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[Source: https://docs.python.org/3/license.html] hdf_compass-0.6.0/additional_legal/wxWidgets_Copyrights_and_Licenses.txt0000666000000000000000000010002212730245342025016 0ustar 00000000000000 Copyrights and Licenses for wxWidgets This page includes the following documents: wxWidgets Copyrights and Licenses wxWindows Library Licence, Version 3.1 GNU Library General Public License The Open Group and DEC Licenses wxWidgets Copyrights and Licenses --------------------------------- Copyright (c) 1992-2013 Julian Smart, Vadim Zeitlin, Stefan Csomor, Robert Roebling, and other members of the wxWidgets team, please see the acknowledgements section below. Portions (c) 1996 Artificial Intelligence Applications Institute Please also see the wxWindows licence files (preamble.txt, lgpl.txt, gpl.txt, licence.txt, licendoc.txt) for conditions of software and documentation use. Note that we use the old name wxWindows in the licence, pending recognition of the new name by OSI. wxWindows Library Licence GNU Library General Public License The Open Group and DEC License Acknowledgements The following is the list of the core, active developers of wxWidgets which keep it running and have provided an invaluable, extensive and high-quality amount of changes over the many of years of wxWidgets' life: Julian Smart Vadim Zeitlin Robert Roebling Robin Dunn Stefan Csomor Vaclav Slavik Paul Cornett Wlodzimierz `ABX' Skiba Chris Elliott David Elliott Kevin Hock Stefan Neis Michael Wetherell We would particularly like to thank the following peoples for their contributions to wxWidgets, and the many others who have been involved in the project over the years. Apologies for any unintentional omissions from this alphabetic list: Yiorgos Adamopoulos, Jamshid Afshar, Alejandro Aguilar-Sierra, AIAI, Patrick Albert, Karsten Ballueder, Mattia Barbon, Michael Bedward, Kai Bendorf, Yura Bidus, Keith Gary Boyce, Chris Breeze, Pete Britton, Ian Brown, C. Buckley, Marco Cavallini, Dmitri Chubraev, Robin Corbet, Cecil Coupe, Andrew Davison, Gilles Depeyrot, Neil Dudman, Hermann Dunkel, Jos van Eijndhoven, Tom Felici, Thomas Fettig, Matthew Flatt, Pasquale Foggia, Josep Fortiana, Todd Fries, Dominic Gallagher, Guillermo Rodriguez Garcia, Wolfram Gloger, Norbert Grotz, Stefan Gunter, Bill Hale, Patrick Halke, Stefan Hammes, Guillaume Helle, Harco de Hilster, Cord Hockemeyer, Markus Holzem, Olaf Klein, Leif Jensen, Bart Jourquin, Guilhem Lavaux, Ron Lee, Jan Lessner, Nicholas Liebmann, Torsten Liermann, Per Lindqvist, Francesco Montorsi, Thomas Runge, Tatu Männistö, Scott Maxwell, Thomas Myers, Oliver Niedung, Ryan Norton, Hernan Otero, Ian Perrigo, Timothy Peters, Giordano Pezzoli, Harri Pasanen, Thomaso Paoletti, Garrett Potts, Marcel Rasche, Dino Scaringella, Jobst Schmalenbach, Arthur Seaton, Paul Shirley, Stein Somers, Petr Smilauer, Neil Smith, Kari Systä, George Tasker, Arthur Tetzlaff-Deas, Jonathan Tonberg, Jyrki Tuomi, Janos Vegh, Andrea Venturoli, David Webster, Otto Wyss, Xiaokun Zhu, Edward Zimmermann. Many thanks also to AIAI for being willing to release the original version of wxWidgets into the public domain, and to our patient partners. `Graphplace', the basis for the wxGraphLayout library, is copyright Dr. Jos T.J. van Eijndhoven of Eindhoven University of Technology. The code has been used in wxGraphLayout (not in wxWidgets anymore) with his permission. We also acknowledge the author of XFIG, the excellent Unix drawing tool, from the source of which we have borrowed some spline drawing code. His copyright is included below. XFig2.1 is copyright (c) 1985 by Supoj Sutanthavibul. Permission to use, copy, modify, distribute, and sell this software and its documentation for any purpose is hereby granted without fee, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation, and that the name of M.I.T. not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. M.I.T. makes no representations about the suitability of this software for any purpose. It is provided "as is" without express or implied warranty. wxWindows Library Licence, Version 3.1 ====================================== Copyright (c) 1998-2005 Julian Smart, Robert Roebling et al Everyone is permitted to copy and distribute verbatim copies of this licence document, but changing it is not allowed. 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END OF TERMS AND CONDITIONS The Open Group and DEC Licenses ------------------------------- Copyright 1987, 1988, 1998 The Open Group Permission to use, copy, modify, distribute, and sell this software and its documentation for any purpose is hereby granted without fee, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation. The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 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All Rights Reserved Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation, and that the name of Digital not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. 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information: additional_legal/h5py_Copyrights_and_Licenses.txt Original source: http://docs.h5py.org/en/latest/licenses.html License type: BSD-style license HydrOffice BAG (hydroffice.bag) Provided by: G.Masetti, B.R.Calder, and contributors Copyright and license information: additional_legal/hydroffice_bag_Copyrights_and_Licenses.txt Original source: https://bitbucket.org/ccomjhc/hyo_bag/raw/tip/COPYING.txt License type: BSD-style license NumPy Provided by: NumPy Developers Copyright and license information: additional_legal/NumPy_Copyright_and_License.txt Original source: http://www.numpy.org/license.html License type: BSD-style license matplotlib Provided by: Matplotlib Development Team Copyright and license information: additional_legal/matplotlib_Copyright_and_License.txt Original source: http://matplotlib.org/users/license.html License type: BSD-style license PyDAP Provided by: Roberto De Almeida Copyright and license information: additional_legal/PyDAP_Copyright_and_License.txt Original source: http://www.pydap.org/license.html License type: BSD-style licensehdf_compass-0.6.0/data/0000777000000000000000000000000012730267653013061 5ustar 00000000000000hdf_compass-0.6.0/data/asc/0000777000000000000000000000000012730267653013627 5ustar 00000000000000hdf_compass-0.6.0/data/asc/sample.asc0000666000000000000000000000030412730245342015564 0ustar 00000000000000ncols 4 nrows 6 xllcorner 0.0 yllcorner 0.0 cellsize 50.0 NODATA_value -9999 -9999 -9999 5 2 -9999 20 100 36 3 8 35 10 32 42 50 6 88 75 27 9 13 5 1 -9999 hdf_compass-0.6.0/data/bag/0000777000000000000000000000000012730267653013612 5ustar 00000000000000hdf_compass-0.6.0/data/bag/bdb_00.bag0000666000000000000000000006674012730245342015317 0ustar 00000000000000HDF  m`TREEHEAPXBAG_root@(hTREE8HEAPXHmetadatatracking_listelevationuncertaintySNOD Hh H Bag Version 1.5.3$tIbad allocationERRO4EVSNOD(  8X hrow col depth  uncertainty   track_codelist_series EV @ Tracking List Length 8$tI$tI   EV HMinimum Elevation Value  L 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86edd853-2b98-4a9f-8618-11e578c43f51engutf8datasetGiuseppe Masetti (gmasetti@ccom.nh)ccom-jhcpostdocprocessor2015-10-05ISO 191152003/Cor.1:2006geometryOnlysurface12row32100column31100point10423000.000000000000,3956300.000000000000 426100.000000000000,3959500.000000000000centerPROJCS["EPSG:32619",GEOGCS["unnamed",DATUM["WGS_1984",SPHEROID["WGS_1984",6378137,298.2572201434276],TOWGS84[0,0,0,0,0,0,0]],PRIMEM["Greenwich",0],UNIT["degree",0.0174532925199433],EXTENSION["Scaler","0,0,0,0.01,0.01,0.0001"],EXTENSION["Source","CARIS"]],PROJECTION["Transverse_Mercator"],PARAMETER["latitude_of_origin",0],PARAMETER["central_meridian",-69],PARAMETER["scale_factor",0.9996],PARAMETER["false_easting",500000],PARAMETER["false_northing",0],UNIT["Meter",1]]WKTVERT_CS["MLW", VERT_DATUM["MLW", 2000]]WKTcaris_00.csar2015-08-15creationGiuseppe Masetti (gmasetti@ccom.nh)ccom-jhcpostdocoriginatorTest abstractunderDevelopmentgrid100engutf8elevationCARIS BASE Editor 4.1.14-69.8516-69.817635.747735.77682015-08-01T14:30:472015-08-15T22:14:53-4692.037109-4525.958984productUncertCSAR5,632datasetMethod: Extract2015-10-05T19:24:36Giuseppe Masetti (gmasetti@ccom.nh)processorSourceSource = K:\Processing\Products\hips\south_area\south_area_cube_100m.csarcreationDesignated soundings applied by automated procedure.0otherRestrictionsFreeunclassifiedTest noteLangsethPlatform Nameinstrument unknowninstrument type unknown hdf_compass-0.6.0/data/hdf5/0000777000000000000000000000000012730267653013707 5ustar 00000000000000hdf_compass-0.6.0/data/hdf5/Download/0000777000000000000000000000000012730267653015456 5ustar 00000000000000hdf_compass-0.6.0/data/hdf5/Download/download_data.py0000666000000000000000000000226112730245342020620 0ustar 00000000000000""" Download additional data files from AWS """ from __future__ import absolute_import, division, print_function import os.path try: import wget except ImportError as e: print("missing wget, try to install it: pip install wget: %s" % e) import sys sys.exit(1) files = [ 'ami_hdf.h5', 'attrfile.h5', 'craterlake.h5', 'compound.h5', 'comp_complex.h5', 'countries.h5', 'hapmap_compressed.h5', 'hdf5_test.h5', 'iso++.h5', 'sequences.h5', 'snps1000_chr22_CEU.h5', 'LD_22_5Kx5K_matrix.h5', # 5 MB 'shuttle_hdf.h5', # 8 MB 'full8_400um.mnc.h5', # 10MB 'DOQ.h5', # 45 MB 'Sample_Urban_Data.h5', # 145 MB 'h5pf_md_manygroupnew2.h5', # 155 MB 'gz6_SCRIS_npp_d20140522_t0754579_e0802557_b13293__noaa_pop.h5', # 187 MB # 'NARA_TWR.h5', # 3 GB! Uncomment if you really want this. ] for filename in files: uri = 'https://s3.amazonaws.com/hdfgroup/data/hdf5test/' + filename print( uri) if os.path.isfile(filename): print(filename, "already downloaded - skipping") else: wget.download(uri, bar=wget.bar_thermometer) print("done!") hdf_compass-0.6.0/data/hdf5/tall.h50000666000000000000000000002014412730245342015071 0ustar 00000000000000HDF  d `HEAP0TREEp HEAP0TREE   SNOD@  HEAP0TREE0 HEAP0TREE x @ SNOD x @ hH  HEAP04TREE  xHEAP0 dTREE SNOD   20000323162808 x  P attr1 1st attribute of dset1.1.1X     $ #(- $*06#*18? (08@H $-6?HQSNODhP  20000323162808` SNOD!  20000323162808 ????ff?33???ٙ?ff?33SNODx! 20000323162808 x=>L>>>L>??L>??fff?g1g2` @ attr1  abcdefghi H attr2  g1.1g1.2dset2.1dset2.2dset1.1.1dset1.1.2g1.2.1 somevalueslink P attr2 2nd attribute of dset1.1.1 g1.2.1 @extlinksomefilesomepathhdf_compass-0.6.0/docs/0000777000000000000000000000000012730267653013100 5ustar 00000000000000hdf_compass-0.6.0/docs/conf.py0000666000000000000000000002226612730245342014376 0ustar 00000000000000# -*- coding: utf-8 -*- # # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. import sys import os import shlex # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. #sys.path.insert(0, os.path.abspath('.')) # -- General configuration ------------------------------------------------ # If your documentation needs a minimal Sphinx version, state it here. #needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.autodoc', ] # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # source_suffix = ['.rst', '.md'] source_suffix = '.rst' # The encoding of source files. #source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = u'HDF Compass' copyright = u'2016, The HDF Group' author = u'The HDF Group' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. version = '0.6' # The full version, including alpha/beta/rc tags. release = '0.6.0b7' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: #today = '' # Else, today_fmt is used as the format for a strftime call. #today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. exclude_patterns = ['_build'] # The reST default role (used for this markup: `text`) to use for all # documents. #default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. #add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). #add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. #show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. #modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. #keep_warnings = False # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. html_theme = 'default' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. #html_theme_options = {} # Add any paths that contain custom themes here, relative to this directory. #html_theme_path = [] # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". #html_title = None # A shorter title for the navigation bar. Default is the same as html_title. #html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. #html_logo = None # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. #html_favicon = None # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the documentation. #html_extra_path = [] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. #html_last_updated_fmt = '%b %d, %Y' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. #html_use_smartypants = True # Custom sidebar templates, maps document names to template names. #html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. #html_additional_pages = {} # If false, no module index is generated. #html_domain_indices = True # If false, no index is generated. #html_use_index = True # If true, the index is split into individual pages for each letter. #html_split_index = False # If true, links to the reST sources are added to the pages. #html_show_sourcelink = True # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. #html_show_sphinx = True # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. #html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. #html_use_opensearch = '' # This is the file name suffix for HTML files (e.g. ".xhtml"). #html_file_suffix = None # Language to be used for generating the HTML full-text search index. # Sphinx supports the following languages: # 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja' # 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr' #html_search_language = 'en' # A dictionary with options for the search language support, empty by default. # Now only 'ja' uses this config value #html_search_options = {'type': 'default'} # The name of a javascript file (relative to the configuration directory) that # implements a search results scorer. If empty, the default will be used. #html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. htmlhelp_basename = 'HDFCompassdoc' # -- Options for LaTeX output --------------------------------------------- latex_elements = { # The paper size ('letterpaper' or 'a4paper'). #'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). #'pointsize': '10pt', # Additional stuff for the LaTeX preamble. #'preamble': '', # Latex figure (float) alignment #'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'HDFCompass.tex', u'HDF Compass Documentation', u'The HDF Group', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. #latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. #latex_use_parts = False # If true, show page references after internal links. #latex_show_pagerefs = False # If true, show URL addresses after external links. #latex_show_urls = False # Documents to append as an appendix to all manuals. #latex_appendices = [] # If false, no module index is generated. #latex_domain_indices = True # -- Options for manual page output --------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'hdfcompass', u'HDF Compass Documentation', [author], 1) ] # If true, show URL addresses after external links. #man_show_urls = False # -- Options for Texinfo output ------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'HDFCompass', u'HDF Compass Documentation', author, 'HDFCompass', 'One line description of project.', 'Miscellaneous'), ] # Documents to append as an appendix to all manuals. #texinfo_appendices = [] # If false, no module index is generated. #texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. #texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. #texinfo_no_detailmenu = False hdf_compass-0.6.0/docs/data_model.rst0000666000000000000000000002515312730245342015720 0ustar 00000000000000Data Model `[developer]` ======================== Introduction ------------ This document describes the publically accessible data model package which is used by HDFCompass to display objects in a file, OpenDAP server or other resource. The data model is implemented as a collection of classes in a top-level Python package, ``compass_model``, which is completely independent of the GUI code. It has no dependencies beyond the Python standard library. This makes it possible to develop and test new plugins independently of GUI development; in particular, the automated Python unit-testing framework can be used, which is impossible for code that depends on the GUI. The classes in ``compass_model`` are abstract, and define a standard interface for objects like containers, regular multidimensional arrays, images, and key/value stores. "Plug-ins" consist of concrete implementations which satisfy this interface. For example, the built-in HDF5 plugin which ships with HDFCompass implements a ``Group`` class which inherits from ``compass_model.Container``, and a Dataset class which inherits from ``compass_model.Array``. The GUI has a collection of viewers which can display any object following the interfaces defined in ``compass_model``. For example, ``compass_model.Container`` implementations are displayed in a browser-style view, with list, icon, and tree displays possible. Likewise, ``compass_model.Array`` implementations are displayed in a spreadsheet-like view, with facilities for plotting data. Multiple concrete classes can handle the same object in a file. For example, an HDF5 image is implemented as a dataset with special attributes. Three classes in the HDF5 plugin are capable of handling such an object, which inherit respectively from ``compass_model.Image``, ``compass_model.Array``, and ``compass_model.KeyValue``; the last represents HDF5 attributes. When an icon in the GUI is double-clicked, the default (last-registered) class is used to open to object in the file. The other classes are made available in a context menu, for example, if the user wants to open an image with the Array viewer or see the HDF5 attributes. Numeric types (integers, floats, multidimensional data) are handled with the NumPy type model, which can represent nearly all formats. Python strings (byte and Unicode) are also supported. Data stores ----------- .. class:: Store Represents a file or remote resource which contains objects. Objects within the store can be retrieved using *keys*, which may be any hashable Python object. For example, an HDF5 store generally uses string keys representing paths in the file, although object and region reference objects are also valid. Objects may be retrieved using the __getitem__ syntax (``obj = store[key]``). The retrieved object is a Node instance. The exact class depends on the order in which Node handlers were registered; see the `push` method below. Methods related to the plugin system ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Typically, a model will implement several classes based on the ``compass_model`` abstract classes such as ``Container`` or ``Array``. This rasises the question: when an object is retrieved from the data store, which class should be used? The answer is that each ``Node`` subclass you write should be "registered" with your ``Store`` subclass, and have a static method called ``canhandle``. When an object is opened, by default the most recently registered class which reports it can understand the object is used. All registered subclasses may be retrieved via the ``gethandlers`` function, which an optionally request that only subclasses capable of handling *key* be returned. This is the basis for the right-click "Open As" menu in the GUI. .. classmethod:: Store.push(nodeclass) Register a Node subclass. These are kept in a list inside the class; when an object is retrieved from the store, the first class for which `nodeclass.canhandle(store, key)` returns True is instantiated and returned. .. method:: Store.__getitem__(key) Open an object in the store, using the last registered class which reports it can open the key. .. method:: Store.gethandlers(key=None) Retrieve all registered Node subclasses, optionally filtering by those which report they can handle *key*. .. method:: Store.__contains__(key) **(Abstract)** True if *key* is exists in the store, False otherwise. Other methods & properties ~~~~~~~~~~~~~~~~~~~~~~~~~~ .. staticmethod:: Store.canhandle(url) **(Abstract)** Return True if this class can make sense of *url*, False otherwise. This method is used by the GUI when determining which Store implementation to use when opening a file. For example, the HDF5 plugin uses ``h5py.is_hdf5(filename)``. .. method:: Store.__init__(url) **(Abstract)** Create a new store instance from the data at *url*. URLs are given in the ``scheme://locator`` fashion. For example, an HDF5 file might be located by ``file:///path/to/file.hdf5``. .. method:: Store.close(): **(Abstract)** Discontinue access to the data store. .. method:: Store.get_parent(key) **(Abstract)** Return the object which contains *key*, or None if no such object exists. .. attribute:: Store.url **(Abstract)** The URL used to open the store .. attribute:: Store.displayname **(Abstract)** A short name used for the store (e.g. ``basename(filepath)``). .. attribute:: Store.root **(Abstract)** A Node instance representing the starting point in the file. For hierarchical formats, this would be the root container. For scalar formats (FITS, for example), this could be e.g. an Array or Image instance. .. attribute:: Store.file_extensions For plugins that support local file access, this is a dictionary mapping file kinds to lists of extensions in "glob" format, e.g. ``{'HDF5 File': ['.h5', '.hdf5']}``. This will be used to populate the filter in the file-open dialog, among other things. Nodes ----- A "node" is any object which lives in the data store. The Node class defined below is the base class for more interesting abstract classes like containers and arrays. It defines much of the interface. .. class:: Node Base class for all objects which live in a data store. You generally shouldn't inherit from Node directly, but from one of the more useful Node subclasses in this file. Direct Node subclasses can't do anything interesting in the GUI; all they do is show up in the browser. .. attribute:: Node.icons Class attribute containing a dict for icon support. Keys should be integers giving icon size; values are a callable returning a byte string with PNG image data. Example: ``icons = {16: get_png_16, 32: get_png_32}``. Since icons are a pain to handle, default icons are provided by ``compass_model`` and this attribute is optional. .. attribute:: Node.classkind **(Abstract)** A short string (2 or 3 words) describing what the class represents. This will show up in e.g. the "Open As" context menu. Example: "HDF5 Image" or "Swath". .. staticmethod:: Node.canhandle(store, key) **(Abstract)** Determine whether this class can usefully represent the object. Keep in mind that keys are not technically required to be strings. .. method:: Node.__init__(store, key): **(Abstract)** Create a new instance representing the object pointed to by *key* in *store*. .. attribute:: Node.key **(Abstract)** Unique key which identifies this object in the store. Keys may be any hashable object, although strings are the most common. .. attribute:: Node.store **(Abstract)** The data store to which the object belongs. .. attribute:: Node.displayname **(Abstract)** A short name for display purposes (16 chars or so; more will be ellipsized). .. attribute:: Node.description **(Abstract)** Descriptive string (possibly multi-line). Containers ---------- .. class:: Container(Node) Represents an object which holds other objects, like an HDF5 group or a filesystem directory. Implementations will be displayed using the browser view. .. method:: Container.__len__() **(Abstract)** Get the number of objects directly attached to the container. .. method:: Container.__getitem__(index) **(Abstract)** Retrieve the node at *index*. Note this returns a Node instance, not a key. Arrays ------ .. class:: Array(Node) The array type represents a multidimensional array, using an interface inspired by Numpy arrays. Implementations will be displayed in a spreadsheet-style viewer with controls for subsetting and plotting. .. attribute:: Array.shape Shape of the array, as a Python tuple. .. attribute:: Array.dtype NumPy data type object representing the type of the array. .. method:: Array.__getitem__(indices) Retrieve data from the array, using the standard array-slicing syntax ``data = array[idx1, idx2, idx3]. *indices* are the slicing arguments. Only integer indexes and slice objects (representing ranges) are supported. Key-Value lists --------------- .. class:: KeyValue(Node) Represents an object which contains a sequence of key: value attributes. Keys must be strings. Values may be Python or NumPy objects. Implementations will be displayed using a list-like control. .. attribute:: KeyValue.keys **(Abstract)** A list containing all (string) keys contained in the object. .. method:: KeyValue.__getitem__(name) **(Abstract)** Retrieve the value associated with string *name*. Images ------ .. class:: Image(Node) Represents an image. The current interface supports only true-color RGB images with the origin at upper left, although this could easily be extended to more complex formats including RGBA or palette-based images. Implementations are displayed in an image viewer. .. attribute:: Image.width Image width in pixels .. attribute:: Image.height Image height in pixels .. attribute:: Image.data Image data. Currently RGB, pixel-interlaced. Top-level functions ------------------- One public function is defined in ``compass_model``: .. function:: push(storeclass) Register a new Store subclass with HDFCompass. When a URL is being opened, the class will be queried (via ``storeclass.canhandle``) to see if it can make sense of the URL.hdf_compass-0.6.0/docs/how_to_contribute.rst0000666000000000000000000000010712730245342017354 0ustar 00000000000000How to contribute `[developer]` =============================== TBDhdf_compass-0.6.0/docs/how_to_freeze.rst0000666000000000000000000000007712730245342016464 0ustar 00000000000000How to freeze `[developer]` =========================== TBDhdf_compass-0.6.0/docs/how_to_install.rst0000666000000000000000000000004512730245342016645 0ustar 00000000000000How to install ============== TBDhdf_compass-0.6.0/docs/how_to_release.rst0000666000000000000000000000133412730245342016621 0ustar 00000000000000How to release `[developer]` ============================ Versioning ---------- You need to install ``bumpversion``. Once installed, you can run something like: ``bumpversion --allow-dirty --new-version 0.6.0.dev0 patch``. The above release value must agree with the variable ``version`` present in the ``conf.py`` under the `docs` folder. PyInstaller ----------- For the `HDFCompass.1file.spec` file, you need to verify that the following parameters are passed to the ``EXE()`` function: * ``console=False``: to avoid that a console window is opened at run-time for standard I/O * ``debug=False``: to avoid that the boot-loader issues progress messages while initializing and starting the bundled app hdf_compass-0.6.0/docs/how_to_use.rst0000666000000000000000000000003512730245342015772 0ustar 00000000000000How to use ========== TBDhdf_compass-0.6.0/docs/index.rst0000666000000000000000000000245212730245342014733 0ustar 00000000000000.. Copyright by The HDF Group. All rights reserved. This file is part of the HDF Compass Viewer. The full HDF Compass copyright notice, including terms governing use, modification, and terms governing use, modification, and redistribution, is contained in the file COPYING, which can be found at the root of the source code distribution tree. If you do not have access to this file, you may request a copy from help@hdfgroup.org. HDF Compass's documentation =========================== This document provide information about the HDF Compass application. In Brief -------- HDF Compass is an experimental viewer program for HDF5 and related formats, designed to complement other more complex applications like HDFView. Strong emphasis is placed on clean minimal design, and maximum extensibility through a plugin system for new formats. HDF Compass is written in Python, but ships as a native application on Windows, OS X, and Linux, by using PyInstaller and Py2App to package the app. Contents -------- .. toctree:: :maxdepth: 2 requirements license how_to_install how_to_use how_to_contribute data_model how_to_release how_to_freeze Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search` hdf_compass-0.6.0/docs/license.rst0000666000000000000000000001251612730245342015250 0ustar 00000000000000License ======= Application License ------------------- Copyright Notice and License Terms for HDF Compass - Viewer for HDF5 and other file formats ----------------------------------------------------------------------------- HDF Compass Copyright 2014-2015 by The HDF Group. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted for any purpose (including commercial purposes) provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions, and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions, and the following disclaimer in the documentation and/or materials provided with the distribution. 3. In addition, redistributions of modified forms of the source or binary code must carry prominent notices stating that the original code was changed and the date of the change. 4. All publications or advertising materials mentioning features or use of this software are asked, but not required, to acknowledge that it was developed by The HDF Group and credit the contributors. 5. Neither the name of The HDF Group, nor the name of any Contributor may be used to endorse or promote products derived from this software without specific prior written permission from The HDF Group or the Contributor, respectively. DISCLAIMER: THIS SOFTWARE IS PROVIDED BY THE HDF GROUP AND THE CONTRIBUTORS "AS IS" WITH NO WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED. In no event shall The HDF Group or the Contributors be liable for any damages suffered by the users arising out of the use of this software, even if advised of the possibility of such damage. Additional Copyright and License Information -------------------------------------------- Copyright and license terms for the following software can be found in the adjacent subdirectory Additional_Legal/. This information was obtained from sources provided by each software package provider at the location specified under "Original source:" and was current as of 19 December 2014. HDF Compass uses selected icons from the following icon sets: KDE Oxygen icon set Provided by: KDE Community Copyright and license information: additional_legal/KDE_Oxygen_Icon_Set_Copyright_and_License.txt Original source: http://www.gnu.org/copyleft/lesser.html (via link from https://techbase.kde.org/Projects/Oxygen/Licensing) License type: GNU LGPL version 3 license HydroPro icon set Provided by: Ben Fleming via MediaDesign Copyright and license information: additional_legal/HydroPro_Icons_Terms.txt Original source: http://www.iconarchive.com/icons/media-design/hydropro/readme.txt License type: Freeware Pre-built HDF Compass binaries include the following software. None of this software is present in whole or in part in the HDF Compass source code. Python interpreter Provided by: Python Software Foundation Copyright and license information: additional_legal/Python_Copyright_and_License.txt Original source: https://docs.python.org/3/license.html License type: BSD-style license wxPython GUI layer Provided by: Julian Smart, Vadim Zeitlin, Stefan Csomor, Robert Roebling, and other members of the wxWidgets team Copyright and license information: additional_legal/wxWidgets_Copyrights_and_Licenses.txt Original source: http://docs.wxwidgets.org/3.0/page_copyright.html License type: GNU LGPL version 2 license with exception PyInstaller runtime support code (Windows & Linux only) Provided by: PyInstaller Development Team Copyright and license information: additional_legal/PyInstaller_Copyrights_and_Licenses.txt Original source: https://github.com/pyinstaller/pyinstaller/blob/develop/COPYING.txt License type: GNU GPL version 2 license with exception HDF5 for Python (h5py) Provided by: Andrew Collette and contributors Copyright and license information: additional_legal/h5py_Copyrights_and_Licenses.txt Original source: http://docs.h5py.org/en/latest/licenses.html License type: BSD-style license HydrOffice BAG (hydroffice.bag) Provided by: G.Masetti, B.R.Calder, and contributors Copyright and license information: additional_legal/hydroffice_bag_Copyrights_and_Licenses.txt Original source: https://bitbucket.org/ccomjhc/hyo_bag/raw/tip/COPYING.txt License type: BSD-style license NumPy Provided by: NumPy Developers Copyright and license information: additional_legal/NumPy_Copyright_and_License.txt Original source: http://www.numpy.org/license.html License type: BSD-style license matplotlib Provided by: Matplotlib Development Team Copyright and license information: additional_legal/matplotlib_Copyright_and_License.txt Original source: http://matplotlib.org/users/license.html License type: BSD-style license PyDAP Provided by: Roberto De Almeida Copyright and license information: additional_legal/PyDAP_Copyright_and_License.txt Original source: http://www.pydap.org/license.html License type: BSD-style licensehdf_compass-0.6.0/docs/make.bat0000777000000000000000000001612412730245342014503 0ustar 00000000000000@ECHO OFF REM Command file for Sphinx documentation if "%SPHINXBUILD%" == "" ( set SPHINXBUILD=sphinx-build ) set BUILDDIR=_build set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . set I18NSPHINXOPTS=%SPHINXOPTS% . if NOT "%PAPER%" == "" ( set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% ) if "%1" == "" goto help if "%1" == "help" ( :help echo.Please use `make ^` where ^ is one of echo. html to make standalone HTML files echo. dirhtml to make HTML files named index.html in directories echo. singlehtml to make a single large HTML file echo. pickle to make pickle files echo. json to make JSON files echo. htmlhelp to make HTML files and a HTML help project echo. qthelp to make HTML files and a qthelp project echo. devhelp to make HTML files and a Devhelp project echo. epub to make an epub echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter echo. text to make text files echo. man to make manual pages echo. texinfo to make Texinfo files echo. gettext to make PO message catalogs echo. changes to make an overview over all changed/added/deprecated items echo. xml to make Docutils-native XML files echo. pseudoxml to make pseudoxml-XML files for display purposes echo. linkcheck to check all external links for integrity echo. doctest to run all doctests embedded in the documentation if enabled echo. coverage to run coverage check of the documentation if enabled goto end ) if "%1" == "clean" ( for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i del /q /s %BUILDDIR%\* goto end ) REM Check if sphinx-build is available and fallback to Python version if any %SPHINXBUILD% 2> nul if errorlevel 9009 goto sphinx_python goto sphinx_ok :sphinx_python set SPHINXBUILD=python -m sphinx.__init__ %SPHINXBUILD% 2> nul if errorlevel 9009 ( echo. echo.The 'sphinx-build' command was not found. 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The message catalogs are in %BUILDDIR%/locale. goto end ) if "%1" == "changes" ( %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes if errorlevel 1 exit /b 1 echo. echo.The overview file is in %BUILDDIR%/changes. goto end ) if "%1" == "linkcheck" ( %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck if errorlevel 1 exit /b 1 echo. echo.Link check complete; look for any errors in the above output ^ or in %BUILDDIR%/linkcheck/output.txt. goto end ) if "%1" == "doctest" ( %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest if errorlevel 1 exit /b 1 echo. echo.Testing of doctests in the sources finished, look at the ^ results in %BUILDDIR%/doctest/output.txt. goto end ) if "%1" == "coverage" ( %SPHINXBUILD% -b coverage %ALLSPHINXOPTS% %BUILDDIR%/coverage if errorlevel 1 exit /b 1 echo. echo.Testing of coverage in the sources finished, look at the ^ results in %BUILDDIR%/coverage/python.txt. goto end ) if "%1" == "xml" ( %SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml if errorlevel 1 exit /b 1 echo. echo.Build finished. The XML files are in %BUILDDIR%/xml. goto end ) if "%1" == "pseudoxml" ( %SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml if errorlevel 1 exit /b 1 echo. echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml. goto end ) :end hdf_compass-0.6.0/docs/requirements.rst0000666000000000000000000000004112730245342016337 0ustar 00000000000000Requirements ============ TBDhdf_compass-0.6.0/HDFCompass.desktop0000666000000000000000000000051212730245342015457 0ustar 00000000000000[Desktop Entry] Version=1.0 Type=Application Name=HDFCompass GenericName=HDFCompass Comment=Viewer program for HDF5 and related formats TryExec=HDFCompass Exec=HDFCompass %f Categories=Development;Science; Keywords=Python;HDF;science;viewer; Icon=HDFCompass Terminal=false StartupNotify=true MimeType=text/x-python; hdf_compass-0.6.0/HDFCompass.icns0000666000000000000000000050751212730245342014756 0ustar 00000000000000icnsJic09B jP ftypjp2 jp2 Ojp2hihdrcolr"cdefjp2cOQ2d#Creator: JasPer Version 1.900.1R \@@HHPHHPHHPHHPHHP]@@HHPHHPHHPHHPHHP]@@HHPHHPHHPHHPHHP]@@HHPHHPHHPHHPHHP ߅O_ߏK%ǓRMDO Mx47ڢ$#aՀyY9K? <> Jw9Y2h%@]c߅O_|ÅcڥjkL`Ö0TT`lh_ Q8]㸏K>CwONWrX=ﺃDWS~&rQ5_7¿GF(h˨]-7cU6,:Y iʲcg֪٫jX7 >Y|m4cD:6POܽcxcׂ!sDb ?a.,5L.`>Qi"_y>G[߅O`* H;8vx`LV_q{Ų4-8?Oo?#w nxxJJ]N¬m3MXSW&W"X8w`Fd? 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The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function, unicode_literals import logging class LoggingFilter(logging.Filter): """ An example of logging filter that disables the logging from a specific module """ def filter(self, record): # print(record.name) if record.name.startswith('hdf_compass.compass_viewer.info'): return False return True # logging settings logger = logging.getLogger() logger.setLevel(logging.NOTSET) ch = logging.StreamHandler() ch.setLevel(logging.DEBUG) # change to WARNING to minimize verbosity, DEBUG for high verbosity ch_formatter = logging.Formatter('%(levelname)-7s %(name)s.%(funcName)s:%(lineno)d > %(message)s') ch.setFormatter(ch_formatter) # ch.addFilter(LoggingFilter()) # uncomment to activate the logging filter logger.addHandler(ch) from hdf_compass import compass_viewer compass_viewer.run() hdf_compass-0.6.0/hdf_compass/0000777000000000000000000000000012730267653014436 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/array_model/0000777000000000000000000000000012730267653016734 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/array_model/model.py0000666000000000000000000002136012730245342020377 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Testing model for array types. """ from __future__ import absolute_import, division, print_function, unicode_literals import numpy as np import os.path as op import logging log = logging.getLogger(__name__) from hdf_compass import compass_model DT_CMP = np.dtype([(b'a', b'i'), (b'b', b'f')]) DATA = {'array://localhost/a_0d': np.array(1), 'array://localhost/a_1d': np.arange(10), 'array://localhost/a_2d': np.arange(10 * 10).reshape((10, 10)), 'array://localhost/a_3d': np.arange(10 * 10 * 10).reshape((10, 10, 10)), 'array://localhost/a_4d': np.arange(10 * 10 * 10 * 10).reshape((10, 10, 10, 10)), 'array://localhost/cmp_0d': np.array((1, 2), dtype=DT_CMP), 'array://localhost/cmp_1d': np.ones((10,), dtype=DT_CMP), 'array://localhost/cmp_2d': np.ones((10, 10), dtype=DT_CMP), 'array://localhost/cmp_3d': np.ones((10, 10, 10), dtype=DT_CMP), 'array://localhost/cmp_4d': np.ones((10, 10, 10, 10), dtype=DT_CMP), 'array://localhost/S_0d': np.array(b"Hello"), 'array://localhost/S_1d': np.array([b"Hello", b"Ciao"]), 'array://localhost/S_2d': np.array([[b"Hello", b"Ciao"], [b"Hello", b"Ciao"]]), 'array://localhost/S_3d': np.array([[[b"Hello", b"Ciao"], [b"Hello", b"Ciao"]], [[b"Hello", b"Ciao"], [b"Hello", b"Ciao"]]]), 'array://localhost/U_1d': np.array(["Hello", "Ciao"]), 'array://localhost/U_2d': np.array([["Hello", "Ciao"], ["Hello", "Ciao"]]), 'array://localhost/U_3d': np.array([[["Hello", "Ciao"], ["Hello", "Ciao"]], [["Hello", "Ciao"], ["Hello", "Ciao"]]]), 'array://localhost/v_0d': np.array('\x01', dtype='|V1'), 'array://localhost/non_square': np.arange(5 * 10).reshape((5, 10)), } class ArrayStore(compass_model.Store): """ A "data store" represented by a set of arrays in memory. Keys are array names as reported in DATA. """ @staticmethod def plugin_name(): return "Array" @staticmethod def plugin_description(): return "A testing plugin used to evaluate the array visualization." def __contains__(self, key): if (key == '/') or (key is None): log.debug("is root: %s" % key) return True return key in DATA @property def url(self): return self._url @property def display_name(self): return "Testing arrays" @property def root(self): return self['/'] @property def valid(self): return self._valid @staticmethod def can_handle(url): if url == "array://localhost": log.debug("able to handle %s? yes" % url) return True log.debug("able to handle %s? no" % url) return False def __init__(self, url): if not self.can_handle(url): raise ValueError(url) self._url = url self._valid = True def close(self): self._valid = False def get_parent(self, key): if key is None: return None if key == "/": return None return self[op.dirname(key)] class ArrayContainer(compass_model.Container): """ Represents a container of in-memory array. """ class_kind = "Array Container" @staticmethod def can_handle(store, key): return (key == '/') or (key is None) def __init__(self, store, key): self._store = store self._key = key self._names = sorted(DATA.keys()) @property def key(self): return None @property def store(self): return self._store @property def display_name(self): return "/" @property def description(self): return self.display_name def __len__(self): return len(DATA) def __iter__(self): for name in self._names: yield self._store[name] def __getitem__(self, idx): key = self._names[idx] return self._store[key] class Array(compass_model.Array): """ An N-D array """ class_kind = "TestArray" @staticmethod def can_handle(store, key): return key in DATA def __init__(self, store, key): self._store = store self._key = key self.data = DATA[key] @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return self.key.rsplit('/', 1)[-1] @property def description(self): return self.display_name @property def shape(self): return self.data.shape @property def dtype(self): return self.data.dtype def __getitem__(self, args): return self.data[args] def is_plottable(self): if self.dtype.kind == 'S': log.debug("Not plottable since ASCII String (characters: %d)" % self.dtype.itemsize) return False if self.dtype.kind == 'U': log.debug("Not plottable since Unicode String (characters: %d)" % self.dtype.itemsize) return False return True class ArrayText(compass_model.Text): """ Represents a text array (both ASCII and UNICODE). """ class_kind = "TestArray [text]" @staticmethod def can_handle(store, key): if key not in DATA: return False if DATA[key].dtype.kind == 'S': # log.debug("ASCII String (characters: %d)" % DATA[key].dtype.itemsize) return True if DATA[key].dtype.kind == 'U': # log.debug("Unicode String (characters: %d)" % DATA[key].dtype.itemsize) return True return False def __init__(self, store, key): self._store = store self._key = key self.data = DATA[key] @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return self.key.rsplit('/', 1)[-1] @property def description(self): return 'Text "%s"' % (self.display_name,) @property def shape(self): return self.data.shape @property def text(self): txt = str() if len(self.shape) == 0: print(self.data) txt += str(self.data) elif len(self.shape) == 1: for el in self.data: txt += el + ",\n" elif len(self.shape) == 2: for i in range(self.shape[0]): for j in range(self.shape[1]): txt += self.data[i, j] + ", " txt += "\n" else: txt = ">> display of more than 2D string array not implemented <<" return txt class ArrayKV(compass_model.KeyValue): class_kind = "Array Key/Value Attrs" @staticmethod def can_handle(store, key): return key in DATA def __init__(self, store, key): self._store = store self._key = key self.data = {'a': np.array((1, 2)), 'b': np.array("Hello"), 'c': np.array('\x01', dtype='|V1')} @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return self.key.rsplit('/', 1)[-1] @property def description(self): return self.display_name @property def keys(self): return self.data.keys() def __getitem__(self, args): return self.data[args] ArrayStore.push(ArrayKV) ArrayStore.push(ArrayContainer) ArrayStore.push(Array) ArrayStore.push(ArrayText) compass_model.push(ArrayStore) hdf_compass-0.6.0/hdf_compass/array_model/test.py0000666000000000000000000000224012730245342020252 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function from hdf_compass.compass_model.test import container, store from hdf_compass.array_model import ArrayStore, ArrayContainer url = "array://localhost" s = store(ArrayStore, url) c = container(ArrayStore, url, ArrayContainer, None)hdf_compass-0.6.0/hdf_compass/array_model/__init__.py0000666000000000000000000000214112730245342021032 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function, unicode_literals from .model import ArrayStore, ArrayContainer, ArrayKV, Array import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler()) hdf_compass-0.6.0/hdf_compass/asc_model/0000777000000000000000000000000012730267653016364 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/asc_model/model.py0000666000000000000000000001307412730245342020032 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ HDF Compass "pilot" plugin for viewing ASCII Grid Data. Subclasses consist of a Container and an Array, representing directories and the ASCII grid data respectively. See: http://en.wikipedia.org/wiki/Esri_grid for a description of the file format """ from __future__ import absolute_import, division, print_function, unicode_literals import os.path as op import linecache import numpy as np import logging log = logging.getLogger(__name__) from hdf_compass import compass_model from hdf_compass.utils import url2path class AsciiGrid(compass_model.Store): """ A "data store" represented by an ascii grid file. """ @staticmethod def plugin_name(): return "Ascii Grid" @staticmethod def plugin_description(): return "A plugin used to browse Ascii Grid." file_extensions = {'ASC File': ['*.asc']} def __contains__(self, key): if key == '/': return True return False @property def url(self): return self._url @property def display_name(self): return op.basename(self._url) @property def root(self): return self['/'] @property def valid(self): return self._valid @staticmethod def can_handle(url): if not url.startswith('file://'): log.debug("able to handle %s? no, not starting with file://" % url) return False if not url.endswith('.asc'): log.debug("able to handle %s? no, missing .asc extension" % url) return False first_line = open(url2path(url)).readline() if first_line.split()[0].upper() != "NCOLS": log.debug("able to handle %s? no, invalid first line" % url) return False log.debug("able to handle %s? yes" % url) return True def __init__(self, url): if not self.can_handle(url): raise ValueError(url) self._url = url self._valid = True def close(self): self._valid = False def get_parent(self, key): return None def getFilePath(self): return url2path(self._url) class ASCFile(compass_model.Array): """ Represents a .asc grid file. """ class_kind = "ASCII Grid File" @staticmethod def can_handle(store, key): if key == '/': return True return False def __init__(self, store, key): self._store = store self._key = key file_path = self._store.getFilePath() self._nrows = int(linecache.getline(file_path, 1).lstrip("ncols")) self._ncols = int(linecache.getline(file_path, 2).lstrip("nrows")) self._data = None @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return self._store.display_name @property def description(self): return 'File "%s", size %d bytes' % (self.display_name, op.getsize(self.key)) @property def shape(self): return self._nrows, self._ncols @property def dtype(self): return np.dtype('float') def __getitem__(self, args): if self._data is None: self._data = np.loadtxt(self._store.getFilePath(), skiprows=6, unpack=True) return self._data[args] class Attributes(compass_model.KeyValue): class_kind = "Attributes of ASC Grid File" @staticmethod def can_handle(store, key): if key == '/': return True return False def __init__(self, store, key): self._store = store self._key = key file_path = self._store.getFilePath() self.data = {'NODATA Value': float(linecache.getline(file_path, 6).lstrip("NODATA_value")), 'cellsize': float(linecache.getline(file_path, 5).lstrip("cellsize")), 'yllcorner': float(linecache.getline(file_path, 4).lstrip("yllcorner")), 'xllcorner': float(linecache.getline(file_path, 3).lstrip("xllcorner"))} @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return self.key @property def description(self): return self.display_name def close(self): self._valid = False @property def keys(self): return self.data.keys() def __getitem__(self, args): return self.data[args] AsciiGrid.push(Attributes) # attribute data AsciiGrid.push(ASCFile) # array compass_model.push(AsciiGrid) hdf_compass-0.6.0/hdf_compass/asc_model/test.py0000666000000000000000000000223412730245342017705 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function import os from hdf_compass.compass_model.test import store from hdf_compass.asc_model import AsciiGrid from hdf_compass.utils import data_url url = os.path.join(data_url(), "asc", "sample.asc") s = store(AsciiGrid, url) hdf_compass-0.6.0/hdf_compass/asc_model/__init__.py0000666000000000000000000000212312730245342020462 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function, unicode_literals from .model import AsciiGrid, ASCFile, Attributes import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler())hdf_compass-0.6.0/hdf_compass/bag_model/0000777000000000000000000000000012730267653016347 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/bag_model/model.py0000666000000000000000000005457312730245342020026 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Implementation of compass_model classes for BAG files. """ from __future__ import absolute_import, division, print_function, unicode_literals from itertools import groupby import sys import os.path as op import posixpath as pp import h5py from hydroffice.bag import is_bag from hydroffice.bag import BAGFile from hydroffice.bag import BAGError from hdf_compass import compass_model from hdf_compass.utils import url2path import logging log = logging.getLogger(__name__) def sort_key(name): """ Sorting key for names in an BAG group. We provide "natural" sort order; e.g. "7" comes before "12". """ return [(int(''.join(g)) if k else ''.join(g)) for k, g in groupby(name, key=unicode.isdigit)] class BAGStore(compass_model.Store): """ Data store implementation using a BAG file (closely mimicking HDF5Store). Keys are the full names of objects in the file. """ @staticmethod def plugin_name(): return "BAG" @staticmethod def plugin_description(): return """A plugin used to browse Open Navigation Surface BAG files. It provides additional features that are not available with the general HDF5 plugin: - View of metadata information as XML (+ content validation). - Plot of elevation and uncertainty using their geographic extent/ The plugin is developed and maintained by G.Masetti [gmasetti@ccom.unh.edu]. """ file_extensions = {'BAG File': ['*.bag']} def __contains__(self, key): return key in self.f @property def url(self): return self._url @property def display_name(self): return op.basename(self.f.filename) @property def root(self): return self['/'] @property def valid(self): return bool(self.f) @staticmethod def can_handle(url): if not url.startswith('file://'): log.debug("able to handle %s? no, invalid url" % url) return False path = url2path(url) if not is_bag(path): log.debug("able to handle %s? no, not a BAG" % url) return False log.debug("able to handle %s? yes" % url) return True def __init__(self, url): if not self.can_handle(url): raise ValueError(url) self._url = url path = url2path(url) self.f = BAGFile(path, 'r') def close(self): self.f.close() def get_parent(self, key): # HDFCompass requires the parent of the root container be None if key == "" or key == "/": return None p_key = pp.dirname(key) if p_key == "": p_key = "/" return self[p_key] class BAGGroup(compass_model.Container): """ Represents an BAG group (closely mimicking HDF5Group). """ class_kind = "BAG Group" @staticmethod def can_handle(store, key): return (key in store) and (isinstance(store.f[key], h5py.Group)) @property def _names(self): # Lazily build the list of names; this helps when browsing big files if self._xnames is None: self._xnames = list(self._group) # Natural sort is expensive if len(self._xnames) < 1000: self._xnames.sort(key=sort_key) return self._xnames def __init__(self, store, key): self._store = store self._key = key self._group = store.f[key] self._xnames = None @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): name = pp.basename(self.key) if name == "": name = '/' return name @property def display_title(self): return "%s %s" % (self.store.display_name, self.key) @property def description(self): return 'Group "%s" (%d members)' % (self.display_name, len(self)) def __len__(self): return len(self._group) def __iter__(self): for name in self._names: yield self.store[pp.join(self.key, name)] def __getitem__(self, idx): name = self._names[idx] return self.store[pp.join(self.key, name)] class BAGRoot(compass_model.Container): """ Represents the BAG root. """ class_kind = "BAG Root" @staticmethod def can_handle(store, key): return (key == "/BAG_root") and (key in store) and (isinstance(store.f[key], h5py.Group)) @property def _names(self): # Lazily build the list of names; this helps when browsing big files if self._xnames is None: self._xnames = list(self._group) # Natural sort is expensive if len(self._xnames) < 1000: self._xnames.sort(key=sort_key) return self._xnames def __init__(self, store, key): self._store = store self._key = key self._group = store.f[key] self._xnames = None @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): name = pp.basename(self.key) return name @property def display_title(self): return "%s %s" % (self.store.display_name, self.key) @property def description(self): return 'Root Group "%s" (%d members)' % (self.display_name, len(self)) def __len__(self): return len(self._group) def __iter__(self): for name in self._names: yield self.store[pp.join(self.key, name)] def __getitem__(self, idx): name = self._names[idx] return self.store[pp.join(self.key, name)] class BAGDataset(compass_model.Array): """ Represents a BAG dataset (closely mimicking HDF5Dataset). """ class_kind = "BAG Dataset" @staticmethod def can_handle(store, key): return key in store and isinstance(store.f[key], h5py.Dataset) def __init__(self, store, key): self._store = store self._key = key self._dset = store.f[key] @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return pp.basename(self.key) @property def description(self): return 'Dataset "%s"' % (self.display_name,) @property def shape(self): return self._dset.shape @property def dtype(self): return self._dset.dtype def __getitem__(self, args): return self._dset[args] def is_plottable(self): if self.dtype.kind == 'S': log.debug("Not plottable since ASCII String (characters: %d)" % self.dtype.itemsize) return False if self.dtype.kind == 'U': log.debug("Not plottable since Unicode String (characters: %d)" % self.dtype.itemsize) return False return True class BAGElevationArray(compass_model.Array): """ Represents a BAG elevation. """ class_kind = "BAG Elevation [array]" @staticmethod def can_handle(store, key): return (key == "/BAG_root/elevation") and (key in store) and (isinstance(store.f[key], h5py.Dataset)) def __init__(self, store, key): self._store = store self._key = key self._dset = store.f.elevation(mask_nan=True) @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return pp.basename(self.key) @property def description(self): return 'Dataset "%s"' % (self.display_name,) @property def shape(self): return self._dset.shape @property def dtype(self): return self._dset.dtype def __getitem__(self, args): return self._dset[args] class BAGElevationGeoArray(compass_model.GeoArray): """ Represents a BAG elevation. """ class_kind = "BAG Elevation [geo array]" @staticmethod def can_handle(store, key): # for GeoSurface we use cartopy that can be challenging to freeze on OSX to dependencies (i.e. geos) try: import cartopy.crs as ccrs except (ImportError, OSError): return False return (key == "/BAG_root/elevation") and (key in store) and (isinstance(store.f[key], h5py.Dataset)) def __init__(self, store, key): self._store = store self._key = key self._dset = store.f.elevation(mask_nan=True) self._meta = store.f.populate_metadata() @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return pp.basename(self.key) @property def description(self): return 'Dataset "%s"' % (self.display_name,) @property def shape(self): return self._dset.shape @property def dtype(self): return self._dset.dtype @property def extent(self): """ Geographic extent as a tuple: (lon_min, lon_max, lon_min, lon_max) """ return self._meta.geo_extent() def __getitem__(self, args): return self._dset[args] class BAGElevation(compass_model.GeoSurface): """ Represents a BAG elevation. """ class_kind = "BAG Elevation" @staticmethod def can_handle(store, key): # for GeoSurface we use cartopy that can be challenging to freeze on OSX to dependencies (i.e. geos) try: import cartopy.crs as ccrs except (ImportError, OSError): return False # for GeoSurface we are using a matplotlib function present after 1.5.x import matplotlib plt_maj, plt_min, _ = matplotlib.__version__.split('.') if (int(plt_maj) == 1) and (int(plt_min) < 5): return False return (key == "/BAG_root/elevation") and (key in store) and (isinstance(store.f[key], h5py.Dataset)) def __init__(self, store, key): self._store = store self._key = key self._dset = store.f.elevation(mask_nan=True) self._meta = store.f.populate_metadata() @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return pp.basename(self.key) @property def description(self): return 'Dataset "%s"' % (self.display_name,) @property def shape(self): return self._dset.shape @property def dtype(self): return self._dset.dtype @property def extent(self): """ Geographic extent as a tuple: (x_min, x_max, y_min, y_max) """ return self._meta.geo_extent() def __getitem__(self, args): return self._dset[args] class BAGUncertaintyArray(compass_model.Array): """ Represents an uncertainty array. """ class_kind = "BAG Uncertainty [array]" @staticmethod def can_handle(store, key): return (key == "/BAG_root/uncertainty") and (key in store) and (isinstance(store.f[key], h5py.Dataset)) def __init__(self, store, key): self._store = store self._key = key self._dset = store.f.uncertainty(mask_nan=True) @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return pp.basename(self.key) @property def description(self): return 'Dataset "%s"' % (self.display_name,) @property def shape(self): return self._dset.shape @property def dtype(self): return self._dset.dtype def __getitem__(self, args): return self._dset[args] class BAGTrackinList(compass_model.Array): """ Represents a BAG tracking list. """ class_kind = "BAG Tracking List" @staticmethod def can_handle(store, key): return (key == "/BAG_root/tracking_list") and (key in store) and (isinstance(store.f[key], h5py.Dataset)) def __init__(self, store, key): self._store = store self._key = key self._dset = store.f.tracking_list() @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return pp.basename(self.key) @property def description(self): return 'Dataset "%s"' % (self.display_name,) @property def shape(self): return self._dset.shape @property def dtype(self): return self._dset.dtype def __getitem__(self, args): return self._dset[args] class BAGMetadataRaw(compass_model.Array): """ Represents a raw BAG metadata. """ class_kind = "BAG Metadata [raw]" @staticmethod def can_handle(store, key): return (key == "/BAG_root/metadata") and (key in store) and (isinstance(store.f[key], h5py.Dataset)) def __init__(self, store, key): self._store = store self._key = key self._dset = store.f.metadata(as_string=False, as_pretty_xml=False) @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return pp.basename(self.key) @property def description(self): return 'Dataset "%s"' % (self.display_name,) @property def shape(self): return self._dset.shape @property def dtype(self): return self._dset.dtype def __getitem__(self, args): return self._dset[args] def is_plottable(self): if self.dtype.kind == 'S': log.debug("Not plottable since ASCII String (characters: %d)" % self.dtype.itemsize) return False if self.dtype.kind == 'U': log.debug("Not plottable since Unicode String (characters: %d)" % self.dtype.itemsize) return False return True class BAGMetadataText(compass_model.Text): """ Represents a text BAG metadata. """ class_kind = "BAG Metadata [text]" @staticmethod def can_handle(store, key): return (key == "/BAG_root/metadata") and (key in store) and (isinstance(store.f[key], h5py.Dataset)) def __init__(self, store, key): self._store = store self._key = key try: self._dset = store.f.metadata(as_string=True, as_pretty_xml=True) except BAGError as e: log.warning("unable to retrieve metadata as xml") self._dset = "" @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return pp.basename(self.key) @property def description(self): return 'Dataset "%s"' % (self.display_name,) @property def text(self): return self._dset class BAGMetadataXml(compass_model.Xml): """ Represents a text BAG metadata. """ class_kind = "BAG Metadata [xml]" @staticmethod def can_handle(store, key): return (key == "/BAG_root/metadata") and (key in store) and (isinstance(store.f[key], h5py.Dataset)) def has_validation(self): """For BAG data there is a known validation mechanism based on XSD and Schematron""" return True def __init__(self, store, key): self._store = store self._key = key try: self._dset = store.f.metadata(as_string=True, as_pretty_xml=True) except BAGError as e: log.warning("unable to retrieve metadata as xml") self._dset = "" @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return pp.basename(self.key) @property def description(self): return 'Dataset "%s"' % (self.display_name,) @property def text(self): return self._dset @property def validation(self): """ Collect a message string with the result of the validation """ return self.store.f.validation_info() class BAGUncertaintyArray(compass_model.Array): """ Represents an uncertainty array. """ class_kind = "BAG Uncertainty [array]" @staticmethod def can_handle(store, key): return (key == "/BAG_root/uncertainty") and (key in store) and (isinstance(store.f[key], h5py.Dataset)) def __init__(self, store, key): self._store = store self._key = key self._dset = store.f.uncertainty(mask_nan=True) @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return pp.basename(self.key) @property def description(self): return 'Dataset "%s"' % (self.display_name,) @property def shape(self): return self._dset.shape @property def dtype(self): return self._dset.dtype def __getitem__(self, args): return self._dset[args] class BAGUncertainty(compass_model.GeoArray): """ Represents a BAG uncertainty. """ class_kind = "BAG Uncertainty" @staticmethod def can_handle(store, key): # for GeoSurface we use cartopy that can be challenging to freeze on OSX to dependencies (i.e. geos) try: import cartopy.crs as ccrs except (ImportError, OSError): return False return (key == "/BAG_root/uncertainty") and (key in store) and (isinstance(store.f[key], h5py.Dataset)) def __init__(self, store, key): self._store = store self._key = key self._dset = store.f.uncertainty(mask_nan=True) self._meta = store.f.populate_metadata() @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return pp.basename(self.key) @property def description(self): return 'Dataset "%s"' % (self.display_name,) @property def shape(self): return self._dset.shape @property def dtype(self): return self._dset.dtype @property def extent(self): """ Geographic extent as a tuple: (x_min, x_max, y_min, y_max) """ return self._meta.geo_extent() def __getitem__(self, args): return self._dset[args] class BAGKV(compass_model.KeyValue): """ A KeyValue node used for BAG attributes (closely mimicking HDF5KV). """ class_kind = "BAG Attributes" @staticmethod def can_handle(store, key): return key in store.f def __init__(self, store, key): log.debug("init") self._store = store self._key = key self._obj = store.f[key] self._names = self._obj.attrs.keys() @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): n = pp.basename(self.key) return n if n != '' else '/' @property def description(self): return self.display_name @property def keys(self): return self._names[:] def __getitem__(self, name): return self._obj.attrs[name] class BAGImage(compass_model.Image): """ BAG true-color images (closely mimicking HDF5Image). """ class_kind = "BAG Truecolor Image" @staticmethod def can_handle(store, key): if key not in store: return False obj = store.f[key] if obj.attrs.get('CLASS') != 'IMAGE': return False if obj.attrs.get('IMAGE_SUBCLASS') != 'IMAGE_TRUECOLOR': return False if obj.attrs.get('INTERLACE_MODE') != 'INTERLACE_PIXEL': return False return True def __init__(self, store, key): log.debug("init") self._store = store self._key = key self._obj = store.f[key] @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): n = pp.basename(self.key) return n if n != '' else '/' @property def description(self): return self.display_name @property def width(self): return self._obj.shape[1] @property def height(self): return self._obj.shape[0] @property def palette(self): return None @property def data(self): return self._obj[:] # Register handlers BAGStore.push(BAGKV) BAGStore.push(BAGDataset) BAGStore.push(BAGElevationArray) BAGStore.push(BAGElevationGeoArray) BAGStore.push(BAGElevation) BAGStore.push(BAGUncertaintyArray) BAGStore.push(BAGUncertainty) BAGStore.push(BAGTrackinList) BAGStore.push(BAGMetadataRaw) BAGStore.push(BAGMetadataText) BAGStore.push(BAGMetadataXml) BAGStore.push(BAGGroup) BAGStore.push(BAGRoot) BAGStore.push(BAGImage) compass_model.push(BAGStore) hdf_compass-0.6.0/hdf_compass/bag_model/test.py0000666000000000000000000000233212730245342017667 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function import os from hdf_compass.compass_model.test import store, container from hdf_compass.bag_model import BAGGroup, BAGStore from hdf_compass.utils import data_url url = os.path.join(data_url(), "bag", "bdb_00.bag") s = store(BAGStore, url) c = container(BAGStore, url, BAGGroup, "/")hdf_compass-0.6.0/hdf_compass/bag_model/__init__.py0000666000000000000000000000220112730245342020442 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function, unicode_literals __version__ = "0.1.4" from .model import BAGStore, BAGDataset, BAGGroup, BAGImage, BAGKV import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler()) hdf_compass-0.6.0/hdf_compass/compass_model/0000777000000000000000000000000012730267653017263 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/compass_model/icons/0000777000000000000000000000000012730267653020376 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/compass_model/icons/array_16.png0000666000000000000000000000144012730245342022516 0ustar 00000000000000PNG  IHDRaIDATxuSKHQ>)ZeI Em 6BЪiD"hVAVE!(h.d`(g9/50.ʽ^\д[kkk-z{|| |;<444‚ ;8du|f#'h4@4rAhs\ DBҦ&vtts8;;+lllBOH(Ihe&tv}}3ѿo`+ H[K]"IENDB`hdf_compass-0.6.0/hdf_compass/compass_model/icons/array_64.png0000666000000000000000000001231012730245342022517 0ustar 00000000000000PNG  IHDR@@iqIDATx UՖϭj YAEe6Nև& qHO C4qF(VhP@A(Pd(((jZp@Ivg{kS?jŋGnݚ#111#rsSSSQGsssC>}/IyĢ˟)))}333vܹ{=:|:A8k?عs]UUU[u+'OtJhѢȺuu\Ю] =|Aiii) ~FGmmm5k6nٲˊj__y啿)' ??)]Z|;x㏗q}U!̙3'M6O4鯹ÜVh,9 Ոc~+D̙3;̼kEc9ĉ"o悃}^y啄UVԩS=//[ sdv  _hu ~ïc1$(8W%=nh駟N֭[=kjj:xbĆl{:@UE+//$=9}:u]Ekɼ w ,ul]OYjη*RҸ@U({nE?k:8奤;ZyRTJ G DǁbWʗ8rN iii^Ȣ:p >`7|c>|w_rX>iҤ+駟Iy,`zOjTccdymڴGc=%\YQn}vcǎУGy 7tÀvpZIB1aΝzŹß~i+V @+,fL*d>}z䑊+,ЋvynRMs˾ŋBhܸq/ү:" nprځ600Qb48#~ a[d4"OC.A ґ@T ߺ{/Sm;oٲeCPw ɰT g5HQAt$! m@zjg$ c  ,,< #Fp,|0`.!=(Z9tZ>lO(ӧORnC1Ca a0 2dka (a87ڛPsg 3ƥ?L#@0qa> 6D.?|jk{͚5t(QDkШ630 <"`lFq%qi7Κð~aц]f1i*]0eʔZPa8)P@d0*4 1c#"Jcc"Ù]pq9j4u k0  dsSOWSOEફJ7tvE,[eéboB2([>[N[| XB-@#oժUh91m 0ϟ?Zlڨ)2:e[nurC1f̷B4r !4cVA!3.DsPUjB %5gB'n9(ƅɀ YkT@EdX@(6m2Q N( ʀyЩX`p„Aa/[o . 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KKKqט xXOqY a* ?:}QhxO (]̺Ri!Kt̫"$ThUiXtep ` XYYyRA...[[[ kCgz;vS^C(3cPcy8wWnŸ@s=.U)ܓ%KIENDB`hdf_compass-0.6.0/hdf_compass/compass_model/icons/license.txt0000666000000000000000000001720612730245342022556 0ustar 00000000000000 GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. This version of the GNU Lesser General Public License incorporates the terms and conditions of version 3 of the GNU General Public License, supplemented by the additional permissions listed below. 0. Additional Definitions. As used herein, "this License" refers to version 3 of the GNU Lesser General Public License, and the "GNU GPL" refers to version 3 of the GNU General Public License. "The Library" refers to a covered work governed by this License, other than an Application or a Combined Work as defined below. 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Each version is given a distinguishing version number. If the Library as you received it specifies that a certain numbered version of the GNU Lesser General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that published version or of any later version published by the Free Software Foundation. If the Library as you received it does not specify a version number of the GNU Lesser General Public License, you may choose any version of the GNU Lesser General Public License ever published by the Free Software Foundation. If the Library as you received it specifies that a proxy can decide whether future versions of the GNU Lesser General Public License shall apply, that proxy's public statement of acceptance of any version is permanent authorization for you to choose that version for the Library.hdf_compass-0.6.0/hdf_compass/compass_model/icons/readme.txt0000666000000000000000000000041112730245342022357 0ustar 00000000000000This folder contains icons from the KDE Oxygen project, used as the default icons for various Node classes. They are packaged up into a .py file by the "package_icons.py" script which comes with HDFCompass. 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The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ The following class definitions represent the pluggable data model. By subclassing various things in this module, and implementing the missing (virtual) methods and properties, you can have the GUI infrastructure display your own objects without writing a single line of wxPython code. GUI support exists for generic kinds of objects including browsable containers, array-like datasets, and images. More importantly, you can add support for entirely new file formats. To implement support for a new kind of "datastore" (HDF5, HDF4, NetCDF, etc.), start by subclassing Store and overriding the appropriate methods and properties. Then, subclass the various Node classes this module provides (Container, Array, Image, etc.) and implement the various virtual bits of those classes as well: class FooStore(compass_model.Store): ... class FooGroup(compass_model.Container): ... class FooDataset(compass_model.Array): ... class FooPicture(compass_model.Image): ... You're not required to do all of them (and of course not all formats provide something like an Image), but the more you implement the more capable the interface will be. So that your Store class knows which kinds of nodes are available to open, manually register your Node subclasses: FooStore.push(FooGroup) FooStore.push(FooDataset) FooStore.push(FooPicture) Finally, let the rest of the world know about your new data store support by calling this module's register() function: compass_model.push(FooStore) You can also extend other peoples' stores. Suppose there's a module for reading HDF5 files, with a store class called foohdf5.HDF5Store, but the author didn't support the HDF5 Image standard. Just write a subclass of Image, and register it with the other person's class: class MyHDF5Image(Image): ... foohdf5.HDF5Store.push(MyHDF5Image) Of course, this assumes you know enough about the internals of the other person's Store to make your new class useful. """ from __future__ import absolute_import, division, print_function, unicode_literals from abc import ABCMeta, abstractmethod, abstractproperty import os import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler()) _stores = [] def push(store): """ Register a new data store class """ _stores.insert(0, store) def get_stores(): """ Get a list containing known data store classes """ return _stores[:] icon_folder = os.path.abspath(os.path.join(os.path.dirname(__file__), 'icons')) class Store(object): """ Represents a data store (i.e. a file or remote resource). """ __metaclass__ = ABCMeta # ------------------------------------------------------------------------- # Plugin support __nodeclasses = None @staticmethod def plugin_name(): """ Short name for the plugin. """ raise NotImplementedError @staticmethod def plugin_description(): """ Plugin description. Return useful info about the plugin as the main functionalities, the author, the support email (if any) """ raise NotImplementedError @classmethod def push(cls, nodeclass): """ Register a Node subclass. When a key is being opened, each subclass is queried in turn. The first one which reports it can handle the key is used. """ if cls.__nodeclasses is None: cls.__nodeclasses = [Unknown] cls.__nodeclasses.insert(0, nodeclass) @abstractmethod def __contains__(self, key): """ Check if a key is valid. """ log.error("to be overloaded") def __getitem__(self, key): """ Return a Node instance for *key*. Figures out the appropriate Node subclass for the object identified by "key", creates an instance and returns it. """ return self.gethandlers(key)[0](self, key) def gethandlers(self, key=None): """ Rather than picking a handler and returning the Node, return a list of all handlers which can do something useful with *key*. If *key* is not specified, returns all handlers """ if self.__nodeclasses is None: self.__nodeclasses = [Unknown] if key is None: return self.__nodeclasses if key not in self: raise KeyError(key) return [nc for nc in self.__nodeclasses if nc.can_handle(self, key)] # End plugin support # ------------------------------------------------------------------------- # For plugins which support local files, this is a dictionary mapping # file kinds to lists of extensions, e.g. {'HDF5 File': ['*.hdf5', '*.h5']} file_extensions = {} @abstractproperty def url(self): """ Identifies the file or Web resource (string). Examples might be "file:///path/to/foo.hdf5" or "http://www.example.com/web/resource" """ raise NotImplementedError @abstractproperty def display_name(self): """ Short name for display purposes. For example, for a file-based store you could implement this with os.path.basename(self.path). """ raise NotImplementedError @abstractproperty def root(self): """ The root node. Serves as the entry point into the resource. Every Store must implement this, and is required to return a Container instance. """ raise NotImplementedError @staticmethod # Python 2.x does not have abstractstatic def can_handle(url): """ Test if this class can open the resource. Returns True or False. Note this may have side effects, but the resource must not be modified. """ raise NotImplementedError @abstractproperty def valid(self): """ True if the store is open and ready for use, False otherwise. """ raise NotImplementedError @abstractmethod def __init__(self, url): """ Open the resource. """ raise NotImplementedError def close(self): """ Discontinue access to the resource. Any further use of this object, or retrieved nodes, is undefined. """ pass def get_parent(self, key): """ Return the parent node of the object identified by *key*. If an object has no parent, or contains itself, this should return None. That way, the "up" arrow on the Container view will be grayed out. """ pass class Node(object): """ Base class for all objects which live in a data store. You generally shouldn't inherit from Node directly, but from one of the more useful Node subclasses in this file. Direct Node subclasses can't do anything interesting in the GUI; all they do is show up in the browser. """ __metaclass__ = ABCMeta # Class attribute containing a dict for icon support. # Keys should be paths to icon files. # Example: icons = {16: png_16, 32: png_32} icons = NotImplemented # A short string (2 or 3 words) describing what the class represents. # This will show up in e.g. the "Open As" context menu. # Example: "HDF5 Image" or "Swath" class_kind = NotImplemented @staticmethod def can_handle(store, key): """ Determine whether this class can usefully represent the object. Keep in mind that keys are not technically required to be strings. """ raise NotImplementedError def __init__(self, store, key): """ Create an instance of this class. Subclasses must not modify the signature. """ raise NotImplementedError @property def key(self): """ Unique key which identifies this object in the store. Keys may be any hashable object, although strings are the most common. """ raise NotImplementedError @property def store(self): """ The data store to which the object belongs. """ raise NotImplementedError @property def display_name(self): """ A short name for display purposes """ raise NotImplementedError @property def display_title(self): """ A longer name appropriate for display in a window title. Defaults to *display_name*. """ return self.display_name @property def description(self): """ Descriptive string (possibly multi-line) """ raise NotImplementedError def preview(self, w, h): """ [Optional] PNG image preview """ return None class Container(Node): """ Represents an object which holds other objects (like an HDF5 group). Subclasses will be displayed using the browser view. """ __metaclass__ = ABCMeta icons = {16: os.path.join(icon_folder, "folder_16.png"), 64: os.path.join(icon_folder, "folder_64.png")} def __len__(self): """ Number of child objects """ raise NotImplementedError def __iter__(self): """ Iterator over child objects. Should yield Nodes, not keys (use your Store.open method). """ raise NotImplementedError def __getitem__(self, idx): """ Open an item by index (necessary to support ListCtrl). Should return a Node, not a key (use your Store.open method). """ raise NotImplementedError class KeyValue(Node): """ Represents an object which contains a sequence of key: value attributes. Keys must be strings. Subclasses will be displayed using a list-like control. """ __metaclass__ = ABCMeta icons = {16: os.path.join(icon_folder, "kv_16.png"), 64: os.path.join(icon_folder, "kv_64.png")} @property def keys(self): """ Return a list of attribute keys. """ raise NotImplementedError def __getitem__(self, name): """ Return the raw attribute value """ raise NotImplementedError class Array(Node): """ Represents a NumPy-style regular, rectangular array. Subclasses will be displayed in a spreadsheet-style viewer. """ __metaclass__ = ABCMeta icons = {16: os.path.join(icon_folder, "array_16.png"), 64: os.path.join(icon_folder, "array_64.png")} @property def shape(self): """ Shape tuple """ raise NotImplementedError @property def dtype(self): """ Data type """ raise NotImplementedError def __getitem__(self, args): """ Retrieve data elements """ raise NotImplementedError def is_plottable(self): """ To be overriden in case that there are cases in which the array is not plottable """ return True class GeoArray(Node): """ Represents a NumPy-style regular, rectangular array with a known geographic extent. """ __metaclass__ = ABCMeta icons = {16: os.path.join(icon_folder, "array_16.png"), 64: os.path.join(icon_folder, "array_64.png")} @property def shape(self): """ Shape tuple """ raise NotImplementedError @property def dtype(self): """ Data type """ raise NotImplementedError @property def extent(self): """ Geographic extent as a tuple: (x_min, x_max, y_min, y_max) """ raise NotImplementedError def __getitem__(self, args): """ Retrieve data elements """ raise NotImplementedError def is_plottable(self): """ To be overriden in case that there are cases in which the array is not plottable """ return True class GeoSurface(Node): """ Represents a NumPy-style regular, rectangular surface with a known geographic extent. """ __metaclass__ = ABCMeta icons = {16: os.path.join(icon_folder, "array_16.png"), 64: os.path.join(icon_folder, "array_64.png")} @property def shape(self): """ Shape tuple """ raise NotImplementedError @property def dtype(self): """ Data type """ raise NotImplementedError def __getitem__(self, args): """ Retrieve data elements """ raise NotImplementedError def is_plottable(self): """ To be overriden in case that there are cases in which the array is not plottable """ return True class Image(Node): """ A single raster image. """ __metaclass__ = ABCMeta icons = {16: os.path.join(icon_folder, "image_16.png"), 64: os.path.join(icon_folder, "image_64.png")} @property def width(self): """ Image width in pixels """ pass @property def height(self): """ Image height in pixels """ pass @property def palette(self): """ Palette array, or None. """ raise NotImplementedError @property def data(self): """ Image data """ class Text(Node): """ A text. """ __metaclass__ = ABCMeta icons = {16: os.path.join(icon_folder, "text_16.png"), 64: os.path.join(icon_folder, "text_64.png")} @property def text(self): """ Text data """ class Xml(Text): """ A XML text. """ __metaclass__ = ABCMeta icons = {16: os.path.join(icon_folder, "xml_16.png"), 64: os.path.join(icon_folder, "xml_64.png")} def has_validation(self): """To be overriden in case that the xml has a known mechanism to be validated""" return False @property def validation(self): """ Validation info """ class Unknown(Node): """ "Last resort" node (and the only concrete class in this module). These can always be created, but do nothing useful. """ icons = {16: os.path.join(icon_folder, "unknown_16.png"), 64: os.path.join(icon_folder, "unknown_64.png")} class_kind = "Unknown" @staticmethod def can_handle(store, key): return True def __init__(self, store, key): self._key = key self._store = store @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): import os.path try: return os.path.basename(str(self.key)) except Exception: return "Unknown" @property def description(self): return "Unknown object" hdf_compass-0.6.0/hdf_compass/compass_model/test.py0000666000000000000000000001661612730245342020615 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Provides support for testing basic properties of data model implementations. Checks to make sure all required properties and methods are implemented, and does basic sanity/consistency checking. More specific tests must be written by plugin authors. The public interface consists of the following functions, each of which provides a TestCase subclass which may be used with unittest: - store - container - array [not implemented] - key-value [not implemented] - image [not implemented] Example, in my_model.test: from hdf_compass.compass_model.test import store, container from hdf_compass.my_model import MyStore, MyContainer URL = "file:///path/to/myfile.ext" store_tests = store(MyStore, URL) container_tests = container(MyStore, URL, MyContainer, "some-key") To run unittest, which discovers classes "store_tests" and "container_tests": $ python -m unittest hdf_compass.my_model.test """ from __future__ import absolute_import, division, print_function import unittest as ut from . import Node, Store # --- Public API -------------------------------------------------------------- def store(store_cls_, url_): """ Construct a TestCase appropriate for a Store subclass. store_cls_: Your compass_model.Store implementation. url_: A URL representing a valid data-store to test against. """ class TestStore(_TestStore): store_cls = store_cls_ url = url_ return TestStore def container(store_cls_, url_, node_cls_, key_): """ Construct a TestCase class appropriate for a Container subclass. store_cls_: Your compass_model.Store implementation. url_: A URL representing a valid data-store to test against. node_cls_: Your compass_model.Container implementation. key_: A valid key which points to a container. """ class TestContainer(_TestContainer): store_cls = store_cls_ url = url_ node_cls = node_cls_ key = key_ return TestContainer # --- End public API ---------------------------------------------------------- class _TestStore(ut.TestCase): """ Base class for testing Stores. """ store_cls = None url = None def setUp(self): self.store = self.store_cls(self.url) def tearDown(self): if self.store.valid: self.store.close() def test_class(self): """ Verify the thing we get from store_cls is actually a Store """ self.assertIsInstance(self.store, Store) def test_url(self): """ Verify store.url produces a string """ self.assertIsInstance(self.store.url, basestring) def test_display_name(self): """ Verify store.display_name produces a string. """ self.assertIsInstance(self.store.display_name, basestring) def test_root(self): """ Verify store.root exists and has no parent """ self.assertIsInstance(self.store.root, Node) self.assertIs(self.store.get_parent(self.store.root.key), None) def test_close_valid(self): """ Verify that store.close() works and is reflected by store.valid """ self.assertTrue(self.store.valid) self.store.close() self.assertFalse(self.store.valid) def test_can_handle(self): """ Verify can_handle() works properly """ self.assertTrue(self.store_cls.can_handle(self.url)) self.assertFalse(self.store_cls.can_handle("file:///no/such/path")) def test_handlers(self): """ The implementation has at least one Node handler registered """ h = self.store.gethandlers() # Test for N > 1 because compass_model.Unknown is always present self.assertGreater(len(h), 1) class _TestNode(ut.TestCase): """ Base class for testing Node objects. """ store_cls = None node_cls = None url = None key = None def setUp(self): self.store = self.store_cls(self.url) self.node = self.node_cls(self.store, self.key) def tearDown(self): if self.store.valid: self.store.close() def test_contains(self): """ Consistency check for store __contains___ """ self.assertTrue(self.key in self.store) self.assertFalse("key_not_in_store" in self.store) def test_icons(self): """ Icon dict is present and contains valid icon paths: keys: int values: icon paths Required sizes: 16x16 and 64x64 """ import os for key, val in self.node_cls.icons.iteritems(): self.assertIsInstance(key, int) self.assertIsInstance(val, unicode) self.assertTrue(os.path.exists(val)) # required resolutions self.assertIn(16, self.node_cls.icons) self.assertIn(64, self.node_cls.icons) def test_class_kind(self): """ class_kind is present, and a string """ self.assertIsInstance(self.node_cls.class_kind, basestring) def test_can_handle(self): """ can_handle() consistency check """ self.assertTrue(self.node_cls.can_handle(self.store, self.key)) self.assertFalse(self.node_cls.can_handle(self.store, "/some/random/key")) def test_key(self): """ Node.key returns a hashable object. We also require that the key be unchanged. """ out = self.node.key hash(out) self.assertEqual(self.node.key, self.key) def test_store(self): """ Node.store returns a data store of the same class and URL. """ self.assertIsInstance(self.node.store, self.store_cls) self.assertEqual(self.node.store.url, self.store.url) def test_display_name(self): """ display_name exists and is a string """ self.assertIsInstance(self.node.display_name, basestring) class _TestContainer(_TestNode): """ Class for testing compass_model.Container implementations. """ def test_len(self): """ Object length is consistent with iter() result """ self.assertGreaterEqual(len(self.node), 0) self.assertEqual(len(self.node), len(list(self.node))) def test_getitem(self): """ __getitem__ works properly """ for idx in xrange(len(self.node)): out = self.node[idx] self.assertIsInstance(out, Node) def test_getitem_exception(self): """ out-of range indices raise IndexError """ with self.assertRaises(IndexError): self.node[len(self.node)] hdf_compass-0.6.0/hdf_compass/compass_model/__init__.py0000666000000000000000000000225012730245342021362 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function, unicode_literals from .model import get_stores, push, Store, Node, Container, KeyValue, \ GeoArray, GeoSurface, Array, Text, Xml, Image, Unknown import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler()) hdf_compass-0.6.0/hdf_compass/compass_viewer/0000777000000000000000000000000012730267653017464 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/compass_viewer/array/0000777000000000000000000000000012730267653020602 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/compass_viewer/array/frame.py0000666000000000000000000003444612730245342022250 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Implements a viewer frame for compass_model.Array. """ from __future__ import absolute_import, division, print_function, unicode_literals import wx import wx.grid from wx.lib.newevent import NewCommandEvent import os import logging log = logging.getLogger(__name__) from ..frame import NodeFrame from .plot import LinePlotFrame, ContourPlotFrame # Indicates that the slicing selection may have changed. # These events are emitted by the SlicerPanel. ArraySlicedEvent, EVT_ARRAY_SLICED = NewCommandEvent() # Menu and button IDs ID_VIS_MENU_PLOT = wx.NewId() class ArrayFrame(NodeFrame): """ Top-level frame displaying objects of type compass_model.Array. From top to bottom, has: 1. Toolbar (see ArrayFrame.init_toolbar) 2. SlicerPanel, with controls for changing what's displayed. 3. An ArrayGrid, which displays the data in a spreadsheet-like view. """ def __init__(self, node, pos=None): """ Create a new array viewer to display the node. """ NodeFrame.__init__(self, node, size=(800, 400), title=node.display_name, pos=pos) self.node = node # Update the menu vis_menu = wx.Menu() if self.node.is_plottable(): vis_menu.Append(ID_VIS_MENU_PLOT, "Plot Data\tCtrl-D") self.add_menu(vis_menu, "Visualize") # Initialize the toolbar self.init_toolbar() # The Slicer is the panel with indexing controls self.slicer = SlicerPanel(self, node.shape, node.dtype.fields is not None) # Create the grid array self.grid = ArrayGrid(self, node, self.slicer) # Sizer for slicer and grid gridsizer = wx.BoxSizer(wx.VERTICAL) gridsizer.Add(self.slicer, 0, wx.EXPAND) gridsizer.Add(self.grid, 1, wx.EXPAND) self.view = gridsizer self.Bind(EVT_ARRAY_SLICED, self.on_sliced) if self.node.is_plottable(): self.Bind(wx.EVT_MENU, self.on_plot, id=ID_VIS_MENU_PLOT) # Workaround for wxPython bug (see SlicerPanel.enable_spinctrls) ID_WORKAROUND_TIMER = wx.NewId() self.Bind(wx.EVT_TIMER, self.on_workaround_timer, id=ID_WORKAROUND_TIMER) self.timer = wx.Timer(self, ID_WORKAROUND_TIMER) self.timer.Start(100) def init_toolbar(self): """ Set up the toolbar at the top of the window. """ t_size = (24, 24) plot_bmp = wx.Bitmap(os.path.join(self.icon_folder, "viz_plot_24.png"), wx.BITMAP_TYPE_ANY) self.toolbar = self.CreateToolBar(wx.TB_HORIZONTAL | wx.NO_BORDER | wx.TB_FLAT | wx.TB_TEXT) self.toolbar.SetToolBitmapSize(t_size) self.toolbar.AddStretchableSpace() if self.node.is_plottable(): self.toolbar.AddLabelTool(ID_VIS_MENU_PLOT, "Plot Data", plot_bmp, shortHelp="Plot data in a popup window", longHelp="Plot the array data in a popup window") self.toolbar.Realize() def on_sliced(self, evt): """ User has chosen to display a different part of the dataset. """ self.grid.Refresh() def on_plot(self, evt): """ User has chosen to plot the current selection """ cols = self.grid.GetSelectedCols() rows = self.grid.GetSelectedRows() # Scalar data can't be line-plotted. if len(self.node.shape) == 0: return # Columns in the view are selected if len(cols) != 0: # The data is compound if self.node.dtype.names is not None: names = [self.grid.GetColLabelValue(x) for x in cols] data = self.node[self.slicer.indices] # -> 1D compound array data = [data[n] for n in names] f = LinePlotFrame(data, names) f.Show() # Plot multiple columns independently else: if len(self.node.shape) == 1: data = [self.node[self.slicer.indices]] else: data = [self.node[self.slicer.indices + (c,)] for c in cols] names = ["Col %d" % c for c in cols] if len(data) > 1 else None f = LinePlotFrame(data, names) f.Show() # Rows in view are selected elif len(rows) != 0: data = [self.node[self.slicer.indices + (slice(None, None, None), r)] for r in rows] names = ["Row %d" % r for r in rows] if len(data) > 1 else None f = LinePlotFrame(data, names) f.Show() # No row or column selection. Plot everything else: data = self.node[self.slicer.indices] # The data is compound if self.node.dtype.names is not None: names = [self.grid.GetColLabelValue(x) for x in xrange(self.grid.GetNumberCols())] data = [data[n] for n in names] f = LinePlotFrame(data, names) f.Show() # Plot 1D elif len(self.node.shape) == 1: f = LinePlotFrame([data]) f.Show() # Plot 2D else: f = ContourPlotFrame(data) f.Show() def on_workaround_timer(self, evt): """ See slicer.enable_spinctrls docs """ self.timer.Destroy() self.slicer.enable_spinctrls() class SlicerPanel(wx.Panel): """ Holds controls for data access. Consult the "indices" property, which returns a tuple of indices that prefix the array. This will be RANK-2 elements long, unless hasfields is true, in which case it will be RANK-1 elements long. """ @property def indices(self): """ A tuple of integer indices appropriate for slicing. Will be RANK-2 elements long, RANK-1 if compound data is in use (hasfields == True). """ return tuple([x.GetValue() for x in self.spincontrols]) def __init__(self, parent, shape, hasfields): """ Create a new slicer panel. parent: The wxPython parent window shape: Shape of the data to visualize hasfields: If True, the data is compound and the grid can only display one axis. So, we should display an extra spinbox. """ wx.Panel.__init__(self, parent) self.shape = shape self.hasfields = hasfields self.spincontrols = [] # Rank of the underlying array rank = len(shape) # Rank displayable in the grid. If fields are present, they occupy # the columns, so the data displayed is actually 1-D. visible_rank = 1 if hasfields else 2 sizer = wx.BoxSizer(wx.HORIZONTAL) # Will arrange the SpinCtrls if rank > visible_rank: infotext = wx.StaticText(self, wx.ID_ANY, "Array Indexing: ") sizer.Add(infotext, 0, flag=wx.EXPAND | wx.ALL, border=10) for idx in xrange(rank - visible_rank): sc = wx.SpinCtrl(self, max=shape[idx] - 1, value="0", min=0) sizer.Add(sc, 0, flag=wx.EXPAND | wx.ALL, border=10) sc.Disable() self.spincontrols.append(sc) self.SetSizer(sizer) self.Bind(wx.EVT_SPINCTRL, self.on_spin) def enable_spinctrls(self): """ Unlock the spin controls. Because of a bug in wxPython on Mac, by default the first spin control has bizarre contents (and control focus) when the panel starts up. Call this after a short delay (e.g. 100 ms) to enable indexing. """ for sc in self.spincontrols: sc.Enable() def on_spin(self, evt): """ Spinbox value changed; notify parent to refresh the grid. """ wx.PostEvent(self, ArraySlicedEvent(self.GetId())) class ArrayGrid(wx.grid.Grid): """ Grid class to display the Array. Cell contents and appearance are handled by the table model in ArrayTable. """ def __init__(self, parent, node, slicer): wx.grid.Grid.__init__(self, parent) table = ArrayTable(node, slicer) self.SetTable(table, True) # Column selection is always allowed selmode = wx.grid.Grid.wxGridSelectColumns # Row selection is forbidden for compound types, and for # scalar/1-D datasets if node.dtype.names is None and len(node.shape) > 1: selmode |= wx.grid.Grid.wxGridSelectRows self.SetSelectionMode(selmode) class LRUTileCache(object): """ Simple tile-based LRU cache which goes between the Grid and the Array object. Caches tiles along the last 1 or 2 dimensions of a dataset. Access is via __getitem__. Because this class exists specifically to support point-based callbacks for the Grid, arguments may only be indices, not slices. """ TILESIZE = 100 # Tiles will have shape (100,) or (100, 100) MAXTILES = 50 # Max number of tiles to retain in the cache def __init__(self, arr): """ *arr* is anything implementing compass_model.Array """ import collections self.cache = collections.OrderedDict() self.arr = arr def __getitem__(self, args): """ Restricted to an index or tuple of indices. """ if not isinstance(args, tuple): args = (args,) # Split off the last 1 or 2 dimensions coarse_position, fine_position = args[0:-2], args[-2:] def clip(x): """ Round down to nearest TILESIZE; takes e.g. 181 -> 100 """ return (x // self.TILESIZE) * self.TILESIZE # Tuple with index of tile corner tile_key = coarse_position + tuple(clip(x) for x in fine_position) # Slice which will be applied to dataset to retrieve tile tile_slice = coarse_position + tuple(slice(clip(x), clip(x) + self.TILESIZE) for x in fine_position) # Index applied to tile to retrieve the desired data point tile_data_index = tuple(x % self.TILESIZE for x in fine_position) # Case 1: Add tile to cache, ejecting oldest tile if needed if not tile_key in self.cache: if len(self.cache) >= self.MAXTILES: self.cache.popitem(last=False) tile = self.arr[tile_slice] self.cache[tile_key] = tile # Case 2: Mark the tile as recently accessed else: tile = self.cache.pop(tile_key) self.cache[tile_key] = tile return tile[tile_data_index] class ArrayTable(wx.grid.PyGridTableBase): """ "Table" class which provides data and metadata for the grid to display. The methods defined here define the contents of the table, as well as the number of rows, columns and their values. """ def __init__(self, node, slicer): """ Create a new Table instance for use with a grid control. node: An compass_model.Array implementation instance. slicer: An instance of SlicerPanel, so we can see what indices the user has requested. """ wx.grid.PyGridTableBase.__init__(self) self.node = node self.slicer = slicer self.rank = len(node.shape) self.names = node.dtype.names self.cache = LRUTileCache(self.node) def GetNumberRows(self): """ Callback for number of rows displayed by the grid control """ if self.rank == 0: return 1 return self.node.shape[-1] def GetNumberCols(self): """ Callback for number of columns displayed by the grid control. Note that if compound data is in use, columns display the field names. """ if self.names is not None: return len(self.names) if self.rank < 2: return 1 return self.node.shape[-2] def GetValue(self, row, col): """ Callback which provides data to the Grid. row, col: Integers giving row and column position (0-based). """ # Scalar case if self.rank == 0: data = self.node[()] if self.names is None: return data return data[col] # 1D case if self.rank == 1: data = self.cache[row] if self.names is None: return data return data[self.names[col]] # ND case. Watch out for compound mode! if self.names is None: args = self.slicer.indices + (col, row) else: args = self.slicer.indices + (row,) data = self.cache[args] if self.names is None: return data return data[self.names[col]] def GetRowLabelValue(self, row): """ Callback for row labels. Row number is used unless the data is scalar. """ if self.rank == 0: return "Value" return str(row) def GetColLabelValue(self, col): """ Callback for column labels. Column number is used, except for scalar or 1D data, or if we're displaying field names in the columns. """ if self.names is not None: return self.names[col] if self.rank == 0 or self.rank == 1: return "Value" return str(col) hdf_compass-0.6.0/hdf_compass/compass_viewer/array/plot.py0000666000000000000000000001561212730245342022126 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Matplotlib window with toolbar. """ from __future__ import absolute_import, division, print_function, unicode_literals import numpy as np import wx import matplotlib.pyplot as plt from matplotlib.figure import Figure from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigCanvas from matplotlib.backends.backend_wx import NavigationToolbar2Wx as NavigationToolbar import logging log = logging.getLogger(__name__) from ..frame import BaseFrame ID_VIEW_CMAP_JET = wx.NewId() # default ID_VIEW_CMAP_BONE = wx.NewId() ID_VIEW_CMAP_GIST_EARTH = wx.NewId() ID_VIEW_CMAP_OCEAN = wx.NewId() ID_VIEW_CMAP_RAINBOW = wx.NewId() ID_VIEW_CMAP_RDYLGN = wx.NewId() ID_VIEW_CMAP_WINTER = wx.NewId() class PlotFrame(BaseFrame): """ Base class for Matplotlib plot windows. Override draw_figure() to plot your figure on the provided axes. """ def __init__(self, data, title="a title"): """ Create a new Matplotlib plotting window for a 1D line plot """ log.debug(self.__class__.__name__) BaseFrame.__init__(self, id=wx.ID_ANY, title=title, size=(800, 400)) self.data = data self.panel = wx.Panel(self) self.dpi = 100 self.fig = Figure((6.0, 4.0), dpi=self.dpi) self.canvas = FigCanvas(self.panel, -1, self.fig) self.axes = self.fig.add_subplot(111) self.toolbar = NavigationToolbar(self.canvas) self.vbox = wx.BoxSizer(wx.VERTICAL) self.vbox.Add(self.canvas, 1, wx.LEFT | wx.TOP | wx.GROW) self.vbox.Add(self.toolbar, 0, wx.EXPAND) self.panel.SetSizer(self.vbox) self.vbox.Fit(self) self.draw_figure() def draw_figure(self): raise NotImplementedError class LinePlotFrame(PlotFrame): def __init__(self, data, names=None, title="Line Plot"): self.names = names PlotFrame.__init__(self, data, title) def draw_figure(self): lines = [self.axes.plot(d)[0] for d in self.data] if self.names is not None: for n in self.names: self.axes.legend(tuple(lines), tuple(self.names)) class ContourPlotFrame(PlotFrame): def __init__(self, data, names=None, title="Contour Plot"): # need to be set before calling the parent (need for plotting) self.colormap = "jet" self.cb = None # matplotlib color-bar PlotFrame.__init__(self, data, title) self.cmap_menu = wx.Menu() self.cmap_menu.Append(ID_VIEW_CMAP_JET, "Jet", kind=wx.ITEM_RADIO) self.cmap_menu.Append(ID_VIEW_CMAP_BONE, "Bone", kind=wx.ITEM_RADIO) self.cmap_menu.Append(ID_VIEW_CMAP_GIST_EARTH, "Gist Earth", kind=wx.ITEM_RADIO) self.cmap_menu.Append(ID_VIEW_CMAP_OCEAN, "Ocean", kind=wx.ITEM_RADIO) self.cmap_menu.Append(ID_VIEW_CMAP_RAINBOW, "Rainbow", kind=wx.ITEM_RADIO) self.cmap_menu.Append(ID_VIEW_CMAP_RDYLGN, "Red-Yellow-Green", kind=wx.ITEM_RADIO) self.cmap_menu.Append(ID_VIEW_CMAP_WINTER, "Winter", kind=wx.ITEM_RADIO) self.add_menu(self.cmap_menu, "Colormap") self.Bind(wx.EVT_MENU, self.on_cmap_jet, id=ID_VIEW_CMAP_JET) self.Bind(wx.EVT_MENU, self.on_cmap_bone, id=ID_VIEW_CMAP_BONE) self.Bind(wx.EVT_MENU, self.on_cmap_gist_earth, id=ID_VIEW_CMAP_GIST_EARTH) self.Bind(wx.EVT_MENU, self.on_cmap_ocean, id=ID_VIEW_CMAP_OCEAN) self.Bind(wx.EVT_MENU, self.on_cmap_rainbow, id=ID_VIEW_CMAP_RAINBOW) self.Bind(wx.EVT_MENU, self.on_cmap_rdylgn, id=ID_VIEW_CMAP_RDYLGN) self.Bind(wx.EVT_MENU, self.on_cmap_winter, id=ID_VIEW_CMAP_WINTER) self.status_bar = wx.StatusBar(self, -1) self.status_bar.SetFieldsCount(2) self.SetStatusBar(self.status_bar) self.canvas.mpl_connect('motion_notify_event', self.update_status_bar) self.canvas.Bind(wx.EVT_ENTER_WINDOW, self.change_cursor) def on_cmap_jet(self, evt): log.debug("cmap: jet") self.colormap = "jet" self._refresh_plot() def on_cmap_bone(self, evt): log.debug("cmap: bone") self.colormap = "bone" self._refresh_plot() def on_cmap_gist_earth(self, evt): log.debug("cmap: gist_earth") self.colormap = "gist_earth" self._refresh_plot() def on_cmap_ocean(self, evt): log.debug("cmap: ocean") self.colormap = "ocean" self._refresh_plot() def on_cmap_rainbow(self, evt): log.debug("cmap: rainbow") self.colormap = "rainbow" self._refresh_plot() def on_cmap_rdylgn(self, evt): log.debug("cmap: RdYlGn") self.colormap = "RdYlGn" self._refresh_plot() def on_cmap_winter(self, evt): log.debug("cmap: winter") self.colormap = "winter" self._refresh_plot() def _refresh_plot(self): self.draw_figure() self.canvas.draw() def draw_figure(self): max_elements = 500 # don't attempt plot more than 500x500 elements rows = self.data.shape[0] cols = self.data.shape[1] row_stride = rows // max_elements + 1 col_stride = cols // max_elements + 1 data = self.data[::row_stride, ::col_stride] xx = np.arange(0, self.data.shape[1], col_stride) yy = np.arange(0, self.data.shape[0], row_stride) img = self.axes.contourf(xx, yy, data, 25, cmap=plt.cm.get_cmap(self.colormap)) self.axes.set_aspect('equal') if self.cb: self.cb.on_mappable_changed(img) else: self.cb = plt.colorbar(img, ax=self.axes) self.cb.ax.tick_params(labelsize=8) def change_cursor(self, event): self.canvas.SetCursor(wx.StockCursor(wx.CURSOR_CROSS)) def update_status_bar(self, event): msg = str() if event.inaxes: x, y = int(event.xdata), int(event.ydata) z = self.data[y, x] msg = "x= %d, y= %d, z= %f" % (x, y, z) self.status_bar.SetStatusText(msg, 1) hdf_compass-0.6.0/hdf_compass/compass_viewer/array/__init__.py0000666000000000000000000000207712730245342022710 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function, unicode_literals from .frame import ArrayFrame import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler())hdf_compass-0.6.0/hdf_compass/compass_viewer/container/0000777000000000000000000000000012730267653021446 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/compass_viewer/container/frame.py0000666000000000000000000002147312730245342023110 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Implements a viewer for compass_model.Container instances. This frame is a simple browser view with back/forward/up controls. Currently list and icon views are supported. """ from __future__ import absolute_import, division, print_function, unicode_literals import wx import os import logging log = logging.getLogger(__name__) from hdf_compass import compass_model from ..frame import NodeFrame from ..events import ID_COMPASS_OPEN from ..events import EVT_CONTAINER_SELECTION from .list import ContainerReportList, ContainerIconList ID_GO_MENU_BACK = wx.NewId() ID_GO_MENU_NEXT = wx.NewId() ID_GO_MENU_UP = wx.NewId() ID_GO_MENU_TOP = wx.NewId() ID_VIEW_MENU_LIST = wx.NewId() ID_VIEW_MENU_ICON = wx.NewId() class ContainerFrame(NodeFrame): """ A frame to display a Container class, and browse its contents. """ def __init__(self, node, pos=None): """ Create a new frame. node: Container instance to display. pos: Screen position at which to display the window. """ NodeFrame.__init__(self, node, size=(800, 400), title=node.display_title, pos=pos) view_menu = wx.Menu() view_menu.Append(ID_VIEW_MENU_LIST, "List view") view_menu.Append(ID_VIEW_MENU_ICON, "Icon view") self.add_menu(view_menu, "View") self.view_menu = view_menu go_menu = wx.Menu() go_menu.Append(ID_GO_MENU_BACK, "Back") go_menu.Append(ID_GO_MENU_NEXT, "Next") go_menu.Append(ID_GO_MENU_UP, "Up") go_menu.Append(ID_GO_MENU_TOP, "Top") self.add_menu(go_menu, "Go") self.go_menu = go_menu self.acc_tbl = wx.AcceleratorTable([ (wx.ACCEL_CMD, wx.WXK_LEFT, ID_GO_MENU_BACK), (wx.ACCEL_CMD, wx.WXK_RIGHT, ID_GO_MENU_NEXT), (wx.ACCEL_CMD, wx.WXK_UP, ID_GO_MENU_UP), (wx.ACCEL_CMD | wx.ACCEL_SHIFT, wx.WXK_UP, ID_GO_MENU_TOP), ]) self.SetAcceleratorTable(self.acc_tbl) self.Bind(wx.EVT_MENU, self.on_open, id=ID_COMPASS_OPEN) self.Bind(EVT_CONTAINER_SELECTION, lambda evt: self.update_info()) self.Bind(wx.EVT_MENU, lambda evt: self.go_back(), id=ID_GO_MENU_BACK) self.Bind(wx.EVT_MENU, lambda evt: self.go_next(), id=ID_GO_MENU_NEXT) self.Bind(wx.EVT_MENU, lambda evt: self.go_up(), id=ID_GO_MENU_UP) self.Bind(wx.EVT_MENU, lambda evt: self.go_top(), id=ID_GO_MENU_TOP) self.Bind(wx.EVT_MENU, lambda evt: self.list_view(), id=ID_VIEW_MENU_LIST) self.Bind(wx.EVT_MENU, lambda evt: self.icon_view(), id=ID_VIEW_MENU_ICON) self.toolbar = self.CreateToolBar(wx.TB_HORIZONTAL | wx.NO_BORDER | wx.TB_FLAT | wx.TB_TEXT) tsize = (24, 24) back_bmp = wx.Bitmap(os.path.join(self.icon_folder, "go_back_24.png"), wx.BITMAP_TYPE_ANY) next_bmp = wx.Bitmap(os.path.join(self.icon_folder, "go_next_24.png"), wx.BITMAP_TYPE_ANY) up_bmp = wx.Bitmap(os.path.join(self.icon_folder, "go_up_24.png"), wx.BITMAP_TYPE_ANY) top_bmp = wx.Bitmap(os.path.join(self.icon_folder, "go_top_24.png"), wx.BITMAP_TYPE_ANY) icon_bmp = wx.Bitmap(os.path.join(self.icon_folder, "view_icon_24.png"), wx.BITMAP_TYPE_ANY) list_bmp = wx.Bitmap(os.path.join(self.icon_folder, "view_list_24.png"), wx.BITMAP_TYPE_ANY) self.toolbar.SetToolBitmapSize(tsize) self.toolbar.AddLabelTool(ID_GO_MENU_BACK, "Back", back_bmp, shortHelp="New", longHelp="Long help for 'New'") self.toolbar.AddLabelTool(ID_GO_MENU_NEXT, "Next", next_bmp, shortHelp="New", longHelp="Long help for 'New'") self.toolbar.AddSeparator() self.toolbar.AddLabelTool(ID_GO_MENU_UP, "Up", up_bmp, shortHelp="New", longHelp="Long help for 'New'") self.toolbar.AddLabelTool(ID_GO_MENU_TOP, "Top", top_bmp, shortHelp="New", longHelp="Long help for 'New'") self.toolbar.AddStretchableSpace() self.toolbar.AddLabelTool(ID_VIEW_MENU_LIST, "List View", list_bmp, shortHelp="New", longHelp="Long help for 'New'") self.toolbar.AddLabelTool(ID_VIEW_MENU_ICON, "Icon View", icon_bmp, shortHelp="New", longHelp="Long help for 'New'") self.toolbar.Realize() self.view = ContainerReportList(self, node) self.history = [node] self.history_ptr = 0 self.update_view() def list_view(self): """ Switch to list view """ if not isinstance(self.view, ContainerReportList): self.view = ContainerReportList(self, self.history[self.history_ptr]) def icon_view(self): """ Switch to icon view """ if not isinstance(self.view, ContainerIconList): self.view = ContainerIconList(self, self.history[self.history_ptr]) # --- Begin history support functions ------------------------------------- @property def node(self): return self.history[self.history_ptr] def go_back(self): """ Go to the previously displayed item """ if self.history_ptr > 0: self.history_ptr -= 1 self.update_view() def go_next(self): """ Go to the next displayed item """ if self.history_ptr < (len(self.history) - 1): self.history_ptr += 1 self.update_view() def go_up(self): """ Go to the enclosing container """ node = self.history[self.history_ptr] parent = node.store.get_parent(node.key) if parent.key != node.key: # at the root item self.go(parent) def go_top(self): """ Go to the root node """ node = self.history[self.history_ptr] parent = node.store.root if parent.key != node.key: # at the root item self.go(parent) def go(self, newnode): """ Go to a particular node. Adds the node to the history. """ del self.history[self.history_ptr + 1:] self.history.append(newnode) self.history_ptr += 1 self.update_view() # --- End history support functions --------------------------------------- def update_view(self): """ Refresh the entire contents of the frame according to self.node. """ self.SetTitle(self.node.display_title) self.view = type(self.view)(self, self.node) self.update_info() can_go_back = self.history_ptr > 0 can_go_next = self.history_ptr < (len(self.history) - 1) can_go_up = self.node.store.get_parent(self.node.key) is not None can_go_top = self.node.key != self.node.store.root.key self.go_menu.Enable(ID_GO_MENU_BACK, can_go_back) self.go_menu.Enable(ID_GO_MENU_NEXT, can_go_next) self.go_menu.Enable(ID_GO_MENU_UP, can_go_up) self.go_menu.Enable(ID_GO_MENU_TOP, can_go_top) self.toolbar.EnableTool(ID_GO_MENU_BACK, can_go_back) self.toolbar.EnableTool(ID_GO_MENU_NEXT, can_go_next) self.toolbar.EnableTool(ID_GO_MENU_UP, can_go_up) self.toolbar.EnableTool(ID_GO_MENU_TOP, can_go_top) icon_view_allowed = len(self.node) <= 1000 self.view_menu.Enable(ID_VIEW_MENU_ICON, icon_view_allowed) self.toolbar.EnableTool(ID_VIEW_MENU_ICON, icon_view_allowed) def update_info(self): """ Refresh the left-hand side information panel, according to the current selection in the view. """ node = self.view.selection if node is None: node = self.node # Nothing selected; show this node's info self.info.display(node) def on_open(self, evt): """ Trap Container open events, so we can browse instead of launching new windows. """ new_node = evt.node log.debug("Got request to open node: %s" % new_node.key) if isinstance(new_node, compass_model.Container): self.go(new_node) else: evt.Skip() hdf_compass-0.6.0/hdf_compass/compass_viewer/container/list.py0000666000000000000000000002043012730245342022761 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Handles list and icon view for Container display. """ from __future__ import absolute_import, division, print_function, unicode_literals import wx import logging log = logging.getLogger(__name__) from hdf_compass import compass_model from ..events import CompassOpenEvent from ..events import ContainerSelectionEvent ID_CONTEXT_MENU_OPEN = wx.NewId() ID_CONTEXT_MENU_OPENWINDOW = wx.NewId() class ContainerList(wx.ListCtrl): """ Base class for list and icons views, both of which use wx.ListCtrl. Defines the current selection (via .selection property) as well as handling item activation (double-click, Enter) and right-click context menu. """ def __init__(self, parent, node, **kwds): wx.ListCtrl.__init__(self, parent, **kwds) self.Bind(wx.EVT_LIST_ITEM_RIGHT_CLICK, self.on_rclick) self.Bind(wx.EVT_LIST_ITEM_ACTIVATED, self.on_activate) self.Bind(wx.EVT_MENU, self.on_context_open, id=ID_CONTEXT_MENU_OPEN) self.Bind(wx.EVT_MENU, self.on_context_openwindow, id=ID_CONTEXT_MENU_OPENWINDOW) self.Bind(wx.EVT_LIST_ITEM_SELECTED, self.hint_select) self.Bind(wx.EVT_LIST_ITEM_DESELECTED, self.hint_select) self.Bind(wx.EVT_LIST_ITEM_FOCUSED, self.hint_select) self.Bind(wx.EVT_LIST_ITEM_ACTIVATED, self.hint_select) @property def selection(self): """ The currently selected item, or None. """ idx = self.GetFirstSelected() if idx < 0: return None return self.node[idx] def hint_select(self, evt): """ Fire off a ContainerSelectionEvent """ wx.PostEvent(self, ContainerSelectionEvent(self.GetId())) evt.Skip() def on_activate(self, evt): """ Emit a CompassOpenEvent when an item is double-clicked. """ # wxPython Mac incorrectly treats a rapid left-right click as activate ms = wx.GetMouseState() if ms.RightIsDown(): return idx = evt.GetIndex() newnode = self.node[idx] pos = wx.GetTopLevelParent(self).GetPosition() evt = CompassOpenEvent(newnode, pos=pos) wx.PostEvent(self, evt) # --------------------------------------------------------- # Context menu support def on_rclick(self, evt): """ Pop up a context menu appropriate for the item """ # Click didn't land on an item idx = evt.GetIndex() if idx < 0: return # The node which was right-clicked in the view. node = self.node[idx] self._menu_node = node # Determine a list of handlers which can understand this object. # We exclude the default handler, "Unknown", as it can't do anything. handlers = [x for x in node.store.gethandlers(node.key) if x != compass_model.Unknown] # This will map menu IDs -> Node subclass handlers self._menu_handlers = {} menu = wx.Menu() menu.Append(ID_CONTEXT_MENU_OPEN, "Open") menu.Append(ID_CONTEXT_MENU_OPENWINDOW, "Open in New Window") if len(handlers) > 0: # Populate the "Open As" submenu, and record what # menu IDs map to what Node subclasses submenu = wx.Menu() for h in handlers: id_ = wx.NewId() self._menu_handlers[id_] = h submenu.Append(id_, h.class_kind) self.Bind(wx.EVT_MENU, self.on_context_openas, id=id_) menu.AppendSubMenu(submenu, "Open As") else: # No handlers were available, so gray out the "Open" entries id1 = wx.NewId() menu.Append(id1, "Open As") menu.Enable(ID_CONTEXT_MENU_OPEN, 0) menu.Enable(ID_CONTEXT_MENU_OPENWINDOW, 0) menu.Enable(id1, 0) self.PopupMenu(menu) del self._menu_node del self._menu_handlers menu.Destroy() def on_context_open(self, evt): """ Called in response to a plain "Open" in the context menu. Posts an event requesting that the node be opened as-is. """ pos = wx.GetTopLevelParent(self).GetPosition() wx.PostEvent(self, CompassOpenEvent(self._menu_node, pos=pos)) def on_context_openwindow(self, evt): """ Called in response to a plain "Open in New Window" in the context menu. Posts an event directly to the app object. """ pos = wx.GetTopLevelParent(self).GetPosition() wx.PostEvent(wx.GetApp(), CompassOpenEvent(self._menu_node, pos=pos)) def on_context_openas(self, evt): """ Called in response to one of the "Open As" context menu items. """ # The "Open As" submenu ID id_ = evt.GetId() # Node which was right-clicked in the view node_being_opened = self._menu_node # The requested Node subclass to instantiate h = self._menu_handlers[id_] # Brand new Node instance of the requested type node_new = h(node_being_opened.store, node_being_opened.key) # Send off a request for it to be opened in the appropriate viewer pos = wx.GetTopLevelParent(self).GetPosition() wx.PostEvent(self, CompassOpenEvent(node_new, pos=pos)) # End context menu support # ------------------------------------------------------------------- class ContainerIconList(ContainerList): """ Icon view of nodes in a Container. """ def __init__(self, parent, node): """ New icon list view """ ContainerList.__init__(self, parent, node, style=wx.LC_ICON | wx.LC_AUTOARRANGE | wx.BORDER_NONE | 0x400) self.node = node self.il = wx.GetApp().imagelists[64] self.SetImageList(self.il, wx.IMAGE_LIST_NORMAL) for item in xrange(len(self.node)): subnode = self.node[item] image_index = self.il.get_index(type(subnode)) self.InsertImageStringItem(item, subnode.display_name, image_index) class ContainerReportList(ContainerList): """ List view of the container's contents. Uses a wxPython virtual list, allowing millions of items in a container without any slowdowns. """ def __init__(self, parent, node): """ Create a new list view. parent: wxPython parent object node: Container instance to be displayed """ ContainerList.__init__(self, parent, node, style=wx.LC_REPORT | wx.LC_VIRTUAL | wx.LC_SINGLE_SEL | wx.BORDER_NONE) self.node = node self.InsertColumn(0, "Name") self.InsertColumn(1, "Kind") self.SetColumnWidth(0, 300) self.SetColumnWidth(1, 200) self.il = wx.GetApp().imagelists[16] self.SetImageList(self.il, wx.IMAGE_LIST_SMALL) self.SetItemCount(len(node)) self.Refresh() def OnGetItemText(self, item, col): """ Callback method to support virtual list ctrl """ if col == 0: return self.node[item].display_name elif col == 1: return type(self.node[item]).class_kind return "" def OnGetItemImage(self, item): """ Callback method to support virtual list ctrl """ subnode = self.node[item] return self.il.get_index(type(subnode)) hdf_compass-0.6.0/hdf_compass/compass_viewer/container/__init__.py0000666000000000000000000000210312730245342023542 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function, unicode_literals from .frame import ContainerFrame import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler())hdf_compass-0.6.0/hdf_compass/compass_viewer/events.py0000666000000000000000000000407512730245342021337 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Defines a small number of custom events, which are useful for the GUI. """ from __future__ import absolute_import, division, print_function, unicode_literals import wx from wx.lib.newevent import NewCommandEvent import logging log = logging.getLogger(__name__) ID_COMPASS_OPEN = wx.NewId() class CompassOpenEvent(wx.PyCommandEvent): """ Event posted when a request has been made to "open" a object in the container. The source should always be ID_COMPASS_OPEN. The type of event is EVT_MENU, because wxPython doesn't like it if we use anything else. When binding handlers, make sure to explicitly specify the source ID (or check it in the callback) to avoid catching these events by mistake. """ def __init__(self, newnode, **kwds): """ Request that *newnode* be displayed by the GUI """ wx.PyCommandEvent.__init__(self, wx.EVT_MENU.typeId, ID_COMPASS_OPEN) self.node = newnode self.kwds = kwds # Hints that the selected item in the view may have changed. # Interested parties should inspect the view to figure out the new selection. ContainerSelectionEvent, EVT_CONTAINER_SELECTION = NewCommandEvent() hdf_compass-0.6.0/hdf_compass/compass_viewer/frame.py0000666000000000000000000004525312730245342021130 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Defines wx.Frame subclasses which are the foundation of the various windows displayed by HDFCompass. Much of the common functionality (e.g. "Open File..." menu item) is implemented here. """ from __future__ import absolute_import, division, print_function, unicode_literals import os import sys from datetime import date import wx import wx.richtext as rtc from wx.lib.pubsub import pub import logging log = logging.getLogger(__name__) from .info import InfoPanel ID_OPEN_RESOURCE = wx.NewId() ID_CLOSE_FILE = wx.NewId() ID_PLUGIN_INFO = wx.NewId() MAX_RECENT_FILES = 8 from hdf_compass import compass_model from hdf_compass.utils import __version__, is_darwin, url2path, path2url from .events import CompassOpenEvent open_frames = 0 # count the open frames class BaseFrame(wx.Frame): """ Base class for all frames used in HDF Compass. Implements common menus including File and Help, and handles their events. When implementing a new viewer window, you should instead inherit from BaseFrame (below), which adds a left-hand side information panel, and participates in the reference counting that automatically shows the initial window when all other frames are closed. """ icon_folder = os.path.abspath(os.path.join(os.path.dirname(__file__), 'icons')) open_frames = 0 # count the number of frames def __init__(self, **kwds): """ Constructor; any keywords are passed on to wx.Frame. """ wx.Frame.__init__(self, None, **kwds) BaseFrame.open_frames += 1 log.debug("new frame -> open frames: %s" % BaseFrame.open_frames) # Frame icon ib = wx.IconBundle() icon_32 = wx.EmptyIcon() icon_32.CopyFromBitmap(wx.Bitmap(os.path.join(self.icon_folder, "favicon_32.png"), wx.BITMAP_TYPE_ANY)) ib.AddIcon(icon_32) icon_48 = wx.EmptyIcon() icon_48.CopyFromBitmap(wx.Bitmap(os.path.join(self.icon_folder, "favicon_48.png"), wx.BITMAP_TYPE_ANY)) ib.AddIcon(icon_48) self.SetIcons(ib) # This is needed to display the app icon on the taskbar on Windows 7 if os.name == 'nt': import ctypes ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID('HDFCompass') self.urlhistory = wx.FileHistory(MAX_RECENT_FILES) self.config = wx.Config("HDFCompass", style=wx.CONFIG_USE_LOCAL_FILE) self.urlhistory.Load(self.config) menubar = wx.MenuBar() # File menu fm = wx.Menu() # Open Recent Menu recent = wx.Menu() self.urlhistory.UseMenu(recent) self.urlhistory.AddFilesToMenu() fm.Append(wx.ID_OPEN, "&Open...\tCtrl-O") fm.Append(ID_OPEN_RESOURCE, "Open &Resource...\tCtrl-R") fm.AppendMenu(wx.ID_ANY, "O&pen Recent", recent) fm.AppendSeparator() fm.Append(wx.ID_CLOSE, "&Close Window\tCtrl-W") fm.Append(ID_CLOSE_FILE, "Close &File\tShift-Ctrl-W") fm.Enable(ID_CLOSE_FILE, False) fm.Append(wx.ID_EXIT, "E&xit", " Terminate the program") menubar.Append(fm, "&File") # Help menu; note that on the Mac, the About entry is automatically # moved to the main application menu by wxPython. help_menu = wx.Menu() help_menu.Append(wx.ID_HELP, "Online &Manual", "Open online documentation") help_menu.Append(ID_PLUGIN_INFO, "&Plugin Info", "Information about the available plugins") help_menu.Append(wx.ID_ABOUT, "&About HDFCompass", "Information about this program") menubar.Append(help_menu, "&Help") self.SetMenuBar(menubar) self.Bind(wx.EVT_MENU, self.on_file_open, id=wx.ID_OPEN) self.Bind(wx.EVT_MENU, self.on_resource_open, id=ID_OPEN_RESOURCE) self.Bind(wx.EVT_MENU, self.on_manual, id=wx.ID_HELP) self.Bind(wx.EVT_MENU, self.on_plugin_info, id=ID_PLUGIN_INFO) self.Bind(wx.EVT_MENU, self.on_about, id=wx.ID_ABOUT) self.Bind(wx.EVT_MENU, self.on_exit, id=wx.ID_EXIT) self.Bind(wx.EVT_MENU, self.on_close, id=wx.ID_CLOSE) self.Bind(wx.EVT_CLOSE, self.on_close) self.Bind(wx.EVT_MENU_RANGE, self.on_url_history, id=wx.ID_FILE1, id2=wx.ID_FILE9) def on_close(self, evt): """ Called on frame closing """ BaseFrame.open_frames -= 1 log.debug("close frame -> open frames: %s" % BaseFrame.open_frames) self.Destroy() if isinstance(self, InitFrame): self.on_exit(evt) def on_exit(self, evt): """ Called on "exit" event from the menu """ log.debug("exit app -> closing all open frames: %s" % BaseFrame.open_frames) wx.GetApp().Exit() def on_manual(self, evt): """ Open the url with the online documentation """ import webbrowser webbrowser.open('http://hdf-compass.readthedocs.org/en/stable/') def on_plugin_info(self, evt): """ Open a tabs frame with info about the available plugins """ plug_info = PluginInfoFrame(self) plug_info.Show() def on_about(self, evt): """ Display an "About" dialog """ info = wx.AboutDialogInfo() info.Name = "HDF Compass" info.Version = __version__ info.Copyright = "(c) 2014-%d The HDF Group" % date.today().year icon_48 = wx.EmptyIcon() icon_48.CopyFromBitmap(wx.Bitmap(os.path.join(self.icon_folder, "favicon_48.png"), wx.BITMAP_TYPE_ANY)) info.SetIcon(icon_48) wx.AboutBox(info) def on_file_open(self, evt): """ Request to open a file via the Open entry in the File menu """ def make_filter_string(): """ Make a wxPython dialog filter string segment from dict """ filter_string = [] hdf_filter_string = [] # put HDF filters in the front for store in compass_model.get_stores(): if len(store.file_extensions) == 0: continue for key in store.file_extensions: s = "{name} ({pattern_c})|{pattern_sc}".format( name=key, pattern_c=",".join(store.file_extensions[key]), pattern_sc=";".join(store.file_extensions[key]) ) if s.startswith("HDF"): hdf_filter_string.append(s) else: filter_string.append(s) filter_string = hdf_filter_string + filter_string filter_string.append('All Files (*.*)|*.*') pipe = "|" return pipe.join(filter_string) wc_string = make_filter_string() dlg = wx.FileDialog(self, "Open Local File", wildcard=wc_string, style=wx.FD_OPEN|wx.FD_FILE_MUST_EXIST) if dlg.ShowModal() != wx.ID_OK: return path = dlg.GetPath() url = path2url(path) self.open_url(url) def on_url_history(self, evt): """ Opens url from history """ fileNum = evt.GetId() - wx.ID_FILE1 url = self.urlhistory.GetHistoryFile(fileNum) self.open_url(url, fileNum) def on_resource_open(self, evt): """ Request to open a URL via the File menu """ dlg = wx.TextEntryDialog(self, 'Enter resource URL:') if dlg.ShowModal() != wx.ID_OK or dlg.GetValue() == "": dlg.Destroy() return url = dlg.GetValue() url = url.strip() # remove any new lines dlg.Destroy() self.open_url(url) def open_url(self, url, fileNum=-1): """ Opens url and saves it to history """ from . import can_open_store, open_store if can_open_store(url): self.urlhistory.AddFileToHistory(url) # add url to top of list self.urlhistory.Save(self.config) self.config.Flush() open_store(url) else: if (fileNum >= 0) and (fileNum < MAX_RECENT_FILES): self.urlhistory.RemoveFileFromHistory(fileNum) self.urlhistory.Save(self.config) self.config.Flush() dlg = wx.MessageDialog(self, 'The following url could not be opened:\n\n%s' % url, 'No handler for url', wx.OK | wx.ICON_INFORMATION) dlg.ShowModal() dlg.Destroy() def add_menu(self, menu, title): """ Add a menu at the appropriate place in the menubar """ mb = self.GetMenuBar() mb.Insert(1, menu, title) class InitFrame(BaseFrame): """ Frame displayed when the application starts up. This includes the menu bar provided by TopFrame. On the Mac, although it still exists (to prevent the application from exiting), the frame is typically not shown. """ def __init__(self): style = wx.DEFAULT_FRAME_STYLE & (~wx.RESIZE_BORDER) & (~wx.MAXIMIZE_BOX) title = "HDF Compass" super(InitFrame, self).__init__(size=(552, 247), title=title, style=style) data = wx.Bitmap(os.path.join(self.icon_folder, "logo.png"), wx.BITMAP_TYPE_ANY) bmp = wx.StaticBitmap(self, wx.ID_ANY, data) # The init frame isn't visible on Mac, so there shouldn't be an # option to close it. "Quit" does the same thing. if is_darwin: mb = self.GetMenuBar() mu = mb.GetMenu(0) mu.Enable(wx.ID_CLOSE, False) self.Center() class NodeFrame(BaseFrame): """ Base class for any frame which displays a Node instance. Provides a "Close file" menu item and manages open data stores. Has three attributes of note: .node: Settable Node instance to display .info: Read-only InfoPanel instance (left-hand sidebar) .view: Settable wx.Panel instance for the right-hand view. In order to coordinate file-close events across multiple frames, a reference-counting system is used. When a new frame that uses a store is created, that store's reference count (in cls._stores) is incremented. When the frame is closed, the store's count is decremented. When the reference count reaches 0 or the "Close File" is selected from the menu, the store is closed and a pubsub notification is sent out to all other frames. They check to see if their .node.store's are valid, and if not, close themselves. """ # --- Store reference-counting methods ------------------------------------ _stores = {} @classmethod def _incref(cls, store): """ Record that a client is using the specified store. """ try: cls._stores[store] += 1 except KeyError: cls._stores[store] = 1 @classmethod def _decref(cls, store): """ Record that a client is finished using the specified store. """ try: val = cls._stores[store] if val == 1: cls._close(store) del cls._stores[store] else: cls._stores[store] = val-1 except KeyError: pass @classmethod def _close(cls, store): """ Manually close the store, and broadcast a pubsub notification. """ cls._stores.pop(store, None) store.close() pub.sendMessage('store.close') # --- End store reference-counting ---------------------------------------- @property def info(self): """ The InfoPanel object used for the left-hand sidebar. """ return self.__info @property def node(self): """ Node instance displayed by the frame. """ return self.__node @node.setter def node(self, newnode): self.__node = newnode @property def view(self): """ Right-hand view """ return self.__view @view.setter def view(self, window): if self.__view is None: self.__sizer.Add(window, 1, wx.EXPAND) else: self.__sizer.Remove(self.__view) self.__view.Destroy() self.__sizer.Add(window, 1, wx.EXPAND) self.__view = window self.Layout() def __init__(self, node, **kwds): """ Constructor. Keywords are passed on to wx.Frame. node: The compass_model.Node instance to display. """ super(NodeFrame, self).__init__(**kwds) # Enable the "Close File" menu entry fm = self.GetMenuBar().GetMenu(0) fm.Enable(ID_CLOSE_FILE, True) # Create the "window" menu to hold "Reopen As" items. wm = wx.Menu() # Determine a list of handlers which can understand this object. # We exclude the default handler, "Unknown", as it can't do anything. # See also container/list.py. handlers = [x for x in node.store.gethandlers(node.key) if x != compass_model.Unknown] # This will map menu IDs -> Node subclass handlers self._menu_handlers = {} # Note there's guaranteed to be at least one entry: the class # being used for the current frame! for h in handlers: id_ = wx.NewId() self._menu_handlers[id_] = h wm.Append(id_, "Reopen as " + h.class_kind) self.Bind(wx.EVT_MENU, self.on_menu_reopen, id=id_) self.GetMenuBar().Insert(1, wm, "&Window") self.__node = node self.__view = None self.__info = InfoPanel(self) self.__sizer = wx.BoxSizer(wx.HORIZONTAL) self.__sizer.Add(self.__info, 0, wx.EXPAND) self.SetSizer(self.__sizer) self.info.display(node) self.Bind(wx.EVT_CLOSE, self.on_close_evt) self.Bind(wx.EVT_MENU, self.on_menu_closefile, id=ID_CLOSE_FILE) self._incref(node.store) pub.subscribe(self.on_notification_closefile, 'store.close') def on_notification_closefile(self): """ Pubsub notification that a file (any file) has been closed """ if not self.node.store.valid: self.Destroy() def on_close_evt(self, evt): """ Window is about to be closed """ self._decref(self.node.store) evt.Skip() def on_menu_closefile(self, evt): """ "Close File" menu item activated. Note we rely on the pubsub message (above) to actually close the frame. """ self._close(self.node.store) def on_menu_reopen(self, evt): """ Called when one of the "Reopen As" menu items is clicked """ # The "Reopen As" submenu ID id_ = evt.GetId() # Present node node_being_opened = self.node # The requested Node subclass to instantiate. h = self._menu_handlers[id_] log.debug('opening: %s %s' % (node_being_opened.store, node_being_opened.key)) # Brand new Node instance of the requested type node_new = h(node_being_opened.store, node_being_opened.key) # Send off a request for it to be opened in the appropriate viewer # Post it directly to the App, or Container will intercept it! pos = wx.GetTopLevelParent(self).GetPosition() wx.PostEvent(wx.GetApp(), CompassOpenEvent(node_new, pos=pos)) class PluginInfoFrame(wx.Frame): icon_folder = os.path.abspath(os.path.join(os.path.dirname(__file__), 'icons')) def __init__(self, parent): # make that the plugin info is displayed in the middle of the screen frame_w = 320 frame_h = 250 x = wx.SystemSettings.GetMetric(wx.SYS_SCREEN_X)//2 - frame_w//2 y = wx.SystemSettings.GetMetric(wx.SYS_SCREEN_Y)//2 - frame_h//2 wx.Frame.__init__(self, parent, title="Plugin Info", pos=(x, y), size=(frame_w, frame_h)) # Frame icon ib = wx.IconBundle() icon_32 = wx.EmptyIcon() icon_32.CopyFromBitmap(wx.Bitmap(os.path.join(self.icon_folder, "favicon_32.png"), wx.BITMAP_TYPE_ANY)) ib.AddIcon(icon_32) icon_48 = wx.EmptyIcon() icon_48.CopyFromBitmap(wx.Bitmap(os.path.join(self.icon_folder, "favicon_48.png"), wx.BITMAP_TYPE_ANY)) ib.AddIcon(icon_48) self.SetIcons(ib) p = wx.Panel(self) nb = wx.Notebook(p) for store in compass_model.get_stores(): try: # log.debug(store.plugin_name()) # log.debug(store.plugin_description()) pnl = wx.Panel(nb) t = rtc.RichTextCtrl(pnl, -1, style=wx.TE_READONLY) t.BeginFontSize(9) t.BeginAlignment(wx.TEXT_ALIGNMENT_CENTRE) t.BeginBold() t.WriteText("Name: ") t.EndBold() t.BeginItalic() t.WriteText(store.plugin_name()) t.EndItalic() t.Newline() t.Newline() t.BeginBold() t.WriteText("Description") t.EndBold() t.Newline() t.BeginItalic() t.WriteText(store.plugin_description()) t.EndItalic() t.Newline() #store.plugin_description(), style=wx.TE_MULTILINE|wx.TE_READONLY|wx.TE_CENTER) szr = wx.BoxSizer() szr.Add(t, 1, wx.ALL|wx.EXPAND, 5) pnl.SetSizer(szr) nb.AddPage(pnl, store.plugin_name()) except NotImplementedError: # skip not implemented plugin name/description log.debug("Not implemented name/description for %s" % store) sizer = wx.BoxSizer() sizer.Add(nb, 1, wx.ALL | wx.EXPAND, 3) p.SetSizer(sizer) hdf_compass-0.6.0/hdf_compass/compass_viewer/geo_array/0000777000000000000000000000000012730267653021434 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/compass_viewer/geo_array/frame.py0000666000000000000000000003452412730245342023077 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Implements a viewer frame for compass_model.Array. """ from __future__ import absolute_import, division, print_function, unicode_literals import wx import wx.grid from wx.lib.newevent import NewCommandEvent import os import logging log = logging.getLogger(__name__) from ..frame import NodeFrame from .plot import LinePlotFrame, ContourPlotFrame # Indicates that the slicing selection may have changed. # These events are emitted by the SlicerPanel. ArraySlicedEvent, EVT_ARRAY_SLICED = NewCommandEvent() # Menu and button IDs ID_VIS_MENU_PLOT = wx.NewId() class GeoArrayFrame(NodeFrame): """ Top-level frame displaying objects of type compass_model.Array. From top to bottom, has: 1. Toolbar (see ArrayFrame.init_toolbar) 2. SlicerPanel, with controls for changing what's displayed. 3. An ArrayGrid, which displays the data in a spreadsheet-like view. """ def __init__(self, node, pos=None): """ Create a new array viewer to display the node. """ NodeFrame.__init__(self, node, size=(800, 400), title=node.display_name, pos=pos) self.node = node # Update the menu vis_menu = wx.Menu() if self.node.is_plottable(): vis_menu.Append(ID_VIS_MENU_PLOT, "Map Data\tCtrl-D") self.add_menu(vis_menu, "Visualize") # Initialize the toolbar self.init_toolbar() # The Slicer is the panel with indexing controls self.slicer = SlicerPanel(self, node.shape, node.dtype.fields is not None) # Create the grid array self.grid = ArrayGrid(self, node, self.slicer) # Sizer for slicer and grid gridsizer = wx.BoxSizer(wx.VERTICAL) gridsizer.Add(self.slicer, 0, wx.EXPAND) gridsizer.Add(self.grid, 1, wx.EXPAND) self.view = gridsizer self.Bind(EVT_ARRAY_SLICED, self.on_sliced) if self.node.is_plottable(): self.Bind(wx.EVT_MENU, self.on_plot, id=ID_VIS_MENU_PLOT) # Workaround for wxPython bug (see SlicerPanel.enable_spinctrls) ID_WORKAROUND_TIMER = wx.NewId() self.Bind(wx.EVT_TIMER, self.on_workaround_timer, id=ID_WORKAROUND_TIMER) self.timer = wx.Timer(self, ID_WORKAROUND_TIMER) self.timer.Start(100) def init_toolbar(self): """ Set up the toolbar at the top of the window. """ t_size = (24, 24) plot_bmp = wx.Bitmap(os.path.join(self.icon_folder, "viz_plot_24.png"), wx.BITMAP_TYPE_ANY) self.toolbar = self.CreateToolBar(wx.TB_HORIZONTAL | wx.NO_BORDER | wx.TB_FLAT | wx.TB_TEXT) self.toolbar.SetToolBitmapSize(t_size) self.toolbar.AddStretchableSpace() if self.node.is_plottable(): self.toolbar.AddLabelTool(ID_VIS_MENU_PLOT, "Map Data", plot_bmp, shortHelp="Map geographic data in a popup window", longHelp="Map the geographic array data in a popup window") self.toolbar.Realize() def on_sliced(self, evt): """ User has chosen to display a different part of the dataset. """ self.grid.Refresh() def on_plot(self, evt): """ User has chosen to plot the current selection """ cols = self.grid.GetSelectedCols() rows = self.grid.GetSelectedRows() # Scalar data can't be line-plotted. if len(self.node.shape) == 0: return # Columns in the view are selected if len(cols) != 0: # The data is compound if self.node.dtype.names is not None: names = [self.grid.GetColLabelValue(x) for x in cols] data = self.node[self.slicer.indices] # -> 1D compound array data = [data[n] for n in names] f = LinePlotFrame(data, names) f.Show() # Plot multiple columns independently else: if len(self.node.shape) == 1: data = [self.node[self.slicer.indices]] else: data = [self.node[self.slicer.indices + (c,)] for c in cols] names = ["Col %d" % c for c in cols] if len(data) > 1 else None f = LinePlotFrame(data, names) f.Show() # Rows in view are selected elif len(rows) != 0: data = [self.node[self.slicer.indices + (slice(None, None, None), r)] for r in rows] names = ["Row %d" % r for r in rows] if len(data) > 1 else None f = LinePlotFrame(data, names) f.Show() # No row or column selection. Plot everything else: data = self.node[self.slicer.indices] # The data is compound if self.node.dtype.names is not None: names = [self.grid.GetColLabelValue(x) for x in xrange(self.grid.GetNumberCols())] data = [data[n] for n in names] f = LinePlotFrame(data, names) f.Show() # Plot 1D elif len(self.node.shape) == 1: f = LinePlotFrame([data]) f.Show() # Plot 2D else: f = ContourPlotFrame(data, extent=self.node.extent) f.Show() def on_workaround_timer(self, evt): """ See slicer.enable_spinctrls docs """ self.timer.Destroy() self.slicer.enable_spinctrls() class SlicerPanel(wx.Panel): """ Holds controls for data access. Consult the "indices" property, which returns a tuple of indices that prefix the array. This will be RANK-2 elements long, unless hasfields is true, in which case it will be RANK-1 elements long. """ @property def indices(self): """ A tuple of integer indices appropriate for slicing. Will be RANK-2 elements long, RANK-1 if compound data is in use (hasfields == True). """ return tuple([x.GetValue() for x in self.spincontrols]) def __init__(self, parent, shape, hasfields): """ Create a new slicer panel. parent: The wxPython parent window shape: Shape of the data to visualize hasfields: If True, the data is compound and the grid can only display one axis. So, we should display an extra spinbox. """ wx.Panel.__init__(self, parent) self.shape = shape self.hasfields = hasfields self.spincontrols = [] # Rank of the underlying array rank = len(shape) # Rank displayable in the grid. If fields are present, they occupy # the columns, so the data displayed is actually 1-D. visible_rank = 1 if hasfields else 2 sizer = wx.BoxSizer(wx.HORIZONTAL) # Will arrange the SpinCtrls if rank > visible_rank: infotext = wx.StaticText(self, wx.ID_ANY, "Array Indexing: ") sizer.Add(infotext, 0, flag=wx.EXPAND | wx.ALL, border=10) for idx in xrange(rank - visible_rank): sc = wx.SpinCtrl(self, max=shape[idx] - 1, value="0", min=0) sizer.Add(sc, 0, flag=wx.EXPAND | wx.ALL, border=10) sc.Disable() self.spincontrols.append(sc) self.SetSizer(sizer) self.Bind(wx.EVT_SPINCTRL, self.on_spin) def enable_spinctrls(self): """ Unlock the spin controls. Because of a bug in wxPython on Mac, by default the first spin control has bizarre contents (and control focus) when the panel starts up. Call this after a short delay (e.g. 100 ms) to enable indexing. """ for sc in self.spincontrols: sc.Enable() def on_spin(self, evt): """ Spinbox value changed; notify parent to refresh the grid. """ wx.PostEvent(self, ArraySlicedEvent(self.GetId())) class ArrayGrid(wx.grid.Grid): """ Grid class to display the Array. Cell contents and appearance are handled by the table model in ArrayTable. """ def __init__(self, parent, node, slicer): wx.grid.Grid.__init__(self, parent) table = ArrayTable(node, slicer) self.SetTable(table, True) # Column selection is always allowed selmode = wx.grid.Grid.wxGridSelectColumns # Row selection is forbidden for compound types, and for # scalar/1-D datasets if node.dtype.names is None and len(node.shape) > 1: selmode |= wx.grid.Grid.wxGridSelectRows self.SetSelectionMode(selmode) class LRUTileCache(object): """ Simple tile-based LRU cache which goes between the Grid and the Array object. Caches tiles along the last 1 or 2 dimensions of a dataset. Access is via __getitem__. Because this class exists specifically to support point-based callbacks for the Grid, arguments may only be indices, not slices. """ TILESIZE = 100 # Tiles will have shape (100,) or (100, 100) MAXTILES = 50 # Max number of tiles to retain in the cache def __init__(self, arr): """ *arr* is anything implementing compass_model.Array """ import collections self.cache = collections.OrderedDict() self.arr = arr def __getitem__(self, args): """ Restricted to an index or tuple of indices. """ if not isinstance(args, tuple): args = (args,) # Split off the last 1 or 2 dimensions coarse_position, fine_position = args[0:-2], args[-2:] def clip(x): """ Round down to nearest TILESIZE; takes e.g. 181 -> 100 """ return (x // self.TILESIZE) * self.TILESIZE # Tuple with index of tile corner tile_key = coarse_position + tuple(clip(x) for x in fine_position) # Slice which will be applied to dataset to retrieve tile tile_slice = coarse_position + tuple(slice(clip(x), clip(x) + self.TILESIZE) for x in fine_position) # Index applied to tile to retrieve the desired data point tile_data_index = tuple(x % self.TILESIZE for x in fine_position) # Case 1: Add tile to cache, ejecting oldest tile if needed if not tile_key in self.cache: if len(self.cache) >= self.MAXTILES: self.cache.popitem(last=False) tile = self.arr[tile_slice] self.cache[tile_key] = tile # Case 2: Mark the tile as recently accessed else: tile = self.cache.pop(tile_key) self.cache[tile_key] = tile return tile[tile_data_index] class ArrayTable(wx.grid.PyGridTableBase): """ "Table" class which provides data and metadata for the grid to display. The methods defined here define the contents of the table, as well as the number of rows, columns and their values. """ def __init__(self, node, slicer): """ Create a new Table instance for use with a grid control. node: An compass_model.Array implementation instance. slicer: An instance of SlicerPanel, so we can see what indices the user has requested. """ wx.grid.PyGridTableBase.__init__(self) self.node = node self.slicer = slicer self.rank = len(node.shape) self.names = node.dtype.names self.cache = LRUTileCache(self.node) def GetNumberRows(self): """ Callback for number of rows displayed by the grid control """ if self.rank == 0: return 1 return self.node.shape[-1] def GetNumberCols(self): """ Callback for number of columns displayed by the grid control. Note that if compound data is in use, columns display the field names. """ if self.names is not None: return len(self.names) if self.rank < 2: return 1 return self.node.shape[-2] def GetValue(self, row, col): """ Callback which provides data to the Grid. row, col: Integers giving row and column position (0-based). """ # Scalar case if self.rank == 0: data = self.node[()] if self.names is None: return data return data[col] # 1D case if self.rank == 1: data = self.cache[row] if self.names is None: return data return data[self.names[col]] # ND case. Watch out for compound mode! if self.names is None: args = self.slicer.indices + (col, row) else: args = self.slicer.indices + (row,) data = self.cache[args] if self.names is None: return data return data[self.names[col]] def GetRowLabelValue(self, row): """ Callback for row labels. Row number is used unless the data is scalar. """ if self.rank == 0: return "Value" return str(row) def GetColLabelValue(self, col): """ Callback for column labels. Column number is used, except for scalar or 1D data, or if we're displaying field names in the columns. """ if self.names is not None: return self.names[col] if self.rank == 0 or self.rank == 1: return "Value" return str(col) hdf_compass-0.6.0/hdf_compass/compass_viewer/geo_array/plot.py0000666000000000000000000002034312730245342022755 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Matplotlib window with toolbar. """ from __future__ import absolute_import, division, print_function, unicode_literals import numpy as np import wx try: # for GeoArray we use cartopy that can be challenging to freeze on OSX to dependencies (i.e. geos) import cartopy.crs as ccrs from cartopy.mpl.gridliner import LONGITUDE_FORMATTER, LATITUDE_FORMATTER except (ImportError, OSError): pass import matplotlib.pyplot as plt from matplotlib.figure import Figure from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigCanvas from matplotlib.backends.backend_wx import NavigationToolbar2Wx as NavigationToolbar import logging log = logging.getLogger(__name__) from ..frame import BaseFrame ID_VIEW_CMAP_JET = wx.NewId() # default ID_VIEW_CMAP_BONE = wx.NewId() ID_VIEW_CMAP_GIST_EARTH = wx.NewId() ID_VIEW_CMAP_OCEAN = wx.NewId() ID_VIEW_CMAP_RAINBOW = wx.NewId() ID_VIEW_CMAP_RDYLGN = wx.NewId() ID_VIEW_CMAP_WINTER = wx.NewId() class PlotFrame(BaseFrame): """ Base class for Matplotlib plot windows. Override draw_figure() to plot your figure on the provided axes. """ def __init__(self, data, title="a title"): """ Create a new Matplotlib plotting window for a 1D line plot """ log.debug(self.__class__.__name__) BaseFrame.__init__(self, id=wx.ID_ANY, title=title, size=(800, 400)) self.data = data self.panel = wx.Panel(self) self.dpi = 100 self.fig = Figure((6.0, 4.0), dpi=self.dpi) self.canvas = FigCanvas(self.panel, -1, self.fig) self.axes = self.fig.add_subplot(111, projection=ccrs.PlateCarree()) self.toolbar = NavigationToolbar(self.canvas) self.vbox = wx.BoxSizer(wx.VERTICAL) self.vbox.Add(self.canvas, 1, wx.LEFT | wx.TOP | wx.GROW) self.vbox.Add(self.toolbar, 0, wx.EXPAND) self.panel.SetSizer(self.vbox) self.vbox.Fit(self) self.draw_figure() def draw_figure(self): raise NotImplementedError class LinePlotFrame(PlotFrame): def __init__(self, data, names=None, title="Line Plot"): self.names = names PlotFrame.__init__(self, data, title) def draw_figure(self): lines = [self.axes.plot(d)[0] for d in self.data] if self.names is not None: for n in self.names: self.axes.legend(tuple(lines), tuple(self.names)) class ContourPlotFrame(PlotFrame): def __init__(self, data, extent, names=None, title="Contour Map"): self.geo_extent = extent log.debug("Extent: %f, %f, %f, %f" % self.geo_extent) # need to be set before calling the parent (need for plotting) self.colormap = "jet" self.cb = None # matplotlib color-bar self.surf = None self.xx = None self.yy = None PlotFrame.__init__(self, data, title) self.cmap_menu = wx.Menu() self.cmap_menu.Append(ID_VIEW_CMAP_JET, "Jet", kind=wx.ITEM_RADIO) self.cmap_menu.Append(ID_VIEW_CMAP_BONE, "Bone", kind=wx.ITEM_RADIO) self.cmap_menu.Append(ID_VIEW_CMAP_GIST_EARTH, "Gist Earth", kind=wx.ITEM_RADIO) self.cmap_menu.Append(ID_VIEW_CMAP_OCEAN, "Ocean", kind=wx.ITEM_RADIO) self.cmap_menu.Append(ID_VIEW_CMAP_RAINBOW, "Rainbow", kind=wx.ITEM_RADIO) self.cmap_menu.Append(ID_VIEW_CMAP_RDYLGN, "Red-Yellow-Green", kind=wx.ITEM_RADIO) self.cmap_menu.Append(ID_VIEW_CMAP_WINTER, "Winter", kind=wx.ITEM_RADIO) self.add_menu(self.cmap_menu, "Colormap") self.Bind(wx.EVT_MENU, self.on_cmap_jet, id=ID_VIEW_CMAP_JET) self.Bind(wx.EVT_MENU, self.on_cmap_bone, id=ID_VIEW_CMAP_BONE) self.Bind(wx.EVT_MENU, self.on_cmap_gist_earth, id=ID_VIEW_CMAP_GIST_EARTH) self.Bind(wx.EVT_MENU, self.on_cmap_ocean, id=ID_VIEW_CMAP_OCEAN) self.Bind(wx.EVT_MENU, self.on_cmap_rainbow, id=ID_VIEW_CMAP_RAINBOW) self.Bind(wx.EVT_MENU, self.on_cmap_rdylgn, id=ID_VIEW_CMAP_RDYLGN) self.Bind(wx.EVT_MENU, self.on_cmap_winter, id=ID_VIEW_CMAP_WINTER) self.status_bar = wx.StatusBar(self, -1) self.status_bar.SetFieldsCount(2) self.SetStatusBar(self.status_bar) self.canvas.mpl_connect('motion_notify_event', self.update_status_bar) self.canvas.Bind(wx.EVT_ENTER_WINDOW, self.change_cursor) def on_cmap_jet(self, evt): log.debug("cmap: jet") self.colormap = "jet" self._refresh_plot() def on_cmap_bone(self, evt): log.debug("cmap: bone") self.colormap = "bone" self._refresh_plot() def on_cmap_gist_earth(self, evt): log.debug("cmap: gist_earth") self.colormap = "gist_earth" self._refresh_plot() def on_cmap_ocean(self, evt): log.debug("cmap: ocean") self.colormap = "ocean" self._refresh_plot() def on_cmap_rainbow(self, evt): log.debug("cmap: rainbow") self.colormap = "rainbow" self._refresh_plot() def on_cmap_rdylgn(self, evt): log.debug("cmap: RdYlGn") self.colormap = "RdYlGn" self._refresh_plot() def on_cmap_winter(self, evt): log.debug("cmap: winter") self.colormap = "winter" self._refresh_plot() def _refresh_plot(self): self.draw_figure() self.canvas.draw() def draw_figure(self): max_elements = 500 # don't attempt plot more than 500x500 elements rows = self.data.shape[0] cols = self.data.shape[1] row_stride = rows // max_elements + 1 col_stride = cols // max_elements + 1 self.surf = self.data[::row_stride, ::col_stride] self.xx = np.linspace(self.geo_extent[0], self.geo_extent[1], self.surf.shape[1]) self.yy = np.linspace(self.geo_extent[2], self.geo_extent[3], self.surf.shape[0]) img = self.axes.contourf(self.xx, self.yy, self.surf, 25, cmap=plt.cm.get_cmap(self.colormap), transform=ccrs.PlateCarree()) self.axes.coastlines(resolution='50m', color='gray', linewidth=1) # add gridlines with labels only on the left and on the bottom grl = self.axes.gridlines(crs=ccrs.PlateCarree(), color='gray', draw_labels=True) grl.xformatter = LONGITUDE_FORMATTER grl.yformatter = LATITUDE_FORMATTER grl.xlabel_style = {'size': 8} grl.ylabel_style = {'size': 8} grl.ylabels_right = False grl.xlabels_top = False if self.cb: self.cb.on_mappable_changed(img) else: self.cb = plt.colorbar(img, ax=self.axes) self.cb.ax.tick_params(labelsize=8) def change_cursor(self, event): self.canvas.SetCursor(wx.StockCursor(wx.CURSOR_CROSS)) @staticmethod def _find_nearest(arr, value): """ Helper function to find the nearest value in an array """ return (np.abs(arr - value)).argmin() def update_status_bar(self, event): msg = str() if event.inaxes: x, y = event.xdata, event.ydata id_y, id_x = self._find_nearest(self.yy, y), self._find_nearest(self.xx, x) # log.debug("id: %f %f" % (id_y, id_x)) z = self.surf[id_y, id_x] msg = "x= %f, y= %f, z= %f" % (x, y, z) self.status_bar.SetStatusText(msg, 1) hdf_compass-0.6.0/hdf_compass/compass_viewer/geo_array/__init__.py0000666000000000000000000000210212730245342023527 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function, unicode_literals from .frame import GeoArrayFrame import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler())hdf_compass-0.6.0/hdf_compass/compass_viewer/geo_surface/0000777000000000000000000000000012730267653021746 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/compass_viewer/geo_surface/frame.py0000666000000000000000000003454212730245342023411 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Implements a viewer frame for compass_model.Array. """ from __future__ import absolute_import, division, print_function, unicode_literals import wx import wx.grid from wx.lib.newevent import NewCommandEvent import os import logging log = logging.getLogger(__name__) from ..frame import NodeFrame from .plot import LinePlotFrame, ContourPlotFrame # Indicates that the slicing selection may have changed. # These events are emitted by the SlicerPanel. ArraySlicedEvent, EVT_ARRAY_SLICED = NewCommandEvent() # Menu and button IDs ID_VIS_MENU_PLOT = wx.NewId() class GeoSurfaceFrame(NodeFrame): """ Top-level frame displaying objects of type compass_model.Array. From top to bottom, has: 1. Toolbar (see ArrayFrame.init_toolbar) 2. SlicerPanel, with controls for changing what's displayed. 3. An ArrayGrid, which displays the data in a spreadsheet-like view. """ def __init__(self, node, pos=None): """ Create a new array viewer to display the node. """ NodeFrame.__init__(self, node, size=(800, 400), title=node.display_name, pos=pos) self.node = node # Update the menu vis_menu = wx.Menu() if self.node.is_plottable(): vis_menu.Append(ID_VIS_MENU_PLOT, "Map Surface\tCtrl-D") self.add_menu(vis_menu, "Visualize") # Initialize the toolbar self.init_toolbar() # The Slicer is the panel with indexing controls self.slicer = SlicerPanel(self, node.shape, node.dtype.fields is not None) # Create the grid array self.grid = ArrayGrid(self, node, self.slicer) # Sizer for slicer and grid gridsizer = wx.BoxSizer(wx.VERTICAL) gridsizer.Add(self.slicer, 0, wx.EXPAND) gridsizer.Add(self.grid, 1, wx.EXPAND) self.view = gridsizer self.Bind(EVT_ARRAY_SLICED, self.on_sliced) if self.node.is_plottable(): self.Bind(wx.EVT_MENU, self.on_plot, id=ID_VIS_MENU_PLOT) # Workaround for wxPython bug (see SlicerPanel.enable_spinctrls) ID_WORKAROUND_TIMER = wx.NewId() self.Bind(wx.EVT_TIMER, self.on_workaround_timer, id=ID_WORKAROUND_TIMER) self.timer = wx.Timer(self, ID_WORKAROUND_TIMER) self.timer.Start(100) def init_toolbar(self): """ Set up the toolbar at the top of the window. """ t_size = (24, 24) plot_bmp = wx.Bitmap(os.path.join(self.icon_folder, "viz_plot_24.png"), wx.BITMAP_TYPE_ANY) self.toolbar = self.CreateToolBar(wx.TB_HORIZONTAL | wx.NO_BORDER | wx.TB_FLAT | wx.TB_TEXT) self.toolbar.SetToolBitmapSize(t_size) self.toolbar.AddStretchableSpace() if self.node.is_plottable(): self.toolbar.AddLabelTool(ID_VIS_MENU_PLOT, "Map Surface", plot_bmp, shortHelp="Map geographic surface in a popup window", longHelp="Map the geographic surface array in a popup window") self.toolbar.Realize() def on_sliced(self, evt): """ User has chosen to display a different part of the dataset. """ self.grid.Refresh() def on_plot(self, evt): """ User has chosen to plot the current selection """ cols = self.grid.GetSelectedCols() rows = self.grid.GetSelectedRows() # Scalar data can't be line-plotted. if len(self.node.shape) == 0: return # Columns in the view are selected if len(cols) != 0: # The data is compound if self.node.dtype.names is not None: names = [self.grid.GetColLabelValue(x) for x in cols] data = self.node[self.slicer.indices] # -> 1D compound array data = [data[n] for n in names] f = LinePlotFrame(data, names) f.Show() # Plot multiple columns independently else: if len(self.node.shape) == 1: data = [self.node[self.slicer.indices]] else: data = [self.node[self.slicer.indices + (c,)] for c in cols] names = ["Col %d" % c for c in cols] if len(data) > 1 else None f = LinePlotFrame(data, names) f.Show() # Rows in view are selected elif len(rows) != 0: data = [self.node[self.slicer.indices + (slice(None, None, None), r)] for r in rows] names = ["Row %d" % r for r in rows] if len(data) > 1 else None f = LinePlotFrame(data, names) f.Show() # No row or column selection. Plot everything else: data = self.node[self.slicer.indices] # The data is compound if self.node.dtype.names is not None: names = [self.grid.GetColLabelValue(x) for x in xrange(self.grid.GetNumberCols())] data = [data[n] for n in names] f = LinePlotFrame(data, names) f.Show() # Plot 1D elif len(self.node.shape) == 1: f = LinePlotFrame([data]) f.Show() # Plot 2D else: f = ContourPlotFrame(data, extent=self.node.extent) f.Show() def on_workaround_timer(self, evt): """ See slicer.enable_spinctrls docs """ self.timer.Destroy() self.slicer.enable_spinctrls() class SlicerPanel(wx.Panel): """ Holds controls for data access. Consult the "indices" property, which returns a tuple of indices that prefix the array. This will be RANK-2 elements long, unless hasfields is true, in which case it will be RANK-1 elements long. """ @property def indices(self): """ A tuple of integer indices appropriate for slicing. Will be RANK-2 elements long, RANK-1 if compound data is in use (hasfields == True). """ return tuple([x.GetValue() for x in self.spincontrols]) def __init__(self, parent, shape, hasfields): """ Create a new slicer panel. parent: The wxPython parent window shape: Shape of the data to visualize hasfields: If True, the data is compound and the grid can only display one axis. So, we should display an extra spinbox. """ wx.Panel.__init__(self, parent) self.shape = shape self.hasfields = hasfields self.spincontrols = [] # Rank of the underlying array rank = len(shape) # Rank displayable in the grid. If fields are present, they occupy # the columns, so the data displayed is actually 1-D. visible_rank = 1 if hasfields else 2 sizer = wx.BoxSizer(wx.HORIZONTAL) # Will arrange the SpinCtrls if rank > visible_rank: infotext = wx.StaticText(self, wx.ID_ANY, "Array Indexing: ") sizer.Add(infotext, 0, flag=wx.EXPAND | wx.ALL, border=10) for idx in xrange(rank - visible_rank): sc = wx.SpinCtrl(self, max=shape[idx] - 1, value="0", min=0) sizer.Add(sc, 0, flag=wx.EXPAND | wx.ALL, border=10) sc.Disable() self.spincontrols.append(sc) self.SetSizer(sizer) self.Bind(wx.EVT_SPINCTRL, self.on_spin) def enable_spinctrls(self): """ Unlock the spin controls. Because of a bug in wxPython on Mac, by default the first spin control has bizarre contents (and control focus) when the panel starts up. Call this after a short delay (e.g. 100 ms) to enable indexing. """ for sc in self.spincontrols: sc.Enable() def on_spin(self, evt): """ Spinbox value changed; notify parent to refresh the grid. """ wx.PostEvent(self, ArraySlicedEvent(self.GetId())) class ArrayGrid(wx.grid.Grid): """ Grid class to display the Array. Cell contents and appearance are handled by the table model in ArrayTable. """ def __init__(self, parent, node, slicer): wx.grid.Grid.__init__(self, parent) table = ArrayTable(node, slicer) self.SetTable(table, True) # Column selection is always allowed selmode = wx.grid.Grid.wxGridSelectColumns # Row selection is forbidden for compound types, and for # scalar/1-D datasets if node.dtype.names is None and len(node.shape) > 1: selmode |= wx.grid.Grid.wxGridSelectRows self.SetSelectionMode(selmode) class LRUTileCache(object): """ Simple tile-based LRU cache which goes between the Grid and the Array object. Caches tiles along the last 1 or 2 dimensions of a dataset. Access is via __getitem__. Because this class exists specifically to support point-based callbacks for the Grid, arguments may only be indices, not slices. """ TILESIZE = 100 # Tiles will have shape (100,) or (100, 100) MAXTILES = 50 # Max number of tiles to retain in the cache def __init__(self, arr): """ *arr* is anything implementing compass_model.Array """ import collections self.cache = collections.OrderedDict() self.arr = arr def __getitem__(self, args): """ Restricted to an index or tuple of indices. """ if not isinstance(args, tuple): args = (args,) # Split off the last 1 or 2 dimensions coarse_position, fine_position = args[0:-2], args[-2:] def clip(x): """ Round down to nearest TILESIZE; takes e.g. 181 -> 100 """ return (x // self.TILESIZE) * self.TILESIZE # Tuple with index of tile corner tile_key = coarse_position + tuple(clip(x) for x in fine_position) # Slice which will be applied to dataset to retrieve tile tile_slice = coarse_position + tuple(slice(clip(x), clip(x) + self.TILESIZE) for x in fine_position) # Index applied to tile to retrieve the desired data point tile_data_index = tuple(x % self.TILESIZE for x in fine_position) # Case 1: Add tile to cache, ejecting oldest tile if needed if not tile_key in self.cache: if len(self.cache) >= self.MAXTILES: self.cache.popitem(last=False) tile = self.arr[tile_slice] self.cache[tile_key] = tile # Case 2: Mark the tile as recently accessed else: tile = self.cache.pop(tile_key) self.cache[tile_key] = tile return tile[tile_data_index] class ArrayTable(wx.grid.PyGridTableBase): """ "Table" class which provides data and metadata for the grid to display. The methods defined here define the contents of the table, as well as the number of rows, columns and their values. """ def __init__(self, node, slicer): """ Create a new Table instance for use with a grid control. node: An compass_model.Array implementation instance. slicer: An instance of SlicerPanel, so we can see what indices the user has requested. """ wx.grid.PyGridTableBase.__init__(self) self.node = node self.slicer = slicer self.rank = len(node.shape) self.names = node.dtype.names self.cache = LRUTileCache(self.node) def GetNumberRows(self): """ Callback for number of rows displayed by the grid control """ if self.rank == 0: return 1 return self.node.shape[-1] def GetNumberCols(self): """ Callback for number of columns displayed by the grid control. Note that if compound data is in use, columns display the field names. """ if self.names is not None: return len(self.names) if self.rank < 2: return 1 return self.node.shape[-2] def GetValue(self, row, col): """ Callback which provides data to the Grid. row, col: Integers giving row and column position (0-based). """ # Scalar case if self.rank == 0: data = self.node[()] if self.names is None: return data return data[col] # 1D case if self.rank == 1: data = self.cache[row] if self.names is None: return data return data[self.names[col]] # ND case. Watch out for compound mode! if self.names is None: args = self.slicer.indices + (col, row) else: args = self.slicer.indices + (row,) data = self.cache[args] if self.names is None: return data return data[self.names[col]] def GetRowLabelValue(self, row): """ Callback for row labels. Row number is used unless the data is scalar. """ if self.rank == 0: return "Value" return str(row) def GetColLabelValue(self, col): """ Callback for column labels. Column number is used, except for scalar or 1D data, or if we're displaying field names in the columns. """ if self.names is not None: return self.names[col] if self.rank == 0 or self.rank == 1: return "Value" return str(col) hdf_compass-0.6.0/hdf_compass/compass_viewer/geo_surface/plot.py0000666000000000000000000002361512730245342023274 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Matplotlib window with toolbar. """ from __future__ import absolute_import, division, print_function, unicode_literals import numpy as np import wx try: # for GeoSurface we use cartopy that can be challenging to freeze on OSX to dependencies (i.e. geos) import cartopy.crs as ccrs from cartopy.mpl.gridliner import LONGITUDE_FORMATTER, LATITUDE_FORMATTER except (ImportError, OSError): pass import matplotlib.pyplot as plt from matplotlib.figure import Figure from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigCanvas from matplotlib.backends.backend_wx import NavigationToolbar2Wx as NavigationToolbar from matplotlib.colors import LinearSegmentedColormap from matplotlib import cm from matplotlib.colors import LightSource import logging log = logging.getLogger(__name__) from ..frame import BaseFrame np.seterr(divide='ignore', invalid='ignore') ID_VIEW_CMAP_BAG = wx.NewId() # default ID_VIEW_CMAP_JET = wx.NewId() ID_VIEW_CMAP_BONE = wx.NewId() ID_VIEW_CMAP_GIST_EARTH = wx.NewId() ID_VIEW_CMAP_OCEAN = wx.NewId() ID_VIEW_CMAP_RAINBOW = wx.NewId() ID_VIEW_CMAP_RDYLGN = wx.NewId() ID_VIEW_CMAP_WINTER = wx.NewId() class PlotFrame(BaseFrame): """ Base class for Matplotlib plot windows. Override draw_figure() to plot your figure on the provided axes. """ def __init__(self, data, title="a title"): """ Create a new Matplotlib plotting window for a 1D line plot """ log.debug(self.__class__.__name__) BaseFrame.__init__(self, id=wx.ID_ANY, title=title, size=(800, 400)) self.data = data self.panel = wx.Panel(self) self.dpi = 100 self.fig = Figure((6.0, 4.0), dpi=self.dpi) self.canvas = FigCanvas(self.panel, -1, self.fig) self.axes = self.fig.add_subplot(111, projection=ccrs.PlateCarree()) self.toolbar = NavigationToolbar(self.canvas) self.vbox = wx.BoxSizer(wx.VERTICAL) self.vbox.Add(self.canvas, 1, wx.LEFT | wx.TOP | wx.GROW) self.vbox.Add(self.toolbar, 0, wx.EXPAND) self.panel.SetSizer(self.vbox) self.vbox.Fit(self) self.draw_figure() def draw_figure(self): raise NotImplementedError class LinePlotFrame(PlotFrame): def __init__(self, data, names=None, title="Line Plot"): self.names = names PlotFrame.__init__(self, data, title) def draw_figure(self): lines = [self.axes.plot(d)[0] for d in self.data] if self.names is not None: for n in self.names: self.axes.legend(tuple(lines), tuple(self.names)) class ContourPlotFrame(PlotFrame): def __init__(self, data, extent, names=None, title="Surface Map"): self.geo_extent = extent log.debug("Extent: %f, %f, %f, %f" % self.geo_extent) # need to be set before calling the parent (need for plotting) self.colormap = LinearSegmentedColormap.from_list("BAG", ["#63006c", "#2b4ef4", "#2f73ff", "#4b8af4", "#bee2bf"]) # register a new colormap cm.register_cmap(cmap=self.colormap) self.cb = None # matplotlib color-bar self.xx = None self.yy = None self.surf = None PlotFrame.__init__(self, data, title) self.cmap_menu = wx.Menu() self.cmap_menu.Append(ID_VIEW_CMAP_BAG, "BAG", kind=wx.ITEM_RADIO) self.cmap_menu.Append(ID_VIEW_CMAP_JET, "Jet", kind=wx.ITEM_RADIO) self.cmap_menu.Append(ID_VIEW_CMAP_BONE, "Bone", kind=wx.ITEM_RADIO) self.cmap_menu.Append(ID_VIEW_CMAP_GIST_EARTH, "Gist Earth", kind=wx.ITEM_RADIO) self.cmap_menu.Append(ID_VIEW_CMAP_OCEAN, "Ocean", kind=wx.ITEM_RADIO) self.cmap_menu.Append(ID_VIEW_CMAP_RAINBOW, "Rainbow", kind=wx.ITEM_RADIO) self.cmap_menu.Append(ID_VIEW_CMAP_RDYLGN, "Red-Yellow-Green", kind=wx.ITEM_RADIO) self.cmap_menu.Append(ID_VIEW_CMAP_WINTER, "Winter", kind=wx.ITEM_RADIO) self.add_menu(self.cmap_menu, "Colormap") self.Bind(wx.EVT_MENU, self.on_cmap_bag, id=ID_VIEW_CMAP_BAG) self.Bind(wx.EVT_MENU, self.on_cmap_jet, id=ID_VIEW_CMAP_JET) self.Bind(wx.EVT_MENU, self.on_cmap_bone, id=ID_VIEW_CMAP_BONE) self.Bind(wx.EVT_MENU, self.on_cmap_gist_earth, id=ID_VIEW_CMAP_GIST_EARTH) self.Bind(wx.EVT_MENU, self.on_cmap_ocean, id=ID_VIEW_CMAP_OCEAN) self.Bind(wx.EVT_MENU, self.on_cmap_rainbow, id=ID_VIEW_CMAP_RAINBOW) self.Bind(wx.EVT_MENU, self.on_cmap_rdylgn, id=ID_VIEW_CMAP_RDYLGN) self.Bind(wx.EVT_MENU, self.on_cmap_winter, id=ID_VIEW_CMAP_WINTER) self.status_bar = wx.StatusBar(self, -1) self.status_bar.SetFieldsCount(2) self.SetStatusBar(self.status_bar) self.canvas.mpl_connect('motion_notify_event', self.update_status_bar) self.canvas.Bind(wx.EVT_ENTER_WINDOW, self.change_cursor) def on_cmap_bag(self, evt): log.debug("cmap: bag") self.colormap = cm.get_cmap("BAG") self._refresh_plot() def on_cmap_jet(self, evt): log.debug("cmap: jet") self.colormap = cm.get_cmap("jet") self._refresh_plot() def on_cmap_bone(self, evt): log.debug("cmap: bone") self.colormap = cm.get_cmap("bone") self._refresh_plot() def on_cmap_gist_earth(self, evt): log.debug("cmap: gist_earth") self.colormap = cm.get_cmap("gist_earth") self._refresh_plot() def on_cmap_ocean(self, evt): log.debug("cmap: ocean") self.colormap = cm.get_cmap("ocean") self._refresh_plot() def on_cmap_rainbow(self, evt): log.debug("cmap: rainbow") self.colormap = cm.get_cmap("rainbow") self._refresh_plot() def on_cmap_rdylgn(self, evt): log.debug("cmap: RdYlGn") self.colormap = cm.get_cmap("RdYlGn") self._refresh_plot() def on_cmap_winter(self, evt): log.debug("cmap: winter") self.colormap = cm.get_cmap("winter") self._refresh_plot() def _refresh_plot(self): self.draw_figure() self.canvas.draw() def draw_figure(self): ls = LightSource(azdeg=315, altdeg=45) self.surf = self.data # try to plot the whole array try: blended_surface = ls.shade(self.surf, cmap=self.colormap, vert_exag=5, blend_mode=b"overlay", vmin=np.nanmin(self.surf), vmax=np.nanmax(self.surf)) # too big, two attempts for sub-sampling except MemoryError: rows = self.data.shape[0] cols = self.data.shape[1] # 1st attempt: <= 1024x1024 try: max_elements = 1024 row_stride = rows // max_elements + 1 col_stride = cols // max_elements + 1 self.surf = self.data[::row_stride, ::col_stride] blended_surface = ls.shade(self.surf, cmap=self.colormap, vert_exag=5, blend_mode=b"overlay", vmin=np.nanmin(self.surf), vmax=np.nanmax(self.surf)) except MemoryError: # 2st attempt: <= 512x512 max_elements = 512 row_stride = rows // max_elements + 1 col_stride = cols // max_elements + 1 self.surf = self.data[::row_stride, ::col_stride] blended_surface = ls.shade(self.surf, cmap=self.colormap, vert_exag=5, blend_mode=b"overlay", vmin=np.nanmin(self.surf), vmax=np.nanmax(self.surf)) log.debug("too big: %s x %s > subsampled to %s x %s" % (self.data.shape[0], self.data.shape[1], self.surf.shape[0], self.surf.shape[1])) self.axes.coastlines(resolution='50m', color='gray', linewidth=1) img = self.axes.imshow(blended_surface, origin='lower', cmap=self.colormap, extent=self.geo_extent, transform=ccrs.PlateCarree()) img.set_clim(vmin=np.nanmin(self.surf), vmax=np.nanmax(self.surf)) # add gridlines with labels only on the left and on the bottom grl = self.axes.gridlines(crs=ccrs.PlateCarree(), color='gray', draw_labels=True) grl.xformatter = LONGITUDE_FORMATTER grl.yformatter = LATITUDE_FORMATTER grl.xlabel_style = {'size': 8} grl.ylabel_style = {'size': 8} grl.ylabels_right = False grl.xlabels_top = False if self.cb: self.cb.on_mappable_changed(img) else: self.cb = plt.colorbar(img, ax=self.axes) self.cb.ax.tick_params(labelsize=8) def change_cursor(self, event): self.canvas.SetCursor(wx.StockCursor(wx.CURSOR_CROSS)) def update_status_bar(self, event): msg = str() if event.inaxes: x, y = event.xdata, event.ydata msg = self.axes.format_coord(x, y) self.status_bar.SetStatusText(msg, 1) hdf_compass-0.6.0/hdf_compass/compass_viewer/geo_surface/__init__.py0000666000000000000000000000210412730245342024043 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function, unicode_literals from .frame import GeoSurfaceFrame import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler())hdf_compass-0.6.0/hdf_compass/compass_viewer/icons/0000777000000000000000000000000012730267653020577 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/compass_viewer/icons/favicon_32.png0000666000000000000000000000514212730245342023227 0ustar 00000000000000PNG  IHDR szzbKGD pHYs  tIME riTXtCommentCreated with GIMPd.e IDATXí{\}?q>{m76M NJJ:ڨPQRTEU#%R(@ *XA`D4&Cf5y9JBtutνq=ڿǣ)M/ ['?}Z&w[|(9vչsۧKvo K^>4:s@{opgv7?|l,?y`퓌(.|{M_d0߻'u<K *&ܵT* 9>mLq֯]Éo߻DvduMs"SC`qqc۴)p5`EjAgod[wN`16_vrҍV?~FAT!X\c^pA €Vˌ²[/o;xCl\ѣGH{F½#(4rY t }ݛRk?ݏ`"t sz3x4^J{5V $0-+{e0 zsUˆz\kտ}׾ߩ=ϽdvTߍ}9lc?XAWJBZ]Y ӕ9RDRbEÜ:]\ǿUh40֋9^l#S(C%J)V8i*=)pl:_%%RI24+j_;Dmtu\{J"!90YT=$%J*Ꜩ%@)V@vZnU+6\@ώ<[;8cdeb O3Z_1 l`{ʟ:aEZ 0Ivrmf2(D.II I"CRoa#C;H(UG11aH%z1d"nI2 RH)bi"7]1w&QC.~o24kGHSRTcx&'9 K\7X4*80JEGNQZ=$K{ ]Zs ) BHTVrsMM=xi60&U3,q.`fWGaؾ#(Ns V6)81v|=/BXl7JX"'R X,,4V2u@S:<\c1SqIj'v\k#D-f`wN( ZaFkIqfUR9RTzgCg:-s8X` y&6&i0AgcKp$AkBy1Sr4ҹ=iϾN,nR?Jm(OYWS-͓q;d:: *[|+O 4BeҽL7F17}gvz~7 SgSX%-qBT BvCWۏ폍ޗ3q[~5 fؗ(חčNXVȢeB2M:Q ejψL0?:'.H[o/~к?ۼKo,C+Wɑ Z/|Џ>C_F{>{b("\IENDB`hdf_compass-0.6.0/hdf_compass/compass_viewer/icons/favicon_48.png0000666000000000000000000001146312730245342023241 0ustar 00000000000000PNG  IHDR00WbKGD pHYs  tIME 5HViTXtCommentCreated with GIMPd.eIDAThyW}?>gfgid,:|c.ۀ $+PS1*$b\X&[–juk=fߑ?zveE6G8IWof{e5\;s5=羑n:|֗`˙+V>6ƍLnŮbKa$X>8_|+M߹_r.˗u6Q\Zȇ/28<:::fmV|WNt]-^{?6\yf롃mP4 F̲RK/9Mg-gxLT>}ߪNسo#AmVAx31G2=yQuP(ҷ*;9<<ˏ>Eqƞ(rQ/T+?w6uݿ-7d9\#rgDatLURʳu~o4)Hu8mAktR%*ѷz`W5Gk}_⮟wp `ra(u䣐B!b2m/ 0m`@QT<ċd4 <|SԷZ#qxhj=! wpgWW/ϲw|"---ڳzA[!?}Qj(+F|*DA@PE:+["]x;)Y^)7}ky>-prx]/\ԓrtپ{/uc )~KD.Q9?`Q<' EB6jp Wu}'OMK1GFbhhRԕ g{#xq}Ozv3{ZRGňR!2\M KyE?}B D378gqƐ#y0da5V-qsFwS~OA* G_g?sOF >{v RӜ=ʱJBК?xfAJ6gq+%J rEvaeIqhch- Xכgtb 3s [Z¿~?wr 8{?iw`B{[j!ha&) gpxHqa_Ӊ1@, )-#BD.)cL%=+fֶĝ\{kN!D?xm]M*%I} 3Q$R5œ)rQcU[E+KBcB H!BùLA>1)뮿{z&~}/k(r@[M̧VqetC(dL$R dH'T<8=bCG6!)5ucfm-ZtQ)W=Ҋ/2NtlI5_OKWV Lr9l8s g)*l_xqn9.k.P KpXk)8cu#S]ӋNq;o>HTnA{tJCWrVJO8Ҍuǖ~|)tb84;c{C5ִSBRc9}uM-Xigq6p쟩sMFt-呃eV*,am]&8G( =A!+!3LK!*< R6wD(lKDdJK)%sj1`,$J U6՘rGvq[bke։Ji-YxɌBm9c )I-tg7W-9_dtp578kZ1gєxA:>O}# ycL`P6J0pX g)E c H)@ qc}9̥L$ymm% z"k228mQ&;%HQ85ĉXDZk4VOB"CJ>3$izJ(.-p^fn-1* 4SZ5k4^m:Ng,jk`hZcZdykp&K'W`)/vᄠ5PଖZ3v`C `hlCcb4&qIbl3=_gClBkMj4fdV5Ar. 4,J8dEfj'dk<ܒ5()XQi7)zJ<=iԱ:bMBי5bz)9Bn ԝMs&`S:w5T5ukEIY󦤤gDZItr6]&1`5H+$F }EC'8PJR ')ژcrr !Omk.fnk831H4Vjh)Iq҈䤤iL[w cL5ԒL)t~SE8']f}k }ɺmZ:K Z )vlk]!/SRHPa@{)" ftKXbE(yTulM-&NЕ RITx+1F XD3x|Z^{gNF?tV'N'XJ||~&f*iJ#I$N& 1=UESly[O ǤsyXgp8 8M1֢ffK1nҊW!UJBOTذQ",0[y =8sHkqiS%)zBZZ l1={'9Cj 7Os#. 9 us#-+ )#(DYiw!CUnhooȉ 9s&)i"56  J9Vv' 33;=wBdvύ;Yj7;0MشM8Scs$϶YI&!ɮtQq0 \FOrb˵F qni[?Dy똤3qs(47:;%JREG'yXS^_} ^~ۙu~ Y(SDﰗk+8\781<:ͪU˩TC#s!sIƼ\TGHPdE8yUu,L^= ɇ?H y{0Z՛PXX& B): ._!T֥f{8g+d"󸰀 윻io{kI%|߇;4L?aEm%nl0:2%84:͹T' o DMs\lO׏`2~?Fr2w'6imNm9g%4 Ps dpXB!r8GyDTbQl62|E3_~W^ )QZV񭗼Con0wX-\NNd-A8U ȵ aUeZ}G%A65moykĉϾOA~zȪ2Gm-ϋ%ZdQVuYİ6 2)t[奍~]x!ŠWo\틌+IENDB`hdf_compass-0.6.0/hdf_compass/compass_viewer/icons/go_back_24.png0000666000000000000000000000217212730245342023170 0ustar 00000000000000PNG  IHDRw=AIDATxڵolSUy{__Cdž01N-f.1hd4 t$:P BŤs`H !QC2 f@ۭk{V@0Fw"f59=Oтm@h`gwSn[0@EPB65[#3iDkR%mڕZтaKinwymij*NNf&3;N.P2?9vm`;˟.x/~:~3:]-(CZ; ͽo<A|qMANCp" "CH@$? d:t]G3o F#1spv%XN,+^˃\))*;y@>PVgMI! 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Refer to "license.txt" for the icon licensing terms. The following images are NOT under the LGPL, and are (c) Heliosphere Research LLC (all rights reserved): logo.png logo.xcfhdf_compass-0.6.0/hdf_compass/compass_viewer/icons/save_24.png0000666000000000000000000000214112730245342022535 0ustar 00000000000000PNG  IHDRw=bKGD pHYs a aJ%tIME #/dIDATHǵKUfz  ~!AMd!_A]{nč 1$$+$p-Џzs[]5 ;}79?7.vY3N9Ky|x>'!T1K˙R՗`揝8~ggfν⡗X;ʶfݓ8ށs7G709{Lɂ?L07sCMQU 35 +ڍ8gѢxx F(`DQ T 2QP"tb7'dF@1osE8z`G"DQ*0[j EHlI$`Em94]@c(ԢH#S2HW"UϿ㽧т,³`^&e${a*LĪRq@dӿpunN5HxIeL)_yo4M `f ^ZWֳszloL-7EfbE~O>m%j*>viXrs/^ﯢlg玝&Xm񈍍?yUeu*ᰩ !cvDbL ر9pӽ{|w Ng8bfuM#UYaJ#]hT;TPICKDR1<bEAHD`{TU  f ňR%$2F꺦k|JYͨ) @=F1L%ISp>;~, Aʲ9ѨcDU),0R[|֤w_><|e˃ݽ{g{ 8DիM3h4*Eyo;-jc`f5pkc?yTo}={f 缪>oH|Y5XL|y2_0 0z|zIENDB`hdf_compass-0.6.0/hdf_compass/compass_viewer/icons/view_icon_24.png0000666000000000000000000000175512730245342023573 0ustar 00000000000000PNG  IHDRw=IDATxڵh[UyiM 4g1̱ڡ( vE2h@D0\n 1wQغvĴM]׼Z;ҭ?{{~/bv "Jnwn~.}WD5_'^;v49Ϻ$IPUuB^óܴO)f yye+PBܜ:ؽ%[AggWiL&Q T,I^tt|T`&x |]>M|;0JRekih}. )R)+[ \o$^]T`kF\ T< N1?/;pM9:}I_KOSA|nLLأjYn.o:*+`x"ӑ(A/]&pOab|X*V00ƫڼWp.PTŌruMk:ż&@$A~ Mz.`X0[ncr#0 UZ$b03K3XiBg{띹ڶT?DM&Ec~=;K3) P? TLwTjދH‘+x?>< ,O_O%Z4nka"p$WJsZs܏B ƃqZ]pF0fGF[itNPMk @' 3.2Nm]4xJ,˲f3T*1}s6ڂ`0R)R]TJN$j>}M^Ƀd2)Rj$4~st݁fd4B&%4&nnnrdǏ$k-;Ps䏋ݫjsg(!E)Zh{{h\.GNyL>Y,kpba2)F(G@9Coz_~/IENDB`hdf_compass-0.6.0/hdf_compass/compass_viewer/icons/view_list_32.png0000666000000000000000000000077412730245342023615 0ustar 00000000000000PNG  IHDR szzIDATxMjPo1jR+X#^ZW݊p$x^@vebԪI_L Uхycf~L`xCpd#%@Ob1i*&;!Iғq 0L=p$(`ˇ@zȲX;f.*B+{dY!:6wi!67AƐ$8rٽ6wiΫ ҿmƲ~DjH4Xb@" CS w տfAN'Zu,KvRVa6r!NuZb@&?*Lu0}!xm\.f>7r܉u P*(AA>_bt ۍBZ8&@<jޯvC$TRSiolG HIENDB`hdf_compass-0.6.0/hdf_compass/compass_viewer/icons/view_tree_32.png0000666000000000000000000000134712730245342023576 0ustar 00000000000000PNG  IHDR szzIDATxŗ?LQǿ?+m( n-5.Eea`a`;@ ,ԁ0ԚŪqМ'RO65|%i]{<U.bԑ0́UU- ˲pԘ <_)dl6g`Y `ssKud(Y*wZ\,(`LUY ^ ey,A28.W1@y hlkk$T_q.45 :jRd$SxCKK"no PWw t"D"`0Hf zX ]]]GwwOxvo-[, Bכq30;;#_}/pn .tfffk`=aaE7߰ʣ×LOO/7iPoKt -W )^PF,7 oZ8`  O/+?l5w4͛Qr " ȑƏu *s' b>} UWwZ$nzX&<< WQP mHK+z( ,ISS,)HSt4 ڹجV6C+\w7fR(7]~ 6ǎҮW)&"''@(eImPFY[*͸hHJ~XGf} {RLȉ>8@uW䖷7$!EJnحYctZa)fU*:X2[Z5~~t$a9“`,wѭBN=[SCN>믩 9a,ql+57ړKM6$2WaIIOXX?<\0̿ssIENDB`hdf_compass-0.6.0/hdf_compass/compass_viewer/icons/viz_plot_32.png0000666000000000000000000000316412730245342023452 0ustar 00000000000000PNG  IHDR szz;IDATx͗KLIǿ` ]b"G7xuP5&ca WeDU8l@FV+":wI1U]}z ~@(,lxtҏ$#>r~#|}{|X,9z(B@ Yl9y"4 nԟ!޽{sXZZbBCx%MI$~= YI!O›7oc!˲jںw*  JsH@wfh(: `:H( '5 pπ;,zuCgC͛ $68晌BZ*xдU>KDp怆 ذa2tP @6a~ދ9 тu\rzŤ$,kh14BF`^)x-BOa;vpΝ;r@(3(f`l,/_zq7.b09c`LA=8y.BSS &@R QYƆ8^v.C} "j:4U3 .Y3ڂ>1 Lզo ֦%%萈۳#x:xaw0[l5*l" L^{z \zOz0qќt-Y@S[ 륣_'Î,x5fI8#N~knJ,MPć (%:h}|ulnIE1feyʋ!` >Jm+T1Y&HeTۧ"ŝ5D *J$dϱh&tt@@ Q@!wϊ7Û1*9Jʹ9:UIE0h I2T]fv*o:DJKypϬO!4'ǁ9hh|{=PX> n Em^-AhɌ+zĶQj,=3hѷ$D P߳ vy;-^Fv_+"?2 ̬dߴ/MQ"JIENDB`hdf_compass-0.6.0/hdf_compass/compass_viewer/image/0000777000000000000000000000000012730267653020546 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/compass_viewer/image/frame.py0000666000000000000000000000450012730245342022200 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Implements a simple true-color image viewer. """ from __future__ import absolute_import, division, print_function, unicode_literals import wx import wx.grid import logging log = logging.getLogger(__name__) from ..frame import NodeFrame class ImageFrame(NodeFrame): """ Top-level frame displaying objects of type compass_model.Image. """ def __init__(self, node, **kwds): """ Create a new array viewer, to display *node*. """ NodeFrame.__init__(self, node, title=node.display_name, size=(800, 400), **kwds) self.node = node p = ImagePanel(self, node) self.view = p class ImagePanel(wx.Panel): """ Panel inside the image viewer pane which displays the image. """ def __init__(self, parent, node): """ Display a true color, pixel-interlaced (not pixel-planar) image """ wx.Panel.__init__(self, parent) b = wx.BitmapFromBuffer(node.width, node.height, node.data) b.CopyFromBuffer(node.data) sizer = wx.BoxSizer(wx.HORIZONTAL) sb = wx.StaticBitmap(self, wx.ID_ANY, b) sizer.AddStretchSpacer() sizer.Add(sb, 1, wx.EXPAND | wx.ALIGN_CENTER | wx.ALIGN_CENTER_VERTICAL) sizer.AddStretchSpacer() sizer2 = wx.BoxSizer(wx.VERTICAL) sizer2.AddStretchSpacer() sizer2.Add(sizer, 1) sizer2.AddStretchSpacer() self.SetSizer(sizer2) hdf_compass-0.6.0/hdf_compass/compass_viewer/image/__init__.py0000666000000000000000000000207712730245342022654 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function, unicode_literals from .frame import ImageFrame import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler())hdf_compass-0.6.0/hdf_compass/compass_viewer/info.py0000666000000000000000000001150312730245342020760 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Defines the left-hand side information panel used to display context info. """ from __future__ import absolute_import, division, print_function, unicode_literals import wx import logging log = logging.getLogger(__name__) from hdf_compass import compass_model from hdf_compass.utils import is_win # Info panel width PANEL_WIDTH = 200 # Size of the main title font FONTSIZE = 16 if is_win else 18 class InfoPanel(wx.Panel): """ Panel displaying general information about the selected object. Designed to be displayed vertically; sets its own width (PANEL_WIDTH). """ def __init__(self, parent): """ Constructor. *parent* should be the containing frame. """ wx.Panel.__init__(self, parent, size=(PANEL_WIDTH, 10), style=wx.BORDER_NONE) font = wx.Font(FONTSIZE, wx.FONTFAMILY_DEFAULT, wx.FONTSTYLE_NORMAL, wx.FONTWEIGHT_NORMAL) # Sidebar title text self.name_text = wx.StaticText(self, style=wx.ALIGN_LEFT | wx.ST_ELLIPSIZE_MIDDLE, size=(PANEL_WIDTH - 40, 30)) self.name_text.SetFont(font) # Sidebar icon (see display method) self.static_bitmap = None # Descriptive text below the icon self.prop_text = wx.StaticText(self, style=wx.ALIGN_LEFT) self.sizer = sizer = wx.BoxSizer(wx.VERTICAL) sizer.Add(self.name_text, 0, wx.LEFT | wx.TOP | wx.RIGHT, border=20) sizer.Add(self.prop_text, 0, wx.LEFT | wx.RIGHT, border=20) sizer.AddStretchSpacer(1) self.SetSizer(sizer) self.SetBackgroundColour(wx.Colour(255, 255, 255)) def display(self, node): """ Update displayed information on the node. See the get* methods for specifics on what's displayed. """ self.name_text.SetLabel(node.display_name) self.prop_text.SetLabel(describe(node)) if self.static_bitmap is not None: self.sizer.Remove(self.static_bitmap) self.static_bitmap.Destroy() # We load the PNG icon directly from the appropriate Node class png = wx.Bitmap(type(node).icons[64], wx.BITMAP_TYPE_ANY) self.static_bitmap = wx.StaticBitmap(self, wx.ID_ANY, png) self.sizer.Insert(1, self.static_bitmap, 0, wx.ALL, border=20) self.sizer.Layout() self.Layout() def describe(node): """ Return a (possibly multi-line) text description of a node. """ desc = "%s\n\n" % type(node).class_kind if isinstance(node, compass_model.Array): desc += "Shape\n%s\n\nType\n%s\n" % \ (node.shape, dtype_text(node.dtype)) elif isinstance(node, compass_model.Container): desc += "%d items\n" % len(node) if not isinstance(node, compass_model.KeyValue): # see if there is a key-value handler for this node handlers = node.store.gethandlers(node.key) for h in handlers: kv_node = h(node.store, node.key) if isinstance(kv_node, compass_model.KeyValue): num_keys = len(kv_node.keys) if num_keys > 0: desc += "\n%d %s\n" % (len(kv_node.keys), type(kv_node).class_kind) return desc def dtype_text(dt): """ String description appropriate for a NumPy dtype """ log.debug("dtype kind: %s, size: %d" % (dt.kind, dt.itemsize)) if dt.names is not None: log.debug("dtype names: %s" % ",".join(n for n in dt.names)) return "Compound (%d fields)" % len(dt.names) if dt.kind == 'f': return "%d-byte floating point" % dt.itemsize if dt.kind == 'u': return "%d-byte unsigned integer" % dt.itemsize if dt.kind == 'i': return "%d-byte signed integer" % dt.itemsize if dt.kind == 'S': return "ASCII String (%d characters)" % dt.itemsize if dt.kind == 'U': return "Unicode String (%d characters)" % dt.itemsize return "Unknown" hdf_compass-0.6.0/hdf_compass/compass_viewer/keyvalue/0000777000000000000000000000000012730267653021311 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/compass_viewer/keyvalue/frame.py0000666000000000000000000000660612730245342022754 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Implements a viewer for key-value stores (instances of compass_model.KeyValue). Keys are strings, values are any data type HDFCompass can understand. Presently this means all NumPy types, plus Python str/unicode. """ from __future__ import absolute_import, division, print_function, unicode_literals import wx import logging log = logging.getLogger(__name__) from ..frame import NodeFrame class KeyValueFrame(NodeFrame): """ A frame to display a list of key/value pairs, their types and shapes. """ def __init__(self, node, pos=None): """ Create a new frame. node: Container instance to display. """ title = 'Attributes of "%s"' % node.display_name NodeFrame.__init__(self, node, size=(800, 400), title=title, pos=pos) self.list = KeyValueList(self, node) self.view = self.list class KeyValueList(wx.ListCtrl): """ A simple list view of key/value attributes """ def __init__(self, parent, node): """ Create a new attribute list view. parent: wxPython parent object node: compass_model.KeyValue instance """ wx.ListCtrl.__init__(self, parent, style=wx.LC_REPORT | wx.LC_SINGLE_SEL | wx.BORDER_NONE | wx.LC_HRULES) self.node = node self.InsertColumn(0, "Name") self.InsertColumn(1, "Value") self.InsertColumn(2, "Type") self.InsertColumn(3, "Shape") names = node.keys values = [self.node[n] for n in names] def itemtext(item, col_id): name = names[item] data = values[item] text = "" if col_id == 0: text = name elif col_id == 1: text = str(data) elif col_id == 2: if hasattr(data, 'dtype'): text = str(data.dtype) else: text = str(type(data)) elif col_id == 3: if hasattr(data, 'shape'): text = str(data.shape) else: text = "()" return text for n in names: row = self.InsertStringItem(9999, n) for col in xrange(1, 4): self.SetStringItem(row, col, itemtext(row, col)) self.SetColumnWidth(0, 200) self.SetColumnWidth(1, wx.LIST_AUTOSIZE) self.SetColumnWidth(2, wx.LIST_AUTOSIZE) self.SetColumnWidth(3, wx.LIST_AUTOSIZE) hdf_compass-0.6.0/hdf_compass/compass_viewer/keyvalue/__init__.py0000666000000000000000000000210412730245342023406 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function, unicode_literals from .frame import KeyValueFrame import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler()) hdf_compass-0.6.0/hdf_compass/compass_viewer/text/0000777000000000000000000000000012730267653020450 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/compass_viewer/text/frame.py0000666000000000000000000001576412730245342022120 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Implements a viewer frame for compass_model.Array. """ from __future__ import absolute_import, division, print_function, unicode_literals import os import logging import wx log = logging.getLogger(__name__) from .text_ctrl import TextViewerFrame, XmlStc from ..frame import NodeFrame # Menu and button IDs ID_SAVE_TEXT_MENU = wx.NewId() ID_VALIDATE_XML_MENU = wx.NewId() ID_SAVE_XML_MENU = wx.NewId() class TextFrame(NodeFrame): icon_folder = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'icons')) """ Top-level frame displaying objects of type compass_model.Text. From top to bottom, has: 1. Toolbar (see TextFrame.init_toolbar) 2. A TextCtrl, which displays the text. """ def __init__(self, node, pos=None): """ Create a new array viewer, to display *node*. """ super(TextFrame, self).__init__(node, size=(800, 400), title=node.display_name, pos=pos) log.debug("init") self.node = node self.txt = wx.TextCtrl(self, 1, style=wx.TE_MULTILINE | wx.TE_READONLY) self.txt.SetValue(node.text) save_menu = wx.Menu() save_menu.Append(ID_SAVE_TEXT_MENU, "Save Text\tCtrl-T") self.add_menu(save_menu, "Save") self.toolbar = None self.init_toolbar() gridsizer = wx.BoxSizer(wx.VERTICAL) gridsizer.Add(self.txt, 1, wx.EXPAND) self.view = gridsizer self.Bind(wx.EVT_MENU, self.on_save, id=ID_SAVE_TEXT_MENU) def init_toolbar(self): """ Set up the toolbar at the top of the window. """ t_size = (24, 24) plot_bmp = wx.Bitmap(os.path.join(self.icon_folder, "save_24.png"), wx.BITMAP_TYPE_ANY) self.toolbar = self.CreateToolBar(wx.TB_HORIZONTAL | wx.NO_BORDER | wx.TB_FLAT | wx.TB_TEXT) self.toolbar.SetToolBitmapSize(t_size) self.toolbar.AddStretchableSpace() self.toolbar.AddLabelTool(ID_SAVE_TEXT_MENU, "Save", plot_bmp, shortHelp="Save Text", longHelp="Extract and save Text on disk") self.toolbar.Realize() def on_save(self, evt): """ User has chosen to save the current Text """ log.debug("saving: %s" % self.node.key) save_file_dialog = wx.FileDialog(self, "Save XML file", "", "text.txt", "Text files (*.txt)|*.txt", wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT) if save_file_dialog.ShowModal() == wx.ID_CANCEL: return # the user changed idea... # save the current contents in the file # this can be done with e.g. wxPython output streams: with open(save_file_dialog.GetPath(), 'w') as fod: fod.write(self.node.text) class XmlFrame(NodeFrame): icon_folder = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'icons')) """ Top-level frame displaying objects of type compass_model.Text. From top to bottom, has: 1. Toolbar (see ArrayFrame.init_toolbar) 2. A TextCtrl, which displays the text. """ def __init__(self, node, pos=None): """ Create a new array viewer, to display *node*. """ super(XmlFrame, self).__init__(node, size=(800, 400), title=node.display_name, pos=pos) log.debug("init") self.node = node self.xml = XmlStc(self, xml_string=self.node.text) self.text_viewer = None save_menu = wx.Menu() save_menu.Append(ID_SAVE_XML_MENU, "Save xml\tCtrl-X") self.add_menu(save_menu, "Save") if self.node.has_validation(): val_menu = wx.Menu() val_menu.Append(ID_VALIDATE_XML_MENU, "Validate xml\tCtrl-V") self.add_menu(val_menu, "Validate") self.toolbar = None self.init_toolbar() gridsizer = wx.BoxSizer(wx.VERTICAL) gridsizer.Add(self.xml, 1, wx.EXPAND) self.view = gridsizer self.Bind(wx.EVT_MENU, self.on_save, id=ID_SAVE_XML_MENU) if self.node.has_validation(): self.Bind(wx.EVT_MENU, self.on_validate, id=ID_VALIDATE_XML_MENU) def init_toolbar(self): """ Set up the toolbar at the top of the window. """ t_size = (24, 24) save_bmp = wx.Bitmap(os.path.join(self.icon_folder, "save_24.png"), wx.BITMAP_TYPE_ANY) if self.node.has_validation(): validate_bmp = wx.Bitmap(os.path.join(self.icon_folder, "xml_validate_24.png"), wx.BITMAP_TYPE_ANY) self.toolbar = self.CreateToolBar(wx.TB_HORIZONTAL | wx.NO_BORDER | wx.TB_FLAT | wx.TB_TEXT) self.toolbar.SetToolBitmapSize(t_size) self.toolbar.AddStretchableSpace() self.toolbar.AddLabelTool(ID_SAVE_XML_MENU, "Save", save_bmp, shortHelp="Save XML", longHelp="Extract and save XML on disk") if self.node.has_validation(): self.toolbar.AddLabelTool(ID_VALIDATE_XML_MENU, "Validate", validate_bmp, shortHelp="Validate XML", longHelp="Validate XML in a popup window") self.toolbar.Realize() def on_validate(self, evt): """ User has chosen to validate the current XML """ if self.node.has_validation(): log.debug("validating: %s" % self.node.key) self.text_viewer = TextViewerFrame(self.node.validation) self.text_viewer.Show() else: log.warning("this node type has not validation: %s" % self.node) def on_save(self, evt): """ User has chosen to save the current XML """ log.debug("saving: %s" % self.node.key) save_file_dialog = wx.FileDialog(self, "Save XML file", "", "text.xml", "Xml files (*.xml)|*.xml", wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT) if save_file_dialog.ShowModal() == wx.ID_CANCEL: return # the user changed idea... # save the current contents in the file # this can be done with e.g. wxPython output streams: with open(save_file_dialog.GetPath(), 'w') as fod: fod.write(self.node.text) hdf_compass-0.6.0/hdf_compass/compass_viewer/text/text_ctrl.py0000666000000000000000000002447712730245342023037 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Implements a viewer frame for compass_model.Array. """ from __future__ import absolute_import, division, print_function, unicode_literals import logging import wx import wx.stc as stc log = logging.getLogger(__name__) from ..frame import BaseFrame if wx.Platform == '__WXMSW__': faces = {'times': 'Times New Roman', 'mono': 'Courier New', 'helv': 'Arial', 'other': 'Comic Sans MS', 'size': 10, 'size2': 8, } else: faces = {'times': 'Times', 'mono': 'Courier', 'helv': 'Helvetica', 'other': 'new century schoolbook', 'size': 13, 'size2': 11, } class TextViewerFrame(BaseFrame): """ Base class for Matplotlib plot windows. Override draw_figure() to plot your figure on the provided axes. """ def __init__(self, data, title="Validation"): """ Create a new Matplotlib plotting window for a 1D line plot """ BaseFrame.__init__(self, id=wx.ID_ANY, title=title, size=(800, 400)) self.data = data self.txt = wx.TextCtrl(self, 1, style=wx.TE_MULTILINE | wx.TE_READONLY) self.txt.SetValue(self.data) gridsizer = wx.BoxSizer(wx.VERTICAL) gridsizer.Add(self.txt, 1, wx.LEFT | wx.TOP | wx.GROW) self.view = gridsizer class XmlStc(stc.StyledTextCtrl): def __init__(self, parent, xml_string, keywords=None): stc.StyledTextCtrl.__init__(self, parent, -1) self.SetLexer(stc.STC_LEX_XML) if keywords is not None: self.SetKeyWords(0, keywords) # Global default styles for all languages self.StyleSetSpec(stc.STC_STYLE_DEFAULT, "face:%(mono)s,size:%(size)d" % faces) self.StyleClearAll() # Reset all to be like the default # Global default styles for all languages self.StyleSetSpec(stc.STC_STYLE_DEFAULT, "face:%(mono)s,size:%(size)d" % faces) self.StyleSetSpec(stc.STC_STYLE_LINENUMBER, "back:#C0C0C0,face:%(helv)s,size:%(size2)d" % faces) self.StyleSetSpec(stc.STC_STYLE_CONTROLCHAR, "face:%(other)s" % faces) self.StyleSetSpec(stc.STC_STYLE_BRACELIGHT, "fore:#FFFFFF,back:#0000FF,bold") self.StyleSetSpec(stc.STC_STYLE_BRACEBAD, "fore:#000000,back:#FF0000,bold") self.StyleSetSpec(stc.STC_H_VALUE, "fore:#0000cc,face:%(helv)s,size:%(size)d" % faces) self.StyleSetSpec(stc.STC_H_DEFAULT, "fore:#0000cc,face:%(helv)s,size:%(size)d" % faces) self.StyleSetSpec(stc.STC_H_ENTITY, "fore:#0000cc,face:%(helv)s,size:%(size)d" % faces) # initial XML tag self.StyleSetSpec(stc.STC_H_XMLSTART, "fore:#ffcccc,bold,face:%(helv)s,size:%(size)d" % faces) self.StyleSetSpec(stc.STC_H_XMLEND, "fore:#ffcccc,bold,face:%(helv)s,size:%(size)d" % faces) # XML tags self.StyleSetSpec(stc.STC_H_TAG, "fore:#555555,face:%(helv)s,size:%(size)d" % faces) self.StyleSetSpec(stc.STC_H_TAGEND, "fore:#555555,face:%(helv)s,size:%(size)d" % faces) self.StyleSetSpec(stc.STC_H_TAGUNKNOWN, "fore:#555555,face:%(helv)s,size:%(size)d" % faces) # XML attributes self.StyleSetSpec(stc.STC_H_ATTRIBUTE, "fore:#BDB76B,face:%(helv)s,size:%(size)d" % faces) self.StyleSetSpec(stc.STC_H_ATTRIBUTEUNKNOWN, "fore:#BDB76B,face:%(helv)s,size:%(size)d" % faces) # XML comments and quotes self.StyleSetSpec(stc.STC_H_COMMENT, "fore:#888888,face:%(helv)s,size:%(size)d" % faces) self.StyleSetSpec(stc.STC_H_SINGLESTRING, "fore:#aa2222,face:%(helv)s,size:%(size)d" % faces) self.StyleSetSpec(stc.STC_H_DOUBLESTRING, "fore:#aa2222,face:%(helv)s,size:%(size)d" % faces) self.StyleSetSpec(stc.STC_H_SGML_SIMPLESTRING, "fore:#aa2222,face:%(helv)s,size:%(size)d" % faces) self.StyleSetSpec(stc.STC_H_SGML_DOUBLESTRING, "fore:#aa2222,face:%(helv)s,size:%(size)d" % faces) # Keyword self.StyleSetSpec(stc.STC_P_WORD, "fore:#990000,size:%(size)d" % faces) # Caret color self.SetCaretForeground("BLUE") # Selection background self.SetSelBackground(1, '#66CCFF') self.SetSelBackground(True, wx.SystemSettings_GetColour(wx.SYS_COLOUR_HIGHLIGHT)) self.SetSelForeground(True, wx.SystemSettings_GetColour(wx.SYS_COLOUR_HIGHLIGHTTEXT)) self.SetProperty("fold", "1") # Enable folding self.SetProperty("fold.html", "1") # Enable folding self.SetProperty("tab.timmy.whinge.level", "1") # Highlight tab/space mixing (shouldn't be any) self.SetMargins(3, 3) # Set left and right margins self.SetMarginType(1, stc.STC_MARGIN_NUMBER) # Set up the numbers in the margin for margin #1 self.SetMarginWidth(1, 40) # Reasonable value for, say, 4-5 digits using a mono font (40 pix) # self.SetViewWhiteSpace(False) self.SetWrapMode(stc.STC_WRAP_WORD) self.SetUseVerticalScrollBar(True) self.SetUseHorizontalScrollBar(True) # Setup a margin to hold fold markers self.SetMarginType(2, stc.STC_MARGIN_SYMBOL) self.SetMarginMask(2, stc.STC_MASK_FOLDERS) self.SetMarginSensitive(2, True) self.SetMarginWidth(2, 15) # marker style self.MarkerDefine(stc.STC_MARKNUM_FOLDEREND, stc.STC_MARK_BOXPLUSCONNECTED, "white", "black") self.MarkerDefine(stc.STC_MARKNUM_FOLDEROPENMID, stc.STC_MARK_BOXMINUSCONNECTED, "white", "black") self.MarkerDefine(stc.STC_MARKNUM_FOLDERMIDTAIL, stc.STC_MARK_TCORNER, "white", "black") self.MarkerDefine(stc.STC_MARKNUM_FOLDERTAIL, stc.STC_MARK_LCORNER, "white", "black") self.MarkerDefine(stc.STC_MARKNUM_FOLDERSUB, stc.STC_MARK_VLINE, "white", "black") self.MarkerDefine(stc.STC_MARKNUM_FOLDER, stc.STC_MARK_BOXPLUS, "white", "#cccccc") self.MarkerDefine(stc.STC_MARKNUM_FOLDEROPEN, stc.STC_MARK_BOXMINUS, "white", "black") stc.EVT_STC_MARGINCLICK(self, -1, self.on_margin_click) self.SetText(xml_string) self.SetEditable(False) def on_margin_click(self, evt): """ Folds and unfolds as needed """ if evt.GetMargin() == 2: if evt.GetShift() and evt.GetControl(): self.fold_all() else: line_clicked = self.LineFromPosition(evt.GetPosition()) if self.GetFoldLevel(line_clicked) & stc.STC_FOLDLEVELHEADERFLAG: if evt.GetShift(): self.SetFoldExpanded(line_clicked, True) self.expand_item(line_clicked, True, True, 1) elif evt.GetControl(): if self.GetFoldExpanded(line_clicked): self.SetFoldExpanded(line_clicked, False) self.expand_item(line_clicked, False, True, 0) else: self.SetFoldExpanded(line_clicked, True) self.expand_item(line_clicked, True, True, 100) else: self.ToggleFold(line_clicked) def fold_all(self): line_count = self.GetLineCount() expanding = True # find out if we are folding or unfolding for line_num in range(line_count): if self.GetFoldLevel(line_num) & stc.STC_FOLDLEVELHEADERFLAG: expanding = not self.GetFoldExpanded(line_num) break line_num = 0 while line_num < line_count: level = self.GetFoldLevel(line_num) if level & stc.STC_FOLDLEVELHEADERFLAG and (level & stc.STC_FOLDLEVELNUMBERMASK) == stc.STC_FOLDLEVELBASE: if expanding: self.SetFoldExpanded(line_num, True) line_num = self.expand_item(line_num, True) line_num -= 1 else: last_child = self.GetLastChild(line_num, -1) self.SetFoldExpanded(line_num, False) if last_child > line_num: self.HideLines(line_num + 1, last_child) line_num += 1 def expand_item(self, line, do_expand, force=False, vis_levels=0, level=-1): last_child = self.GetLastChild(line, level) line += 1 while line <= last_child: if force: if vis_levels > 0: self.ShowLines(line, line) else: self.HideLines(line, line) else: if do_expand: self.ShowLines(line, line) if level == -1: level = self.GetFoldLevel(line) if level & stc.STC_FOLDLEVELHEADERFLAG: if force: if vis_levels > 1: self.SetFoldExpanded(line, True) else: self.SetFoldExpanded(line, False) line = self.expand_item(line, do_expand, force, vis_levels - 1) else: if do_expand and self.GetFoldExpanded(line): line = self.expand_item(line=line, do_expand=True, force=force, vis_levels=(vis_levels - 1)) else: line = self.expand_item(line=line, do_expand=False, force=force, vis_levels=(vis_levels - 1)) else: line += 1 return line hdf_compass-0.6.0/hdf_compass/compass_viewer/text/__init__.py0000666000000000000000000000033212730245342022546 0ustar 00000000000000from __future__ import absolute_import, division, print_function, unicode_literals from .frame import TextFrame, XmlFrame import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler()) hdf_compass-0.6.0/hdf_compass/compass_viewer/viewer.py0000666000000000000000000002105112730245342021325 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Main module for HDFCompass. Defines the App class, along with supporting infrastructure. """ from __future__ import absolute_import, division, print_function, unicode_literals # Must be at the top, to ensure we're the first to call matplotlib.use. import matplotlib matplotlib.use('WXAgg') import sys import wx import logging log = logging.getLogger(__name__) from hdf_compass import compass_model from hdf_compass import utils from .events import ID_COMPASS_OPEN from . import container, array, geo_surface, geo_array, keyvalue, image, frame, text __version__ = utils.__version__ class CompassImageList(wx.ImageList): """ A specialized type of image list, to support icons from Node subclasses. Instances of this class hold only square icons, of the size specified when created. The appropriate icon index for a particular Node subclass is retrieved using get_index(nodeclass). Image addition and indexing is completely bootstrapped; there's no need to manually add or register Node classes with this class. Just call get_index and the object will figure it out. """ def __init__(self, size): """ Create a new list holding square icons of the given size. """ wx.ImageList.__init__(self, size, size) self._indices = {} self._size = size def get_index(self, node_class): """ Retrieve an index appropriate for the given Node subclass. """ if node_class not in self._indices: png = wx.Bitmap(node_class.icons[self._size], wx.BITMAP_TYPE_ANY) idx = self.Add(png) self._indices[node_class] = idx return self._indices[node_class] class CompassApp(wx.App): """ The main application object for HDFCompass. This mainly handles ID_COMPASS_OPEN events, which are requests to launch a new window viewing a particular node. Also contains a dict of CompassImageLists, indexed by image width. """ def __init__(self, redirect): """ Constructor. If *redirect*, show a windows with console output. """ wx.App.__init__(self, redirect) self.imagelists = {} for size in (16, 24, 32, 48, 64): self.imagelists[size] = CompassImageList(size) self.Bind(wx.EVT_MENU, self.on_compass_open, id=ID_COMPASS_OPEN) self.SetAppName("HDFCompass") def on_compass_open(self, evt): """ A request has been made to open a node from somewhere in the GUI """ open_node(evt.node, evt.kwds.get('pos')) def MacOpenFile(self, filename): """ A file has been dropped onto the app icon """ url = 'file://' + filename open_store(url) def open_node(node, pos=None): """ Open a viewer frame appropriate for the given Node instance. node: Node instance to open pos: 2-tuple with current window position (used to avoid overlap). """ if pos is not None: # The thing we get from GetPosition isn't really a tuple, so # you have to manually cast entries to int or it silently fails. new_pos =(int(pos[0])+40, int(pos[1])+40) else: new_pos = None log.debug("Top-level open called for %s" % node) if isinstance(node, compass_model.Container): f = container.ContainerFrame(node, pos=new_pos) f.Show() elif isinstance(node, compass_model.GeoSurface): f = geo_surface.GeoSurfaceFrame(node, pos=new_pos) f.Show() elif isinstance(node, compass_model.GeoArray): f = geo_array.GeoArrayFrame(node, pos=new_pos) f.Show() elif isinstance(node, compass_model.Array): f = array.ArrayFrame(node, pos=new_pos) f.Show() elif isinstance(node, compass_model.Xml): f = text.XmlFrame(node, pos=new_pos) f.Show() elif isinstance(node, compass_model.Text): f = text.TextFrame(node, pos=new_pos) f.Show() elif isinstance(node, compass_model.KeyValue): f = keyvalue.KeyValueFrame(node, pos=new_pos) f.Show() elif isinstance(node, compass_model.Image): f = image.ImageFrame(node, pos=pos) f.Show() else: pass def open_store(url): """ Open the url using the first matching registered Store class. Returns True if the url was successfully opened, False otherwise. """ stores = [x for x in compass_model.get_stores() if x.can_handle(url)] if len(stores) > 0: instance = stores[0](url) open_node(instance.root) return True return False def can_open_store(url): """ checks url for first matching registered Store class. Returns True if the url can be successfully opened, False otherwise. """ stores = [x for x in compass_model.get_stores() if x.can_handle(url)] if len(stores) > 0: instance = stores[0](url) return True return False def load_plugins(): """ Helper function that attempts to load all the plugins """ # provide some info about the env in use import platform log.debug("Python %s %s on %s %s (%s)" % (platform.python_version(), platform.architecture()[0], platform.uname()[0], platform.uname()[2], platform.uname()[4])) import numpy log.debug("numpy %s" % numpy.__version__) log.debug("matplotlib %s" % matplotlib.__version__) log.debug("wxPython %s" % wx.__version__) from hdf_compass import compass_model try: from hdf_compass import filesystem_model except ImportError: log.warning("Filesystem plugin: NOT loaded") try: from hdf_compass import array_model except ImportError: log.warning("Array plugin: NOT loaded") try: from hdf_compass import hdf5_model import h5py log.debug("h5py %s" % h5py.__version__) except ImportError: log.warning("HDF5 plugin: NOT loaded") try: from hdf_compass import bag_model from hydroffice import bag from lxml import etree log.debug("hydroffice.bag %s" % bag.__version__) log.debug("lxml %s (libxml %s, libxslt %s)" % (etree.__version__, ".".join(str(i) for i in etree.LIBXML_VERSION), ".".join(str(i) for i in etree.LIBXSLT_VERSION))) except (ImportError, OSError): log.warning("BAG plugin: NOT loaded") try: from hdf_compass import asc_model except ImportError: log.warning("Ascii grid: plugin NOT loaded") try: from hdf_compass import opendap_model from pydap import lib log.debug("pydap %s (protocol %s)" % (".".join(str(i) for i in lib.__version__), ".".join(str(i) for i in lib.__dap__))) except ImportError: log.warning("Opendap plugin: NOT loaded") from hdf_compass import hdf5rest_model try: from hdf_compass import hdf5rest_model except ImportError: log.warning("HDF5 REST: plugin NOT loaded") def run(): """ Run HDFCompass. Handles all command-line arguments, etc. """ import os.path as op app = CompassApp(False) load_plugins() urls = sys.argv[1:] for url in urls: if "://" not in url: # assumed to be file path url = utils.path2url(op.abspath(url)) if not open_store(url): log.warning('Failed to open "%s"; no handlers' % url) f = frame.InitFrame() if utils.is_darwin: wx.MenuBar.MacSetCommonMenuBar(f.GetMenuBar()) else: f.Show() app.MainLoop() hdf_compass-0.6.0/hdf_compass/compass_viewer/__init__.py0000666000000000000000000000214312730245342021564 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function, unicode_literals from .viewer import run, can_open_store, open_store, CompassApp import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler()) hdf_compass-0.6.0/hdf_compass/compass_viewer/__main__.py0000666000000000000000000000335112730245342021547 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function, unicode_literals import logging class LoggingFilter(logging.Filter): """ An example of logging filter that disables the logging from a specific module """ def filter(self, record): # print(record.name) if record.name.startswith('hdf_compass.compass_viewer.info'): return False return True # logging settings logger = logging.getLogger() logger.setLevel(logging.NOTSET) ch = logging.StreamHandler() ch.setLevel(logging.DEBUG) # change to WARNING to minimize verbosity, DEBUG for high verbosity ch_formatter = logging.Formatter('%(levelname)-7s %(name)s.%(funcName)s:%(lineno)d > %(message)s') ch.setFormatter(ch_formatter) # ch.addFilter(LoggingFilter()) # uncomment to activate the logging filter logger.addHandler(ch) from . import run run() hdf_compass-0.6.0/hdf_compass/filesystem_model/0000777000000000000000000000000012730267653020002 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/filesystem_model/model.py0000666000000000000000000001150312730245342021443 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Example data model which represents the file system. Subclasses just two node types: Container and Array, representing directories and files respectively. """ from __future__ import absolute_import, division, print_function, unicode_literals import os import os.path as op import numpy as np import logging log = logging.getLogger(__name__) from hdf_compass import compass_model class Filesystem(compass_model.Store): """ A "data store" represented by the file system. Keys are absolute paths on the local file system. """ @staticmethod def plugin_name(): return "Filesystem" @staticmethod def plugin_description(): return "A plugin used to browse local files and folders." def __contains__(self, key): return op.exists(key) @property def url(self): return self._url @property def display_name(self): return "Local file system" @property def root(self): return self['/'] @property def valid(self): return self._valid @staticmethod def can_handle(url): if url == "file://localhost": log.debug("able to handle %s? yes" % url) return True log.debug("able to handle %s? no" % url) return False def __init__(self, url): if not self.can_handle(url): raise ValueError(url) self._url = url self._valid = True def close(self): self._valid = False def get_parent(self, key): if key == "/": return None return self[op.dirname(key)] class Directory(compass_model.Container): """ Represents a directory in the filesystem. """ class_kind = "Directory" @staticmethod def can_handle(store, key): return op.isdir(key) def __init__(self, store, key): self._store = store self._key = key try: self._names = os.listdir(key) except OSError: # Permissions, etc. self._names = [] @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): bn = op.basename(self.key) if len(bn) == 0: return "/" return bn @property def description(self): return 'Folder "%s" (%d members)' % (self.display_name, len(self)) def __len__(self): return len(self._names) def __iter__(self): for name in self._names: key = op.join(self.key, name) yield self._store[key] def __getitem__(self, idx): key = op.join(self.key, self._names[idx]) return self._store[key] class File(compass_model.Array): """ Represents a file (all loaded as an array of bytes) """ class_kind = "File" @staticmethod def can_handle(store, key): return op.isfile(key) def __init__(self, store, key): self._store = store self._key = key @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return op.basename(self.key) @property def description(self): return 'File "%s", size %d bytes' % (self.display_name, op.getsize(self.key)) @property def shape(self): return (op.getsize(self.key),) @property def dtype(self): return np.dtype('u1') def __getitem__(self, args): try: with open(self.key, 'rb') as f: data = np.fromstring(f.read(), dtype='u1') except (OSError, IOError): data = np.zeros((len(self),), dtype='u1') return data[args] Filesystem.push(File) Filesystem.push(Directory) compass_model.push(Filesystem) hdf_compass-0.6.0/hdf_compass/filesystem_model/test.py0000666000000000000000000000223312730245342021322 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function from hdf_compass.compass_model.test import container, store from hdf_compass.filesystem_model import Filesystem, Directory url = "file://localhost" s = store(Filesystem, url) c = container(Filesystem, url, Directory, "/") hdf_compass-0.6.0/hdf_compass/filesystem_model/__init__.py0000666000000000000000000000212212730245342022077 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function, unicode_literals from .model import Filesystem, Directory, File import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler()) hdf_compass-0.6.0/hdf_compass/hdf5rest_model/0000777000000000000000000000000012730267653017342 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/hdf5rest_model/hdf5dtype.py0000666000000000000000000004263012730245342021604 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of H5Serv (HDF5 REST Server) Service, Libraries and # # Utilities. The full HDF5 REST Server copyright notice, including # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ This class is used to map between HDF5 type representations and numpy types """ import numpy as np from h5py.h5t import special_dtype from h5py.h5t import check_dtype from h5py.h5r import Reference from h5py.h5r import RegionReference """ Convert the given type item to a predefined type string for predefined integer and floating point types ("H5T_STD_I64LE", et. al). For compound types, recursively iterate through the typeItem and do same conversion for fields of the compound type. """ def getTypeResponse(typeItem): response = None if 'uuid' in typeItem: # committed type, just return uuid response = 'datatypes/' + typeItem['uuid'] elif typeItem['class'] == 'H5T_INTEGER' or typeItem['class'] == 'H5T_FLOAT': # just return the class and base for pre-defined types response = {} response['class'] = typeItem['class'] response['base'] = typeItem['base'] elif typeItem['class'] == 'H5T_OPAQUE': response = {} response['class'] = 'H5T_OPAQUE' response['size'] = typeItem['size'] elif typeItem['class'] == 'H5T_REFERENCE': response = {} response['class'] = 'H5T_REFERENCE' response['base'] = typeItem['base'] elif typeItem['class'] == 'H5T_COMPOUND': response = {} response['class'] = 'H5T_COMPOUND' fieldList = [] for field in typeItem['fields']: fieldItem = { } fieldItem['name'] = field['name'] fieldItem['type'] = getTypeResponse(field['type']) # recursive call fieldList.append(fieldItem) response['fields'] = fieldList else: response = {} # otherwise, return full type for k in typeItem.keys(): if k == 'base': if type(typeItem[k]) == dict: response[k] = getTypeResponse(typeItem[k]) # recursive call else: response[k] = typeItem[k] # predefined type elif k not in ('size', 'base_size'): response[k] = typeItem[k] return response """ Return type info. For primitive types, return string with typename For compound types return array of dictionary items """ def getTypeItem(dt): type_info = {} if len(dt) <= 1: type_info = getTypeElement(dt) else: names = dt.names type_info['class'] = 'H5T_COMPOUND' fields = [] for name in names: field = { 'name': name } field['type'] = getTypeElement(dt[name]) fields.append(field) type_info['fields'] = fields return type_info """ Get element type info - either a complete type or element of a compound type Returns dictionary Note: only getTypeItem should call this! """ def getTypeElement(dt): if len(dt) > 1: raise Exception("unexpected numpy type passed to getTypeElement") type_info = {} if dt.kind == 'O': # numpy object type - assume this is a h5py variable length extension h5t_check = check_dtype(vlen=dt) if h5t_check is not None: if h5t_check == str: type_info['class'] = 'H5T_STRING' type_info['length'] = 'H5T_VARIABLE' type_info['charSet'] = 'H5T_CSET_ASCII' type_info['strPad'] = 'H5T_STR_NULLTERM' elif h5t_check == unicode: type_info['class'] = 'H5T_STRING' type_info['length'] = 'H5T_VARIABLE' type_info['charSet'] = 'H5T_CSET_UTF8' type_info['strPad'] = 'H5T_STR_NULLTERM' elif type(h5t_check) == np.dtype: # vlen data type_info['class'] = 'H5T_VLEN' type_info['size'] = 'H5T_VARIABLE' type_info['base'] = getBaseType(h5t_check) else: #unknown vlen type raise TypeError("Unknown h5py vlen type: " + h5t_check) else: # check for reference type h5t_check = check_dtype(ref=dt) if h5t_check is not None: type_info['class'] = 'H5T_REFERENCE' if h5t_check is Reference: type_info['base'] = 'H5T_STD_REF_OBJ' # objref elif h5t_check is RegionReference: type_info['base'] = 'H5T_STD_REF_DSETREG' # region ref else: raise TypeError("unexpected reference type") else: raise TypeError("unknown object type") elif dt.kind == 'V': baseType = getBaseType(dt) if dt.shape: # array type type_info['dims'] = dt.shape type_info['class'] = 'H5T_ARRAY' type_info['base'] = baseType elif baseType['class'] == 'H5T_OPAQUE': # expecting this to be an opaque type type_info = baseType # just promote the base type else: raise TypeError("unexpected Void type") elif dt.kind == 'S': # String type baseType = getBaseType(dt) type_info = baseType # just use base type elif dt.kind == 'U': # Unicode String type baseType = getBaseType(dt) type_info = baseType # just use base type elif dt.kind == 'i' or dt.kind == 'u': # integer type baseType = getBaseType(dt) # numpy integer type - but check to see if this is the hypy # enum extension mapping = check_dtype(enum=dt) if mapping: # yes, this is an enum! type_info['class'] = 'H5T_ENUM' type_info['mapping'] = mapping type_info['base'] = baseType else: type_info = baseType # just use base type elif dt.kind == 'f': # floating point type baseType = getBaseType(dt) type_info = baseType # just use base type else: # unexpected kind raise TypeError("unexpected dtype kind: " + dt.kind) return type_info """ Get Base type info for given type element. """ def getBaseType(dt): if len(dt) > 1: raise TypeError("unexpected numpy type passed to getTypeElement") predefined_int_types = { 'int8': 'H5T_STD_I8', 'uint8': 'H5T_STD_U8', 'int16': 'H5T_STD_I16', 'uint16': 'H5T_STD_U16', 'int32': 'H5T_STD_I32', 'uint32': 'H5T_STD_U32', 'int64': 'H5T_STD_I64', 'uint64': 'H5T_STD_U64' } predefined_float_types = { 'float32': 'H5T_IEEE_F32', 'float64': 'H5T_IEEE_F64' } type_info = {} #type_info['base_size'] = dt.base.itemsize # primitive type if dt.base.kind == 'S': # Fixed length string type type_info['class'] = 'H5T_STRING' type_info['charSet'] = 'H5T_CSET_ASCII' type_info['length'] = dt.base.itemsize type_info['strPad'] = 'H5T_STR_NULLPAD' elif dt.base.kind == 'V': type_info['class'] = 'H5T_OPAQUE' type_info['size'] = dt.itemsize type_info['tag'] = '' # todo - determine tag elif dt.base.kind == 'i' or dt.base.kind == 'u': type_info['class'] = 'H5T_INTEGER' byteorder = 'LE' if dt.base.byteorder == '>': byteorder = 'BE' if dt.base.name in predefined_int_types: #maps to one of the HDF5 predefined types type_info['base'] = predefined_int_types[dt.base.name] + byteorder elif dt.base.kind == 'f': type_info['class'] = 'H5T_FLOAT' byteorder = 'LE' if dt.base.byteorder == '>': byteorder = 'BE' if dt.base.name in predefined_float_types: #maps to one of the HDF5 predefined types type_info['base'] = predefined_float_types[dt.base.name] + byteorder elif dt.base.kind == 'O': # check for reference type h5t_check = check_dtype(ref=dt) if h5t_check is not None: type_info['class'] = 'H5T_REFERENCE' if h5t_check is Reference: type_info['base'] = 'H5T_STD_REF_OBJ' # objref elif h5t_check is RegionReference: type_info['base'] = 'H5T_STD_REF_DSETREG' # region ref else: raise TypeError("unexpected reference type") else: raise TypeError("unknown object type") else: # unexpected kind raise TypeError("unexpected dtype base kind: " + dt.base.kind) return type_info def getNumpyTypename(hdf5TypeName, typeClass=None): predefined_int_types = { 'H5T_STD_I8': 'i1', 'H5T_STD_U8': 'u1', 'H5T_STD_I16': 'i2', 'H5T_STD_U16': 'u2', 'H5T_STD_I32': 'i4', 'H5T_STD_U32': 'u4', 'H5T_STD_I64': 'i8', 'H5T_STD_U64': 'u8' } predefined_float_types = { 'H5T_IEEE_F32': 'f4', 'H5T_IEEE_F64': 'f8' } if len(hdf5TypeName) < 3: raise Exception("Type Error: invalid typename: ") endian = '<' # default endian key = hdf5TypeName if hdf5TypeName.endswith('LE'): key = hdf5TypeName[:-2] elif hdf5TypeName.endswith('BE'): key = hdf5TypeName[:-2] endian = '>' if key in predefined_int_types and (typeClass == None or typeClass == 'H5T_INTEGER'): return endian + predefined_int_types[key] if key in predefined_float_types and (typeClass == None or typeClass == 'H5T_FLOAT'): return endian + predefined_float_types[key] raise TypeError("Type Error: invalid type") def createBaseDataType(typeItem): dtRet = None if type(typeItem) == str or type(typeItem) == unicode: # should be one of the predefined types dtName = getNumpyTypename(typeItem) dtRet = np.dtype(dtName) return dtRet # return predefined type if type(typeItem) != dict: raise TypeError("Type Error: invalid type") if 'class' not in typeItem: raise KeyError("'class' not provided") typeClass = typeItem['class'] dims = '' if 'dims' in typeItem: dims = None if type(typeItem['dims']) == int: dims = (typeItem['dims']) # make into a tuple elif type(typeItem['dims']) not in (list, tuple): raise TypeError("expected list or integer for dims") else: dims = typeItem['dims'] dims = str(tuple(dims)) if typeClass == 'H5T_INTEGER': if 'base' not in typeItem: raise KeyError("'base' not provided") baseType = getNumpyTypename(typeItem['base'], typeClass='H5T_INTEGER') dtRet = np.dtype(dims + baseType) elif typeClass == 'H5T_FLOAT': if 'base' not in typeItem: raise KeyError("'base' not provided") baseType = getNumpyTypename(typeItem['base'], typeClass='H5T_FLOAT') dtRet = np.dtype(dims + baseType) elif typeClass == 'H5T_STRING': if 'length' not in typeItem: raise KeyError("'length' not provided") if 'charSet' not in typeItem: raise KeyError("'charSet' not provided") if typeItem['length'] == 'H5T_VARIABLE': if dims: raise TypeError("ArrayType is not supported for variable len types") if typeItem['charSet'] == 'H5T_CSET_ASCII': dtRet = special_dtype(vlen=str) elif typeItem['charSet'] == 'H5T_CSET_UTF8': dtRet = special_dtype(vlen=unicode) else: raise TypeError("unexpected 'charSet' value") else: nStrSize = typeItem['length'] if type(nStrSize) != int: raise TypeError("expecting integer value for 'length'") type_code = None if typeItem['charSet'] == 'H5T_CSET_ASCII': type_code = 'S' elif typeItem['charSet'] == 'H5T_CSET_UTF8': raise TypeError("fixed-width unicode strings are not supported") else: raise TypeError("unexpected 'charSet' value") dtRet = np.dtype(dims + type_code + str(nStrSize)) # fixed size string elif typeClass == 'H5T_VLEN': if dims: raise TypeError("ArrayType is not supported for variable len types") if 'base' not in typeItem: raise KeyError("'base' not provided") baseType = createBaseDataType(typeItem['base']) dtRet = special_dtype(vlen=np.dtype(baseType)) elif typeClass == 'H5T_OPAQUE': if dims: raise TypeError("Opaque Type is not supported for variable len types") if 'size' not in typeItem: raise KeyError("'size' not provided") nSize = int(typeItem['size']) if nSize <= 0: raise TypeError("'size' must be non-negative") dtRet = np.dtype('V' + str(nSize)) elif typeClass == 'H5T_ARRAY': if not dims: raise KeyError("'dims' must be provided for array types") if 'base' not in typeItem: raise KeyError("'base' not provided") arrayBaseType = typeItem['base'] if type(arrayBaseType) is dict: if "class" not in arrayBaseType: raise KeyError("'class' not provided for array base type") if arrayBaseType["class"] not in ('H5T_INTEGER', 'H5T_FLOAT', 'H5T_STRING'): raise TypeError("Array Type base type must be integer, float, or string") baseType = createDataType(arrayBaseType) dtRet = np.dtype(dims+baseType.str) return dtRet # return predefined type elif typeClass == 'H5T_REFERENCE': if 'base' not in typeItem: raise KeyError("'base' not provided") if typeItem['base'] == 'H5T_STD_REF_OBJ': dtRet = special_dtype(ref=Reference) elif typeItem['base'] == 'H5T_STD_REF_DSETREG': dtRet = special_dtype(ref=RegionReference) else: raise TypeError("Invalid base type for reference type") else: raise TypeError("Invalid type class") return dtRet def createDataType(typeItem): dtRet = None if type(typeItem) == str or type(typeItem) == unicode: # should be one of the predefined types dtName = getNumpyTypename(typeItem) dtRet = np.dtype(dtName) return dtRet # return predefined type if type(typeItem) != dict: raise TypeError("invalid type") if 'class' not in typeItem: raise KeyError("'class' not provided") typeClass = typeItem['class'] if typeClass == 'H5T_COMPOUND': if 'fields' not in typeItem: raise KeyError("'fields' not provided for compound type") fields = typeItem['fields'] if type(fields) is not list: raise TypeError("Type Error: expected list type for 'fields'") if not fields: raise KeyError("no 'field' elements provided") subtypes = [] for field in fields: if type(field) != dict: raise TypeError("Expected dictionary type for field") if 'name' not in field: raise KeyError("'name' missing from field") if 'type' not in field: raise KeyError("'type' missing from field") field_name = field['name'] if type(field_name) == unicode: # convert to ascii ascii_name = field_name.encode('ascii') if ascii_name != field_name: raise TypeError("non-ascii field name not allowed") field['name'] = ascii_name dt = createDataType(field['type']) # recursive call if dt is None: raise Exception("unexpected error") subtypes.append((field['name'], dt)) # append tuple dtRet = np.dtype(subtypes) else: dtRet = createBaseDataType(typeItem) # create non-compound dt return dtRet hdf_compass-0.6.0/hdf_compass/hdf5rest_model/model.py0000666000000000000000000003345212730245342021012 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Implementation of compass_model classes for HDF5 REST API. """ from __future__ import absolute_import, division, print_function, unicode_literals from itertools import groupby import sys import os.path as op import posixpath as pp import json import requests import numpy as np import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler()) # Py2App can't successfully import otherwise from hdf_compass import compass_model from hdf_compass.utils import url2path from . import hdf5dtype def get_json(endpoint, domain=None, uri=None): # try to do a GET from the domain req = endpoint if uri is not None: req += uri headers = {} if domain is not None: headers['host'] = domain log.debug("GET: " + req) rsp = requests.get(req, headers=headers, verify=False) log.debug("RSP: " + str(rsp.status_code) + ':' + rsp.text) if rsp.status_code != 200: raise IOError(rsp.reason) rsp_json = json.loads(rsp.text) return rsp_json def sort_key(name): """ Sorting key for names in an HDF5 group. We provide "natural" sort order; e.g. "7" comes before "12". """ return [(int(''.join(g)) if k else ''.join(g)) for k, g in groupby(name, key=unicode.isdigit)] class HDF5RestStore(compass_model.Store): """ Data store implementation for an HDF Service endpoint Keys are valid h5paths to the object: e.g.: /g1 /g1/dset1.1 /g1/dtype Values are URI's to the resource /groups/ /datasets/ /datatypes/ """ @staticmethod def plugin_name(): return "HDF5 Rest" @staticmethod def plugin_description(): return "A plugin used to access HDF Services." def __contains__(self, key): if key in self.f: return True try: pkey = self.get_parent(key) except KeyError: return False if pkey not in self.f: # assumes that we've loaded any parents, before querying for children return False pkey_uri = self.f[pkey] if not pkey_uri.startswith("/groups/"): # if the parent is not a group, this is not a valid key return False # do a get on the link name linkname = pp.basename(key) contains = False try: link_json = self.get(pkey_uri + "/links/" + linkname) if link_json["class"] == "H5L_TYPE_HARD": log.debug("add key to store:" + key) self.f[key] = '/' + link_json["collection"] + '/' + link_json["id"] contains = True else: pass # todo support soft/external links except IOError: # invalid link # todo - verify it is a 404 log.debug("invalid key:"+key) return contains @property def url(self): return self._url @property def display_name(self): if self.domain: return self.domain else: return self.endpoint @property def root(self): return self['/'] @property def valid(self): return '/' in self.f @staticmethod def can_handle(url): log.debug("hdf5rest can_handle: " + url) try: flag = True rsp_json = get_json(url) for key in ("root", "created", "hrefs", "lastModified"): if key not in rsp_json: flag = False break log.debug("able to handle %s? %r" % (url, flag)) return flag except Exception: log.debug("able to handle %s? no" % url) return False return True def __init__(self, url): if not self.can_handle(url): raise ValueError(url) self._url = url # extract domain if there's a "host" query param queryParam = "host=" nindex = url.find('?' + queryParam) if nindex < 0: nindex = url.find('&' + queryParam) if nindex > 0: domain = url[(nindex + len(queryParam) + 1):] # trim any additional query params nindex = domain.find('&') if nindex > 0: domain = domain[:nindex] self._domain = domain else: self._domain = None nindex = url.find('?') if nindex < 0: self._endpoint = url else: self._endpoint = url[:(nindex)] if self._endpoint.endswith('/'): # trim any trailing '/' self._endpoint = self._endpoint[:-1] self.cache = {} # http cache rsp = self.get('/') self.f = {} self.f['/'] = "/groups/" + rsp['root'] @property def endpoint(self): return self._endpoint @property def domain(self): return self._domain @property def objid(self): return self._objid def get(self, uri): if uri in self.cache: rsp = self.cache[uri] else: rsp = get_json(self.endpoint, domain=self.domain, uri=uri) self.cache[uri] = rsp return rsp def close(self): self.f = {} # clear the key store def get_parent(self, key): # HDFCompass requires the parent of the root container be None if key == "" or key == "/": return None pkey = pp.dirname(key) if pkey == "": pkey = "/" if pkey not in self.f: # is it possible to get to a key without traversing the parents? # if so, we should query the server for the given path raise KeyError("parent not found: " + pkey) return self[pkey] class HDF5RestGroup(compass_model.Container): """ Represents an HDF5 group, to be displayed in the browser view. """ class_kind = "HDF5 Group" @staticmethod def can_handle(store, key): return key in store and store.f[key].startswith("/groups/") def get_names(self): # Lazily build the list of names; this helps when browsing big files if self._xnames is None: rsp = self.store.get(self._uri + "/links") self._xnames = [] links = rsp["links"] log.debug("got %d links for key: %s" % (len(links), self._key)) for link in links: name = link["title"] self._xnames.append(name) link_key = pp.join(self.key, name) if link_key not in self.store.f: if link["class"] == "H5L_TYPE_HARD": log.debug("add key to store:" + link_key) self.store.f[link_key] = '/' + link["collection"] + '/' + link["id"] else: pass # todo support soft/external links # Natural sort is expensive if len(self._xnames) < 1000: self._xnames.sort(key=sort_key) return self._xnames def __init__(self, store, key): self._store = store self._key = key self._uri = store.f[key] self._xnames = None rsp = store.get(self._uri) self._count = rsp["linkCount"] log.debug("new group node: " + self._key) self.get_names() @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): name = pp.basename(self.key) if name == "": name = '/' return name @property def display_title(self): return "%s %s" % (self.store.display_name, self.key) @property def description(self): return 'Group "%s" (%d members)' % (self.display_name, len(self)) def __len__(self): return self._count def __iter__(self): for name in self._xnames: yield self.store[pp.join(self.key, name)] def __getitem__(self, idx): name = self._xnames[idx] return self.store[pp.join(self.key, name)] class HDF5RestDataset(compass_model.Array): """ Represents an HDF5 dataset. """ class_kind = "HDF5 Dataset" @staticmethod def can_handle(store, key): return key in store and store.f[key].startswith("/datasets/") def __init__(self, store, key): self._store = store self._key = key self._uri = store.f[key] rsp = store.get(self._uri) shape_json = rsp["shape"] if shape_json["class"] == "H5S_SCALAR": self._shape = () elif shape_json["class"] == "H5S_SIMPLE": self._shape = shape_json["dims"] else: raise IOError("Unexpected shape class: " + shape_json["class"]) type_json = rsp["type"] self._dtype = hdf5dtype.createDataType(type_json) @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return pp.basename(self.key) @property def description(self): return 'Dataset "%s"' % (self.display_name,) @property def shape(self): return self._shape @property def dtype(self): return self._dtype def __getitem__(self, args): log.debug("getitem: " + str(args)) req = self._uri + "/value" rank = len(self._shape) if rank > 0: sel_query = '[' for dim in range(rank): if dim < len(args): s = args[dim] else: s = slice(0, self._shape[dim]) sel_query += str(s.start) sel_query += ':' if s.stop > self._shape[dim]: sel_query += str(self._shape[dim]) else: sel_query += str(s.stop) sel_query += ',' sel_query = sel_query[:-1] # trim trailing comma sel_query += ']' req += "?select=" + sel_query rsp = self.store.get(req) value = rsp["value"] arr = np.array(value, dtype=self._dtype) return arr def is_plottable(self): if self.dtype.kind == 'S': log.debug("Not plottable since ASCII String (characters: %d)" % self.dtype.itemsize) return False if self.dtype.kind == 'U': log.debug("Not plottable since Unicode String (characters: %d)" % self.dtype.itemsize) return False return True class HDF5RestKV(compass_model.KeyValue): """ A KeyValue node used for HDF5 attributes. """ class_kind = "HDF5 Attributes" @staticmethod def can_handle(store, key): canhandle = False if key in store: uri = store.f[key] if uri.startswith("/groups/"): canhandle = True elif uri.startswith("/datasets/"): canhandle = True elif uri.startswith("/datatypes/"): canhandle = True return canhandle def __init__(self, store, key): self._store = store self._key = key self._uri = store.f[key] rsp = store.get(self._uri + "/attributes") attributes = rsp["attributes"] names = [] for attr in attributes: names.append(attr["name"]) self._names = names @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): n = pp.basename(self.key) return n if n != '' else '/' @property def description(self): return self.display_name @property def keys(self): return self._names[:] def __getitem__(self, name): rsp = self._store.get(self._uri + "/attributes/" + name) type_json = rsp["type"] value_json = rsp["value"] arr_dtype = hdf5dtype.createDataType(type_json) arr = np.array(value_json, dtype=arr_dtype) return arr # Register handlers HDF5RestStore.push(HDF5RestKV) HDF5RestStore.push(HDF5RestDataset) #HDF5RestStore.push(HDF5Text) HDF5RestStore.push(HDF5RestGroup) #HDF5RestStore.push(HDF5Image) compass_model.push(HDF5RestStore) hdf_compass-0.6.0/hdf_compass/hdf5rest_model/test.py0000666000000000000000000000270712730245342020670 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## # # Run test, from hdf-compass directory:: # python -m unittest hdf_compass.my_model.test # from __future__ import absolute_import, division, print_function from hdf_compass.compass_model.test import container, store from hdf_compass.hdf5rest_model import HDF5RestGroup, HDF5RestStore from hdf_compass.utils import data_url import os # use this url if you are running h5serv locally url = "http://127.0.0.1:5000" #url = "https://data.hdfgroup.org:7258/?host=tall.test.data.hdfgroup.org" s = store(HDF5RestStore, url) c = container(HDF5RestStore, url, HDF5RestGroup, "/") hdf_compass-0.6.0/hdf_compass/hdf5rest_model/__init__.py0000666000000000000000000000216012730245342021441 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function, unicode_literals from .model import HDF5RestStore, HDF5RestGroup, HDF5RestDataset, HDF5RestKV import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler()) hdf_compass-0.6.0/hdf_compass/hdf5_model/0000777000000000000000000000000012730267653016444 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/hdf5_model/model.py0000666000000000000000000002404612730245342020113 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Implementation of compass_model classes for HDF5 files. """ from __future__ import absolute_import, division, print_function, unicode_literals from itertools import groupby import sys import os.path as op import posixpath as pp import h5py import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler()) # Py2App can't successfully import otherwise from hdf_compass import compass_model from hdf_compass.utils import url2path def sort_key(name): """ Sorting key for names in an HDF5 group. We provide "natural" sort order; e.g. "7" comes before "12". """ return [(int(''.join(g)) if k else ''.join(g)) for k, g in groupby(name, key=unicode.isdigit)] class HDF5Store(compass_model.Store): """ Data store implementation using an HDF5 file. Keys are the full names of objects in the file. """ @staticmethod def plugin_name(): return "HDF5" @staticmethod def plugin_description(): return "A plugin used to browse HDF5 files." file_extensions = {'HDF5 File': ['*.hdf5', '*.h5']} def __contains__(self, key): return key in self.f @property def url(self): return self._url @property def display_name(self): return op.basename(self.f.filename) @property def root(self): return self['/'] @property def valid(self): return bool(self.f) @staticmethod def can_handle(url): if not url.startswith('file://'): log.debug("able to handle %s? no, not starting with file://" % url) return False path = url2path(url) if not h5py.is_hdf5(path): log.debug("able to handle %s? no, not hdf5 file" % url) return False log.debug("able to handle %s? yes" % url) return True def __init__(self, url): if not self.can_handle(url): raise ValueError(url) self._url = url path = url2path(url) self.f = h5py.File(path, 'r') def close(self): self.f.close() def get_parent(self, key): # HDFCompass requires the parent of the root container be None if key == "" or key == "/": return None pkey = pp.dirname(key) if pkey == "": pkey = "/" return self[pkey] class HDF5Group(compass_model.Container): """ Represents an HDF5 group, to be displayed in the browser view. """ class_kind = "HDF5 Group" @staticmethod def can_handle(store, key): return key in store and isinstance(store.f[key], h5py.Group) @property def _names(self): # Lazily build the list of names; this helps when browsing big files if self._xnames is None: self._xnames = list(self._group) # Natural sort is expensive if len(self._xnames) < 1000: self._xnames.sort(key=sort_key) return self._xnames def __init__(self, store, key): self._store = store self._key = key self._group = store.f[key] self._xnames = None @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): name = pp.basename(self.key) if name == "": name = '/' return name @property def display_title(self): return "%s %s" % (self.store.display_name, self.key) @property def description(self): return 'Group "%s" (%d members)' % (self.display_name, len(self)) def __len__(self): return len(self._group) def __iter__(self): for name in self._names: yield self.store[pp.join(self.key, name)] def __getitem__(self, idx): name = self._names[idx] return self.store[pp.join(self.key, name)] class HDF5Dataset(compass_model.Array): """ Represents an HDF5 dataset. """ class_kind = "HDF5 Dataset" @staticmethod def can_handle(store, key): return key in store and isinstance(store.f[key], h5py.Dataset) def __init__(self, store, key): self._store = store self._key = key self._dset = store.f[key] @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return pp.basename(self.key) @property def description(self): return 'Dataset "%s"' % (self.display_name,) @property def shape(self): return self._dset.shape @property def dtype(self): return self._dset.dtype def __getitem__(self, args): return self._dset[args] def is_plottable(self): if self.dtype.kind == 'S': log.debug("Not plottable since ASCII String (characters: %d)" % self.dtype.itemsize) return False if self.dtype.kind == 'U': log.debug("Not plottable since Unicode String (characters: %d)" % self.dtype.itemsize) return False return True class HDF5Text(compass_model.Text): """ Represents a text array (both ASCII and UNICODE). """ class_kind = "HDF5 Dataset[text]" @staticmethod def can_handle(store, key): if key in store and isinstance(store.f[key], h5py.Dataset): if store.f[key].dtype.kind == 'S': # log.debug("ASCII String (characters: %d)" % DATA[key].dtype.itemsize) return True if store.f[key].dtype.kind == 'U': # log.debug("Unicode String (characters: %d)" % DATA[key].dtype.itemsize) return True return False def __init__(self, store, key): self._store = store self._key = key self.data = store.f[key] @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return pp.basename(self.key) @property def description(self): return 'Text "%s"' % (self.display_name,) @property def shape(self): return self.data.shape @property def text(self): txt = str() if len(self.shape) == 0: # print(type(self.data)) txt += str(self.data[()]) elif len(self.shape) == 1: for el in self.data: txt += el + ", \n" elif len(self.shape) == 2: for i in range(self.shape[0]): for j in range(self.shape[1]): txt += self.data[i, j] + ", " txt += "\n" else: txt = ">> display of more than 2D string array not implemented <<" return txt class HDF5KV(compass_model.KeyValue): """ A KeyValue node used for HDF5 attributes. """ class_kind = "HDF5 Attributes" @staticmethod def can_handle(store, key): return key in store.f def __init__(self, store, key): self._store = store self._key = key self._obj = store.f[key] self._names = self._obj.attrs.keys() @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): n = pp.basename(self.key) return n if n != '' else '/' @property def description(self): return self.display_name @property def keys(self): return self._names[:] def __getitem__(self, name): return self._obj.attrs[name] class HDF5Image(compass_model.Image): """ True-color images. """ class_kind = "HDF5 Truecolor Image" @staticmethod def can_handle(store, key): if key not in store: return False obj = store.f[key] if obj.attrs.get('CLASS') != 'IMAGE': return False if obj.attrs.get('IMAGE_SUBCLASS') != 'IMAGE_TRUECOLOR': return False if obj.attrs.get('INTERLACE_MODE') != 'INTERLACE_PIXEL': return False return True def __init__(self, store, key): self._store = store self._key = key self._obj = store.f[key] @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): n = pp.basename(self.key) return n if n != '' else '/' @property def description(self): return self.display_name @property def width(self): return self._obj.shape[1] @property def height(self): return self._obj.shape[0] @property def palette(self): return None @property def data(self): return self._obj[:] # Register handlers HDF5Store.push(HDF5KV) HDF5Store.push(HDF5Dataset) HDF5Store.push(HDF5Text) HDF5Store.push(HDF5Group) HDF5Store.push(HDF5Image) compass_model.push(HDF5Store) hdf_compass-0.6.0/hdf_compass/hdf5_model/test.py0000666000000000000000000000234212730245342017765 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function from hdf_compass.compass_model.test import container, store from hdf_compass.hdf5_model import HDF5Group, HDF5Store from hdf_compass.utils import data_url import os url = os.path.join(data_url(), "hdf5", "tall.h5") s = store(HDF5Store, url) c = container(HDF5Store, url, HDF5Group, "/") hdf_compass-0.6.0/hdf_compass/hdf5_model/__init__.py0000666000000000000000000000214012730245342020541 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function, unicode_literals from .model import HDF5Store, HDF5Group, HDF5Dataset, HDF5KV import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler()) hdf_compass-0.6.0/hdf_compass/opendap_model/0000777000000000000000000000000012730267653017244 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/opendap_model/model.py0000666000000000000000000002006712730245342020712 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function, unicode_literals import posixpath as pp import numpy as np import pydap as dap from pydap.client import open_url from pydap.proxy import ArrayProxy import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler()) from hdf_compass import compass_model def check_key(key, dataset): if '/' not in key: return key, dataset new_dataset = dataset[key.split('/')[0]] return key.split('/')[1], new_dataset class Server(compass_model.Store): """ Represents the remote OpENDAP server to be accessed """ @staticmethod def plugin_name(): return "OpENDAP" @staticmethod def plugin_description(): return "A plugin used to access OpENDAP Servers." def __contains__(self, key): if '/' not in key: return key in self.dataset new_dset = self.dataset[key.split('/')[0]] new_key = key.rsplit('/')[1] return new_key in new_dset @staticmethod def can_handle(url): try: flag = isinstance(open_url(url), dap.model.DatasetType) log.debug("able to handle %s? %r" % (url, flag)) return flag except Exception: log.debug("able to handle %s? no" % url) return False def __init__(self, url): if not self.can_handle(url): raise ValueError(url) self._url = url self._valid = True self._dataset = open_url(self.url) self._datalength = len(self._dataset.data) self._dataset.setdefault('') def close(self): self._valid = False def get_parent(self, key): return None @property def url(self): return self._url @property def display_name(self): return self.dataset.name @property def root(self): return self[''] @property def valid(self): return self._valid @property def dataset(self): return self._dataset @property def datalength(self): return self._datalength class Dataset(compass_model.Container): """ Represents Dataset/DatasetType Object in OpENDAP/Pydap. """ class_kind = "Dataset" def __len__(self): return self._store.datalength def __getitem__(self, index): name = self._dset.keys()[index] return self.store[pp.join(self.key, name)] def __iter__(self): pass @staticmethod def can_handle(store, key): return key == '' def __init__(self, store, key): if not key == '': raise ValueError("A Dataset object may only represent the root group") self._store = store self._key = key self._url = store.url self._dset = store.dataset @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return self._dset.name @property def description(self): return "A Pydap DatasetType Object." @property def dset(self): return self._dset class Structure(compass_model.Container): """ Represents Structure/StructureType Object in OpENDAP/Pydap. """ class_kind = "Structure/Grid/Sequence" def __len__(self): return len(self._dset.data) def __getitem__(self, index): name = self._dset.keys()[index] return self.store[pp.join(self.key, name)] def __iter__(self): pass @staticmethod def can_handle(store, key): new_key, new_dset = check_key(key, store.dataset) try: return new_key in new_dset and isinstance(new_dset[new_key], dap.model.StructureType) except isinstance(new_dset[new_key], dap.model.DatasetType): return False def __init__(self, store, key): new_key, new_dset = check_key(key, store.dataset) self._store = store self._key = new_key self._url = store.url self._dset = new_dset[new_key] @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return self._dset.name @property def description(self): return "A Pydap StructureType Object." class Base(compass_model.Array): """ Represents Array/BaseType Object in OpENDAP/Pydap. """ class_kind = "Array" @property def shape(self): return self._shape @property def dtype(self): return np.dtype(self._dtype.typecode) def __getitem__(self, index): if self._data is None: self._data = ArrayProxy(self._id, self._url, self._shape)[:] return self._data[index] @staticmethod def can_handle(store, key): new_key, new_dset = check_key(key, store.dataset) return new_key in new_dset and isinstance(new_dset[new_key], dap.model.BaseType) def __init__(self, store, key): new_key, new_dset = check_key(key, store.dataset) self._store = store self._key = new_key self._url = store.url self._id = new_dset[new_key].id self._shape = new_dset[new_key].shape self._dtype = new_dset[new_key].type self._name = new_dset[new_key].name self._data = None @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return self._name @property def description(self): return "A Pydap BaseType Object." def is_plottable(self): if self.dtype.kind == 'S': log.debug("Not plottable since ASCII String (characters: %d)" % self.dtype.itemsize) return False if self.dtype.kind == 'U': log.debug("Not plottable since Unicode String (characters: %d)" % self.dtype.itemsize) return False return True class Attributes(compass_model.KeyValue): """ Represents the Attributes member of Pydap Objects. """ class_kind = "Attributes" @property def keys(self): return self._keys.keys() def __getitem__(self, name): return self._keys[name] @staticmethod def can_handle(store, key): new_key, new_dset = check_key(key, store.dataset) return new_key != '' def __init__(self, store, key): new_key, new_dset = check_key(key, store.dataset) self._store = store self._key = new_key self._keys = new_dset[self._key].attributes @property def key(self): return self._key @property def store(self): return self._store @property def display_name(self): return "%s Attributes" % self._key @property def description(self): return "Attributes of %s" % self._key # Register Handlers Server.push(Attributes) Server.push(Dataset) Server.push(Structure) Server.push(Base) compass_model.push(Server) hdf_compass-0.6.0/hdf_compass/opendap_model/test.py0000666000000000000000000000046012730245342020564 0ustar 00000000000000from hdf_compass.compass_model.test import container, store from hdf_compass.opendap_model import Server, Dataset url = "http://test.opendap.org/opendap/hyrax/data/hdf5/grid_1_2d.h5" s_1 = store(Server, url) url = "http://test.opendap.org/opendap/hyrax/data/nc/bears.nc" s_2 = store(Server, url)hdf_compass-0.6.0/hdf_compass/opendap_model/__init__.py0000666000000000000000000000214112730245342021342 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function, unicode_literals from .model import Server, Dataset, Structure, Attributes, Base import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler())hdf_compass-0.6.0/hdf_compass/utils/0000777000000000000000000000000012730267653015576 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass/utils/utils.py0000666000000000000000000000404412730245342017301 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ Implementation of utils and helper functions """ from __future__ import absolute_import, division, print_function, unicode_literals import sys import os import logging log = logging.getLogger(__name__) is_darwin = sys.platform == 'darwin' is_win = sys.platform == 'win32' is_linux = sys.platform == 'linux2' def url2path(url): """ Helper function that returns the file path from an url, dealing with Windows peculiarities """ if is_win: return url.replace('file:///', '') else: return url.replace('file://', '') def path2url(path): """ Helper function that returns the url from a file path, dealing with Windows peculiarities """ if is_win: return 'file:///' + path else: return 'file://' + path def data_url(): """ Helper function used to return the url to the project data folder """ prj_root_folder = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir)) data_folder = os.path.join(prj_root_folder, "data") if not os.path.exists(data_folder): raise RuntimeError("data path %s does not exist" % data_folder) return path2url(data_folder) hdf_compass-0.6.0/hdf_compass/utils/__init__.py0000666000000000000000000000221512730245342017676 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## from __future__ import absolute_import, division, print_function, unicode_literals import logging log = logging.getLogger(__name__) log.addHandler(logging.NullHandler()) from .utils import is_darwin, is_win, is_linux, url2path, path2url, data_url __version__ = "0.6.0" hdf_compass-0.6.0/hdf_compass/__init__.py0000666000000000000000000000042212730245342016534 0ustar 00000000000000""" HDFCompass Namespace """ from __future__ import absolute_import, division, print_function try: import pkg_resources pkg_resources.declare_namespace(__name__) except ImportError: import pkgutil __path__ = pkgutil.extend_path(__path__, __name__) hdf_compass-0.6.0/hdf_compass.egg-info/0000777000000000000000000000000012730267653016130 5ustar 00000000000000hdf_compass-0.6.0/hdf_compass.egg-info/dependency_links.txt0000666000000000000000000000000112730267653022176 0ustar 00000000000000 hdf_compass-0.6.0/hdf_compass.egg-info/entry_points.txt0000666000000000000000000000010212730267653021417 0ustar 00000000000000[gui_scripts] HDFCompass = hdf_compass.compass_viewer.viewer:run hdf_compass-0.6.0/hdf_compass.egg-info/namespace_packages.txt0000666000000000000000000000001412730267653022456 0ustar 00000000000000hdf_compass hdf_compass-0.6.0/hdf_compass.egg-info/PKG-INFO0000666000000000000000000001257112730267653017233 0ustar 00000000000000Metadata-Version: 1.1 Name: hdf-compass Version: 0.6.0 Summary: An experimental viewer program for HDF5 and related formats. Home-page: https://github.com/HDFGroup/hdf-compass/ Author: HDFGroup Author-email: help@hdfgroup.org License: BSD-like license Description: HDF Compass =========== .. image:: https://badge.fury.io/py/hdf_compass.svg :target: https://badge.fury.io/py/hdf_compass :alt: PyPI Status .. image:: https://readthedocs.org/projects/hdf-compass/badge/?version=stable :target: http://hdf-compass.readthedocs.org/en/stable/?badge=stable :alt: Stable Documentation Status .. image:: https://readthedocs.org/projects/hdf-compass/badge/?version=latest :target: http://hdf-compass.readthedocs.org/en/latest/?badge=latest :alt: Latest Documentation Status .. image:: https://ci.appveyor.com/api/projects/status/tfg350xo8t7h70ix?svg=true :target: https://ci.appveyor.com/project/giumas/hdf-compass :alt: AppVeyor Status .. image:: https://travis-ci.org/giumas/hdf-compass.svg?branch=develop :target: https://travis-ci.org/giumas/hdf-compass :alt: Travis-CI Status Welcome to the project! HDF Compass is an experimental viewer program for HDF5 and related formats, designed to complement other more complex applications like HDFView. Strong emphasis is placed on clean minimal design, and maximum extensibility through a plugin system for new formats. HDF Compass is written in Python, but ships as a native application on Windows, OS X, and Linux, by using PyInstaller and Py2App to package the app. Binary executables are available for Windows (Windows 7 or later) and Mac OS X (Yosemite or later) at the Project Page listed below. Bug reports and pull requests are welcome! For non-trivial PRs please open an issue first, so the core developers can give feedback on your idea. Development Environment ----------------------- You will need: * `Python 2.7 `_ *(support for Python 3.4+ in progress)* * `NumPy `_ * `Matplotlib `_ * `wxPython Phoenix 3.0.2 `_ *(later releases have not been tested)* * `Cartopy `_ * `h5py `_ *[HDF plugin]* * `hydroffice.bag `_ *[BAG plugin]* * `Pydap `_ *[OPeNDAP plugin]* * `Requests `_ *[HDF Rest API plugin]* For packaging the app: * `PyInstaller `_ (Linux & Windows, experimental for OS X) *(>= 3.0)* * `Py2App `_ (OS X) Running the Program ------------------- ``$ python HDFCompass.py`` Note: If you are using the Anaconda distribution on the Mac, you will see the message: "This program needs access to the screen. Please run with a Framework build of python...". In this case use the pythonw command: ``$ pythonw HDFCompass.py`` Note: on Mac, HDF Compass doesn't create an initial window, use the system Application menu to open a file or remote resource. Packaging on OS X ----------------- ``$ python setup.py py2app`` Packaging on Windows -------------------- Single-file: ``$ pyinstaller --clean -y HDFCompass.1file.spec`` Single-folder (useful for debugging the ``pyinstaller`` settings): ``$ pyinstaller --clean -y HDFCompass.1folder.spec`` Other info ---------- * Github: `http://github.com/HDFGroup/hdf-compass `_ * Project page: `https://www.hdfgroup.org/projects/compass/ `_ * License: BSD-like HDF Group license (See `COPYING `_) Keywords: data hdf bag ascii grid opendap Platform: UNKNOWN Classifier: Development Status :: 4 - Beta Classifier: Intended Audience :: Science/Research Classifier: Natural Language :: English Classifier: License :: OSI Approved :: BSD License Classifier: Operating System :: OS Independent Classifier: Programming Language :: Python Classifier: Programming Language :: Python :: 2 Classifier: Programming Language :: Python :: 2.7 Classifier: Topic :: Scientific/Engineering :: Information Analysis Classifier: Topic :: Office/Business :: Office Suites Classifier: Topic :: Utilities hdf_compass-0.6.0/hdf_compass.egg-info/requires.txt0000666000000000000000000000020112730267653020521 0ustar 00000000000000numpy matplotlib>=1.5 h5py wxPython==3.0.2 requests [BAG] hydroffice.bag>=0.2.10 [GeoNodes] cartopy[plotting] [OpenDAP] pydap hdf_compass-0.6.0/hdf_compass.egg-info/SOURCES.txt0000666000000000000000000001203412730267653020014 0ustar 00000000000000COPYING HDFCompass.desktop HDFCompass.icns HDFCompass.ico HDFCompass.py MANIFEST.in README.rst README.txt setup.cfg setup.py additional_legal/HydroPro_Icons_Terms.txt additional_legal/KDE_Oxygen_Icon_Set_Copyright_and_License.txt additional_legal/NumPy_Copyright_and_License.txt additional_legal/PyDAP_Copyright_and_License.txt additional_legal/PyInstaller_Copyrights_and_Licenses.txt additional_legal/Python_Copyright_and_License.txt additional_legal/cartopy_Copyrights_and_Licenses.txt additional_legal/h5py_Copyrights_and_Licenses.txt additional_legal/hydroffice_bag_Copyrights_and_Licenses.txt additional_legal/matplotlib_Copyright_and_License.txt additional_legal/wxWidgets_Copyrights_and_Licenses.txt data/asc/sample.asc data/bag/bdb_00.bag data/hdf5/tall.h5 data/hdf5/Download/download_data.py docs/conf.py docs/data_model.rst docs/how_to_contribute.rst docs/how_to_freeze.rst docs/how_to_install.rst docs/how_to_release.rst docs/how_to_use.rst docs/index.rst docs/license.rst docs/make.bat docs/requirements.rst hdf_compass/__init__.py hdf_compass.egg-info/PKG-INFO hdf_compass.egg-info/SOURCES.txt hdf_compass.egg-info/dependency_links.txt hdf_compass.egg-info/entry_points.txt hdf_compass.egg-info/namespace_packages.txt hdf_compass.egg-info/requires.txt hdf_compass.egg-info/top_level.txt hdf_compass/array_model/__init__.py hdf_compass/array_model/model.py hdf_compass/array_model/test.py hdf_compass/asc_model/__init__.py hdf_compass/asc_model/model.py hdf_compass/asc_model/test.py hdf_compass/bag_model/__init__.py hdf_compass/bag_model/model.py hdf_compass/bag_model/test.py hdf_compass/compass_model/__init__.py hdf_compass/compass_model/model.py hdf_compass/compass_model/test.py hdf_compass/compass_model/icons/array_16.png hdf_compass/compass_model/icons/array_64.png hdf_compass/compass_model/icons/folder_16.png hdf_compass/compass_model/icons/folder_64.png hdf_compass/compass_model/icons/image_16.png hdf_compass/compass_model/icons/image_64.png hdf_compass/compass_model/icons/kv_16.png hdf_compass/compass_model/icons/kv_64.png hdf_compass/compass_model/icons/license.txt hdf_compass/compass_model/icons/readme.txt hdf_compass/compass_model/icons/text_16.png hdf_compass/compass_model/icons/text_64.png hdf_compass/compass_model/icons/unknown_16.png hdf_compass/compass_model/icons/unknown_64.png hdf_compass/compass_model/icons/xml_16.png hdf_compass/compass_model/icons/xml_64.png hdf_compass/compass_viewer/__init__.py hdf_compass/compass_viewer/__main__.py hdf_compass/compass_viewer/events.py hdf_compass/compass_viewer/frame.py hdf_compass/compass_viewer/info.py hdf_compass/compass_viewer/viewer.py hdf_compass/compass_viewer/array/__init__.py hdf_compass/compass_viewer/array/frame.py hdf_compass/compass_viewer/array/plot.py hdf_compass/compass_viewer/container/__init__.py hdf_compass/compass_viewer/container/frame.py hdf_compass/compass_viewer/container/list.py hdf_compass/compass_viewer/geo_array/__init__.py hdf_compass/compass_viewer/geo_array/frame.py hdf_compass/compass_viewer/geo_array/plot.py hdf_compass/compass_viewer/geo_surface/__init__.py hdf_compass/compass_viewer/geo_surface/frame.py hdf_compass/compass_viewer/geo_surface/plot.py hdf_compass/compass_viewer/icons/favicon_32.png hdf_compass/compass_viewer/icons/favicon_48.png hdf_compass/compass_viewer/icons/go_back_24.png hdf_compass/compass_viewer/icons/go_back_32.png hdf_compass/compass_viewer/icons/go_next_24.png hdf_compass/compass_viewer/icons/go_next_32.png hdf_compass/compass_viewer/icons/go_top_24.png hdf_compass/compass_viewer/icons/go_top_32.png hdf_compass/compass_viewer/icons/go_up_24.png hdf_compass/compass_viewer/icons/go_up_32.png hdf_compass/compass_viewer/icons/license.txt hdf_compass/compass_viewer/icons/logo.png hdf_compass/compass_viewer/icons/readme.txt hdf_compass/compass_viewer/icons/save_24.png hdf_compass/compass_viewer/icons/view_icon_24.png hdf_compass/compass_viewer/icons/view_icon_32.png hdf_compass/compass_viewer/icons/view_list_24.png hdf_compass/compass_viewer/icons/view_list_32.png hdf_compass/compass_viewer/icons/view_tree_32.png hdf_compass/compass_viewer/icons/viz_plot_24.png hdf_compass/compass_viewer/icons/viz_plot_32.png hdf_compass/compass_viewer/icons/xml_validate_24.png hdf_compass/compass_viewer/image/__init__.py hdf_compass/compass_viewer/image/frame.py hdf_compass/compass_viewer/keyvalue/__init__.py hdf_compass/compass_viewer/keyvalue/frame.py hdf_compass/compass_viewer/text/__init__.py hdf_compass/compass_viewer/text/frame.py hdf_compass/compass_viewer/text/text_ctrl.py hdf_compass/filesystem_model/__init__.py hdf_compass/filesystem_model/model.py hdf_compass/filesystem_model/test.py hdf_compass/hdf5_model/__init__.py hdf_compass/hdf5_model/model.py hdf_compass/hdf5_model/test.py hdf_compass/hdf5rest_model/__init__.py hdf_compass/hdf5rest_model/hdf5dtype.py hdf_compass/hdf5rest_model/model.py hdf_compass/hdf5rest_model/test.py hdf_compass/opendap_model/__init__.py hdf_compass/opendap_model/model.py hdf_compass/opendap_model/test.py hdf_compass/utils/__init__.py hdf_compass/utils/utils.py tests/HDFCompassTestLog.rst tests/HDFCompassTestPlan.rst tests/sample.aschdf_compass-0.6.0/hdf_compass.egg-info/top_level.txt0000666000000000000000000000001412730267653020655 0ustar 00000000000000hdf_compass hdf_compass-0.6.0/MANIFEST.in0000666000000000000000000000060512730245342013676 0ustar 00000000000000# Include the license file include COPYING include additional_legal/*.* include README.txt include HDFCompass.desktop include HDFCompass.ico include HDFCompass.icns include HDFCompass.py recursive-include tests *.* recursive-include docs *.* prune docs/_build include data/asc/*.* include data/bag/*.* include data/hdf5/*.* include data/hdf5/Download/download_data.pyhdf_compass-0.6.0/PKG-INFO0000666000000000000000000001257112730267653013253 0ustar 00000000000000Metadata-Version: 1.1 Name: hdf_compass Version: 0.6.0 Summary: An experimental viewer program for HDF5 and related formats. Home-page: https://github.com/HDFGroup/hdf-compass/ Author: HDFGroup Author-email: help@hdfgroup.org License: BSD-like license Description: HDF Compass =========== .. image:: https://badge.fury.io/py/hdf_compass.svg :target: https://badge.fury.io/py/hdf_compass :alt: PyPI Status .. image:: https://readthedocs.org/projects/hdf-compass/badge/?version=stable :target: http://hdf-compass.readthedocs.org/en/stable/?badge=stable :alt: Stable Documentation Status .. image:: https://readthedocs.org/projects/hdf-compass/badge/?version=latest :target: http://hdf-compass.readthedocs.org/en/latest/?badge=latest :alt: Latest Documentation Status .. image:: https://ci.appveyor.com/api/projects/status/tfg350xo8t7h70ix?svg=true :target: https://ci.appveyor.com/project/giumas/hdf-compass :alt: AppVeyor Status .. image:: https://travis-ci.org/giumas/hdf-compass.svg?branch=develop :target: https://travis-ci.org/giumas/hdf-compass :alt: Travis-CI Status Welcome to the project! HDF Compass is an experimental viewer program for HDF5 and related formats, designed to complement other more complex applications like HDFView. Strong emphasis is placed on clean minimal design, and maximum extensibility through a plugin system for new formats. HDF Compass is written in Python, but ships as a native application on Windows, OS X, and Linux, by using PyInstaller and Py2App to package the app. Binary executables are available for Windows (Windows 7 or later) and Mac OS X (Yosemite or later) at the Project Page listed below. Bug reports and pull requests are welcome! For non-trivial PRs please open an issue first, so the core developers can give feedback on your idea. Development Environment ----------------------- You will need: * `Python 2.7 `_ *(support for Python 3.4+ in progress)* * `NumPy `_ * `Matplotlib `_ * `wxPython Phoenix 3.0.2 `_ *(later releases have not been tested)* * `Cartopy `_ * `h5py `_ *[HDF plugin]* * `hydroffice.bag `_ *[BAG plugin]* * `Pydap `_ *[OPeNDAP plugin]* * `Requests `_ *[HDF Rest API plugin]* For packaging the app: * `PyInstaller `_ (Linux & Windows, experimental for OS X) *(>= 3.0)* * `Py2App `_ (OS X) Running the Program ------------------- ``$ python HDFCompass.py`` Note: If you are using the Anaconda distribution on the Mac, you will see the message: "This program needs access to the screen. Please run with a Framework build of python...". In this case use the pythonw command: ``$ pythonw HDFCompass.py`` Note: on Mac, HDF Compass doesn't create an initial window, use the system Application menu to open a file or remote resource. Packaging on OS X ----------------- ``$ python setup.py py2app`` Packaging on Windows -------------------- Single-file: ``$ pyinstaller --clean -y HDFCompass.1file.spec`` Single-folder (useful for debugging the ``pyinstaller`` settings): ``$ pyinstaller --clean -y HDFCompass.1folder.spec`` Other info ---------- * Github: `http://github.com/HDFGroup/hdf-compass `_ * Project page: `https://www.hdfgroup.org/projects/compass/ `_ * License: BSD-like HDF Group license (See `COPYING `_) Keywords: data hdf bag ascii grid opendap Platform: UNKNOWN Classifier: Development Status :: 4 - Beta Classifier: Intended Audience :: Science/Research Classifier: Natural Language :: English Classifier: License :: OSI Approved :: BSD License Classifier: Operating System :: OS Independent Classifier: Programming Language :: Python Classifier: Programming Language :: Python :: 2 Classifier: Programming Language :: Python :: 2.7 Classifier: Topic :: Scientific/Engineering :: Information Analysis Classifier: Topic :: Office/Business :: Office Suites Classifier: Topic :: Utilities hdf_compass-0.6.0/README.rst0000666000000000000000000000724712730245342013640 0ustar 00000000000000HDF Compass =========== .. image:: https://badge.fury.io/py/hdf_compass.svg :target: https://badge.fury.io/py/hdf_compass :alt: PyPI Status .. image:: https://readthedocs.org/projects/hdf-compass/badge/?version=stable :target: http://hdf-compass.readthedocs.org/en/stable/?badge=stable :alt: Stable Documentation Status .. image:: https://readthedocs.org/projects/hdf-compass/badge/?version=latest :target: http://hdf-compass.readthedocs.org/en/latest/?badge=latest :alt: Latest Documentation Status .. image:: https://ci.appveyor.com/api/projects/status/tfg350xo8t7h70ix?svg=true :target: https://ci.appveyor.com/project/giumas/hdf-compass :alt: AppVeyor Status .. image:: https://travis-ci.org/giumas/hdf-compass.svg?branch=develop :target: https://travis-ci.org/giumas/hdf-compass :alt: Travis-CI Status Welcome to the project! HDF Compass is an experimental viewer program for HDF5 and related formats, designed to complement other more complex applications like HDFView. Strong emphasis is placed on clean minimal design, and maximum extensibility through a plugin system for new formats. HDF Compass is written in Python, but ships as a native application on Windows, OS X, and Linux, by using PyInstaller and Py2App to package the app. Binary executables are available for Windows (Windows 7 or later) and Mac OS X (Yosemite or later) at the Project Page listed below. Bug reports and pull requests are welcome! For non-trivial PRs please open an issue first, so the core developers can give feedback on your idea. Development Environment ----------------------- You will need: * `Python 2.7 `_ *(support for Python 3.4+ in progress)* * `NumPy `_ * `Matplotlib `_ * `wxPython Phoenix 3.0.2 `_ *(later releases have not been tested)* * `Cartopy `_ * `h5py `_ *[HDF plugin]* * `hydroffice.bag `_ *[BAG plugin]* * `Pydap `_ *[OPeNDAP plugin]* * `Requests `_ *[HDF Rest API plugin]* For packaging the app: * `PyInstaller `_ (Linux & Windows, experimental for OS X) *(>= 3.0)* * `Py2App `_ (OS X) Running the Program ------------------- ``$ python HDFCompass.py`` Note: If you are using the Anaconda distribution on the Mac, you will see the message: "This program needs access to the screen. Please run with a Framework build of python...". In this case use the pythonw command: ``$ pythonw HDFCompass.py`` Note: on Mac, HDF Compass doesn't create an initial window, use the system Application menu to open a file or remote resource. Packaging on OS X ----------------- ``$ python setup.py py2app`` Packaging on Windows -------------------- Single-file: ``$ pyinstaller --clean -y HDFCompass.1file.spec`` Single-folder (useful for debugging the ``pyinstaller`` settings): ``$ pyinstaller --clean -y HDFCompass.1folder.spec`` Other info ---------- * Github: `http://github.com/HDFGroup/hdf-compass `_ * Project page: `https://www.hdfgroup.org/projects/compass/ `_ * License: BSD-like HDF Group license (See `COPYING `_) hdf_compass-0.6.0/README.txt0000666000000000000000000000204012615776327013647 0ustar 00000000000000This is the source code repository for HDF Compass, a viewer program for HDF and HDF-related files. The project is divided into components, each of which is a top-level Python package: compass_viewer The GUI viewer application, based on wxPython. The file HDFCompass.py is a two-line script that launches the viewer, and is provided as the entry point for Py2App and PyInstaller. compass_model Defines the classes available for the pluggable data model. This is the main dependency for plugins. The interfaces defined in compass_model are implemented by plugins, and those implementations are called by the viwer to populate the various views in HDFCompass (container, array, etc.). hdf5_model A basic HDF5 plugin, using h5py. filesystem_model An example filesystem plugin. Access through the GUI by opening the resource "file://localhost". array_model An example/debugging array plugin. Access through the GUI by opening the resource "array://localhost".hdf_compass-0.6.0/setup.cfg0000666000000000000000000000041212730267653013766 0ustar 00000000000000[bumpversion] current_version = 0.6.0 files = setup.py hdf_compass/utils/__init__.py docs/conf.py HDFCompass.1file.spec [bdist_wheel] universal = 1 [metadata] description-file = README.rst [egg_info] tag_build = tag_date = 0 tag_svn_revision = 0 hdf_compass-0.6.0/setup.py0000666000000000000000000001130212730245342013646 0ustar 00000000000000############################################################################## # Copyright by The HDF Group. # # All rights reserved. # # # # This file is part of the HDF Compass Viewer. The full HDF Compass # # copyright notice, including terms governing use, modification, and # # terms governing use, modification, and redistribution, is contained in # # the file COPYING, which can be found at the root of the source code # # distribution tree. If you do not have access to this file, you may # # request a copy from help@hdfgroup.org. # ############################################################################## """ A setuptools based setup module. See: https://packaging.python.org/en/latest/distributing.html https://github.com/pypa/sampleproject Run `python setup.py --help-commands` for available options """ from __future__ import absolute_import, division, print_function # unicode_literals import os import sys # To use a consistent encoding from codecs import open # Always prefer setuptools over distutils from setuptools import setup, find_packages # --------------------------------------------------------------------------- # Some helper stuff # --------------------------------------------------------------------------- here = os.path.abspath(os.path.dirname(__file__)) def txt_read(*paths): """ Build a file path from *paths* and return the textual contents """ with open(os.path.join(here, *paths), encoding='utf-8') as f: return f.read() # --------------------------------------------------------------------------- # Populate dictionary with settings # --------------------------------------------------------------------------- # Create a dict with the basic information that is passed to setup after keys are added. setup_args = dict() setup_args['name'] = 'hdf_compass' # The adopted versioning scheme follow PEP40 setup_args['version'] = '0.6.0' setup_args['url'] = 'https://github.com/HDFGroup/hdf-compass/' setup_args['license'] = 'BSD-like license' setup_args['author'] = 'HDFGroup' setup_args['author_email'] = 'help@hdfgroup.org' # # descriptive stuff # description = 'An experimental viewer program for HDF5 and related formats.' setup_args['description'] = description setup_args['long_description'] = txt_read('README.rst') setup_args['classifiers'] = \ [ # https://pypi.python.org/pypi?%3Aaction=list_classifiers 'Development Status :: 4 - Beta', 'Intended Audience :: Science/Research', 'Natural Language :: English', 'License :: OSI Approved :: BSD License', 'Operating System :: OS Independent', 'Programming Language :: Python', 'Programming Language :: Python :: 2', 'Programming Language :: Python :: 2.7', # 'Programming Language :: Python :: 3', # 'Programming Language :: Python :: 3.4', 'Topic :: Scientific/Engineering :: Information Analysis', 'Topic :: Office/Business :: Office Suites', 'Topic :: Utilities' ] setup_args['keywords'] = "data hdf bag ascii grid opendap" # # code stuff # # requirements setup_args['setup_requires'] =\ [ "setuptools", "wheel", ] setup_args['install_requires'] =\ [ "numpy", "matplotlib>=1.5", "h5py", "wxPython==3.0.2", "requests" ] setup_args['extras_require'] =\ { "GeoNodes": ["cartopy[plotting]", ], # required for visualization of GeoArray and GeoSurface nodes "BAG": ["hydroffice.bag>=0.2.10", ], # required by BAG plugin "OpenDAP": ["pydap", ], # required by OpenDAP plugin } # hdf_compass namespace, packages and other files setup_args['namespace_packages'] = ['hdf_compass'] setup_args['packages'] = find_packages(exclude=["*.tests", "*.tests.*", "tests.*", "tests", "*.test*", ]) setup_args['package_data'] =\ { '': ['icons/*.png', 'icons/*.ico', 'icons/*.icns', 'icons/*.txt'], } setup_args['data_files'] = [] setup_args['entry_points'] =\ { 'gui_scripts': ['HDFCompass = hdf_compass.compass_viewer.viewer:run'], } # --------------------------------------------------------------------------- # Do the actual setup now # --------------------------------------------------------------------------- setup(**setup_args) hdf_compass-0.6.0/tests/0000777000000000000000000000000012730267653013312 5ustar 00000000000000hdf_compass-0.6.0/tests/HDFCompassTestLog.rst0000666000000000000000000003235712730245342017276 0ustar 00000000000000As of Oct. 19\ :sup:`th`, 2015 1) Files under ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/HDFCompass/kent-files/ A) Directory /hdf5-handler-fake +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | Files | Issues-view | Issues -plot | +==============================+========================================================================================+=============================================+ | Comp\_complex.h5 | 1. Datatype cmp1 treats an HDF5 Attributes | Two lines are plotted, which | | | | | | | 2. No information about compound datatype cmp1, cmp2 | doesn’t make sense | | | | | | | 3. Attribute of phony\_compound\_var | | | | | | | | DIMENSION\_LIST Value doesn’t make sense. | | | | | | | | 4. The value of phony\_compound\_var | | | | | | | | Is not right | | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | comp\_scalar.h5 | All right | No plot | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | comp\_complex\_scalar.h5 | Only display the first element of the member | No plot | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | Compound\_more\_types.h5 | No data is displayed | Crash the compass when clicking plot data | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | D\_compound.h5 | OK | No plot | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | D\_dset\_many.h5 | OK and fast | OK | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | D\_link\_hard.h5 | https://github.com/HDFGroup/hdf-compass/issues/90 | N/A | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | D\_link\_soft.h5 | https://github.com/HDFGroup/hdf-compass/issues/91 | N/A | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | D\_objref.h5 | https://github.com/HDFGroup/hdf-compass/issues/92 | N/A | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | D\_regref.h5 | https://github.com/HDFGroup/hdf-compass/issues/93 | N/A | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | Grid\_1\_2d.h5 | Ok but the display of HDF5 string dataset is all in one. | OK | | | | | | | https://github.com/HDFGroup/hdf-compass/issues/94 | | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | Grid\_1\_3d\_xyz\_aug.h5 | Object reference issues discovered by others | OK | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | Nc4\_group\_atomic.h5 | Object reference issues discovered by others | N/A | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | Nc4\_group\_comp.h5 | Wait | N/A | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | Nest\_comp\_scalar.h5 | Wait | N/A | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | Ntypes.h5 | See issues 95-99 | N/A | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | t\_flatten\_name\_clash.h5 | OK | N/A | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | t\_link\_comment.h5 | Comment doesn’t show up, no need to report this since comment is deprecated in HDF5. | N/A | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | T\_vl\_string\_cstr.h5 | Covered | N/A | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | T\_space\_null.h5 | OK | N/A | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ | T\_space\_zero.h5 | OK | N/A | +------------------------------+----------------------------------------------------------------------------------------+---------------------------------------------+ B) Directory /hdf5-testing-files +---------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------+----------------+ | Files | Issues-view | Issues -plot | +===============================================================================================================+====================================================================================+================+ | Charsets.h5 | ok | | +---------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------+----------------+ | tldoublebad.h5 | Cannot open by h5dump, the file may be corrupted tldouble.h5 is under /testfiles | | +---------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------+----------------+ | tldouble.h5 | Cannot open the file | | +---------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------+----------------+ | tbigdims.h5 | Crash the testing machine | | +---------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------+----------------+ | tfilters.h5 | OK | | +---------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------+----------------+ | This may wrap up the testing for all the fake files. | | | | | | | | STOP testing and wait for the lead to review the testing plan and provide the guidelines for the next step. | | | +---------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------+----------------+ C) Directory /hdf5-real-files hdf_compass-0.6.0/tests/HDFCompassTestPlan.rst0000666000000000000000000003260112730245342017437 0ustar 00000000000000HDF Compass Test Plan ===================== The test plan includes Testing environment, Installation, Basic functionality, Basic viewer tests, Plug-in tests, and a table to carry out a test with a sample file. kyang2014 write comments starting with kyang2014: kyang2014: From the ticket and JR's comments(https://github.com/HDFGroup/hdf-compass/issues/71) , it seems this is just for the release validation. The tester doesn't need to build HDFCompass from the source. The developer will provide the binaries to the tester. I. Testing environment 1) Platforms +----------------+----------------------------------+ | **Platform** | **Versions** | +================+==================================+ | Mac OS | MacOS 10.8, 10.9, 10.10, 10.11 | +----------------+----------------------------------+ | Windows | 7,8 and 10 | +----------------+----------------------------------+ | Linux | 64-bit CentOS 6 and 7? | +----------------+----------------------------------+ kyang2014: Do we need the Python,h5py etc. versions? Seems that we don't need these information just for this purpose? 2) Where to obtain the testing files kyang2014: May use Amazon S3 or google cloud or azure. I put some testing files for a quick test under ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/HDFCompass/kent-files/ II. Installation +----------------+-------------------------------------------+ | **Platform** | **Experience** | +================+===========================================+ | Mac OS | ? | +----------------+-------------------------------------------+ | Windows | Download and follow the instructions | +----------------+-------------------------------------------+ | Linux | may need to install python dependencies | +----------------+-------------------------------------------+   III. Basic functionality 1) Launch HDFCompass Click HDFCompass icon or type HDFCompass.exe under the command-line to see if the program can get started. 2) Menu Tests +-----------------+------------------------+----------------------------------+ | **File Menu** | **File Menu Hotkey** | **About HDFCompass** | +=================+========================+==================================+ | Open | Ctrl- O | HDFCompass Version number(0.5) | | | | | | | | @2014-2015 The HDF Group | +-----------------+------------------------+----------------------------------+ | Open Resource | Ctrl-R | | +-----------------+------------------------+----------------------------------+ | Close Window | Ctrl-W | | +-----------------+------------------------+----------------------------------+ | Close File | Shift-Ctrl-W | | +-----------------+------------------------+----------------------------------+ | Exit |   | | +-----------------+------------------------+----------------------------------+ 3) Toolbar Icon displays (On mac). Can drag files to Toolbar?   IV. Basic viewer Tests 1) Basic Tests A) +--------------------+--------------------------------------------------------------------+-----------------------------------------+----------------------------+--------------------------------+--------------------------------------+ | **Platform** | **HDF5 Group** | **HDF5 Group Attributes** | **HDF5 Dataset** | **HDF5 Dataset Plots** | **HDF5 Dataset Attributes** | +====================+====================================================================+=========================================+============================+================================+======================================+ | (items to check) | 1. Tree view or List view | 1. Click  "Reopen as HDF5 Attributes" | name, shape,type, values | Plot by clicking "Plot Data" | Click  "Reopen as HDF5 Attributes" | | | | | | | | | | 2. Name and Kind | 2. name, values,type and shapes | | Icons on the Plot windows | name, value, type, values | | | | | | | | | | 3. Click "Reopen as HDF5 Group"  to check if it is still working | | | | | +--------------------+--------------------------------------------------------------------+-----------------------------------------+----------------------------+--------------------------------+--------------------------------------+ | Windows 7 |   |   |   |   |   | +--------------------+--------------------------------------------------------------------+-----------------------------------------+----------------------------+--------------------------------+--------------------------------------+ | Linux CentOS 6 |   |   |   |   |   | +--------------------+--------------------------------------------------------------------+-----------------------------------------+----------------------------+--------------------------------+--------------------------------------+ | MacOS 10.10 |   |   |   |   |   | +--------------------+--------------------------------------------------------------------+-----------------------------------------+----------------------------+--------------------------------+--------------------------------------+ | ....... |   |   |   |   |   | +--------------------+--------------------------------------------------------------------+-----------------------------------------+----------------------------+--------------------------------+--------------------------------------+ B) On each window, check the "Go" icon 2) Advanced Tests Same as the above but may need to provide the information that needs specific attentions for some tests. kyang2014: Do we want to test if one can open an HDF5 file >1 times at the same time? 3) Files for the basic Tests A) Really basic one: A file that just includes one group, one HDF5 dataset of 2-D floating-point array, a string attribute under the group and an integer attribute for the dataset. B) Basic tests: a) Dataset: One group, one scalar, one 1-D array and one 3-D floating-point array. b) Group: multi-groups(no cycle) c) Attributes: Attributes of different types, from int8(signed and unsigned) to int64, floating-points, HDF5 string under a group d) Compound datatype datasets: a simple one and a nested one datasets as well as a simple and a nested attributes   C) Advanced tests: a) HDF5 object references: One dataset and one attribute b) HDF5 region references: One dataset and one attribute c) HDF5 softlink and hardlink: Links for groups and datasets d) HDF5 external links: Link to datasets and groups from another HDF5 file(Will this work?) e) HDF5 Image, table, packed table kyang2014: f) to i) should be more advanced. f) HDF5 datatypes(advanced): f1) HDF5 string: variable length string with different pad options, fixed-size string with different pad options f2) Big endian and Little endian mixed f3) Bitfield, enum, opaque and even array type g) HDF5 datasets(advanced) g1) HDF5 datasets applied to different filters and storage: gzip(different levels), shuffle, nbit, scaleoffset, szip, chunking, compact  g2) One 4-D and one 5-D array(Mainly for the plot feature) g3) Unlimited dimension HDF5 datasets : 1-D and 2-D h) HDF5 spaces(advanced) h1) Null space i) Stress tests: i1)Giant dataset > 4GB i2) Many attributes i3) Many objects kyang2014: Need to get approved to implement the above testing plan. In the mean time, I've just tried out the HDFCompass with some files I collected by my own. Issues I found are submitted to github issues 87-99. My own testing files(included a few from JR) can be found under ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/HDFCompass/kent-files/ V. Plug-in Tests 1) OPeNDAP kyang2014: *Needs the clarification about the purpose of OPeNDAP plug-in. DAP is a protocol. Various formats such as netCDF, HDF4, HDF5, grib, excel etc. can be accessed via DAP. Also there are different DAP implementations. Different DAP implementations may provide different output. So we need to clarify what implementation we should test.* *Unidata's THREDDS(java) and OPeNDAP's Hyrax(C++) are two major ones. A python implementation(pydap) is also available. * *Also the OPeNDAP plug-in uses Pydap underneath to access the DAP data. The Pydap client may also have its own limitation(See the last section of kyang2014's comments for issue 60. Since the HDF group implemented HDF modules for Hyrax, so first we should target the HDF5 files served via Hyrax implementation of OPeNDAP. A) Testing the access of HDF5 via Hyrax Hyrax provides an option to dynamically enable different outputs. To serve our NASA customers, we implement an option(CF option) in addition to the default option for Hyrax output. In my view, default option is more fit for HDFCompass although the CF option may be more practical for users.Since the output is different for different options, we need to provide the expected output for different options.  The testing files can be found under ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/HDFCompass/kent-files/hdf5-handler-fake/ A1) Default option a) DAP2 testing This mapping keeps the original HDF5 structure via DAP2. d_compound.h5 d_group.h5 d_objref.h5 d_regref.h5 d_link_soft.h5 d_link_hard.h5 d_int.h5 t_string.h5 t_vl_string.h5 b) DAP4 testing Prerequiste: Pydap supports DAP4 d_compound.h5 d_group.h5 d_objref.h5 d_regref.h5 d_link_soft.h5 d_link_hard.h5 d_int.h5 d_int64.h5 t_string_cstr.h5 t_vl_string_cstr.h5 nc4_group_atomic.h5 nc4_group_comp.h5   A2) CF option The output is more like netCDF output, which is like a subset of HDF5. The variable/attribute names are following CF conventions. Groups are flattened out. Bunch of datatypes not supported by CF are ignored. Some customized features specifically requested from NASA are also added. The DAP4 output is strictly mapped from the DAP2 output. So the testing files are the same. t_float.h5 t_group_scalar_attrs.h5 t_int.h5 t_2d_2dll.nc4.h5 t_cf_1dll.h5 t_size8.h5 t_string.h5 t_unsupported.h5 t_vl_string.h5 t_name_clash.h5 t_non_cf_char.h5 t_fillvalue_2d_2x2y.nc4.h5 grid_1_2d.h5 B) (Maybe) Testing the access of HDF4 via Hyrax C) (Maybe) Testing the access of HDF5 via THREDDS D) (Maybe) Testing the access of netCDF via THREDDS ....... 2) ASCII Grid sample.asc can be found under the test directory. kyang2014: Just have a check with the sample.asc of this plug-in. Actually I don't think the plot is right although the data values in the viewer looks like corresponding to the sample.asc. The problem is the starting point of the plot index. HDFcompass starting from the upper-left corner with index (0,0). The (0,0) in the ASCII Grid should start from lower-left. So the plot is upside-down.This example shows the compass contour plot feature is not sufficient. The contour plot is not appropriate. The plot should be like the one at  https://en.wikipedia.org/wiki/Esri_grid. This Basic testing for this plug-in is relatively easy. It just needs three tests. 1) Sample.asc 2) Sample.asc with xllcorner as 300.00 and yllcorner as 200.00 3) Sample.asc without having NODATA\_Value VI. An example to check the functionality of the basic viewer kyang2014: Fill in the information later if necessary         hdf_compass-0.6.0/tests/sample.asc0000666000000000000000000000030412730245342015247 0ustar 00000000000000ncols 4 nrows 6 xllcorner 0.0 yllcorner 0.0 cellsize 50.0 NODATA_value -9999 -9999 -9999 5 2 -9999 20 100 36 3 8 35 10 32 42 50 6 88 75 27 9 13 5 1 -9999