Create branch for release 0.9.7.
* [r11257]
doc/Downloads/index_text.php,
doc/Home/news_text.php,
doc/News/index_text.php:
Updated release date and download links.
* [r11256]
doc/Downloads/existingpython_text.php,
setup.py:
Explicitly state we have tested Python 2.5 and 2.6.
* [r11255]
param/tk.py:
Removed unused variables and imports.
* [r11254]
param/__init__.py:
Do not pickle Filename's search paths.
* [r11253]
param/__init__.py:
Removed unused import and fixed name error.
* [r11252]
external/Makefile:
Clarification of comment.
* [r11251]
topo/misc/inlinec.py:
Hack to allow weave to work when the user name contains a
space.
* [r11250]
param/parameterized.py:
Removed unused variable.
* [r11249]
topo/base/arrayutil.py:
Removed duplicate import.
* [r11248]
topo/base/sheet.py:
Removed unused imports.
* [r11247]
topo/base/cf.py:
Removed unused import.
* [r11246]
topo/plotting/bitmap.py:
Simplified finding default title font.
* [r11245]
topo/command/basic.py:
Only warn about missing gnosis.xml if trying to save a
snapshot with xml=True.
* [r11244]
doc/Downloads/existingpython_text.php,
doc/Downloads/index_text.php:
Simplified download instructions (only mention graphical
installers, since presumably people using the commandline
already know what to do).
* [r11243]
doc/Downloads/index_text.php:
Removed mac installer section. EPD includes only Tk 8.4.
* [r11242]
setup.py:
Removed no-longer-needed link to doozy for getting extra
packages.
2010-07-17 ceball
* [r11241]
Makefile:
More files to keep (that are cleaned by distclean).
2010-07-16 ceball
* [r11240]
Makefile,
doc/Downloads/index_text.php:
Updated DEB and RPM links to match release candidates.
* [r11239]
doc/Downloads/existingpython_text.php,
doc/Downloads/index_text.php:
Simplified pypi download links.
* [r11238]
Makefile:
More to clean for release (no sounds/ dir, remove windows
installer stuff).
* [r11237]
external/Makefile:
More to clean and uninstall (zlib, m4).
* [r11236]
doc/buildbot/dot-dput.cf:
Updated for stable repository.
2010-07-16 ceball
* [r11234]
doc/Downloads/index_text.php:
Added comment.
* [r11233]
doc/Downloads/existingpython_text.php,
doc/FAQ/index_text.php,
setup.py:
Made easy_install do bare minimum by default for maximum
chance of success.
2010-07-15 ceball
* [r11232]
/trunk/topographica-win:
Removing obsolete topographica-win.
* [r11231]
param/__init__.py:
Default param.normalize_path.prefix is now os.getcwd(),
rather than being empty. Should have no effect on
Topographica because Topographica sets prefix on startup to
~/topographica.
* [r11230]
Makefile:
Fixed typo.
* [r11229]
topo/command/basic.py:
Added documentation about alteration of
param.norm_path.prefix.
* [r11228]
topo/tkgui/topoconsole.py:
Fix how help pages are looked up (checked on SVN version and
Ubuntu version).
* [r11227]
doc/Team_Members/index_text.php:
Removed dead link.
* [r11226]
topo/misc/genexamples.py:
Minor simplification.
* [r11225]
topo/misc/genexamples.py:
Removed no-longer-necessary hack for Windows quoting.
* [r11224]
doc/Tutorials/gcal_text.php,
doc/Tutorials/lissom_oo_or_text.php,
topo/command/basic.py:
Simplified typ-generation command.
* [r11223]
doc/News/index_text.php:
Corrected news items.
* [r11222]
topo/misc/legacy.py:
Added support for fixedpoint not existing as an importable
module (instead being topo.misc.fixedpoint).
* [r11221]
topo/tests/gca_lissom.ty_DATA,
topo/tests/gcal.ty_DATA:
Renamed data file to match GCAL.
* [r11220]
topo/tests/hierarchical.ty_DATA,
topo/tests/lissom_oo_or.ty_DATA,
topo/tests/lissom_or.ty_DATA,
topo/tests/som_retinotopy.ty_DATA,
topo/tests/sullivan_neurocomputing04.ty_DATA:
Updated saved test data to use gmpy. No change to results.
* [r11219]
topo/misc/inlinec.py:
Removed stray print statement.
* [r11218]
doc/User_Manual/batch_text.php,
doc/User_Manual/commandline_text.php:
Documented default output path of ~/topographica.
* [r11217]
topo/tests/test_script.py:
Check that output_directory is respected.
* [r11216]
doc/Makefile:
Added param module to reference manual.
* [r11215]
Makefile,
topo/tests/test_script.py:
Added test of run_batch(); SF 2564343.
* [r11214]
doc/Tutorials:
Updated files to ignore.
* [r11213]
doc/Tutorials/index_text.php:
Restored lissom_oo_or name.
* [r11212]
doc/User_Manual/batch_text.php,
doc/User_Manual/commandline_text.php,
doc/User_Manual/patterns_text.php:
Updated how to start topographica.
2010-07-14 ceball
* [r11211]
topo/misc/inlinec.py:
Apart from testing that weave can be imported, test that
compiler works.
* [r11210]
examples/lissom_or_movie.ty:
Removed application_path.
* [r11209]
doc/Downloads/win32notes_text.php:
Minor cleanup.
* [r11208]
doc/Tutorials/som_retinotopy_text.php:
Fixed copy-paste error.
* [r11207]
doc/Downloads/existingpython_text.php,
doc/Downloads/index_text.php:
Updated installation locations.
* [r11206]
doc/Downloads/index_text.php:
Added links to deb and rpm files.
* [r11205]
Makefile:
Added RPM spec generation, suitable as input to OpenSUSE
build service.
* [r11204]
doc/buildbot/master.cfg:
Cleaned up packages and archives slaves.
* [r11203]
Makefile:
Fixed pypi upload.
* [r11202]
external/Makefile:
Include fixedpoint module in topo/misc, so we can assume it
always exists (in case gmpy is not available). Removed
fixedpoint from default build target in Makefile.
* [r11201]
topo/__init__.py,
topo/misc/fixedpoint.py,
topo/misc/util.py:
Include fixedpoint module in topo/misc, so we can assume it
always exists (in case gmpy is not available). Removed
fixedpoint from default build target in Makefile.
* [r11200]
Makefile:
Updated name for GCAL in tests.
* [r11199]
Makefile:
Commented out problematic pypi upload target.
* [r11198]
Makefile,
doc/Developer_Manual/releases_text.php,
doc/Downloads/bzr_text.php,
doc/Downloads/git_text.php:
Removing topographica-win/
* [r11197]
Makefile,
doc/Downloads/index_text.php,
setup.py,
topographica.ico,
windows_postinstall.py:
Makefile can now generate Windows installer (on linux).
2010-07-13 jbednar
* [r11196]
examples/gcal.ty:
Renamed gca_lissom to gcal
* [r11195]
doc/Tutorials/images/gcal_activity_010000.png,
doc/Tutorials/images/gcal_activity_010000_or.png,
doc/Tutorials/images/gcal_cf_center_010000.png,
doc/Tutorials/images/gcal_cf_center_010000_or.png,
doc/Tutorials/images/gcal_cf_vertical_010000_or.png,
doc/Tutorials/images/gcal_natural_image_oo_or.png,
doc/Tutorials/images/gcal_network_diagram.png,
doc/Tutorials/images/gcal_or_pref_010000.png,
doc/Tutorials/images/gcal_ormap_ft.png,
doc/Tutorials/images/gcal_projection_010000.png,
doc/Tutorials/images/gcal_test_pattern.png:
\R\e\n\a\m\e\d\ \g\c\a\_\l\i\s\s\o\m\ \t\o\ \g\c\a\l
* [r11194]
doc/Tutorials/lissom_oo_or_text.php,
examples/README.txt:
Renamed gca_lissom to gcal
* [r11193]
doc/News/index_text.php,
doc/Tutorials/gca_lissom_text.php,
doc/Tutorials/gcal_text.php,
doc/Tutorials/images/gca_lissom_activity_010000.png,
doc/Tutorials/images/gca_lissom_activity_010000_or.png,
doc/Tutorials/images/gca_lissom_cf_center_010000.png,
doc/Tutorials/images/gca_lissom_cf_center_010000_or.png,
doc/Tutorials/images/gca_lissom_cf_vertical_010000_or.png,
doc/Tutorials/images/gca_lissom_network_diagram.png,
doc/Tutorials/images/gca_lissom_or_pref_010000.png,
doc/Tutorials/images/gca_lissom_ormap_ft.png,
doc/Tutorials/images/gca_lissom_projection_010000.png,
doc/Tutorials/images/gca_lissom_test_pattern.png,
doc/Tutorials/images/gca_natural_image_oo_or.png,
doc/Tutorials/index_text.php,
examples/Makefile,
examples/gca_lissom.ty,
topo/misc/genexamples.py:
Renamed gca_lissom to gcal
2010-07-13 ceball
* [r11192]
doc/Reference_Manual:
More to ignore.
* [r11191]
doc/Reference_Manual:
More to ignore.
* [r11190]
doc/Developer_Manual/installation_text.php:
Removed duplicate suggestion to run 'make tests'.
* [r11189]
setup.py:
Minor changes to pypi info.
2010-07-12 jbednar
* [r11188]
doc/Tutorials/gca_lissom_text.php,
doc/Tutorials/index_text.php:
Changed GCA to GCAL
2010-07-10 jbednar
* [r11187]
doc/Tutorials/som_retinotopy_text.php:
Updated instructions for 0.9.7
* [r11186]
doc/Tutorials/gca_lissom_text.php,
doc/Tutorials/images/gca_lissom_activity_010000.png,
doc/Tutorials/images/gca_lissom_activity_010000_or.png,
doc/Tutorials/images/gca_lissom_cf_center_010000.png,
doc/Tutorials/images/gca_lissom_cf_center_010000_or.png,
doc/Tutorials/images/gca_lissom_cf_vertical_010000_or.png,
doc/Tutorials/images/gca_lissom_network_diagram.png,
doc/Tutorials/images/gca_lissom_or_pref_010000.png,
doc/Tutorials/images/gca_lissom_ormap_ft.png,
doc/Tutorials/images/gca_lissom_projection_010000.png,
doc/Tutorials/images/gca_natural_image_oo_or.png,
doc/Tutorials/index_text.php:
Updated GCA tutorial images, and changed text to match
* [r11185]
Makefile:
Made update setup.py's version number
* [r11184]
doc/Tutorials/gca_lissom_text.php,
doc/Tutorials/lissom_oo_or_text.php:
Made gca and lissom tutorials match
2010-07-10 ceball
* [r11183]
param/parameterized.py:
Reverted r11145: parameter repr() returned to original, and
full parameter declaration not used in commandline help.
Opened SF 3027874.
* [r11182]
setup.py:
Updated version number.
2010-07-10 jbednar
* [r11181]
doc/User_Manual/scripts_text.php:
Added link target
* [r11180]
doc/Tutorials/lissom_oo_or_text.php:
Added link to copying examples and encouragd people to read
the .ty file.
* [r11179]
doc/Developer_Manual/installation_text.php:
Suggested linking to topographica script
* [r11178]
doc/Downloads/win32notes_text.php:
Fixed space problem
* [r11177]
doc/Downloads/existingpython_text.php,
doc/Downloads/index_text.php,
doc/Home/index_text.php,
doc/News/index_text.php,
doc/Tutorials/lissom_oo_or_text.php,
doc/User_Manual/plotting_text.php:
Tweaked text for new release
* [r11176]
topo/misc/genexamples.py:
Added notes
2010-07-10 ceball
* [r11175]
topo/misc/genexamples.py:
Fixed typo.
2010-07-10 jbednar
* [r11174]
topo/command/basic.py:
Imported generate from misc.genexamples to simplify the
tutorials
2010-07-10 ceball
* [r11173]
topo/misc/genexamples.py:
Restored missing examples location.
* [r11172]
topo/misc/genexamples.py:
Fixed error in path.
* [r11171]
doc/Tutorials/lissom_oo_or_text.php:
Updated tutorial for path locations.
* [r11170]
doc/Developer_Manual/installation_text.php:
Updated space and time requirements for building.
* [r11169]
Makefile:
Made mktemp command compatible with Mac.
2010-07-10 jbednar
* [r11168]
Makefile,
doc/Home/news_text.php,
doc/News/index_text.php:
Updated release number
* [r11167]
README.txt:
Minor updates
* [r11166]
/trunk/topographica-win/common/setup.py,
/trunk/topographica-win/create_installer/topographica.iss:
Changed release to 0.9.7.
2010-07-10 ceball
* [r11165]
topo/misc/genexamples.py,
topo/tkgui/topoconsole.py:
Missed from previous commit.
* [r11164]
doc/Downloads/win32notes_text.php,
doc/Tutorials/lissom_oo_or_text.php,
doc/User_Manual/scripts_text.php:
Intermediate checkin: updating instructions for runing
topographica and generating saved networks.
* [r11163]
topo/tkgui/topoconsole.py:
Updated file locations.
* [r11162]
topo/misc/genexamples.py:
Added copy_examples() function.
* [r11161]
topo/__init__.py:
Print message about creating ~/topographica.
* [r11160]
topo/tests/test_script.py:
Fixed another path error.
* [r11159]
external/Makefile:
Patch to allow PIL to build on a Mac with Fink (or possibly
Macports) installed.
2010-07-10 jbednar
* [r11158]
doc/FAQ/index_text.php,
doc/Future_Work/index_text.php,
doc/Reference_Manual/index_text.php,
doc/User_Manual/overview_text.php,
doc/User_Manual/scripts_text.php:
Cleaned up docs
2010-07-09 ceball
* [r11157]
topo/tests/test_script.py:
Fixed paths.
2010-07-09 jbednar
* [r11156]
ChangeLog.txt:
Added recent revisions
* [r11155]
topo/pattern/audio.py,
topo/transferfn/optimized.py:
Added alerts
* [r11154]
topo/command/analysis.py:
Minor cleanup of organization
* [r11153]
examples/lissom_whisker_barrels.ty:
Minor cleanup
2010-07-09 ceball
* [r11152] Makefile,
topo/tests/__init__.py,
topo/tests/test_script.py:
Semi-permanent test data is stored in 'default output path'/tests
(created if necessary). Locations of test data being read and
saved are now printed. Updated test paths.
* [r11151] topo/misc/genexamples.py:
Made find_examples() and print_examples() functions.
2010-07-09 jbednar
* [r11150] examples/lissom_whisker_barrels.ty:
Further cleanup
2010-07-09 ceball
* [r11149] topo/tests/gca_lissom.ty_SPEEDDATA,
topo/tests/lissom_fsa.ty_SPEEDDATA:
Removed 'speed data', which should not be checked in (it is
machine-specific).
2010-07-09 jbednar
* [r11148] examples/lissom_whisker_barrels.ty:
Partly cleaned up to match conventions
* [r11147] examples/lissom_whisker_barrels.ty:
Partly cleaned up to match conventions
* [r11146] examples/lissom_whisker_barrels.ty:
Slightly corrected version from Stuart
2010-07-09 ceball
* [r11145] param/parameterized.py:
Added repr() for Parameter, so they are represented reasonably.
When displayed as part of help(parameterized), parameters'
default values, bounds, etc, will be shown.
* [r11144]
doc/Developer_Manual/imports_text.php,
param/parameterized.py,
topo/analysis/vision.py,
topo/command/basic.py,
topo/command/pylabplot.py,
topo/misc/commandline.py,
topo/tests/__init__.py,
topo/tkgui/topoconsole.py:
Added Command(ParameterizedFunction) class. Commands should
inherit from this class, so that exceptions when calling them can
be handled gracefully. Added mechanism to allow code that depends
on an optional module to create classes etc to be run, deferring
the ImportException to the point of use (allows user to learn
about possibilties even if he/she is missing an optional module).
Made Matplotlib be optional.
* [r11143] topo/misc/genexamples.py:
Print where the examples were found. Also some cleaning and
corrections.
2010-07-08 ceball
* [r11142]
doc/Developer_Manual/installation_text.php:
Minor tidying.
2010-07-07 ceball
* [r11139] topo/misc/genexamples.py:
Added missing path.
* [r11138] examples/run.py,
topo/misc/genexamples.py:
Moved examples/run.py to topo/misc/genexamples.py, and made it
work however Topographica was installed.
* [r11137] Makefile,
contrib/jaanalysis.py,
contrib/jacommands.py,
contrib/jsldefs.py,
contrib/modelfit.py,
contrib/surround_analysis.py,
doc/Developer_Manual/coding_text.php,
examples/lissom_or_movie.ty,
param/__init__.py,
param/tk.py,
topo/__init__.py,
topo/analysis/vision.py,
topo/command/analysis.py,
topo/command/basic.py,
topo/command/pylabplot.py,
topo/misc/__init__.py,
topo/misc/commandline.py,
topo/misc/filepath.py,
topo/misc/trace.py,
topo/pattern/audio.py,
topo/pattern/image.py,
topo/plotting/bitmap.py,
topo/plotting/plotfilesaver.py,
topo/plotting/plotgroup.py,
topo/tests/testCompositeSheetMasks.txt,
topo/tests/test_map_measurement.py,
topo/tests/test_script.py,
topo/tests/testbitmap.py,
topo/tests/testimage.py,
topo/tests/testplotfilesaver.py,
topo/tests/testsnapshots.py,
topo/tkgui/editor.py,
topo/tkgui/templateplotgrouppanel.py,
topo/tkgui/topoconsole.py:
Moved resolve_path, normalize_path, and Filename out of
topo.misc.filepath and into topo.param. Cleaned up 'special
paths' (application_path, output_path, package_path).
* [r11136] doc/Developer_Manual,
doc/Downloads,
doc/Downloads/git_text.php:
Updated ignore lists and added comment.
* [r11135] doc/Developer_Manual/index_text.php,
doc/Developer_Manual/installation_text.php,
doc/Developer_Manual/revisioncontrol_text.php,
doc/Downloads/bzr_text.php,
doc/Downloads/cvs_text.php,
doc/Downloads/existingpython_text.php,
doc/Downloads/git_text.php,
doc/Downloads/index_text.php,
doc/FAQ/index_text.php:
Reorganized download documentation. 'Basic' installation page is
supposed to be simpler, but with the chance for developers or
experienced python users to jump to more complex options.
2010-07-07 jbednar
* [r11134] topo/pattern/audio.py:
Tweaked error message
* [r11133] topo/pattern/audio.py:
Restored old error handling for when pyaudiolab is not present
* [r11132] doc/News/index_text.php:
Removed note
* [r11131] topo/command/analysis.py:
Cleaned up formatting
* [r11130] topo/pattern/basic.py:
Changed default min_frequency to a nonzero value to make it work
with log10, so that AudioFile can be instantiated with default
parameters
* [r11129] topo/base/projection.py:
Removed unused parameters
* [r11128] topo/tests/testaudio.py:
Brought Audio test up to date
* [r11127] topo/tkgui/editor.py,
topo/tkgui/topoconsole.py,
topo/transferfn/optimized.py:
Removed unused import
2010-07-06 ceball
* [r11126] setup.py:
setup.py now installs examples to
prefix/share/topographica/examples.
2010-07-05 ceball
* [r11125] examples/lissom.ty:
Corrected out-of-date name for individual normalization.
* [r11124] param/__init__.py:
Fixed bug where default value was a list.
2010-07-05 jbednar
* [r11123] topo/pattern/basic.py:
Cleaned up docs and comments. Marked PowerSpectrum and
Spectrogram abstract for now, as they are not useful in the GUI.
Provided a more useful default for PowerSpectrum.window_length.
Removed default value for the signal argument, as it is not
currently usable with default values anyway. Added sanity check
on window size.
* [r11122] topo/pattern/audio.py:
Made AudioFile and AudioFolder disappear entirely if pyaudiolab
is not available.
2010-07-05 ceball
* [r11121] contrib/basic.py,
contrib/lissom_rgb.ty,
examples/gca_lissom.ty,
examples/lissom.ty,
param/__init__.py,
topo/coordmapper/basic.py,
topo/pattern/image.py,
topo/plotting/plotgroup.py,
topo/tests/testEnumerationParameter.txt,
topo/tkgui/editor.py:
Simplified param.ObjectSelector by removing 'allow_None'.
param.ObjectSelector now restricts values to be among specified
objects by default (whereas if no objects are supplied, values
are not restricted).
2010-07-05 jbednar
* [r11120] doc/Makefile:
Enabled classtrees in reference manual
* [r11119] topo/command/basic.py:
Force non-XML pickles to be opened in binary mode on all
platforms
2010-07-05 ceball
* [r11118]
topo/tests/testEnumerationParameter.txt:
Updated test after removing param.Enumeration.
* [r11117] param/__init__.py:
Temporary fix to ObjectSelector: when check_value() is called as
the parameter is being created, and the default value fails the
check, attrib_name has not yet been set.
* [r11116] param/tk.py:
Added missing return statement, which had been preventing
topoconsole's 'refresh_plots_menu() from working under some
circumstances.
* [r11115] contrib/basic.py,
contrib/lissom_rgb.ty,
examples/gca_lissom.ty,
examples/lissom.ty,
param/__init__.py,
topo/coordmapper/basic.py,
topo/misc/legacy.py,
topo/pattern/basic.py,
topo/pattern/image.py,
topo/tkgui/editor.py:
Removed redundant param.Enumeration (replaced with
param.ObjectSelector); SF 2630230.
* [r11114] topo/command/pylabplot.py:
File missed from previous commit (svn does some strange
things...).
* [r11113] external/Makefile:
Made python depend on zlib, since we are now including zlib (and
Python skips building some modules if zlib is not available).
* [r11112] doc/FAQ/index_text.php,
doc/User_Manual/commandline_text.php,
doc/User_Manual/noise_text.php,
doc/User_Manual/overview_text.php,
doc/User_Manual/patterns_text.php,
doc/User_Manual/plotting_text.php,
doc/buildbot/bbanalysis.py,
topo/tests/reference/lissom_fsa_reference.ty:
Updated documentation after recent reorganizations.
* [r11111] examples/lissom.ty,
examples/run.py,
topo/analysis/vision.py,
topo/command/pylabplots.py,
topo/misc/legacy.py,
topo/sheet/slissom.py,
topo/tests/gui_tests.py,
topo/tests/test_map_measurement.py,
topo/tests/testimage.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/templateplotgrouppanel.py:
Renamed topo.command.pylabplots to topo.command.pylabplot (SF
2631254).
* [r11110] topo/misc/generatorsheet.py,
topo/sheet/basic.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/testpattern.py:
Moved definition of GeneratorSheet from topo.sheet to
topo.misc.generatorsheet so that it can be used independently of
importing topo.sheet library (partially addresses SF 2657028).
* [r11109] Makefile:
Fixed missing argument from recent change.
* [r11108] contrib/cc_lesi_final.ty,
contrib/cc_lesi_final_new.ty,
contrib/cc_lesi_oo_or.ty,
contrib/cc_lesi_oo_or_new.ty,
contrib/cc_lissom_oo_or_simple_rv.ty,
contrib/gc_alissom.ty,
contrib/gc_lissom_oo_or_homeostatic_new.ty,
contrib/jacommands.py,
contrib/jm_cc_lissom.ty,
contrib/lesi_whisker_barrels.ty,
contrib/lissom_oo_or_homeostatic.ty,
contrib/lissom_oo_or_homeostatic_tracked.ty,
contrib/lissom_oo_or_homeostatic_tracked_new.ty,
contrib/lissom_oo_or_noshrinking.ty,
contrib/modelfit.py,
contrib/sparse_connectivity_LESI.ty,
contrib/sparse_connectivity_model.ty,
contrib/species_cf_jitter.ty,
contrib/species_lat_jitter.ty,
contrib/species_pf_jitter.ty,
examples/gca_lissom.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty,
examples/sullivan_neurocomputing04.ty,
topo/misc/legacy.py,
topo/pattern/basic.py,
topo/transferfn/basic.py,
topo/transferfn/misc.py:
Moved TransferFns with complex dependencies out of
transferfn.basic into transferfn.misc. Fixes SF 2945499.
2010-07-04 ceball
* [r11107] examples/leaky_lissom_or.ty,
examples/lissom_whisker_barrels.ty,
examples/obermayer_pnas90.ty,
examples/saccade_demo.ty:
Examples missed from previous commit.
* [r11106] contrib/basic.py,
contrib/cc_lesi_final.ty,
contrib/cc_lesi_final_new.ty,
contrib/cc_lesi_oo_or.ty,
contrib/cc_lesi_oo_or_new.ty,
contrib/cc_lissom_oo_or_simple_rv.ty,
contrib/gc_alissom.ty,
contrib/gc_lissom_oo_or_homeostatic_new.ty,
contrib/helper.py,
contrib/jacommands.py,
contrib/jm_cc_lissom.ty,
contrib/jm_plotting.py,
contrib/lesi.ty,
contrib/lesi_judethesisversion.ty,
contrib/lesi_whisker_barrels.ty,
contrib/lgn_lateral.ty,
contrib/lissom_oo_or_homeostatic.ty,
contrib/lissom_oo_or_homeostatic_tracked.ty,
contrib/lissom_oo_or_homeostatic_tracked_new.ty,
contrib/lissom_oo_or_noshrinking.ty,
contrib/lissom_oo_or_noshrinking_latswitch.ty,
contrib/lissom_or_noshrinking.ty,
contrib/lissom_or_noshrinking_latswitch.ty,
contrib/modelfit.py,
contrib/sparse_connectivity_LESI.ty,
contrib/sparse_connectivity_model.ty,
contrib/species_cf_jitter.ty,
contrib/species_lat_jitter.ty,
contrib/species_pf_jitter.ty,
contrib/surround_analysis.py,
topo/analysis/vision.py,
topo/command/analysis.py,
topo/coordmapper/basic.py,
topo/misc/__init__.py,
topo/misc/legacy.py,
topo/misc/numbergenerator.py,
topo/pattern/basic.py,
topo/tests/gui_tests.py,
topo/tests/testCompositePatternGenerators.txt,
topo/tests/testDynamicParameter.txt,
topo/tests/testNumberParameter.txt,
topo/tests/test_pattern_present.txt,
topo/tests/testcfsom.py,
topo/tests/testgmpynumber.txt,
topo/tests/testparameterizedobject.py,
topo/tests/testpatterngenerator.py,
topo/transferfn/basic.py:
Removed topo.misc.numbergenerator (SF 2631258).
* [r11105] Makefile,
create_topographica_script.py:
When Topographica and its dependencies are built from source,
Python's site.USER_SITE is ignored by passing '-s' to Python.
Fixes sf.net bug 2965099.
* [r11104]
doc/Developer_Manual/revisioncontrol_text.php:
Fixed typo.
* [r11103] param/tk.py:
Added GUI support for Filename parameter. Fixes sf.net bugs
2970815 and 2725796.
2010-07-04 jbednar
* [r11102] doc/Home/news_text.php,
doc/News/index_text.php:
Brought news up to date
* [r11101] topo/pattern/basic.py:
Cleaned up whitespace
* [r11100] ChangeLog.txt:
Updated to r11099
2010-07-02 ceball
* [r11099] Makefile:
Fixed typo.
* [r11098] Makefile:
Should have been included in the previous commit.
* [r11097] Makefile:
Fixed quotation marks error.
* [r11096] Makefile:
Cleaned up deb generation, adding support for 'release' debs.
2010-07-01 ceball
* [r11095] debian/control:
Added python-dev dependency to Ubuntu package.
2010-06-30 ceball
* [r11094] doc/Forums/index_text.php,
doc/Forums/problems_text.php:
Removed out-of-date link to Windows Forum, and improved links to
bug reports and feature requests.
2010-06-29 ceball
* [r11093] /branches/kkudryavtsev_branch:
Removed Konstantin's aborted MPI branch (latest version is
http://gitorious.org/topographica, mpi2 branch).
* [r11092] doc/buildbot/master.cfg:
Doozy was upgraded to Ubuntu 10.04.
2010-06-23 ceball
* [r11091] doc/buildbot/master.cfg:
Added Lucid to list of debs to be uploaded.
2010-06-22 ceball
* [r11090] topo/base/simulation.py,
topo/command/basic.py,
topo/misc/picklemain.py:
Added ALERTs.
2010-06-20 ceball
* [r11089] doc/buildbot/master.cfg:
Added generation of Reference Manual to one builder (also
uploaded to buildbot.topographica.org/doc/).
2010-06-17 ceball
* [r11088] topo/base/functionfamily.py,
topo/responsefn/optimized.py:
Added comments.
* [r11087] external/zlib-1.2.5.tar.gz:
Identical version of zlib, but extracted and recompressed on a
linux machine (apparently there is some problem with gzip on
recent linux;
https://bugs.launchpad.net/ubuntu/+source/gzip/+bug/524366).
Fixes bug 3015804.
* [r11086] Makefile:
Fixed Ubuntu version name errors.
* [r11085] Makefile:
Fixed quoting mistake.
* [r11084] Makefile:
Ubuntu package moved to 'Lucid' (10.04 LTS). Not yet tested.
* [r11083]
doc/Developer_Manual/optimization_text.php:
Added comment.
* [r11082]
doc/Developer_Manual/optimization_text.php:
Updated optimization page and tried to make the example coherent.
* [r11081]
doc/Developer_Manual/optimization_text.php:
Fixed various typos and updated a link.
2010-06-13 ceball
* [r11080] external:
More to ignore.
2010-06-04 antolikjan
* [r11074] topo/analysis/vision.py:
small changes to complexity analysis
2010-06-03 jbednar
* [r11073] topo/transferfn/basic.py:
Made HomeostaticResponse picklable even before first use, so that
run_batch (which presents an initial test pattern) would work for
gca_lissom.ty
2010-05-28 jbednar
* [r11072] examples/gca_lissom.ty:
Added ALERT
* [r11071] topo/transferfn/basic.py:
Minor doc and formatting cleanup. Removed unused sheet_name
parameter
2010-05-27 ceball
* [r11070] topo/pattern/random.py:
Added ALERT.
* [r11069] examples/gca_lissom.ty,
topo/base/arrayutil.py,
topo/tests/gca_lissom.ty_DATA,
topo/transferfn/basic.py:
New version to match GCA paper. Intermediate checkin - some
documentation and minor changes to come.
* [r11068] external/Makefile,
external/zlib-1.2.5.tar.gz:
Added zlib (a not-always-available dependency of libpng).
* [r11067] external/Makefile,
external/m4-1.4.9.tar.gz:
Added M4 (a not-always-available dependency of GMP).
2010-05-18 ceball
* [r11059] topo/tests/utils.py:
Added note.
2010-05-09 ceball
* [r11042] doc/buildbot/master.cfg:
Added Ubuntu server buildslave (no X server installed).
2010-05-07 ceball
* [r11040]
topo/tests/testparametersframe_tk.py:
Change missed from r11038.
2010-05-06 ceball
* [r11039] Makefile,
external/Makefile:
Added variable 'GUI' to control whether or not to build tk and
related packages.
* [r11038] topo/tests/__init__.py,
topo/tests/testmatplotlib_tk.py,
topo/tests/testmatplotlibtk.py,
topo/tests/testparameterizedobject_tk.py,
topo/tests/testparametersframe.py,
topo/tests/testparametersframe_tk.py,
topo/tests/testtkparameterizedobject.py:
Test files that import Tkinter now have a name that ends in '_tk'
so that importing them can be avoided if tk is not available.
* [r11037] param/external.py:
Removed dependency of param.external on Tkinter.
2010-04-10 ceball
* [r11028] topo/command/basic.py:
When snapshot fails to load, show original error as well the one
raised after legacy support has been loaded.
2010-04-10 bilalkhancnsg
* [r11027] contrib/lissom_audio.ty,
topo/command/analysis.py:
Removed svn tagging accidentally left in command.analysis
* [r11021] sounds/sine_waves/00020hz.wav,
sounds/sine_waves/*.wav,
sounds/square_waves/*.wav,
Old sound files deleted.
* [r11020] sounds/complex/ReadMe.txt,
sounds/complex/daisy.wav,
sounds/sine_waves/ReadMe.txt,
sounds/sine_waves/normalized,
sounds/sine_waves/normalized/*_sine.wav,
sounds/sine_waves/raw,
sounds/sine_waves/raw/*_sine.wav,
sounds/square_waves/ReadMe.txt,
sounds/square_waves/normalized,
sounds/square_waves/normalized/*_square.wav,
sounds/square_waves/raw,
sounds/square_waves/raw/*_square.wav,
Added normalised versions of sine and square waves, updated
ReadMe files accordingly.
* [r11019] topo/analysis/featureresponses.py,
topo/pattern/audio.py,
topo/pattern/basic.py:
Minor spacing corrections.
* [r11018] topo/command/analysis.py:
Modified frequency map measurement to use Line instead of
RawRectangle, added a selectivity as well as preference output
* [r11017] topo/pattern/audio.py:
Added ability to multiplicatively amplify a frequency range.
Changed AudioFolder to employ AudioFile, previous concat of audio
signal behavior does not scale.
* [r11016] topo/pattern/audio.py:
Updated AudioFile to use new Spectrogram/PowerSpectrum structure.
AudioFile now outputs in dB.
* [r11015] topo/pattern/basic.py:
Segmented PowerSpectrum for cleaner inheritance, fixed window
overlap bug where sample window shrunk instead of overlapping.
Updated Spectrogram to use new PowerSpectrum
* [r11014] topo/pattern/basic.py:
Added precendence values for sigmoidedDoG pattern params, removed
eroneous sigmoid x offset from sigmoidedDog.
2010-04-09 bilalkhancnsg
* [r11013] topo/pattern/basic.py:
Added dedicted difference of gaussians pattern
* [r11012] topo/pattern/basic.py:
Replaced rectangular smoothing window with a simpler
implementation.
* [r11011] topo/pattern/basic.py:
Removed log gaussian and difference of log gaussians, they don't
work predictably
* [r11010] topo/misc/patternfn.py:
Removed log gaussian function, it doesnt work predictably
2010-04-05 ceball
* [r11009] topo/transferfn/basic.py:
Added comment about ActivityAveragingTF.
2010-03-31 ceball
* [r11008] topo/base/simulation.py:
Added enhancement note.
2010-03-26 ceball
* [r11007] topo/base/arrayutil.py:
No visible change (renamed internal variable).
* [r11006] topo/base/arrayutil.py:
Simplified array_argmax(). Should be no change to results.
* [r11005] topo/base/arrayutil.py:
Simplified clip_lower() and clip_upper(). New implementation is
presumably faster, but I have not verified that. Should be no
change to any results.
* [r11004] topo/pattern/image.py:
Simpified PatternSampler.__call__() (no longer any need to create
'empty' pattern sample in advance). Should be no change to
results.
* [r11003] topo/pattern/image.py:
Simplified image sampling (also gives vast speedup for presenting
images). Should cause no change to results.
2010-03-19 aplebe
* [r11002] topo/command/key_angles.png:
initial static image for angle prefernce map
* [r11001] topo/command/analysis.py:
Added preference map for angle between two segments,
independently from the
segment orientations, and related image with hue coding of the
angles
2010-03-18 ceball
* [r11000] COPYING.txt,
LICENSE.txt, README.txt,
debian/copyright,
doc/Team_Members/index_text.php,
setup.py,
topo/__init__.py:
Changed from GPL to BSD license. Changed copyright statement to
refer to 'Topographica Developers' (individuals are listed on the
Team Members page).
2010-03-15 jbednar
* [r10999] sounds/sine_waves/ReadMe.txt,
sounds/square_waves/ReadMe.txt:
Fixed missing newlines
2010-03-14 ceball
* [r10998] topo/misc/legacy.py:
Leagacy support for OneDPowerSpectrum->Spectrogram.
* [r10997] topo/misc/commandline.py:
Fixed typo (resulting in IPython being unavailable; sf.net bug
2969832).
2010-03-14 bilalkhancnsg
* [r10996] topo/pattern/audio.py:
Corrected typo.
* [r10995] contrib/lissom_audio.ty,
topo/pattern/audio.py:
Added ability for pattern.audio to load a folder of sound files
back to back, sample rates must be consistent between files. Can
also specify a length of gap to insert between each consecutive
sound file. Updated lissom_audio to use new audio load methods.
* [r10994] topo/pattern/basic.py:
Changed the 'fft results to sheet mapping' so it takes into
account ALL amplitudes when drawing on the sheet, this fixes the
previous erroneous behaviour where only a tiny subset of
amplitudes were employed which caused the bulk of information to
be lost, hence distinct bands were seen even on pure tone ffts.
It also fixes the problem where the sheet needed normalisation
before anything was visible. Lastly it fixes corollary discrete
frequency problems since the frequency is now continuous along
the sheet (the resolution is directly proportional to the density
of the sheet). As a consequence changed lin and logspace mapping
such that it now returns all possible frequency indices between
user specified min and max (unconstrained by sheet divisions). It
also now rounds properly (used to use floor to get int index
values). Made some commenting clearer.
* [r10993] topo/command/analysis.py:
Added class to measure frequency preference maps in mgb and a1.
2010-03-13 ceball
* [r10991] Makefile:
Fixed bug where system python was being used to create
topographica script, rather than Topographica's python. Changed
'other python' target to use the 'other python' to create the
topographica script.
2010-03-13 bilalkhancnsg
* [r10990] topo/pattern/basic.py:
Removed the overridden size parameter from LogGaussian.
* [r10989] topo/misc/patternfn.py:
Added a line to sigmoid to explain what is meant by axis.
* [r10987] sounds/sine_waves/ReadMe.txt,
sounds/square_waves/*.wav,
sounds/square_waves/ReadMe.txt:
Added ReadMe files to the sine and square wave sound file folders
explaining the format and how they were generated. Added square
waves for each frequency currently in sine waves.
* [r10985] topo/pattern/basic.py:
Defined a new kind of smoothing window, rectangular, which
actually means no smoothing is applied. Set this to be the
default.
* [r10984] topo/pattern/audio.py:
Changed class name from Spectrogram back to Audio (Audio now
inherits from Spectrogram). Removed all spectrogram specific
code, retaining only that relevant to the importing of audio
files.
* [r10983] topo/pattern/basic.py:
Moved Spectrogram from topo.pattern.audio to topo.pattern.basic.
Spectrogram inherits from new PowerSpectrum, so code content
remains largely unchanged, merely restructured to fit the new
PowerSpectrum. The changes that have occurred: Spectrogram now
pushes new data onto the left side, with older information on the
right, and frequencies go from lowest at the bottom to highest at
the top - this is how it should have been all along.
* [r10982] topo/pattern/basic.py:
Renamed class OneDPowerSpectrum to PowerSpectrum. Combined its
methods _generate_frequency_indices and _create_indices. Shifted
fft calculation into its own function for cleaner inheritance.
Commented everything, as a result found and corrected bug where
default window parameters were not being overridden in
PowerSpectrum.
* [r10981] topo/plotting/plotgroup.py:
Minor typo correction
2010-03-12 ceball
* [r10980] external/Makefile:
Removed unused variable (was for building via msys on Windows,
which does not work).
* [r10979] MANIFEST.in,
Makefile,
create_topographica_script.py,
setup.py:
Fixed some recently introduced bugs in setup.py-related commands.
2010-03-11 jbednar
* [r10978] topo/misc/patternfn.py:
Minor updates and fixes to messages and documentation
* [r10977] topo/misc/commandline.py,
topo/misc/patternfn.py:
Minor updates and fixes to messages and documentation
* [r10976] Makefile,
topo/__init__.py:
Minor updates and fixes to messages and documentation
2010-03-11 bilalkhancnsg
* [r10975] contrib/lissom_audio.ty,
topo/pattern/audio.py:
Modified paths in lissom audio to reflect new sounds folder
structure, modified pattern.audio to use a log space for
spctrogram.
* [r10974] topo/pattern/basic.py:
Added class for Sigmoided Difference of Log Gaussians.
* [r10973] sounds/multipletones,
sounds/puretones,
sounds/sine_waves,
sounds/sine_waves/*.wav,
sounds/square_waves,
sounds/square_waves/sqr-100Hz.wav,
sounds/square_waves/sqr-1kHz.wav:
Could not locate the original source to credit for the pure tone
sound files so i generated a new one of each. The waveforms of
mine appear to be a little cleaner also. Renamed pure tone to
sine wave and multiple tone to square wave as this is far
clearer.
* [r10972] topo/misc/patternfn.py,
topo/pattern/basic.py:
Added class for logarithmic gaussian pattern in
topo.pattern.basic. Added log_gaussian function to
topo.misc.patternfn
* [r10971] topo/misc/patternfn.py,
topo/pattern/audio.py,
topo/pattern/basic.py:
Removed spectrogram code from OneDPowerSpectrum, as the name
implies it should only return a one dimensional structure.
Spectrogram code is now in pattern/audio. Fft no longer employs a
smoothing function (i.e. it operates on a rectangualr window)
which produces slightly better results. Moved fft calculation to
its own method to make inheritence cleaner. In pattern/audio
renamed class Audio to class Spectrogram as this is really what
it should have been doing all along (and is now doing). Moved the
function aspect of the sigmoid pattern to topo/patternfn as this
is conforms to how every other class is doing it.
2010-03-10 jbednar
* [r10970]
doc/Developer_Manual/optimization_text.php:
Minor fixes
2010-03-10 ceball
* [r10969] setup.py:
Minor alterations to setup.py
* [r10968] setup.py:
Fixed typo.
* [r10967] setup.py:
Minor updates to docs.
* [r10966] setup.py:
Remove capitalization of 'topographica' package name.
* [r10965] setup.py:
Uncommented code that was disabled for testing (should have been
part of previous commit).
* [r10964] setup.py:
Support easy_install without depending on setuptools.
* [r10963] Makefile,
create_topographica_script.py:
Fixed bugs with svnversion variables.
2010-03-10 bilalkhancnsg
* [r10962] sounds/complex,
sounds/complex/daisy.wav,
sounds/daisy.wav,
sounds/multipletones,
sounds/multipletones/sqr-100Hz.wav,
sounds/multipletones/sqr-1kHz.wav,
sounds/puretones,
sounds/puretones/*.wav,
sounds/sqr-1kHz.wav,
sounds/test.wav:
Added 20 sound files of pure tones of ascending frequency ranging
from 20Hz to 20000Hz to a folder named 'puretones', added 2 sound
files of square waves (test of multiple frequencies) to the
'multipletones' folder, and finally, created a folder named
'complex' to house the spectral and termporally variant rich test
sound (daisy).
2010-03-07 ceball
* [r10961] setup.py:
Added description for pypi page.
* [r10960] MANIFEST.in,
Makefile, setup.py:
More minor packaging cleanup.
* [r10959] Makefile,
setup.py:
Packaging cleanup.
* [r10958] topo/__init__.py,
topo/misc/commandline.py,
topo/tests/__init__.py:
Allow Topographica to run without gmpy or fixedpoint.
* [r10957] external/Makefile:
fixedpoint-uninstall was leaving files behind.
* [r10956] MANIFEST.in,
Makefile,
create_topographica_script.py,
setup.py:
Simplified distutils pypi commands.
2010-03-06 ceball
* [r10955] topo/misc/commandline.py:
Made IPython be optional.
* [r10954] MANIFEST.in:
Added missing file.
* [r10953] MANIFEST.in,
Makefile, _setup.py,
external/Makefile,
setup.py, setup_app.py,
setup_exe.py,
setup_ez.py:
Focus on Python's distutils only: drop setuptools, easy_install,
py2exe, and py2app (all of which are incompatible with code in
Topographica or at least one of its dependencies in various
ways). Also, removed incomplete support for building via MSYS on
Windows.
2010-03-03 bilalkhancnsg
* [r10951] sounds/daisy.wav:
Added a new test sound: the song Daisy Bell, this allows us to
see how the audio pattern generator holds up to a more complex
spectrogram. (Daisy Bell in tribute to the IBM 704 which in 1962
became the first ever computer to 'sing')
* [r10950] topo/command/analysis.py:
Modified the _feature_list method of class measure_rfs such that
it no longer assumes a square sheet
2010-03-02 bilalkhancnsg
* [r10949] topo/pattern/basic.py:
Commented out Gamma for now, it't not presently needed and
requires more time to fix than i can currently give it.
2010-03-02 jbednar
* [r10948] topo/pattern/basic.py:
Cleaned up docstrings
2010-03-02 bilalkhancnsg
* [r10947] topo/command/basic.py:
Added an extra section to the documentation of method
pattern_present explaining the back arrow history mechanism
availible in the gui to view just presented patterns. Removed the
time.sleep command added to pattern_present which attempted to
achieve similar functionality.
* [r10946] topo/analysis/featureresponses.py:
Reverted class Feature to its previous state, the modification of
parameter 'range' was duplication of the functionality provided
by the parameter 'value'.
* [r10944] topo/pattern/basic.py:
Changed the name of GammaDistribution to Gamma. Gamma now
utilises the SciPy implementation for the generalised gamma
distribution. Accordingly much improved the documentation for
Gamma.
* [r10943] topo/misc/patternfn.py:
Removed my implementations of gamma and factorial in favour of
those from scipy, the scipy versions are one liners so they're
now placed directly in topo.pattern.basic where they're utilised.
2010-03-01 jbednar
* [r10942] topo/misc/patternfn.py,
topo/pattern/basic.py:
Cleaned up docstrings and comments
2010-03-01 bilalkhancnsg
* [r10941] topo/command/analysis.py,
topo/command/basic.py,
topo/misc/patternfn.py:
CORRECTION TO REVISION 10936: misunderstood the CEBENHANCEMENT
about visualising motion, changed the code to reflect this
* [r10939] topo/pattern/basic.py:
Added a Gamma Distribution class to utilise the gamma function
from topo.misc.patternfn. Changed the default x position of
SigmoidedDoG from -1.5 to 0. Changed the gaussians such that
modifying the global size parameter multiplies the individual
size of both.
* [r10938] topo/misc/patternfn.py:
Added new definitions for gamma and recursive factorial (which is
employed by gamma). Note that gamma is one dimensional.
* [r10937] topo/misc/patternfn.py:
Added new definitions for gamma and recursive factorial (which is
employed by gamma). Note that gamma is one dimensional.
* [r10936] topo/command/basic.py:
Added ability to slow down presentation of patterns in
pattern_present so as to be able to visualise them
* [r10935] topo/analysis/featureresponses.py:
Added ability for the class FeatureMaps to accept single values
for its range
2010-02-25 jbednar
* [r10934] topo/coordmapper/basic.py:
Fixed ConstantMapper parameter bounds and documentation
2010-02-23 jbednar
* [r10933] examples/obermayer_pnas90.ty:
Removed outdated reference to topo.param that prevented it from
being run
2010-02-23 ceball
* [r10932] external/Cython-0.12.1.tar.gz,
external/Cython-0.9.8.1.1.tar.gz,
external/Makefile:
Upgraded Cython to 0.12.1.
2010-02-21 ceball
* [r10929] debian/install.ex,
debian/menu.ex,
debian/topographica.desktop:
(Ubuntu package) Added files for creating menu entry in the
future - currently unused.
* [r10928] Makefile:
(Ubuntu package) Add tk-tile as dependency for Ubuntu 8.04.
2010-02-18 ceball
* [r10926] doc/buildbot/master.cfg:
(Buildbot) Fixed another typo.
* [r10925] doc/buildbot/master.cfg:
(buildbot) Fixed typos.
2010-02-17 ceball
* [r10924] doc/buildbot/master.cfg:
(Buildbot) Fixed package uploading.
2010-02-16 ceball
* [r10923] Makefile:
(Ubuntu package) Fixed path error for rpm creation.
* [r10922] doc/buildbot/master.cfg:
Added deb and rpm generation.
2010-02-16 antolikjan
* [r10921] topo/command/pylabplots.py:
improved plotting of modulation ratios
* [r10920] topo/analysis/vision.py:
improved plotting of modulation ratio histograms
2010-02-16 ceball
* [r10919] Makefile:
(Ubuntu package) Renamed a target.
* [r10918] Makefile:
(Ubuntu package) Removed 'PRERELEASE' variable.
2010-02-15 ceball
* [r10917] Makefile:
(Ubuntu package) debuild source after binaries, so checksums
match for subsequent dput.
* [r10916] Makefile:
(Ubuntu package) Restored hardy deb.
* [r10915] debian/pyversions:
(Ubuntu package) File removed from previous commit.
* [r10914] debian/control:
(Ubuntu package) Fix python dependency confusion.
* [r10913] Makefile:
Added some notes.
* [r10912] Makefile:
Fixed typo.
* [r10911] Makefile:
(Ubuntu package) Commented out Hardy package building.
* [r10910] Makefile,
doc/buildbot/dot-dput.cf:
(Ubuntu package) Cleanup plus generation of rpm files.
2010-02-13 ceball
* [r10909] debian/control:
(Ubuntu package) Attempt to allow building on Hardy (LTS).
* [r10908] Makefile:
(Ubuntu package) Continued attempt to upload debs for multiple
versions of Ubuntu.
* [r10907] Makefile:
(Ubuntu package) Attempt to upload debs for multiple versions of
Ubuntu.
* [r10906] Makefile:
(Ubuntu package) Automated process now working for Ubuntu Jaunty
target.
* [r10905] Makefile:
(Ubuntu package) Attempt to create Ubuntu Jaunty deb.
* [r10904] Makefile:
(Ubuntu package) Continued attempting to get automatic PPA upload
to work.
* [r10903] Makefile:
(Ubuntu package) Testing PPA.
* [r10902] Makefile:
(Ubuntu package) Simplified the commands.
* [r10901] Makefile:
(Ubuntu package) Create valid changelog.
* [r10900] Makefile:
(Ubuntu package) Fixed mistake in previous commit.
* [r10899] Makefile,
debian/changelog:
(Ubuntu package) Continued attempting to automate deb creation.
* [r10898] debian/control,
debian/rules:
Reverted earlier confused change of pycentral to pysupport.
2010-02-12 ceball
* [r10897] debian/pyversions:
(Ubuntu packaging) Fixed syntax error.
* [r10896] Makefile,
debian/pyversions:
More deb packaging updates.
* [r10895] Makefile,
debian/control:
More updates for Karmic Koala build machine.
* [r10894] create_topographica_script.py:
Fixed typo in previous commit.
* [r10893] Makefile,
create_topographica_script.py:
Began implementing deb creation via Makefile.
* [r10892] debian/compat,
debian/rules:
Updates for Ubuntu Karmic Koala (as the packaging machine).
2010-02-10 jbednar
* [r10891] contrib/lissom_audio.ty,
topo/pattern/audio.py,
topo/pattern/basic.py:
Cleaned up formatting and docstrings to match Topographica
conventions. Should be no change in behavior apart from the
arrangement in the Model Editor
2010-02-10 bilalkhancnsg
* [r10890] contrib/lissom_audio.ty,
topo/pattern/basic.py:
SigmoidedDoG now with doc info, which lissom audio now employs as
its weights generator
* [r10889] contrib/lissom_audio.ty,
topo/pattern/basic.py:
lissom audio sans happyface, and SigmoidedDoG pattern working
* [r10888] topo/pattern/basic.py:
SigmoidedDoGs changed to SigmoidedDoG since it now only employs
one diff of gaussians
2010-02-09 ceball
* [r10887]
topo/tests/reference/lissom_oo_or_reference.ty:
Change missed from previous commit.
* [r10886]
topo/tests/reference/lissom_oo_dr_reference.ty,
topo/tests/reference/lissom_or_reference.ty,
topo/tests/reference/topo_or_defs.py:
Changes missed when converting CFProjection's n_units() method to
an attribute.
2010-02-05 ceball
* [r10885] doc/Downloads/git_text.php:
Some updates about sharing work.
2010-02-04 ceball
* [r10884] external:
Updated ignore list.
2010-02-04 jbednar
* [r10883]
doc/Developer_Manual/revisioncontrol_text.php:
Fixed apparent typo
2010-02-04 ceball
* [r10882] external/Makefile:
Added Python 2.5 directories to clean and uninstall.
* [r10881] doc/buildbot/index.html,
doc/buildbot/master.cfg:
Made current svn documentation available from buildbot.
2010-02-03 bilalkhancnsg
* [r10880] topo/pattern/basic.py:
Updated doc info for Sigmoid and SigmoidedDoGs, changed param
names in SigmoidedDoGs to be generic and also changed soft and
hard bounds to reasonable values
* [r10879] contrib/lissom_audio.ty,
topo/misc/patternfn.py,
topo/pattern/basic.py:
Added new pattern (Sigmoid) for generating sigmoids along the
horizontal, and added a new pattern (SigmoidedDoGs) consisting of
two differences of gaussians summed and subsequently multiplied
by a sigmoid
2010-02-02 ceball
* [r10878] doc/buildbot/master.cfg:
New Mac buildslave does not yet have necessary tools installed to
build docs, so stop warning (it's not a failure of docs to build
on Mac). No slow-tests on Windows, because msys shell interacts
badly with buildbot, giving false failures.
* [r10877] doc/buildbot/index.html:
Updated links.
2010-02-01 ceball
* [r10876] param/tk.py:
Restored compatibility setting for Tk versions less than 8.5 (for
Windows).
* [r10875] external/Makefile:
Try to address mysterious, intermittent buildbot error by
avoiding pipe in matplotlib unpacking.
* [r10874] topo/misc/legacy.py:
Added legacy support for CFProjection's n_units() method being
removed (r10871).
2010-01-31 ceball
* [r10873] topo/projection/basic.py:
Fixed bug in n_bytes() (hadn't been updated after flattening cfs
list.
* [r10872] topo/base/cf.py,
topo/base/projection.py:
Minor changes to comments.
* [r10871] topo/base/cf.py,
topo/sheet/lissom.py:
Made CFProjection's n_units() method into an attribute, since the
number of units is fixed (should make distribution easier).
ResizableCFProjection's n_units is updated when the bounds are
changed.
* [r10870] topo/base/cf.py:
CFProjection.n_units() uses the mask template to count the number
of units, rather than the mask of the central CF. Should be no
change to existing simulations.
* [r10869] topo/projection/basic.py:
Fixed bug where incorrect mask was being stored on shared cf;
this resulted in n_units() returning the wrong value (but this
had no effect on existing simulations because learning is not
implemented for shared weight CFPs).
* [r10868] topo/base/cf.py:
Removed proj from CFIter.
* [r10867] topo/base/cf.py,
topo/learningfn/optimized.py,
topo/learningfn/projfn.py,
topo/responsefn/optimized.py,
topo/responsefn/projfn.py,
topo/transferfn/optimized.py:
Use flatcfs and flattened activity array (see svn r10838). Use
cf_type stored in CFIter rather than from projection.
* [r10866] topo/base/cf.py,
topo/learningfn/optimized.py,
topo/learningfn/projfn.py:
CFPLearningFn.constant_sum_connection_rate() takes n_units
directly, rather than proj then accessing proj.n_units(), so that
CFIter only needs to store n_units.
* [r10865] topo/base/cf.py:
Made CFIter store activity, flatcfs, and mask (in preparation for
it no longer storing the projection).
* [r10864] topo/base/cf.py:
Fixed CFPLearningFn call signature.
2010-01-28 ceball
* [r10862] Makefile:
Pylint warnings should not appear as errors until we have
eliminated all of the invalid warnings.
2010-01-27 ceball
* [r10861] _setup.py,
external/Makefile,
external/Python-2.5.1.tgz,
external/Python-2.6.4.tgz,
external/Python_64bit_pickle.diff,
external/Tkinter_bool_none.diff,
external/freetype-2.3.9.tar.gz,
external/idle_tk8.5.patch,
external/libpng-1.2.40.tar.gz,
external/numpy-1.2.1.tar.gz,
external/numpy-1.3.0.tar.gz,
setup_app.py,
setup_exe.py,
setup_ez.py:
Upgraded to Python 2.6. Includes: upgrade to numpy 1.3 (necessary
for Windows and Mac); freetype and libpng so they are no longer
dependencies that must be installed from elsewhere.
(I.e. merge branch 'python26' from ceball_fiver.)
2010-01-16 bilalkhancnsg
* [r10859] contrib/lissom_audio.ty,
topo/pattern/audio.py,
topo/pattern/basic.py:
the audio pattern generator now populates a sheet with a
spectrogram, new signal transforms are pushed to the right,
oldest fall off the left, size of history is dictated by sheet
size
2010-01-15 aplebe
* [r10858] topo/transferfn/optimized.py:
Added a check on the cumulative weight value in
CFPOF_DivisiveNormalizeL1_opt
and CFPOF_DivisiveNormalizeL1, to avoid dividing by 0 - it is
especially
deceitful for the optimized version, because no error is issued
and "NaN"
non-value are stored in the weights
2010-01-14 jbednar
* [r10857]
topo/tests/lissom_oo_or_t000100.00_Size_Tuning.data:
Checked in new data for buildbot to pass; must be verified by J.
Antolik
* [r10856] doc/Home/index_text.php:
Removed outdated qualifier
* [r10855] doc/Home/news_text.php,
doc/News/index_text.php:
Cleaned up news for publishing
* [r10854] topo/base/simulation.py:
Added alert
* [r10853] topo/pattern/audio.py:
Clarified how Audio differs from OneDPowerSpectrum
2010-01-13 jbednar
* [r10852] doc/News/index_text.php:
First pass at list of recent post-0.9.6 features
* [r10851] ChangeLog.txt:
Brought up to date as of 9 Jan 2010
2010-01-11 bilalkhancnsg
* [r10850] examples/run.py:
Commented a path check in examples/run.py when debugging on my
system, accidently uploaded it in that state. Now back to as it
should be
2010-01-10 bilalkhancnsg
* [r10849] contrib/lissom_audio.ty,
examples/run.py,
sounds/sqr-1kHz.wav:
1. Connected Cochlea to MGBv with correct edge adjustments,
connected MGBv to A1 with correct edge adjustments, put in
lateral excitory and inhibitory connections in A1 as in V1, not
sure about these entirely at this stage. 2. Sounds can now be
placed in the sounds folder and loaded into the file, currently
there is a 1kHz square wave and a small drumbeat in there. 3.
Cochlea sheet gets populated with the frequency bands (fourier
analysis), these are passed up to the MGBv and from there to A1 -
i see the patterns of activity pass up but am not sure its 100%
correct at this stage (not quite sure how it should look)
2010-01-09 bilalkhancnsg
2010-01-09 jbednar
* [r10846] ChangeLog.txt:
Brought up to date as of 11 Dec 2009
* [r10845] topo/base/cf.py:
Upgraded alert
2010-01-05 antolikjan
* [r10841] topo/base/cf.py:
bug correction
2010-01-05 aplebe
* [r10840] topo/pattern/basic.py:
Minor modification of GaussiansCorner: two additional parameters,
the internal
angle and the control on the intersection points of the two
Gaussians. Now it is
possible to combina e cross shape, as before, and also a corner
shape, with
arbitrary angle. The dafault values of the new parameters
preserve
the behaviour of the previous version of the pattern.
2009-12-29 ceball
* [r10838] topo/base/cf.py,
topo/base/projection.py,
topo/learningfn/optimized.py,
topo/learningfn/projfn.py,
topo/learningfn/som.py,
topo/misc/legacy.py,
topo/responsefn/optimized.py,
topo/sheet/basic.py,
topo/sheet/optimized.py,
topo/tests/testcf.py,
topo/transferfn/optimized.py:
Added flatcfs and made CFIter use it. Adjusted
CFPOF_DivisiveNormalizeL1_opt, CFPLF_Hebbian_opt,
CFPRF_DotProduct_opt, and optimized joint normalization to use
flatcfs. Removed CFProjection's _cfs attribute.
* [r10837] topo/base/cf.py,
topo/base/projection.py:
Removed MaskedCFIter. CFIter is now MaskedCFIter, unless
ignore_sheet_mask is True. Simplified CFIter.
* [r10836] topo/base/cf.py,
topo/base/projection.py,
topo/learningfn/optimized.py,
topo/sheet/optimized.py,
topo/transferfn/optimized.py:
CFPOF_DivisiveNormalizeL1_opt, CFPLF_Hebbian_opt, and optimized
joint normalization now respect the sheet mask.
* [r10835] topo/base/cf.py,
topo/base/projection.py,
topo/projection/basic.py,
topo/sheet/basic.py,
topo/sheet/lissom.py,
topo/sheet/optimized.py,
topo/transferfn/optimized.py:
Moved 'activity masking' into CFIter and made active_units_mask
be a switch for apply_learn_output_fns and weight normalization.
* [r10834] topo/base/cf.py,
topo/learningfn/optimized.py,
topo/projection/basic.py,
topo/sheet/basic.py,
topo/sheet/optimized.py,
topo/transferfn/optimized.py:
Tried to document the 'activity mask' used to decide whether or
not to apply weights_output_fns. Added ALERTs about sheet mask
being ignored by several functions.
2009-12-11 antolikjan
* [r10831] topo/command/pylabplots.py:
added frequency to features of orientation contrast measurement
2009-12-04 ceball
* [r10830] topo/misc/util.py:
Added to comment.
2009-12-03 ceball
* [r10827] contrib/parameter_analysis,
contrib/parameter_analysis.cfg,
doc/User_Manual/batch_text.php:
Added 'parameter_analysis' script for generating simple reports
from collections of batch runs.
2009-12-02 ceball
* [r10826] contrib/parameter_search:
parameter_search prints where output will go.
* [r10825] contrib/parameter_search,
contrib/parameter_search.cfg:
Updated parameter_search to allow it to be used simultaneously
from the same directory by different machines (by distinguishing
the names of generated scripts; this makes it clearer anyway).
2009-11-30 ceball
* [r10822] topo/command/basic.py:
Silently ignore parameter names in param_formatter.map that are
not present among the actual params.
* [r10821] topo/command/basic.py:
Added ALERT.
* [r10820] topo/misc/picklemain.py:
When pickling main, skip items beginning with an underscore.
Unlikely to have any effect on existing code.
* [r10819] topo/misc/legacy.py:
Added missing import.
2009-11-30 jbednar
* [r10818] doc/Downloads/index_text.php:
Added m4 to ubuntu prerequisites
* [r10817] topo/pattern/basic.py:
Minor fixes to comments
2009-11-30 ceball
* [r10816] topo/pattern/basic.py:
Added comment.
* [r10815] topo/pattern/audio.py,
topo/pattern/basic.py:
Removed warnings.
* [r10814] topo/pattern/audio.py,
topo/pattern/basic.py:
Moved OneDPowerSpectrum into topo/pattern/basic.py.
* [r10813] topo/pattern/audio.py:
Finished implementing Audio and OneDPowerSpectrum pattern
generators.
2009-11-29 ceball
* [r10812] topo/command/basic.py:
Allow specification of order for params in run_batch's directory
name.
2009-11-28 antolikjan
* [r10810] topo/command/pylabplots.py:
bug correction in orientation contrast
* [r10809] topo/command/pylabplots.py:
bug correction in orientation contrast
* [r10807] topo/command/pylabplots.py:
minor changes to orientation contrast analysis
* [r10806] topo/command/pylabplots.py:
made orientation center an explicit parameter in orientation
contrast analysis
2009-11-27 ceball
* [r10805] doc/Downloads/git_text.php:
Added git admin info for sf.net.
2009-11-26 ceball
* [r10804] topo/base/cf.py:
Fixed bug in change_bounds() introduced in r10792.
* [r10803] topo/command/basic.py:
Fixed saving of script parameters that were specified to
run_batch().
* [r10802] topo/command/basic.py:
Allow run_batch's directory name to use abbreviated parameter
names.
* [r10801] topo/command/basic.py:
Made order_params_by_name() actually sort the names.
* [r10800] topo/command/basic.py:
Added dirname_params_filter to run_batch(), allowing control over
how parameters will appear in the output directory name.
* [r10799] topo/command/basic.py:
Added notes.
* [r10798] param/parameterized.py,
topo/tests/testparameterizedobject.py:
Allow ParameterizedFunction.instance()s to pickle.
* [r10797]
topo/tests/testparameterizedobject.py:
Repeat ParameterizedFunction tests on an instance (previously,
only the class was tested).
* [r10796]
topo/tests/testparameterizedobject.py:
Minor alteration to test to make it easier to subclass.
2009-11-24 ceball
* [r10794] topo/pattern/audio.py:
Cleaned up formatting (no other change).
2009-11-24 ceball
* [r10792] topo/base/cf.py,
topo/projection/basic.py:
Allow ConnectionFields to be instantiated easily by fixing
default arguments to __init__.
2009-11-21 antolikjan
* [r10790] topo/transferfn/basic.py:
corrected bug in HalfRectify
* [r10789] topo/transferfn/basic.py:
added gain to HalfRectify
2009-11-21 ceball
* [r10787] doc/Downloads/git_text.php:
Added missing 'fetch' command and some formatting to git
documentation.
2009-11-20 ceball
* [r10786] Makefile,
_setup.py,
create_topographica_script.py,
setup.py, setup_exe.py,
setup_ez.py:
Made a python script to create the topographica script. Now there
is only one routine to create the topographica script (except
that topographica-win also needs to be adjusted to use the new
script). Added 'topographica-other-python' target to Makefile,
for creating the topographica script when using some external
python interpreter.
* [r10785] doc/Downloads/git_text.php:
Added more git documentation.
2009-11-18 ceball
* [r10782] external/Makefile,
external/weave_keyerror.patch:
Fix KeyError problem with weave and Python 2.6
(http://projects.scipy.org/scipy/ticket/855).
* [r10781] param/tk.py:
Fixed multiple 'ignored' Exception RuntimeErrors when starting
the gui with Python 2.6.
2009-11-18 KKudryavtsev
* [r10780] /branches/kkudryavtsev_branch/topographica/mpidemo*:
Created branch for MPI work
2009-11-17 KKudryavtsev
* [r10779] /branches/kkudryavtsev_branch:
* [r10778]
contrib/cc_lissom_oo_or_simple_rv.ty,
contrib/gc_lissom_oo_or_homeostatic_new.ty,
contrib/lgn_lateral.ty,
contrib/sparse_connectivity_model.ty,
examples/lissom_oo_or.ty,
examples/tiny.ty,
external/Makefile,
mpidemo, setup_ez.py:
* [r10777] examples/lissom_oo_or.ty,
examples/tiny.ty,
external/Makefile,
mpidemo*:
Mistakenly added files to trunk instead of branch
2009-11-17 ceball
* [r10775] topo/command/basic.py:
Added option to run_batch() for saving global_params to a pickle
for future inspection.
* [r10774] topo/command/basic.py:
Added more info for git vc info in run_batch().
* [r10773] topo/command/basic.py:
Added more information about the version of Topographica used for
batch runs.
* [r10772] topo/command/basic.py:
Added information about host to batch output.
2009-11-16 ceball
* [r10771] Makefile:
Restored xvfb-run's -a option, accidentally removed in a previous
commit.
* [r10770] Makefile:
Restored warning if xvfb-run not found.
* [r10769] Makefile:
Tried to simplify detection of xvfb-run.
* [r10768] external:
Updated ignore list.
* [r10767] external/libsndfile-1.0.20.tar.gz,
external/scikits.audiolab-0.10.2.tar.gz,
external/setuptools-0.6c11.tar.gz,
sounds/test.wav:
Fixed svn:mime-type on recently added files.
* [r10766] Makefile:
Try to use xvfb-run for tests.
* [r10765] external/Makefile,
sounds, sounds/test.wav,
topo/pattern/audio.py,
topo/tests/__init__.py,
topo/tests/testaudio.py:
Added sounds/ directory, and test sound from scikits.audiolab.
Added test file for audio.py.
* [r10764] external/Makefile,
topo/pattern/audio.py:
Updated to new API for scikits.audiolab.
* [r10763] external/Makefile,
external/libsndfile-1.0.17.tar.gz,
external/libsndfile-1.0.20.tar.gz,
external/pyaudiolab-0.6.6.tar.gz,
external/scikits.audiolab-0.10.2.tar.gz,
external/setuptools-0.6c11.tar.gz,
topo/pattern/audio.py:
Updated topo.pattern.audio and its dependencies to the stage that
at least the Audio PatternGenerator can be called without error.
2009-11-12 jbednar
* [r10756] topo/base/cf.py,
topo/command/analysis.py,
topo/plotting/plot.py,
topo/plotting/plotgroup.py:
Fix Projection Activity plots to show the correct label for the
source of the projection
2009-11-12 ceball
* [r10752] topo/tests/testplotfilesaver.py:
Minor change to error message.
* [r10751] topo/tests/testplotfilesaver.py:
Improved error message.
2009-11-10 ceball
* [r10747] topo/command/basic.py:
Extended VC info to include 'svn info' and 'svn status' (or
equivalents).
* [r10746] topo/command/basic.py:
Fixed longstanding bug where 'Differences from' prefix could be
printed at the end of the diff file.
* [r10745] topo/command/basic.py:
Added support for git and bzr version control systems when
recording diffs.
2009-11-07 ceball
* [r10741] param/tk.py:
GUI does not suspend when there is an error.
* [r10740] topo/command/analysis.py:
Fix for SF.net 2872925: no more 'Projection Activity errors for
mousing'.
2009-11-04 kkudryavtsev
* [r10738]
doc/Developer_Manual/optimization_text.php:
New version of optimisation page from Developers Manual
2009-11-04 ceball
* [r10737] examples/lissom.ty:
Added notes about some known problems with the CR model in this
file (fixed in other versions).
2009-11-04 ceball
* [r10734] external/Makefile:
Updated note about MPI on DICE, and updated OpenMPI uninstall.
* [r10733] param:
Added files to ignore.
* [r10732] external:
More to ignore.
* [r10731]
external/PyFlakes-divmod_r17780.tar.gz:
Fixed error in directory name.
* [r10730] external/Makefile,
external/PyFlakes-divmod_r17780.tar.gz,
external/pyflakes-0.3.0.tar.gz:
Updated PyFlakes to a recent SVN version.
2009-11-03 ceball
* [r10725] external/Makefile,
external/pyflakes-0.3.0.tar.gz:
Added pyflakes (another tool like Lint).
* [r10724] external/Makefile:
Added to comment about MPI on Eddie.
* [r10723] external/Makefile,
external/Twisted-8.2.0.tar.gz,
external/foolscap-0.4.2.tar.gz,
external/ipython-0.10.tar.gz,
external/ipython-0.8.4.tar.gz,
external/pyOpenSSL-0.9.tar.gz,
external/zope.interface-3.3.0.tar.gz:
Upgraded to IPython 0.10. Added optional dependencies for
parallel IPython. Reverted r10721 (environment variables removed
in that commit are required under Ubuntu, at least). Added
various missing items from the 'clean' and 'uninstall' lists.
* [r10722] external/Makefile:
Minor alterations to comments.
* [r10721] external/Makefile:
Minor simplification.
* [r10720] external/Makefile:
Fixed typo.
2009-11-03 ceball
* [r10717] external/Makefile:
Fixed system MPI build of mpi4py, and added notes.
2009-11-03 ceball
* [r10715] external/Makefile,
external/mpi4py-1.1.0.tar.gz,
external/openmpi-1.3.3.tar.gz:
'make -C external mpi4py' seems to work on DICE and Ubuntu. Also
added a second mpi4py section, for using the system MPI (which I
couldn't get to work on DICE).
2009-11-02 ceball
* [r10710] external/Makefile:
Added sections for OpenMPI and mpi4py (but haven't uploaded
binaries).
2009-11-01 jbednar
* [r10702] topo/sheet/basic.py:
Fixed typo in debug message
2009-11-01 ceball
* [r10701] doc/buildbot/master.cfg:
Buildslave 'sunny' upgraded to latest Ubuntu (9.10).
* [r10700] topo/tkgui/topoconsole.py:
Allow printing of full traceback from errors that occur during
gui callbacks.
2009-11-01 ceball
* [r10698] param/tk.py,
topo/tests/testparametersframe.py,
topo/tests/testtkparameterizedobject.py,
topo/tkgui/__init__.py:
Allow param.tk to work with an external Tkinter.Tk instance.
2009-10-31 ceball
* [r10694] external/Makefile,
external/ipythonTk.diff,
external/ipythonTk.tar.gz,
external/ipython_view.diff,
topo/misc/commandline.py,
topo/tkgui/__init__.py,
topo/tkgui/topoconsole.py:
Removed IPythonTk-related code (which was all experimental: there
is too much to do to make it complete).
* [r10693] contrib/complex_shapes_analysis.py,
contrib/expressionparam.py,
contrib/jm_plotting.py,
contrib/jsldefs.py,
contrib/rgbimages.py:
Changes in contrib/ missed when moving topo.param to param.
2009-10-29 ceball
* [r10687] doc/Future_Work/current_text.php:
Cleaned up by moving some tasks to trackers and reorganizing some
of the comments. Added my non-phd-related Topographica tasks
(commented out, until they find a better home).
* [r10686] doc/Downloads/git_text.php,
doc/Future_Work/current_text.php:
Moved some git notes to the git document; deleted obsolete notes.
* [r10685] doc/Forums/index_text.php:
Replaced tracker links with ones that show only open items, and
have the items ordered by priority.
2009-10-28 ceball
* [r10675] doc/Downloads/git_text.php:
Documented how to handle rebasing when the remote repository is
shared.
* [r10674] doc/FAQ/index_text.php:
Removed platform-specific FAQ. Only contained one entry (for
Mac), and that was out of date.
* [r10673] Makefile:
Added to notes.
* [r10672] topo/__init__.py,
topo/analysis/featureresponses.py,
topo/analysis/vision.py,
topo/base/__init__.py,
topo/base/arrayutil.py,
topo/base/boundingregion.py,
topo/base/cf.py,
topo/base/functionfamily.py,
topo/base/patterngenerator.py,
topo/base/projection.py,
topo/base/sheet.py,
topo/base/sheetview.py,
topo/base/simulation.py,
topo/command/analysis.py,
topo/command/basic.py,
topo/command/pylabplots.py,
topo/coordmapper/basic.py,
topo/ep/basic.py,
topo/learningfn/basic.py,
topo/learningfn/optimized.py,
topo/learningfn/projfn.py,
topo/learningfn/som.py,
topo/misc/commandline.py,
topo/misc/filepath.py,
topo/misc/legacy.py,
topo/misc/picklemain.py,
topo/misc/robotics.py,
topo/misc/trace.py,
topo/misc/util.py,
topo/numbergen/basic.py,
topo/pattern/audio.py,
topo/pattern/basic.py,
topo/pattern/image.py,
topo/pattern/random.py,
topo/pattern/rds.py,
topo/plotting/bitmap.py,
topo/plotting/palette.py,
topo/plotting/plot.py,
topo/plotting/plotfilesaver.py,
topo/plotting/plotgroup.py,
topo/projection/basic.py,
topo/responsefn/optimized.py,
topo/responsefn/projfn.py,
topo/sheet/basic.py,
topo/sheet/lissom.py,
topo/sheet/optimized.py,
topo/sheet/saccade.py,
topo/sheet/slissom.py,
topo/tests/__init__.py,
topo/tests/testCompositeParameter.txt,
topo/tests/testDynamicParameter.txt,
topo/tests/testEnumerationParameter.txt,
topo/tests/testNumberParameter.txt,
topo/tests/testParamOverrides.txt,
topo/tests/test_map_measurement.py,
topo/tests/testcfsom.py,
topo/tests/testgmpynumber.txt,
topo/tests/testparameterizedobject.py,
topo/tests/testparametersframe.py,
topo/tests/testplot.py,
topo/tests/testsheetview.py,
topo/tests/testtkparameterizedobject.py,
topo/tkgui/__init__.py,
topo/tkgui/editor.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/templateplotgrouppanel.py,
topo/tkgui/testpattern.py,
topo/tkgui/topoconsole.py,
topo/transferfn/basic.py,
topo/transferfn/optimized.py:
Whole directory missed from r10668. Subversion appears to have
trouble tracking directory moves!
2009-10-27 ceball
* [r10671] Makefile:
make clean-pyc now removes pyc files from main directory.
* [r10670] _setup.py:
Updated setup.py code for separate param package.
* [r10669] param/parameterized.py:
Revert an unrelated change accidentally included in the previous
checkin.
* [r10668] contrib/cbmisc.py,
contrib/cc_lesi_final.ty,
contrib/cc_lesi_oo_or.ty,
contrib/cc_lesi_oo_or_new.ty,
contrib/cc_lissom_oo_or_simple_rv.ty,
contrib/expressionparam.py,
contrib/hegdeessen.py,
contrib/jacommands.py,
contrib/jj_tiny.ty,
contrib/jm_cc_lissom.ty,
contrib/jm_cf_matrix.py,
contrib/jsldefs.py,
contrib/lesi_whisker_barrels.ty,
contrib/lissom_happyface.ty,
contrib/lissom_or_noshrinking_latswitch.ty,
contrib/lissom_rgb.ty,
contrib/rgbimages.py,
contrib/sparse_connectivity_LESI.ty,
contrib/sparse_connectivity_model.ty,
contrib/surround_analysis.py,
contrib/tracker.py,
doc/Developer_Manual/gui_text.php,
doc/FAQ/index_text.php,
doc/News/index_text.php,
doc/Reference_Manual/index_text.php,
doc/User_Manual/commandline_text.php,
doc/User_Manual/interfacing_text.php,
doc/User_Manual/overview_text.php,
doc/User_Manual/parameters_text.php,
doc/User_Manual/scripts_text.php,
examples/gca_lissom.ty,
examples/goodhill_network90.ty,
examples/hierarchical.ty,
examples/leaky_lissom_or.ty,
examples/lissom.ty,
examples/lissom_fsa.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/lissom_whisker_barrels.ty,
examples/obermayer_pnas90.ty,
examples/perrinet_retina.ty,
examples/saccade_demo.ty,
examples/som_retinotopy.ty,
examples/sullivan_neurocomputing04.ty,
examples/tiny.ty, param,
param/__init__.py,
param/external.py,
param/externaltk,
param/externaltk/README,
param/externaltk/scrodget-2.1,
param/externaltk/scrodget-2.1/pkgIndex.tcl,
param/externaltk/scrodget-2.1/scrodget.tcl,
param/externaltk/snit-2.2.1,
param/externaltk/snit-2.2.1/main1.tcl,
param/externaltk/snit-2.2.1/main1_83.tcl,
param/externaltk/snit-2.2.1/main2.tcl,
param/externaltk/snit-2.2.1/pkgIndex.tcl,
param/externaltk/snit-2.2.1/snit.tcl,
param/externaltk/snit-2.2.1/snit2.tcl,
param/externaltk/snit-2.2.1/snit_tcl83_utils.tcl,
param/externaltk/snit-2.2.1/validate.tcl,
param/externaltk/tooltip-1.4,
param/externaltk/tooltip-1.4/pkgIndex.tcl,
param/externaltk/tooltip-1.4/tipstack.tcl,
param/externaltk/tooltip-1.4/tooltip.tcl,
param/parameterized.py,
param/tk.py, topo/param:
Moved topo.param to param.
2009-10-27 jbednar
* [r10666] topo/pattern/basic.py:
Fixed TwoRectangles to allow non-square patterns
2009-10-27 antolikjan
* [r10665] topo/sheet/basic.py:
made continuos to activate during learning step
2009-10-12 ceball
* [r10636] doc/buildbot/master.cfg:
cider.csres was updated to OS X 10.6 (Snow Leopard).
2009-10-09 ceball
* [r10634] setup.py:
Added note about creating pypi entry.
* [r10633] _setup.py,
debian/control,
external/Makefile,
setup_app.py,
setup_ez.py,
topo/param/externaltk/README:
Updated information about external packages.
* [r10632] doc/Downloads/index_text.php:
Added missing dependency from Ubuntu example.
* [r10631] external/Makefile,
topo/param/externaltk,
topo/param/externaltk/scrodget-2.1,
topo/param/externaltk/scrodget-2.1/pkgIndex.tcl,
topo/param/externaltk/scrodget-2.1/scrodget.tcl,
topo/param/externaltk/snit-2.2.1,
topo/param/externaltk/snit-2.2.1/main1.tcl,
topo/param/externaltk/snit-2.2.1/main1_83.tcl,
topo/param/externaltk/snit-2.2.1/main2.tcl,
topo/param/externaltk/snit-2.2.1/pkgIndex.tcl,
topo/param/externaltk/snit-2.2.1/snit.tcl,
topo/param/externaltk/snit-2.2.1/snit2.tcl,
topo/param/externaltk/snit-2.2.1/snit_tcl83_utils.tcl,
topo/param/externaltk/snit-2.2.1/validate.tcl,
topo/param/externaltk/tooltip-1.4,
topo/param/externaltk/tooltip-1.4/pkgIndex.tcl,
topo/param/externaltk/tooltip-1.4/tipstack.tcl,
topo/param/externaltk/tooltip-1.4/tooltip.tcl,
topo/param/tk.py,
topo/tkgui/__init__.py:
Moved snit, scrodget, and tooltip into topo.param so that they do
not appear as external dependencies.
* [r10630] doc/Downloads/git_text.php:
Fixed a few formatting errors.
2009-10-04 ceball
* [r10628] Makefile:
Added info about rpm generation.
* [r10627] Makefile,
debian/python-scrodget.debhelper.log,
debian/python-scrodget.postinst.debhelper,
debian/python-scrodget.preinst.debhelper,
debian/python-scrodget.prerm.debhelper,
debian/python-scrodget.substvars:
Cleaned up debian/ directory.
* [r10626] external:
Updated ignore list.
* [r10625] debian/control:
Updated package dependencies (scrodget, not pyscrodget).
* [r10624] _setup.py,
setup_ez.py:
Updated info about scrodget.
* [r10623] external/Makefile,
external/pyscrodget-0.0.2_2.1.tar.gz,
external/scrodget-2.1.tar.gz,
topo/param/tk.py:
Moved pyscrodget wrapper to topo.param.tk.
* [r10622] Makefile:
Added transcript of uploading .deb based on svn version of
Topographica.
* [r10621] Makefile:
More to clean.
* [r10620] external:
More to ignore.
2009-10-03 ceball
* [r10619] Makefile:
Added info about signing deb.
* [r10618] Makefile:
Corrected ppa upload command.
* [r10617] Makefile:
Minor addition.
* [r10616] Makefile,
debian/changelog,
debian/docs:
Added doc/ and examples/ to deb package.
* [r10615] Makefile,
debian, debian/changelog,
debian/compat,
debian/control,
debian/copyright,
debian/docs,
debian/pycompat,
debian/python-scrodget.debhelper.log,
debian/python-scrodget.postinst.debhelper,
debian/python-scrodget.preinst.debhelper,
debian/python-scrodget.prerm.debhelper,
debian/python-scrodget.substvars,
debian/rules:
Sketch of creating an Ubuntu deb file.
* [r10614] _setup.py,
setup.py, setup_app.py:
Topographica's 'python setup.py install' can work on Ubuntu 9.04
and Mac OS X 10.6 (with MacPorts).
* [r10613] external/Makefile,
topo/__init__.py,
topo/base/sheetcoords.py,
topo/param/__init__.py,
topo/param/parameterized.py:
Added some notes relating to Python 2.6.
2009-10-01 ceball
* [r10612] setup_ez.py:
First version that appears to work, depending only on Python,
Tcl/Tk, and GMP.
* [r10611] topo/__init__.py:
Support setuptools-based installations of PIL.
* [r10610] topo/misc/legacy.py,
topo/pattern/image.py:
Removed old 'Image=FileImage' hack.
2009-09-30 ceball
* [r10608] doc/Downloads/git_text.php:
Added more info to git docs about sharing.
* [r10607] doc/Downloads/git_text.php:
Added more to git docs.
* [r10606] doc/Downloads/git_text.php:
Added more to git docs.
* [r10605] doc/Downloads/git_text.php:
Added clarification.
* [r10604] doc/Downloads/git_text.php:
Updated sharing command.
* [r10603] doc/Downloads/git_text.php:
Added warning.
* [r10602] doc/Downloads/git_text.php:
Added more info about sharing git repository.
* [r10601] doc/Downloads/git_text.php:
Began extending git documentation to cover more advanced usage.
* [r10600] external/Makefile:
Added link to relevant mailing list item.
* [r10599] external/Makefile,
external/matplotlib-0.91.4.tar.gz,
external/matplotlib-0.99.1.1.tar.gz,
topo/command/pylabplots.py:
Upgraded to matplotlib 0.99.1.1.
* [r10598] doc/buildbot/index.html,
doc/buildbot/master.cfg:
Added jupiter3 buildslave.
2009-09-26 ceball
* [r10597] external/Makefile,
external/weave.diff:
Changes missed from r10596 (patch to make weave not depend on
scipy).
* [r10596] external/Makefile:
Fixed installation of weave. SF 2791212 is now fixed.
2009-09-24 antolikjan
* [r10595] external/Makefile:
corrected dependency of weave on old scipy
2009-09-23 antolikjan
* [r10594] external/Makefile,
external/numpy-1.1.1.tar.gz,
external/numpy-1.2.1.tar.gz,
external/numpy.diff,
external/scipy-0.5.2.tar.gz,
external/scipy-0.7.1.tar.gz,
external/scipy-site.cfg:
Upgraded numpy and scipy, and edited the example scipy-site.cfg
to be suitable for DICE.
2009-09-22 jbednar
* [r10592] topo/plotting/plotgroup.py:
Trivial fixes to comments and docstrings
2009-09-18 ceball
* [r10589] topo/base/boundingregion.py,
topo/pattern/image.py:
Small changes reducing attribute lookups inside two particular
loops, improving the performance of the Image pattern generators.
* [r10588] topo/transferfn/basic.py:
Clean up DivisiveNormalizeLinf (to use numpy max and abs; vastly
improves performance).
2009-09-17 ceball
* [r10587] doc/buildbot/master.cfg:
buildbot: examples/ and doc/ no longer split from 'python
setup.py install' archive.
* [r10586] Makefile:
Archive produced for 'python setup.py install' now contains
examples/ and doc/.
* [r10585] topo/param/tk.py:
If Topographica doesn't have 'grab', don't try to get grab for
window causing the error.
2009-09-16 ceball
* [r10583] doc/buildbot/master.cfg:
Added archive-making slave.
2009-09-13 ceball
* [r10580] setup_ez.py:
Various updates. Getting closer to working...
* [r10579] doc/Developer_Manual:
More to ignore.
* [r10578] external:
Updated files to ignore.
* [r10577] Makefile:
First go at making archives suitable for packaging.
* [r10576] _setup.py,
setup.py:
setup.py fixes.
* [r10575] topo/command/analysis.py:
Renamed variable (to avoid potential clash). Should be no visible
change.
2009-09-02 ceball
* [r10566] topo/tkgui/topoconsole.py:
Added ALERT.
* [r10565] topo/base/projection.py,
topo/base/sheet.py,
topo/sheet/basic.py:
Moved definition of output_fns to Sheet. (Fixes problem where
state_push()/pop() assume output_fns are present in Sheet.)
2009-08-30 ceball
* [r10564] topo/command/pylabplots.py,
topo/plotting/plotgroup.py:
Minor clarifcation of docs.
* [r10563] topo/plotting/plotgroup.py:
Renamed normalize='Joint' to normalize='JointProjections'.
* [r10562] topo/plotting/plotgroup.py:
Renamed normalize='All' to normalize='AllTogether'.
* [r10561] topo/command/analysis.py,
topo/command/pylabplots.py,
topo/plotting/plotgroup.py,
topo/sheet/basic.py:
Renamed normalize='Independent' to normalize='Individually'.
* [r10560] topo/tkgui/topoconsole.py:
Hide any error generated while trying to find an appropriate
status bar for displaying messages.
* [r10559] topo/param/tk.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/topoconsole.py:
Progress bars, messages, warnings, and errors should now display
on the appropriate status bar. This is quite a significant
change, and is likely to need tuning based on feedback from
users.
* [r10558] topo/param/__init__.py,
topo/tkgui/projectionpanel.py:
Hacked support for exclusive right and top bounds when editing
parameters in the GUI.
2009-08-03 jbednar
* [r10542] examples/lissom.ty:
Fixed outdated dims='All' to work as dims=[] instead. Fixed SF
map measurement to set frequencies parameter before instantiation
of measure_sine_pref, so that the value will be respected.
* [r10541] topo/command/analysis.py:
Added PhaseDisparity Preference&Selectivity plot
2009-08-03 jbednar
* [r10537] doc/Downloads/index_text.php,
topo/transferfn/basic.py:
Minor fix to doc
2009-08-02 antolikjan
* [r10536] contrib/jacommands.py:
Added new pattern generator - Expander - increases size of
patterns
2009-07-30 ceball
* [r10535] topo/base/simulation.py:
Added note.
* [r10534] doc/Downloads/index_text.php:
Mentioned about using a 64-bit platform for large simulations.
2009-07-29 jbednar
* [r10533] contrib/basic.py,
contrib/cc_lesi_oo_or.ty,
contrib/cc_lissom_oo_or_simple_rv.ty,
contrib/jsldefs.py,
contrib/lesi_judethesisversion.ty,
contrib/lesi_whisker_barrels.ty,
contrib/lissom.ty,
contrib/lissom_oo_or_homeostatic.ty,
contrib/lissom_oo_or_homeostatic_tracked.ty,
contrib/lissom_rgb.ty,
contrib/modelfit.py,
contrib/rgbhsv.py,
contrib/sparse_connectivity_LESI.ty,
contrib/sparse_connectivity_model.ty,
contrib/species_cf_jitter.ty,
contrib/species_lat_jitter.ty,
contrib/species_pf_jitter.ty,
examples/leaky_lissom_or.ty,
examples/lissom.ty,
examples/lissom_oo_or_cr.ty,
examples/lissom_whisker_barrels.ty,
examples/perrinet_retina_pynest.py,
examples/sullivan_neurocomputing04.ty,
examples/tiny.ty,
topo/analysis/featureresponses.py,
topo/analysis/vision.py,
topo/base/cf.py,
topo/base/sheetcoords.py,
topo/base/sheetview.py,
topo/command/analysis.py,
topo/command/basic.py,
topo/command/pylabplots.py,
topo/coordmapper/basic.py,
topo/learningfn/basic.py,
topo/learningfn/optimized.py,
topo/learningfn/projfn.py,
topo/learningfn/som.py,
topo/pattern/basic.py,
topo/plotting/bitmap.py,
topo/plotting/palette.py,
topo/plotting/plot.py,
topo/plotting/plotgroup.py,
topo/projection/basic.py,
topo/responsefn/optimized.py,
topo/responsefn/projfn.py,
topo/sheet/lissom.py,
topo/sheet/slissom.py,
topo/tests/testoutputfnsbasic.py,
topo/tests/testplot.py,
topo/tests/testplotgroup.py,
topo/tests/testsheet.py,
topo/tests/testsheetview.py,
topo/tests/testtkparameterizedobject.py,
topo/tkgui/editor.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/testpattern.py,
topo/tkgui/topoconsole.py,
topo/transferfn/basic.py:
Expanded tabs to spaces to avoid problems with some editors
* [r10532] contrib/hegdeessen.py:
Fixed typos
2009-07-28 ceball
* [r10531] topo/analysis/featureresponses.py:
Fixed variable name. (Hue map measurement for separate R, G, and
B retinas has presumably been broken since I added support for
hue map measurement using a single RGB retina.)
2009-07-27 ceball
* [r10530] topo/plotting/bitmap.py:
When enlarging an image by an integer factor, avoid PIL by using
numpy (PIL has a bug). Mitigates SF 2820821.
2009-07-26 ceball
* [r10529] topo/misc/commandline.py,
topo/tkgui/__init__.py,
topo/tkgui/topoconsole.py:
Simplified dock-by-default for -G option.
* [r10528] topo/plotting/plot.py:
Fix for 1962478 ('Status bar information bug on the map
window'). Actually caused by TemplatePlot instances sharing the
same view_dict (the Sheet's sheet_views dictionary).
2009-07-25 ceball
* [r10527] topo/plotting/plotgroup.py:
Fixed mistake in r10524 (mistakenly introduced a space into plot
labels).
* [r10526] topo/analysis/featureresponses.py:
Set MeasureResponseCommand's pattern_presenter parameter to
instantiate its value, since the value will be mutable.
* [r10525] contrib/cbmisc.py:
Updated my analysis function.
2009-07-24 ceball
* [r10524] examples/lissom.ty,
topo/command/analysis.py,
topo/command/pylabplots.py,
topo/plotting/plot.py,
topo/plotting/plotgroup.py,
topo/tkgui/testpattern.py:
Implemented joint normalization for plotting (SF 1829844).
Includes some clean-up of the PlotGroup classes. Various parts of
plotgroup.py and plot.py still require cleaning, and the GUI's
normalization widget placement also needs to be sorted out.
* [r10523] topo/param/__init__.py:
Fix for SF 2661510. (Intermediate checkin: will be cleaned up.
2009-07-23 ceball
* [r10522] doc/Downloads/git_text.php:
Added link and hint.
* [r10521] topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py:
Fixed GUI's dynamic coordinates: now there is no systematic
offset (SF 2127012), and coordinates work on projection and CF
panels (ALERT). Also: changed plot borders to be drawn by tk
rather than by us.
* [r10520] _setup.py:
Removed package that no longer exists.
* [r10519] topo/command/basic.py:
Added comment about pickling.
* [r10518] Makefile:
File missed from previous commit.
* [r10517] external/Makefile,
external/idle_tk8.5.patch:
Experimental: 'make topographicagui; ./topographicagui' to try
using Topographica with IDLE.
* [r10516] external/Makefile,
external/ipythonTk.diff,
external/ipythonTk.tar.gz,
external/ipython_view.diff,
topo/ipythonTk,
topo/tkgui/topoconsole.py:
Moved topo.ipythonTk to an external package (plus patches to fix
some problems). The package contains unmodified copies of
ipython_view.py from Accerciser and ipythonTk.py from CCP1GUI.
ipython_view.py is now part of new IPython releases, so we should
just use IPython's version eventaully. (IPython focuses on wx,
though, so there is no equivalent of ipythonTk.py in IPython.)
2009-07-22 ceball
* [r10515] topo/tkgui/__init__.py:
File missed from previous commit.
* [r10514] topo/misc/commandline.py:
Hack to allow -G to have windows docked by default.
* [r10513] topo/ipythonTk/ipython_view.py:
ipythonTk: Apparently fixed tab completion.
2009-07-17 jmoudrik
* [r10512] contrib/jm_plotting.py:
Added title for the Phase preference scatter plot
2009-07-15 antolikjan
* [r10511] contrib/modelfit.py:
added backpropagation
2009-07-14 antolikjan
* [r10510]
contrib/cc_lissom_oo_or_simple_rv.ty:
switching back to uncorrelated
2009-07-13 antolikjan
* [r10509] contrib/modelfit.py:
changed default density
* [r10508] contrib/modelfit.py:
added learning rate parameter'
* [r10507] contrib/modelfit.py:
made the file 'executable'
* [r10506] contrib/modelfit.py:
added external parameters
2009-07-13 ceball
* [r10505] topo/param/parameterized.py:
Updated comment.
2009-07-13 machalekj
* [r10504] contrib/complex_shapes_analysis.py:
Added python header info to analysis plots.
2009-07-12 machalekj
* [r10503] contrib/complex_shapes_analysis.py,
contrib/hegdeessen.py:
Modification of Hegde and Van Essen stimuli as were used in
complex shapes analysis in bachalor thesis of Machalek. Added
script with analysis plots.
2009-07-12 jmoudrik
* [r10502] contrib/jm_analysis.py,
contrib/jm_cc_lissom.ty,
contrib/jm_cf_matrix.py,
contrib/jm_plotting.py,
contrib/jm_smooth.py:
Merged jm_smooth into jm_analysis; jm_analysis splitted to
analysis and plotting (jm_plotting).
Added an extension of complex cell model.
2009-07-12 antolikjan
* [r10501] contrib/gc_alissom.ty:
increased the retinal density in order to improve RV LGN response
2009-07-11 antolikjan
* [r10500]
contrib/cc_lissom_oo_or_simple_rv.ty:
switching of correlated RV
2009-07-09 ceball
* [r10499] contrib/cbmisc.py:
Updated my analysis functions.
2009-07-09 antolikjan
* [r10498] contrib/modelfit.py:
new models
2009-07-08 ceball
* [r10497] contrib/cbmisc.py:
Added function to create single-eye plotgroups. Added function I
use for OR/OD/CR simulations.
* [r10496] topo/analysis/featureresponses.py:
Added generator_sheets parameter to MeasureResponseCommand, to
simplify setting this parameter on the PatternPresenter.
* [r10495] topo/analysis/featureresponses.py:
Added sheet_views_prefix to allow distinction between e.g.
OrientationPreference and LeftRetina OrientationPreference.
* [r10494] topo/analysis/featureresponses.py:
Put blank patterns in GeneratorSheets that are not being used.
* [r10493] topo/analysis/featureresponses.py:
Added generator_sheets parameter to PatternPresenter (allowing
restriction of set of GeneratorSheets).
* [r10492] topo/analysis/featureresponses.py:
Set instantiate=True for pattern_presenter pararameter of
SinusoidalMeasureResponseCommand (since it defaults to a mutable
object).
2009-07-07 jbednar
* [r10491] examples/lissom.ty:
Added speed parameter, and allowed linear interpolation between
integer values
* [r10490] topo/misc/util.py:
Added linearly_interpolate
2009-07-03 ceball
* [r10489] contrib/parameter_search,
contrib/parameter_search.cfg:
Tidying. Should be no visible change.
* [r10488] contrib/parameter_search,
contrib/parameter_search.cfg:
Saves combinations file. Saves command used to launch
parameter_search. Saves everything (all run_batch() directories,
combinations file, etc) into one directory.
* [r10487] contrib/parameter_search,
contrib/parameter_search.cfg:
Added ability to pass dirname_prefix to run_batch().
* [r10486] topo/command/basic.py:
Added name_time_format parameter to run_batch().
* [r10485] topo/command/basic.py:
Added optional dirname_prefix to run_batch().
2009-07-01 ceball
* [r10484] topo/base/cf.py:
Removed unused import.
* [r10483] topo/base/sheetview.py:
Replaced tabs with spaces.
* [r10482] topo/base/sheetcoords.py:
Removed unused import.
2009-07-01 antolikjan
* [r10481]
contrib/cc_lissom_oo_or_simple_rv.ty:
Minnor changes
2009-06-30 ceball
* [r10480] doc/Downloads/git_text.php,
doc/Downloads/index_text.php:
Updated some documentation relating to git.
2009-06-26 ceball
* [r10479] topo/base/cf.py,
topo/misc/legacy.py,
topo/projection/basic.py,
topo/tests/testcf.py:
ConnectionField no longer stores x and y.
* [r10478] topo/base/sheet.py:
Removed never-been-used sheet_offset() method.
* [r10477] examples/hierarchical.ty,
examples/lissom.ty,
examples/lissom_fsa.ty,
examples/lissom_oo_or.ty,
examples/lissom_oo_or_cr.ty,
examples/lissom_or.ty,
examples/lissom_whisker_barrels.ty,
topo/base/cf.py,
topo/projection/basic.py,
topo/tests/reference/lissom_fsa_reference.ty,
topo/tests/reference/lissom_oo_dr_reference.ty,
topo/tests/reference/lissom_oo_or_reference.ty,
topo/tests/reference/lissom_or_reference.ty:
Added ResizableCFProjection and removed bounds-changing-related
code from CFProjection and ConnectionField.
* [r10476] topo/base/cf.py:
Added _generate_coords() method to CFProjection, with the
intention of allowing subclasses to e.g. store the generated
coords. Improved simple_vectorize() to handle functions with any
number of outputs.
* [r10475] topo/base/sheet.py:
Added method to get arrays of X and Y sheet coordinates.
* [r10474] topo/base/cf.py,
topo/projection/basic.py:
Tried to simplify CFProjection by adding a _create_cf() method
and avoiding a visible loop through the dest sheet units.
* [r10473] topo/base/sheet.py:
Added ALERT.
2009-06-26 antolikjan
* [r10472]
contrib/cc_lissom_oo_or_simple_rv.ty:
Minor changes
2009-06-25 ceball
* [r10471] topo/param/__init__.py:
Added ALERT.
2009-06-25 antolikjan
* [r10470] contrib/jacommands.py:
variouse changes to surround analysis
* [r10469] topo/command/pylabplots.py:
corrected the units in measure_orientation_contrast
* [r10468] contrib/gc_alissom.ty:
Minor changes
2009-06-23 ceball
* [r10467] topo/base/cf.py,
topo/base/sheetcoords.py,
topo/plotting/plot.py,
topo/plotting/plotgroup.py,
topo/projection/basic.py,
topo/tests/testsheet.py:
Slice no longer stores bounds. Reduces memory usage (as recorded
in 'memuse_rSlice_no_bounds.out'). Could increase plotting times
- not sure.
* [r10466] topo/base/cf.py:
Corrected an error in CFProjection.change_bounds(): the
bounds_template that is stored after changing bounds is now that
which corresponds exactly to the slice. Should make no change to
any of our simulations, because the correct slice was being
passed to the ConnectionField; CFProjection's bounds_template is
not currently used by anything after the point it is stored.
2009-06-23 antolikjan
* [r10465] contrib/modelfit.py:
Added motion to the model
* [r10464] contrib/gc_alissom.ty:
Overhaul of gain control and consequently parameters
* [r10463]
contrib/cc_lissom_oo_or_simple_rv.ty:
Overhaul of gain control and consequently parameters
* [r10462] contrib/jacommands.py:
GC update and LGN channel randomization updates
* [r10461] topo/command/basic.py:
Adding the wipe_out_activity and clear_even_queue into the
analysis pre-presentation hooks
* [r10460] topo/sheet/basic.py:
Addjusted the JointNormalizingCFSheet_Continuous such that it
works more in line with LISSOM
* [r10459] topo/analysis/featureresponses.py:
pre presentation hooks are now set in different place
* [r10458] topo/tkgui/testpattern.py:
Adjusted test pattern so it clears the activity and state of the
network properly before presenting stimulus
2009-06-19 ceball
* [r10457] doc/buildbot/master.cfg:
Fixed 'warn on errors' in various cases (e.g. for make lint-base,
which niow only causes warnings even if pylint reports errors
with the code).
2009-06-18 jbednar
* [r10456] topo/responsefn/optimized.py:
Replaced C code with macros; verified that the .cpp code did not
change
* [r10455] topo/misc/inlinec.py:
Added macro for looking up contiguous array from slot
* [r10454] topo/responsefn/optimized.py:
Further reorganized C code to match macros
* [r10453] topo/responsefn/optimized.py:
Reorganized C code to match macros
2009-06-18 ceball
* [r10452] topo/tests/test_script.py:
Run current density combinations to 20000 rather than 1000.
2009-06-17 ceball
* [r10451] external:
Ignore guppy.
* [r10450] external/Makefile,
external/logilab-astng-0.17.2.tar.gz,
external/logilab-astng-0.19.0.tar.gz,
external/logilab-common-0.25.0.tar.gz,
external/logilab-common-0.41.0.tar.gz,
external/pylint-0.14.0.tar.gz,
external/pylint-0.18.0.tar.gz:
Upgraded pylint.
2009-06-17 antolikjan
* [r10449] contrib/gc_alissom.ty:
added two new natural image datasets
2009-06-16 antolikjan
* [r10448] contrib/cc_lesi_oo_or_new.ty:
made V1 complex inh neurons have external parameter defining
their threshold
2009-06-16 machalekj
* [r10447] contrib/hegdeessen.py:
48 Grating and 80 contour stimuli used in Hegde and Van Essen
works. 5 new patterns classes added.
2009-06-15 antolikjan
* [r10446] contrib/cc_lesi_oo_or_new.ty:
made V1 complex inh neurons have external parameter defining
their threshold
* [r10445] topo/command/pylabplots.py:
Modified the Orientation Contrast analysis so it better reflects
the published figures
* [r10444] contrib/jacommands.py:
Added surround modulation analysis batch test
* [r10443] contrib/cc_lesi_oo_or.ty:
minor parameter changes
* [r10442] topo/pattern/basic.py:
Removed some spurious parameters in the OrientationContrast
pattern
2009-06-15 ceball
* [r10441] topo/base/cf.py,
topo/misc/legacy.py,
topo/projection/basic.py:
ConnectionField no longer stores input_sheet.
* [r10440] topo/projection/basic.py:
Fixed SharedWeightCFProjection.n_bytes(): count
input_sheet_slice, not weights_slice.
2009-06-14 ceball
* [r10439] topo/misc/legacy.py:
File missed from the previous checkin.
* [r10438] topo/base/cf.py,
topo/projection/basic.py:
ConnectionField no longer stores weights_slice.
* [r10437] topo/projection/basic.py:
Fixed error in recent commit.
* [r10436] topo/base/cf.py,
topo/misc/legacy.py,
topo/projection/basic.py:
Made ConnectionField no longer have a __dict__ (to save memory).
* [r10435] examples/saccade_demo.ty,
topo/base/cf.py,
topo/projection/basic.py:
Moved min_matrix_radius from cf to projection.
* [r10434] topo/base/cf.py,
topo/param/parameterized.py,
topo/projection/basic.py:
Made ConnectionField inherit from object rather than
Parameterized (to reduce memory usage). Intermediate checkin:
added slots for all attributes except _has_norm_total; still have
to remove __dict__.
* [r10433] topo/misc/legacy.py:
Added support for __setstate__ for classes that used to - but no
longer - have __setstate__.
* [r10432] topo/misc/legacy.py:
Removed stray import.
2009-06-14 antolikjan
* [r10431]
contrib/cc_lissom_oo_or_simple_rv.ty:
made LGN center size external parameter
2009-06-14 jbednar
* [r10430] topo/learningfn/optimized.py,
topo/responsefn/optimized.py,
topo/sheet/optimized.py,
topo/transferfn/optimized.py:
Changed double * to npfloat * to allow changing float type ;
should be no change in function or performance
* [r10429] topo/sheet/basic.py:
Removed unused import
2009-06-13 jbednar
* [r10428] topo/learningfn/optimized.py:
Simplified C code based on new macros in c_header
* [r10427] topo/misc/inlinec.py:
Added c_header with declarations and macros
* [r10426] topo/learningfn/optimized.py:
Reordered statements and renamed temporaries to match macro
version to be checked in next, to allow direct comparison of .cpp
code
* [r10425] topo/base/sheet.py:
Made numpy float type explicit
2009-06-13 ceball
* [r10424] doc/Downloads/index_text.php,
external/Makefile:
Added documentation about package required for antialiased fonts
(fixes SF 2791479).
* [r10423] _setup.py:
Added list of dependencies in the form of what I had to install
on Ubuntu 9.04.
2009-06-12 jbednar
* [r10422]
doc/Developer_Manual/memuse_text.php:
Fixed typo
* [r10421] topo/analysis/featureresponses.py:
Removed changes from r10404, making a correct fix for RF plots
instead
* [r10420] doc/shared/util.php:
Added fns for building the Developer Manual
* [r10419] topo/command/basic.py:
Added docstring
* [r10418] doc/Developer_Manual/index_text.php,
doc/Developer_Manual/memuse_text.php,
doc/Developer_Manual/optimization_text.php,
topo/misc/memuse.py:
Added documentation about optimizing memory usage
2009-06-12 judelaw
* [r10417] contrib/laminar_oo_or.ty,
contrib/laminar_or.ty,
contrib/lissom_oo_or_species.ty,
contrib/lissom_oo_or_species_tracked.ty,
contrib/species_lateral_sparsity.ty:
removed old versions replaced by newer files
* [r10416] contrib/lesi_judethesisversion.ty:
Version which matches simulations presented in thesis
* [r10415] contrib/species_lat_jitter.ty:
Updated to match simulations presented in thesis
* [r10414] contrib/species_pf_jitter.ty:
Updated to match simulations presented in thesis
* [r10413] contrib/jsldefs.py,
contrib/lesi.ty,
contrib/species_cf_jitter.ty,
topo/command/pylabplots.py,
topo/coordmapper/basic.py:
added NormalJitter for jitter chosen from a Normal distribution
* [r10412] topo/base/arrayutil.py:
added clip_upper function
* [r10411] topo/transferfn/basic.py:
added Threshold function that sets values below a particular
value to zero but leaves others unchanged
* [r10410] topo/analysis/featureresponses.py:
added multiplier and offset parameters to Feature class so that
individual SheetViews can be maipulated separately for each
feature
2009-06-12 ceball
* [r10409] topo/param/tk.py:
Fixed typo.
* [r10408] topo/param/tk.py:
Fixed part of SF bug 2805379 (only Parameterized classes can be
represented by ClassSelector, but GUI was attempting to use
ClassSelector for e.g. floats when editing a list).
2009-06-11 jbednar
* [r10407] topo/misc/memuse.py:
Made topsize work for small-size process ids
2009-06-11 ceball
* [r10406] Makefile,
topo/tkgui/topoconsole.py:
Allow exit status to be passed to quit_topographica(), and use it
for gui-tests.
* [r10405] topo/tkgui/topoconsole.py:
Attempt to fix strange Windows 'unusual termination' error: one
cause of the error is quitting with matplotlib windows open.
2009-06-11 jbednar
* [r10404] topo/analysis/featureresponses.py:
Updated ReverseCorrelation to match recent changes to
FeatureResponses; may help fix RF plots
* [r10403] topo/analysis/featureresponses.py:
Suppressed message about number of test patterns being printed
* [r10402] topo/misc/memuse.py:
Shortened default message length
* [r10401] topo/projection/basic.py:
Removed Python variables from n_bytes so that it more accurately
reflects weight and activity array sizes
* [r10400] topo/misc/memuse.py:
Initial version; code for measuring memry usage
* [r10399] topo/misc/asizeof.py:
Copied recipe
http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/546530
verbatim
2009-06-11 ceball
* [r10398] external/Makefile,
external/guppy-r70.tar.gz:
Added guppy (which provides heapy, for memory profiling), from
https://guppy-pe.svn.sourceforge.net/svnroot/guppy-pe/trunk/guppy
r70.
* [r10397] topo/tests/test_map_measurement.py:
Added support for Parameterized BoundingRegions in pickled map
test data.
2009-06-10 ceball
* [r10396] topo/base/boundingregion.py:
Removed redundant __init__ methods.
* [r10395] topo/base/boundingregion.py,
topo/misc/legacy.py,
topo/param/parameterized.py:
BoundingRegion is now just an object (no longer inherits from
Parameterized). Reduces memory consumption of "./topographica -i
-p 'cortex_density=retina_density=1' -p lgn_density=20 -p
'dims=[or,od,dr,cr,sf]' examples/lissom.ty" from 435 to 334 MB
(as reported by top). Also added legacy support.
* [r10394] topo/tests/testsnapshots.py:
Added preferred search_path. (Avoids conflict with any unrelated
testsnapshot.typ that happens to be in a default search path.)
* [r10393] topo/base/sheetcoords.py:
Added __slots__ to Slice. Reduces memory consumption of
"./topographica -i -p 'cortex_density=retina_density=1' -p
lgn_density=20 -p 'dims=[or,od,dr,cr,sf]' examples/lissom.ty"
from 525 to 435 MB (as reported by top).
2009-06-10 jbednar
* [r10392] topo/base/cf.py,
topo/base/projection.py,
topo/projection/basic.py:
Made n_bytes be implemented at the Projection level
* [r10391] topo/projection/basic.py:
Added missing n_conns method
2009-06-10 antolikjan
* [r10390]
contrib/cc_lissom_oo_or_simple_rv.ty:
made sure all random generators are seeded
2009-06-10 ceball
* [r10389] topo/base/sheetcoords.py:
Added ALERT.
2009-06-09 jbednar
* [r10388] topo/command/basic.py:
Added print_sizes command, which is now called in run_batch (but
can also be called explicitly)
* [r10387] topo/projection/basic.py:
Added more SharedCF overhead
* [r10386] topo/base/cf.py:
Minor cleanup
* [r10385] topo/base/cf.py,
topo/base/projection.py,
topo/base/sheet.py,
topo/command/basic.py,
topo/projection/basic.py:
Added n_bytes() and n_conns() methods and global commands to
calculate memory size and number of connections in the current
simulation
2009-06-09 ceball
* [r10384] contrib/parameter_search,
contrib/parameter_search.cfg:
Moved some options into a config file.
2009-06-08 ceball
* [r10383] contrib/parameter_search:
Minor simplification.
* [r10382] contrib/parameter_search:
Use simpler string formatting.
* [r10381] setup_app.py:
Added notes.
* [r10380]
external/pyscrodget-0.0.2_2.1.tar.gz:
Accidentally left in the build/ directory in previous version.
* [r10379] _setup.py,
setup.py, setup_app.py,
setup_exe.py,
setup_ez.py:
Added create_topographica_script() to _setup.py. Previously, the
topographica script had to be created by make before running
setup.
2009-06-06 ceball
* [r10378] doc/Future_Work/current_text.php,
setup_app.py:
Added info about icons from future work doc.
* [r10377] setup_app.py:
Began attempting to include external packages.
* [r10376] setup_ez.py:
Added docstring.
* [r10375] Makefile,
easysetup.py,
setup_app.py,
setup_exe.py,
setup_ez.py,
win_build_exe.py:
Made setup script naming more consistent. Added beginnings of
py2app script.
* [r10374] Makefile:
More files to delete from distribution.
* [r10373] doc/Downloads/index_text.php:
Added comment.
2009-06-05 ceball
* [r10372] topo/plotting/plotgroup.py:
Fixed bogus 'self'.
* [r10371] easysetup.py,
setup.py:
Added some documentation.
* [r10370] easysetup.py:
Fixed typos.
* [r10369] _setup.py,
easysetup.py, setup.py:
Moved code common to distutils and setuptools into _setup.py.
* [r10368] easysetup.py:
Beginnings of 'easy_install topographica'
* [r10367] topo/misc/filepath.py:
Removed erroneous use of set() (search paths were not being
searched in order). It doesn't matter if a path appears more than
once.
* [r10366] topo/misc/filepath.py:
Fixed (presumably accidental) mutable default argument.
* [r10365] topo/tests/testsnapshots.py:
Simplified paths.
* [r10364] topo/misc/filepath.py:
Added output_path to resolve_path()'s list of search_paths.
* [r10363]
topo/tests/testCompositeSheetMasks.txt:
Fixed path.
* [r10362] topo/tests/__init__.py:
Skip gmpy/Number tests if gmpy not available.
* [r10361] topo/tests/testNumberParameter.txt,
topo/tests/testgmpynumber.txt:
Split gmpy/Number tests from other Number tests.
* [r10360] setup.py:
Added more missing files.
* [r10359] topo/analysis/vision.py,
topo/command/analysis.py,
topo/tests/testbitmap.py,
topo/tests/testimage.py,
topo/tkgui/plotgrouppanel.py:
Cleaned up file paths.
2009-06-05 antolikjan
* [r10358]
contrib/cc_lissom_oo_or_simple_rv.ty:
added missing import
2009-06-05 ceball
* [r10357]
external/pyscrodget-0.0.2_2.1.tar.gz:
Forgot to gzip previous version.
* [r10356]
external/pyscrodget-0.0.2_2.1.tar.gz:
Minor update to path finding.
* [r10355] topo/plotting/bitmap.py:
Added level to vera.ttf detection hack, so that vera.ttf can be
found when topo is installed as a package.
* [r10354] setup.py:
Added missing files.
* [r10353]
external/pyscrodget-0.0.2_2.1.tar.gz:
Corrected typo in package info.
* [r10352] external/Makefile,
external/pyscrodget-0.0.1_2.1.tar.gz,
external/pyscrodget-0.0.2_2.1.tar.gz:
Minor alterations to pyscrodget package.
* [r10351] topo/misc/filepath.py:
Expanded comment.
* [r10350] external/Makefile,
external/Tile.py,
external/odict.py,
topo/param/external.py,
topo/param/tk.py,
topo/tkgui/editor.py,
topo/tkgui/topoconsole.py:
Moved odict and tilewrapper to topo.param.external module.
* [r10349] setup.py:
Added a comment.
* [r10348] setup.py,
topo/misc/filepath.py,
topo/tests/testsnapshots.py:
Fixed error introduced into testsnapshots (I mistakenly thought
testsnapshot.typ was checked in).
2009-06-04 ceball
* [r10347] topo/tests/testplotfilesaver.py:
Simplified temporary file handling.
* [r10346] topo/tests/testsnapshots.py:
Use resolve_path() to locate the snapshot file.
* [r10345] setup.py:
Added some notes.
* [r10344] topo/tests/testsnapshots.py:
Removed out-of-date ALERT.
* [r10343] topo/command/basic.py:
Tried to simplify handling snapshots that might or might not be
xml, when gnosis (for xml pickles) might or might not be
available. Will probably have to revisit this if we also add
hdf5.
* [r10342] topo/param/tk.py:
Adjustment to paths now that package_path is available.
* [r10341] topo/misc/commandline.py,
topo/tests/test_map_measurement.py,
topo/tkgui/topoconsole.py:
Adjustment to paths now that topo.misc.filepath.package_path is
available. Not yet complete: other uses of
application_path/normalize_path/resolve_path might need to be
updated.
* [r10340] topo/plotting/bitmap.py:
Added comment.
* [r10339] topo/misc/filepath.py:
Added 'package_path' (the location of the topo module), which is
often what is needed when 'application_path' is currently used.
(Some uses of 'application_path' should be 'output_path'.)
* [r10338] topo/tests/testplotfilesaver.py:
Cleaned up temporary file creation.
* [r10337] topo/param/tk.py:
Removed unused output_path variable.
* [r10336] topo/misc/trace.py:
Removed unused import.
* [r10335] setup.py,
topo/__init__.py:
Added missing numbergen package.
* [r10334] topo/misc/util.py:
Made pstats & cProfile dependencies optional.
* [r10333] topo/misc/filepath.py:
topo.misc.filepath.output_path is set to ~/topographica if the
application_path is not writable.
2009-06-04 antolikjan
* [r10332]
contrib/cc_lissom_oo_or_simple_rv.ty:
change of default parameters
* [r10331]
contrib/cc_lissom_oo_or_simple_rv.ty:
Added intrinsic noise and parametrization of V1 afferent extents
2009-06-04 ceball
* [r10330] setup.py:
Added installation of topographica script.
* [r10329] topo/misc/inlinec.py:
Check for scipy.weave if weave module is not found (for e.g.
Ubuntu package).
* [r10328] topo/command/basic.py:
Removed topo.command.basic's dependency on gnosis module (making
it optional).
* [r10327] setup.py:
Initial version.
2009-06-04 jbednar
* [r10326] doc/User_Manual/overview_text.php:
Added note about one-to-one and all-to-all connections
2009-06-03 jbednar
* [r10325] contrib/jj_tiny.ty:
Added missing imports
* [r10324] contrib/jj_tiny.ty:
Simple starting point for John to optimize
2009-05-31 ceball
* [r10323] doc/buildbot/master.cfg:
svn backup and build scheduled at different times. Skip docs on
mac build.
* [r10322] topo/__init__.py,
topo/misc/legacy.py:
Replace gmpy.mpq with fixedpoint.FixedPoint if gmpy is
unavailable.
* [r10321] topo/misc/util.py:
Added warning.
* [r10320] topo/misc/legacy.py,
topo/misc/util.py:
More advanced module faking: the fake module is not created until
an attempt is made to import the module. So far, only gmpy faking
uses this. Should make no visible change to legacy support for
gmpy.
* [r10319] topo/misc/legacy.py:
Removed testing code (accidentally left in).
2009-05-29 jbednar
* [r10318] topo/analysis/featureresponses.py:
Cleaned up docstring
2009-05-28 ceball
* [r10317] doc/buildbot/master.cfg:
Set up windows build. Added svn checkout retries (to avoid
clobbering the checkout quite so readily). Reduced frequency of
performance tests. The windows build's VM is on doozy, so added
doozy_lock to windows build.
* [r10316] doc/Downloads/index_text.php:
Updated info about using fink to build docs.
2009-05-28 antolikjan
* [r10315] contrib/gc_alissom.ty:
change the default parameters of retinal waves
2009-05-28 ceball
* [r10314] topo/misc/legacy.py:
Fixed support for no gmpy.mpq: numbers like '5/7' couldn't be
parsed by FixedPoint, so the number is first eval'd (using float
division).
* [r10313] external/gmpy-1.04.tar.gz:
Latest release of gmpy.
* [r10312]
topo/tests/reference/topo_or_defs.py:
Corrected typo.
* [r10311]
topo/tests/reference/topo_or_defs.py:
Updated output_fn -> output_fns.
* [r10310]
topo/tests/reference/lissom_oo_dr_reference.ty,
topo/tests/reference/lissom_oo_or_reference.ty,
topo/tests/reference/lissom_or_reference.ty:
Updated output_fn to output_fns.
* [r10309] doc/buildbot/index.html:
Various simplifications.
* [r10308] doc/buildbot/master.cfg:
Cleaned up. Added Ubuntu 9.04 builder.
2009-05-28 jbednar
* [r10307] doc/buildbot/master.cfg:
Fixed typo
2009-05-27 ceball
* [r10306] doc/buildbot/master.cfg:
Simplification of builders.
2009-05-27 jmoudrik
* [r10305] contrib/jm_analysis.py,
contrib/jm_cf_matrix.py,
contrib/jm_smooth.py:
files for complex analysis and an improved CFProjection
2009-05-27 ceball
* [r10304] topo/misc/legacy.py:
Added missing import statement.
* [r10303] doc/buildbot/doozy-buildbot.tac:
Removed out-of-date file.
* [r10302] doc/buildbot/index.html:
Updated links.
* [r10301] doc/buildbot/master.cfg:
Beginnings of reorganization. Added new machines cider (OS X) and
light (Windows XP).
* [r10300] doc/buildbot/master.cfg:
Unoptimized train-tests TESTDP reverted to 5. Changes have been
running on buildbot for a while.
2009-05-26 antolikjan
* [r10299] topo/command/pylabplots.py:
added parameter to size tuning curve measurment function which
defines the size of the maximum disk grating
* [r10298] contrib/jacommands.py:
added surround modulation analysis function
* [r10297] contrib/cc_lesi_oo_or_new.ty:
removed double retina
* [r10296] contrib/gc_alissom.ty:
made Hysteresis optional
* [r10295] topo/analysis/featureresponses.py:
deleted the debugging info and renamed num_repetitions to
repetitions
2009-05-26 ceball
* [r10294]
doc/Developer_Manual/testing_text.php:
Added note.
* [r10293] doc/Downloads/index_text.php:
Minor reorganization.
2009-05-24 jbednar
* [r10292] external/Makefile,
external/gmp-4.2.2.tar.gz,
external/gmp-4.3.1.tar.gz:
Upgraded gmp to 4.3.1 to fix CPU detection problem on some Macs
2009-05-22 antolikjan
* [r10291] topo/command/analysis.py:
Set correct default duration for corner orientation map
measurement
2009-05-21 antolikjan
* [r10290] topo/analysis/featureresponses.py:
Implemented the repetitions paradigm
2009-05-20 antolikjan
* [r10289]
contrib/cc_lissom_oo_or_simple_rv.ty:
Made only single fake retina
* [r10288] contrib/cc_lesi_oo_or_new.ty:
changed default contrasts where tuning curves are measured
* [r10287] contrib/jacommands.py:
made hysteresis in V2 reset
2009-05-18 jbednar
* [r10286] topo/projection/basic.py:
Clarified docstring
2009-05-17 jbednar
* [r10285]
/releases/0.9.6/topographica/doc/User_Manual/overview_text.php:
Added note about one-to-one and all-to-all connections
2009-05-15 antolikjan
* [r10284] contrib/jacommands.py:
switched off V1 plasticity in outputfn after adding V2
* [r10283] contrib/jacommands.py:
changes to AddV2 function
* [r10282] contrib/jacommands.py:
changes to AddV2 function
* [r10281] contrib/v2_cc_lesi_oo_or.ty:
loads a simulation, adds V2
2009-05-11 antolikjan
* [r10280] contrib/cc_lesi_oo_or_new.ty:
Added SimpleHomeoLinear
2009-05-09 jbednar
* [r10279] ChangeLog.txt:
Added recent changes
2009-05-06 ceball
* [r10278] contrib/parameter_search:
Minor fix to work with Python 2.3.
* [r10277] contrib/parameter_search:
Minor correction in docstring.
* [r10276] doc/Downloads/git_text.php:
Removed draft notes that were turning into a git tutorial.
2009-05-04 jbednar
* [r10275]
contrib/gc_lissom_oo_or_homeostatic_new.ty,
contrib/laminar_oo_or.ty,
contrib/laminar_or.ty,
contrib/lesi.ty,
contrib/lesi_whisker_barrels.ty,
contrib/lgn_lateral.ty,
contrib/lissom_oo_or_homeostatic.ty,
contrib/lissom_oo_or_homeostatic_tracked.ty,
contrib/lissom_oo_or_homeostatic_tracked_new.ty,
contrib/lissom_oo_or_noshrinking.ty,
contrib/lissom_oo_or_noshrinking_latswitch.ty,
contrib/lissom_oo_or_species.ty,
contrib/lissom_oo_or_species_tracked.ty,
contrib/lissom_or_noshrinking.ty,
contrib/lissom_or_noshrinking_latswitch.ty,
contrib/sparse_connectivity_LESI.ty,
contrib/sparse_connectivity_model.ty,
contrib/species_cf_jitter.ty,
contrib/species_lateral_sparsity.ty:
Fixed outdated ref to topo.sheet.generator
* [r10274] contrib/gc_alissom.ty:
Fixed typo
* [r10273] contrib/cc_lesi_oo_or_new.ty:
Added newlines
* [r10272] topo/command/basic.py:
Formatted docstring
2009-05-04 ceball
* [r10271] doc/buildbot/master.cfg:
Reduced accuracy of unoptimized tests and altered an email
address. Changes have been live on buildbot for at least a month.
2009-05-03 antolikjan
* [r10270] contrib/gc_alissom.ty:
switched of attribute tracking when fixed treshold output
function is active
* [r10269] contrib/cc_lesi_oo_or_new.ty:
reduced number of contrasts at which tuning curves are computed
2009-05-02 antolikjan
* [r10268] contrib/cc_lesi_oo_or_new.ty:
complex cell model with exactly the same connectivity (except
strength) as in the lesi model in layer 2/3
2009-05-01 antolikjan
* [r10267] topo/analysis/vision.py:
Corrected potential division by zero bug
2009-04-30 antolikjan
* [r10266] contrib/gc_alissom.ty:
Added fixed treshold output function
* [r10265] topo/transferfn/basic.py:
Extended HalfRectify with random treshold
2009-04-30 ceball
* [r10264] contrib/parameter_search:
Added note.
2009-04-30 antolikjan
* [r10263] contrib/gc_alissom.ty:
Removed JointScaling_opt
* [r10262] contrib/jacommands.py:
Corrected SimpleHomeoLinear to set the initial y_avg to MU
2009-04-30 jbednar
* [r10261] doc/Tutorials/lissom_oo_or_text.php:
Minor clarification
* [r10260] Makefile:
Delete generated info directory from distribution
* [r10259] topo/sheet/optimized.py:
Removed unnecessary JointScaling_Opt class, and clarified
docstring for LISSOM_Opt
2009-04-29 antolikjan
* [r10258] contrib/cc_lesi_oo_or.ty:
allowd for homeostasis also in layer 4C
2009-04-29 ceball
* [r10257] contrib/parameter_search:
Corrected path to python.
2009-04-29 antolikjan
* [r10256] contrib/gc_alissom.ty:
changed the t_init parameter
* [r10255] contrib/jacommands.py:
corrected bug with state_push/pop stack
2009-04-29 ceball
* [r10254] contrib/parameter_search:
Tidied up script and documentation; should be no visible change.
2009-04-29 antolikjan
* [r10253] topo/analysis/vision.py:
made the modulation ratio to scale to 0-1.0 scale in order to
achieve correct plotting
* [r10252]
contrib/cc_lissom_oo_or_simple_rv.ty:
corrected bug with external parametriazation
2009-04-29 ceball
* [r10251] contrib/parameter_search:
Removed out-of-date note.
2009-04-28 ceball
* [r10250] contrib/parameter_search:
Initial version of script to help start multiple batch
simulations.
2009-04-27 ceball
* [r10249] topo/param/tk.py,
topo/tkgui/plotgrouppanel.py:
Addition to SF 2122761: pre_plot_hooks etc now also do not
scroll.
2009-04-26 ceball
* [r10248] topo/command/basic.py:
Added max_name_length parameter to run_batch() to avoid
generating experiment directory names that are too long for the
filesystem.
2009-04-25 jbednar
* [r10247] topo/transferfn/basic.py:
Clarified docs
2009-04-25 ceball
* [r10246] topo/param/tk.py,
topo/tkgui/plotgrouppanel.py:
Fix SF 2122761: PlotGroup control buttons now do not scroll.
* [r10245] topo/param/tk.py:
Simplification - no visible change.
2009-04-23 ceball
* [r10244] topo/param/parameterized.py:
Minor clarification.
2009-04-20 antolikjan
* [r10243] contrib/jacommands.py:
Corrected a bug
* [r10242] topo/transferfn/basic.py:
Corrected docstring of state_push/pop in TranfserFnWithState
* [r10241] topo/base/sheet.py:
state_push/pop in Sheet now checks for existing state_push/pop
function in output functions
2009-04-17 ceball
* [r10240] examples/gca_lissom.ty:
Added missing import.
2009-04-16 antolikjan
* [r10239] topo/sheet/optimized.py:
corrected bug with importing of JointScaling
* [r10238] contrib/gc_alissom.ty:
Chaneged JointScaling to JointScaling_Opt
* [r10237] topo/sheet/optimized.py:
Added optimized version of JointScaling
* [r10236] topo/base/sheet.py:
state_push/pop in Sheet now check whether a given output function
is of class TransferFnWithState begfore it calls its
state_push/pop
* [r10235] topo/base/functionfamily.py:
Removed the stat_push/pop from TransferFn (they were moved to
TransferFnWithState)
* [r10234] topo/transferfn/basic.py:
Removed IntrinsicNoise function, moved the definition of
state_push/pop into TranfserFnWithState, and made Hysteresis have
sheet_name parameter
* [r10233] contrib/gc_alissom.ty:
Replaced the IntrinsicNoise transfer function with existing
composite equivalent
2009-04-12 jbednar
* [r10232] topo/transferfn/basic.py:
Cleaned up docs and fixed spelling error on parameter
2009-04-10 antolikjan
* [r10231] topo/transferfn/basic.py:
corrected the IntrinsicNoise OF
* [r10230] contrib/gc_alissom.ty:
changed the default analysis input scale
2009-04-09 antolikjan
* [r10229] topo/transferfn/basic.py:
Added Intrinsic Noise output function and corrected some issues
with state_push/pop
* [r10228] topo/analysis/vision.py:
corrected the measure_and_analyze_complexity to be derived from
the right class
* [r10227] contrib/jacommands.py:
various minor changes
* [r10226] contrib/gc_alissom.ty:
added intrinsic noise and made relative adaptation and gain
control optional
* [r10225]
contrib/cc_lissom_oo_or_simple_rv.ty:
added external parameter
* [r10224] topo/base/sheet.py:
Made sheet to call state_push/pop on all output functions when
its state_push/pop is called
2009-04-06 antolikjan
* [r10223] contrib/gc_alissom.ty:
made the size of V1 to be external parameter
2009-04-04 ceball
* [r10222]
/releases/0.9.6/topographica-win/common/python_topo.tar.gz:
Added missing python25.dll
* [r10221] /trunk/topographica-win/create_installer/README.txt:
Added 10217 from 0.9.6 (note in release instructions).
* [r10220]
/trunk/topographica-win/create_installer/topographica.iss:
Added a step to instructions for Windows release.
2009-04-04 antolikjan
* [r10219]
contrib/cc_lissom_oo_or_simple_rv.ty:
added external parameters
* [r10218] contrib/cc_lesi_oo_or.ty:
added external parameters
2009-04-04 ceball
* [r10217]
/releases/0.9.6/topographica-win/create_installer/README.txt:
Added note.
2009-04-03 ceball
* [r10216] topo/learningfn/optimized.py:
Added ALERT.
* [r10215] /releases/0.9.6/topographica/examples/gca_lissom.ty:
Applied r10212 from trunk: in gca_lissom, "replaced
CFPLF_Scaled_opt with CFPLF_Hebbian_opt - we do not use different
learning rates for individual neurons anymore".
2009-04-03 antolikjan
* [r10214] contrib/cc_lesi_oo_or.ty:
change of default parameters
* [r10213] contrib/cc_lesi_oo_or.ty:
allowed for changing the lateral connections learning rate
* [r10212] examples/gca_lissom.ty:
replaced CFPLF_Scaled_opt with CFPLF_Hebbian_opt - we do not use
different learning rates for individual neurons anymore
2009-04-02 ceball
* [r10211]
/releases/0.9.6/topographica/doc/User_Manual/noise_text.php:
Applied change that was missed from r10209 (r10203 - class name
qualification in the noise documentation).
* [r10210]
/releases/0.9.6/topographica/topo/tkgui/templateplotgrouppanel.py:
Applied r10202 from trunk ('Applied strength-only hack to
refresh_plots() (previously, it was only applied to
redraw_plots()). Fixes SF 2724032.')
* [r10209]
/releases/0.9.6/topographica/doc/User_Manual/noise_text.php:
Applied r10183, r10204, and r10205 from trunk (fixes to noise
documentation).
* [r10208] /releases/0.9.6/topographica/Makefile:
Applied r10167 and r10168 from trunk ("Added separate
win-distclean target so that python_topo/ can be preserved during
distclean on Windows. (Want to keep the binaries for Windows
distribution, but usually during clean we do want to remove
python_topo/)").
* [r10207] /releases/0.9.6/topographica/examples/Makefile:
Applied r10164 from trunk ("Removed references to cfsom_or").
* [r10206]
/releases/0.9.6/topographica/topo/tests/test_map_measurement.py:
Applied r10161 from trunk ("Removed 'Retinotopy' from the list of
map measurements to test").
* [r10205] doc/User_Manual/noise_text.php:
Commented out 'weight adjustment noise' example, since this
specific code cannot currently be used.
* [r10204] doc/User_Manual/noise_text.php:
Described how to get dynamic numbers for weight generation.
* [r10203] doc/User_Manual/noise_text.php:
Qualified some names with the module (e.g. PatternCombine ->
transferfn.PatternCombine.
2009-04-01 ceball
* [r10202]
topo/tkgui/templateplotgrouppanel.py:
Applied strength-only hack to refresh_plots() (previously, it was
only applied to redraw_plots()). Fixes SF 2724032.
* [r10201] /trunk/topographica-win/README.txt,
/trunk/topographica-win/common/python_topo.tar.gz,
/trunk/topographica-win/common/setup.py,
/trunk/topographica-win/create_installer/README.txt,
/trunk/topographica-win/create_installer/prepare_for_installer.bat,
/trunk/topographica-win/create_installer/topographica.iss,
/trunk/topographica-win/create_python_topo/PIL-1.1.5.win32-py2.5.exe,
/trunk/topographica-win/create_python_topo/PIL-1.1.6.win32-py2.5.exe,
/trunk/topographica-win/create_python_topo/README.txt,
/trunk/topographica-win/create_python_topo/distutils_compiler_quoting.diff,
/trunk/topographica-win/create_python_topo/pyreadline-1.5-win32-setup.exe,
/trunk/topographica-win/create_python_topo/setup.bat,
/trunk/topographica-win/setup_cvs_copy/README.txt,
/trunk/topographica-win/setup_cvs_copy/setup.bat,
/trunk/topographica-win/util/gzip.exe:
Merged changes r10135:10191 from releases/0.9.6/topographica-win
into the trunk version of topographica-win.
* [r10200] /releases/0.9.6/topographica/Makefile:
Applied 10199 from trunk: fixes missing images/ellen_arthur.pgm.
* [r10199] Makefile:
Preserve images/ellen_arthur.pgm in release distribtions. Fixes
SF 2724036.
2009-03-31 jbednar
* [r10198] /releases/0.9.6/topographica/examples/som_retinotopy.ty:
Fixed density to match tutorial
* [r10197] examples/som_retinotopy.ty:
Fixed cortex_density; in r9809 it was mistakenly set to 48
instead of 10.
2009-03-30 antolikjan
* [r10196] topo/transferfn/basic.py:
made Hysteresis to push/pop state
* [r10195] topo/base/functionfamily.py:
Introduced push pop function for all output fns
* [r10194] topo/analysis/vision.py:
Made the measure_and_analyse_complexity be a measure_or_pref
class
* [r10193] contrib/jacommands.py:
Big revamp after the move from Eclipse to command line svn
* [r10192]
contrib/cc_lissom_oo_or_simple_rv.ty:
Changed to use shouval dataset
2009-03-28 ceball
* [r10191] /releases/0.9.6/topographica-win/common/setup.py:
Fixed a typo.
* [r10190]
/releases/0.9.6/topographica-win/common/python_topo.tar.gz:
Updated with recent changes.
* [r10189]
/releases/0.9.6/topographica-win/create_python_topo/setup.bat:
Fixed a typo resulting in odict being missed (odict isn't missing
from existing binaries because it was copied in manually).
* [r10188]
/releases/0.9.6/topographica-win/create_python_topo/README.txt:
Fixed a typo.
* [r10187]
/releases/0.9.6/topographica-win/create_python_topo/setup.bat:
Correction to location of weave's compiled code cache.
* [r10186]
/releases/0.9.6/topographica-win/create_python_topo/distutils_compiler_quoting.patch:
Deletion missed from an earlier commit.
* [r10185] /releases/0.9.6/topographica-win/common/setup.py:
Added extra directory to PATH (required for non-admin Vista
users?).
2009-03-28 machalekj
* [r10184] contrib/basic.py,
contrib/hegdeessen.py,
contrib/patternfn.py:
Implementation of Hegde and Van Essen grating and contour
stimuli. Four new basic patterns added to allow this.
2009-03-26 jbednar
* [r10183] doc/User_Manual/noise_text.php:
Clarified how scale and offset work
* [r10182] topo/base/projection.py:
Fixed whitespace
2009-03-24 antolikjan
* [r10181] contrib/cc_lesi_oo_or.ty:
the lesie version of the complex cell model
2009-03-23 ceball
* [r10180] contrib/cbmisc.py,
contrib/rgbhsv.py,
contrib/rgbimages.py:
Reorganization of some of my code.
* [r10179] examples/gca_lissom.ty:
Fixed another typo in code ('Nature' dataset can now be used).
* [r10178] examples/gca_lissom.ty:
Fixed typo in code (p.lgn_density was being ignored).
2009-03-18 ceball
* [r10177]
/releases/0.9.6/topographica-win/create_python_topo/pyreadline-1.5-win32-setup.exe,
/releases/0.9.6/topographica-win/create_python_topo/setup.bat:
Added pyreadline.
2009-03-18 antolikjan
* [r10176] contrib/jacommands.py:
made the lgn channel afferent strength normalization uniform
random
2009-03-18 ceball
* [r10175]
/releases/0.9.6/topographica-win/create_python_topo/distutils_compiler_quoting.diff,
/releases/0.9.6/topographica-win/create_python_topo/setup.bat:
Changed distutils_compiler_quoting patch into a format that works
with the Windows version of patch.
* [r10174]
/releases/0.9.6/topographica-win/create_python_topo/distutils_compiler_quoting.patch,
/releases/0.9.6/topographica-win/create_python_topo/setup.bat:
http://bugs.python.org/issue4508
* [r10173]
/releases/0.9.6/topographica-win/create_installer/topographica.iss:
Removed debugging test.
* [r10172]
/releases/0.9.6/topographica-win/create_installer/topographica.iss:
Added check for required Windows system dlls; if they are
missing, and the user is not running the installation program as
a Power User or Administrator, the installation is aborted (with
a message to that effect, and the instruction to re-run with
appropriate privileges). Also updated paths to match my current
setup.
2009-03-16 ceball
* [r10171]
/releases/0.9.6/topographica-win/setup_cvs_copy/README.txt:
Added more info.
* [r10170]
/releases/0.9.6/topographica-win/create_installer/topographica.iss:
Added conditional installation of some required .dll files.
* [r10169]
/releases/0.9.6/topographica-win/create_installer/README.txt:
Updated to use win-distclean.
* [r10168] Makefile:
Fixed command for renaming.
* [r10167] Makefile:
Added separate win-distclean target so that python_topo/ can be
preserved during distclean on Windows. (Want to keep the binaries
for Windows distribution, but usually during clean we do want to
remove python_topo/.)
* [r10166]
/releases/0.9.6/topographica-win/create_installer/prepare_for_installer.bat:
Minor clarification.
* [r10165]
doc/Developer_Manual/releases_text.php:
Minor updates.
* [r10164] examples/Makefile:
Removed references to cfsom_or.
* [r10163]
/releases/0.9.6/topographica-win/create_installer/README.txt,
/releases/0.9.6/topographica-win/create_installer/topographica.iss:
Clarified instructions.
* [r10162]
/releases/0.9.6/topographica-win/create_installer/README.txt:
Clarified documentation.
* [r10161] topo/tests/test_map_measurement.py:
Removed 'Retinotopy' from the list of map measurements to test.
2009-03-15 ceball
* [r10160]
/releases/0.9.6/topographica-win/setup_cvs_copy/README.txt:
Fixed typo.
* [r10159]
/releases/0.9.6/topographica-win/create_installer/README.txt:
Cut down on duplicated instructions.
* [r10158] topo/numbergen/basic.py:
Fixed syntax and import error.
* [r10157]
/releases/0.9.6/topographica-win/setup_cvs_copy/setup.bat:
Correction to printed instruction.
2009-03-14 ceball
* [r10156] /releases/0.9.6/topographica-win/common/setup.py:
Added missing newline character.
2009-03-14 jbednar
* [r10155] /releases/0.9.6/topographica/examples/gca_lissom.ty,
/releases/0.9.6/topographica/examples/lissom_oo_or.ty,
/releases/0.9.6/topographica/examples/tiny.ty,
/releases/0.9.6/topographica/topo/base/patterngenerator.py,
/releases/0.9.6/topographica/topo/tkgui/plotgrouppanel.py:
Ported bugfixes from the main branch
* [r10154] topo/numbergen/basic.py:
Minor clarifications to docstrings; added softbounds
2009-03-13 ceball
* [r10153] topo/analysis/featureresponses.py:
For 'hue', PatternPresenter detects whether there are three
separate retinas for the color dimension, allowing e.g.
measure_hue_pref() to work with a single, color retina, or with
three separate retinas. (Should be no change to the measurement
for each case.)
* [r10152] topo/analysis/featureresponses.py:
Simplifications - should be no visible change.
2009-03-12 ceball
* [r10151] examples/lissom.ty:
Added ALERT.
* [r10150] contrib/rgbimages.py:
Added handling of cache parameter to ColorImage.
* [r10149] doc/Future_Work/current_text.php:
Test commit.
2009-03-11 antolikjan
* [r10148] contrib/gc_alissom.ty:
parameter changes
2009-03-10 jbednar
* [r10147] /releases/0.9.6/topographica/doc/shared/trailer.php:
Updated sf.net logo as they requested
2009-03-09 ceball
* [r10146] contrib/rgbimages.py:
Now uses weave versions of rgb/hsv conversion functions.
* [r10145] /releases/0.9.6/topographica-win/README.txt,
/releases/0.9.6/topographica-win/create_python_topo/README.txt:
Clarified and moved note about running setup.bat files.
* [r10144]
/releases/0.9.6/topographica-win/common/python_topo.tar.gz:
Updated external packages.
* [r10143]
/releases/0.9.6/topographica-win/create_python_topo/setup.bat:
Added odict
* [r10142]
/releases/0.9.6/topographica-win/setup_cvs_copy/README.txt:
Added a note about MSVCP71.DLL
* [r10141]
/releases/0.9.6/topographica-win/create_python_topo/README.txt,
/releases/0.9.6/topographica-win/create_python_topo/setup.bat:
Simplified instructions.
* [r10140] /releases/0.9.6/topographica-win/util/gzip.exe:
Added gzip.
* [r10139]
/releases/0.9.6/topographica-win/create_python_topo/setup.bat:
Minor alteration to text.
* [r10138]
/releases/0.9.6/topographica-win/create_python_topo/README.txt:
Minor addition to text.
* [r10137]
/releases/0.9.6/topographica-win/create_python_topo/setup.bat:
Missed from previous commit.
* [r10136]
/releases/0.9.6/topographica-win/create_python_topo/PIL-1.1.5.win32-py2.5.exe,
/releases/0.9.6/topographica-win/create_python_topo/PIL-1.1.6.win32-py2.5.exe:
Updated to PIL 1.16
* [r10135] doc/Downloads/cvs_text.php:
Fixed links.
2009-03-09 jbednar
* [r10134] doc/User_Manual/noise_text.php:
Fixed typo
2009-03-08 jbednar
* [r10133] topo/base/patterngenerator.py:
Made __setup_xy and __create_and_rotate_coordinate_arrays not be
private, because it prevented __call__ from being reimplemented
with minor changes in a subclass
2009-03-06 jbednar
* [r10132] topo/base/patterngenerator.py,
topo/tests/lissom_oo_or_t000100.00_Retinotopy.data:
Changed mask_shape to calculate its x, y, and orientation
relative to those of the owning pattern, to allow the mask to be
offset or a different size from the main pattern. These
parameters were previously ignored, and they must now be set to
1.0, 1.0, and 0.0 to get the same results as before. Thus it is
possible for this change to change results for a pattern using
mask_shape, but the old behavior should be easily obtainable by
adding parameter settings.
* [r10131] topo/analysis/featureresponses.py,
topo/command/pylabplots.py,
topo/misc/legacy.py,
topo/pattern/basic.py:
Added explicit size specification for pattern masks, so that they
can later respect their given size
* [r10130] topo/command/pylabplots.py:
Reverted Rectangle to RawRectangle to make tests pass
* [r10129] doc/News/index_text.php:
Added list of new pattern generators, as a comment
* [r10128] doc/News/index_text.php:
Added list of new pattern generators, as a comment
* [r10127] contrib/lissom_happyface.ty,
examples/leaky_lissom_or.ty,
topo/analysis/featureresponses.py,
topo/command/pylabplots.py,
topo/misc/legacy.py,
topo/misc/patternfn.py,
topo/pattern/basic.py,
topo/tests/testpatterngenerator.py:
Moved Arc, Curve, and SmoothedRectangle classes into topo/,
renaming the old Rectangle class to RawRectangle (possibly to be
removed?), and changing SmoothedRectangle to Rectangle. Old code
that uses Rectangle will now have a small amount of smoothing by
default; to avoid this change Rectangle to RawRectangle in the
old code, or set smoothing to zero.
* [r10126] contrib/lissom_happyface.ty:
Major cleanup of documentation, spacing, floating-point errors
for parameter values of 0.0, and parameter names. Changed default
smoothing values, arc_end to arc_length
* [r10125] topo/base/patterngenerator.py,
topo/misc/patternfn.py,
topo/pattern/basic.py:
Increased soft bounds on size and aspect_ratio to make working
with them in the GUI easier. Added guards for case of zero
smoothing, to avoid floating-point errors in extreme cases. Fixes
HACKALERT.
2009-03-05 jbednar
* [r10124] topo/pattern/basic.py:
Added ExponentialDecay pattern.
* [r10123] examples/gca_lissom.ty,
topo/tests/gca_lissom.ty_DATA:
Changed y position seed to match lissom_oo_or.ty; will change
results
* [r10122] topo/misc/patternfn.py:
Fixed errors in Gabor when aspect_ratio or size was zero
* [r10121] topo/misc/patternfn.py:
Added ExponentialDecay pattern. Fixed errors in Gaussian when
aspect_ratio or size was zero
2009-03-04 rczhao
* [r10120] contrib/lissom_happyface.ty:
Replaced Boolean parameter in class Curve with Enumeration.
2009-03-03 ceball
* [r10119] contrib/rgbhsv.py:
File missed from previous checkin (r10118).
* [r10118] contrib/rgbimages.py:
Undid changes to ColorImage from 10111. Corrected how mask,
scale, offset, output_fns are applied. (Also changed from RGB
values on [0,255] to [0,1]; I'd misread the colorsys module
documentation.)
2009-03-03 rczhao
* [r10117] contrib/lissom_happyface.ty:
Revised class Curve and function arc_by_center so that Curve can
draw both constant-length and constant-width curves.
2009-03-03 jbednar
* [r10116] topo/tkgui/editor.py:
Added import removed in previous revision; was breaking gui-tests
2009-03-03 ceball
* [r10115] examples/tiny.ty:
Fixed list of imports.
2009-03-03 jbednar
* [r10114]
doc/Developer_Manual/optimization_text.php:
Fixed attribution
* [r10113] topo/tkgui/editor.py:
Removed duplicate importing of sheets and projections
* [r10112] examples/gca_lissom.ty,
examples/lissom_oo_or.ty:
Fixed area scaling; had not been using the right area or number
of inputs for large areas
2009-03-02 ceball
* [r10111] contrib/rgbimages.py:
Simplified code for ColorImage by overriding __call__ instead of
function().
* [r10110] contrib/rgbimages.py:
Fixed ColorImage: scale, offset, mask, and output_fns were not
being applied to the color channels.
2009-02-27 ceball
* [r10109] topo/command/analysis.py:
save_plotgroup() now uses Parameterized's set_param() method to
set parameters on the plotgroup, thereby giving an error if the
wrong name is given for a plotgroup parameter (e.g.
save_plotgroup('Activity',normalized=True).
* [r10108] topo/param/parameterized.py:
Added set_param() method to Parameterized, for use when setting
parameters (instead of setattr(), which does not check for that
the named attribute is actually a Parameter).
2009-02-27 jbednar
* [r10107] examples/gca_lissom.ty:
Added support for area parameter
* [r10106] topo/tkgui/plotgrouppanel.py:
Made it possible to open Test Pattern window for a simulation
created in the Model Editor
2009-02-25 jbednar
* [r10105] topo/pattern/basic.py:
Added HalfPlane pattern from Stuart
2009-02-24 jbednar
* [r10104] contrib/lissom_happyface.ty:
Fixed RectangleWithSmoothing to be smoothed in both directions.
Changed Arc.arc_end to increase from zero as angles do. Fixed
hiding of Curve.arc_end.
2009-02-24 rczhao
* [r10103] contrib/lissom_happyface.ty:
Revised Arc class and rectangle()
2009-02-23 ceball
* [r10102] contrib/lissom_rgb.ty:
Updated dataset=Gaussian to work with color retina.
* [r10101] contrib/rgbimages.py,
topo/analysis/featureresponses.py:
Added ListGenerator, to create lists dynamically. Changed
ExtendToRGB's channel_strengths to relative_channel_strengths.
* [r10100] images/mcgill/foliage_b/01.png,
images/mcgill/foliage_b/02.png,
images/mcgill/foliage_b/03.png,
images/mcgill/foliage_b/04.png,
images/mcgill/foliage_b/05.png,
images/mcgill/foliage_b/06.png,
images/mcgill/foliage_b/07.png,
images/mcgill/foliage_b/08.png,
images/mcgill/foliage_b/09.png,
images/mcgill/foliage_b/10.png,
images/mcgill/foliage_b/11.png,
images/mcgill/foliage_b/12.png,
images/mcgill/foliage_b/13.png,
images/mcgill/foliage_b/14.png,
images/mcgill/foliage_b/15.png,
images/mcgill/foliage_b/16.png,
images/mcgill/foliage_b/17.png,
images/mcgill/foliage_b/18.png,
images/mcgill/foliage_b/19.png,
images/mcgill/foliage_b/20.png,
images/mcgill/foliage_b/21.png,
images/mcgill/foliage_b/22.png,
images/mcgill/foliage_b/23.png,
images/mcgill/foliage_b/24.png,
images/mcgill/foliage_b/25.png:
Added single-file (i.e. color) versions of existing images (the
existing images will be deleted in the future).
* [r10099] examples/lissom.ty:
Simplified parentheses.
* [r10098] topo/base/projection.py:
Simplified SheetMask's sheet and data properties by making them
both overridable properties. Should be no visible change.
* [r10097] topo/param/parameterized.py,
topo/pattern/image.py:
Renamed Oproperty to overridable_property, and cleaned up docs
and spacing.
2009-02-23 jbednar
* [r10096] contrib/rgbimages.py:
Fixed typo
2009-02-23 ceball
* [r10095] topo/pattern/image.py:
Added comment.
* [r10094] topo/pattern/image.py:
Fixed error deleting PatternSampler's cache of the image.
* [r10093] contrib/rgbimages.py,
topo/pattern/image.py:
Simplified PatternSampler by removing the caching of image array.
(The cache no longer appeared to be having much of an impact on
performance, since PIL.Image can now be efficiently converted to
an array.) Created base class ImageSampler, from which
PatternSampler and FastImageSampler (formerly FastPatternSampler)
now inherit. Simplified GenericImage's _get_image().
* [r10092] topo/base/projection.py,
topo/param/parameterized.py:
Added Oproperty, an implementation of 'property' that allows
subclasses to override the get/set/del methods.
* [r10091] contrib/rgbimages.py:
Updated docs.
* [r10090] contrib/lissom_rgb.ty:
Initial version.
* [r10089] contrib/rgbimages.py:
Added ALERT, plus minor cleanup (should be no visible change).
* [r10088] topo/param/tk.py:
Fixed bug with ListWidget where e.g. right clicking on output_fns
list in the Test Pattern window caused an error. (The 'disabled'
attribute was not being created during __init__.)
2009-02-21 rczhao
* [r10087] contrib/lissom_happyface.ty:
Many improvements.
2009-02-20 ceball
* [r10086] contrib/rgbimages.py:
Simplified application of channel_strengths (now applies in both
color and monochrome cases.
* [r10085] contrib/rgbimages.py:
If ColorImage gets a grayscale image, sets R, G, and B channels
to the same (each to 1/3 of grayscale) rather than giving an
error.
* [r10084] examples/lissom.ty:
Removed accidentally duplicated line (which I think was having no
effect).
* [r10083] topo/command/analysis.py,
topo/command/basic.py,
topo/command/pylabplots.py,
topo/param/parameterized.py:
Fixed problem that became apparent in r10076: e.g. p.x=y (where p
is a ParamOverrides instance) would be lost when passing on p via
**p, because p.x did not result in x being put into the
ParamOverrides dictionary (it was only set as an attribute, and
hence was lost on converting ParamOverrides to a dictionary via
**). ParamOverrides now inserts into its dictionary any attribute
that does not start with an underscore. Genuine attributes of
ParamOverrides (e.g. extra_keywords) have now been renamed to
begin with an underscore (this is better anyway because it
reduces the chance for a parameter to have the same name as an
attribute of ParamOverrides).
2009-02-19 ceball
* [r10082] topo/pattern/image.py:
Added ALERT.
* [r10081] contrib/rgbimages.py:
Simplified RotatedHuesImage's random number generation.
* [r10080] contrib/rgbimages.py:
ParamOverrides-related renaming for consistency. Should be no
visible change.
* [r10079] topo/pattern/image.py:
Removed ability to override PatternSampler's parameter when
calling it (was unused).
* [r10078] contrib/rgbimages.py,
topo/pattern/image.py:
Removed PatternSampler's _initialize_image() method, and made its
whole_pattern_output_fns and background_value_fn be constant
parameters.
* [r10077] topo/param/tk.py:
Added support to ListWidget for constant List parameters (i.e.
don't show a popup menu for a right click if the parameter is
constant).
2009-02-19 jbednar
* [r10076] topo/pattern/basic.py,
topo/pattern/random.py,
topo/pattern/rds.py:
Updated to use cleaner parameter accessing style and to fix cases
where parameters supplied in the call to a PatternGenerator
instance would be ignored. Should be no change in results except
for cases where instances were called with explicit parameters
2009-02-19 ceball
* [r10075] contrib/rgbimages.py:
Restored line that went missing sometime recently.
* [r10074] topo/pattern/basic.py:
Removed unused parameter.
* [r10073] topo/pattern/image.py:
Made ParamOverrides-related naming more consistent. Should be no
visible change.
* [r10072] topo/pattern/basic.py:
Some patterns' __call__ methods were ignoring some parameters if
they were passed in.
* [r10071] topo/pattern/basic.py:
Made ParamOverrides-related naming more consistent. Should be no
visible change.
* [r10070] topo/base/patterngenerator.py:
Minor code simplification.
* [r10069] topo/base/patterngenerator.py:
Fixed bug in Constant pattern generator; since output_fn was
changed to output_fns, Constant has not been working whenever it
has had any output_fns.
* [r10068] topo/base/patterngenerator.py:
Made ParamOverrides-related naming more consistent. Should be no
visible change.
* [r10067] topo/pattern/image.py:
Ensure FileImage's _get_image() uses a filename that's passed
into __call__().
2009-02-18 jbednar
* [r10066] contrib/rgbimages.py:
Cleaned up docs, some code
2009-02-18 ceball
* [r10065] contrib/rgbimages.py:
Made ExtendToRGB have red, green, blue attributes on creation.
* [r10064] topo/sheet/basic.py:
Added ALERT.
* [r10063] topo/analysis/featureresponses.py:
Added commented-out code for measuring hue maps with a single
color retina.
* [r10062] contrib/rgbimages.py:
More simplification. Should be no visible change.
* [r10061] contrib/rgbimages.py:
Simplified ColorImageSheet: automatically wraps input_generator
in ExtendToRGB.
* [r10060] contrib/rgbimages.py:
More renaming of variables.
* [r10059] contrib/rgbimages.py,
topo/command/analysis.py:
Various RGB-related renaming and documentation.
* [r10058] contrib/rgbimages.py:
Simplified ColorImage after recent changes to GenericImage.
* [r10057] topo/pattern/image.py:
Made PatternSampler's __call__ not change the supplied x and y
matrices. (Changing the supplied x any matrices prevents their
reuse e.g. in a subclass of GenericImage that makes more than one
sample.)
* [r10056] topo/pattern/image.py:
Reverted change accidentally introduced during recent
reorganization.
* [r10055] topo/pattern/image.py:
Added to comment.
2009-02-18 jbednar
* [r10054] contrib/lissom_happyface.ty:
Reorganized Arc; added Curve class; still needs more work
2009-02-18 antolikjan
* [r10053]
contrib/cc_lissom_oo_or_simple_rv.ty:
decreased the density of retina to increase speed
2009-02-18 rczhao
* [r10052] contrib/lissom_happyface.ty:
Arc class now can draw an arc by either specifying start and end
radian, or by specifying the arc width and height.
2009-02-18 antolikjan
* [r10051] topo/command/pylabplots.py:
made the tuning curves plotting use larger fonts and thicker
plots lines
2009-02-18 ceball
* [r10050] topo/pattern/image.py,
topo/tests/testimage.py:
Simplified GenericImage and PatternSampler by removing duplicate
parameters size_normalization and whole_image_output_fns from
GenericImage.
* [r10049] topo/pattern/image.py:
Intermediate checkin: changing GenericImage to have a
PatternSampler instance, rather than creating one from a type
each time. Should simplify code and cut down on parameter
duplication.
* [r10048] examples/lissom.ty:
Removed redundant check.
2009-02-18 jbednar
* [r10047] topo/pattern/image.py:
Fixed formatting of docstrings; minor clarifications
* [r10046] topo/plotting/bitmap.py:
Removed unused import
2009-02-18 ceball
* [r10045] topo/pattern/image.py:
Changed some of PatternSampler's various method arguments to be
parameters. Should be no visible change.
2009-02-17 ceball
* [r10044] topo/pattern/image.py:
Restored Float argument accidentally deleted in previous commit.
* [r10043] topo/pattern/image.py:
Simplified converting PIL Image into array (became possible after
upgrading to PIL 1.1.6). Should be no visible change.
* [r10042] examples/lissom.ty:
Fixed typo.
* [r10041] contrib/rgbimages.py:
Code simplification: no visible change.
2009-02-17 antolikjan
* [r10040] contrib/gc_alissom.ty:
selectivity multiplier change
2009-02-17 ceball
* [r10039] examples/lissom.ty:
Updated doc (for script-level parameters).
2009-02-16 ceball
* [r10038] contrib/rgbimages.py:
Corrected import.
2009-02-13 rczhao
* [r10037] contrib/lissom_happyface.ty:
A LISSOM-based happy face (cartoon face with a curved mouth)
simulation.
2009-02-12 jbednar