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Merge branch 'debian' into debian_proper

* debian: (177 commits)
  Update Debian packaging.
  Update news item.
  Prepare release.
  Update changelog.
  NF: confusion.plot(): explicit control over alpha level of numbers
  confusion.plot: text labels are colored with colors of limits in cmap
  NF: disabled test for confusion.plot (based on cell data confusion)
  RF: confusion.plot -- more stable colorbar size, etc
  BF+NF: RF: confusion.plot works fine with provided labels order, NF: sets argument
  NF: confusion.plot() inspired by Ingo
  NF: some pieces migrated from frontier's paper code
  BF: needed to assign axis limits prior to each axis creation
  NF: Let plotBars() pass kwargs to pylab.bars().
  adjusted untraining in sg.SVM
  NF+BF: MappedClassifierSensitivityAnalyzer so now FeatSelClassifiers return appropriate sensitivity
  RF: more informative msg whenever detrend per chunk fails
  BF: maskmapper.reverse didn't care about the size of the 1D data
  RF+NF: stats carry mean values, TPR=0 iff P=0, use alignment within table
  NF: adding lightweight markup for table2string
  NF: now we can assign new labels_map to Dataset at runtime ;-)
  ...
  • Loading branch information...
mih committed Sep 19, 2008
2 parents b8395e3 + 7fd021f commit 942059ce23afadb1b0a876fec04da7f5181ed28d
Showing with 6,664 additions and 619 deletions.
  1. +35 −1 Changelog
  2. +10 −4 Makefile
  3. +6 −3 TODO
  4. +1,452 −0 data/attributes_literal.txt
  5. BIN data/tueb_meg.dat.gz
  6. +152 −0 data/tueb_meg_coord.xyz
  7. +7 −0 debian/changelog
  8. +1 −1 debian/control
  9. +2 −1 debian/rules
  10. +5 −0 doc/_templates/indexsidebar.html
  11. +27 −0 doc/authors.txt
  12. +9 −4 doc/conf.py
  13. +23 −0 doc/datasets.txt
  14. +53 −0 doc/devguide.txt
  15. +7 −4 doc/examples/clfs_examples.py
  16. +70 −0 doc/examples/erp_plot.py
  17. 0 doc/examples/kerneldemo.py
  18. 0 doc/examples/projections.py
  19. +16 −10 doc/examples/sensanas.py
  20. 0 doc/examples/smellit.py
  21. +4 −34 doc/examples/svdclf.py
  22. +47 −0 doc/examples/topo_plot.py
  23. +51 −0 doc/faq.txt
  24. +193 −3 doc/featsel.txt
  25. +91 −22 doc/index.txt
  26. +83 −10 doc/installation.txt
  27. +8 −6 doc/intro.txt
  28. +12 −0 doc/publications.txt
  29. +9 −3 mvpa/__init__.py
  30. +34 −12 mvpa/algorithms/cvtranserror.py
  31. +8 −7 mvpa/base/__init__.py
  32. +76 −0 mvpa/base/dochelpers.py
  33. +3 −2 mvpa/base/externals.py
  34. +2 −2 mvpa/clfs/_svmbase.py
  35. +106 −11 mvpa/clfs/base.py
  36. +196 −7 mvpa/clfs/distance.py
  37. +197 −81 mvpa/clfs/gpr.py
  38. +37 −8 mvpa/clfs/kernel.py
  39. +3 −0 mvpa/clfs/libsmlr/__init__.py
  40. +47 −5 mvpa/clfs/libsvm/svm.py
  41. +46 −20 mvpa/clfs/model_selector.py
  42. +55 −16 mvpa/clfs/sg/svm.py
  43. +20 −5 mvpa/clfs/smlr.py
  44. +45 −4 mvpa/clfs/stats.py
  45. +276 −45 mvpa/clfs/transerror.py
  46. +7 −5 mvpa/clfs/warehouse.py
  47. +563 −31 mvpa/datasets/base.py
  48. +227 −0 mvpa/datasets/channel.py
  49. +13 −38 mvpa/datasets/eep.py
  50. +9 −0 mvpa/datasets/mapped.py
  51. +42 −6 mvpa/datasets/miscfx.py
  52. +10 −3 mvpa/datasets/miscfx_sp.py
  53. +8 −3 mvpa/datasets/nifti.py
  54. +3 −0 mvpa/datasets/splitter.py
  55. +3 −0 mvpa/featsel/base.py
  56. +9 −1 mvpa/mappers/mask.py
  57. +6 −1 mvpa/measures/anova.py
  58. +63 −17 mvpa/measures/base.py
  59. +14 −9 mvpa/measures/corrcoef.py
  60. +465 −0 mvpa/measures/irelief.py
  61. +5 −0 mvpa/misc/cmdline.py
  62. +2 −2 mvpa/misc/data_generators.py
  63. +73 −16 mvpa/misc/io/base.py
  64. +2 −2 mvpa/misc/io/meg.py
  65. +1 −1 mvpa/misc/param.py
  66. +126 −0 mvpa/misc/plot/base.py
  67. +271 −87 mvpa/misc/plot/erp.py
  68. +212 −0 mvpa/misc/plot/topo.py
  69. +10 −0 mvpa/misc/state.py
  70. +23 −0 mvpa/misc/support.py
  71. +5 −1 mvpa/misc/transformers.py
  72. +10 −3 mvpa/suite.py
  73. +17 −8 setup.py
  74. +5 −0 tests/main.py
  75. +14 −2 tests/test_clf.py
  76. +2 −2 tests/test_config.py
  77. +55 −13 tests/test_datameasure.py
  78. +269 −27 tests/test_dataset.py
  79. +29 −0 tests/test_datasetfx.py
  80. +8 −1 tests/test_datasetfx_sp.py
  81. +27 −1 tests/test_eepdataset.py
  82. +1 −1 tests/test_iohelpers.py
  83. +60 −2 tests/test_kernel.py
  84. +12 −0 tests/test_maskeddataset.py
  85. +39 −0 tests/test_meg.py
  86. +6 −2 tests/test_niftidataset.py
  87. +15 −0 tests/test_smlr.py
  88. +18 −1 tests/test_stats.py
  89. +2 −2 tests/test_svdmapper.py
  90. +70 −0 tests/test_svm.py
  91. +272 −0 tests/test_transerror.py
  92. +6 −0 tests/tests_warehouse.py
  93. +31 −0 tools/mpkg_wrapper.py
View
@@ -23,12 +23,46 @@ Unreleased changes
Changes described here are not yet released, but available from VCS
repository.
- * None.
+ * None yet.
Releases
========
+* 0.3.1 (Sun, 14 Sep 2008)
+
+ * New manual section about feature selection with a focus on RFE.
+ Contributed by James M. Hughes.
+ * New dataset type `ChannelDataset` for data structured in channels. Might
+ be useful for data modalities like EEG and MEG. This dataset includes
+ support for common preprocessing steps like resampling and baseline
+ signal substraction.
+ * Plotting of topographies on heads. Thanks to Ingo Fründ for contributing
+ this code. Additionally, a new example shows how to do such plots.
+ * New general purpose function for generating barplots and candlestick plots
+ with error bars (`plotBars()`).
+ * Dataset supports mapping of string labels onto numerical labels, removing
+ the need to perform this mapping manually in user code. 'clfs_examples.py'
+ is adjusted accordingly to demonstrate the new feature.
+ * New Classifier.summary() method to dump classifier settings.
+ * Improved and more flexible plotERPs().
+ * New I-RELIEF sensitivity analyzer.
+ * Added visualization of confusion matrices via `ConfusionMatrix.plot()`
+ inspired by Ingo Fründ.
+ * The PyMVPA version is now globally available in `mvpa.pymvpa_version`.
+ * BugFix: TuebingenMEG reader failed in some cases.
+ * Several improvements (docs and implementation) for building PyMVPA on
+ MacOS X.
+ * New convenience accessor methods (`select()`, `where()` and
+ `__getitem__()`) for the `Dataset` base class.
+ * New `seed()` function to configure the random number generators from user
+ code.
+ * Added reader for a MEG sensor locations format
+ (`TuebingenMEGSensorLocations`).
+ * Initial model selection support for GRP (using openopt).
+ * And tons of minor bugfixes, additional tests and improved documentation.
+
+
* 0.3.0 (Mon, 18 Aug 2008)
* Import of binary EEP files (used by EEProbe) and EEPDataset class.
View
@@ -194,12 +194,13 @@ testapiref: apidoc
test: unittests testmanual testsuite testapiref testexamples
$(COVERAGE_REPORT): build
+ @echo "Generating coverage data and report. Takes awhile. No progress output."
@cd tests && { \
- export PYTHONPATH=..; \
- python-coverage -x main.py; \
- python-coverage -r -i -o /usr >| ../$(COVERAGE_REPORT); \
+ export PYTHONPATH=.. MVPA_DEBUG=.* MVPA_DEBUG_METRICS=ALL; \
+ python-coverage -x main.py >/dev/null 2>&1; \
+ python-coverage -r -i -o /usr,/var >| ../$(COVERAGE_REPORT); \
grep -v '100%$$' ../$(COVERAGE_REPORT); \
- python-coverage -a -i -o /usr; }
+ python-coverage -a -i -o /usr,/var ; }
#
@@ -245,6 +246,11 @@ bdist_rpm: 3rd
--packager "PyMVPA Authors <pkg-exppsy-pymvpa@lists.alioth.debian.org>" \
--vendor "PyMVPA Authors <pkg-exppsy-pymvpa@lists.alioth.debian.org>"
+# build MacOS installer -- depends on patched bdist_mpkg for Leopard
+bdist_mpkg: 3rd
+ python tools/mpkg_wrapper.py setup.py build_ext
+ python tools/mpkg_wrapper.py setup.py install
+
#
# Data
View
9 TODO
@@ -15,8 +15,11 @@
TODO
****
+ * OptimizedClassifier: to automatically select the model in an easy and
+ non-biased(i.e. non-cheating) way, so it could become a part of any
+ more advanced pipeline as a regular classifier
+ * Add ability to add/modify custom attributes to a dataset instance
* IPython mode
- * Add ability to add/modify custom attributes to a dataset.
* Possibly make NiftiDataset default to float32 when it sees that the data are
- ints.
- * Along with ICA mapper, we should add a PLS mapper.
+ ints
+ * Along with ICA mapper, we should add a PLS mapper
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