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ENH: modelines for all the files

whenever there was already an utf-8 codepage mode for a file -- it was
absorbed.  if there were modelines -- they should have been kept

For accomplishing the mission following commands were used:

find -iname *.py ! -path "./build/*" ! -path "./debian/*" ! -path "./.pc/*" ! -path "./newdoc/sphinxext/*" | xargs grep -L '#!' | xargs sed -i '1s|.|# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-\n# vi: set ft=python sts=4 ts=4 sw=4 et:\n&|' | head
find -iname *.py ! -path "./build/*" ! -path "./debian/*" ! -path "./.pc/*" ! -path "./newdoc/sphinxext/*" | xargs grep -l '#!' | xargs sed -i '2s|.|# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-\n# vi: set ft=python sts=4 ts=4 sw=4 et:\n&|' | head

and then manual eyeballing and tune ups in emacs
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1 parent e093c1a commit 43214511ace27006c8245e75293300867230a005 @yarikoptic yarikoptic committed
Showing with 600 additions and 6 deletions.
  1. +2 −0 build_helpers.py
  2. +2 −1 doc/conf.py
  3. +2 −0 doc/devel/guidelines/elegant.py
  4. +2 −0 doc/neurospin/datasets/viz_volume_data.py
  5. +2 −0 doc/neurospin/datasets/viz_volume_field.py
  6. +2 −0 doc/neurospin/datasets/viz_volume_grid.py
  7. +2 −0 doc/neurospin/datasets/viz_volume_img.py
  8. +2 −0 doc/neurospin/plots/enn_demo.py
  9. +2 −0 doc/neurospin/plots/surrogate_array.py
  10. +2 −0 doc/sphinxext/autosummary.py
  11. +2 −0 doc/sphinxext/autosummary_generate.py
  12. +2 −0 doc/sphinxext/docscrape.py
  13. +2 −0 doc/sphinxext/docscrape_sphinx.py
  14. +2 −0 doc/sphinxext/inheritance_diagram.py
  15. +2 −0 doc/sphinxext/ipython_console_highlighting.py
  16. +2 −0 doc/sphinxext/mathmpl.py
  17. +2 −0 doc/sphinxext/numpydoc.py
  18. +2 −0 doc/sphinxext/only_directives.py
  19. +2 −0 doc/sphinxext/plot_directive.py
  20. +2 −0 doc/users/plots/amplitudes.py
  21. +2 −0 doc/users/plots/block.py
  22. +2 −0 doc/users/plots/event.py
  23. +2 −0 doc/users/plots/event_amplitude.py
  24. +2 −0 doc/users/plots/hrf.py
  25. +2 −0 doc/users/plots/hrf_delta.py
  26. +2 −0 doc/users/plots/hrf_different.py
  27. +2 −0 doc/users/plots/neuronal_block.py
  28. +2 −0 doc/users/plots/neuronal_event.py
  29. +2 −0 doc/users/plots/random_amplitudes.py
  30. +2 −0 doc/users/plots/random_amplitudes_times.py
  31. +2 −0 doc/users/plots/sinusoidal.py
  32. +2 −1 doc/www/conf.py
  33. +2 −0 examples/affine_registration.py
  34. +2 −0 examples/compute_fmri_contrast.py
  35. +2 −0 examples/create_fmri_model.py
  36. +2 −0 examples/create_tempimage.py
  37. +2 −0 examples/data_package/nipy-examplepkg/setup.py
  38. +2 −0 examples/fiac/fiac_example.py
  39. +2 −0 examples/fiac/fiac_util.py
  40. +2 −0 examples/fiac/parallel_run.py
  41. +2 −0 examples/fiac/view_contrasts_3d.py
  42. +2 −0 examples/formula/fir.py
  43. +2 −0 examples/formula/multi_session_contrast.py
  44. +2 −0 examples/formula/parametric_design.py
  45. +2 −0 examples/formula/simple_contrast.py
  46. +2 −0 examples/image_fromarray.py
  47. +2 −0 examples/interfaces/process_fiac.py
  48. +2 −0 examples/neurospin/bayesian_gaussian_mixtures.py
  49. +2 −0 examples/neurospin/bayesian_structural_analysis.py
  50. +2 −0 examples/neurospin/blob_extraction.py
  51. +2 −0 examples/neurospin/clustering_comparisons.py
  52. +2 −0 examples/neurospin/demo_dmtx.py
  53. +2 −0 examples/neurospin/dimension_reduction.py
  54. +2 −0 examples/neurospin/example_glm.py
  55. +2 −0 examples/neurospin/gaussian_mixture_models.py
  56. +2 −0 examples/neurospin/glm_lowlevel.py
  57. +2 −0 examples/neurospin/group_reproducibility_analysis.py
  58. +2 −0 examples/neurospin/hierarchical_rois.py
  59. +2 −0 examples/neurospin/histogram_fits.py
  60. +2 −0 examples/neurospin/multi_subject_parcelation.py
  61. +2 −0 examples/neurospin/need_data/bayesian_structural_analaysis.py
  62. +2 −0 examples/neurospin/need_data/demo_blob_from_image.py
  63. +2 −0 examples/neurospin/need_data/demo_roi.py
  64. +2 −0 examples/neurospin/need_data/demo_ward_clustering.py
  65. +2 −0 examples/neurospin/need_data/erp.py
  66. +2 −0 examples/neurospin/need_data/example_localizer_glm.py
  67. +2 −0 examples/neurospin/need_data/example_roi_and_glm.py
  68. +2 −0 examples/neurospin/need_data/get_data_light.py
  69. +2 −0 examples/neurospin/need_data/group_reproducibility_analysis.py
  70. +2 −0 examples/neurospin/need_data/histogram_fits.py
  71. +2 −0 examples/neurospin/need_data/parcel_intra.py
  72. +2 −0 examples/neurospin/need_data/permutation_test.py
  73. +2 −0 examples/neurospin/need_data/script_parcel_multisubj.py
  74. +2 −0 examples/neurospin/need_data/viz.py
  75. +2 −0 examples/neurospin/neurospy/makeParadigmFile.py
  76. +2 −0 examples/neurospin/neurospy/script_first_level_bigrams.py
  77. +2 −0 examples/neurospin/neurospy/script_first_level_fiac.py
  78. +2 −0 examples/neurospin/neurospy/script_first_level_localizer.py
  79. +2 −0 examples/neurospin/neurospy/script_retino.py
  80. +2 −0 examples/neurospin/neurospy/script_surface_localizer.py
  81. +2 −0 examples/neurospin/permutation_test_fakedata.py
  82. +2 −0 examples/neurospin/two_sample_mixed_effects.py
  83. +2 −0 examples/neurospin/ward_clustering.py
  84. +2 −0 examples/neurospin/watershed_labeling.py
  85. +2 −0 examples/nonrigid_registration.py
  86. +2 −0 examples/onesample_group.py
  87. +2 −0 examples/space_time_realign.py
  88. +2 −1 newdoc/conf.py
  89. +2 −1 nipy/__init__.py
  90. +2 −0 nipy/algorithms/__init__.py
  91. +2 −0 nipy/algorithms/diagnostics/__init__.py
  92. +2 −0 nipy/algorithms/diagnostics/screens.py
  93. +2 −0 nipy/algorithms/diagnostics/setup.py
  94. +2 −0 nipy/algorithms/diagnostics/tests/test_screen.py
  95. +2 −0 nipy/algorithms/diagnostics/tests/test_time_difference.py
  96. +2 −0 nipy/algorithms/diagnostics/timediff.py
  97. +2 −0 nipy/algorithms/diagnostics/tsdiffplot.py
  98. +2 −0 nipy/algorithms/fwhm.py
  99. +2 −0 nipy/algorithms/interpolation.py
  100. +2 −0 nipy/algorithms/kernel_smooth.py
  101. +2 −0 nipy/algorithms/resample.py
  102. +2 −0 nipy/algorithms/setup.py
  103. +2 −0 nipy/algorithms/statistics/__init__.py
  104. +2 −0 nipy/algorithms/statistics/classification.py
  105. +2 −0 nipy/algorithms/statistics/nlsmodel.py
  106. +2 −0 nipy/algorithms/statistics/onesample.py
  107. +2 −0 nipy/algorithms/statistics/regression.py
  108. +2 −0 nipy/algorithms/statistics/rft.py
  109. +2 −0 nipy/algorithms/statistics/setup.py
  110. +2 −0 nipy/algorithms/statistics/tests/__init__.py
  111. +2 −0 nipy/algorithms/statistics/tests/test_intrinsic_volumes.py
  112. +2 −0 nipy/algorithms/statistics/tests/test_rft.py
  113. +2 −0 nipy/algorithms/statistics/utils.py
  114. +2 −0 nipy/algorithms/tests/test_kernel_smooth.py
  115. +2 −0 nipy/algorithms/tests/test_resample.py
  116. +2 −0 nipy/core/__init__.py
  117. +2 −0 nipy/core/api.py
  118. +2 −0 nipy/core/image/__init__.py
  119. +2 −0 nipy/core/image/affine_image.py
  120. +2 −0 nipy/core/image/generators.py
  121. +2 −0 nipy/core/image/image.py
  122. +2 −0 nipy/core/image/image_list.py
  123. +2 −0 nipy/core/image/roi.py
  124. +2 −0 nipy/core/image/setup.py
  125. +2 −0 nipy/core/image/tests/test_affine_image.py
  126. +2 −0 nipy/core/image/tests/test_generators.py
  127. +2 −0 nipy/core/image/tests/test_image.py
  128. +2 −0 nipy/core/image/tests/test_image_list.py
  129. +2 −0 nipy/core/image/tests/test_rollaxis.py
  130. +2 −0 nipy/core/image/tests/test_xyz_image.py
  131. +2 −0 nipy/core/image/tests/test_xyz_image_fmri.py
  132. +2 −0 nipy/core/reference/__init__.py
  133. +2 −0 nipy/core/reference/array_coords.py
  134. +2 −0 nipy/core/reference/coordinate_map.py
  135. +2 −0 nipy/core/reference/coordinate_system.py
  136. +2 −0 nipy/core/reference/setup.py
  137. +2 −0 nipy/core/reference/slices.py
  138. +2 −0 nipy/core/reference/tests/matrix_groups.py
  139. +2 −0 nipy/core/reference/tests/test_array_coords.py
  140. +2 −0 nipy/core/reference/tests/test_coordinate_map.py
  141. +2 −0 nipy/core/reference/tests/test_parametrized_surface.py
  142. +2 −0 nipy/core/reference/tests/test_slices.py
  143. +2 −0 nipy/core/setup.py
  144. +2 −0 nipy/core/transforms/affines.py
  145. +2 −0 nipy/core/transforms/setup.py
  146. +2 −0 nipy/core/transforms/tests/test_affines.py
  147. +2 −0 nipy/externals/__init__.py
  148. +2 −1 nipy/externals/argparse.py
  149. +2 −0 nipy/fixes/scipy/setup.py
  150. +2 −0 nipy/fixes/scipy/stats/models/__init__.py
  151. +2 −0 nipy/fixes/scipy/stats/models/descriptors.py
  152. +2 −0 nipy/fixes/scipy/stats/models/family/__init__.py
  153. +2 −0 nipy/fixes/scipy/stats/models/family/family.py
  154. +2 −0 nipy/fixes/scipy/stats/models/family/links.py
  155. +2 −0 nipy/fixes/scipy/stats/models/family/varfuncs.py
  156. +2 −0 nipy/fixes/scipy/stats/models/glm.py
  157. +2 −0 nipy/fixes/scipy/stats/models/info.py
  158. +2 −0 nipy/fixes/scipy/stats/models/model.py
  159. +2 −0 nipy/fixes/scipy/stats/models/regression.py
  160. +2 −0 nipy/fixes/scipy/stats/models/tests/exampledata.py
  161. +2 −0 nipy/fixes/scipy/stats/models/tests/rmodelwrap.py
  162. +2 −0 nipy/fixes/scipy/stats/models/tests/test_anova.py
  163. +2 −0 nipy/fixes/scipy/stats/models/tests/test_glm.py
  164. +2 −0 nipy/fixes/scipy/stats/models/tests/test_matrix_rank.py
  165. +2 −0 nipy/fixes/scipy/stats/models/tests/test_regression.py
  166. +2 −0 nipy/fixes/scipy/stats/models/tests/test_utils.py
  167. +2 −0 nipy/fixes/scipy/stats/models/utils.py
  168. +2 −0 nipy/fixes/scipy/stats/setup.py
  169. +2 −0 nipy/fixes/setup.py
  170. +2 −0 nipy/interfaces/__init__.py
  171. +2 −0 nipy/interfaces/matlab.py
  172. +2 −0 nipy/interfaces/setup.py
  173. +2 −0 nipy/interfaces/spm.py
  174. +2 −0 nipy/interfaces/tests/test_mlabtemp.py
  175. +2 −0 nipy/io/__init__.py
  176. +2 −0 nipy/io/api.py
  177. +2 −0 nipy/io/files.py
  178. +2 −0 nipy/io/imageformats/analyze.py
  179. +2 −0 nipy/io/imageformats/batteryrunners.py
  180. +2 −0 nipy/io/imageformats/binaryheaders.py
  181. +2 −0 nipy/io/imageformats/eulerangles.py
  182. +2 −0 nipy/io/imageformats/filename_parser.py
  183. +2 −0 nipy/io/imageformats/filetuples.py
  184. +2 −0 nipy/io/imageformats/funcs.py
  185. +2 −0 nipy/io/imageformats/header_ufuncs.py
  186. +2 −0 nipy/io/imageformats/headers.py
  187. +2 −0 nipy/io/imageformats/imageglobals.py
  188. +2 −0 nipy/io/imageformats/loadsave.py
  189. +2 −0 nipy/io/imageformats/minc.py
  190. +2 −0 nipy/io/imageformats/nifti1.py
  191. +2 −0 nipy/io/imageformats/orientations.py
  192. +2 −0 nipy/io/imageformats/quaternions.py
  193. +2 −0 nipy/io/imageformats/setup.py
  194. +2 −0 nipy/io/imageformats/spatialimages.py
  195. +2 −0 nipy/io/imageformats/spm2analyze.py
  196. +2 −0 nipy/io/imageformats/spm99analyze.py
  197. +2 −0 nipy/io/imageformats/testing/__init__.py
  198. +2 −0 nipy/io/imageformats/testing/_paramtestpy2.py
  199. +2 −0 nipy/io/imageformats/testing/_paramtestpy3.py
  200. +2 −0 nipy/io/imageformats/testing/lightunit.py
  201. +2 −0 nipy/io/imageformats/testing/nosepatch.py
  202. +2 −0 nipy/io/imageformats/tests/test_analyze.py
  203. +2 −0 nipy/io/imageformats/tests/test_batteryrunners.py
  204. +2 −0 nipy/io/imageformats/tests/test_binary.py
  205. +2 −1 nipy/io/imageformats/tests/test_compat.py
  206. +2 −0 nipy/io/imageformats/tests/test_endiancodes.py
  207. +2 −0 nipy/io/imageformats/tests/test_euler.py
  208. +2 −0 nipy/io/imageformats/tests/test_filetuples.py
  209. +2 −0 nipy/io/imageformats/tests/test_funcs.py
  210. +2 −0 nipy/io/imageformats/tests/test_image_load_save.py
  211. +2 −0 nipy/io/imageformats/tests/test_minc.py
  212. +2 −0 nipy/io/imageformats/tests/test_nifti1.py
  213. +2 −0 nipy/io/imageformats/tests/test_orientations.py
  214. +2 −0 nipy/io/imageformats/tests/test_quaternions.py
  215. +2 −0 nipy/io/imageformats/tests/test_recoder.py
  216. +2 −0 nipy/io/imageformats/tests/test_spm2analyze.py
  217. +2 −0 nipy/io/imageformats/tests/test_spm99analyze.py
  218. +2 −0 nipy/io/imageformats/tests/test_types_filenames.py
  219. +2 −0 nipy/io/imageformats/tests/test_utils.py
  220. +2 −0 nipy/io/imageformats/volumeutils.py
  221. +2 −0 nipy/io/nifti_ref.py
  222. +2 −0 nipy/io/setup.py
  223. +2 −0 nipy/io/tests/test_image_io.py
  224. +2 −0 nipy/io/tests/test_nifti_ref.py
  225. +2 −0 nipy/io/tests/test_save.py
  226. +2 −0 nipy/modalities/__init__.py
  227. +2 −0 nipy/modalities/fmri/__init__.py
  228. +2 −0 nipy/modalities/fmri/aliased.py
  229. +2 −0 nipy/modalities/fmri/api.py
  230. +2 −0 nipy/modalities/fmri/design.py
  231. +2 −0 nipy/modalities/fmri/fmri.py
  232. +2 −0 nipy/modalities/fmri/fmristat/__init__.py
  233. +2 −0 nipy/modalities/fmri/fmristat/api.py
  234. +2 −0 nipy/modalities/fmri/fmristat/delay.py
  235. +2 −0 nipy/modalities/fmri/fmristat/hrf.py
  236. +2 −0 nipy/modalities/fmri/fmristat/model.py
  237. +2 −0 nipy/modalities/fmri/fmristat/setup.py
  238. +2 −0 nipy/modalities/fmri/fmristat/tests/FIACdesigns.py
  239. +2 −0 nipy/modalities/fmri/fmristat/tests/test_FIAC.py
  240. +2 −0 nipy/modalities/fmri/fmristat/tests/test_hrf.py
  241. +2 −0 nipy/modalities/fmri/fmristat/tests/test_iterables.py
  242. +2 −0 nipy/modalities/fmri/fmristat/tests/test_model.py
  243. +2 −0 nipy/modalities/fmri/fmristat/utils.py
  244. +2 −0 nipy/modalities/fmri/formula.py
  245. +2 −0 nipy/modalities/fmri/hrf.py
  246. +2 −0 nipy/modalities/fmri/pca.py
  247. +2 −0 nipy/modalities/fmri/setup.py
  248. +2 −0 nipy/modalities/fmri/spm/__init__.py
  249. +2 −0 nipy/modalities/fmri/spm/correlation.py
  250. +2 −0 nipy/modalities/fmri/spm/example.py
  251. +2 −0 nipy/modalities/fmri/spm/model.py
  252. +2 −0 nipy/modalities/fmri/spm/reml.py
  253. +2 −0 nipy/modalities/fmri/spm/trace.py
  254. +2 −0 nipy/modalities/fmri/tests/test_aliases.py
  255. +2 −0 nipy/modalities/fmri/tests/test_fmri.py
  256. +2 −0 nipy/modalities/fmri/tests/test_formula.py
  257. +2 −0 nipy/modalities/fmri/tests/test_iterators.py
  258. +2 −0 nipy/modalities/fmri/tests/test_pca.py
  259. +2 −0 nipy/modalities/fmri/tests/test_pca_image.py
  260. +2 −0 nipy/modalities/fmri/tests/test_utils.py
  261. +2 −0 nipy/modalities/fmri/utils.py
  262. +2 −0 nipy/modalities/setup.py
  263. +2 −0 nipy/neurospin/__init__.py
  264. +2 −0 nipy/neurospin/bindings/__init__.py
  265. +2 −0 nipy/neurospin/bindings/benchmarks/bench_numpy.py
  266. +2 −0 nipy/neurospin/bindings/setup.py
  267. +2 −0 nipy/neurospin/bindings/tests/test_numpy.py
  268. +2 −0 nipy/neurospin/clustering/__init__.py
  269. +2 −0 nipy/neurospin/clustering/benchmarks/bench_bootstrap_hc.py
  270. +2 −0 nipy/neurospin/clustering/bgmm.py
  271. +2 −0 nipy/neurospin/clustering/bootstrap_hc.py
  272. +2 −0 nipy/neurospin/clustering/clustering.py
  273. +2 −0 nipy/neurospin/clustering/ggmixture.py
  274. +2 −0 nipy/neurospin/clustering/gmm.py
  275. +2 −0 nipy/neurospin/clustering/hierarchical_clustering.py
  276. +2 −0 nipy/neurospin/clustering/tests/test_bgmm.py
  277. +2 −0 nipy/neurospin/clustering/tests/test_bootstrap_hc.py
  278. +2 −0 nipy/neurospin/clustering/tests/test_hierarchical_clustering.py
  279. +2 −0 nipy/neurospin/datasets/__init__.py
  280. +2 −0 nipy/neurospin/datasets/converters.py
  281. +2 −0 nipy/neurospin/datasets/setup.py
  282. +2 −0 nipy/neurospin/datasets/tests/test_converters.py
  283. +2 −0 nipy/neurospin/datasets/transforms/affine_transform.py
  284. +2 −0 nipy/neurospin/datasets/transforms/affine_utils.py
  285. +2 −0 nipy/neurospin/datasets/transforms/setup.py
  286. +2 −0 nipy/neurospin/datasets/transforms/tests/test_affine_utils.py
  287. +2 −0 nipy/neurospin/datasets/transforms/tests/test_transform.py
  288. +2 −0 nipy/neurospin/datasets/transforms/transform.py
  289. +2 −0 nipy/neurospin/datasets/volumes/__init__.py
  290. +2 −0 nipy/neurospin/datasets/volumes/setup.py
  291. +2 −0 nipy/neurospin/datasets/volumes/tests/test_volume_data.py
  292. +2 −0 nipy/neurospin/datasets/volumes/tests/test_volume_field.py
  293. +2 −0 nipy/neurospin/datasets/volumes/tests/test_volume_grid.py
  294. +2 −0 nipy/neurospin/datasets/volumes/tests/test_volume_img.py
  295. +2 −0 nipy/neurospin/datasets/volumes/volume_data.py
  296. +2 −0 nipy/neurospin/datasets/volumes/volume_field.py
  297. +2 −0 nipy/neurospin/datasets/volumes/volume_grid.py
  298. +2 −0 nipy/neurospin/datasets/volumes/volume_img.py
  299. +2 −0 nipy/neurospin/eda/dimension_reduction.py
  300. +2 −0 nipy/neurospin/eda/tests/test_dr.py
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2 build_helpers.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Build helpers for setup.py
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3 doc/conf.py
@@ -1,4 +1,5 @@
-# -*- coding: utf-8 -*-
+# emacs: -*- coding: utf-8; mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
#
# sampledoc documentation build configuration file, created by
# sphinx-quickstart on Tue Jun 3 12:40:24 2008.
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2 doc/devel/guidelines/elegant.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import matplotlib.pyplot as plt
plt.plot([1,2,3], [4,5,6])
plt.ylabel('some more numbers')
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2 doc/neurospin/datasets/viz_volume_data.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Use Mayavi to visualize the structure of a VolumeData
"""
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2 doc/neurospin/datasets/viz_volume_field.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Use Mayavi to visualize the structure of a VolumeData
"""
View
2 doc/neurospin/datasets/viz_volume_grid.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Use Mayavi to visualize the structure of a VolumeGrid
"""
View
2 doc/neurospin/datasets/viz_volume_img.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Use Mayavi to visualize the structure of a VolumeImg
"""
View
2 doc/neurospin/plots/enn_demo.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
x = np.c_[np.random.normal(size=1e4),
np.random.normal(scale=4, size=1e4)]
View
2 doc/neurospin/plots/surrogate_array.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
import pylab as pl
View
2 doc/sphinxext/autosummary.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
===========
autosummary
View
2 doc/sphinxext/autosummary_generate.py
@@ -1,4 +1,6 @@
#!/usr/bin/env python
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
r"""
autosummary_generate.py OPTIONS FILES
View
2 doc/sphinxext/docscrape.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Extract reference documentation from the NumPy source tree.
"""
View
2 doc/sphinxext/docscrape_sphinx.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import re, inspect, textwrap, pydoc
import sphinx
from docscrape import NumpyDocString, FunctionDoc, ClassDoc
View
2 doc/sphinxext/inheritance_diagram.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Defines a docutils directive for inserting inheritance diagrams.
View
2 doc/sphinxext/ipython_console_highlighting.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""reST directive for syntax-highlighting ipython interactive sessions.
"""
View
2 doc/sphinxext/mathmpl.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import os
import sys
try:
View
2 doc/sphinxext/numpydoc.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
========
numpydoc
View
2 doc/sphinxext/only_directives.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
#
# A pair of directives for inserting content that will only appear in
# either html or latex.
View
2 doc/sphinxext/plot_directive.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
A special directive for generating a matplotlib plot.
View
2 doc/users/plots/amplitudes.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This figure is meant to represent an event-type design with
events at times [0,4,8,12,16] and amplitudes [0,1.1,2.3,0.9,0.3].
View
2 doc/users/plots/block.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This figure is meant to represent an event-type with Faces presented
at times [0,4,8,12,16] and Objects presented at [2,6,10,14,18].
View
2 doc/users/plots/event.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This figure is meant to represent an event-type with Faces presented
at times [0,4,8,12,16] and Objects presented at [2,6,10,14,18].
View
2 doc/users/plots/event_amplitude.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
import pylab
View
2 doc/users/plots/hrf.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Plot of the canonical Glover HRF
"""
View
2 doc/users/plots/hrf_delta.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This plot demonstrates a neuronal model that is a sum
of delta functions times coefficient values
View
2 doc/users/plots/hrf_different.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This example uses a different HRF for different event types
"""
View
2 doc/users/plots/neuronal_block.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This figure is meant to represent the neuronal block model
with Faces at times [0,4,8,12,16] and Objects presented at [2,6,10,14,18]
View
2 doc/users/plots/neuronal_event.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This figure is meant to represent the neuronal event-related model
View
2 doc/users/plots/random_amplitudes.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This figure is meant to represent an event-type design with
events at times [0,4,8,12,16] and random amplitudes
View
2 doc/users/plots/random_amplitudes_times.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This figure is meant to represent an event-type design with
events at random times centered [0,2,4,6,8] and random
View
2 doc/users/plots/sinusoidal.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This figure is meant to represent a continuous
stimulus having two features, Orientation and Contrast
View
3 doc/www/conf.py
@@ -1,4 +1,5 @@
-# -*- coding: utf-8 -*-
+# emacs: -*- coding: utf-8; mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
#
#
# All configuration values have a default value; values that are commented out
View
2 examples/affine_registration.py
@@ -1,4 +1,6 @@
#!/usr/bin/env python
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This script requires the nipy-data package to run. It is an example of
inter-subject affine registration using two MR-T1 images from the
View
2 examples/compute_fmri_contrast.py
@@ -1,4 +1,6 @@
#!/usr/bin/env python
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This script requires the nipy-data package to run. It is an example of
using a general linear model in single-subject fMRI data analysis
View
2 examples/create_fmri_model.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
import sympy as sym
from numpy.random import randn
View
2 examples/create_tempimage.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""This example shows how to create a temporary image to use during processing.
The array is filled with zeros.
View
2 examples/data_package/nipy-examplepkg/setup.py
@@ -1,4 +1,6 @@
#!/usr/bin/env python
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
''' Installation script for nipy examplepkg package '''
import os
from os.path import join as pjoin
View
2 examples/fiac/fiac_example.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Example analyzing the FIAC dataset with NIPY.
"""
#-----------------------------------------------------------------------------
View
2 examples/fiac/fiac_util.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Support utilities for FIAC example, mostly path management.
The purpose of separating these is to keep the main example code as readable as
View
2 examples/fiac/parallel_run.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Script to run the main analyses in parallel, using the IPython machinery.
"""
#-----------------------------------------------------------------------------
View
2 examples/fiac/view_contrasts_3d.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""A quick and dirty example of using Mayavi to overlay anatomy and activation.
"""
#-----------------------------------------------------------------------------
View
2 examples/formula/fir.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
import sympy
from nipy.modalities.fmri import formula, utils, hrf
View
2 examples/formula/multi_session_contrast.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
import sympy
from nipy.modalities.fmri import formula, utils, hrf
View
2 examples/formula/parametric_design.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
In this example, we create a regression model for
an event-related design in which the response
View
2 examples/formula/simple_contrast.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
import nipy.testing as niptest
import sympy
View
2 examples/image_fromarray.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Create a nifti image from a numpy array and an affine transform."""
import os
View
2 examples/interfaces/process_fiac.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
''' Single subject analysis script for SPM / FIAC '''
import sys
from os.path import join as pjoin
View
2 examples/neurospin/bayesian_gaussian_mixtures.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Example of a demo that fits a Bayesian Gaussian Mixture Model (GMM)
to a dataset.
View
2 examples/neurospin/bayesian_structural_analysis.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This scipt generates a noisy activation image image
and applies the bayesian structural analysis on it
View
2 examples/neurospin/blob_extraction.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This scipt generates a noisy activation image image
and extracts the blobs from it.
View
2 examples/neurospin/clustering_comparisons.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Simple demo that partitions a smooth field into 10 clusters
In that case, Ward's clustering behaves best, by far.
View
2 examples/neurospin/demo_dmtx.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Examples of design matrices specification and and computation
(event-related design, FIR design, etc)
View
2 examples/neurospin/dimension_reduction.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Example of dimension reduction on a swiss roll using Isomap.
Bertrand Thirion, 2008-2010
View
2 examples/neurospin/example_glm.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This is an example where
1. An sequence of fMRI volumes are simulated
View
2 examples/neurospin/gaussian_mixture_models.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Example of a demo that fits a Gaussian Mixture Model (GMM) to a dataset
The possible number of clusters is in the [1,10] range
View
2 examples/neurospin/glm_lowlevel.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This example routine simulates a number of pure Gaussian white noise
signals, then fits each one in terms of two regressors: a constant baseline,
View
2 examples/neurospin/group_reproducibility_analysis.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Example of script to analyse the reproducibility in group studies
using a bootstrap procedure
View
2 examples/neurospin/hierarchical_rois.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
__doc__ = \
"""
Example of a script that crates a 'hierarchical roi' structure
View
2 examples/neurospin/histogram_fits.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
__doc__ = \
"""
Example of a script that perfoms histogram analysis of an activation
View
2 examples/neurospin/multi_subject_parcelation.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This script contains a quick demo on a multi'subject parcellation
on a toy 2D example.
View
2 examples/neurospin/need_data/bayesian_structural_analaysis.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Example of a script that uses the BSA (Bayesian Structural Analysis)
-- nipy.neurospin.spatial_models.bayesian_structural_analysis --
View
2 examples/neurospin/need_data/demo_blob_from_image.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This scipt generates a noisy activation image image
and extracts the blob from it.
View
2 examples/neurospin/need_data/demo_roi.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This is a little demo that simply shows ROI manipulation within
the nipy framework
View
2 examples/neurospin/need_data/demo_ward_clustering.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This is a little demo that simply shows the effect of ward clustering
on an fMRI dataset
View
2 examples/neurospin/need_data/erp.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
from nipy.neurospin.glm import glm
from time import time
View
2 examples/neurospin/need_data/example_localizer_glm.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Example of (step-by-step) GLM application and result creation.
More specifically,
View
2 examples/neurospin/need_data/example_roi_and_glm.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This is an example where
1. An sequence of fMRI volumes are loaded
View
2 examples/neurospin/need_data/get_data_light.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Get two images from the web (one mask image and one spmT image) and
put them in the dir: ~/.nipy/tests/data
View
2 examples/neurospin/need_data/group_reproducibility_analysis.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Example of script to analyse the reproducibility in group studies
using a bootstrap procedure
View
2 examples/neurospin/need_data/histogram_fits.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Example of a script that perfoms histogram analysis of an activation image.
This is based on a real fMRI image
View
2 examples/neurospin/need_data/parcel_intra.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Example of script to parcellate the data from one subject,
using various algorithms.
View
2 examples/neurospin/need_data/permutation_test.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
from nipy.neurospin.group.permutation_test import permutation_test_onesample
View
2 examples/neurospin/need_data/script_parcel_multisubj.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Example of script to parcellate mutli-subject data
author: Bertrand Thirion, 2005-2009
View
2 examples/neurospin/need_data/viz.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Example of activation image vizualization
with nip.neurospin vizualization tools
View
2 examples/neurospin/neurospy/makeParadigmFile.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
import csv
View
2 examples/neurospin/neurospy/script_first_level_bigrams.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Script that perform the first-level analysis of a dataset of the FIAC
Last updated by B.Thirion
View
2 examples/neurospin/neurospy/script_first_level_fiac.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Script that perform the first-level analysis of a dataset of the FIAC
Last updated by B.Thirion
View
2 examples/neurospin/neurospy/script_first_level_localizer.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Script that perform the first-level analysis of a dataset of the FIAC
Last updated by B.Thirion
View
2 examples/neurospin/neurospy/script_retino.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Script that performs the GLM analysis on the cortical surface
In order to obtain retinotopic maps
View
2 examples/neurospin/neurospy/script_surface_localizer.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Script that perform the first-level analysis of a dataset of the localizer
Here the analysis is perfomed on the cortical of one hemisphere.
View
2 examples/neurospin/permutation_test_fakedata.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
from nipy.neurospin.group import permutation_test as PT
View
2 examples/neurospin/two_sample_mixed_effects.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Demo two sample mixed effect models;
"""
View
2 examples/neurospin/ward_clustering.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Demo ward clustering on a graph:
various ways of forming clusters and dendrogram
View
2 examples/neurospin/watershed_labeling.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This scipt generates a noisy activation image image
and performs a watershed segmentation in it.
View
2 examples/nonrigid_registration.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
from nipy.neurospin.registration import *
View
2 examples/onesample_group.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
import nipy.neurospin.statistical_mapping as sm
View
2 examples/space_time_realign.py
@@ -1,4 +1,6 @@
#!/usr/bin/env python
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This script requires the nipy-data package to run. It is an example of
simultaneous motion correction and slice timing correction in
View
3 newdoc/conf.py
@@ -1,4 +1,5 @@
-# -*- coding: utf-8 -*-
+# emacs: -*- coding: utf-8; mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
#
# nipy documentation build configuration file, created by
# sphinx-quickstart on Mon Jul 20 12:30:18 2009.
View
3 nipy/__init__.py
@@ -1,4 +1,5 @@
-# -*- coding: utf-8 -*-
+# emacs: -*- coding: utf-8; mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set fileencoding=utf-8 ft=python sts=4 ts=4 sw=4 et:
"""
Neuroimaging tools for Python (NIPY).
View
2 nipy/algorithms/__init__.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Package containing generic algorithms such as registration, statistics,
simulation, etc.
View
2 nipy/algorithms/diagnostics/__init__.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
# Initialization for diagnostics package
from .timediff import time_slice_diffs
View
2 nipy/algorithms/diagnostics/screens.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
''' Diagnostic 4d image screen '''
from os.path import join as pjoin
View
2 nipy/algorithms/diagnostics/setup.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import os.path
import numpy.core
View
2 nipy/algorithms/diagnostics/tests/test_screen.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
""" Testing diagnostic screen
"""
View
2 nipy/algorithms/diagnostics/tests/test_time_difference.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
""" Testing tsdiffana
"""
View
2 nipy/algorithms/diagnostics/timediff.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
''' Time series diagnostics
These started life as ``tsdiffana.m`` - see
View
2 nipy/algorithms/diagnostics/tsdiffplot.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
''' plot tsdiffana parameters '''
import numpy as np
View
2 nipy/algorithms/fwhm.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This module provides classes and definitions for using full width at half
maximum (FWHM) to be used in conjunction with Gaussian Random Field Theory
View
2 nipy/algorithms/interpolation.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Image interpolators using ndimage.
"""
View
2 nipy/algorithms/kernel_smooth.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
TODO
"""
View
2 nipy/algorithms/resample.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Some simple examples and utility functions for resampling.
"""
View
2 nipy/algorithms/setup.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('algorithms', parent_package, top_path)
View
2 nipy/algorithms/statistics/__init__.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
TODO
"""
View
2 nipy/algorithms/statistics/classification.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
TODO
"""
View
2 nipy/algorithms/statistics/nlsmodel.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
TODO
"""
View
2 nipy/algorithms/statistics/onesample.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
TODO
"""
View
2 nipy/algorithms/statistics/regression.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This module provides various convenience functions for extracting
statistics from regression analysis techniques to model the
View
2 nipy/algorithms/statistics/rft.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
__docformat__ = 'restructuredtext'
"""
View
2 nipy/algorithms/statistics/setup.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
def configuration(parent_package='',top_path=None):
View
2 nipy/algorithms/statistics/tests/__init__.py
@@ -1,2 +1,4 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import nipy.algorithms.statistics.tests.test_rft
import nipy.algorithms.statistics.tests.test_intrinsic_volumes
View
2 nipy/algorithms/statistics/tests/test_intrinsic_volumes.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
import numpy.linalg as L
import numpy.random as R
View
2 nipy/algorithms/statistics/tests/test_rft.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
from scipy.special import gammaln, hermitenorm
import scipy.stats
View
2 nipy/algorithms/statistics/utils.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
# Taken from python doc site, exists in python2.6
View
2 nipy/algorithms/tests/test_kernel_smooth.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
from numpy.random import random_integers as randint
View
2 nipy/algorithms/tests/test_resample.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
View
2 nipy/core/__init__.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Package containing core nipy classes.
"""
View
2 nipy/core/api.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Pseudo-package for all of the core symbols from the image object and its
reference system. Use this module for importing core names into your
View
2 nipy/core/image/__init__.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
The Image class provides the interface which should be used
by users at the application level. The image provides a coordinate map,
View
2 nipy/core/image/affine_image.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
The base image interface.
"""
View
2 nipy/core/image/generators.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This module defines a few common generators that may be useful
for Image instances.
View
2 nipy/core/image/image.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This module defines the Image class, as well as two functions that create Image instances.
View
2 nipy/core/image/image_list.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
from copy import copy
import numpy as np
View
2 nipy/core/image/roi.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Template region of interest (ROI) module
"""
View
2 nipy/core/image/setup.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('image', parent_package, top_path)
View
2 nipy/core/image/tests/test_affine_image.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipy.testing import *
from nipy.core.image import affine_image
View
2 nipy/core/image/tests/test_generators.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
from nipy.testing import *
View
2 nipy/core/image/tests/test_image.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import warnings
import numpy as np
View
2 nipy/core/image/tests/test_image_list.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
from nipy.core.image.image_list import ImageList
View
2 nipy/core/image/tests/test_rollaxis.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This test basically just plays around with image.rollaxis.
View
2 nipy/core/image/tests/test_xyz_image.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import copy
from nipy.core.image import xyz_image
View
2 nipy/core/image/tests/test_xyz_image_fmri.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipy.testing import *
import numpy as np
View
2 nipy/core/reference/__init__.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Frame of reference/coordinates package.
View
2 nipy/core/reference/array_coords.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Some CoordinateMaps have a domain that are 'array' coordinates,
hence the function of the CoordinateMap can be evaluated at these
View
2 nipy/core/reference/coordinate_map.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This module describes two types of *mappings*:
View
2 nipy/core/reference/coordinate_system.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
CoordinateSystems are used to represent the space in which the image resides.
View
2 nipy/core/reference/setup.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('reference', parent_package, top_path)
View
2 nipy/core/reference/slices.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
A set of methods to get coordinate maps which represent slices in space.
View
2 nipy/core/reference/tests/matrix_groups.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This module is essentially a test of the AffineTransform object to
see if it can succinctly describe an object like a matrix group.
View
2 nipy/core/reference/tests/test_array_coords.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
""" Testing array coords
"""
View
2 nipy/core/reference/tests/test_coordinate_map.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
from nipy.testing import (assert_true, assert_equal, assert_raises,
assert_false, assert_array_equal,
View
2 nipy/core/reference/tests/test_parametrized_surface.py
@@ -1,3 +1,5 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Parametrized surfaces using a CoordinateMap
"""
View