Merge pull request #307 from hanke/v24docfix

WiP: Kitchen sink of updates for v2.4

Makefile

@@ -469,7 +469,7 @@ testexamples: te-svdclf te-smlr te-sensanas te-pylab_2d \
               te-erp_plot te-match_distribution te-permutation_test \
               te-searchlight_minimal te-smlr te-start_easy te-topo_plot \
               te-gpr te-gpr_model_selection0 te-mri_plot te-searchlight \
-              te-clfs_examples
+              te-eventrelated te-clfs_examples
 
 testdocstrings: dt-mvpa
 

bin/pymvpa2-tutorial

@@ -107,24 +107,22 @@ def main():
     if notebook_srcdir is False:
         notebook_srcdir = '/usr/share/doc/python-mvpa2/notebooks'
     # assemble session dir
-    for dir in ('data', 'results'):
-        src = os.path.join(os.path.abspath(tutorial_datadir), dir)
-        dst = os.path.join(os.path.abspath(workdir), dir)
-        if os.path.lexists(dst):
-            print "Use existing tutorial '%s' path at '%s'." \
-                  % (dir, dst)
-            continue
+    dst = os.path.join(os.path.abspath(workdir), 'data')
+    src = os.path.abspath(tutorial_datadir)
+    if os.path.lexists(dst):
+        print "Use existing tutorial data path at '%s'." % (dst,)
+    else:
         if not os.path.exists(src):
-            # only the data dir is absolutely critical
-            if dir == 'data':
-                print "Cannot find tutorial data at '%s'" % src
-                sys.exit(1)
-            else:
-                continue
-        if hasattr(os, 'symlink'):
-            os.symlink(src, dst)
+            print "Cannot find tutorial data at '%s'" % (src,)
+            sys.exit(1)
         else:
-            shutil.copytree(src, dst)
+            if hasattr(os, 'symlink'):
+                os.symlink(src, dst)
+            else:
+                shutil.copytree(src, dst)
+    # point pymvpa to the personalized folder
+    os.environ['MVPA_LOCATION_TUTORIAL_DATA'] = dst
+    # prep IPython call
     ipy_args = sys.argv[1:]
     ipy_args.append('--quiet')
     if not sum([arg.startswith('--pylab') for arg in ipy_args]):

doc/Makefile

@@ -40,20 +40,14 @@ SPHINXEXT_PATH=$(shell python -c 'import sphinx.ext; from distutils.version impo
 generate: generate-stamp
 generate-stamp: cache_intersphinx
 	mkdir -p $(BUILDDIR)
-	@MVPA_EXTERNALS_RAISE_EXCEPTION=off \
-		PYTHONPATH=$(CURDIR)/sphinxext:$(CURDIR)/..:$(PYTHONPATH) \
-		$(PYTHON) $(SPHINXEXT_PATH)/autosummary/generate.py \
-		-t $(CURDIR)/templates -o source/generated source/*.rst
-	# wipe everything that is not pymvpa to prevent suffering from the bugs
-	# of other in subsequent stages
-	find source/generated -type f ! -name 'mvpa*' -delete
+	mkdir -p source/generated
 	set -e; set -o pipefail; for man in $(BUILDDIR)/man/pymvpa*; do \
 		manfile=$$(basename $${man}) ; \
 		cmd=$${manfile#pymvpa2-*} ; \
 		cmd=$${cmd%*.1} ; \
 		man2html $${man} | sed -n '/<HR>/{:a;n;/<HR>/b;p;ba}' | sed -n '/<A NAME/{:a;n;/This document was created by/b;p;ba}' > source/generated/$${manfile}.html ; \
 		underline="*****************$$(echo $${cmd} | tr A-Za-z0-9 \*)" ; \
-		echo ".. index:: command line, $${cmd}\n.. _chap_cmdline_$${cmd}\n\n$${underline}\nMan page for \`\`$${cmd}\`\`\n$${underline}\n\n.. raw:: html\n   :file: $${manfile}.html\n" > source/generated/cmd_$${cmd}.rst ; \
+		printf ".. index:: command line, $${cmd}\n.. _chap_cmdline_$${cmd}:\n\n$${underline}\nMan page for \`\`$${cmd}\`\`\n$${underline}\n\n.. raw:: html\n   :file: $${manfile}.html\n" > source/generated/cmd_$${cmd}.rst ; \
 	done
 	@touch $@
 

doc/examples/cmdline/fmri_analyses.sh

@@ -6,7 +6,7 @@ set -u
 # BOILERPLATE
 
 # where is the data; support standard env variable switch
-dataroot=${MVPA_DATA_ROOT:-"mvpa2/data/openfmri"}
+dataroot=${MVPA_DATA_ROOT:-"mvpa2/data/haxby2001"}
 
 # where to place output; into tmp by default
 outdir=${MVPA_EXAMPLE_WORKDIR:-}

doc/examples/eventrelated.py

@@ -21,7 +21,7 @@
 
 from mvpa2.suite import *
 
-ds = load_datadb_tutorial_data(roi=(36,38,39,40))
+ds = load_tutorial_data(roi=(36,38,39,40))
 
 """
 
@@ -137,7 +137,7 @@
 """
 
 clf = LinearCSVMC()
-sclf = SplitClassifier(clf, enable_ca=['confusion'])
+sclf = SplitClassifier(clf, enable_ca=['stats'])
 
 # Compute sensitivity, which internally trains the classifier
 analyzer = sclf.get_sensitivity_analyzer()
@@ -150,7 +150,7 @@
 
 """
 
-print sclf.ca.confusion
+print sclf.ca.stats
 
 """
 

doc/examples/mri_plot.py

@@ -37,8 +37,8 @@
 from mvpa2.suite import *
 
 # load PyMVPA example dataset
-datapath = os.path.join(mvpa2.cfg.get('location', 'tutorial data'), 'data')
-dataset = load_datadb_tutorial_data(roi='gray')
+datapath = os.path.join(mvpa2.cfg.get('location', 'tutorial data'), 'haxby2001')
+dataset = load_tutorial_data(roi='gray')
 
 # do chunkswise linear detrending on dataset
 poly_detrend(dataset, chunks_attr='chunks')

doc/examples/rsa_fmri.py

@@ -29,6 +29,7 @@
 
 import numpy as np
 import pylab as pl
+from os.path import join as pjoin
 from mvpa2 import cfg
 
 """
@@ -39,9 +40,9 @@
 """
 
 # load dataset -- ventral and occipital ROIs
-from mvpa2.misc.data_generators import load_datadb_tutorial_data
-from mvpa2 import pymvpa_datadbroot
-ds = load_datadb_tutorial_data(roi=(15, 16, 23, 24, 36, 38, 39, 40, 48))
+from mvpa2.datasets.sources.native import load_tutorial_data
+datapath = pjoin(cfg.get('location', 'tutorial data'))
+ds = load_tutorial_data(roi=(15, 16, 23, 24, 36, 38, 39, 40, 48))
 
 """
 We only do minimal pre-processing: linear trend removal and Z-scoring all voxel
@@ -204,25 +205,23 @@ def plot_mtx(mtx, labels, title):
 # plot the spatial distribution using NiPy
 vol = ds.a.mapper.reverse1(slres_tdsm.samples[0])
 import nibabel as nb
-from os.path import join as pjoin
-anat = nb.load(pjoin(pymvpa_datadbroot, 'tutorial_data', 'tutorial_data',
-                     'data', 'sub001', 'anatomy', 'highres001.nii.gz'))
+anat = nb.load(pjoin(datapath, 'sub001', 'anatomy', 'highres001.nii.gz'))
 
 from nipy.labs.viz_tools.activation_maps import plot_map
 pl.figure(figsize=(15,4))
 sp = pl.subplot(121)
 pl.title('Distribution of target similarity structure correlation')
 slices = plot_map(
             vol,
-            ds.a.imghdr.get_best_affine(),
-             cut_coords=np.array((12,-42,-20)),
-             threshold=.5,
-             cmap="bwr",
-             vmin=0,
-             vmax=1.,
-             axes=sp,
-             anat=anat.get_data(),
-             anat_affine=anat.get_affine(),
+            ds.a.imgaffine,
+            cut_coords=np.array((12,-42,-20)),
+            threshold=.5,
+            cmap="bwr",
+            vmin=0,
+            vmax=1.,
+            axes=sp,
+            anat=anat.get_data(),
+            anat_affine=anat.get_affine(),
          )
 img = pl.gca().get_images()[1]
 cax = pl.axes([.05, .05, .05, .9])

doc/examples/searchlight.py

@@ -44,8 +44,8 @@
 selectivity contrast for voxels ventral temporal cortex."""
 
 # data path
-datapath = os.path.join(mvpa2.cfg.get('location', 'tutorial data'), 'data')
-dataset = load_datadb_tutorial_data(
+datapath = os.path.join(mvpa2.cfg.get('location', 'tutorial data'), 'haxby2001')
+dataset = load_tutorial_data(
         roi='brain',
         add_fa={'vt_thr_glm': os.path.join(datapath, 'sub001', 'masks',
                                                      'orig', 'vt.nii.gz')})

doc/source/cmdline.rst

@@ -69,6 +69,7 @@ Create, modify and convert datasets
    generated/cmd_select
    generated/cmd_preproc
    generated/cmd_dump
+   generated/cmd_describe
 
 Perform analyses
 ----------------
@@ -86,6 +87,8 @@ Auxilliary command
    generated/cmd_info
    generated/cmd_exec
    generated/cmd_atlaslabeler
+   generated/cmd_ofmotionqc
+   generated/cmd_ttest
 
 .. _cmdline_example_scripts:
 

doc/source/conf.py

@@ -73,10 +73,10 @@
 
 # the following doesn't work with sphinx < 1.0, but will make a separate
 # sphinx-autogen run obsolete in the future
-#autosummary_generate = True
+autosummary_generate = True
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ['../templates']
 
 # The suffix of source filenames.
 source_suffix = '.rst'
@@ -89,7 +89,7 @@
 
 # General substitutions.
 project = 'PyMVPA'
-copyright = '2006-2013, PyMVPA Authors'
+copyright = '2006-2015, PyMVPA Authors'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

doc/source/datadb/haxby2001.rst

@@ -88,7 +88,7 @@ Instructions
   ...                   targets=attrs.labels, chunks=attrs.chunks,
   ...                   mask=os.path.join(subjpath, 'mask4_vt.nii.gz'))
   >>> print ds
-  <Dataset: 1452x577@int16, <sa: chunks,targets,time_coords,time_indices>, <fa: voxel_indices>, <a: imghdr,imgtype,mapper,voxel_dim,voxel_eldim>>
+  <Dataset: 1452x577@int16, <sa: chunks,targets,time_coords,time_indices>, <fa: voxel_indices>, <a: imgaffine,imghdr,imgtype,mapper,voxel_dim,voxel_eldim>>
 
 
 References

doc/source/datadb/tutorial_data.rst

@@ -62,7 +62,7 @@ Tarballs are available at:
 Tarball Content
 ===============
 
-data/
+haxby2001/
   Contains data files:
 
   bold.nii.gz
@@ -169,7 +169,7 @@ Instructions
 
   >>> from mvpa2.suite import *
   >>> datapath = os.path.join(pymvpa_datadbroot, 'tutorial_data',
-  ...                         'tutorial_data', 'data')
+  ...                         'tutorial_data', 'haxby2001')
   >>> attrs = SampleAttributes(os.path.join(datapath, 'attributes.txt'))
   >>> ds = fmri_dataset(samples=os.path.join(datapath, 'bold.nii.gz'),
   ...                   targets=attrs.targets, chunks=attrs.chunks,

doc/source/index.rst

@@ -6,7 +6,7 @@ PyMVPA is a Python_ package intended to ease statistical learning analyses of
 large datasets. It offers an extensible framework with a high-level interface
 to a broad range of algorithms for classification, regression, feature
 selection, data import and export. It is designed to integrate well with
-related software packages, such as scikit-learn_, and MDP_. While it is not
+related software packages, such as scikit-learn_, shogun_, MDP_, etc. While it is not
 limited to the neuroimaging domain, it is eminently suited for such datasets.
 PyMVPA is free software and requires nothing but free-software to run.
 
@@ -111,6 +111,9 @@ here.
 
 * 3dsvm_: AFNI_ plugin to apply support vector machine classifiers to fMRI data.
 
+* CoSMoMVPA_: Matlab/Octave toolbox designed after PyMVPA and with good
+  interoperability with PyMVPA.
+
 * Elefant_: Efficient Learning, Large-scale Inference, and Optimization
   Toolkit.  Multi-purpose open source library for machine learning.
 
@@ -121,6 +124,9 @@ here.
 * `MVPA Toolbox`_: Matlab-based toolbox to facilitate multi-voxel pattern
   analysis of fMRI neuroimaging data.
 
+* nilearn_: `scikit-learn`_ based Python module for fast and easy statistical
+  learning on NeuroImaging data.
+
 * NiPy_: Project with growing functionality to analyze brain imaging data. NiPy_
   is heavily connected to SciPy and lots of functionality developed within
   NiPy becomes part of SciPy.

doc/source/link_names.txt

@@ -93,6 +93,7 @@
 
 .. Not so python imaging projects
 .. _Caret: http://brainvis.wustl.edu/wiki/index.php/Caret:About
+.. _CoSMoMVPA: http://www.github.com/CoSMoMVPA
 .. _matlab: http://www.mathworks.com
 .. _spm: http://www.fil.ion.ucl.ac.uk/spm
 .. _spm8: http://www.fil.ion.ucl.ac.uk/spm/software/spm8
@@ -116,7 +117,7 @@
 .. _PyML: http://pyml.sourceforge.net
 .. _MVPA Toolbox: http://www.csbmb.princeton.edu/mvpa/
 .. _scikit-learn: http://scikit-learn.org
-
+.. _nilearn: http://nilearn.github.io
 
 .. File formats
 .. _DICOM: http://medical.nema.org/
@@ -142,6 +143,7 @@
 .. _Debian: http://www.debian.org
 .. _`Debian project`: http://www.debian.org
 .. _Ubuntu: http://www.ubuntu.com
+.. _Xubuntu: http://www.xubuntu.org
 .. _exppsy: http://alioth.debian.org/projects/pkg-exppsy
 .. _`Debian Med`: http://debian-med.alioth.debian.org
 .. _`Debian Science`: http://wiki.debian.org/DebianScience
@@ -151,6 +153,18 @@
 .. _Lin4Neuro: http://www.nemotos.net/lin4neuro
 .. _fail2ban: http://www.fail2ban.org
 
+.. Debian releases
+.. _Debian 6.0 (squeeze): http://www.debian.org/releases/squeeze
+.. _Debian 7.0 (wheezy): http://www.debian.org/releases/wheezy
+.. _Debian 7.8 (wheezy): http://www.debian.org/releases/wheezy
+.. _Debian 8.0 (jessie): http://www.debian.org/releases/jessie
+
+.. Desktop environments
+.. _GNOME: http://www.gnome.org/
+.. _GNOME3: http://www.gnome.org/gnome-3/
+.. _XFCE: http://www.xfce.org/
+.. _XFCE4: http://www.xfce.org/
+
 .. Functional imaging labs
 .. _`functional imaging laboratory`: http://www.fil.ion.ucl.ac.uk
 .. _FMRIB: http://www.fmrib.ox.ac.uk
@@ -199,6 +213,7 @@
 .. |ITP| replace:: :abbr:`ITP (Intent to Package)`
 .. |RFP| replace:: :abbr:`RFP (Request for packaging)`
 .. |DBTS| replace:: :abbr:`DBTS (Debian Bug Tracking System)`
+.. _debian-installer: http://www.debian.org/devel/debian-installer/
 
 .. mailing lists
 .. _neurodebian-users: http://lists.alioth.debian.org/mailman/listinfo/neurodebian-users

doc/source/modref.rst

@@ -69,6 +69,8 @@ Datasets: Input, Output, Storage and Preprocessing
    datasets.cosmo
    datasets.eeglab
    datasets.miscfx
+   datasets.sources.native
+   datasets.sources.openfmri
    datasets.sources.skl_data
 
 
@@ -287,4 +289,6 @@ Basic Plotting Utilities
    support.nibabel.surf_caret
    support.nibabel.surf_gifti
    support.nibabel.surf
-
+
+
+.. include:: link_names.txt