Merge remote-tracking branch 'upstream/master'

Conflicts:
	nibabel/nicom/tests/test_dicomwrappers.py

Author: embaker

.gitmodules

@@ -10,3 +10,6 @@
 [submodule "nibabel-data/nitest-freesurfer"]
 	path = nibabel-data/nitest-freesurfer
 	url = https://bitbucket.org/nipy/nitest-freesurfer.git
+[submodule "nibabel-data/parrec_oblique"]
+	path = nibabel-data/parrec_oblique
+	url = https://github.com/grlee77/parrec_oblique.git

.mailmap

@@ -29,3 +29,5 @@ Basile Pinsard <[email protected]> bpinsard <[email protected]>
 Nguyen, Ly <[email protected]> lxn2 <[email protected]>
 Ben Cipollini <[email protected]> Ben Cipollini <[email protected]>
 Chris Markiewicz <[email protected]> Christopher J. Markiewicz <[email protected]>
+Chris Markiewicz <[email protected]> Christopher J. Markiewicz <[email protected]>
+Chris Markiewicz <[email protected]> Chris Johnson <[email protected]>

.travis.yml

@@ -3,6 +3,7 @@
 # munges each line before executing it to print out the exit status.  It's okay
 # for it to be on multiple physical lines, so long as you remember: - There
 # can't be any leading "-"s - All newlines will be removed, so use ";"s
+
 language: python
 
 # Run jobs on container-based infrastructure, can be overridden per job
@@ -11,20 +12,19 @@ sudo: false
 cache:
   directories:
     - $HOME/.cache/pip
-
 addons:
   apt:
     packages:
       - libhdf5-serial-dev
-
+      # For numpy --pre wheels
+      - libatlas-base-dev
 env:
     global:
         - DEPENDS="numpy scipy matplotlib h5py"
         - PYDICOM=1
         - INSTALL_TYPE="setup"
 python:
     - 2.6
-    - 3.2
     - 3.3
     - 3.4
     - 3.5
@@ -37,14 +37,26 @@ matrix:
     - python: 2.7
       env:
         - DEPENDS=numpy==1.5.1 PYDICOM=0
+    # Absolute minimum dependencies plus oldest MPL
+    - python: 2.7
+      env:
+        - DEPENDS=numpy==1.5.1 matplotlib==1.3.1 PYDICOM=0
     # Minimum pydicom dependency
     - python: 2.7
       env:
         - DEPENDS="numpy==1.5.1 pydicom==0.9.7"
+    # test against numpy 1.7
+    - python: 2.7
+      env:
+        - DEPENDS="numpy==1.7.1"
     # pydicom 1.0 (currently unreleased)
     - python: 2.7
       env:
         - PYDICOM="v1.0"
+    # test against pre-release builds
+    - python: 2.7
+      env:
+        - EXTRA_PIP_FLAGS="--pre"
     # Documentation doctests
     - python: 2.7
       env:
@@ -58,14 +70,20 @@ matrix:
     - python: 2.7
       env:
         - INSTALL_TYPE=requirements
+    - python: 2.7
+      env:
+        - STYLE=1
+    - python: 3.5
+      env:
+        - STYLE=1
 before_install:
     - source tools/travis_tools.sh
     - virtualenv --python=python venv
     - source venv/bin/activate
     - python --version # just to check
-    - pip install -U pip  # upgrade to latest pip to find 3.5 wheels
-    - retry pip install nose # always
-    - wheelhouse_pip_install $DEPENDS
+    - pip install -U pip wheel  # upgrade to latest pip find 3.5 wheels; wheel to avoid errors
+    - retry pip install nose flake8  # always
+    - wheelhouse_pip_install $EXTRA_PIP_FLAGS $DEPENDS
     # pydicom <= 0.9.8 doesn't install on python 3
     - if [ "${TRAVIS_PYTHON_VERSION:0:1}" == "2" ]; then
         if [ "$PYDICOM" == "1" ]; then
@@ -77,6 +95,7 @@ before_install:
     - if [ "${COVERAGE}" == "1" ]; then
       pip install coverage;
       pip install coveralls;
+      pip install codecov;
       fi
 # command to install dependencies
 install:
@@ -86,33 +105,42 @@ install:
       elif [ "$INSTALL_TYPE" == "sdist" ]; then
           python setup_egg.py egg_info  # check egg_info while we're here
           python setup_egg.py sdist
-          wheelhouse_pip_install dist/*.tar.gz
+          wheelhouse_pip_install $EXTRA_PIP_FLAGS dist/*.tar.gz
       elif [ "$INSTALL_TYPE" == "wheel" ]; then
           pip install wheel
           python setup_egg.py bdist_wheel
-          wheelhouse_pip_install dist/*.whl
+          wheelhouse_pip_install $EXTRA_PIP_FLAGS dist/*.whl
       elif [ "$INSTALL_TYPE" == "requirements" ]; then
-          wheelhouse_pip_install -r requirements.txt
+          wheelhouse_pip_install $EXTRA_PIP_FLAGS -r requirements.txt
           python setup.py install
       fi
     # Point to nibabel data directory
     - export NIBABEL_DATA_DIR="$PWD/nibabel-data"
 # command to run tests, e.g. python setup.py test
 script:
-    # Change into an innocuous directory and find tests from installation
-    - mkdir for_testing
-    - cd for_testing
-    - if [ "${COVERAGE}" == "1" ]; then
-      cp ../.coveragerc .;
-      COVER_ARGS="--with-coverage --cover-package nibabel";
-      fi
-    - if [ "$DOC_DOC_TEST" == "1" ]; then
-      pip install sphinx;
-      cd ../doc;
-      make html;
-      make doctest;
+    - |
+      if [ "${STYLE}" == "1" ]; then
+          # Run styles only on core nibabel code.
+          flake8 nibabel
       else
-      nosetests --with-doctest $COVER_ARGS nibabel;
+          # Change into an innocuous directory and find tests from installation
+          mkdir for_testing
+          cd for_testing
+          if [ "${COVERAGE}" == "1" ]; then
+              cp ../.coveragerc .;
+              COVER_ARGS="--with-coverage --cover-package nibabel";
+          fi
+          if [ "$DOC_DOC_TEST" == "1" ]; then
+              cd ../doc;
+              pip install -r ../doc-requirements.txt
+              make html;
+              make doctest;
+          else
+              nosetests --with-doctest $COVER_ARGS nibabel;
+          fi
       fi
 after_success:
-    - if [ "${COVERAGE}" == "1" ]; then coveralls; fi
+    - if [ "${COVERAGE}" == "1" ]; then coveralls; codecov; fi
+
+notifications:
+    webhooks: http://nipy.bic.berkeley.edu:54856/travis

Changelog

@@ -26,6 +26,8 @@ References like "pr/298" refer to github pull request numbers.
 
 * Upcoming
 
+  * Read and write support for DICOM tags in NIfTI Extended Header using
+    pydicom (pr/296);
   * Trackvis reader will now allow final streamline to have fewer points that
     tne numbe declared in the header, with ``strict=False`` argument to
     ``read`` function;
@@ -34,6 +36,19 @@ References like "pr/298" refer to github pull request numbers.
     are raising a DataError if the track is truncated when ``strict=True``
     (the default), rather than a TypeError when trying to create the points
     array.
+
+* 2.0.2 (Monday 23 November 2015)
+
+  * Fix for integer overflow on large images (pr/325) (MB);
+  * Fix for Freesurfer nifti files with unusual dimensions (pr/332) (Chris
+    Markiewicz);
+  * Fix typos on benchmarks and tests (pr/336, pr/340, pr/347) (Chris
+    Markiewicz);
+  * Fix Windows install script (pr/339) (MB);
+  * Support for Python 3.5 (pr/363) (MB) and numpy 1.10 (pr/358) (Chris
+    Markiewicz);
+  * Update pydicom imports to permit version 1.0 (pr/379) (Chris Markiewicz);
+  * Workaround for Python 3.5.0 gzip regression (pr/383) (Ben Cipollini).
   * tripwire.TripWire object now raises subclass of AttributeError when trying
     to get an attribute, rather than a direct subclass of Exception.  This
     prevents Python 3.5 triggering the tripwire when doing inspection prior to

bin/nib-dicomfs

@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!python
 # emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##

bin/nib-ls

@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!python
 # emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
@@ -13,7 +13,7 @@ Output a summary table for neuroimaging files (resolution, dimensionality, etc.)
 from __future__ import division, print_function, absolute_import
 
 __author__ = 'Yaroslav Halchenko'
-__copyright__ = 'Copyright (c) 2011-2012 Yaroslav Halchenko ' \
+__copyright__ = 'Copyright (c) 2011-2015 Yaroslav Halchenko ' \
                 'and NiBabel contributors'
 __license__ = 'MIT'
 
@@ -141,6 +141,10 @@ def get_opt_parser():
                dest="verbose", default=0,
                help="Make more noise.  Could be specified multiple times"),
 
+        Option("-H", "--header-fields",
+               dest="header_fields", default='',
+               help="Header fields (comma separated) to be printed as well (if present)"),
+
         Option("-s", "--stats",
                action="store_true", dest='stats', default=False,
                help="Output basic data statistics"),
@@ -180,6 +184,23 @@ def proc_file(f, opts):
     else:
         row += [ '' ]
 
+    if opts.header_fields:
+        # signals "all fields"
+        if opts.header_fields == 'all':
+            # TODO: might vary across file types, thus prior sensing
+            # would be needed
+            header_fields = h.keys()
+        else:
+            header_fields = opts.header_fields.split(',')
+
+        for f in header_fields:
+            if not f: # skip empty
+                continue
+            try:
+                row += [str(h[f])]
+            except (KeyError, ValueError):
+                row += [ 'error' ]
+
     try:
         if (hasattr(h, 'get_qform') and hasattr(h, 'get_sform')
             and (h.get_qform() != h.get_sform()).any()):

bin/nib-nifti-dx

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!python
 # emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##

bin/parrec2nii

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!python
 """PAR/REC to NIfTI converter
 """
 from __future__ import division, print_function, absolute_import
@@ -8,6 +8,7 @@ import numpy as np
 import numpy.linalg as npl
 import sys
 import os
+import csv
 import nibabel
 import nibabel.parrec as pr
 from nibabel.parrec import one_line
@@ -66,6 +67,18 @@ def get_opt_parser():
                    """The magnetic field strength of the recording, only needed
                    for --dwell-time. The field strength must be supplied
                    because it is not encoded in the PAR/REC format.""")))
+    p.add_option(
+        Option("-i", "--volume-info", action="store_true", dest="vol_info",
+               default=False,
+               help=one_line(
+                   """Export .PAR volume labels corresponding to the fourth
+                   dimension of the data.  The dimension info will be stored in
+                   CSV format with the first row containing dimension labels
+                   and the subsequent rows (one per volume), the corresponding
+                   indices.  Only labels that vary along the 4th dimension are
+                   exported (e.g. for a single volume structural scan there
+                   are no dynamic labels and no output file will be created).
+                   """)))
     p.add_option(
         Option("--origin", action="store", dest="origin", default="scanner",
                help=one_line(
@@ -113,6 +126,13 @@ def get_opt_parser():
                default=False,
                help=one_line("""Overwrite file if it exists. Default:
                              False""")))
+    p.add_option(
+        Option("--strict-sort", action="store_true", dest="strict_sort",
+               default=False,
+               help=one_line("""Use additional keys in determining the order
+                to sort the slices within the .REC file.  This may be necessary
+                for more complicated scans with multiple echos,
+                cardiac phases, ASL label states, etc.""")))
     return p
 
 
@@ -148,7 +168,8 @@ def proc_file(infile, opts):
     infile = fname_ext_ul_case(infile)
     pr_img = pr.load(infile,
                      permit_truncated=opts.permit_truncated,
-                     scaling=scaling)
+                     scaling=scaling,
+                     strict_sort=opts.strict_sort)
     pr_hdr = pr_img.header
     affine = pr_hdr.get_affine(origin=opts.origin)
     slope, intercept = pr_hdr.get_data_scaling(scaling)
@@ -185,7 +206,7 @@ def proc_file(infile, opts):
 
     bvals, bvecs = pr_hdr.get_bvals_bvecs()
     if not opts.keep_trace:  # discard Philips DTI trace if present
-        if bvals is not None:
+        if bvecs is not None:
             bad_mask = np.logical_and(bvals != 0, (bvecs == 0).all(axis=1))
             if bad_mask.sum() > 0:
                 pl = 's' if bad_mask.sum() != 1 else ''
@@ -229,6 +250,14 @@ def proc_file(infile, opts):
     if opts.bvs:
         if bvals is None and bvecs is None:
             verbose('No DTI volumes detected, bvals and bvecs not written')
+        elif bvecs is None:
+            verbose('DTI volumes detected, but no diffusion direction info was'
+                    'found.  Writing .bvals file only.')
+            with open(basefilename + '.bvals', 'w') as fid:
+                # np.savetxt could do this, but it's just a loop anyway
+                for val in bvals:
+                    fid.write('%s ' % val)
+                fid.write('\n')
         else:
             verbose('Writing .bvals and .bvecs files')
             # Transform bvecs with reorientation affine
@@ -246,6 +275,17 @@ def proc_file(infile, opts):
                         fid.write('%s ' % val)
                     fid.write('\n')
 
+    # export data labels varying along the 4th dimensions if requested
+    if opts.vol_info:
+        labels = pr_img.header.get_volume_labels()
+        if len(labels) > 0:
+            vol_keys = list(labels.keys())
+            with open(basefilename + '.ordering.csv', 'w') as csvfile:
+                csvwriter = csv.writer(csvfile, delimiter=',')
+                csvwriter.writerow(vol_keys)
+                for vals in zip(*[labels[k] for k in vol_keys]):
+                    csvwriter.writerow(vals)
+
     # write out dwell time if requested
     if opts.dwell_time:
         try:

dev-requirements.txt

@@ -0,0 +1,3 @@
+# Requirements for running tests
+-r requirements.txt
+nose

doc-requirements.txt

@@ -0,0 +1,6 @@
+# Requirements for building docs
+-r requirements.txt
+sphinx
+numpydoc
+texext
+matplotlib>=1.3