Merge remote-tracking branch 'origin/master' into chris-master

* origin/master: (76 commits)
  STY: Clearer conditional
  FIX: Fix for NumPy deprecation
  Better handle pathological filenames
  BF: flake8 the import
  BF(PY3): just catch all Exceptions, patch builtins module now provided in py3k
  BF: be resilient to optional module non-ImportError exceptions upon import
  better file checks - path.exists is try/except for os.stat anyways!
  Using another existing exception, and shorter message
  removing unnecessary space that nibabel checks dont like
  merging with upstream master to undo changes not ready to PR/merge
  detecting if the input is empty early on! Apparently no one needed it ;)
  DOC: rewrite first line of function docstring
  CI: Remove duplicate Travis entry [skip ci]
  mv test of failure + rm redundant tests
  COV: Omit tests, drop obsolete omissions
  add: tests for `nibabel.save`
  TEST: Delete arrayproxies, allowing Windows to close filehandles
  Revert "FIX: Give Windows time to decide files are closed"
  bf: preserve error output if not valid klass
  fix: use correct CIFTI intent names
  ...

Author: yarikoptic

.coveragerc

@@ -5,5 +5,4 @@ include = */nibabel/*, */nisext/*
 omit =
     */externals/*
     */benchmarks/*
-    */ast.py
-    */codegen.py
+    */tests/*

.travis.yml

@@ -14,9 +14,8 @@ cache:
     - $HOME/.cache/pip
 env:
     global:
-        - DEPENDS="six numpy scipy matplotlib h5py pillow"
+        - DEPENDS="six numpy scipy matplotlib h5py pillow pydicom"
         - OPTIONAL_DEPENDS=""
-        - PYDICOM=1
         - INSTALL_TYPE="setup"
         - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
         - PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com"
@@ -34,27 +33,23 @@ matrix:
     # Absolute minimum dependencies
     - python: 2.7
       env:
-        - DEPENDS="numpy==1.7.1" PYDICOM=0
+        - DEPENDS="numpy==1.7.1"
     # Absolute minimum dependencies plus oldest MPL
     # Check these against:
     # nibabel/info.py
     # doc/source/installation.rst
     # requirements.txt
     - python: 2.7
       env:
-        - DEPENDS="numpy==1.7.1 matplotlib==1.3.1" PYDICOM=0
+        - DEPENDS="numpy==1.7.1 matplotlib==1.3.1"
     # Minimum pydicom dependency
     - python: 2.7
       env:
-        - DEPENDS="numpy==1.7.1 pydicom==0.9.7 pillow==2.6"
-    # test against numpy 1.7
-    - python: 2.7
-      env:
-        - DEPENDS="numpy==1.7.1"
-    # pydicom 1.0 (currently unreleased)
-    - python: 2.7
+        - DEPENDS="numpy==1.7.1 pydicom==0.9.9 pillow==2.6"
+    # pydicom master branch
+    - python: 3.5
       env:
-        - PYDICOM="v1.0"
+        - DEPENDS="numpy git+https://github.com/pydicom/pydicom.git@master"
     # test 2.7 against pre-release builds of everything
     - python: 2.7
       env:
@@ -102,14 +97,6 @@ before_install:
     - pip install -U pip wheel  # needed at one point
     - retry pip install nose flake8 mock  # always
     - pip install $EXTRA_PIP_FLAGS $DEPENDS $OPTIONAL_DEPENDS
-    # pydicom <= 0.9.8 doesn't install on python 3
-    - if [ "${TRAVIS_PYTHON_VERSION:0:1}" == "2" ]; then
-        if [ "$PYDICOM" == "1" ]; then
-            pip install pydicom;
-        elif [ "$PYDICOM" == "v1.0" ]; then
-            pip install git+https://github.com/darcymason/pydicom.git@43f278444d5cb2e4648135d3edcd430c363c6975;
-        fi
-      fi
     - if [ "${COVERAGE}" == "1" ]; then
       pip install coverage;
       pip install coveralls;

doc/source/installation.rst

@@ -90,7 +90,7 @@ Requirements
 *  NumPy_ 1.7.1 or greater
 *  Six_ 1.3 or greater
 *  SciPy_ (optional, for full SPM-ANALYZE support)
-*  PyDICOM_ 0.9.7 or greater (optional, for DICOM support)
+*  PyDICOM_ 0.9.9 or greater (optional, for DICOM support)
 *  `Python Imaging Library`_ (optional, for PNG conversion in DICOMFS)
 *  nose_ 0.11 or greater (optional, to run the tests)
 *  mock_ (optional, to run the tests)

nibabel/analyze.py

@@ -1086,10 +1086,6 @@ def to_file_map(self, file_map=None):
         # Write header
         hdr.write_to(hdrf)
         # Write image
-        shape = hdr.get_data_shape()
-        if data.shape != shape:
-            raise HeaderDataError('Data should be shape (%s)' %
-                                  ', '.join(str(s) for s in shape))
         # Seek to writing position, get there by writing zeros if seek fails
         seek_tell(imgf, hdr.get_data_offset(), write0=True)
         # Write array data

nibabel/cifti2/cifti2.py

@@ -1384,6 +1384,9 @@ def to_file_map(self, file_map=None):
         header = self._nifti_header
         extension = Cifti2Extension(content=self.header.to_xml())
         header.extensions.append(extension)
+        # if intent code is not set, default to unknown CIFTI
+        if header.get_intent()[0] == 'none':
+            header.set_intent('NIFTI_INTENT_CONNECTIVITY_UNKNOWN')
         data = reshape_dataobj(self.dataobj,
                                (1, 1, 1, 1) + self.dataobj.shape)
         # If qform not set, reset pixdim values so Nifti2 does not complain

nibabel/cifti2/parse_cifti2.py

@@ -52,27 +52,27 @@ def _mangle(self, value):
     # The codes below appear on the CIFTI-2 standard
     # http://www.nitrc.org/plugins/mwiki/index.php/cifti:ConnectivityMatrixFileFormats
     # https://www.nitrc.org/forum/attachment.php?attachid=341&group_id=454&forum_id=1955
-    (3000, 'dense fiber/fan samples', (), 'NIFTI_INTENT_CONNECTIVITY_UNKNOWN'),
-    (3001, 'dense connectivity', (), 'NIFTI_INTENT_CONNECTIVITY_DENSE'),
-    (3002, 'dense data series/fiber fans', (),
+    (3000, 'ConnUnknown', (), 'NIFTI_INTENT_CONNECTIVITY_UNKNOWN'),
+    (3001, 'ConnDense', (), 'NIFTI_INTENT_CONNECTIVITY_DENSE'),
+    (3002, 'ConnDenseSeries', (),
      'NIFTI_INTENT_CONNECTIVITY_DENSE_SERIES'),
-    (3003, 'parcellated connectivity', (),
+    (3003, 'ConnParcels', (),
      'NIFTI_INTENT_CONNECTIVITY_PARCELLATED'),
-    (3004, 'parcellated data series', (),
+    (3004, 'ConnParcelSries', (),
      "NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SERIES"),
-    (3006, 'dense scalar', (),
+    (3006, 'ConnDenseScalar', (),
      'NIFTI_INTENT_CONNECTIVITY_DENSE_SCALARS'),
-    (3007, 'dense label', (),
+    (3007, 'ConnDenseLabel', (),
      'NIFTI_INTENT_CONNECTIVITY_DENSE_LABELS'),
-    (3008, 'parcellated scalar', (),
+    (3008, 'ConnParcelScalr', (),
      'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SCALAR'),
-    (3009, 'parcellated dense connectivity', (),
+    (3009, 'ConnParcelDense', (),
      'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_DENSE'),
-    (3010, 'dense parcellated connectivity', (),
+    (3010, 'ConnDenseParcel', (),
      'NIFTI_INTENT_CONNECTIVITY_DENSE_PARCELLATED'),
-    (3011, 'parcellated connectivity series', (),
+    (3011, 'ConnPPSr', (),
      'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_PARCELLATED_SERIES'),
-    (3012, 'parcellated connectivity scalar', (),
+    (3012, 'ConnPPSc', (),
      'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_PARCELLATED_SCALAR')))
 
 

nibabel/cifti2/tests/test_new_cifti2.py

@@ -8,6 +8,7 @@
 """
 import numpy as np
 
+import nibabel as nib
 from nibabel import cifti2 as ci
 from nibabel.tmpdirs import InTemporaryDirectory
 
@@ -212,10 +213,14 @@ def test_dtseries():
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(13, 9)
     img = ci.Cifti2Image(data, hdr)
+    img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_DENSE_SERIES')
 
     with InTemporaryDirectory():
         ci.save(img, 'test.dtseries.nii')
-        img2 = ci.load('test.dtseries.nii')
+        img2 = nib.load('test.dtseries.nii')
+        assert_equal(img2.nifti_header.get_intent()[0],
+                     'ConnDenseSeries')
+        assert_true(isinstance(img2, ci.Cifti2Image))
         assert_true((img2.get_data() == data).all())
         check_series_map(img2.header.matrix.get_index_map(0))
         check_geometry_map(img2.header.matrix.get_index_map(1))
@@ -231,10 +236,13 @@ def test_dscalar():
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(2, 9)
     img = ci.Cifti2Image(data, hdr)
+    img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_DENSE_SCALARS')
 
     with InTemporaryDirectory():
         ci.save(img, 'test.dscalar.nii')
-        img2 = ci.load('test.dscalar.nii')
+        img2 = nib.load('test.dscalar.nii')
+        assert_equal(img2.nifti_header.get_intent()[0], 'ConnDenseScalar')
+        assert_true(isinstance(img2, ci.Cifti2Image))
         assert_true((img2.get_data() == data).all())
         check_scalar_map(img2.header.matrix.get_index_map(0))
         check_geometry_map(img2.header.matrix.get_index_map(1))
@@ -250,10 +258,13 @@ def test_dlabel():
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(2, 9)
     img = ci.Cifti2Image(data, hdr)
+    img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_DENSE_LABELS')
 
     with InTemporaryDirectory():
         ci.save(img, 'test.dlabel.nii')
-        img2 = ci.load('test.dlabel.nii')
+        img2 = nib.load('test.dlabel.nii')
+        assert_equal(img2.nifti_header.get_intent()[0], 'ConnDenseLabel')
+        assert_true(isinstance(img2, ci.Cifti2Image))
         assert_true((img2.get_data() == data).all())
         check_label_map(img2.header.matrix.get_index_map(0))
         check_geometry_map(img2.header.matrix.get_index_map(1))
@@ -267,10 +278,13 @@ def test_dconn():
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(9, 9)
     img = ci.Cifti2Image(data, hdr)
+    img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_DENSE')
 
     with InTemporaryDirectory():
         ci.save(img, 'test.dconn.nii')
-        img2 = ci.load('test.dconn.nii')
+        img2 = nib.load('test.dconn.nii')
+        assert_equal(img2.nifti_header.get_intent()[0], 'ConnDense')
+        assert_true(isinstance(img2, ci.Cifti2Image))
         assert_true((img2.get_data() == data).all())
         assert_equal(img2.header.matrix.get_index_map(0),
                      img2.header.matrix.get_index_map(1))
@@ -287,10 +301,13 @@ def test_ptseries():
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(13, 3)
     img = ci.Cifti2Image(data, hdr)
+    img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SERIES')
 
     with InTemporaryDirectory():
         ci.save(img, 'test.ptseries.nii')
-        img2 = ci.load('test.ptseries.nii')
+        img2 = nib.load('test.ptseries.nii')
+        assert_equal(img2.nifti_header.get_intent()[0], 'ConnParcelSries')
+        assert_true(isinstance(img2, ci.Cifti2Image))
         assert_true((img2.get_data() == data).all())
         check_series_map(img2.header.matrix.get_index_map(0))
         check_parcel_map(img2.header.matrix.get_index_map(1))
@@ -306,10 +323,13 @@ def test_pscalar():
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(2, 3)
     img = ci.Cifti2Image(data, hdr)
+    img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SCALAR')
 
     with InTemporaryDirectory():
         ci.save(img, 'test.pscalar.nii')
-        img2 = ci.load('test.pscalar.nii')
+        img2 = nib.load('test.pscalar.nii')
+        assert_equal(img2.nifti_header.get_intent()[0], 'ConnParcelScalr')
+        assert_true(isinstance(img2, ci.Cifti2Image))
         assert_true((img2.get_data() == data).all())
         check_scalar_map(img2.header.matrix.get_index_map(0))
         check_parcel_map(img2.header.matrix.get_index_map(1))
@@ -325,10 +345,13 @@ def test_pdconn():
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(2, 3)
     img = ci.Cifti2Image(data, hdr)
+    img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED_DENSE')
 
     with InTemporaryDirectory():
         ci.save(img, 'test.pdconn.nii')
         img2 = ci.load('test.pdconn.nii')
+        assert_equal(img2.nifti_header.get_intent()[0], 'ConnParcelDense')
+        assert_true(isinstance(img2, ci.Cifti2Image))
         assert_true((img2.get_data() == data).all())
         check_geometry_map(img2.header.matrix.get_index_map(0))
         check_parcel_map(img2.header.matrix.get_index_map(1))
@@ -344,10 +367,13 @@ def test_dpconn():
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(2, 3)
     img = ci.Cifti2Image(data, hdr)
+    img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_DENSE_PARCELLATED')
 
     with InTemporaryDirectory():
         ci.save(img, 'test.dpconn.nii')
         img2 = ci.load('test.dpconn.nii')
+        assert_equal(img2.nifti_header.get_intent()[0], 'ConnDenseParcel')
+        assert_true(isinstance(img2, ci.Cifti2Image))
         assert_true((img2.get_data() == data).all())
         check_parcel_map(img2.header.matrix.get_index_map(0))
         check_geometry_map(img2.header.matrix.get_index_map(1))
@@ -367,6 +393,8 @@ def test_plabel():
     with InTemporaryDirectory():
         ci.save(img, 'test.plabel.nii')
         img2 = ci.load('test.plabel.nii')
+        assert_equal(img.nifti_header.get_intent()[0], 'ConnUnknown')
+        assert_true(isinstance(img2, ci.Cifti2Image))
         assert_true((img2.get_data() == data).all())
         check_label_map(img2.header.matrix.get_index_map(0))
         check_parcel_map(img2.header.matrix.get_index_map(1))
@@ -380,10 +408,13 @@ def test_pconn():
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(3, 3)
     img = ci.Cifti2Image(data, hdr)
+    img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED')
 
     with InTemporaryDirectory():
         ci.save(img, 'test.pconn.nii')
         img2 = ci.load('test.pconn.nii')
+        assert_equal(img.nifti_header.get_intent()[0], 'ConnParcels')
+        assert_true(isinstance(img2, ci.Cifti2Image))
         assert_true((img2.get_data() == data).all())
         assert_equal(img2.header.matrix.get_index_map(0),
                      img2.header.matrix.get_index_map(1))
@@ -401,10 +432,14 @@ def test_pconnseries():
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(3, 3, 13)
     img = ci.Cifti2Image(data, hdr)
+    img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED_'
+                                'PARCELLATED_SERIES')
 
     with InTemporaryDirectory():
         ci.save(img, 'test.pconnseries.nii')
         img2 = ci.load('test.pconnseries.nii')
+        assert_equal(img.nifti_header.get_intent()[0], 'ConnPPSr')
+        assert_true(isinstance(img2, ci.Cifti2Image))
         assert_true((img2.get_data() == data).all())
         assert_equal(img2.header.matrix.get_index_map(0),
                      img2.header.matrix.get_index_map(1))
@@ -423,10 +458,14 @@ def test_pconnscalar():
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(3, 3, 13)
     img = ci.Cifti2Image(data, hdr)
+    img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED_'
+                                'PARCELLATED_SCALAR')
 
     with InTemporaryDirectory():
         ci.save(img, 'test.pconnscalar.nii')
         img2 = ci.load('test.pconnscalar.nii')
+        assert_equal(img.nifti_header.get_intent()[0], 'ConnPPSc')
+        assert_true(isinstance(img2, ci.Cifti2Image))
         assert_true((img2.get_data() == data).all())
         assert_equal(img2.header.matrix.get_index_map(0),
                      img2.header.matrix.get_index_map(1))

nibabel/deprecated.py

@@ -31,10 +31,6 @@ class ModuleProxy(object):
     def __init__(self, module_name):
         self._module_name = module_name
 
-    def __hasattr__(self, key):
-        mod = __import__(self._module_name, fromlist=[''])
-        return hasattr(mod, key)
-
     def __getattr__(self, key):
         mod = __import__(self._module_name, fromlist=[''])
         return getattr(mod, key)

nibabel/filename_parser.py

@@ -147,8 +147,7 @@ def parse_filename(filename,
                    types_exts,
                    trailing_suffixes,
                    match_case=False):
-    ''' Splits filename into tuple of
-    (fileroot, extension, trailing_suffix, guessed_name)
+    '''Split filename into fileroot, extension, trailing suffix; guess type.
 
     Parameters
     ----------
@@ -265,9 +264,14 @@ def splitext_addext(filename,
     for ext in addexts:
         if endswith(filename, ext):
             extpos = -len(ext)
-            addext = filename[extpos:]
-            filename = filename[:extpos]
+            filename, addext = filename[:extpos], filename[extpos:]
             break
     else:
         addext = ''
-    return os.path.splitext(filename) + (addext,)
+    # os.path.splitext() behaves unexpectedly when filename starts with '.'
+    extpos = filename.rfind('.')
+    if extpos < 0 or filename.strip('.') == '':
+        root, ext = filename, ''
+    else:
+        root, ext = filename[:extpos], filename[extpos:]
+    return (root, ext, addext)