Merge pull request #599 from matthew-brett/pydicom-compatibility

MRG: refactoring for pydicom 1.0

Make tests pass against pydicom 1.0.

Refactor CI to test pydicom master, as suggested by pydicom folks.

Update minimum pydicom dependency to 0.9.9 (previous versions no longer install).

Author: matthew-brett

.travis.yml

@@ -14,9 +14,8 @@ cache:
     - $HOME/.cache/pip
 env:
     global:
-        - DEPENDS="six numpy scipy matplotlib h5py pillow"
+        - DEPENDS="six numpy scipy matplotlib h5py pillow pydicom"
         - OPTIONAL_DEPENDS=""
-        - PYDICOM=1
         - INSTALL_TYPE="setup"
         - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
         - PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com"
@@ -34,29 +33,29 @@ matrix:
     # Absolute minimum dependencies
     - python: 2.7
       env:
-        - DEPENDS="numpy==1.7.1" PYDICOM=0
+        - DEPENDS="numpy==1.7.1"
     # Absolute minimum dependencies plus oldest MPL
     # Check these against:
     # nibabel/info.py
     # doc/source/installation.rst
     # requirements.txt
     - python: 2.7
       env:
-        - DEPENDS="numpy==1.7.1 matplotlib==1.3.1" PYDICOM=0
+        - DEPENDS="numpy==1.7.1 matplotlib==1.3.1"
     # Minimum pydicom dependency
     - python: 2.7
       env:
-        - DEPENDS="numpy==1.7.1 pydicom==0.9.7 pillow==2.6"
+        - DEPENDS="numpy==1.7.1 pydicom==0.9.9 pillow==2.6"
     # test against numpy 1.7
     - python: 2.7
       env:
         - DEPENDS="numpy==1.7.1"
-    # pydicom 1.0 (currently unreleased)
-    - python: 2.7
+    # pydicom master branch
+    - python: 3.5
       env:
-        - PYDICOM="v1.0"
-    # test 2.7 against pre-release builds of everything
-    - python: 2.7
+        - DEPENDS="numpy git+https://github.com/pydicom/pydicom.git@master"
+    # test 3.5 against pre-release builds of everything
+    - python: 3.5
       env:
         - EXTRA_PIP_FLAGS="$PRE_PIP_FLAGS"
     # test 3.5 against pre-release builds of everything
@@ -102,14 +101,6 @@ 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/info.py

@@ -187,7 +187,7 @@ def cmp_pkg_version(version_str, pkg_version_str=__version__):
 # requirements.txt
 # .travis.yml
 NUMPY_MIN_VERSION = '1.7.1'
-PYDICOM_MIN_VERSION = '0.9.7'
+PYDICOM_MIN_VERSION = '0.9.9'
 SIX_MIN_VERSION = '1.3'
 
 # Main setup parameters

nibabel/nicom/dicomwrappers.py

@@ -21,7 +21,7 @@
 from .dwiparams import B2q, nearest_pos_semi_def, q2bg
 from ..openers import ImageOpener
 from ..onetime import setattr_on_read as one_time
-from ..pydicom_compat import pydicom
+from ..pydicom_compat import tag_for_keyword
 
 
 class WrapperError(Exception):
@@ -517,7 +517,7 @@ def image_shape(self):
         # Determine if one of the dimension indices refers to the stack id
         dim_seq = [dim.DimensionIndexPointer
                    for dim in self.get('DimensionIndexSequence')]
-        stackid_tag = pydicom.datadict.tag_for_name('StackID')
+        stackid_tag = tag_for_keyword('StackID')
         # remove the stack id axis if present
         if stackid_tag in dim_seq:
             stackid_dim_idx = dim_seq.index(stackid_tag)

nibabel/nicom/tests/test_dicomwrappers.py

@@ -9,7 +9,8 @@
 
 import numpy as np
 
-from nibabel.pydicom_compat import have_dicom, pydicom, read_file, dicom_test
+from nibabel.pydicom_compat import (have_dicom, pydicom, read_file, dicom_test,
+                                    tag_for_keyword)
 
 from .. import dicomwrappers as didw
 from .. import dicomreaders as didr
@@ -416,8 +417,8 @@ def __init__(self, div, sid):
     dim_idx_seq = [DimIdxSeqElem()] * num_of_frames
     # add an entry for StackID into the DimensionIndexSequence
     if sid_dim is not None:
-        sid_tag = pydicom.datadict.tag_for_name('StackID')
-        fcs_tag = pydicom.datadict.tag_for_name('FrameContentSequence')
+        sid_tag = tag_for_keyword('StackID')
+        fcs_tag = tag_for_keyword('FrameContentSequence')
         dim_idx_seq[sid_dim] = DimIdxSeqElem(sid_tag, fcs_tag)
     # create the PerFrameFunctionalGroupsSequence
     frames = [PerFrmFuncGrpSeqElem(div, sid)

nibabel/pydicom_compat.py

@@ -10,17 +10,18 @@
 * pydicom : pydicom module or dicom module or None of not importable;
 * read_file : ``read_file`` function if pydicom or dicom module is importable
   else None;
+* tag_for_keyword : ``tag_for_keyword`` function if pydicom or dicom module
+  is importable else None;
 * dicom_test : test decorator that skips test if dicom not available.
 """
 
-# Module does (apparently) unused imports; stop flake8 complaining
+# Module has (apparently) unused imports; stop flake8 complaining
 # flake8: noqa
 
 import numpy as np
 
 have_dicom = True
-read_file = None
-pydicom = None
+pydicom = read_file = tag_for_keyword = None
 
 try:
     import dicom as pydicom
@@ -38,6 +39,14 @@
 else:  # dicom module available
     read_file = pydicom.read_file
 
+if have_dicom:
+    try:
+        # Versions >= 1.0
+        tag_for_keyword = pydicom.datadict.tag_for_keyword
+    except AttributeError:
+        # Versions < 1.0 - also has more search options.
+        tag_for_keyword = pydicom.datadict.tag_for_name
+
 
 # test decorator that skips test if dicom not available.
 dicom_test = np.testing.dec.skipif(not have_dicom,