Merge branch 'fix/ImportsFromNipypeTesting' into fix/MinorErrorsNewInstaller

Author: oesteban

CHANGES

@@ -1,6 +1,7 @@
 Upcoming release 0.13
 =====================
 
+* ENH: Add AFNI 3dNote interface (https://github.com/nipy/nipype/pull/1637)
 * FIX: Minor bugfixes related to unicode literals (https://github.com/nipy/nipype/pull/1656)
 * ENH: Add a DVARS calculation interface (https://github.com/nipy/nipype/pull/1606)
 * ENH: New interface to b0calc of FSL-POSSUM (https://github.com/nipy/nipype/pull/1399)

docker/nipype_test/Dockerfile_py27

@@ -40,7 +40,8 @@ RUN chmod +x /usr/bin/run_*
 # Speed up building
 RUN mkdir -p /root/src/nipype
 COPY requirements.txt /root/src/nipype/requirements.txt
-RUN pip install -r /root/src/nipype/requirements.txt
+RUN pip install -r /root/src/nipype/requirements.txt && \
+    sed -i 's/\(backend *: \).*$/\1Agg/g' /usr/local/miniconda/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc
 
 # Re-install nipype
 COPY . /root/src/nipype

docker/nipype_test/Dockerfile_py34

@@ -45,7 +45,8 @@ RUN rm -r ${FSLDIR}/bin/imglob && \
 # Speed up building
 RUN mkdir -p /root/src/nipype
 COPY requirements.txt /root/src/nipype/requirements.txt
-RUN pip install -r /root/src/nipype/requirements.txt
+RUN pip install -r /root/src/nipype/requirements.txt && \
+    sed -i 's/\(backend *: \).*$/\1Agg/g' /usr/local/miniconda/lib/python3.4/site-packages/matplotlib/mpl-data/matplotlibrc
 
 # Re-install nipype
 COPY . /root/src/nipype

docker/nipype_test/Dockerfile_py35

@@ -43,7 +43,8 @@ RUN rm -r ${FSLDIR}/bin/imglob && \
 # Speed up building
 RUN mkdir -p /root/src/nipype
 COPY requirements.txt /root/src/nipype/requirements.txt
-RUN pip install -r /root/src/nipype/requirements.txt
+RUN pip install -r /root/src/nipype/requirements.txt && \
+    sed -i 's/\(backend *: \).*$/\1Agg/g' /usr/local/miniconda/lib/python3.5/site-packages/matplotlib/mpl-data/matplotlibrc
 
 # Re-install nipype
 COPY . /root/src/nipype

nipype/interfaces/afni/__init__.py

@@ -15,5 +15,5 @@
                          Fim, BlurInMask, Autobox, TCorrMap, Bandpass, Retroicor,
                          TCorrelate, TCorr1D, BrickStat, ROIStats, AutoTcorrelate,
                          AFNItoNIFTI, Eval, Means, Hist, FWHMx, OutlierCount,
-                         QualityIndex)
+                         QualityIndex, Notes)
 from .svm import (SVMTest, SVMTrain)

nipype/interfaces/afni/preprocess.py

@@ -20,7 +20,7 @@
 from ...utils.filemanip import (load_json, save_json, split_filename)
 from ..base import (
     CommandLineInputSpec, CommandLine, Directory, TraitedSpec,
-    traits, isdefined, File, InputMultiPath, Undefined)
+    traits, isdefined, File, InputMultiPath, Undefined, Str)
 
 from .base import (
     AFNICommandBase, AFNICommand, AFNICommandInputSpec, AFNICommandOutputSpec,
@@ -2102,7 +2102,6 @@ class CalcInputSpec(AFNICommandInputSpec):
     other = File(desc='other options', argstr='')
 
 
-
 class Calc(AFNICommand):
     """This program does voxel-by-voxel arithmetic on 3D datasets
 
@@ -2326,7 +2325,7 @@ class AutoboxInputSpec(AFNICommandInputSpec):
                 cropping box, and will clip off small isolated blobs.""")
 
 
-class AutoboxOuputSpec(TraitedSpec):  # out_file not mandatory
+class AutoboxOutputSpec(TraitedSpec):  # out_file not mandatory
     x_min = traits.Int()
     x_max = traits.Int()
     y_min = traits.Int()
@@ -2357,7 +2356,7 @@ class Autobox(AFNICommand):
 
     _cmd = '3dAutobox'
     input_spec = AutoboxInputSpec
-    output_spec = AutoboxOuputSpec
+    output_spec = AutoboxOutputSpec
 
     def aggregate_outputs(self, runtime=None, needed_outputs=None):
         outputs = self._outputs()
@@ -2923,7 +2922,6 @@ class OutlierCountOutputSpec(TraitedSpec):
         keep_extension=False, position=-1, desc='capture standard output')
 
 
-
 class OutlierCount(CommandLine):
     """Create a 3D dataset from 2D image files using AFNI to3d command
 
@@ -2989,8 +2987,7 @@ class QualityIndexInputSpec(CommandLineInputSpec):
 
 
 class QualityIndexOutputSpec(TraitedSpec):
-    out_file = File(desc='file containing the caputured standard output')
-
+    out_file = File(desc='file containing the captured standard output')
 
 
 class QualityIndex(CommandLine):
@@ -3013,3 +3010,56 @@ class QualityIndex(CommandLine):
     _cmd = '3dTqual'
     input_spec = QualityIndexInputSpec
     output_spec = QualityIndexOutputSpec
+
+
+class NotesInputSpec(AFNICommandInputSpec):
+    in_file = File(desc='input file to 3dNotes',
+                   argstr='%s',
+                   position=-1,
+                   mandatory=True,
+                   exists=True,
+                   copyfile=False)
+    add = Str(desc='note to add',
+              argstr='-a "%s"')
+    add_history = Str(desc='note to add to history',
+                      argstr='-h "%s"',
+                      xor=['rep_history'])
+    rep_history = Str(desc='note with which to replace history',
+                      argstr='-HH "%s"',
+                      xor=['add_history'])
+    delete = traits.Int(desc='delete note number num',
+                        argstr='-d %d')
+    ses = traits.Bool(desc='print to stdout the expanded notes',
+                      argstr='-ses')
+    out_file = File(desc='output image file name',
+                    argstr='%s')
+
+
+class Notes(CommandLine):
+    """
+    A program to add, delete, and show notes for AFNI datasets.
+
+    For complete details, see the `3dNotes Documentation.
+    <http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dNotes.html>
+
+    Examples
+    ========
+
+    >>> from nipype.interfaces import afni
+    >>> notes = afni.Notes()
+    >>> notes.inputs.in_file = "functional.HEAD"
+    >>> notes.inputs.add = "This note is added."
+    >>> notes.inputs.add_history = "This note is added to history."
+    >>> notes.cmdline #doctest: +IGNORE_UNICODE
+    '3dNotes -a "This note is added." -h "This note is added to history." functional.HEAD'
+    >>> res = notes.run() # doctest: +SKIP
+    """
+
+    _cmd = '3dNotes'
+    input_spec = NotesInputSpec
+    output_spec = AFNICommandOutputSpec
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['out_file'] = os.path.abspath(self.inputs.in_file)
+        return outputs

nipype/interfaces/afni/tests/test_auto_Notes.py

@@ -0,0 +1,52 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ....testing import assert_equal
+from ..preprocess import Notes
+
+
+def test_Notes_inputs():
+    input_map = dict(add=dict(argstr='-a "%s"',
+    ),
+    add_history=dict(argstr='-h "%s"',
+    xor=[u'rep_history'],
+    ),
+    args=dict(argstr='%s',
+    ),
+    delete=dict(argstr='-d %d',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='%s',
+    copyfile=False,
+    mandatory=True,
+    position=-1,
+    ),
+    out_file=dict(argstr='%s',
+    ),
+    outputtype=dict(),
+    rep_history=dict(argstr='-HH "%s"',
+    xor=[u'add_history'],
+    ),
+    ses=dict(argstr='-ses',
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = Notes.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+
+def test_Notes_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = Notes.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value