Merge branch 'master' into fix/py2functions

Author: mgxd

.zenodo.json

@@ -518,6 +518,11 @@
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",
       "orcid": "0000-0002-5312-6729"
+    },
+    {
+      "affiliation": "University of Amsterdam",
+      "name": "Lukas Snoek",
+      "orcid": "0000-0001-8972-204X"
     }
   ],
   "keywords": [

doc/images/nipype_architecture_overview2.png

@@ -7,9 +7,13 @@ def test_ACompCor_inputs():
     input_map = dict(components_file=dict(usedefault=True,
     ),
     header_prefix=dict(),
+    high_pass_cutoff=dict(usedefault=True,
+    ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
+    ignore_initial_volumes=dict(usedefault=True,
+    ),
     mask_files=dict(),
     mask_index=dict(requires=['mask_files'],
     xor=['merge_method'],
@@ -19,11 +23,16 @@ def test_ACompCor_inputs():
     ),
     num_components=dict(usedefault=True,
     ),
+    pre_filter=dict(usedefault=True,
+    ),
     realigned_file=dict(mandatory=True,
     ),
     regress_poly_degree=dict(usedefault=True,
     ),
-    use_regress_poly=dict(usedefault=True,
+    repetition_time=dict(),
+    save_pre_filter=dict(),
+    use_regress_poly=dict(deprecated='0.15.0',
+    new_name='pre_filter',
     ),
     )
     inputs = ACompCor.input_spec()
@@ -35,6 +44,7 @@ def test_ACompCor_inputs():
 
 def test_ACompCor_outputs():
     output_map = dict(components_file=dict(),
+    pre_filter_file=dict(),
     )
     outputs = ACompCor.output_spec()
 

doc/images/nipype_architecture_overview2.svg

@@ -7,9 +7,13 @@ def test_TCompCor_inputs():
     input_map = dict(components_file=dict(usedefault=True,
     ),
     header_prefix=dict(),
+    high_pass_cutoff=dict(usedefault=True,
+    ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
+    ignore_initial_volumes=dict(usedefault=True,
+    ),
     mask_files=dict(),
     mask_index=dict(requires=['mask_files'],
     xor=['merge_method'],
@@ -21,11 +25,16 @@ def test_TCompCor_inputs():
     ),
     percentile_threshold=dict(usedefault=True,
     ),
+    pre_filter=dict(usedefault=True,
+    ),
     realigned_file=dict(mandatory=True,
     ),
     regress_poly_degree=dict(usedefault=True,
     ),
-    use_regress_poly=dict(usedefault=True,
+    repetition_time=dict(),
+    save_pre_filter=dict(),
+    use_regress_poly=dict(deprecated='0.15.0',
+    new_name='pre_filter',
     ),
     )
     inputs = TCompCor.input_spec()
@@ -38,6 +47,7 @@ def test_TCompCor_inputs():
 def test_TCompCor_outputs():
     output_map = dict(components_file=dict(),
     high_variance_masks=dict(),
+    pre_filter_file=dict(),
     )
     outputs = TCompCor.output_spec()
 

nipype/algorithms/confounds.py

@@ -80,7 +80,7 @@ def test_compcor_no_regress_poly(self):
         self.run_cc(CompCor(realigned_file=self.realigned_file,
                             mask_files=self.mask_files,
                             mask_index=0,
-                            use_regress_poly=False),
+                            pre_filter=False),
                     [['0.4451946442', '-0.7683311482'],
                      ['-0.4285129505', '-0.0926034137'],
                      ['0.5721540256', '0.5608764842'],

nipype/algorithms/tests/test_auto_ACompCor.py

@@ -105,7 +105,7 @@ def get_nipype_gitversion():
 PYTEST_MIN_VERSION = '3.0'
 FUTURE_MIN_VERSION = '0.16.0'
 SIMPLEJSON_MIN_VERSION = '3.8.0'
-PROV_MIN_VERSION = '1.5.0'
+PROV_VERSION = '1.5.0'
 CLICK_MIN_VERSION = '6.6.0'
 
 NAME = 'nipype'
@@ -136,7 +136,7 @@ def get_nipype_gitversion():
     'traits>=%s' % TRAITS_MIN_VERSION,
     'future>=%s' % FUTURE_MIN_VERSION,
     'simplejson>=%s' % SIMPLEJSON_MIN_VERSION,
-    'prov>=%s' % PROV_MIN_VERSION,
+    'prov==%s' % PROV_VERSION,
     'click>=%s' % CLICK_MIN_VERSION,
     'funcsigs',
     'pytest>=%s' % PYTEST_MIN_VERSION,

nipype/algorithms/tests/test_auto_TCompCor.py

@@ -15,9 +15,10 @@
                          Maskave, Means, OutlierCount,
                          QualityIndex, ROIStats, Retroicor,
                          Seg, SkullStrip, TCorr1D, TCorrMap, TCorrelate,
-                         TShift, Volreg, Warp, QwarpPlusMinus)
+                         TShift, Volreg, Warp, QwarpPlusMinus, Qwarp)
 from .svm import (SVMTest, SVMTrain)
-from .utils import (AFNItoNIFTI, Autobox, BrickStat, Calc, Copy, Edge3,
-                    Eval, FWHMx,
-                    MaskTool, Merge, Notes, Refit, Resample, TCat, TStat, To3D,
-                    Unifize, ZCutUp, GCOR,)
+from .utils import (AFNItoNIFTI, Autobox, Axialize, BrickStat, Calc, Cat, Copy,
+                    Edge3, Eval, FWHMx, MaskTool, Merge, Notes, NwarpApply,
+                    Refit, Resample, TCat, TStat, To3D, Unifize, ZCutUp, GCOR,
+                    Zcat, Zeropad)
+from .model import (Deconvolve, Remlfit)

nipype/algorithms/tests/test_compcor.py

@@ -10,7 +10,8 @@
 from sys import platform
 
 from ... import logging
-from ...utils.filemanip import split_filename
+from ...utils.filemanip import split_filename, fname_presuffix
+
 from ..base import (
     CommandLine, traits, CommandLineInputSpec, isdefined, File, TraitedSpec)
 from ...external.due import BibTeX
@@ -70,7 +71,7 @@ def version():
         return tuple(v)
 
     @classmethod
-    def outputtype_to_ext(cls, outputtype):
+    def output_type_to_ext(cls, outputtype):
         """Get the file extension for the given output type.
 
         Parameters
@@ -217,7 +218,7 @@ def set_default_output_type(cls, outputtype):
 
     def _overload_extension(self, value, name=None):
         path, base, _ = split_filename(value)
-        return os.path.join(path, base + Info.outputtype_to_ext(self.inputs.outputtype))
+        return os.path.join(path, base + Info.output_type_to_ext(self.inputs.outputtype))
 
     def _list_outputs(self):
         outputs = super(AFNICommand, self)._list_outputs()
@@ -231,6 +232,51 @@ def _list_outputs(self):
                         outputs[name] = outputs[name] + "+orig.BRIK"
         return outputs
 
+    def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True,
+                   ext=None):
+        """Generate a filename based on the given parameters.
+
+        The filename will take the form: cwd/basename<suffix><ext>.
+        If change_ext is True, it will use the extentions specified in
+        <instance>intputs.output_type.
+
+        Parameters
+        ----------
+        basename : str
+            Filename to base the new filename on.
+        cwd : str
+            Path to prefix to the new filename. (default is os.getcwd())
+        suffix : str
+            Suffix to add to the `basename`.  (defaults is '' )
+        change_ext : bool
+            Flag to change the filename extension to the FSL output type.
+            (default True)
+
+        Returns
+        -------
+        fname : str
+            New filename based on given parameters.
+
+        """
+
+        if basename == '':
+            msg = 'Unable to generate filename for command %s. ' % self.cmd
+            msg += 'basename is not set!'
+            raise ValueError(msg)
+        if cwd is None:
+            cwd = os.getcwd()
+        if ext is None:
+            ext = Info.output_type_to_ext(self.inputs.outputtype)
+        if change_ext:
+            if suffix:
+                suffix = ''.join((suffix, ext))
+            else:
+                suffix = ext
+        if suffix is None:
+            suffix = ''
+        fname = fname_presuffix(basename, suffix=suffix,
+                                use_ext=False, newpath=cwd)
+        return fname
 
 def no_afni():
     """ Checks if AFNI is available """