Merge remote-tracking branch 'upstream/master' into update_petsurfer

Author: effigies

.zenodo.json

@@ -911,6 +911,11 @@
       "name": "Wu, Jianxiao",
       "orcid": "0000-0002-4866-272X",
     },
+    {
+      "affiliation": "Lund University",
+      "name": "Anijärv, Toomas Erik",
+      "orcid": "0000-0002-3650-4230",
+    },
   ],
   "keywords": [
     "neuroimaging",

nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py

@@ -37,7 +37,6 @@ def test_Generate5tt_inputs():
         ),
         in_file=dict(
             argstr="%s",
-            extensions=None,
             mandatory=True,
             position=-2,
         ),

nipype/interfaces/mrtrix3/tests/test_auto_MRTransform.py

@@ -12,15 +12,13 @@ def test_MRTransform_inputs():
         ),
         debug=dict(
             argstr="-debug",
-            position=1,
         ),
         environ=dict(
             nohash=True,
             usedefault=True,
         ),
         flip_x=dict(
             argstr="-flipx",
-            position=1,
         ),
         grad_file=dict(
             argstr="-grad %s",
@@ -45,12 +43,10 @@ def test_MRTransform_inputs():
         ),
         invert=dict(
             argstr="-inverse",
-            position=1,
         ),
         linear_transform=dict(
             argstr="-linear %s",
             extensions=None,
-            position=1,
         ),
         nthreads=dict(
             argstr="-nthreads %d",
@@ -71,26 +67,21 @@ def test_MRTransform_inputs():
         ),
         quiet=dict(
             argstr="-quiet",
-            position=1,
         ),
         reference_image=dict(
             argstr="-reference %s",
             extensions=None,
-            position=1,
         ),
         replace_transform=dict(
             argstr="-replace",
-            position=1,
         ),
         template_image=dict(
             argstr="-template %s",
             extensions=None,
-            position=1,
         ),
         transformation_file=dict(
             argstr="-transform %s",
             extensions=None,
-            position=1,
         ),
     )
     inputs = MRTransform.input_spec()

nipype/interfaces/mrtrix3/utils.py

@@ -11,6 +11,7 @@
     traits,
     TraitedSpec,
     File,
+    Directory,
     InputMultiPath,
     isdefined,
 )
@@ -224,13 +225,19 @@ class Generate5ttInputSpec(MRTrix3BaseInputSpec):
         "fsl",
         "gif",
         "freesurfer",
+        "hsvs",
         argstr="%s",
         position=-3,
         mandatory=True,
         desc="tissue segmentation algorithm",
     )
-    in_file = File(
-        exists=True, argstr="%s", mandatory=True, position=-2, desc="input image"
+    in_file = traits.Either(
+        File(exists=True),
+        Directory(exists=True),
+        argstr="%s",
+        mandatory=True,
+        position=-2,
+        desc="input image / directory",
     )
     out_file = File(argstr="%s", mandatory=True, position=-1, desc="output image")
 
@@ -822,13 +829,11 @@ class MRTransformInputSpec(MRTrix3BaseInputSpec):
     )
     invert = traits.Bool(
         argstr="-inverse",
-        position=1,
         desc="Invert the specified transform before using it",
     )
     linear_transform = File(
         exists=True,
         argstr="-linear %s",
-        position=1,
         desc=(
             "Specify a linear transform to apply, in the form of a 3x4 or 4x4 ascii file. "
             "Note the standard reverse convention is used, "
@@ -838,38 +843,32 @@ class MRTransformInputSpec(MRTrix3BaseInputSpec):
     )
     replace_transform = traits.Bool(
         argstr="-replace",
-        position=1,
         desc="replace the current transform by that specified, rather than applying it to the current transform",
     )
     transformation_file = File(
         exists=True,
         argstr="-transform %s",
-        position=1,
         desc="The transform to apply, in the form of a 4x4 ascii file.",
     )
     template_image = File(
         exists=True,
         argstr="-template %s",
-        position=1,
         desc="Reslice the input image to match the specified template image.",
     )
     reference_image = File(
         exists=True,
         argstr="-reference %s",
-        position=1,
         desc="in case the transform supplied maps from the input image onto a reference image, use this option to specify the reference. Note that this implicitly sets the -replace option.",
     )
     flip_x = traits.Bool(
         argstr="-flipx",
-        position=1,
         desc="assume the transform is supplied assuming a coordinate system with the x-axis reversed relative to the MRtrix convention (i.e. x increases from right to left). This is required to handle transform matrices produced by FSL's FLIRT command. This is only used in conjunction with the -reference option.",
     )
     quiet = traits.Bool(
         argstr="-quiet",
-        position=1,
         desc="Do not display information messages or progress status.",
     )
-    debug = traits.Bool(argstr="-debug", position=1, desc="Display debugging messages.")
+    debug = traits.Bool(argstr="-debug", desc="Display debugging messages.")
 
 
 class MRTransformOutputSpec(TraitedSpec):

nipype/interfaces/utility/csv.py

@@ -2,6 +2,7 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """CSV Handling utilities
 """
+import csv
 from ..base import traits, TraitedSpec, DynamicTraitedSpec, File, BaseInterface
 from ..io import add_traits
 
@@ -13,6 +14,7 @@ class CSVReaderInputSpec(DynamicTraitedSpec, TraitedSpec):
     header = traits.Bool(
         False, usedefault=True, desc="True if the first line is a column header"
     )
+    delimiter = traits.String(",", usedefault=True, desc="Delimiter to use.")
 
 
 class CSVReader(BaseInterface):
@@ -52,14 +54,11 @@ def _append_entry(self, outputs, entry):
             outputs[key].append(value)
         return outputs
 
-    def _parse_line(self, line):
-        line = line.replace("\n", "")
-        entry = [x.strip() for x in line.split(",")]
-        return entry
-
     def _get_outfields(self):
         with open(self.inputs.in_file) as fid:
-            entry = self._parse_line(fid.readline())
+            reader = csv.reader(fid, delimiter=self.inputs.delimiter)
+
+            entry = next(reader)
             if self.inputs.header:
                 self._outfields = tuple(entry)
             else:
@@ -82,10 +81,10 @@ def _list_outputs(self):
         for key in self._outfields:
             outputs[key] = []  # initialize outfields
         with open(self.inputs.in_file) as fid:
-            for line in fid.readlines():
+            reader = csv.reader(fid, delimiter=self.inputs.delimiter)
+            for entry in reader:
                 if self.inputs.header and isHeader:  # skip header line
                     isHeader = False
                     continue
-                entry = self._parse_line(line)
                 outputs = self._append_entry(outputs, entry)
         return outputs

nipype/interfaces/utility/tests/test_auto_CSVReader.py

@@ -4,6 +4,9 @@
 
 def test_CSVReader_inputs():
     input_map = dict(
+        delimiter=dict(
+            usedefault=True,
+        ),
         header=dict(
             usedefault=True,
         ),

nipype/interfaces/utility/tests/test_csv.py

@@ -26,3 +26,44 @@ def test_csvReader(tmpdir):
                 assert out.outputs.column_0 == ["foo", "bar", "baz"]
                 assert out.outputs.column_1 == ["hello", "world", "goodbye"]
                 assert out.outputs.column_2 == ["300.1", "5", "0.3"]
+
+
+def test_csvReader_quoted(tmpdir):
+    header = "files,labels,erosion\n"
+    lines = ['foo,"hello, world",300.1\n']
+
+    name = tmpdir.join("testfile.csv").strpath
+    with open(name, "w") as fid:
+        reader = utility.CSVReader()
+        fid.writelines(lines)
+        fid.flush()
+        reader.inputs.in_file = name
+        out = reader.run()
+
+        assert out.outputs.column_0 == ["foo"]
+        assert out.outputs.column_1 == ["hello, world"]
+        assert out.outputs.column_2 == ["300.1"]
+
+
+def test_csvReader_tabs(tmpdir):
+    header = "files\tlabels\terosion\n"
+    lines = ["foo\thello\t300.1\n", "bar\tworld\t5\n", "baz\tgoodbye\t0.3\n"]
+    for x in range(2):
+        name = tmpdir.join("testfile.csv").strpath
+        with open(name, "w") as fid:
+            reader = utility.CSVReader(delimiter="\t")
+            if x % 2 == 0:
+                fid.write(header)
+                reader.inputs.header = True
+            fid.writelines(lines)
+            fid.flush()
+            reader.inputs.in_file = name
+            out = reader.run()
+            if x % 2 == 0:
+                assert out.outputs.files == ["foo", "bar", "baz"]
+                assert out.outputs.labels == ["hello", "world", "goodbye"]
+                assert out.outputs.erosion == ["300.1", "5", "0.3"]
+            else:
+                assert out.outputs.column_0 == ["foo", "bar", "baz"]
+                assert out.outputs.column_1 == ["hello", "world", "goodbye"]
+                assert out.outputs.column_2 == ["300.1", "5", "0.3"]