Merge branch 'master' into replace_imghdr

Author: effigies

nipype/algorithms/misc.py

@@ -684,7 +684,7 @@ def _run_interface(self, runtime):
 
         output_array = merge_csvs(self.inputs.in_files)
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".csv":
+        if ext != ".csv":
             ext = ".csv"
 
         out_file = op.abspath(name + ext)
@@ -725,7 +725,7 @@ def _run_interface(self, runtime):
     def _list_outputs(self):
         outputs = self.output_spec().get()
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".csv":
+        if ext != ".csv":
             ext = ".csv"
         out_file = op.abspath(name + ext)
         outputs["csv_file"] = out_file
@@ -771,7 +771,7 @@ class AddCSVColumn(BaseInterface):
     def _run_interface(self, runtime):
         in_file = open(self.inputs.in_file)
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".csv":
+        if ext != ".csv":
             ext = ".csv"
         out_file = op.abspath(name + ext)
 
@@ -791,7 +791,7 @@ def _run_interface(self, runtime):
     def _list_outputs(self):
         outputs = self.output_spec().get()
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".csv":
+        if ext != ".csv":
             ext = ".csv"
         out_file = op.abspath(name + ext)
         outputs["csv_file"] = out_file

nipype/algorithms/modelgen.py

@@ -161,7 +161,7 @@ def bids_gen_info(
     for bids_event_file in bids_event_files:
         with open(bids_event_file) as f:
             f_events = csv.DictReader(f, skipinitialspace=True, delimiter="\t")
-            events = [{k: v for k, v in row.items()} for row in f_events]
+            events = list(f_events)
         if not condition_column:
             condition_column = "_trial_type"
             for i in events:

nipype/algorithms/tests/test_CompCor.py

@@ -287,9 +287,9 @@ def run_cc(
                 components_metadata = [
                     line.rstrip().split("\t") for line in metadata_file
                 ]
-                components_metadata = {
-                    i: j for i, j in zip(components_metadata[0], components_metadata[1])
-                }
+                components_metadata = dict(
+                    zip(components_metadata[0], components_metadata[1])
+                )
                 assert components_metadata == expected_metadata
 
         return ccresult

nipype/algorithms/tests/test_modelgen.py

@@ -122,7 +122,7 @@ def test_modelgen_spm_concat(tmpdir):
     s = SpecifySPMModel()
     s.inputs.input_units = "secs"
     s.inputs.concatenate_runs = True
-    setattr(s.inputs, "output_units", "secs")
+    s.inputs.output_units = "secs"
     assert s.inputs.output_units == "secs"
     s.inputs.functional_runs = [filename1, filename2]
     s.inputs.time_repetition = 6
@@ -147,7 +147,7 @@ def test_modelgen_spm_concat(tmpdir):
     )
 
     # Test case of scans as output units instead of seconds
-    setattr(s.inputs, "output_units", "scans")
+    s.inputs.output_units = "scans"
     assert s.inputs.output_units == "scans"
     s.inputs.subject_info = deepcopy(info)
     res = s.run()

nipype/interfaces/afni/base.py

@@ -326,6 +326,4 @@ def _cmd_prefix(self):
 
 def no_afni():
     """Check whether AFNI is not available."""
-    if Info.version() is None:
-        return True
-    return False
+    return Info.version() is None

nipype/interfaces/afni/model.py

@@ -636,7 +636,7 @@ def _parse_inputs(self, skip=None):
     def _list_outputs(self):
         outputs = self.output_spec().get()
 
-        for key in outputs.keys():
+        for key in outputs:
             if isdefined(self.inputs.get()[key]):
                 outputs[key] = os.path.abspath(self.inputs.get()[key])
 
@@ -722,7 +722,7 @@ class Synthesize(AFNICommand):
     def _list_outputs(self):
         outputs = self.output_spec().get()
 
-        for key in outputs.keys():
+        for key in outputs:
             if isdefined(self.inputs.get()[key]):
                 outputs[key] = os.path.abspath(self.inputs.get()[key])
 

nipype/interfaces/afni/utils.py

@@ -234,7 +234,7 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None):
             m = re.search(pattern, line)
             if m:
                 d = m.groupdict()
-                outputs.trait_set(**{k: int(d[k]) for k in d.keys()})
+                outputs.trait_set(**{k: int(v) for k, v in d.items()})
         return outputs
 
 
@@ -3244,11 +3244,11 @@ def _run_interface(self, runtime):
             for line in runtime.stdout.split("\n")
             if line.strip().startswith("GCOR = ")
         ][-1]
-        setattr(self, "_gcor", float(gcor_line[len("GCOR = ") :]))
+        self._gcor = float(gcor_line[len("GCOR = ") :])
         return runtime
 
     def _list_outputs(self):
-        return {"out": getattr(self, "_gcor")}
+        return {"out": self._gcor}
 
 
 class AxializeInputSpec(AFNICommandInputSpec):

nipype/interfaces/ants/segmentation.py

@@ -194,7 +194,7 @@ def _format_arg(self, opt, spec, val):
                         priors_paths[0] % i for i in range(1, n_classes + 1)
                     ]
 
-                if not all([os.path.exists(p) for p in priors_paths]):
+                if not all(os.path.exists(p) for p in priors_paths):
                     raise FileNotFoundError(
                         "One or more prior images do not exist: "
                         "%s." % ", ".join(priors_paths)

nipype/interfaces/ants/utils.py

@@ -536,7 +536,7 @@ def _format_arg(self, opt, spec, val):
         return super()._format_arg(opt, spec, val)
 
     def _list_outputs(self):
-        return getattr(self, "_output")
+        return self._output
 
 
 class AverageAffineTransformInputSpec(ANTSCommandInputSpec):

nipype/interfaces/base/core.py

@@ -486,7 +486,7 @@ def load_inputs_from_json(self, json_file, overwrite=True):
         if not overwrite:
             def_inputs = list(self.inputs.get_traitsfree().keys())
 
-        new_inputs = list(set(list(inputs_dict.keys())) - set(def_inputs))
+        new_inputs = set(inputs_dict) - set(def_inputs)
         for key in new_inputs:
             if hasattr(self.inputs, key):
                 setattr(self.inputs, key, inputs_dict[key])

nipype/interfaces/base/specs.py

@@ -177,19 +177,15 @@ def get_traitsfree(self, **kwargs):
 
     def _clean_container(self, objekt, undefinedval=None, skipundefined=False):
         """Convert a traited object into a pure python representation."""
-        if isinstance(objekt, TraitDictObject) or isinstance(objekt, dict):
+        if isinstance(objekt, (TraitDictObject, dict)):
             out = {}
             for key, val in list(objekt.items()):
                 if isdefined(val):
                     out[key] = self._clean_container(val, undefinedval)
                 else:
                     if not skipundefined:
                         out[key] = undefinedval
-        elif (
-            isinstance(objekt, TraitListObject)
-            or isinstance(objekt, list)
-            or isinstance(objekt, tuple)
-        ):
+        elif isinstance(objekt, (TraitListObject, list, tuple)):
             out = []
             for val in objekt:
                 if isdefined(val):
@@ -387,7 +383,7 @@ def __deepcopy__(self, memo):
         dup_dict = deepcopy(self.trait_get(), memo)
         # access all keys
         for key in self.copyable_trait_names():
-            if key in self.__dict__.keys():
+            if key in self.__dict__:
                 _ = getattr(self, key)
         # clone once
         dup = self.clone_traits(memo=memo)

nipype/interfaces/base/support.py

@@ -16,6 +16,7 @@
 import platform
 
 from ... import logging, config
+from ...utils.datetime import utcnow
 from ...utils.misc import is_container, rgetcwd
 from ...utils.filemanip import md5, hash_infile
 
@@ -72,15 +73,15 @@ def __enter__(self):
         if self._runtime.redirect_x:
             self._runtime.environ["DISPLAY"] = config.get_display()
 
-        self._runtime.startTime = dt.isoformat(dt.utcnow())
+        self._runtime.startTime = dt.isoformat(utcnow())
         self._resmon.start()
         # TODO: Perhaps clean-up path and ensure it exists?
         os.chdir(self._runtime.cwd)
         return self._runtime
 
     def __exit__(self, exc_type, exc_value, exc_tb):
         """Tear-down interface execution."""
-        self._runtime.endTime = dt.isoformat(dt.utcnow())
+        self._runtime.endTime = dt.isoformat(utcnow())
         timediff = parseutc(self._runtime.endTime) - parseutc(self._runtime.startTime)
         self._runtime.duration = (
             timediff.days * 86400 + timediff.seconds + timediff.microseconds / 1e6
@@ -99,7 +100,7 @@ def __exit__(self, exc_type, exc_value, exc_tb):
                 traceback.format_exception(exc_type, exc_value, exc_tb)
             )
             # Gather up the exception arguments and append nipype info.
-            exc_args = exc_value.args if getattr(exc_value, "args") else tuple()
+            exc_args = exc_value.args or ()
             exc_args += (
                 f"An exception of type {exc_type.__name__} occurred while "
                 f"running interface {self._runtime.interface}.",

nipype/interfaces/cmtk/cmtk.py

@@ -77,7 +77,7 @@ def get_rois_crossed(pointsmm, roiData, voxelSize):
         x = int(pointsmm[j, 0] / float(voxelSize[0]))
         y = int(pointsmm[j, 1] / float(voxelSize[1]))
         z = int(pointsmm[j, 2] / float(voxelSize[2]))
-        if not roiData[x, y, z] == 0:
+        if roiData[x, y, z] != 0:
             rois_crossed.append(roiData[x, y, z])
     rois_crossed = list(
         dict.fromkeys(rois_crossed).keys()
@@ -91,7 +91,7 @@ def get_connectivity_matrix(n_rois, list_of_roi_crossed_lists):
         for idx_i, roi_i in enumerate(rois_crossed):
             for idx_j, roi_j in enumerate(rois_crossed):
                 if idx_i > idx_j:
-                    if not roi_i == roi_j:
+                    if roi_i != roi_j:
                         connectivity_matrix[roi_i - 1, roi_j - 1] += 1
     connectivity_matrix = connectivity_matrix + connectivity_matrix.T
     return connectivity_matrix
@@ -248,7 +248,7 @@ def cmat(
                     axis=1,
                 )
             )
-            G.nodes[int(u)]["dn_position"] = tuple([xyz[0], xyz[2], -xyz[1]])
+            G.nodes[int(u)]["dn_position"] = (xyz[0], xyz[2], -xyz[1])
 
     if intersections:
         iflogger.info("Filtering tractography from intersections")
@@ -371,7 +371,7 @@ def cmat(
             di["fiber_length_mean"] = 0
             di["fiber_length_median"] = 0
             di["fiber_length_std"] = 0
-        if not u == v:  # Fix for self loop problem
+        if u != v:  # Fix for self loop problem
             G.add_edge(u, v, **di)
             if "fiblist" in d:
                 numfib.add_edge(u, v, weight=di["number_of_fibers"])
@@ -400,7 +400,7 @@ def cmat(
             pickle.dump(I, f, pickle.HIGHEST_PROTOCOL)
 
     path, name, ext = split_filename(matrix_mat_name)
-    if not ext == ".mat":
+    if ext != ".mat":
         ext = ".mat"
         matrix_mat_name = matrix_mat_name + ext
 
@@ -608,7 +608,7 @@ def _run_interface(self, runtime):
 
         matrix_mat_file = op.abspath(self.inputs.out_matrix_mat_file)
         path, name, ext = split_filename(matrix_mat_file)
-        if not ext == ".mat":
+        if ext != ".mat":
             ext = ".mat"
             matrix_mat_file = matrix_mat_file + ext
 
@@ -673,7 +673,7 @@ def _list_outputs(self):
 
         matrix_mat_file = op.abspath(self.inputs.out_matrix_mat_file)
         path, name, ext = split_filename(matrix_mat_file)
-        if not ext == ".mat":
+        if ext != ".mat":
             ext = ".mat"
             matrix_mat_file = matrix_mat_file + ext
 
@@ -1070,7 +1070,7 @@ def create_nodes(roi_file, resolution_network_file, out_filename):
                 np.where(np.flipud(roiData) == int(d["dn_correspondence_id"])), axis=1
             )
         )
-        G.nodes[int(u)]["dn_position"] = tuple([xyz[0], xyz[2], -xyz[1]])
+        G.nodes[int(u)]["dn_position"] = (xyz[0], xyz[2], -xyz[1])
     with open(out_filename, 'wb') as f:
         pickle.dump(G, f, pickle.HIGHEST_PROTOCOL)
     return out_filename

nipype/interfaces/cmtk/convert.py

@@ -194,17 +194,17 @@ def _run_interface(self, runtime):
             for data in self.inputs.data_files:
                 _, data_name, _ = split_filename(data)
                 cda = cf.CData(name=data_name, src=data, fileformat="NumPy")
-                if not string.find(data_name, "lengths") == -1:
+                if 'lengths' in data_name:
                     cda.dtype = "FinalFiberLengthArray"
-                if not string.find(data_name, "endpoints") == -1:
+                if 'endpoints' in data_name:
                     cda.dtype = "FiberEndpoints"
-                if not string.find(data_name, "labels") == -1:
+                if 'labels' in data_name:
                     cda.dtype = "FinalFiberLabels"
                 a.add_connectome_data(cda)
 
         a.print_summary()
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".cff":
+        if ext != '.cff':
             ext = ".cff"
         cf.save_to_cff(a, op.abspath(name + ext))
 
@@ -213,7 +213,7 @@ def _run_interface(self, runtime):
     def _list_outputs(self):
         outputs = self._outputs().get()
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".cff":
+        if ext != '.cff':
             ext = ".cff"
         outputs["connectome_file"] = op.abspath(name + ext)
         return outputs
@@ -281,7 +281,7 @@ def _run_interface(self, runtime):
         metadata.set_email("My Email")
 
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".cff":
+        if ext != '.cff':
             ext = ".cff"
         cf.save_to_cff(newcon, op.abspath(name + ext))
 
@@ -290,7 +290,7 @@ def _run_interface(self, runtime):
     def _list_outputs(self):
         outputs = self._outputs().get()
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".cff":
+        if ext != '.cff':
             ext = ".cff"
         outputs["connectome_file"] = op.abspath(name + ext)
         return outputs

nipype/interfaces/cmtk/nx.py

@@ -166,8 +166,8 @@ def average_networks(in_files, ntwk_res_file, group_id):
         for edge in edges:
             data = ntwk.edge[edge[0]][edge[1]]
             if ntwk.edge[edge[0]][edge[1]]["count"] >= count_to_keep_edge:
-                for key in list(data.keys()):
-                    if not key == "count":
+                for key in data:
+                    if key != "count":
                         data[key] = data[key] / len(in_files)
                 ntwk.edge[edge[0]][edge[1]] = data
                 avg_ntwk.add_edge(edge[0], edge[1], **data)
@@ -183,8 +183,8 @@ def average_networks(in_files, ntwk_res_file, group_id):
         avg_edges = avg_ntwk.edges()
         for edge in avg_edges:
             data = avg_ntwk.edge[edge[0]][edge[1]]
-            for key in list(data.keys()):
-                if not key == "count":
+            for key in data:
+                if key != "count":
                     edge_dict[key] = np.zeros(
                         (avg_ntwk.number_of_nodes(), avg_ntwk.number_of_nodes())
                     )
@@ -342,7 +342,7 @@ def add_node_data(node_array, ntwk):
     node_ntwk = nx.Graph()
     newdata = {}
     for idx, data in ntwk.nodes(data=True):
-        if not int(idx) == 0:
+        if int(idx) != 0:
             newdata["value"] = node_array[int(idx) - 1]
             data.update(newdata)
             node_ntwk.add_node(int(idx), **data)
@@ -354,7 +354,7 @@ def add_edge_data(edge_array, ntwk, above=0, below=0):
     data = {}
     for x, row in enumerate(edge_array):
         for y in range(np.max(np.shape(edge_array[x]))):
-            if not edge_array[x, y] == 0:
+            if edge_array[x, y] != 0:
                 data["value"] = edge_array[x, y]
                 if data["value"] <= below or data["value"] >= above:
                     if edge_ntwk.has_edge(x + 1, y + 1):

nipype/interfaces/dcmstack.py

@@ -152,7 +152,7 @@ def _run_interface(self, runtime):
         meta_filter = dcmstack.make_key_regex_filter(exclude_regexes, include_regexes)
         stack = dcmstack.DicomStack(meta_filter=meta_filter)
         for src_path in src_paths:
-            if not puremagic.what(src_path) == "gif":
+            if puremagic.what(src_path) != "gif":
                 src_dcm = pydicom.dcmread(src_path, force=self.inputs.force_read)
                 stack.add_dcm(src_dcm)
         nii = stack.to_nifti(embed_meta=True)

nipype/interfaces/diffusion_toolkit/dti.py

@@ -97,7 +97,7 @@ class DTIRecon(CommandLine):
     def _create_gradient_matrix(self, bvecs_file, bvals_file):
         _gradient_matrix_file = "gradient_matrix.txt"
         with open(bvals_file) as fbvals:
-            bvals = [val for val in re.split(r"\s+", fbvals.readline().strip())]
+            bvals = fbvals.readline().strip().split()
         with open(bvecs_file) as fbvecs:
             bvecs_x = fbvecs.readline().split()
             bvecs_y = fbvecs.readline().split()