Merge pull request #3674 from DimitriPapadopoulos/PERF

STY: Apply ruff/Perflint rules (PERF)

Author: effigies

nipype/algorithms/confounds.py

@@ -1290,11 +1290,8 @@ def combine_mask_files(mask_files, mask_method=None, mask_index=None):
         raise ValueError(
             f"mask_index {mask_index} must be less than number of mask files {len(mask_files)}"
         )
-    masks = []
     if mask_method == "none":
-        for filename in mask_files:
-            masks.append(nb.load(filename))
-        return masks
+        return [nb.load(filename) for filename in mask_files]
 
     if mask_method == "union":
         mask = None

nipype/algorithms/misc.py

@@ -549,11 +549,9 @@ def maketypelist(rowheadings, shape, extraheadingBool, extraheading):
     if rowheadings:
         typelist.append(("heading", "a40"))
     if len(shape) > 1:
-        for idx in range(1, (min(shape) + 1)):
-            typelist.append((str(idx), float))
+        typelist.extend((str(idx), float) for idx in range(1, (min(shape) + 1)))
     else:
-        for idx in range(1, (shape[0] + 1)):
-            typelist.append((str(idx), float))
+        typelist.extend((str(idx), float) for idx in range(1, (shape[0] + 1)))
     if extraheadingBool:
         typelist.append((extraheading, "a40"))
     iflogger.info(typelist)
@@ -714,8 +712,7 @@ def _run_interface(self, runtime):
                 mx = shape[0]
             else:
                 mx = 1
-            for idx in range(mx):
-                extrafieldlist.append(self.inputs.extra_field)
+            extrafieldlist.extend(self.inputs.extra_field for idx in range(mx))
             iflogger.info(len(extrafieldlist))
             output[extraheading] = extrafieldlist
         iflogger.info(output)

nipype/algorithms/modelgen.py

@@ -473,15 +473,15 @@ def _generate_design(self, infolist=None):
         """Generate design specification for a typical fmri paradigm"""
         realignment_parameters = []
         if isdefined(self.inputs.realignment_parameters):
-            for parfile in self.inputs.realignment_parameters:
-                realignment_parameters.append(
-                    np.apply_along_axis(
-                        func1d=normalize_mc_params,
-                        axis=1,
-                        arr=np.loadtxt(parfile),
-                        source=self.inputs.parameter_source,
-                    )
+            realignment_parameters.extend(
+                np.apply_along_axis(
+                    func1d=normalize_mc_params,
+                    axis=1,
+                    arr=np.loadtxt(parfile),
+                    source=self.inputs.parameter_source,
                 )
+                for parfile in self.inputs.realignment_parameters
+            )
         outliers = []
         if isdefined(self.inputs.outlier_files):
             for filename in self.inputs.outlier_files:

nipype/interfaces/ants/registration.py

@@ -190,10 +190,11 @@ def _transformation_constructor(self):
         delta_time = self.inputs.delta_time
         symmetry_type = self.inputs.symmetry_type
         retval = ["--transformation-model %s" % model]
-        parameters = []
-        for elem in (step_length, time_step, delta_time, symmetry_type):
-            if elem is not traits.Undefined:
-                parameters.append("%#.2g" % elem)
+        parameters = [
+            "%#.2g" % elem
+            for elem in (step_length, time_step, delta_time, symmetry_type)
+            if elem is not traits.Undefined
+        ]
         if len(parameters) > 0:
             if len(parameters) > 1:
                 parameters = ",".join(parameters)
@@ -1134,8 +1135,7 @@ def _format_registration(self):
         retval = []
         for ii in range(len(self.inputs.transforms)):
             retval.append("--transform %s" % (self._format_transform(ii)))
-            for metric in self._format_metric(ii):
-                retval.append("--metric %s" % metric)
+            retval.extend("--metric %s" % metric for metric in self._format_metric(ii))
             retval.append("--convergence %s" % self._format_convergence(ii))
             if isdefined(self.inputs.sigma_units):
                 retval.append(

nipype/interfaces/ants/segmentation.py

@@ -813,16 +813,15 @@ def _list_outputs(self):
             os.getcwd(),
             self.inputs.out_prefix + "BrainSegmentation0N4." + self.inputs.image_suffix,
         )
-        posteriors = []
-        for i in range(len(self.inputs.segmentation_priors)):
-            posteriors.append(
-                os.path.join(
-                    os.getcwd(),
-                    self.inputs.out_prefix
-                    + "BrainSegmentationPosteriors%02d." % (i + 1)
-                    + self.inputs.image_suffix,
-                )
+        posteriors = [
+            os.path.join(
+                os.getcwd(),
+                self.inputs.out_prefix
+                + "BrainSegmentationPosteriors%02d." % (i + 1)
+                + self.inputs.image_suffix,
             )
+            for i in range(len(self.inputs.segmentation_priors))
+        ]
         outputs["BrainSegmentationPosteriors"] = posteriors
         outputs["CorticalThickness"] = os.path.join(
             os.getcwd(),
@@ -1488,15 +1487,13 @@ class JointFusion(ANTSCommand):
 
     def _format_arg(self, opt, spec, val):
         if opt == "exclusion_image_label":
-            retval = []
-            for ii in range(len(self.inputs.exclusion_image_label)):
-                retval.append(
-                    "-e {}[{}]".format(
-                        self.inputs.exclusion_image_label[ii],
-                        self.inputs.exclusion_image[ii],
-                    )
+            return " ".join(
+                "-e {}[{}]".format(
+                    self.inputs.exclusion_image_label[ii],
+                    self.inputs.exclusion_image[ii],
                 )
-            return " ".join(retval)
+                for ii in range(len(self.inputs.exclusion_image_label))
+            )
         if opt == "patch_radius":
             return f"-p {self._format_xarray(val)}"
         if opt == "search_radius":

nipype/interfaces/base/core.py

@@ -1047,10 +1047,11 @@ def __init__(self, check_import=True, *args, **kwargs):
         if check_import:
             import pkgutil
 
-            failed_imports = []
-            for pkg in (self._pkg,) + tuple(self.imports):
-                if pkgutil.find_loader(pkg) is None:
-                    failed_imports.append(pkg)
+            failed_imports = [
+                pkg
+                for pkg in (self._pkg,) + tuple(self.imports)
+                if pkgutil.find_loader(pkg) is None
+            ]
             if failed_imports:
                 iflogger.warning(
                     "Unable to import %s; %s interface may fail to run",

nipype/interfaces/cmtk/cmtk.py

@@ -328,9 +328,11 @@ def cmat(
     else:
         final_fibers_indices = final_fibers_idx
 
-    for idx in final_fibers_indices:
+    finalfiberlength.extend(
         # compute length of fiber
-        finalfiberlength.append(length(fib[idx][0]))
+        length(fib[idx][0])
+        for idx in final_fibers_indices
+    )
 
     # convert to array
     final_fiberlength_array = np.array(finalfiberlength)
@@ -463,9 +465,7 @@ def cmat(
 def save_fibers(oldhdr, oldfib, fname, indices):
     """Stores a new trackvis file fname using only given indices"""
     hdrnew = oldhdr.copy()
-    outstreams = []
-    for i in indices:
-        outstreams.append(oldfib[i])
+    outstreams = [oldfib[i] for i in indices]
     n_fib_out = len(outstreams)
     hdrnew["n_count"] = n_fib_out
     iflogger.info("Writing final non-orphan fibers as %s", fname)

nipype/interfaces/dipy/simulate.py

@@ -222,20 +222,17 @@ def _run_interface(self, runtime):
         mevals = [sf_evals] * nsticks + [[ba_evals[d]] * 3 for d in range(nballs)]
 
         b0 = b0_im.get_fdata()[msk > 0]
-        args = []
-        for i in range(nvox):
-            args.append(
-                {
-                    "fractions": fracs[i, ...].tolist(),
-                    "sticks": [
-                        tuple(dirs[i, j : j + 3]) for j in range(nsticks + nballs)
-                    ],
-                    "gradients": gtab,
-                    "mevals": mevals,
-                    "S0": b0[i],
-                    "snr": self.inputs.snr,
-                }
-            )
+        args = [
+            {
+                "fractions": fracs[i, ...].tolist(),
+                "sticks": [tuple(dirs[i, j : j + 3]) for j in range(nsticks + nballs)],
+                "gradients": gtab,
+                "mevals": mevals,
+                "S0": b0[i],
+                "snr": self.inputs.snr,
+            }
+            for i in range(nvox)
+        ]
 
         n_proc = self.inputs.n_proc
         if n_proc == 0:

nipype/interfaces/freesurfer/preprocess.py

@@ -594,10 +594,10 @@ def _list_outputs(self):
                     raise Exception(
                         "Not taking frame manipulations into account- please warn the developers"
                     )
-                outfiles = []
                 outfile = self._get_outfilename()
-                for i in range(tp):
-                    outfiles.append(fname_presuffix(outfile, suffix="%03d" % (i + 1)))
+                outfiles = [
+                    fname_presuffix(outfile, suffix="%03d" % (i + 1)) for i in range(tp)
+                ]
                 outfile = outfiles
         outputs["out_file"] = outfile
         return outputs

nipype/interfaces/fsl/fix.py

@@ -105,11 +105,11 @@ class TrainingSetCreator(BaseInterface):
     _always_run = True
 
     def _run_interface(self, runtime):
-        mel_icas = []
-        for item in self.inputs.mel_icas_in:
-            if os.path.exists(os.path.join(item, "hand_labels_noise.txt")):
-                mel_icas.append(item)
-
+        mel_icas = [
+            item
+            for item in self.inputs.mel_icas_in
+            if os.path.exists(os.path.join(item, "hand_labels_noise.txt"))
+        ]
         if len(mel_icas) == 0:
             raise Exception(
                 "%s did not find any hand_labels_noise.txt files in the following directories: %s"
@@ -119,10 +119,11 @@ def _run_interface(self, runtime):
         return runtime
 
     def _list_outputs(self):
-        mel_icas = []
-        for item in self.inputs.mel_icas_in:
-            if os.path.exists(os.path.join(item, "hand_labels_noise.txt")):
-                mel_icas.append(item)
+        mel_icas = [
+            item
+            for item in self.inputs.mel_icas_in
+            if os.path.exists(os.path.join(item, "hand_labels_noise.txt"))
+        ]
         outputs = self._outputs().get()
         outputs["mel_icas_out"] = mel_icas
         return outputs

nipype/interfaces/io.py

@@ -959,10 +959,7 @@ def _list_outputs(self):
             if isdefined(self.inputs.bucket_path):
                 template = os.path.join(self.inputs.bucket_path, template)
             if not args:
-                filelist = []
-                for fname in bkt_files:
-                    if re.match(template, fname):
-                        filelist.append(fname)
+                filelist = [fname for fname in bkt_files if re.match(template, fname)]
                 if len(filelist) == 0:
                     msg = "Output key: {} Template: {} returned no files".format(
                         key,
@@ -2720,16 +2717,14 @@ class JSONFileGrabber(IOBase):
     def _list_outputs(self):
         import simplejson
 
-        outputs = {}
         if isdefined(self.inputs.in_file):
             with open(self.inputs.in_file) as f:
-                data = simplejson.load(f)
+                outputs = simplejson.load(f)
 
-            if not isinstance(data, dict):
+            if not isinstance(outputs, dict):
                 raise RuntimeError("JSON input has no dictionary structure")
-
-            for key, value in list(data.items()):
-                outputs[key] = value
+        else:
+            outputs = {}
 
         if isdefined(self.inputs.defaults):
             defaults = self.inputs.defaults

nipype/interfaces/mne/base.py

@@ -132,9 +132,7 @@ def _list_outputs(self):
                 if val:
                     value_list = simplify_list(val)
                     if isinstance(value_list, list):
-                        out_files = []
-                        for value in value_list:
-                            out_files.append(op.abspath(value))
+                        out_files = [op.abspath(value) for value in value_list]
                     elif isinstance(value_list, (str, bytes)):
                         out_files = op.abspath(value_list)
                     else:

nipype/interfaces/nilearn.py

@@ -98,9 +98,7 @@ class SignalExtraction(NilearnBaseInterface, SimpleInterface):
     def _run_interface(self, runtime):
         maskers = self._process_inputs()
 
-        signals = []
-        for masker in maskers:
-            signals.append(masker.fit_transform(self.inputs.in_file))
+        signals = [masker.fit_transform(self.inputs.in_file) for masker in maskers]
         region_signals = np.hstack(signals)
 
         output = np.vstack((self.inputs.class_labels, region_signals.astype(str)))
@@ -127,10 +125,10 @@ def _process_inputs(self):
         else:  # 4d labels
             n_labels = label_data.shape[3]
             if self.inputs.incl_shared_variance:  # independent computation
-                for img in nli.iter_img(label_data):
-                    maskers.append(
-                        nl.NiftiMapsMasker(self._4d(img.dataobj, img.affine))
-                    )
+                maskers.extend(
+                    nl.NiftiMapsMasker(self._4d(img.dataobj, img.affine))
+                    for img in nli.iter_img(label_data)
+                )
             else:  # one computation fitting all
                 maskers.append(nl.NiftiMapsMasker(label_data))
 

nipype/interfaces/nipy/model.py

@@ -138,10 +138,7 @@ def _run_interface(self, runtime):
             hpf = 0
             drift_model = "Blank"
 
-        reg_names = []
-        for reg in session_info[0]["regress"]:
-            reg_names.append(reg["name"])
-
+        reg_names = [reg["name"] for reg in session_info[0]["regress"]]
         reg_vals = np.zeros((nscans, len(reg_names)))
         for i in range(len(reg_names)):
             reg_vals[:, i] = np.array(session_info[0]["regress"][i]["val"]).reshape(

nipype/pipeline/engine/utils.py

@@ -1489,13 +1489,12 @@ def clean_working_directory(
                     files2remove.append(f)
     else:
         if not str2bool(config["execution"]["keep_inputs"]):
-            input_files = []
-            inputdict = inputs.trait_get()
-            input_files.extend(walk_outputs(inputdict))
-            input_files = [path for path, type in input_files if type == "f"]
-            for f in walk_files(cwd):
-                if f in input_files and f not in needed_files:
-                    files2remove.append(f)
+            input_files = {
+                path for path, type in walk_outputs(inputs.trait_get()) if type == "f"
+            }
+            files2remove.extend(
+                f for f in walk_files(cwd) if f in input_files and f not in needed_files
+            )
     logger.debug("Removing files: %s", ";".join(files2remove))
     for f in files2remove:
         os.remove(f)
@@ -1717,9 +1716,7 @@ def topological_sort(graph, depth_first=False):
     components = nx.connected_components(G)
     for desc in components:
         group += 1
-        indices = []
-        for node in desc:
-            indices.append(nodesort.index(node))
+        indices = [nodesort.index(node) for node in desc]
         nodes.extend(
             np.array(nodesort)[np.array(indices)[np.argsort(indices)]].tolist()
         )