STY: Black

Author: mgxd

nibabies/cli/parser.py

@@ -68,8 +68,9 @@ def _slice_time_ref(value, parser):
         try:
             value = float(value)
         except ValueError:
-            raise parser.error("Slice time reference must be number, 'start', or 'middle'. "
-                               f"Received {value}.")
+            raise parser.error(
+                "Slice time reference must be number, 'start', or 'middle'. " f"Received {value}."
+            )
         if not 0 <= value <= 1:
             raise parser.error(f"Slice time reference must be in range 0-1. Received {value}.")
         return value
@@ -325,9 +326,9 @@ def _slice_time_ref(value, parser):
         default=None,
         type=SliceTimeRef,
         help="The time of the reference slice to correct BOLD values to, as a fraction "
-             "acquisition time. 0 indicates the start, 0.5 the midpoint, and 1 the end "
-             "of acquisition. The alias `start` corresponds to 0, and `middle` to 0.5. "
-             "The default value is 0.5.",
+        "acquisition time. 0 indicates the start, 0.5 the midpoint, and 1 the end "
+        "of acquisition. The alias `start` corresponds to 0, and `middle` to 0.5. "
+        "The default value is 0.5.",
     )
     g_conf.add_argument(
         "--dummy-scans",

nibabies/workflows/bold/outputs.py

@@ -10,7 +10,7 @@
 
 
 def prepare_timing_parameters(metadata):
-    """ Convert initial timing metadata to post-realignment timing metadata
+    """Convert initial timing metadata to post-realignment timing metadata
     In particular, SliceTiming metadata is invalid once STC or any realignment is applied,
     as a matrix of voxels no longer corresponds to an acquisition slice.
     Therefore, if SliceTiming is present in the metadata dictionary, and a sparse
@@ -53,11 +53,17 @@ def prepare_timing_parameters(metadata):
     """
     timing_parameters = {
         key: metadata[key]
-        for key in ("RepetitionTime", "VolumeTiming", "DelayTime",
-                    "AcquisitionDuration", "SliceTiming")
-        if key in metadata}
+        for key in (
+            "RepetitionTime",
+            "VolumeTiming",
+            "DelayTime",
+            "AcquisitionDuration",
+            "SliceTiming",
+        )
+        if key in metadata
+    }
 
-    run_stc = "SliceTiming" in metadata and 'slicetiming' not in config.workflow.ignore
+    run_stc = "SliceTiming" in metadata and "slicetiming" not in config.workflow.ignore
     timing_parameters["SliceTimingCorrected"] = run_stc
 
     if "SliceTiming" in timing_parameters:

nibabies/workflows/bold/stc.py

@@ -63,7 +63,7 @@ def init_bold_stc_wf(metadata, name="bold_stc_wf"):
     frac = config.workflow.slice_time_ref
     tzero = np.round(first + frac * (last - first), 3)
 
-    afni_ver = ''.join('%02d' % v for v in afni.Info().version() or [])
+    afni_ver = "".join("%02d" % v for v in afni.Info().version() or [])
     workflow = Workflow(name=name)
     workflow.__desc__ = f"""\
 BOLD runs were slice-time corrected to {tzero:0.3g}s ({frac:g} of slice acquisition range
@@ -72,7 +72,7 @@ def init_bold_stc_wf(metadata, name="bold_stc_wf"):
     inputnode = pe.Node(niu.IdentityInterface(fields=["bold_file", "skip_vols"]), name="inputnode")
     outputnode = pe.Node(niu.IdentityInterface(fields=["stc_file"]), name="outputnode")
 
-    LOGGER.log(25, f'BOLD series will be slice-timing corrected to an offset of {tzero:.3g}s.')
+    LOGGER.log(25, f"BOLD series will be slice-timing corrected to an offset of {tzero:.3g}s.")
 
     # It would be good to fingerprint memory use of afni.TShift
     slice_timing_correction = pe.Node(