maint: revise shebangs/attribution, add dependencies

nireports/interfaces/viz.py

@@ -1,7 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 #
-# Copyright 2021 The NiPreps Developers <[email protected]>
+# Copyright 2023 The NiPreps Developers <[email protected]>
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -20,12 +20,15 @@
 #
 #     https://www.nipreps.org/community/licensing/
 #
+# STATEMENT OF CHANGES: This file was ported carrying over full git history from MRIQC,
+# another NiPreps project licensed under the Apache-2.0 terms, and has been changed since.
+# The original file this work derives from is found at:
+# https://github.com/nipreps/mriqc/blob/1ffd4c8d1a20b44ebfea648a7b12bb32a425d4ec/
+# mriqc/interfaces/viz.py
 """Visualization interfaces."""
-from io import open  # pylint: disable=W0622
 from pathlib import Path
 
 import numpy as np
-from mriqc.viz.utils import plot_mosaic, plot_segmentation, plot_spikes
 from nipype.interfaces.base import (
     BaseInterfaceInputSpec,
     File,
@@ -35,16 +38,14 @@
     traits,
 )
 
+from nireports.reportlets.mriqc.utils import plot_mosaic, plot_segmentation, plot_spikes
+
 
 class PlotContoursInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True, desc="File to be plotted")
-    in_contours = File(
-        exists=True, mandatory=True, desc="file to pick the contours from"
-    )
+    in_contours = File(exists=True, mandatory=True, desc="file to pick the contours from")
     cut_coords = traits.Int(8, usedefault=True, desc="number of slices")
-    levels = traits.List(
-        [0.5], traits.Float, usedefault=True, desc="add a contour per level"
-    )
+    levels = traits.List([0.5], traits.Float, usedefault=True, desc="add a contour per level")
     colors = traits.List(
         ["r"],
         traits.Str,
@@ -159,9 +160,7 @@ def _run_interface(self, runtime):
             cmap=self.inputs.cmap,
             annotate=self.inputs.annotate,
         )
-        self._results["out_file"] = str(
-            (Path(runtime.cwd) / self.inputs.out_file).resolve()
-        )
+        self._results["out_file"] = str((Path(runtime.cwd) / self.inputs.out_file).resolve())
         return runtime
 
 
@@ -175,9 +174,7 @@ class PlotSpikesOutputSpec(TraitedSpec):
 
 
 class PlotSpikes(SimpleInterface):
-    """
-    Plot slices of a dataset with spikes
-    """
+    """Plot slices of a dataset with spikes."""
 
     input_spec = PlotSpikesInputSpec
     output_spec = PlotSpikesOutputSpec
@@ -189,8 +186,7 @@ def _run_interface(self, runtime):
         spikes_list = np.loadtxt(self.inputs.in_spikes, dtype=int).tolist()
         # No spikes
         if not spikes_list:
-            with open(out_file, "w") as f:
-                f.write("<p>No high-frequency spikes were found in this dataset</p>")
+            Path(out_file).write_text("<p>No high-frequency spikes were found in this dataset</p>")
             return runtime
 
         spikes_list = [tuple(i) for i in np.atleast_2d(spikes_list).tolist()]

nireports/reportlets/mriqc/svg.py

@@ -1,7 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 #
-# Copyright 2021 The NiPreps Developers <[email protected]>
+# Copyright 2023 The NiPreps Developers <[email protected]>
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -20,6 +20,11 @@
 #
 #     https://www.nipreps.org/community/licensing/
 #
+# STATEMENT OF CHANGES: This file was ported carrying over full git history from MRIQC,
+# another NiPreps project licensed under the Apache-2.0 terms, and has been changed since.
+# The original file this work derives from is found at:
+# https://github.com/nipreps/mriqc/blob/1ffd4c8d1a20b44ebfea648a7b12bb32a425d4ec/
+# mriqc/viz/svg.py
 """SVG handling utilities."""
 
 
@@ -59,9 +64,7 @@ def combine_svg(svg_list, axis="vertical"):
             for i, els in enumerate(sizes):
                 scales[i] = ref_size[0] / els[0]
 
-        newsizes = [
-            tuple(size) for size in np.array(sizes) * np.array(scales)[..., np.newaxis]
-        ]
+        newsizes = [tuple(size) for size in np.array(sizes) * np.array(scales)[..., np.newaxis]]
         totalsize = [newsizes[0][0], np.sum(newsizes, axis=0)[1]]
 
     elif axis == "horizontal":
@@ -72,9 +75,7 @@ def combine_svg(svg_list, axis="vertical"):
             for i, els in enumerate(sizes):
                 scales[i] = ref_size[1] / els[1]
 
-        newsizes = [
-            tuple(size) for size in np.array(sizes) * np.array(scales)[..., np.newaxis]
-        ]
+        newsizes = [tuple(size) for size in np.array(sizes) * np.array(scales)[..., np.newaxis]]
         totalsize = [np.sum(newsizes, axis=0)[0], newsizes[0][1]]
 
     # Compose the views panel: total size is the width of

nireports/reportlets/mriqc/utils.py

@@ -1,7 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 #
-# Copyright 2021 The NiPreps Developers <[email protected]>
+# Copyright 2023 The NiPreps Developers <[email protected]>
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -20,6 +20,11 @@
 #
 #     https://www.nipreps.org/community/licensing/
 #
+# STATEMENT OF CHANGES: This file was ported carrying over full git history from MRIQC,
+# another NiPreps project licensed under the Apache-2.0 terms, and has been changed since.
+# The original file this work derives from is found at:
+# https://github.com/nipreps/mriqc/blob/1ffd4c8d1a20b44ebfea648a7b12bb32a425d4ec/
+# mriqc/viz/utils.py
 """Visualization utilities."""
 import math
 import os.path as op
@@ -396,9 +401,7 @@ def plot_mosaic(
             )
             naxis += 1
 
-    fig.subplots_adjust(
-        left=0.05, right=0.95, bottom=0.05, top=0.95, wspace=0.05, hspace=0.05
-    )
+    fig.subplots_adjust(left=0.05, right=0.95, bottom=0.05, top=0.95, wspace=0.05, hspace=0.05)
 
     if title:
         fig.suptitle(title, fontsize="10")
@@ -516,9 +519,7 @@ def _calc_fd(fd_file, fd_radius):
     translations = np.transpose(np.abs(np.diff(cols[0:3, :])))
     rotations = np.transpose(np.abs(np.diff(cols[3:6, :])))
 
-    fd_power = np.sum(translations, axis=1) + (fd_radius * pi / 180) * np.sum(
-        rotations, axis=1
-    )
+    fd_power = np.sum(translations, axis=1) + (fd_radius * pi / 180) * np.sum(rotations, axis=1)
 
     # FD is zero for the first time point
     fd_power = np.insert(fd_power, 0, 0)
@@ -556,16 +557,12 @@ def plot_segmentation(anat_file, segmentation, out_file, **kwargs):
 
     anat_ras = nb.as_closest_canonical(nb.load(anat_file))
     anat_ras_plumb = anat_ras.__class__(
-        anat_ras.dataobj,
-        _dicom_real_to_card(anat_ras.affine),
-        anat_ras.header
+        anat_ras.dataobj, _dicom_real_to_card(anat_ras.affine), anat_ras.header
     )
 
     seg_ras = nb.as_closest_canonical(nb.load(segmentation))
     seg_ras_plumb = seg_ras.__class__(
-        seg_ras.dataobj,
-        _dicom_real_to_card(seg_ras.affine),
-        seg_ras.header
+        seg_ras.dataobj, _dicom_real_to_card(seg_ras.affine), seg_ras.header
     )
 
     if kwargs.get("saturate", False):

setup.cfg

@@ -20,10 +20,14 @@ classifiers =
 [options]
 python_requires = >= 3.7
 install_requires =
+    matplotlib >= 3.4.2
     nibabel >= 3.0.1
     nipype
+    numpy
     pybids
     pyyaml
+    seaborn
+    svgutils >= 0.3.4
 packages = find:
 
 [options.package_data]