Merge pull request #473 from effigies/mnt/nireports

rf: Transition from niworkflows reporting interfaces

Author: effigies

docs/conf.py

@@ -48,6 +48,7 @@
     "nilearn",
     "nipy",
     "nitime",
+    "nireports",
     "pandas",
     "seaborn",
     "skimage",

docs/requirements.txt

@@ -18,4 +18,3 @@ sphinx >= 7.2.2
 sphinx-argparse
 sphinxcontrib-apidoc
 templateflow
-traits < 6.4

pyproject.toml

@@ -27,6 +27,7 @@ dependencies = [
     "nibabel >= 3.0",
     "nipype >= 1.8.5",
     "migas >= 0.4.0",
+    "nireports >= 24.1.0",
     "niworkflows >= 1.7.0",
     "nitransforms >= 24.1.0",
     "numpy >= 1.22",

sdcflows/interfaces/reportlets.py

@@ -26,7 +26,7 @@
 from nilearn.image import threshold_img, load_img
 from niworkflows import NIWORKFLOWS_LOG
 from niworkflows.utils.images import rotation2canonical, rotate_affine
-from niworkflows.viz.utils import cuts_from_bbox, compose_view
+from nireports.reportlets.utils import cuts_from_bbox, compose_view
 from nipype.interfaces.base import File, isdefined, traits
 from nipype.interfaces.mixins import reporting
 

sdcflows/tests/test_transform.py

@@ -29,6 +29,7 @@
 from nitransforms.linear import LinearTransformsMapping
 from skimage.morphology import ball
 import scipy.ndimage as nd
+from nireports.interfaces.reporting.base import SimpleBeforeAfterRPT as SimpleBeforeAfter
 
 from sdcflows import transform as tf
 from sdcflows.interfaces.bspline import bspline_grid
@@ -120,10 +121,6 @@ def test_displacements_field(tmpdir, testdata_dir, outdir, pe_dir, rotation, fli
     assert np.all((np.sqrt(((ours - theirs) ** 2).sum()) / ours.size) < 1e-1)
 
     if outdir:
-        from niworkflows.interfaces.reportlets.registration import (
-            SimpleBeforeAfterRPT as SimpleBeforeAfter,
-        )
-
         orientation = "".join([ax[bool(f)] for ax, f in zip(("RL", "AP", "SI"), flip)])
 
         SimpleBeforeAfter(
@@ -204,10 +201,6 @@ def test_apply_transform(tmpdir, outdir, datadir, pe0, hmc, fmap):
         error = np.sqrt(((corrected.dataobj - realigned.dataobj) ** 2))
 
         if outdir:
-            from niworkflows.interfaces.reportlets.registration import (
-                SimpleBeforeAfterRPT as SimpleBeforeAfter,
-            )
-
             # Do not include the first volume in the average to enhance differences
             realigned_data = np.asanyarray(corrected.dataobj)[..., 1:].mean(-1)
             realigned_data[realigned_data < 0] = 0
@@ -241,10 +234,6 @@ def test_apply_transform(tmpdir, outdir, datadir, pe0, hmc, fmap):
         error_margin = 200  # test oracle is pretty bad here - needs revision.
 
         if outdir:
-            from niworkflows.interfaces.reportlets.registration import (
-                SimpleBeforeAfterRPT as SimpleBeforeAfter,
-            )
-
             # Do not include the first volume in the average to enhance differences
             realigned_data = np.asanyarray(corrected.dataobj)[..., 1:].mean(-1)
             realigned_data[realigned_data < 0] = 0

sdcflows/viz/utils.py

@@ -47,7 +47,7 @@ def plot_registration(
     import matplotlib.pyplot as plt
     from nilearn.plotting import plot_anat
     from svgutils.transform import SVGFigure
-    from niworkflows.viz.utils import robust_set_limits, extract_svg, SVGNS
+    from nireports.reportlets.utils import robust_set_limits, extract_svg, SVGNS
 
     plot_params = plot_params or {}
 

sdcflows/workflows/apply/tests/test_correction.py

@@ -25,6 +25,7 @@
 import pytest
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu
+from nireports.interfaces.reporting.base import SimpleBeforeAfterRPT as SimpleBeforeAfter
 from sdcflows.workflows.apply.correction import init_unwarp_wf
 
 
@@ -58,9 +59,6 @@ def test_unwarp_wf(tmpdir, datadir, workdir, outdir, with_affine):
         )
 
     if outdir:
-        from niworkflows.interfaces.reportlets.registration import (
-            SimpleBeforeAfterRPT as SimpleBeforeAfter,
-        )
         from ...outputs import DerivativesDataSink
         from ....interfaces.reportlets import FieldmapReportlet
 

sdcflows/workflows/apply/tests/test_registration.py

@@ -26,6 +26,7 @@
 
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu
+from nireports.interfaces.reporting.base import SimpleBeforeAfterRPT as SimpleBeforeAfter
 
 from ...fit.fieldmap import init_magnitude_wf
 from ..registration import init_coeff2epi_wf
@@ -70,9 +71,6 @@ def test_registration_wf(tmpdir, datadir, workdir, outdir):
     # fmt: on
 
     if outdir:
-        from niworkflows.interfaces.reportlets.registration import (
-            SimpleBeforeAfterRPT as SimpleBeforeAfter,
-        )
         from ...outputs import DerivativesDataSink
 
         report = pe.Node(

sdcflows/workflows/tests/test_ancillary.py

@@ -24,7 +24,7 @@
 import pytest
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu
-from niworkflows.interfaces.reportlets.masks import SimpleShowMaskRPT
+from nireports.interfaces.reporting.masks import SimpleShowMaskRPT
 from ..ancillary import init_brainextraction_wf
 
 

sdcflows/workflows/tests/test_integration.py

@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Test the base workflow."""
+
 from pathlib import Path
 import json
 import pytest
@@ -31,7 +32,7 @@
 from sdcflows.interfaces.reportlets import FieldmapReportlet
 from sdcflows.workflows.apply import correction as swac
 from sdcflows.workflows.apply import registration as swar
-from niworkflows.interfaces.reportlets.registration import (
+from nireports.interfaces.reporting.base import (
     SimpleBeforeAfterRPT as SimpleBeforeAfter,
 )