Feat: Implement a visualisation feature to NiTransforms

.circleci/config.yml

@@ -142,7 +142,8 @@ jobs:
               -v /tmp/data/nitransforms-tests:/data -e TEST_DATA_HOME=/data \
               -e COVERAGE_FILE=/tmp/summaries/.pytest.coverage \
               -v /tmp/fslicense/license.txt:/opt/freesurfer/license.txt:ro \
-              -v /tmp/tests:/tmp nitransforms:latest \
+              -v /tmp/tests:/tmp -e TEST_OUTPUT_DIR=/tmp/artifacts \
+              nitransforms:latest \
               pytest --junit-xml=/tmp/summaries/pytest.xml \
                      --cov nitransforms --cov-report xml:/tmp/summaries/unittests.xml \
                      nitransforms/

nitransforms/conftest.py

@@ -9,6 +9,8 @@
 _data = None
 _brainmask = None
 _testdir = Path(os.getenv("TEST_DATA_HOME", "~/.nitransforms/testdata")).expanduser()
+_outdir = os.getenv("TEST_OUTPUT_DIR", None)
+
 _datadir = Path(__file__).parent / "tests" / "data"
 
 
@@ -45,6 +47,12 @@ def testdata_path():
     return _testdir
 
 
+@pytest.fixture
+def output_path():
+    """Return an output folder."""
+    return Path(_outdir) if _outdir is not None else None
+
+
 @pytest.fixture
 def get_testdata():
     """Generate data in the requested orientation."""

nitransforms/io/afni.py

@@ -198,7 +198,7 @@ def from_image(cls, imgobj):
         hdr = imgobj.header.copy()
         shape = hdr.get_data_shape()
 
-        if len(shape) != 5 or shape[-2] != 1 or not shape[-1] in (2, 3):
+        if len(shape) != 5 or shape[-2] != 1 or shape[-1] not in (2, 3):
             raise TransformFileError(
                 'Displacements field "%s" does not come from AFNI.'
                 % imgobj.file_map["image"].filename

nitransforms/io/fsl.py

@@ -180,7 +180,7 @@ def from_image(cls, imgobj):
         hdr = imgobj.header.copy()
         shape = hdr.get_data_shape()
 
-        if len(shape) != 4 or not shape[-1] in (2, 3):
+        if len(shape) != 4 or shape[-1] not in (2, 3):
             raise TransformFileError(
                 'Displacements field "%s" does not come from FSL.' %
                 imgobj.file_map['image'].filename)

nitransforms/io/itk.py

@@ -337,7 +337,7 @@ def from_image(cls, imgobj):
         hdr = imgobj.header.copy()
         shape = hdr.get_data_shape()
 
-        if len(shape) != 5 or shape[-2] != 1 or not shape[-1] in (2, 3):
+        if len(shape) != 5 or shape[-2] != 1 or shape[-1] not in (2, 3):
             raise TransformFileError(
                 'Displacements field "%s" does not come from ITK.'
                 % imgobj.file_map["image"].filename

nitransforms/tests/test_vis.py

@@ -0,0 +1,171 @@
+import numpy as np
+import matplotlib.pyplot as plt
+import pytest
+
+import nibabel as nb
+from nitransforms.nonlinear import DenseFieldTransform
+from nitransforms.vis import PlotDenseField, format_axes
+
+
+def test_read_path(data_path):
+    "Check that filepaths are a supported method for loading "
+    "and reading transforms with PlotDenseField"
+    PlotDenseField(transform=data_path / "ds-005_sub-01_from-OASIS_to-T1_warp_fsl.nii.gz")
+
+
+def test_slice_values():
+    """Check that ValueError is issued if negative slices are provided"""
+    with pytest.raises(ValueError):
+        PlotDenseField(
+            transform=np.zeros((10, 10, 10, 3)),
+            reference=nb.Nifti1Image(np.zeros((10, 10, 10, 3)), np.eye(4), None),
+        ).test_slices(
+            xslice=-1,
+            yslice=-1,
+            zslice=-1,
+        )
+
+    "Check that IndexError is issued if provided slices are beyond range of transform dimensions"
+    xfm = DenseFieldTransform(
+        field=np.zeros((10, 10, 10, 3)),
+        reference=nb.Nifti1Image(np.zeros((10, 10, 10, 3)), np.eye(4), None),
+    )
+    for idx in range(0,3):
+        if idx == 0:
+            i, j, k = 1, 0, 0
+        elif idx == 1:
+            i, j, k = 0, 1, 0
+        elif idx == 2:
+            i, j, k = 0, 0, 1
+
+        with pytest.raises(IndexError):
+            PlotDenseField(
+                transform=xfm._field,
+                reference=xfm._reference,
+            ).test_slices(
+                xslice=xfm._field.shape[0] + i,
+                yslice=xfm._field.shape[1] + j,
+                zslice=xfm._field.shape[2] + k,
+            )
+
+
+def test_show_transform(data_path, output_path):
+    PlotDenseField(
+        transform=data_path / "ds-005_sub-01_from-OASIS_to-T1_warp_fsl.nii.gz"
+    ).show_transform(
+        xslice=45,
+        yslice=50,
+        zslice=55,
+    )
+    if output_path is not None:
+        plt.savefig(output_path / "show_transform.svg", bbox_inches="tight")
+    else:
+        plt.show()
+
+
+def test_plot_distortion(data_path, output_path):
+    fig, axes = plt.subplots(1, 3, figsize=(12, 4))
+    PlotDenseField(
+        transform=data_path / "ds-005_sub-01_from-OASIS_to-T1_warp_fsl.nii.gz"
+    ).plot_distortion(
+        axes=axes,
+        xslice=50,
+        yslice=50,
+        zslice=50,
+        show_grid=True,
+        show_brain=True,
+    )
+    if output_path is not None:
+        plt.savefig(output_path / "plot_distortion.svg", bbox_inches="tight")
+    else:
+        plt.show()
+
+
+def test_empty_quiver():
+    fig, axes = plt.subplots(1, 3, figsize=(12, 4), tight_layout=True)
+    PlotDenseField(
+        transform=np.zeros((10, 10, 10, 3)),
+        reference=nb.Nifti1Image(np.zeros((10, 10, 10, 3)), np.eye(4), None),
+    ).plot_quiverdsm(
+        axes=axes,
+        xslice=5,
+        yslice=5,
+        zslice=5,
+    )
+
+
+def test_plot_quiverdsm(data_path, output_path):
+    fig, axes = plt.subplots(1, 3, figsize=(12, 4))
+    PlotDenseField(
+        transform=data_path / "ds-005_sub-01_from-OASIS_to-T1_warp_fsl.nii.gz"
+    ).plot_quiverdsm(
+        axes=axes,
+        xslice=50,
+        yslice=50,
+        zslice=50,
+    )
+
+    if output_path is not None:
+        plt.savefig(output_path / "plot_quiverdsm.svg", bbox_inches="tight")
+    else:
+        plt.show()
+
+
+def test_3dquiver(data_path, output_path):
+    with pytest.raises(NotImplementedError):
+        fig = plt.figure()
+        axes = fig.add_subplot(projection='3d')
+        PlotDenseField(
+            transform=data_path / "ds-005_sub-01_from-OASIS_to-T1_warp_fsl.nii.gz",
+        ).plot_quiverdsm(
+            axes=axes,
+            xslice=None,
+            yslice=None,
+            zslice=None,
+            three_D=True
+        )
+        format_axes(axes)
+
+    if output_path is not None:
+        plt.savefig(output_path / "plot_3dquiver.svg", bbox_inches="tight")
+    else:
+        plt.show()
+
+
+def test_coeffs(data_path, output_path):
+    fig, axes = plt.subplots(3, 3, figsize=(10, 9))
+    PlotDenseField(
+        transform=data_path / "ds-005_sub-01_from-OASIS_to-T1_warp_fsl.nii.gz"
+    ).plot_coeffs(
+        fig=fig,
+        axes=axes,
+        xslice=50,
+        yslice=50,
+        zslice=50,
+    )
+
+    if output_path is not None:
+        plt.savefig(output_path / "plot_coeffs.svg", bbox_inches="tight")
+    else:
+        plt.show()
+
+
+def test_plot_jacobian(data_path, output_path):
+    fig, axes = plt.subplots(1, 3, figsize=(12, 5))
+    PlotDenseField(
+        transform=data_path / "ds-005_sub-01_from-OASIS_to-T1_warp_fsl.nii.gz"
+    ).plot_jacobian(
+        axes=axes,
+        xslice=50,
+        yslice=50,
+        zslice=50,
+    )
+
+    if output_path is not None:
+        plt.savefig(output_path / "plot_jacobian.svg", bbox_inches="tight")
+    else:
+        plt.show()
+
+
+if __name__ == "__main__":
+    pytest.main([__file__])