enh: Further additions to test_vis, output path for figures added to …

…conftest

.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

@@ -1,37 +1,120 @@
+import numpy as np
 import matplotlib.pyplot as plt
-import pytest, unittest
-from pathlib import Path
+import pytest
 
+import nibabel as nb
+from nitransforms.nonlinear import DenseFieldTransform
 from nitransforms.vis import PlotDenseField
 
-test_dir = Path("tests/data/")
-test_file = Path("ds-005_sub-01_from-OASIS_to-T1_warp_fsl.nii.gz")
 
-xfm = Path(test_dir/test_file)
+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(xfm, xslice, yslice, zslice, is_deltas=True):
+
+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"""
+    with pytest.raises(IndexError):
+        xfm = DenseFieldTransform(
+            field=np.zeros((10, 10, 10, 3)),
+            reference=nb.Nifti1Image(np.zeros((10, 10, 10, 3)), np.eye(4), None),
+        )
+        PlotDenseField(
+            transform=xfm._field,
+            reference=xfm._reference,
+        ).test_slices(
+            xslice=xfm._field.shape[0]+1,
+            yslice=xfm._field.shape[1]+1,
+            zslice=xfm._field.shape[2]+1,
+        )
+
+
+def test_show_transform(data_path, output_path):
     PlotDenseField(
-        path_to_file=Path(xfm),
-        is_deltas=is_deltas, 
-    ).test_slices(
-        xslice=xslice,
-        yslice=yslice,
-        zslice=zslice,
+        transform = data_path / "ds-005_sub-01_from-OASIS_to-T1_warp_fsl.nii.gz"
+    ).show_transform(
+        xslice=50,
+        yslice=50,
+        zslice=50,
     )
+    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,
+    )
+    if output_path is not None:
+        plt.savefig(output_path / "show_transform.svg", bbox_inches="tight")
+    else:
+        plt.show()
+
 
-def test_show_transform(xfm, xslice=50, yslice=50, zslice=50, is_deltas=True):
+def test_plot_quiverdsm(data_path, output_path):
     fig, axes = plt.subplots(1, 3, figsize=(12, 4))
     PlotDenseField(
-        path_to_file=Path(xfm),
-        is_deltas=is_deltas, 
+        transform = data_path / "ds-005_sub-01_from-OASIS_to-T1_warp_fsl.nii.gz"
     ).plot_quiverdsm(
         axes=axes,
-        xslice=xslice,
-        yslice=yslice,
-        zslice=zslice,
+        xslice=50,
+        yslice=50,
+        zslice=50,
     )
-    plt.show()
+    if output_path is not None:
+        plt.savefig(output_path / "show_transform.svg", bbox_inches="tight")
+    else:
+        plt.show()
+
+
+def test_3dquiver(data_path, output_path):
+    with pytest.raises(NotImplementedError):
+        fig = plt.figure()
+        axes = plt.subplots(projection='3d')
+        PlotDenseField(
+            transform = data_path / "ds-005_sub-01_from-OASIS_to-T1_warp_fsl.nii.gz"
+        ).plot_quiverdsm(axes=axes, three_D=True)
+
+    if output_path is not None:
+        plt.savefig(output_path / "show_transform.svg", bbox_inches="tight")
+    else:
+        plt.show()
+
+
+def test_plot_jacobian(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_jacobian(
+        axes=axes,
+        xslice=50,
+        yslice=50,
+        zslice=50,
+    )
+    if output_path is not None:
+        plt.savefig(output_path / "show_transform.svg", bbox_inches="tight")
+    else:
+        plt.show()
+
 
-test_slice_values(xfm, 50, -50, 50) #should raise ValueError
-test_slice_values(xfm, 500, 50, 50) #should raise IndexError
-test_show_transform(Path("tests/data/ds-005_sub-01_from-OASIS_to-T1_warp_fsl.nii.gz"))
+if __name__ == "__main__":
+    pytest.main([__file__])

nitransforms/vis.py

@@ -9,7 +9,6 @@
 
 from itertools import product
 
-from nitransforms.base import TransformError
 from nitransforms.nonlinear import DenseFieldTransform
 
 class PlotDenseField():
@@ -27,26 +26,35 @@ class PlotDenseField():
     Parameters
     ----------
 
-    path_to_file: :obj:`str`
+    transform: :obj:`str`
         Path from which the trasnformation file should be read.
     is_deltas: :obj:`bool`
         Whether the field is a displacement field or a deformations field. Default = True
     """
-    __slots__ = ('_path_to_file', '_xfm', '_voxel_size')
+    __slots__ = ('_transform', '_xfm', '_voxel_size')
 
-    def __init__(self, path_to_file, is_deltas=True):
-        self._path_to_file = path_to_file
+    def __init__(self, transform, is_deltas=True, reference=None):
+        self._transform = transform
         self._xfm = DenseFieldTransform(
-            self._path_to_file,
+            field=self._transform,
             is_deltas=is_deltas,
+            reference=reference
         )
-        self._voxel_size = nb.load(path_to_file).header.get_zooms()
+        try:
+            """if field provided by path"""
+            self._voxel_size = nb.load(transform).header.get_zooms()
+        except:
+            """if field provided by numpy array (eg tests)"""
+            deltas = []
+            for i in range(self._xfm.ndim):
+                deltas.append((np.max(self._xfm._field[i]) - np.min(self._xfm._field[i])) / len(self._xfm._field[i]))
+
+            assert np.all(deltas == deltas[0])
+            assert np.mean(deltas) == deltas[0]
+
+            deltas.append(0)
+            self._voxel_size = deltas        
 
-        if self._xfm._field.shape[-1] != self._xfm.ndim:
-            raise TransformError(
-                "The number of components of the field (%d) does not match "
-                "the number of dimensions (%d)" % (self._xfm._field.shape[-1], self._xfm.ndim)
-            )
 
     def show_transform(self, xslice, yslice, zslice, scaling=1, show_brain=True, show_grid=True, lw=0.1, save_to_path=None):
         """
@@ -73,7 +81,7 @@ def show_transform(self, xslice, yslice, zslice, scaling=1, show_brain=True, sho
         >>> plt.show()
 
         >>> PlotDenseField(
-        ...     path_to_file = "test_dir/someones-displacement-field.nii.gz",
+        ...     transform = "test_dir/someones-displacement-field.nii.gz",
         ...     is_deltas = True,
         ... ).show_transform(
         ...     xslice = 70,
@@ -92,7 +100,7 @@ def show_transform(self, xslice, yslice, zslice, scaling=1, show_brain=True, sho
             figsize=(9,9),
             gs_rows=3,
             gs_cols=3,
-            suptitle="Dense Field Transform \n" + os.path.basename(self._path_to_file),
+            suptitle="Dense Field Transform \n" + os.path.basename(self._transform),
         )
         fig.subplots_adjust(bottom=0.15)
 
@@ -143,7 +151,7 @@ def plot_distortion(self, axes, xslice, yslice, zslice, show_brain=True, show_gr
         Example:
         fig, axes = plt.subplots(1, 3, figsize=(15, 5), tight_layout=True)
         PlotDenseField(
-            path_to_file="test_dir/someones-displacement-field.nii.gz",
+            transform="test_dir/someones-displacement-field.nii.gz",
             is_deltas=True,
         ).plot_distortion(
             axes=[axes[2], axes[1], axes[0]],
@@ -215,7 +223,7 @@ def plot_quiverdsm(self, axes, xslice, yslice, zslice, scaling=1, three_D=False,
         Example:
         fig, axes = plt.subplots(1, 3, figsize=(15, 5), tight_layout=True)
         PlotDenseField(
-            path_to_file="test_dir/someones-displacement-field.nii.gz",
+            transform="test_dir/someones-displacement-field.nii.gz",
             is_deltas=True,
         ).plot_quiverdsm(
             axes=[axes[2], axes[1], axes[0]],
@@ -230,7 +238,7 @@ def plot_quiverdsm(self, axes, xslice, yslice, zslice, scaling=1, three_D=False,
         #Example 2: 3D quiver
         fig = plt.figure()
         ax = fig.add_subplot(projection='3d')
-        PlotDenseField(path_to_file, is_deltas=True).plot_quiverdsm(
+        PlotDenseField(transform, is_deltas=True).plot_quiverdsm(
             ax,
             xslice=None,
             yslice=None,
@@ -310,7 +318,7 @@ def plot_jacobian(self, axes, xslice, yslice, zslice, show_titles=True):
         Example:
         fig, axes = plt.subplots(1, 3, figsize=(15, 5), tight_layout=True)
         PlotDenseField(
-            path_to_file="test_dir/someones-displacement-field.nii.gz",
+            transform="test_dir/someones-displacement-field.nii.gz",
             is_deltas=True,
         ).plot_jacobian(
             axes=[axes[2], axes[1], axes[0]],