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enh: added tests for codecov
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Julien Marabotto authored and Julien Marabotto committed Jul 19, 2024
1 parent 2384469 commit c25a501
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23 changes: 18 additions & 5 deletions docs/notebooks/Visualizing transforms.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -302,7 +302,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 16,
"metadata": {},
"outputs": [
{
Expand All @@ -325,6 +325,7 @@
" zslice=zslice,\n",
" lw=0.25,\n",
" show_brain=False,\n",
" show_grid=True,\n",
")\n",
"plt.show()"
]
Expand Down Expand Up @@ -453,24 +454,36 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 17,
"metadata": {},
"outputs": [
{
"ename": "TypeError",
"evalue": "PlotDenseField.plot_coeffs() missing 1 required positional argument: 'axes'",
"evalue": "'list' object cannot be interpreted as an integer",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[12], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mpdf_3d\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mplot_coeffs\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 2\u001b[0m \u001b[43m \u001b[49m\u001b[43mxslice\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mxslice\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 3\u001b[0m \u001b[43m \u001b[49m\u001b[43myslice\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43myslice\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 4\u001b[0m \u001b[43m \u001b[49m\u001b[43mzslice\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mzslice\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 5\u001b[0m \u001b[43m)\u001b[49m\n\u001b[1;32m 6\u001b[0m plt\u001b[38;5;241m.\u001b[39mshow()\n",
"\u001b[0;31mTypeError\u001b[0m: PlotDenseField.plot_coeffs() missing 1 required positional argument: 'axes'"
"Cell \u001b[0;32mIn[17], line 2\u001b[0m\n\u001b[1;32m 1\u001b[0m fig, axes \u001b[38;5;241m=\u001b[39m plt\u001b[38;5;241m.\u001b[39msubplots(\u001b[38;5;241m1\u001b[39m, \u001b[38;5;241m3\u001b[39m, figsize\u001b[38;5;241m=\u001b[39m(\u001b[38;5;241m12\u001b[39m, \u001b[38;5;241m4\u001b[39m), tight_layout\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[0;32m----> 2\u001b[0m \u001b[43mpdf_3d\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mplot_coeffs\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 3\u001b[0m \u001b[43m \u001b[49m\u001b[43maxes\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43maxes\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 4\u001b[0m \u001b[43m \u001b[49m\u001b[43mxslice\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mxslice\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 5\u001b[0m \u001b[43m \u001b[49m\u001b[43myslice\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43myslice\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 6\u001b[0m \u001b[43m \u001b[49m\u001b[43mzslice\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mzslice\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 7\u001b[0m \u001b[43m)\u001b[49m\n\u001b[1;32m 8\u001b[0m plt\u001b[38;5;241m.\u001b[39mshow()\n",
"File \u001b[0;32m~/workspace/nitransforms/nitransforms/vis.py:398\u001b[0m, in \u001b[0;36mPlotDenseField.plot_coeffs\u001b[0;34m(self, axes, xslice, yslice, zslice, show_titles)\u001b[0m\n\u001b[1;32m 395\u001b[0m xslice, yslice, zslice \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtest_slices(xslice, yslice, zslice)\n\u001b[1;32m 396\u001b[0m planes, titles \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_planes(xslice, yslice, zslice)\n\u001b[0;32m--> 398\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m index, (ax, plane) \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28;43menumerate\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43maxes\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mplanes\u001b[49m\u001b[43m)\u001b[49m:\n\u001b[1;32m 399\u001b[0m x, y, z, u, v, w \u001b[38;5;241m=\u001b[39m plane\n\u001b[1;32m 401\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m index \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m0\u001b[39m:\n",
"\u001b[0;31mTypeError\u001b[0m: 'list' object cannot be interpreted as an integer"
]
},
{
"data": {
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",
"text/plain": [
"<Figure size 1200x400 with 3 Axes>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"fig, axes = plt.subplots(1, 3, figsize=(12, 4), tight_layout=True)\n",
"pdf_3d.plot_coeffs(\n",
" fig=fig,\n",
" axes=axes,\n",
" xslice=xslice,\n",
" yslice=yslice,\n",
Expand Down
34 changes: 33 additions & 1 deletion nitransforms/tests/test_vis.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@

import nibabel as nb
from nitransforms.nonlinear import DenseFieldTransform
from nitransforms.vis import PlotDenseField
from nitransforms.vis import PlotDenseField, format_axes


def test_read_path(data_path):
Expand Down Expand Up @@ -81,6 +81,19 @@ def test_plot_distortion(data_path, output_path):
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(
Expand Down Expand Up @@ -111,13 +124,32 @@ def test_3dquiver(data_path, output_path):
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(
Expand Down

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