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Julien MarabottoJulien Marabotto
Julien Marabotto
authored and
Julien Marabotto
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enh: added tests for codecov
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‎docs/notebooks/Visualizing transforms.ipynb‎

Lines changed: 18 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -302,7 +302,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 10,
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"execution_count": 16,
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"metadata": {},
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"outputs": [
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{
@@ -325,6 +325,7 @@
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" zslice=zslice,\n",
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" lw=0.25,\n",
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" show_brain=False,\n",
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" show_grid=True,\n",
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")\n",
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"plt.show()"
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]
@@ -453,24 +454,36 @@
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},
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{
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"cell_type": "code",
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"execution_count": 12,
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"execution_count": 17,
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"metadata": {},
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"outputs": [
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{
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"ename": "TypeError",
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"evalue": "PlotDenseField.plot_coeffs() missing 1 required positional argument: 'axes'",
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"evalue": "'list' object cannot be interpreted as an integer",
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"output_type": "error",
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"traceback": [
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"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)",
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"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",
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"\u001b[0;31mTypeError\u001b[0m: PlotDenseField.plot_coeffs() missing 1 required positional argument: 'axes'"
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"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",
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"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",
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"\u001b[0;31mTypeError\u001b[0m: 'list' object cannot be interpreted as an integer"
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]
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},
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{
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"data": {
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"image/png": 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",
475+
"text/plain": [
476+
"<Figure size 1200x400 with 3 Axes>"
477+
]
478+
},
479+
"metadata": {},
480+
"output_type": "display_data"
469481
}
470482
],
471483
"source": [
472484
"fig, axes = plt.subplots(1, 3, figsize=(12, 4), tight_layout=True)\n",
473485
"pdf_3d.plot_coeffs(\n",
486+
" fig=fig,\n",
474487
" axes=axes,\n",
475488
" xslice=xslice,\n",
476489
" yslice=yslice,\n",

‎nitransforms/tests/test_vis.py‎

Lines changed: 33 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44

55
import nibabel as nb
66
from nitransforms.nonlinear import DenseFieldTransform
7-
from nitransforms.vis import PlotDenseField
7+
from nitransforms.vis import PlotDenseField, format_axes
88

99

1010
def test_read_path(data_path):
@@ -81,6 +81,19 @@ def test_plot_distortion(data_path, output_path):
8181
plt.show()
8282

8383

84+
def test_empty_quiver():
85+
fig, axes = plt.subplots(1, 3, figsize=(12, 4), tight_layout=True)
86+
PlotDenseField(
87+
transform=np.zeros((10, 10, 10, 3)),
88+
reference=nb.Nifti1Image(np.zeros((10, 10, 10, 3)), np.eye(4), None),
89+
).plot_quiverdsm(
90+
axes=axes,
91+
xslice=5,
92+
yslice=5,
93+
zslice=5,
94+
)
95+
96+
8497
def test_plot_quiverdsm(data_path, output_path):
8598
fig, axes = plt.subplots(1, 3, figsize=(12, 4))
8699
PlotDenseField(
@@ -111,13 +124,32 @@ def test_3dquiver(data_path, output_path):
111124
zslice=None,
112125
three_D=True
113126
)
127+
format_axes(axes)
114128

115129
if output_path is not None:
116130
plt.savefig(output_path / "plot_3dquiver.svg", bbox_inches="tight")
117131
else:
118132
plt.show()
119133

120134

135+
def test_coeffs(data_path, output_path):
136+
fig, axes = plt.subplots(3, 3, figsize=(10, 9))
137+
PlotDenseField(
138+
transform=data_path / "ds-005_sub-01_from-OASIS_to-T1_warp_fsl.nii.gz"
139+
).plot_coeffs(
140+
fig=fig,
141+
axes=axes,
142+
xslice=50,
143+
yslice=50,
144+
zslice=50,
145+
)
146+
147+
if output_path is not None:
148+
plt.savefig(output_path / "plot_coeffs.svg", bbox_inches="tight")
149+
else:
150+
plt.show()
151+
152+
121153
def test_plot_jacobian(data_path, output_path):
122154
fig, axes = plt.subplots(1, 3, figsize=(12, 5))
123155
PlotDenseField(

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