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kostrykinkostrykin
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Fix bugs, add segmentation example
1 parent 1f64e45 commit c9284c6

10 files changed

Lines changed: 265 additions & 161 deletions

‎examples/cells.ipynb‎

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‎examples/cthead.ipynb‎

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‎examples/introduction.ipynb‎

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"id": "3bf7058d",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-05-09T09:12:49.023933Z",
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"iopub.status.busy": "2025-05-09T09:12:49.023707Z",
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"iopub.status.idle": "2025-05-09T09:12:49.585847Z",
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"shell.execute_reply": "2025-05-09T09:12:49.585428Z"
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"iopub.execute_input": "2025-05-09T15:53:15.629826Z",
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"iopub.status.busy": "2025-05-09T15:53:15.629624Z",
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"shell.execute_reply": "2025-05-09T15:53:16.192906Z"
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},
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"vscode": {
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"id": "cd38b675",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-05-09T09:12:49.587247Z",
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"iopub.status.busy": "2025-05-09T09:12:49.587030Z",
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"iopub.status.idle": "2025-05-09T09:12:49.589118Z",
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"shell.execute_reply": "2025-05-09T09:12:49.588780Z"
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"iopub.execute_input": "2025-05-09T15:53:16.194832Z",
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"iopub.status.busy": "2025-05-09T15:53:16.194658Z",
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"iopub.status.idle": "2025-05-09T15:53:16.196728Z",
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"shell.execute_reply": "2025-05-09T15:53:16.196424Z"
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@@ -84,10 +84,10 @@
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"id": "8518d1b2",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-05-09T09:12:49.590271Z",
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"iopub.status.busy": "2025-05-09T09:12:49.590024Z",
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"iopub.status.idle": "2025-05-09T09:12:49.592062Z",
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"iopub.execute_input": "2025-05-09T15:53:16.198185Z",
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"iopub.status.busy": "2025-05-09T15:53:16.198082Z",
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"iopub.status.idle": "2025-05-09T15:53:16.200110Z",
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"shell.execute_reply": "2025-05-09T15:53:16.199808Z"
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"id": "df9403bf",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-05-09T09:12:49.593234Z",
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"iopub.status.busy": "2025-05-09T09:12:49.592987Z",
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"iopub.status.idle": "2025-05-09T09:12:49.597666Z",
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"shell.execute_reply": "2025-05-09T09:12:49.597336Z"
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"iopub.execute_input": "2025-05-09T15:53:16.201610Z",
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"iopub.status.busy": "2025-05-09T15:53:16.201420Z",
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"iopub.status.idle": "2025-05-09T15:53:16.205859Z",
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"shell.execute_reply": "2025-05-09T15:53:16.205516Z"
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"languageId": "plaintext"
@@ -133,7 +133,7 @@
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{
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"data": {
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"text/plain": [
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"<libcarna._spatial.geometry.<locals>.Geometry at 0x704a26a4aab0>"
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"<libcarna._spatial.geometry.<locals>.Geometry at 0x773c0acaebd0>"
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]
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},
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"execution_count": 4,
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"id": "4a1a1c31",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-05-09T09:12:49.598829Z",
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"iopub.status.busy": "2025-05-09T09:12:49.598572Z",
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"iopub.status.idle": "2025-05-09T09:12:49.600643Z",
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"iopub.execute_input": "2025-05-09T15:53:16.207368Z",
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"iopub.status.busy": "2025-05-09T15:53:16.207160Z",
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"shell.execute_reply": "2025-05-09T15:53:16.208827Z"
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"vscode": {
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"id": "0ca491a8",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-05-09T09:12:49.601752Z",
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"iopub.execute_input": "2025-05-09T15:53:16.210634Z",
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"iopub.status.busy": "2025-05-09T15:53:16.210433Z",
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"id": "37ff9c22",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-05-09T09:12:49.681256Z",
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{
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"data": {
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"text/plain": [
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"<matplotlib.image.AxesImage at 0x704a268ea570>"
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"<matplotlib.image.AxesImage at 0x773c0ab534a0>"
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]
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},
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"execution_count": 7,
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"id": "10ab7a0a",
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"metadata": {
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"execution": {
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"iopub.execute_input": "2025-05-09T09:12:49.778128Z",
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"iopub.status.busy": "2025-05-09T09:12:49.778007Z",
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"shell.execute_reply": "2025-05-09T09:12:49.925715Z"
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"iopub.execute_input": "2025-05-09T15:53:16.396152Z",
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"iopub.status.busy": "2025-05-09T15:53:16.395998Z",
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"shell.execute_reply": "2025-05-09T15:53:16.533160Z"
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"vscode": {
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"languageId": "plaintext"

‎misc/libcarna/_dvr.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -39,7 +39,7 @@ def __init__(
3939
cmap: str | libcarna.base.ColorMap | None = None,
4040
clim: tuple[float | None, float | None] | None = None,
4141
sr: int = libcarna.presets.VolumeRenderingStage.DEFAULT_SAMPLE_RATE,
42-
transl: float = libcarna.presets.DVRStage.DEFAULT_TRANSLUCENCY,
42+
transl: float = 0,
4343
diffuse: float = libcarna.presets.DVRStage.DEFAULT_DIFFUSE_LIGHT,
4444
):
4545
super().__init__(geometry_type)

‎misc/libcarna/_mask_renderer.py‎

Lines changed: 6 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,8 @@ class mask_renderer(libcarna.presets.MaskRenderingStage):
77
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Arguments:
99
geometry_type: Geometry type to be rendered.
10-
mask_role: Mask role to be used.
10+
sr: Sample rate for volume rendering. Larger values result in higher quality and less artifacts, but slower
11+
rendering.
1112
color: Color to use for the mask.
1213
fill: If `True`, the mask is filled. If `False`, only the borders are rendered.
1314
@@ -27,12 +28,13 @@ class mask_renderer(libcarna.presets.MaskRenderingStage):
2728
def __init__(
2829
self,
2930
geometry_type: int,
30-
mask_role: int = libcarna.presets.MaskRenderingStage.DEFAULT_ROLE_MASK,
3131
*,
32+
sr: int = libcarna.presets.VolumeRenderingStage.DEFAULT_SAMPLE_RATE,
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color: libcarna.color = libcarna.presets.MaskRenderingStage.DEFAULT_COLOR,
3334
fill: bool = False,
3435
):
35-
super().__init__(geometry_type, mask_role)
36+
super().__init__(geometry_type, mask_role=0)
37+
self.sample_rate = sr
3638
self.color = color
3739
self.filling = fill
3840

@@ -42,7 +44,7 @@ def replicate(self):
4244
"""
4345
return mask_renderer(
4446
self.geometry_type,
45-
self.mask_role,
47+
sr=self.sample_rate,
4648
color=self.color,
4749
fill=self.filling,
4850
)

‎src/py/presets.cpp‎

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Original file line numberDiff line numberDiff line change
@@ -245,7 +245,7 @@ PYBIND11_MODULE( presets, m )
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"mask_role",
246246
VIEW_DELEGATE( MaskRenderingStageView, maskRenderingStage().maskRole )
247247
)
248-
.def_property(
248+
.def_property( // TODO: This shouldn't be a property, see comment above.
249249
"color",
250250
VIEW_DELEGATE( MaskRenderingStageView, maskRenderingStage().color() ),
251251
VIEW_DELEGATE( MaskRenderingStageView, maskRenderingStage().setColor( color ), const LibCarna::base::Color& color )

‎test/results/expected/test_integration.MaskRenderingStage.test.png‎

-51 Bytes
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‎test/results/expected/test_integration.MaskRenderingStage.test__animated.png‎

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‎test/test_mask_renderer.py‎

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Original file line numberDiff line numberDiff line change
@@ -6,15 +6,14 @@ class mask_renderer(testsuite.LibCarnaTestCase):
66

77
def test__replicate(self):
88
GEOMETRY_TYPE_VOLUME = 1
9-
MASK_ROLE = 2
109
mask_renderer1 = libcarna.mask_renderer(
1110
GEOMETRY_TYPE_VOLUME,
12-
MASK_ROLE,
11+
sr=500,
1312
color=libcarna.color.RED,
1413
fill=True,
1514
)
1615
mask_renderer2 = mask_renderer1.replicate()
1716
self.assertEqual(mask_renderer2.geometry_type, GEOMETRY_TYPE_VOLUME)
18-
self.assertEqual(mask_renderer2.mask_role, MASK_ROLE)
17+
self.assertEqual(mask_renderer2.sample_rate, 500)
1918
self.assertEqual(mask_renderer2.color, libcarna.color.RED)
2019
self.assertEqual(mask_renderer2.filling, True)

‎test/test_spatial.py‎

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Original file line numberDiff line numberDiff line change
@@ -51,7 +51,7 @@ def setUp(self):
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def test__transform_into_voxels_from(self):
5252
np.testing.assert_array_almost_equal(
5353
self.volume.transform_into_voxels_from(self.root).point(),
54-
(32., 24., 5., 1.),
54+
(32., 24., 5.,),
5555
)
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5757
def test__extent(self):

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