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Adding more examples to the gallery #80

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cb6103a
add notebooks
kolibril13 Aug 7, 2024
dbc2498
add torso notebook
kolibril13 Aug 14, 2024
2d11956
rearranged file structure and fixed lint issues
bcalford Nov 2, 2024
2c55814
clearned notebook outputs
bcalford Nov 2, 2024
b3f5cf3
created file download function py file
bcalford Nov 8, 2024
c7f18fe
implements data download into each example
bcalford Dec 2, 2024
b3bfada
Merge branch 'main' into gallery1
bcalford Dec 2, 2024
881baef
lint fixes
bcalford Dec 2, 2024
5c7f4d3
lint fixes
bcalford Dec 2, 2024
44487b9
restructure and rename download_images to download_dataset
bcalford Dec 2, 2024
d339246
Update src/ipyniivue/download_dataset.py
bcalford Dec 5, 2024
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33 changes: 23 additions & 10 deletions examples/additive_voxels.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,26 @@
"metadata": {},
"outputs": [],
"source": [
"!mkdir -p ../images/\n",
"path = \"https://github.com/niivue/niivue/raw/main/demos/images/\"\n",
"!wget {path}narps-4735_50GV-hypo1_unthresh.nii.gz -P ../images/\n",
"!wget {path}narps-4965_9U7M-hypo1_unthresh.nii.gz -P ../images/\n",
"!wget {path}mni152.nii.gz -P ../images/"
"from pathlib import Path\n",
"\n",
"import ipyniivue\n",
"from ipyniivue import NiiVue, download_dataset\n",
"\n",
"# GitHub API URL for the base folder\n",
"BASE_API_URL = (\n",
" \"https://api.github.com/repos/niivue/niivue/contents/packages/niivue/demos/images\"\n",
")\n",
"DATA_FOLDER = Path(ipyniivue.__file__).parent / \"images\""
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Downloads all data for examples\n",
"download_dataset(f\"{BASE_API_URL}\", DATA_FOLDER)"
]
},
{
Expand All @@ -19,20 +34,18 @@
"metadata": {},
"outputs": [],
"source": [
"from ipyniivue import NiiVue\n",
"\n",
"# based on https://niivue.github.io/niivue/features/additive.voxels.html\n",
"\n",
"volumes = [\n",
" {\"path\": \"../images/mni152.nii.gz\"},\n",
" {\"path\": DATA_FOLDER / \"mni152.nii.gz\"},\n",
" {\n",
" \"path\": \"../images/narps-4965_9U7M-hypo1_unthresh.nii.gz\",\n",
" \"path\": DATA_FOLDER / \"narps-4965_9U7M-hypo1_unthresh.nii.gz\",\n",
" \"colormap\": \"red\",\n",
" \"cal_min\": 2,\n",
" \"cal_max\": 4,\n",
" },\n",
" {\n",
" \"path\": \"../images/narps-4735_50GV-hypo1_unthresh.nii.gz\",\n",
" \"path\": DATA_FOLDER / \"narps-4735_50GV-hypo1_unthresh.nii.gz\",\n",
" \"colormap\": \"green\",\n",
" \"cal_min\": 2,\n",
" \"cal_max\": 4,\n",
Expand Down
39 changes: 23 additions & 16 deletions examples/basic_multiplanar.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -6,10 +6,26 @@
"metadata": {},
"outputs": [],
"source": [
"!mkdir -p ../images/\n",
"path = \"https://github.com/niivue/niivue/raw/main/demos/images/\"\n",
"!wget {path}mni152.nii.gz -P ../images/\n",
"!wget {path}hippo.nii.gz -P ../images/"
"from pathlib import Path\n",
"\n",
"import ipyniivue\n",
"from ipyniivue import NiiVue, SliceType, download_dataset\n",
"\n",
"# GitHub API URL for the base folder\n",
"BASE_API_URL = (\n",
" \"https://api.github.com/repos/niivue/niivue/contents/packages/niivue/demos/images\"\n",
")\n",
"DATA_FOLDER = Path(ipyniivue.__file__).parent / \"images\""
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Downloads all data for examples\n",
"download_dataset(f\"{BASE_API_URL}\", DATA_FOLDER)"
]
},
{
Expand All @@ -18,19 +34,17 @@
"metadata": {},
"outputs": [],
"source": [
"from ipyniivue import NiiVue, SliceType\n",
"\n",
"# based on https://niivue.github.io/niivue/features/basic.multiplanar.html\n",
"\n",
"volumes = [\n",
" {\n",
" \"path\": \"../images/mni152.nii.gz\",\n",
" \"path\": DATA_FOLDER / \"mni152.nii.gz\",\n",
" \"colormap\": \"gray\",\n",
" \"visible\": True,\n",
" \"opacity\": 1.0,\n",
" },\n",
" {\n",
" \"path\": \"../images/hippo.nii.gz\",\n",
" \"path\": DATA_FOLDER / \"hippo.nii.gz\",\n",
" \"colormap\": \"red\",\n",
" \"visible\": True,\n",
" \"opacity\": 1,\n",
Expand Down Expand Up @@ -89,14 +103,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.3"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
"state": {},
"version_major": 2,
"version_minor": 0
}
"version": "3.11.6"
}
},
"nbformat": 4,
Expand Down
97 changes: 97 additions & 0 deletions examples/mesh_and_volume.ipynb
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Original file line number Diff line number Diff line change
@@ -0,0 +1,97 @@
{
"cells": [
{
"cell_type": "code",
"execution_count": null,
"id": "593d466e-6bf6-47df-ba63-23b627f41da0",
"metadata": {},
"outputs": [],
"source": [
"from pathlib import Path\n",
"\n",
"import ipyniivue\n",
"from ipyniivue import NiiVue, SliceType, download_dataset\n",
"\n",
"# GitHub API URL for the base folder\n",
"BASE_API_URL = (\n",
" \"https://api.github.com/repos/niivue/niivue/contents/packages/niivue/demos/images\"\n",
")\n",
"DATA_FOLDER = Path(ipyniivue.__file__).parent / \"images\""
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "a09b7f2a-d0f7-4337-bfcc-ce5152fa9e79",
"metadata": {},
"outputs": [],
"source": [
"# Downloads all data for examples\n",
"download_dataset(f\"{BASE_API_URL}\", DATA_FOLDER)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "71c2f1ec-fdbf-4aae-8d09-77fd5988e11c",
"metadata": {},
"outputs": [],
"source": [
"# based on https://github.com/niivue/ipyniivue/blob/main/original_gallery.md#tractography-tck-trk-trx-vtk\n",
"\n",
"volumes = [\n",
" {\n",
" \"path\": DATA_FOLDER / \"mni152.nii.gz\",\n",
" \"colormap\": \"gray\",\n",
" \"visible\": True,\n",
" \"opacity\": 1.0,\n",
" },\n",
"]\n",
"\n",
"nv = NiiVue(slice_type=SliceType.MULTIPLANAR)\n",
"nv.load_volumes(volumes)\n",
"\n",
"nv.load_meshes(\n",
" [\n",
" {\n",
" \"path\": DATA_FOLDER / \"BrainMesh_ICBM152.lh.mz3\",\n",
" \"rgba255\": [255, 255, 255, 255],\n",
" }\n",
" ]\n",
")\n",
"\n",
"\n",
"nv"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "851a559d-59e8-40bc-b1f0-9380f9844855",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.6"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
46 changes: 26 additions & 20 deletions examples/mesh_layers.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -3,15 +3,31 @@
{
"cell_type": "code",
"execution_count": null,
"id": "6606a337-3243-4041-a7b7-ec64136f245c",
"id": "69a4c0b3",
"metadata": {},
"outputs": [],
"source": [
"!mkdir -p ../images/\n",
"path = \"https://github.com/niivue/niivue/raw/main/demos/images/\"\n",
"!wget {path}BrainMesh_ICBM152.lh.mz3 -P ../images/\n",
"!wget {path}CIT168.mz3 -P ../images/\n",
"!wget {path}BrainMesh_ICBM152.lh.motor.mz3 -P ../images/"
"from pathlib import Path\n",
"\n",
"import ipyniivue\n",
"from ipyniivue import NiiVue, download_dataset\n",
"\n",
"# GitHub API URL for the base folder\n",
"BASE_API_URL = (\n",
" \"https://api.github.com/repos/niivue/niivue/contents/packages/niivue/demos/images\"\n",
")\n",
"DATA_FOLDER = Path(ipyniivue.__file__).parent / \"images\""
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "eaca0a33-87c7-437f-b9b5-a0c967a44faf",
"metadata": {},
"outputs": [],
"source": [
"# Downloads all data for examples\n",
"download_dataset(f\"{BASE_API_URL}\", DATA_FOLDER)"
]
},
{
Expand All @@ -21,14 +37,12 @@
"metadata": {},
"outputs": [],
"source": [
"from ipyniivue import NiiVue\n",
"\n",
"nv = NiiVue(\n",
" show_3d_crosshair=True, back_color=(1, 1, 1, 1), mesh_x_ray=0.3, is_colorbar=True\n",
")\n",
"\n",
"mesh_layer = {\n",
" \"path\": \"../images/BrainMesh_ICBM152.lh.motor.mz3\",\n",
" \"path\": DATA_FOLDER / \"BrainMesh_ICBM152.lh.motor.mz3\",\n",
" \"cal_min\": 0.5,\n",
" \"cal_max\": 5.5,\n",
" \"useNegativeCmap\": True,\n",
Expand All @@ -38,11 +52,11 @@
"nv.load_meshes(\n",
" [\n",
" {\n",
" \"path\": \"../images/BrainMesh_ICBM152.lh.mz3\",\n",
" \"path\": DATA_FOLDER / \"BrainMesh_ICBM152.lh.mz3\",\n",
" \"rgba255\": [255, 255, 255, 255],\n",
" \"layers\": [mesh_layer],\n",
" },\n",
" {\"path\": \"../images/CIT168.mz3\", \"rgba255\": [0, 0, 255, 255]},\n",
" {\"path\": DATA_FOLDER / \"CIT168.mz3\", \"rgba255\": [0, 0, 255, 255]},\n",
" ]\n",
")\n",
"\n",
Expand All @@ -56,16 +70,8 @@
"metadata": {},
"outputs": [],
"source": [
"nv.meshes[0].rgba255 = [0, 0, 0, 0]"
"nv.meshes[0].rgba255 = [200, 200, 200, 0]"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "811a654f",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand Down
76 changes: 76 additions & 0 deletions examples/prototypes/meshes_(GIfTI, FreeSurfer, MZ3, OBJ, STL, legacy VTK).ipynb
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Original file line number Diff line number Diff line change
@@ -0,0 +1,76 @@
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "ab4d7045b8204843842d751f2bfe810f",
"version_major": 2,
"version_minor": 1
},
"text/plain": [
"NiiVue(height=300)"
]
},
"execution_count": 1,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from ipyniivue import NiiVue\n",
"\n",
"# based on https://github.com/niivue/ipyniivue/blob/main/original_gallery.md#meshes-gifti-freesurfer-mz3-obj-stl-legacy-vtk\n",
"nv = NiiVue(\n",
" show_3d_crosshair=True, back_color=(1, 1, 1, 1), mesh_x_ray=0.3, is_colorbar=True\n",
")\n",
"\n",
"nv.load_meshes(\n",
" [\n",
" {\n",
" \"path\": \"images/BrainMesh_ICBM152.lh.mz3\",\n",
" \"rgba255\": [222, 164, 164, 255],\n",
" },\n",
" {\"path\": \"images/CIT168.mz3\", \"rgba255\": [0, 0, 255, 255]},\n",
" ]\n",
")\n",
"\n",
"nv\n",
"\n",
"# nv1.setMeshShader(nv1.meshes[0].id, \"Outline\"); does not seem to exist yet."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.6"
}
},
"nbformat": 4,
"nbformat_minor": 4
}
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