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DOC: Add registration parameters notebook #27

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Merged
thewtex merged 6 commits into from
Jan 22, 2020
Merged

DOC: Add registration parameters notebook #27

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712b379
DOC: Add registration parameters notebook
thewtex Jan 17, 2020
0e5a954
DOC: Require itk-elastix>=0.5.1 on Binder
thewtex Jan 20, 2020
af693a2
DOC: Require itkwidgets>=0.25.1
thewtex Jan 20, 2020
b44ffc0
DOC: Notebook content for serializing ParameterObject's
thewtex Jan 20, 2020
c3520b7
DOC: Use compare widget in notebooks
thewtex Jan 20, 2020
8987e97
DOC: Link to elastix manual and elastix parameter file database
thewtex Jan 20, 2020
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -16,3 +16,4 @@ tools/
zstd-1.2.0-linux.tar
zstd-1.2.0-linux/
.ipynb_checkpoints/
examples/Parameters.*.txt
4 changes: 2 additions & 2 deletions binder/requirements.txt
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@@ -1,11 +1,11 @@
itk-elastix>=0.5.0
itk-elastix>=0.5.1
itk>=5.1rc1.post1
itk-core>=5.1rc1.post1
itk-numerics>=5.1rc1.post1
itk-filtering>=5.1rc1.post1
itk-registration>=5.1rc1.post1
itk-segmentation>=5.1rc1.post1
itkwidgets>=0.24.2
itkwidgets>=0.25.1
jupyterlab==1.2.5
imageio
ipywidgets>=7.5.1
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125 changes: 28 additions & 97 deletions examples/0_HelloRegistrationWorld.ipynb
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Expand Up @@ -9,12 +9,12 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"import itk\n",
"from itkwidgets import view, checkerboard"
"from itkwidgets import view, compare, checkerboard"
]
},
{
Expand All @@ -30,80 +30,41 @@
"source": [
"In image registration, we typically identify the two images as the fixed and moving image. Our goal is to find the spatial transformation that makes the moving image align with the fixed image.\n",
"\n",
"First, let's load our **fixed image**."
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"fixed = itk.imread('data/CT_2D_head_fixed.mha', itk.F)"
"First, let's load our **fixed image** and the image we will align to our fixed image, the **moving image**."
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@dzenanz dzenanz Jan 20, 2020

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Weird sentence

]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "e4158972d1a04e098425a4f40d0e7c4b",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageF2; proxy o…"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"view(fixed, ui_collapsed=True)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"And the image we will align to our fixed image, the **moving image**."
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"fixed = itk.imread('data/CT_2D_head_fixed.mha', itk.F)\n",
"moving = itk.imread('data/CT_2D_head_moving.mha', itk.F)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "7a65180dd10d4e2ba85b81ade160e3ab",
"model_id": "b3ebeb5e96b64508a72580cd02bf86c3",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageF2; proxy o…"
"AppLayout(children=(HBox(children=(Label(value='Link:'), Checkbox(value=False, description='cmap'), Checkbox(v…"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"view(moving, ui_collapsed=True)"
"compare(fixed, moving, ui_collapsed=True)"
]
},
{
Expand All @@ -115,13 +76,13 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "8c8f18d0f55344e7b3eb44b56a1f0bb6",
"model_id": "9c0aa44dab00479eb61af83594bab01a",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -139,7 +100,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -156,37 +117,37 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 7,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "ec232d21042e4f159272bec55c8a24a0",
"model_id": "30f9e21a18aa4ba3bbd0b07122785301",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageF2; proxy o…"
"AppLayout(children=(HBox(children=(Label(value='Link:'), Checkbox(value=False, description='cmap'), Checkbox(v…"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"view(registered_moving, ui_collapsed=True)"
"compare(fixed, registered_moving, ui_collapsed=True)"
]
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 8,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "a6e2d7c491ba4d50b45b35e03e85a475",
"model_id": "4aea9949acf8440d88d0e2106f41f21e",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -211,79 +172,48 @@
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
"fixed = itk.imread('data/CT_3D_lung_fixed.mha', itk.F)"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "92cdb0e11f354bd49916557e2d6be968",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageF3; proxy o…"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"view(fixed)"
]
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"fixed = itk.imread('data/CT_3D_lung_fixed.mha', itk.F)\n",
"moving = itk.imread('data/CT_3D_lung_moving.mha', itk.F)"
]
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "b52c532b5c724faaa5d22cbe4460a504",
"model_id": "3435f5147c574e35b581944cb40a3177",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageF3; proxy o…"
"AppLayout(children=(HBox(children=(Label(value='Link:'), Checkbox(value=True, description='cmap'), Checkbox(va…"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"view(moving)"
"# A human lung at different time points\n",
"compare(fixed, moving, link_cmap=True, link_gradient_opacity=True)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"execution_count": 13,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "103b7484068044fb84ed5f7911aad9d1",
"model_id": "b0bba114c9a44411880775350294b876",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -305,7 +235,8 @@
"metadata": {},
"outputs": [],
"source": [
"# With the default, conservative parameters, this can take a few minutes\n# on a low-compute-power system.\n",
"# With the default, conservative parameters, this can take a few minutes\n",
"# on a low-compute-power system.\n",
"registered = itk.elastix_registration_method(fixed, moving)"
]
},
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