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DOC: Use compare widget in notebooks
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@thewtex
thewtex committed Jan 20, 2020
1 parent 9e5e12d commit e76fbf0
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125 changes: 28 additions & 97 deletions examples/0_HelloRegistrationWorld.ipynb
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Original file line number Diff line number Diff line change
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**."
]
},
{
"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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