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thewtex/itk-dask-blogpost.ipynb

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Created March 3, 2023 12:43
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ITK + Dask notebooks (August 2022)
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itk-dask-blogpost.ipynb
{
"cells": [
{
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"execution_count": 1,
"id": "1e772694",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"/home/genevieb/em95/miniconda/conda/envs/itk-dask/bin/python\r\n"
]
}
],
"source": [
"!which python"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "a1a0ad7e",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"# packages in environment at /home/genevieb/em95/miniconda/conda/envs/itk-dask:\r\n",
"itk 5.3rc4.post2 pypi_0 pypi\r\n",
"itk-core 5.3rc4.post2 pypi_0 pypi\r\n",
"itk-filtering 5.3rc4.post2 pypi_0 pypi\r\n",
"itk-io 5.3rc4.post2 pypi_0 pypi\r\n",
"itk-numerics 5.3rc4.post2 pypi_0 pypi\r\n",
"itk-registration 5.3rc4.post2 pypi_0 pypi\r\n",
"itk-segmentation 5.3rc4.post2 pypi_0 pypi\r\n"
]
}
],
"source": [
"!conda list | grep itk"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "e99e08b3",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"TiffTag 32781: coercing invalid ASCII to bytes\n",
"TiffTag 32781: coercing invalid ASCII to bytes\n",
"TiffTag 32781: coercing invalid ASCII to bytes\n",
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]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"(101, 64, 64)\n"
]
}
],
"source": [
"import tifffile\n",
"\n",
"psf_filename = \"psfs_z0p1/PSF_488nm_dz100nm.tif\"\n",
"psf = tifffile.imread(psf_filename)\n",
"print(psf.shape)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "835cdf9d",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/genevieb/em95/miniconda/conda/envs/itk-dask/lib/python3.10/site-packages/scipy/__init__.py:146: UserWarning: A NumPy version >=1.16.5 and <1.23.0 is required for this version of SciPy (detected version 1.23.1\n",
" warnings.warn(f\"A NumPy version >={np_minversion} and <{np_maxversion}\"\n",
"TiffTag 32781: coercing invalid ASCII to bytes\n",
"TiffTag 32781: coercing invalid ASCII to bytes\n",
"TiffTag 32781: coercing invalid ASCII to bytes\n",
"TiffTag 32781: coercing invalid ASCII to bytes\n"
]
},
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"text/plain": [
"dask.array<imread, shape=(199, 201, 1024, 768), dtype=uint16, chunksize=(1, 201, 1024, 768), chunktype=numpy.ndarray>"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from dask.array.image import imread\n",
"\n",
"raw_filename = \"raw-488nm/*.tif\"\n",
"imgs = imread(raw_filename)\n",
"imgs"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "f125a926",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"TiffTag 32781: coercing invalid ASCII to bytes\n",
"TiffTag 32781: coercing invalid ASCII to bytes\n",
"TiffTag 32781: coercing invalid ASCII to bytes\n",
"TiffTag 32781: coercing invalid ASCII to bytes\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"(201, 1024, 768)\n"
]
}
],
"source": [
"single_img_filename = \"raw-488nm/ex6-2_CamB_ch0_CAM1_stack0000_488nm_0000000msec_0001291795msecAbs_000x_000y_000z_0000t.tif\"\n",
"img = tifffile.imread(single_img_filename)\n",
"print(img.shape)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "5b43d300",
"metadata": {},
"outputs": [],
"source": [
"from skimage import restoration\n",
"\n",
"deconvolved_RL = restoration.richardson_lucy(img, psf, num_iter=30)\n",
"print(deconvolved_RL.shape)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "2ca2a48b",
"metadata": {},
"outputs": [
{
"ename": "AttributeError",
"evalue": "'itkRichardsonLucyDeconvolutionImageFilterIUS3IUS3' object has no attribute 'SetKernel'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)",
"Input \u001b[0;32mIn [6]\u001b[0m, in \u001b[0;36m<cell line: 3>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mitk\u001b[39;00m\n\u001b[0;32m----> 3\u001b[0m deconvolved_RLitk\u001b[38;5;241m=\u001b[39m \u001b[43mitk\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrichardson_lucy_deconvolution_image_filter\u001b[49m\u001b[43m(\u001b[49m\u001b[43mimg\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mkernel\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mpsf\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43miterations\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m 4\u001b[0m \u001b[38;5;28mprint\u001b[39m(deconvoled_RLitk\u001b[38;5;241m.\u001b[39mshape)\n",
"File \u001b[0;32m~/em95/miniconda/conda/envs/itk-dask/lib/python3.10/site-packages/itk/support/helpers.py:139\u001b[0m, in \u001b[0;36maccept_array_like_xarray_torch.<locals>.image_filter_wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 135\u001b[0m kwargs[key] \u001b[38;5;241m=\u001b[39m image\n\u001b[1;32m 137\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m have_xarray_input \u001b[38;5;129;01mor\u001b[39;00m have_torch_input \u001b[38;5;129;01mor\u001b[39;00m have_array_input:\n\u001b[1;32m 138\u001b[0m \u001b[38;5;66;03m# Convert output itk.Image's to numpy.ndarray's\u001b[39;00m\n\u001b[0;32m--> 139\u001b[0m output \u001b[38;5;241m=\u001b[39m \u001b[43mimage_filter\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;28;43mtuple\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43margs_list\u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 140\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(output, \u001b[38;5;28mtuple\u001b[39m):\n\u001b[1;32m 141\u001b[0m output_list \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(output)\n",
"File \u001b[0;32m~/em95/miniconda/conda/envs/itk-dask/lib/python3.10/site-packages/itk/itkRichardsonLucyDeconvolutionImageFilterPython.py:876\u001b[0m, in \u001b[0;36mrichardson_lucy_deconvolution_image_filter\u001b[0;34m(number_of_iterations, stop_iteration, size_greatest_prime_factor, boundary_condition, kernel_image, normalize, output_region_mode, *args, **kwargs)\u001b[0m\n\u001b[1;32m 873\u001b[0m specified_kwarg_typehints \u001b[38;5;241m=\u001b[39m { k:v \u001b[38;5;28;01mfor\u001b[39;00m (k,v) \u001b[38;5;129;01min\u001b[39;00m kwarg_typehints\u001b[38;5;241m.\u001b[39mitems() \u001b[38;5;28;01mif\u001b[39;00m kwarg_typehints[k] \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m\u001b[38;5;241m.\u001b[39m }\n\u001b[1;32m 874\u001b[0m kwargs\u001b[38;5;241m.\u001b[39mupdate(specified_kwarg_typehints)\n\u001b[0;32m--> 876\u001b[0m instance \u001b[38;5;241m=\u001b[39m \u001b[43mitk\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mRichardsonLucyDeconvolutionImageFilter\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mNew\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 877\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m instance\u001b[38;5;241m.\u001b[39m__internal_call__()\n",
"File \u001b[0;32m~/em95/miniconda/conda/envs/itk-dask/lib/python3.10/site-packages/itk/support/template_class.py:735\u001b[0m, in \u001b[0;36mitkTemplate.New\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m 732\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mitk\u001b[39;00m\n\u001b[1;32m 734\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m itk\u001b[38;5;241m.\u001b[39mTemplateTypeError(\u001b[38;5;28mself\u001b[39m, input_type)\n\u001b[0;32m--> 735\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[43m[\u001b[49m\u001b[38;5;28;43mlist\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mkeys\u001b[49m\u001b[43m)\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m]\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mNew\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/em95/miniconda/conda/envs/itk-dask/lib/python3.10/site-packages/itk/itkRichardsonLucyDeconvolutionImageFilterPython.py:802\u001b[0m, in \u001b[0;36mitkRichardsonLucyDeconvolutionImageFilterIUS3IUS3.New\u001b[0;34m(*args, **kargs)\u001b[0m\n\u001b[1;32m 800\u001b[0m obj \u001b[38;5;241m=\u001b[39m itkRichardsonLucyDeconvolutionImageFilterIUS3IUS3\u001b[38;5;241m.\u001b[39m__New_orig__()\n\u001b[1;32m 801\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mitk\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01msupport\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m template_class\n\u001b[0;32m--> 802\u001b[0m \u001b[43mtemplate_class\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mNew\u001b[49m\u001b[43m(\u001b[49m\u001b[43mobj\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 803\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m obj\n",
"File \u001b[0;32m~/em95/miniconda/conda/envs/itk-dask/lib/python3.10/site-packages/itk/support/template_class.py:800\u001b[0m, in \u001b[0;36mNew\u001b[0;34m(self, *args, **kargs)\u001b[0m\n\u001b[1;32m 797\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mNew\u001b[39m(\u001b[38;5;28mself\u001b[39m, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkargs):\n\u001b[1;32m 798\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mitk\u001b[39;00m\n\u001b[0;32m--> 800\u001b[0m \u001b[43mitk\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mset_inputs\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mkargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 802\u001b[0m \u001b[38;5;66;03m# now, try to add observer to display progress\u001b[39;00m\n\u001b[1;32m 803\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mauto_progress\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m kargs\u001b[38;5;241m.\u001b[39mkeys():\n",
"File \u001b[0;32m~/em95/miniconda/conda/envs/itk-dask/lib/python3.10/site-packages/itk/support/extras.py:1508\u001b[0m, in \u001b[0;36mset_inputs\u001b[0;34m(new_itk_object, inargs, inkargs)\u001b[0m\n\u001b[1;32m 1506\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m attribName\u001b[38;5;241m.\u001b[39mislower():\n\u001b[1;32m 1507\u001b[0m attribName \u001b[38;5;241m=\u001b[39m _snake_to_camel(attribName)\n\u001b[0;32m-> 1508\u001b[0m attrib \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mgetattr\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mnew_itk_object\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mSet\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m+\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mattribName\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1510\u001b[0m \u001b[38;5;66;03m# Do not use try-except mechanism as this leads to\u001b[39;00m\n\u001b[1;32m 1511\u001b[0m \u001b[38;5;66;03m# segfaults. Instead limit the number of types that are\u001b[39;00m\n\u001b[1;32m 1512\u001b[0m \u001b[38;5;66;03m# tested. The list of tested type could maybe be replaced by\u001b[39;00m\n\u001b[1;32m 1513\u001b[0m \u001b[38;5;66;03m# a test that would check for iterables.\u001b[39;00m\n\u001b[1;32m 1514\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mitk\u001b[39;00m\n",
"\u001b[0;31mAttributeError\u001b[0m: 'itkRichardsonLucyDeconvolutionImageFilterIUS3IUS3' object has no attribute 'SetKernel'"
]
}
],
"source": [
"import itk\n",
"\n",
"deconvolved_RLitk = itk.richardson_lucy_deconvolution_image_filter(img, kernel=psf, iterations=1)\n",
"print(deconvoled_RLitk.shape)"
]
},
{
"cell_type": "code",
"execution_count": 18,
"id": "e38c2f4d",
"metadata": {},
"outputs": [
{
"data": {
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"text/plain": [
"dask.array<rechunk-merge, shape=(199, 201, 1024, 768), dtype=uint16, chunksize=(1, 201, 512, 384), chunktype=numpy.ndarray>"
]
},
"execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import dask.array as da\n",
"\n",
"imgs = da.rechunk(imgs)\n",
"imgs"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "dc3ee594",
"metadata": {},
"outputs": [],
"source": [
"import itk\n",
"\n",
"deconvolved = da.map_blocks(itk.richardson_lucy_deconvolution_image_filter, imgs, kernel=psf, iterations=1, dtype=np.float32)\n",
"deconvolved"
]
}
],
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},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.4"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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