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add demo #4

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167 changes: 167 additions & 0 deletions scripts/data_format.ipynb
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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"from aicsimageio import AICSImage\n",
"from aicsimageio.writers import OmeTiffWriter\n",
"from aicsimageio.types import PhysicalPixelSizes\n",
"from pathlib import Path\n",
"import numpy as np"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"base_path = \"/mnt/eternus/share/immun_project/\"\n",
"cut_path = base_path / Path(\"cut\")\n",
"new_path = base_path / Path(\"source_cut\")\n",
"\n",
"filenames = sorted(cut_path.glob(\"*_DAPI.tif\"))"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n",
"/mnt/eternus/anaconda3_shared/envs/jc_im2im_dev/lib/python3.9/site-packages/ome_types/_convenience.py:105: FutureWarning: The default XML parser will be changing from 'xmlschema' to 'lxml' in version 0.4.0. To silence this warning, please provide the `parser` argument, specifying either 'lxml' (to opt into the new behavior), or'xmlschema' (to retain the old behavior).\n",
" d = to_dict(os.fspath(xml), parser=parser, validate=validate)\n"
]
}
],
"source": [
"for fn in filenames:\n",
" fn_base = fn.stem[:-5]\n",
" dapi = AICSImage(fn).get_image_data(\"YX\", Z=0, T=0, C=0)\n",
" CD64 = AICSImage(cut_path / f\"{fn_base}_CD64.tif\").get_image_data(\"YX\", Z=0, T=0, C=0)\n",
" TMEM119 = AICSImage(cut_path / f\"{fn_base}_TMEM119.tif\").get_image_data(\"YX\", Z=0, T=0, C=0)\n",
" merged = np.stack([dapi, CD64, TMEM119], axis=0)\n",
" out_fn = new_path / f\"{fn_base}.tiff\"\n",
" OmeTiffWriter.save(merged, out_fn, dim_order=\"CYX\", physical_pixel_sizes=[PhysicalPixelSizes(0, 0.325, 0.325)], channel_names=[[\"DAPI\", \"CD64\", \"TMEM119\"]])"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"0.325\n",
"0.325\n",
"<Dimensions [T: 1, C: 3, Z: 1, Y: 2600, X: 2600]>\n"
]
}
],
"source": [
"reader = AICSImage(out_fn)\n",
"print(reader.physical_pixel_sizes.Y)\n",
"print(reader.physical_pixel_sizes.X)\n",
"print(reader.dims)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"img_DAPI = reader.get_image_data(\"YX\", C=reader.channel_names.index(\"DAPI\"), T=0, Z=0)\n",
"img_CD64 = reader.get_image_data(\"YX\", C=reader.channel_names.index(\"CD64\"), T=0, Z=0)\n",
"img_TMEM119 = reader.get_image_data(\"YX\", C=reader.channel_names.index(\"TMEM119\"), T=0, Z=0)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "jc_im2im_dev",
"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": "3.9.15"
},
"orig_nbformat": 4,
"vscode": {
"interpreter": {
"hash": "50fa6b3a3d2c08b8f5587b2999a963caca3e95136a1c3abe22c8121754c6ac26"
}
}
},
"nbformat": 4,
"nbformat_minor": 2
}