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test images from FIRE #119

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0b69530
test images from FIRE
jburel Aug 25, 2022
9ea50b1
add info
jburel Aug 25, 2022
7de3667
add info
jburel Aug 25, 2022
37f1bcc
add option to load tile
jburel Aug 25, 2022
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370 changes: 370 additions & 0 deletions Load_FIRE.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"id": "5da62504",
"metadata": {},
"source": [
"## Connect to IDR"
]
},
{
"cell_type": "code",
"execution_count": 16,
"id": "3e1ec8b6",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"True\n"
]
}
],
"source": [
"from omero.gateway import BlitzGateway\n",
"HOST = 'ws://idr.openmicroscopy.org/omero-ws'\n",
"conn = BlitzGateway('public', 'public',\n",
" host=HOST, secure=True)\n",
"print(conn.connect())\n",
"conn.c.enableKeepAlive(60)"
]
},
{
"cell_type": "markdown",
"id": "46f1f8d0",
"metadata": {},
"source": [
"## Connect to IDR testing "
]
},
{
"cell_type": "code",
"execution_count": 17,
"id": "27861120",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"True\n"
]
}
],
"source": [
"HOST = 'ws://idr-testing.openmicroscopy.org/omero-ws'\n",
"conn_testing = BlitzGateway('public', 'public',\n",
" host=HOST, secure=True)\n",
"print(conn_testing.connect())\n",
"conn_testing.c.enableKeepAlive(60)"
]
},
{
"cell_type": "markdown",
"id": "682a9ddb",
"metadata": {},
"source": [
"## Load an image\n",
"\n",
"We load information about the image but **not** the binary data. An image is a 5D-object\n",
"The size of a plane is 1024x1024"
]
},
{
"cell_type": "code",
"execution_count": 42,
"id": "0f8964ac",
"metadata": {},
"outputs": [],
"source": [
"# For the test an image from idr0067, idr0082, idr0117 should be used.\n",
"image_id = 9846309 # idr0067 9846282->idr0082"
]
},
{
"cell_type": "code",
"execution_count": 43,
"id": "3fe79a7a",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"S156_HandE.ndpi [0]\n"
]
}
],
"source": [
"image = conn.getObject(\"Image\", image_id)\n",
"print(image.getName())"
]
},
{
"cell_type": "code",
"execution_count": 44,
"id": "c04bbd1f",
"metadata": {},
"outputs": [],
"source": [
"image_testing = conn_testing.getObject(\"Image\", image_id)"
]
},
{
"cell_type": "code",
"execution_count": 45,
"id": "639d759f",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Size Z: 1, Size C: 3, Size T: 3\n"
]
}
],
"source": [
"print(\"Size Z: %s, Size C: %s, Size T: %s\" % (image.getSizeZ(), image.getSizeC(), image.getSizeC()))"
]
},
{
"cell_type": "markdown",
"id": "c564e823",
"metadata": {},
"source": [
"## Load the binary data\n",
"\n",
"To access the binary data, we need to load the `pixels` object from the image and retrieve the plane(s)"
]
},
{
"cell_type": "code",
"execution_count": 46,
"id": "7901bf45",
"metadata": {},
"outputs": [],
"source": [
"def load_plane(image, z, c, t, tile=None):\n",
" pixels = image.getPrimaryPixels()\n",
" if tile is not None:\n",
" print(tile)\n",
" return pixels.getTile(z, c, t, tile)\n",
" return pixels.getPlane(z, c, t)"
]
},
{
"cell_type": "code",
"execution_count": 54,
"id": "1a47b60c",
"metadata": {},
"outputs": [],
"source": [
"tile = (0, 0, 5000, 5000)"
]
},
{
"cell_type": "code",
"execution_count": 55,
"id": "ade36464",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"(0, 0, 5000, 5000)\n",
"(5000, 5000)\n",
"CPU times: user 1.81 s, sys: 179 ms, total: 1.99 s\n",
"Wall time: 4.21 s\n"
]
}
],
"source": [
"%%time\n",
"# Load from idr\n",
"plane = load_plane(image, 0, 0, 0, tile)\n",
"print(plane.shape)"
]
},
{
"cell_type": "code",
"execution_count": 56,
"id": "cd0bcf37",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"(0, 0, 5000, 5000)\n",
"CPU times: user 1.81 s, sys: 162 ms, total: 1.97 s\n",
"Wall time: 4.01 s\n"
]
}
],
"source": [
"%%time\n",
"# Load from idr-testing\n",
"plane_testing = load_plane(image_testing, 0, 0, 0, tile)"
]
},
{
"cell_type": "markdown",
"id": "7494df01",
"metadata": {},
"source": [
"To load multiple planes use ``pixels.getPlanes()``"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "146e0d0b",
"metadata": {},
"outputs": [],
"source": [
"zct_list = [(0, 0, 0), (1, 0, 0)]"
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "aff55fee",
"metadata": {},
"outputs": [],
"source": [
"def load_planes(image, zct_list):\n",
" pixels = image.getPrimaryPixels()\n",
" return pixels.getPlanes(zct_list)"
]
},
{
"cell_type": "code",
"execution_count": 12,
"id": "c77e4820",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"CPU times: user 233 µs, sys: 26 µs, total: 259 µs\n",
"Wall time: 285 µs\n"
]
}
],
"source": [
"%%time\n",
"# Load from idr\n",
"planes = load_planes(image, zct_list)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "6c53867b",
"metadata": {},
"outputs": [],
"source": [
"%%time\n",
"# Load from idr-testing\n",
"planes_testing = load_planes(image_testing, zct_list)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "1c71b06d",
"metadata": {},
"outputs": [],
"source": [
"def load_5D_array(image):\n",
" pixels = image.getPrimaryPixels()\n",
" size_z = image.getSizeZ()\n",
" size_c = image.getSizeC()\n",
" size_t = image.getSizeT()\n",
" #z, t, c = 0, 0, 0 # first plane of the image\n",
"\n",
" zct_list = []\n",
" for t in range(size_t):\n",
" for c in range(size_c): # all channels\n",
" for z in range(size_z): # get the Z-stack\n",
" zct_list.append((z, c, t))\n",
"\n",
" # Load all the planes as YX numpy array\n",
" return pixels.getPlanes(zct_list)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "efd67ee3",
"metadata": {},
"outputs": [
{
"ename": "KeyboardInterrupt",
"evalue": "",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)",
"File \u001b[0;32m<timed exec>:2\u001b[0m, in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n",
"File \u001b[0;32m~/opt/anaconda3/envs/stardist/lib/python3.9/site-packages/omero/gateway/__init__.py:7466\u001b[0m, in \u001b[0;36m_PixelsWrapper.getTiles\u001b[0;34m(self, zctTileList)\u001b[0m\n\u001b[1;32m 7464\u001b[0m z, c, t, tile \u001b[38;5;241m=\u001b[39m zctTile\n\u001b[1;32m 7465\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m tile \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m-> 7466\u001b[0m rawPlane \u001b[38;5;241m=\u001b[39m \u001b[43mrawPixelsStore\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgetPlane\u001b[49m\u001b[43m(\u001b[49m\u001b[43mz\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mc\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mt\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 7467\u001b[0m planeY \u001b[38;5;241m=\u001b[39m sizeY\n\u001b[1;32m 7468\u001b[0m planeX \u001b[38;5;241m=\u001b[39m sizeX\n",
"File \u001b[0;32m~/opt/anaconda3/envs/stardist/lib/python3.9/site-packages/omero/gateway/__init__.py:4793\u001b[0m, in \u001b[0;36mOmeroGatewaySafeCallWrapper.__call__\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m 4791\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m__call__\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[39mkwargs):\n\u001b[1;32m 4792\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m-> 4793\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mf\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 4794\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 4795\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdebug(e\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__class__\u001b[39m\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__name__\u001b[39m, args, kwargs)\n",
"File \u001b[0;32m~/opt/anaconda3/envs/stardist/lib/python3.9/site-packages/omero_api_RawPixelsStore_ice.py:1199\u001b[0m, in \u001b[0;36mRawPixelsStorePrx.getPlane\u001b[0;34m(self, z, c, t, _ctx)\u001b[0m\n\u001b[1;32m 1198\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mgetPlane\u001b[39m(\u001b[38;5;28mself\u001b[39m, z, c, t, _ctx\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m):\n\u001b[0;32m-> 1199\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43m_M_omero\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mapi\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mRawPixelsStore\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_op_getPlane\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43minvoke\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m(\u001b[49m\u001b[43m(\u001b[49m\u001b[43mz\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mc\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mt\u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m_ctx\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n",
"\u001b[0;31mKeyboardInterrupt\u001b[0m: "
]
}
],
"source": [
"%%time\n",
"# Load from idr\n",
"planes = load_5D_array(image)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "c42ca39c",
"metadata": {},
"outputs": [],
"source": [
"%%time\n",
"# Load from idr-testing\n",
"planes_testing = load_5D_array(image_testing)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "65f6bd08",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python [conda env:stardist]",
"language": "python",
"name": "conda-env-stardist-py"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.0"
}
},
"nbformat": 4,
"nbformat_minor": 5
}