{
"cells": [
{
"cell_type": "code",
"execution_count": 127,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"loadLibrary\n",
"remoteSourcesURL https://git0.fmf.uni-lj.si/studen/nixSuite/raw/master/remoteResources/resources.json\n",
"{'labkeyInterface': {'url': 'https://git0.fmf.uni-lj.si/studen/labkeyInterface/archive/master.zip', 'branch': 'master', 'modules': []}, 'irAEMM': {'url': 'https://git0.fmf.uni-lj.si/studen/iraemm/archive/master.zip', 'branch': 'master', 'modules': ['iraemmBrowser']}, 'SlicerLabkeyExtension': {'url': 'https://git0.fmf.uni-lj.si/studen/SlicerLabkeyExtension/archive/SlicerExtensionIndex.zip', 'branch': 'SlicerExtensionIndex', 'modules': ['labkeyBrowser']}, 'limfomiPET': {'url': 'https://git0.fmf.uni-lj.si/studen/limfomiPET/archive/master.zip', 'branch': 'master', 'modules': ['imageBrowser', 'segmentationBrowser']}, 'parseConfig': {'url': 'https://git0.fmf.uni-lj.si/studen/parseConfig/archive/master.zip', 'branch': 'master', 'modules': []}, 'orthancInterface': {'url': 'https://git0.fmf.uni-lj.si/studen/orthancInterface/archive/master.zip', 'branch': 'master', 'modules': []}}\n",
"{'url': 'https://git0.fmf.uni-lj.si/studen/labkeyInterface/archive/master.zip', 'branch': 'master', 'modules': []}\n",
"File /home/studen/temp/labkeyInterface.zip: True\n"
]
}
],
"source": [
"import sys\n",
"import os\n",
"import SimpleITK\n",
"import numpy\n",
"import matplotlib.pyplot\n",
"import subprocess\n",
"import json\n",
"import config\n",
"import getData\n",
"import segmentation\n",
"import importlib\n",
"importlib.reload(segmentation)\n",
"importlib.reload(getData)\n",
"importlib.reload(config)\n",
"\n",
"sys.path.append(os.path.join(os.path.expanduser('~'),'software','src','|ixSuite','wrapper'))\n",
"import nixWrapper\n",
"nixWrapper.loadLibrary('labkeyInterface')\n",
"import labkeyInterface\n",
"import labkeyFileBrowser\n",
"import labkeyDatabaseBrowser\n",
"\n",
"#manipulate segmentations\n",
"#rewrite this\n",
"#nim=getPatientNIM(pId)\n",
"\n"
]
},
{
"cell_type": "code",
"execution_count": 116,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"loadLibrary\n",
"remoteSourcesURL https://git0.fmf.uni-lj.si/studen/nixSuite/raw/master/remoteResources/resources.json\n",
"{'labkeyInterface': {'url': 'https://git0.fmf.uni-lj.si/studen/labkeyInterface/archive/master.zip', 'branch': 'master', 'modules': []}, 'irAEMM': {'url': 'https://git0.fmf.uni-lj.si/studen/iraemm/archive/master.zip', 'branch': 'master', 'modules': ['iraemmBrowser']}, 'SlicerLabkeyExtension': {'url': 'https://git0.fmf.uni-lj.si/studen/SlicerLabkeyExtension/archive/SlicerExtensionIndex.zip', 'branch': 'SlicerExtensionIndex', 'modules': ['labkeyBrowser']}, 'limfomiPET': {'url': 'https://git0.fmf.uni-lj.si/studen/limfomiPET/archive/master.zip', 'branch': 'master', 'modules': ['imageBrowser', 'segmentationBrowser']}, 'parseConfig': {'url': 'https://git0.fmf.uni-lj.si/studen/parseConfig/archive/master.zip', 'branch': 'master', 'modules': []}, 'orthancInterface': {'url': 'https://git0.fmf.uni-lj.si/studen/orthancInterface/archive/master.zip', 'branch': 'master', 'modules': []}}\n",
"{'url': 'https://git0.fmf.uni-lj.si/studen/labkeyInterface/archive/master.zip', 'branch': 'master', 'modules': []}\n",
"File /home/studen/temp/labkeyInterface.zip: True\n",
"User: andrej studen CSRF: e682a2d778135e99c8f86ab87bcc8e47\n"
]
}
],
"source": [
"#\n",
"\n",
"fsetup='../template/cardiacSPECT.json'\n",
"with open(fsetup,'r') as f:\n",
" setup=json.load(f)\n",
"\n",
"db,fb=getData.connectDB(setup['network']) \n",
" \n"
]
},
{
"cell_type": "code",
"execution_count": 130,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{'date': '2022/12/06 00:00:00', 'lsid': 'urn:lsid:ijs.si:Study.Data-113:5006.MM.2.0000', 'visitName': 'OBR', '_labkeyurl_nmMasterOrthancId': 'https://orthanc.fmf.uni-lj.si/series/49464cfb-e53fb7b5-f8d4f7fc-c762f334-f1dc3863/archive', '_labkeyurl_PatientId': '/labkey/dinamic_spect/Patients/study-participant.view?participantId=MM', 'PatientId': 'MM', 'ctOrthancId': 'a226533f-2ec5d437-1c74d352-17bd6dca-dc719b60', 'nmCorrDataOrthancId': '7d5a1513-67b10c30-c0decf1c-2305db38-8c0e3128', '_labkeyurl_nmCorrDataOrthancId': 'https://orthanc.fmf.uni-lj.si/series/7d5a1513-67b10c30-c0decf1c-2305db38-8c0e3128/archive', '_labkeyurl_ctOrthancId': 'https://orthanc.fmf.uni-lj.si/series/a226533f-2ec5d437-1c74d352-17bd6dca-dc719b60/archive', 'nmMasterOrthancId': '49464cfb-e53fb7b5-f8d4f7fc-c762f334-f1dc3863', 'SequenceNum': 2.0}\n",
"5\n"
]
}
],
"source": [
"def guessSegmentation(db,setup,pId='MM',visitName='MIR',sx=32,sy=31,sz=31):\n",
"\n",
" idFilter={'variable':'PatientId','value':pId,'oper':'eq'}\n",
" visitFilter={'variable':'visitName','value':visitName,'oper':'eq'} \n",
" rows=getData.getPatients(db,setup,[idFilter,visitFilter])\n",
" r=rows[0] \n",
" pixels=segmentation.guessPixelPosition4(sx,sy,sz) \n",
" segmentation.updateSegmentation(db,setup,r,pixels)\n",
"\n",
"#guessSegmentation(db,setup,sz=32,sx=33)\n",
"def doPlotSegmentation(db,fb,setup,pId='MM',visitName='MIR',vmax=1000):\n",
" idFilter={'variable':'PatientId','value':pId,'oper':'eq'}\n",
" visitFilter={'variable':'visitName','value':visitName,'oper':'eq'} \n",
" rows=getData.getPatients(db,setup,[idFilter,visitFilter])\n",
" r=rows[0] \n",
" segmentation.plotSegmentation(db,fb,r,setup,vmax)\n",
"\n",
"def getRow(db,setup,pId='MM',visitName='MIR'):\n",
" idFilter={'variable':'PatientId','value':pId,'oper':'eq'}\n",
" visitFilter={'variable':'visitName','value':visitName,'oper':'eq'} \n",
" rows=getData.getPatients(db,setup,[idFilter,visitFilter])\n",
" return rows[0] \n",
" \n",
"\n",
"pId='MM'\n",
"visitName='OBR'\n",
"#guessSegmentation(db,setup,pId,visitName,sx=32,sy=31,sz=33)\n",
"#doPlotSegmentation(db,fb,setup,pId,visitName,vmax=500)\n",
"r=getRow(db,setup,pId,visitName)\n",
"print(r)\n",
"x=segmentation.loadSegmentation(db,fb,r,setup)\n",
"print(x.shape[0])"
]
},
{
"cell_type": "code",
"execution_count": 80,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"******10KF_MIR******\n",
"******10KF_OBR******\n",
"******MM_MIR******\n",
"******MM_MIR1******\n",
"******MM_OBR******\n"
]
},
{
"ename": "FileNotFoundError",
"evalue": "[Errno 2] No such file or directory: '/home/studen/temp/dynamicSPECT/MM_OBR/MM_OBR_Segmentation.txt'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[80], line 5\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m r \u001b[38;5;129;01min\u001b[39;00m rows:\n\u001b[1;32m 4\u001b[0m \u001b[38;5;28mprint\u001b[39m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m******\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m******\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(config\u001b[38;5;241m.\u001b[39mgetCode(r,setup)))\n\u001b[0;32m----> 5\u001b[0m \u001b[43msegmentation\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mwriteSegmentation\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdb\u001b[49m\u001b[43m,\u001b[49m\u001b[43mr\u001b[49m\u001b[43m,\u001b[49m\u001b[43msetup\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/software/src/dynamicSPECT/pythonScripts/segmentation.py:152\u001b[0m, in \u001b[0;36mwriteSegmentation\u001b[0;34m(db, r, setup)\u001b[0m\n\u001b[1;32m 149\u001b[0m v[region,\u001b[38;5;241m0\u001b[39m]\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mfloat\u001b[39m(qr[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mz\u001b[39m\u001b[38;5;124m'\u001b[39m])\n\u001b[1;32m 150\u001b[0m \u001b[38;5;66;03m#for i in range(len(rows)):\u001b[39;00m\n\u001b[1;32m 151\u001b[0m \u001b[38;5;66;03m# print(v[i,:])\u001b[39;00m\n\u001b[0;32m--> 152\u001b[0m \u001b[43mnumpy\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msavetxt\u001b[49m\u001b[43m(\u001b[49m\u001b[43mos\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpath\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mjoin\u001b[49m\u001b[43m(\u001b[49m\u001b[43mlocDir\u001b[49m\u001b[43m,\u001b[49m\u001b[43mfileName\u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\u001b[43mv\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m<__array_function__ internals>:5\u001b[0m, in \u001b[0;36msavetxt\u001b[0;34m(*args, **kwargs)\u001b[0m\n",
"File \u001b[0;32m/usr/lib/python3/dist-packages/numpy/lib/npyio.py:1368\u001b[0m, in \u001b[0;36msavetxt\u001b[0;34m(fname, X, fmt, delimiter, newline, header, footer, comments, encoding)\u001b[0m\n\u001b[1;32m 1365\u001b[0m fname \u001b[38;5;241m=\u001b[39m os_fspath(fname)\n\u001b[1;32m 1366\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m _is_string_like(fname):\n\u001b[1;32m 1367\u001b[0m \u001b[38;5;66;03m# datasource doesn't support creating a new file ...\u001b[39;00m\n\u001b[0;32m-> 1368\u001b[0m \u001b[38;5;28;43mopen\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mfname\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mwt\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m\u001b[38;5;241m.\u001b[39mclose()\n\u001b[1;32m 1369\u001b[0m fh \u001b[38;5;241m=\u001b[39m np\u001b[38;5;241m.\u001b[39mlib\u001b[38;5;241m.\u001b[39m_datasource\u001b[38;5;241m.\u001b[39mopen(fname, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mwt\u001b[39m\u001b[38;5;124m'\u001b[39m, encoding\u001b[38;5;241m=\u001b[39mencoding)\n\u001b[1;32m 1370\u001b[0m own_fh \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m\n",
"\u001b[0;31mFileNotFoundError\u001b[0m: [Errno 2] No such file or directory: '/home/studen/temp/dynamicSPECT/MM_OBR/MM_OBR_Segmentation.txt'"
]
}
],
"source": [
"#rarely used. Mostly, segmentation points are edited in LabKey\n",
"rows=getData.getPatients(db,setup)\n",
"for r in rows:\n",
" print('******{}******'.format(config.getCode(r,setup)))\n",
" segmentation.writeSegmentation(db,r,setup)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"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": "3.10.6"
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"nbformat": 4,
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