{
"cells": [
{
"cell_type": "code",
"execution_count": 96,
"id": "067cdb44-f8d5-4175-bb11-0447c187b5f7",
"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']}, '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 C:\\Users\\studen\\temp\\labkeyInterface.zip: True\n"
]
}
],
"source": [
"#this fills SUVanalysis\n",
"import runStat\n",
"#runStat.main('../templates/statistics.json')\n"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "89889edb-533e-4bde-9514-22f40cceb2ab",
"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 C:\\Users\\studen\\temp\\labkeyInterface.zip: True\n",
"User: andrej studen CSRF: 9470c83e5b000aff6a021aa7ff1307a9\n",
"True\n",
"Failed to find segmentation for 4763/18/VISIT_1\n",
"No segmentation for 4763/18/VISIT_1\n",
"Failed to find segmentation for 4763/18/VISIT_2\n",
"No segmentation for 4763/18/VISIT_2\n",
"Failed to find segmentation for 4763/18/VISIT_3\n",
"No segmentation for 4763/18/VISIT_3\n",
"Failed to find segmentation for 8294/16/VISIT_1\n",
"No segmentation for 8294/16/VISIT_1\n",
"segmentationNotDone: 4\n",
"backupFileOK: 0\n",
"noSubstitute: 0\n",
"substituteFileOK: 0\n",
"substituteFileMissing: 0\n",
"segmentationOK: 41\n",
"all: 45\n"
]
}
],
"source": [
"import statUtils\n",
"import SimpleITK\n",
"import os\n",
"setup=statUtils.loadSetup(\"../templates/statistics.json\")\n",
"db,fb=statUtils.connectDB('onko-nix')\n",
"project='limfomiPET/EANM'\n",
"blankFilter={'variable':'MTV','value':'x','oper':'isblank'}\n",
"ds=db.selectRows(project,'study','analysis1',[blankFilter])\n",
"\n",
"localSeg=os.path.join(os.path.expanduser('~'),'Downloads','Segmentation_20230417')\n",
"print(os.path.isdir(localSeg))\n",
"\n",
"entries=ds['rows']\n",
"outcomes={'segmentationNotDone':0,'backupFileOK':0,'noSubstitute':0,'substituteFileOK':0,'substituteFileMissing':0,'segmentationOK':0,'all':0}\n",
"\n",
"doModify=False\n",
"\n",
"for entry in entries:\n",
" id=entry['ParticipantId']\n",
" setup.update({'db':db,'fb':fb})\n",
" idFilter={'variable':'ParticipantId','value':id,'oper':'eq'}\n",
" #visitFilter={'variable':'visitCode','value':'VISIT_1','oper':'eq'}\n",
" ds=db.selectRows(setup['project'],'study',setup['imagingDataset'],[idFilter])\n",
" rows=ds['rows']\n",
" for r in rows:\n",
" outcomes['all']+=1\n",
" segPaths=statUtils.getSegmentations(setup,r)\n",
" if not \"NONE\" in segPaths.values():\n",
" #print('Segmentation {}/{} OK.'.format(r['ParticipantId'],r['visitCode']))\n",
" outcomes['segmentationOK']+=1\n",
" continue\n",
" \n",
" #get file name\n",
" qFilter=[{'variable':x,'value':r[x],'oper':'eq'} for x in ['ParticipantId','visitCode']]\n",
" qFilter.append({'variable':'User','value':'1037','oper':'eq'})\n",
" dsSeg=db.selectRows(setup['project'],'study','Segmentations',qFilter)\n",
" \n",
" n=len(dsSeg['rows'])\n",
" if n==0:\n",
" print('No segmentation for {}/{}'.format(r['ParticipantId'],r['visitCode']))\n",
" outcomes['segmentationNotDone']+=1\n",
" continue\n",
" if n>1:\n",
" print('Multiple segmentations for {}/{}'.format(r['ParticipantId'],r['visitCode']))\n",
" break\n",
" \n",
" segEntry=dsSeg['rows'][0]\n",
" file=segEntry['latestFile']\n",
" localPath=os.path.join(localSeg,file)\n",
" found=os.path.isfile(localPath)\n",
" print('[{}] {}'.format(os.path.isfile(localPath),file))\n",
" \n",
" if found:\n",
" print('Original local file found')\n",
" pathList=[setup['imageDir'],segEntry['patientCode'],segEntry['visitCode'],'Segmentations']\n",
" remotePath=fb.buildPathURL(setup['project'],pathList)\n",
" remotPath+='/'+file\n",
" fb.writeFileToFile(localPath,remotePath)\n",
" outcomes['backupFileOK']+=1\n",
" continue\n",
"\n",
" #get alternate file (one before the last)\n",
" fileFilter={'variable':'segmentation','value':file,'oper':'eq'}\n",
" dsLSeg=db.selectRows(setup['project'],'lists','segmentationList',[fileFilter])\n",
" key=dsLSeg['rows'][0]['Key']\n",
" #here we look at a previous key\n",
" keyFilter={'variable':'Key','value':'{}'.format(key-1),'oper':'eq'}\n",
" qFilter.append(keyFilter)\n",
" dsLSeg=db.selectRows(setup['project'],'lists','segmentationList',qFilter)\n",
" if len(dsLSeg['rows'])>0:\n",
" file1=dsLSeg['rows'][0]['segmentation']\n",
" else:\n",
" print('No subsitute found')\n",
" #remove vacant pointers to valid segmentations\n",
" if doModify:\n",
" db.modifyRows('delete',setup['project'],'study','Segmentations',[segEntry])\n",
" outcomes['noSubstitute']+=1\n",
" continue\n",
" \n",
" \n",
" localPath=os.path.join(localSeg,file1)\n",
" found=os.path.isfile(localPath)\n",
" if found:\n",
" print('Substitute file found')\n",
" pathList=[setup['imageDir'],segEntry['patientCode'],segEntry['visitCode'],'Segmentations']\n",
" remotePath=fb.buildPathURL(setup['project'],pathList)\n",
" remotePath+='/'+file1\n",
" fb.writeFileToFile(localPath,remotePath)\n",
" print('[{}] Uploaded {}'.format(fb.entryExists(remotePath),remotePath))\n",
" segEntry['latestFile']=file1\n",
" segEntry['comments']='substitute'\n",
" outcomes['substituteFileOK']+=1\n",
" if doModify:\n",
" db.modifyRows('update',setup['project'],'study','Segmentations',[segEntry])\n",
" else:\n",
" print('Substitute file not available')\n",
" #remove vacant pointers to valid segmentations\n",
" if doModify:\n",
" db.modifyRows('delete',setup['project'],'study','Segmentations',[segEntry])\n",
" outcomes['substituteFileMissing']+=1\n",
" \n",
" \n",
" #print('[{}] {}'.format(os.path.isfile(localPath),file1))\n",
" \n",
" #seg={x:SimpleITK.ReadImage(segPaths[x]) for x in segPaths}\n",
" #for x in seg:\n",
" # ids=statUtils.getSegments(seg[x])\n",
" # for id in ids:\n",
" # print('{} {}'.format(id,ids[id]))\n",
"for x in outcomes:\n",
" print('{}: {}'.format(x,outcomes[x]))"
]
},
{
"cell_type": "code",
"execution_count": 47,
"id": "3be1c0f3-034c-4de0-947e-d2293693b057",
"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 C:\\Users\\studen\\temp\\labkeyInterface.zip: True\n",
"User: andrej studen CSRF: 0a0a0c1f37e17fbbd02c2a2670aa2879\n",
"Segmentation_1487_17-VISIT_1_adoma_322.nrrd\n",
"Segmentation_1645_17-VISIT_1_adoma_357.nrrd\n",
"Segmentation_1645_17-VISIT_2_adoma_360.nrrd\n",
"Segmentation_1731_17-VISIT_1_adoma_318.nrrd\n",
"Segmentation_1837_16-VISIT_1_adoma_310.nrrd\n",
"Segmentation_1837_16-VISIT_2_adoma_312.nrrd\n",
"Segmentation_2180_17-VISIT_1_adoma_340.nrrd\n",
"Segmentation_2294_16-VISIT_1_adoma_350.nrrd\n",
"Segmentation_2294_16-VISIT_2_adoma_352.nrrd\n",
"Segmentation_2589_16-VISIT_1_adoma_348.nrrd\n",
"Segmentation_4081_16-VISIT_1_adoma_306.nrrd\n",
"Segmentation_4081_16-VISIT_2_adoma_308.nrrd\n",
"Segmentation_4679_17-VISIT_1_adoma_342.nrrd\n",
"Segmentation_4679_17-VISIT_2_adoma_344.nrrd\n",
"Segmentation_5389_16-VISIT_1_adoma_354.nrrd\n",
"Segmentation_5916_17-VISIT_1_adoma_314.nrrd\n",
"Segmentation_5916_17-VISIT_2_adoma_316.nrrd\n",
"Segmentation_6435_16-VISIT_1_adoma_326.nrrd\n",
"Segmentation_653_97-VISIT_1_adoma_346.nrrd\n",
"Segmentation_7268_16-VISIT_1_adoma_331.nrrd\n",
"Segmentation_7268_16-VISIT_2_adoma_333.nrrd\n",
"Segmentation_8154_16-VISIT_1_adoma_364.nrrd\n"
]
}
],
"source": [
"#correct Version numbers (forgot to do that in updates, just changed latestFile, but not numeric version)\n",
"import statUtils\n",
"import re\n",
"setup=statUtils.loadSetup(\"../templates/statistics.json\")\n",
"db,fb=statUtils.connectDB('onko-nix')\n",
"subFilter={'variable':'comments','value':'substitute','oper':'eq'}\n",
"dsSeg=db.selectRows(setup['project'],'study','Segmentations',[subFilter])\n",
"for r in dsSeg['rows']:\n",
" f=r['latestFile']\n",
" print(f)\n",
" g=re.sub(r'^.*_([0-9]*).nrrd$',r'\\1',f)\n",
" key=int(g)\n",
" if key!=r['version']:\n",
" print('Version mismatch {}/{}'.format(key,r['version']))\n",
" r['version']=key\n",
" db.modifyRows('update',setup['project'],'study','Segmentations',[r])"
]
},
{
"cell_type": "code",
"execution_count": 23,
"id": "551c17b2-e4f4-4e63-bb8b-b5b0ff95854c",
"metadata": {},
"outputs": [
{
"ename": "TypeError",
"evalue": "in method 'Threshold', argument 1 of type 'itk::simple::Image const &'",
"output_type": "error",
"traceback": [
"\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[1;31mTypeError\u001b[0m Traceback (most recent call last)",
"\u001b[1;32m<ipython-input-23-895f684012f3>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[0;32m 1\u001b[0m \u001b[0mlabel\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;36m4\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 2\u001b[1;33m \u001b[0mcc\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mSimpleITK\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mThreshold\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mseg\u001b[0m\u001b[1;33m,\u001b[0m\u001b[0mlower\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mlabel\u001b[0m\u001b[1;33m,\u001b[0m\u001b[0mupper\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mlabel\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 3\u001b[0m \u001b[0mccFilter\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mSimpleITK\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mConnectedComponentImageFilter\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 4\u001b[0m \u001b[0mcc1\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mccFilter\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mExecute\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mcc\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 5\u001b[0m \u001b[0mprint\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mccFilter\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mGetObjectCount\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;32mc:\\users\\studen\\appdata\\local\\programs\\python\\python39\\lib\\site-packages\\SimpleITK\\SimpleITK.py\u001b[0m in \u001b[0;36mThreshold\u001b[1;34m(image1, lower, upper, outsideValue)\u001b[0m\n\u001b[0;32m 22557\u001b[0m \u001b[1;32mdef\u001b[0m \u001b[0mThreshold\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mimage1\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mlower\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;36m0.0\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mupper\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;36m1.0\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0moutsideValue\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;36m0.0\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 22558\u001b[0m \u001b[1;34mr\"\"\"Threshold(Image image1, double lower=0.0, double upper=1.0, double outsideValue=0.0) -> Image\"\"\"\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m> 22559\u001b[1;33m \u001b[1;32mreturn\u001b[0m \u001b[0m_SimpleITK\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mThreshold\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mimage1\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mlower\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mupper\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0moutsideValue\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 22560\u001b[0m \u001b[1;32mclass\u001b[0m \u001b[0mThresholdMaximumConnectedComponentsImageFilter\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mImageFilter\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 22561\u001b[0m \u001b[1;34mr\"\"\"Proxy of C++ itk::simple::ThresholdMaximumConnectedComponentsImageFilter class.\"\"\"\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;31mTypeError\u001b[0m: in method 'Threshold', argument 1 of type 'itk::simple::Image const &'"
]
}
],
"source": [
"label=4\n",
"cc=SimpleITK.Threshold(seg,lower=label,upper=label)\n",
"ccFilter=SimpleITK.ConnectedComponentImageFilter()\n",
"cc1=ccFilter.Execute(cc)\n",
"print(ccFilter.GetObjectCount())\n",
"ccNumpy=SimpleITK.GetArrayFromImage(cc)\n",
"print(numpy.max(ccNumpy))\n",
"ccNumpy[ccNumpy==label]=1\n",
"print(len(ccNumpy[ccNumpy==1]))\n",
"petNumpy=SimpleITK.GetArrayFromImage(pet)\n",
"\n",
"#matplotlib.pyplot.imshow(numpy.sum(petNumpy,1)[400:550,:])\n",
"#matplotlib.pyplot.imshow(numpy.sum(ccNumpy[:,160:161,:],1)[400:550,:])\n",
"matplotlib.pyplot.imshow(petNumpy[400:550,160,:])\n",
"matplotlib.pyplot.imshow(ccNumpy[400:550,160,:],alpha=0.3)\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "6edd77c8-57d1-4503-96ad-69ff5fd4b07d",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"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": "3.9.0"
}
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"nbformat": 4,
"nbformat_minor": 5
}