{
"cells": [
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
" warnings.warn(\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"User: andrej studen CSRF: 1f11a0b613d172716bb47acf122d5106\n"
]
}
],
"source": [
"import sys\n",
"import os\n",
"import SimpleITK\n",
"import numpy\n",
"import matplotlib.pyplot\n",
"import subprocess\n",
"sys.path.append(os.path.join(os.path.expanduser('~'),'software','src','nixSuite','wrapper'))\n",
"import nixWrapper\n",
"nixWrapper.loadLibrary('labkeyInterface')\n",
"import labkeyInterface\n",
"net=labkeyInterface.labkeyInterface()\n",
"fconfig=os.path.join(os.path.expanduser('~'),'.labkey','network.json')\n",
"net.init(fconfig)\n",
"net.getCSRF()\n",
"import labkeyFileBrowser\n",
"sys.path.append(os.getcwd())\n",
"import downloadPatient\n",
"fb=labkeyFileBrowser.labkeyFileBrowser(net)\n",
"project='dinamic_spect/Patients'\n",
"locDir=os.path.join(os.path.expanduser('~'),'temp','dynamicSPECT')\n",
"import labkeyDatabaseBrowser\n",
"db=labkeyDatabaseBrowser.labkeyDB(net)\n",
"ds=db.selectRows(project,'study','Imaging',[])\n",
"patients=[row['aliasID'] for row in ds['rows']]"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"#doAnalysis\n",
"import subprocess\n",
"\n",
"patients=list(set(patients))\n",
"#this is if IVF is inferred from locations\n",
"runScript='doPixelAnalysis.sh'\n",
"#this is if IVF is taken from clusters\n",
"runScript='doPixelIVFAnalysis.sh'\n",
"scriptPath=os.path.join(os.path.expanduser('~'),\\\n",
" 'scripts','dynamicSPECT',runScript)\n",
"#patients1=['10KFMIR']\n",
"patients1=patients\n",
"for pId in patients1:\n",
" if pId.find('8')==0:\n",
" continue\n",
" for sigma2 in [0.1,1.0,4.0]:\n",
" print('{}/{}'.format(pId,sigma2))\n",
" subprocess.run([scriptPath,pId,str(sigma2)], \\\n",
" check=True, stdout=subprocess.PIPE)\n",
" \n",
" "
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [],
"source": [
"def getPatientNIM(id):\n",
" f=os.path.join(locDir,id,id+'Volume19.nrrd')\n",
" im=SimpleITK.ReadImage(f)\n",
" nim=SimpleITK.GetArrayFromImage(im)\n",
" return nim\n",
"\n",
"def getIWeights(locDir,p,nclass,realizationId,ic):\n",
" fname='{}_{}_{}_center{}_centerWeigth.nrrd'.\\\n",
" format(p,nclass,realizationId+1,ic+1)\n",
" uFile=os.path.join(locDir,p,fname)\n",
" \n",
" imU=SimpleITK.ReadImage(uFile)\n",
" return SimpleITK.GetArrayFromImage(imU)\n",
"\n",
"\n",
"\n",
"#gets weights by class for a particular realization and sigma2 averaging\n",
"def getWeights(project,locDir,p,nclass,realizationId,sigma2,na):\n",
" #for w1, classes are in 0 to nclass-1 space\n",
" idFilter={'variable':'aliasID','value':p,'oper':'eq'}\n",
" ds=db.selectRows(project,'study','Segmentation',[idFilter])\n",
" pts={r['regionId']:[float(x) for x in [r['x'],r['y'],r['z']]] for r in ds['rows']}\n",
" \n",
" w={region:numpy.zeros(nclass) for region in pts}\n",
" na2=0.5*(na-1)\n",
" \n",
" for c in numpy.arange(nclass):\n",
" fname='{}_{}_{}_center{}_centerWeigth.nrrd'.\\\n",
" format(p,nclass,realizationId+1,c+1)\n",
" uFile=os.path.join(locDir,p,fname)\n",
" \n",
" imU=SimpleITK.ReadImage(uFile)\n",
" nU=SimpleITK.GetArrayFromImage(imU)\n",
" \n",
" \n",
" for region in w:\n",
" #print(pts[region])\n",
" idx=[int(x) for x in pts[region]]\n",
" #print(nU[tuple(idx)])\n",
" \n",
" #gaussian weighted summation of surrounding pixels\n",
" fidx=numpy.zeros(3)\n",
" fs=0\n",
" for i in numpy.arange(na):\n",
" fidx[0]=idx[0]+(i-na2)\n",
" for j in numpy.arange(na):\n",
" fidx[1]=idx[1]+(j-na2)\n",
" for k in numpy.arange(na):\n",
" fidx[2]=idx[2]+(k-na2)\n",
" fidx=[int(x) for x in fidx]\n",
" fw=numpy.array(fidx)-numpy.array(pts[region])\n",
" fw=numpy.exp(-0.5*sum(fw*fw)/sigma2);\n",
" fs+=fw\n",
" w[region][c]+=fw*nU[tuple(fidx)]\n",
" #print('{}/{}: {:.2f} {:.2g}'.format(idx,fidx,fw,nU[tuple(fidx)]))\n",
" w[region][c]/=fs\n",
" \n",
" \n",
" return w\n",
"\n",
"#gets fitPar for a particular realization\n",
"def getFitPar(locDir,p,nclass,realizationId):\n",
" #fitGoodnes A tau alpha delay [k1 BVF k2 delay]xNcenters\n",
" fname='{}_{}_{}_fitParFinal.txt'.format(p,nclass,realizationId+1)\n",
" uFile=os.path.join(locDir,p,fname)\n",
" return numpy.genfromtxt(uFile,delimiter='\\t')\n",
"\n",
"def getFitParIVF(locDir,p,nclass,realizationId):\n",
" #fitGoodnes A tau alpha delay [k1 BVF k2 delay]xNcenters\n",
" fname='{}_{}_{}_IVF_fitParFinal.txt'.format(p,nclass,realizationId+1)\n",
" uFile=os.path.join(locDir,p,fname)\n",
" return numpy.genfromtxt(uFile,delimiter='\\t')\n",
"\n",
"def getFitParPixel(locDir,p,nclass,sigma2):\n",
" sigmaCode='{:.2f}'.format(sigma2)\n",
" sigmaCode=sigmaCode.replace(\".\",\"p\")\n",
" fname='{}_{}_{}_Pixel_fitParFinal.txt'.format(p,nclass,sigmaCode)\n",
" uFile=os.path.join(locDir,p,fname)\n",
" return numpy.genfromtxt(uFile,delimiter='\\t')\n",
"\n",
"def getFitParPixelIVF(locDir,p,nclass,sigma2):\n",
" sigmaCode='{:.2f}'.format(sigma2)\n",
" sigmaCode=sigmaCode.replace(\".\",\"p\")\n",
" fname='{}_{}_{}_PixelIVF_fitParFinal.txt'.format(p,nclass,sigmaCode)\n",
" uFile=os.path.join(locDir,p,fname)\n",
" return numpy.genfromtxt(uFile,delimiter='\\t')\n",
"\n",
"def getK1(fitPar,iclass):\n",
" #fitGoodnes A tau alpha delay [k1 BVF k2 delay]xNcenters\n",
" #0 to nclass-1 space\n",
" return fitPar[4*iclass+5]\n",
"\n",
"def calculateK1(w,fitPar):\n",
" k1={region:{'M':0,'W':0} for region in w}\n",
" for region in w:\n",
" cmax=numpy.argmax(w[region])\n",
" k1[region]['M']=getK1(fitPar,cmax)\n",
" fs=0\n",
" for c in numpy.arange(len(w[region])):\n",
" fs+=w[region][c]*getK1(fitPar,c)\n",
" k1[region]['W']=fs\n",
" return k1\n",
"\n",
"def getPatientValuesByNclass(project,locDir,p,nclass,nrealizations,sigma2,na):\n",
" k1={}\n",
" for i in numpy.arange(nrealizations):\n",
" w=getWeights(project,locDir,p,nclass,i,sigma2,na)\n",
" fitPar=getFitParIVF(locDir,p,nclass,i)\n",
" qk1=calculateK1(w,fitPar)\n",
" for region in w:\n",
" for type in qk1[region]:\n",
" try:\n",
" k1[region][type].append(qk1[region][type])\n",
" except KeyError:\n",
" k1={region:{type:[] for type in qk1[region]} for region in w}\n",
" print(type)\n",
" k1[region][type].append(qk1[region][type])\n",
" print('[{}] {}/{}'.format(nclass,i+1,nrealizations))\n",
" return k1 \n",
"\n",
"def getSummaryPatientValuesByNclass(project,locDir,p,nclass,nrealizations,sigma2,na):\n",
" k1=getPatientValuesByNclass(project,locDir,p,nclass,nrealizations,sigma2,na)\n",
" avgType=['M','W']\n",
" summaryK1={type:{region:{\n",
" 'mean':numpy.mean(k1[region][type]), \n",
" 'std':numpy.std(k1[region][type]), \n",
" 'median':numpy.median(k1[region][type])} for region in k1}\n",
" for type in avgType}\n",
" \n",
" return summaryK1\n",
"\n",
"def fullSummary(project,locDir,patientList,classes,nr,sigma2,na):\n",
" return \\\n",
" {p:{c:getSummaryPatientValuesByNclass(project,locDir,p,c,nr,sigma2,na) for c in classes} for p in patientList}\n",
" \n",
"def storeSummary(db,project,locDir,k1,sigma2,na):\n",
" dsM=db.selectRows(project,'study','Imaging',[])\n",
" for p in k1:\n",
" idFilter={'variable':'aliasID','value':p,'oper':'eq'}\n",
" for c in k1[p]:\n",
" cFilter={'variable':'nclass','value':str(c),'oper':'eq'}\n",
" for t in k1[p][c]:\n",
" tFilter={'variable':'option','value':t,'oper':'eq'}\n",
" for r in k1[p][c][t]:\n",
" rFilter={'variable':'regionId','value':str(r),'oper':'eq'}\n",
" ds=db.selectRows(project,'study','Summary',[idFilter,cFilter,tFilter,rFilter])\n",
" if len(ds['rows'])>0:\n",
" qrow=ds['rows'][0]\n",
" mode='update'\n",
" else:\n",
" frow=[r for r in dsM['rows'] if r['aliasID']==p]\n",
" qrow={'aliasID':p,'nclass':c,'option':t,'regionId':r}\n",
" qrow['SequenceNum']=frow[0]['SequenceNum']+c+0.001*r\n",
" if t=='M':\n",
" qrow['SequenceNum']+=0.0001\n",
" qrow['PatientId']=frow[0]['PatientId']\n",
" mode='insert'\n",
" for v in k1[p][c][t][r]:\n",
" qrow[v]=k1[p][c][t][r][v]\n",
" qrow['sigma2']=sigma2\n",
" qrow['na']=na\n",
" db.modifyRows(mode,project,'study','Summary',[qrow])\n",
" \n",
"def summaryPixelIVF(project,locDir,patientList,sigma2List,na):\n",
" return \\\n",
" {p:{sigma2:getPixelIVF(project,locDir,p,sigma2,na) for sigma2 in sigma2List} for p in patientList}\n",
" \n",
"def storeIVF(db,project,locDir,k1):\n",
" dsM=db.selectRows(project,'study','Imaging',[])\n",
" for p in k1:\n",
" idFilter={'variable':'aliasID','value':p,'oper':'eq'}\n",
" for s2 in k1[p]:\n",
" sigmaFilter={'variable':'sigma2','value':str(s2),'oper':'eq'}\n",
" for r in k1[p][s2]:\n",
" rFilter={'variable':'regionId','value':str(r),'oper':'eq'}\n",
" typeFilter={'variable':'option','value':'D','oper':'eq'}\n",
" ds=db.selectRows(project,'study','Summary',[idFilter,sigmaFilter,rFilter,typeFilter])\n",
" if len(ds['rows'])>0:\n",
" qrow=ds['rows'][0]\n",
" mode='update'\n",
" else:\n",
" frow=[r for r in dsM['rows'] if r['aliasID']==p]\n",
" qrow={'aliasID':p,'sigma2':s2,'regionId':r}\n",
" qrow['SequenceNum']=40+frow[0]['SequenceNum']+0.01*r+0.001*s2\n",
" qrow['PatientId']=frow[0]['PatientId']\n",
" mode='insert'\n",
" qrow['mean']=k1[p][s2][r]\n",
" qrow['na']=7\n",
" qrow['nclass']=16\n",
" qrow['option']='D'\n",
" db.modifyRows(mode,project,'study','Summary',[qrow])\n",
"\n",
"def getPixelIVF(project,locDir,p,sigma2,na):\n",
" fitPar=getFitParPixelIVF(locDir,p,16,sigma2)\n",
" idFilter={'variable':'aliasID','value':p,'oper':'eq'}\n",
" ds=db.selectRows(project,'study','Segmentation',[idFilter])\n",
" k1={r['regionId']:getK1(fitPar,r['regionId']) for r in ds['rows']}\n",
" return k1"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
" warnings.warn(\n"
]
},
{
"name": "stdout",
"output_type": "stream",
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]
},
{
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"text": [
"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
" warnings.warn(\n"
]
},
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},
{
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"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
" warnings.warn(\n"
]
},
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"User: andrej studen CSRF: c657389564fed0b694336b89d39c0420\n",
"User: andrej studen CSRF: 2093d35a0e8d12d4b823bcbe3d88c029\n",
"User: andrej studen CSRF: 280154139aafb3b3b634ee95b8e9ab57\n",
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"User: andrej studen CSRF: 1421c672da3f24ef0fcc88856bd6ee8f\n",
"User: andrej studen CSRF: 14c225d796c6043b3e5895efdffdb21b\n",
"User: andrej studen CSRF: f6c7073ea9c5ac49f73bccabf1e5ce32\n",
"User: andrej studen CSRF: 00d051a4ca90b7d5b2b6fbb98a64d1e5\n",
"User: andrej studen CSRF: 9de2c0c544a0a1e5e25d102a7f490af7\n",
"User: andrej studen CSRF: db3f905d4d2a91387b4a4dd5fdec2aba\n",
"User: andrej studen CSRF: 650be1f5cddf9d6ef804f847ee666d4d\n",
"User: andrej studen CSRF: efca2dd889ff0ab6b4ae640acdddf6fa\n",
"User: andrej studen CSRF: 82ae1e1be2e5912efe2a1b49238a206c\n",
"User: andrej studen CSRF: d72754e75d53233d77a795f58d698de0\n"
]
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"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
" warnings.warn(\n"
]
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"User: andrej studen CSRF: 012811adf1c147f0b7a45d71bdf3b4e3\n",
"User: andrej studen CSRF: 64f045d8063aa4c01895d45a6b8d456f\n",
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"User: andrej studen CSRF: b8bb560ed73640520bc0ee0e1bd56a96\n",
"User: andrej studen CSRF: e5f13c276bf403a0b4c0d00242f4c245\n",
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"User: andrej studen CSRF: f14daed93cdda355636efc83f91bc4bd\n",
"User: andrej studen CSRF: 2b8f86d836619f0e092e49361c497856\n",
"User: andrej studen CSRF: 97d444338e73180829b1ba13be8f7820\n",
"User: andrej studen CSRF: b45fbd7a5ae4ecce144421e12c7493ce\n",
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]
},
{
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"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
" warnings.warn(\n"
]
},
{
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"User: andrej studen CSRF: e340dc16fd94c9bbdb7120f40781cb9d\n",
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"User: andrej studen CSRF: 47e2a13f0dffcd5660f5d503b444c4fc\n",
"User: andrej studen CSRF: b61e170856634306c33249818ef56497\n",
"User: andrej studen CSRF: 39f89e811018698c4f9f7d63febf61cd\n",
"User: andrej studen CSRF: a4b02789ce9a1726224ed97740c37944\n",
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"User: andrej studen CSRF: 539ab75da7ff122af12d9aa0d39c75fe\n",
"User: andrej studen CSRF: 4300f33dc41bf4f849a80ae7c996cc3a\n",
"User: andrej studen CSRF: d497e04a6079e10b5d74fd0e2112b657\n",
"User: andrej studen CSRF: 5192bea7856131302ad4cf2666737223\n",
"User: andrej studen CSRF: 9e632649bda175f287124046168a2e0d\n",
"User: andrej studen CSRF: cdacc232d34f2c3ac108d0e7776a5e55\n",
"User: andrej studen CSRF: 94d7fc9b06ea4de6f0158edfa8c5b982\n",
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]
},
{
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"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
" warnings.warn(\n"
]
},
{
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"User: andrej studen CSRF: 7b01cca5c97a00f4d513669d06ed4937\n",
"User: andrej studen CSRF: 5edf9222fc17a03b1bdfe2a77b4a9513\n",
"User: andrej studen CSRF: 1c4f28b912da6a0d1401bd6c47986a42\n",
"User: andrej studen CSRF: 490bdf1edf9f916538024986ff68982f\n",
"User: andrej studen CSRF: 3f08b9e414d2334d15122157a2a06edb\n",
"User: andrej studen CSRF: 245cd211aa6161b1e9d5ee6bd564e7f2\n",
"User: andrej studen CSRF: 88a6f2412b48859a5c4c65f0d405b4f0\n",
"User: andrej studen CSRF: 878ef0c26a71c3a02d5609395880501b\n",
"User: andrej studen CSRF: cb46b4c8014b55e112559791b22696b8\n",
"User: andrej studen CSRF: 907a5eaec3739e15d292915ec0423b1c\n",
"User: andrej studen CSRF: a5cf3f93dc9b944f70ec7a7ca87d78f9\n",
"User: andrej studen CSRF: 1b0166366696fb72fb1e911fb0cf2c25\n",
"User: andrej studen CSRF: 3ccff50b4979bda949dfff4f53a7a708\n",
"User: andrej studen CSRF: c25e00daf08b5c6019d2227a216e8dc1\n",
"User: andrej studen CSRF: f11a39cac798ad686e479ef5d5131df3\n",
"User: andrej studen CSRF: 7a9734fd95031ec04f12a796372a507a\n",
"User: andrej studen CSRF: ac853942d51bab33ca1d514f0cbcdfa6\n",
"User: andrej studen CSRF: 28e816b593e280402052c5b2b2a7efb6\n",
"User: andrej studen CSRF: 15cae34beb97379c8b6547ed4cbd6af3\n",
"User: andrej studen CSRF: bd3fd702e6d0523d4a368a0d7fae2f30\n",
"User: andrej studen CSRF: 6660cb2f84bb8f3750ec5ec05d3162e5\n",
"User: andrej studen CSRF: a5df32f6e3971bc670bdaa399f475988\n",
"User: andrej studen CSRF: 333c7237fbe437bda97ac879b0910ddb\n",
"User: andrej studen CSRF: 0fa34ae60f37f609204dc4a69fc3989f\n",
"User: andrej studen CSRF: 0bc15c1728a458659024553ab0b41865\n",
"User: andrej studen CSRF: f4044c498adbb046748be02e202452cf\n",
"User: andrej studen CSRF: 9bfc37782ee8fc36c2f731f902d31f64\n",
"User: andrej studen CSRF: db807ee35692973297b8dea4785aade6\n"
]
}
],
"source": [
"pat=[p for p in patients if p.find('8')!=0]\n",
"k1=summaryPixelIVF(project,locDir,pat,[0.1],7)\n",
"storeIVF(db,project,locDir,k1)"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
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"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
" warnings.warn(\n"
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"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
" warnings.warn(\n"
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"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
" warnings.warn(\n"
]
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"User: andrej studen CSRF: 9e41ce7fbf9783b102145634ae6107ab\n",
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"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
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"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
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"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
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"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
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"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
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"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
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]
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"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
" warnings.warn(\n"
]
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]
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"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
" warnings.warn(\n"
]
},
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]
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"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
" warnings.warn(\n"
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"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
" warnings.warn(\n"
]
},
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]
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"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
" warnings.warn(\n"
]
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]
}
],
"source": [
"pat=[p for p in patients if p.find('8')!=0]\n",
"k1=fullSummary(project,locDir,pat,[10],20,0.1,3)\n",
"storeSummary(db,project,locDir,k1,0.1,3)\n"
]
},
{
"cell_type": "code",
"execution_count": 107,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{'M': {0: {'mean': 0.005371908478823275, 'std': 0.0005748154115907079, 'median': 0.00504829351328475}, 1: {'mean': 0.00398706780698255, 'std': 0.0008592694250527332, 'median': 0.003388404180814905}, 2: {'mean': 0.0037767548460013053, 'std': 0.0006276175516250823, 'median': 0.004138535106155311}, 3: {'mean': 0.0045120019537560705, 'std': 0.0007593001890057208, 'median': 0.004904191257967345}, 4: {'mean': 0.0031040814064716474, 'std': 0.0001765662651125499, 'median': 0.00301590732317976}, 5: {'mean': 0.0045120019537560705, 'std': 0.0007593001890057208, 'median': 0.004904191257967345}, 6: {'mean': 0.0031040814064716474, 'std': 0.0001765662651125499, 'median': 0.00301590732317976}, 7: {'mean': 0.0031040814064716474, 'std': 0.0001765662651125499, 'median': 0.00301590732317976}, 8: {'mean': 0.0031040814064716474, 'std': 0.0001765662651125499, 'median': 0.00301590732317976}, 9: {'mean': 0.0031040814064716474, 'std': 0.0001765662651125499, 'median': 0.00301590732317976}, 10: {'mean': 0.0034925792443534615, 'std': 0.000712836434502568, 'median': 0.003230836321052485}, 11: {'mean': 0.002942684869416924, 'std': 8.584987083884881e-05, 'median': 0.002954897966504385}, 12: {'mean': 0.002942684869416924, 'std': 8.584987083884881e-05, 'median': 0.002954897966504385}, 13: {'mean': 0.0038874562766629287, 'std': 0.0008528550492831983, 'median': 0.003379357792522795}, 14: {'mean': 0.0031040814064716474, 'std': 0.0001765662651125499, 'median': 0.00301590732317976}, 15: {'mean': 0.002184062672680895, 'std': 4.336506662161737e-05, 'median': 0.00218645043494317}}, 'W': {0: {'mean': 0.005931986370752202, 'std': 0.00019139810809457942, 'median': 0.005930116066388524}, 1: {'mean': 0.003749548513649944, 'std': 0.0002816147776747823, 'median': 0.003861192537029771}, 2: {'mean': 0.003727806875027615, 'std': 0.0003322774172470865, 'median': 0.003940037177277234}, 3: {'mean': 0.004167914310279712, 'std': 0.0003870638820251826, 'median': 0.004406229257514758}, 4: {'mean': 0.003022912024319836, 'std': 6.624420546066359e-05, 'median': 0.0030077717895602004}, 5: {'mean': 0.0041797131569875105, 'std': 0.00046772875608648833, 'median': 0.004479721774912185}, 6: {'mean': 0.003247813763947978, 'std': 5.8068068873377935e-05, 'median': 0.0032274876165731556}, 7: {'mean': 0.0030447606235200955, 'std': 0.00011810157358104187, 'median': 0.00298593361254862}, 8: {'mean': 0.0032165663666835617, 'std': 5.5061408735894747e-05, 'median': 0.0031890549872549408}, 9: {'mean': 0.0033939676098046906, 'std': 4.4627474787750075e-05, 'median': 0.003381235252182444}, 10: {'mean': 0.0034631266888655184, 'std': 0.00011706013950740912, 'median': 0.003482031844177046}, 11: {'mean': 0.00362500279071822, 'std': 0.0001368698874922536, 'median': 0.0036780213624651305}, 12: {'mean': 0.0032147639914663546, 'std': 0.00012959835042494118, 'median': 0.0032326569794918335}, 13: {'mean': 0.003665605915324069, 'std': 0.00017376818980351577, 'median': 0.003724704287518482}, 14: {'mean': 0.0033597397409155273, 'std': 5.3618215779729534e-05, 'median': 0.0033406114442330387}, 15: {'mean': 0.0021692854905642515, 'std': 8.516403911876423e-06, 'median': 0.0021676539137135773}}}\n"
]
}
],
"source": [
"print(k1)"
]
},
{
"cell_type": "code",
"execution_count": 56,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"0.02223504\n",
"0.02223504\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
" warnings.warn(\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"0.4418241525813627\n",
"0.34392268845874496\n",
"0.44668512187675746\n",
"0.4277373071517828\n",
"0.3922308796145302\n",
"0.35643425292374326\n",
"0.3692802456593414\n",
"0.31520469737807355\n",
"0.4654286761032285\n",
"0.7829711283052362\n",
"0.29574684452011624\n",
"0.32465688583552055\n",
"0.4998691162413557\n",
"0.45862342417011315\n",
"0.5354598797118066\n",
"0.29275341177289665\n"
]
},
{
"data": {
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wGGYK4383QgJw+nonUAAAAABJRU5ErkJggg==\n",
"text/plain": [
"<Figure size 432x288 with 1 Axes>"
]
},
"metadata": {
"needs_background": "light"
},
"output_type": "display_data"
},
{
"data": {
"image/png": "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\n",
"text/plain": [
"<Figure size 432x288 with 1 Axes>"
]
},
"metadata": {
"needs_background": "light"
},
"output_type": "display_data"
}
],
"source": [
"import matplotlib\n",
"p='7TMOBR'\n",
"sy=28\n",
"realizationId=5\n",
"nclass=30\n",
"nu=getIWeights(locDir,p,30,realizationId,4)\n",
"nim=getPatientNIM(p)\n",
"cut0=20\n",
"w0=20\n",
"cut1=0\n",
"fw=40\n",
"idx=[7,28,34]\n",
"print(nu[7,28,34])\n",
"print(nu[tuple(idx)])\n",
"w=getWeights(project,locDir,p,nclass,realizationId,0.1,7)\n",
"for r in w:\n",
" print(numpy.max(w[r]))\n",
"matplotlib.pyplot.imshow(nu[:,sy,cut0:cut0+w0])\n",
"matplotlib.pyplot.show()\n",
"matplotlib.pyplot.imshow(nim[:,sy,cut0:cut0+w0])\n",
"matplotlib.pyplot.show()"
]
},
{
"cell_type": "code",
"execution_count": 93,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
" warnings.warn(\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"M\n",
"[10] 20/20\n",
"[20] 20/20\n",
"[30] 20/20\n"
]
}
],
"source": [
"k1=combinePatient(project,locDir,'7TMMIR',[10,20,30],20,4.0,7)"
]
},
{
"cell_type": "code",
"execution_count": 94,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{0: 0.006172951839546806, 1: 0.0011293802007511504, 2: 0.0034521499735888144, 3: 0.0042544572958967365, 4: 0.0035312206174353085, 5: 0.0042544572958967365, 6: 0.0030514161815550344, 7: 0.0013307214487837872, 8: 0.003330571003684981, 9: 0.0031176179941574842, 10: 0.0020333718489625023, 11: 0.00333907520086298, 12: 0.007351435428832242, 13: 0.0038036462072787995, 14: 0.003625240367164753, 15: 0.0028970199562430546}\n",
"{0: 0.0006961087295939239, 1: 0.00031228541489592706, 2: 0.0004510546128805069, 3: 0.0005051282237067151, 4: 0.0004762660491350051, 5: 0.0005051282237067151, 6: 0.0005505760968232114, 7: 0.00032581639272840707, 8: 0.0005191027850853616, 9: 0.0007540860325457227, 10: 0.00032310962085205355, 11: 0.00038986355593399486, 12: 0.0027199019036271716, 13: 0.000548794240952012, 14: 0.0005487268424526743, 15: 0.0006667221336658735}\n"
]
}
],
"source": [
"avgType=['M','W']\n",
"meanK1={type:{region:numpy.mean(k1[region][type]) for region in k1} for type in avgType}\n",
"stdK1={type:{region:numpy.std(k1[region][type]) for region in k1} for type in avgType}\n",
"print(meanK1['M'])\n",
"print(stdK1['M'])\n"
]
},
{
"cell_type": "code",
"execution_count": 79,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[0.00252038792282219, 0.00151611481573515, 0.00254164182147798, 0.00186663983190471, 0.00404895113316396, 0.0020328762566657, 0.00190085158556521, 0.00249521000442543, 0.00157109119636192, 0.00386999102896687, 0.00282258552513781, 0.00334338605677939, 0.00304450254908494, 0.00187659097886802, 0.00202826225861249, 0.0016204124091652]\n",
"0.00252038792282219 0 0.00544315853082935\n",
"0.00151611481573515 8 0.00204586967629601\n",
"0.00254164182147798 1 0.00249553160944056\n",
"0.00186663983190471 8 0.00204586967629601\n",
"0.00404895113316396 7 0.00310949812694919\n",
"0.0020328762566657 8 0.00204586967629601\n",
"0.00190085158556521 2 0.0025554273008312\n",
"0.00249521000442543 7 0.00310949812694919\n",
"0.00157109119636192 9 0.00148953599268332\n",
"0.00386999102896687 0 0.00544315853082935\n",
"0.00282258552513781 7 0.00310949812694919\n",
"0.00334338605677939 1 0.00249553160944056\n",
"0.00304450254908494 1 0.00249553160944056\n",
"0.00187659097886802 2 0.0025554273008312\n",
"0.00202826225861249 8 0.00204586967629601\n",
"0.0016204124091652 9 0.00148953599268332\n"
]
},
{
"data": {
"image/png": 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\n",
"text/plain": [
"<Figure size 432x288 with 1 Axes>"
]
},
"metadata": {
"needs_background": "light"
},
"output_type": "display_data"
}
],
"source": [
"#k1=combinePatient(project,locDir,'7TMMIR',[10],20,4.0,7)\n",
"realizationId=3\n",
"c=10\n",
"p='7TMOBR'\n",
"w=getWeights(project,locDir,p,c,realizationId,0.1,3)\n",
"wc={region:numpy.argmax(w[region]) for region in w}\n",
"fitPar=getFitParIVF(locDir,p,c,realizationId)\n",
"qk1=calculateK1(w,fitPar)\n",
"k1p=getPixelIVF(project,locDir,p,4.0,7)\n",
"pk=list(k1p.values())\n",
"print(pk)\n",
"ck=[qk1[region]['M'] for region in qk1]\n",
"matplotlib.pyplot.scatter(ck,pk)\n",
"for region in w:\n",
" print('{} {} {}'.format(k1p[region],wc[region],qk1[region]['M']))"
]
},
{
"cell_type": "code",
"execution_count": 136,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/usr/lib/python3/dist-packages/urllib3/connection.py:391: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
" warnings.warn(\n"
]
}
],
"source": [
"k1p=getPixelIVF(project,locDir,'7TMMIR',4.0,7)"
]
},
{
"cell_type": "code",
"execution_count": 156,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"0.00252038792282219 0.00821063685487176 0.000769278586995102/0.0003330083431359072\n",
"0.00151611481573515 3.10567836690838e-05 7.88785113142985e-06/1.9000844446763202e-06\n",
"0.00254164182147798 3.10567836690838e-05 7.88785113142985e-06/1.9000844446763202e-06\n",
"0.00186663983190471 0.00821063685487176 0.000769278586995102/0.0001671052167808519\n",
"0.00404895113316396 0.0122210526169817 0.000769278586995102/0.0001671052167808519\n",
"0.0020328762566657 0.0329991638607282 0.00219782291835452/0.0009453421745505919\n",
"0.00190085158556521 3.10567836690838e-05 7.88785113142985e-06/1.9000844446763202e-06\n",
"0.00249521000442543 0.0170371097144494 0.000769278586995102/0.0001671052167808519\n",
"0.00157109119636192 3.10567836690838e-05 7.88785113142985e-06/1.9000844446763202e-06\n",
"0.00386999102896687 0.22232351448649 0.00260465709367942/0.0010770771831046689\n",
"0.00282258552513781 0.0261881964613408 0.002167764950618855/0.0006606993805304795\n",
"0.00334338605677939 0.00388464867694823 7.88785113142985e-06/0.0003179710076941252\n",
"0.00304450254908494 3.10567836690838e-05 7.88785113142985e-06/1.9000844446763202e-06\n",
"0.00187659097886802 3.10567836690838e-05 7.88785113142985e-06/1.9000844446763202e-06\n",
"0.00202826225861249 3.10567836690838e-05 0.000769278586995102/0.0007166763218796836\n",
"0.0016204124091652 0.0261881964613408 0.002167764950618855/0.0007016445972818652\n"
]
}
],
"source": [
"for r in k1:\n",
" print('{} {} {}/{}'.format(k1p[r], qk1[r]['M'] ,numpy.median(k1[r]['M'][10:20]),numpy.std(k1[r]['M'])))"
]
},
{
"cell_type": "code",
"execution_count": 45,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array([0., 0., 0.])"
]
},
"execution_count": 45,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"numpy.zeros(3)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
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