assignOrthancStudy.ipynb 63 KB
import sys
import os
import SimpleITK
import numpy
import matplotlib.pyplot
import subprocess
import json
import chardet
import re
import getData
import segmentation
import importlib
import datetime
sys.path.append(os.path.join(os.path.expanduser('~'),'software','src','nixSuite','wrapper'))
import nixWrapper
nixWrapper.loadLibrary('labkeyInterface')
import labkeyInterface
import labkeyFileBrowser
import labkeyDatabaseBrowser
nixWrapper.loadLibrary('orthancInterface')
import orthancInterface
import orthancFileBrowser
import orthancDatabaseBrowser
def configFile(server):
return os.path.join(os.path.expanduser('~'),'.labkey',"{}.json".format(server))
def connectDB(server):
fconfig=configFile(server)
net=labkeyInterface.labkeyInterface()
net.init(fconfig)
net.getCSRF()
return labkeyDatabaseBrowser.labkeyDB(net)
def connectFB(server):
fconfig=configFile(server)
net=labkeyInterface.labkeyInterface()
net.init(fconfig)
net.getCSRF()
return labkeyFileBrowser.labkeyFileBrowser(net)
def connectOrthanc(server):
fconfig=configFile(server)
net=orthancInterface.orthancInterface()
net.init(fconfig)
return orthancDatabaseBrowser.orthancDB(net)
#manipulate segmentations
#rewrite this
#nim=getPatientNIM(pId)
loadLibrary
remoteSourcesURL https://git0.fmf.uni-lj.si/studen/nixSuite/raw/master/remoteResources/resources.json
{'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': []}, 'dynamicSPECT': {'url': 'https://git0.fmf.uni-lj.si/studen/dynamicSPECT/archive/master.zip', 'branch': 'master', 'modules': ['imageBrowser']}}
{'url': 'https://git0.fmf.uni-lj.si/studen/labkeyInterface/archive/master.zip', 'branch': 'master', 'modules': []}
File /home/studen/temp/labkeyInterface.zip: True
loadLibrary
remoteSourcesURL https://git0.fmf.uni-lj.si/studen/nixSuite/raw/master/remoteResources/resources.json
{'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': []}, 'dynamicSPECT': {'url': 'https://git0.fmf.uni-lj.si/studen/dynamicSPECT/archive/master.zip', 'branch': 'master', 'modules': ['imageBrowser']}}
{'url': 'https://git0.fmf.uni-lj.si/studen/orthancInterface/archive/master.zip', 'branch': 'master', 'modules': []}
File /home/studen/temp/orthancInterface.zip: True
#figure out and set studyId from seriesId
#below - assingOrthancId from date
def assignFromSeriesId():
db=connectDB('merlin')
orthanc=connectOrthanc('merlin')
project='/dinamic_spect/Patients'
dataset='Imaging1'
ds=db.selectRows(project,'study',dataset,'')
for r in ds['rows']:
se=orthanc.getSeriesData(r['nmCorrDataOrthancId'])
r['studyOrthancId']=se['ParentStudy']
db.modifyRows('update',project,'study',dataset,[r])
def sortStudies(orthanc,xs,f):
xm={}
for x in xs:
sd=f(orthanc.getStudyData(x))
try:
xm[sd].append(x)
except KeyError:
xm[sd]=[x]
return xm
#extractors as 3rd arguments to sortStudies;
#they operate on sdata as returned by orthancDatabaseBrowser
def getStudyDate(sdata):
return sdata['MainDicomTags']['StudyDate']
def getBirthYear(sdata):
return sdata['PatientMainDicomTags']['PatientBirthDate'][0:4]
#implementation of sortStudies by studyDate
def studyMap(orthanc):
xs=orthanc.getList('studies')
return sortStudies(orthanc,xs,getStudyDate)
def assignFromDate(modifyRows=False):
db=connectDB('labkey-ukc')
orthanc=connectOrthanc('labkey-ukc')
project='dynamicSPECT/cardiacSPECT'
dataset='Imaging1'
oStudies=studyMap(orthanc)
ds=db.selectRows(project,'study',dataset,'')
print('Study date candidates: {}'.format(list(oStudies.keys())))
for r in ds['rows']:
sid=r['studyOrthancId']
patientId=r['patientCode']
visit=r['visitCode']
if not patientId:
patientId=r['PatientId']
code=f'{patientId}/{visit}'
if sid:
print(f'SET [{code}] ID:{sid}')
continue
sdate=r['imagingDate']
try:
studies=oStudies[sdate]
except:
print(f'FAIL [{code}] @ {sdate} study date not found'.format(patientId,sdate))
continue
if len(studies)==1:
r['studyOrthancId']=studies[0]
studyId=studies[0]
print(f'OK [{code}] @ {sdate} found {studyId}')
if modifyRows:
ds=db.modifyRows('update',project,'study',dataset,[r])
continue
print(f'\t [{code}] @ {sdate} multiple matches: {len(studies)}')
xm=sortStudies(orthanc,studies,getBirthYear)
#bdate=patientId[2:]
#select only numeric glyphs
bdate=re.sub(r'[^0-9]*','',patientId)
#filter on bdate
try:
xmPrime=xm[bdate]
except KeyError:
print(f'FAIL [{code}] @ {sdate} no birth year {bdate}')
continue
#unique solution
if len(xmPrime)==1:
studyId=xmPrime[0]
print(f'OK [{code}] @ {sdate} match birth year {bdate}: {studyId}')
r['studyOrthancId']=xmPrime[0]
if modifyRows:
ds=db.modifyRows('update',project,'study',dataset,[r])
continue
#print(xm)
print(f'FAIL [{code}] @ {sdate} birth year {bdate} multiple: {xmPrime}')
assignFromDate(False) User: andrej studen CSRF: 07c44a2191bd67a30f42f1696b4b3fdf Study date candidates: ['20190514', '20190513', '20220819', '20221129', '20221206', '20220512', '20230830', '20230515', '20190903', '20210202', '20210203', '20190902', '20210423', '20210421', '20220217', '20220215', '20210219', '20210216', '20220708', '20220706', '20200618', '20200619', '20210528', '20210526', '20210212', '20210209', '20190326', '20190327', '20200304', '20200305', '20190826', '20190827', '20210521', '20210519'] SET [10KF/MIR] ID:992c0733-b219b554-7ffbb1eb-e29d0606-63a62c51 SET [10KF/OBR] ID:8de576d0-e88601c2-5317457b-47705c87-60c15eee FAIL [FJ1943/MIR1] @ 20190309 study date not found FAIL [FJ1943/OBR1] @ 20190209 study date not found SET [FJ1943/MIR2] ID:79bcca93-9a5b01f7-516b7ea0-4e5ff2b1-7a1bdaac SET [FJ1943/OBR2] ID:4b1cde0a-72e63430-a9a00264-8861a4cb-a46377cd SET [JA1960/OBR1] ID:b6c889de-f8d38668-e7a15a74-c8530db3-08388687 FAIL [JA1960/MIR1] @ 20210424 study date not found SET [JA1960/OBR2] ID:adcd3506-691a5541-220c8aa1-b0f796fb-fa2db1cd SET [JA1960/MIR2] ID:84791e18-eefcd3cd-4c16e1ff-eaf2b9b4-ee8051a0 SET [JD1971/MIR1] ID:6b4eacd2-2fbf8ef0-ee0ee52b-5dc1e26c-0ae36a23 SET [JD1971/OBR1] ID:18a061b9-db13bed9-90bb43ea-c7f044c4-a86cfd3e SET [JD1971/MIR2] ID:8b017f66-1598a87d-1b8a3c3f-fe9f1ed5-0344686a SET [JD1971/OBR2] ID:72a6e5cd-0d1cac70-0f38027c-5c1c7d8a-f6eba43b SET [JD1973/MIR1] ID:670e9d2a-c1feec4b-99757eaf-997f73e8-8df2742a SET [JD1973/OBR1] ID:96c75aa9-0a16ea6e-d080cd60-29ffddf5-ef3c3f05 SET [JD1973/MIR2] ID:9ae9acd5-5063fedb-0e0d7a72-29f3a951-1ff5fb6d SET [JD1973/OBR2] ID:36a0503d-220a1996-fec9b6ff-29de8388-a3cf3788 SET [JI1943/MIR1] ID:345ed9ec-ec584712-87154bb0-1e6cb5a8-065443eb SET [JI1943/OBR1] ID:fb51a384-24bf561a-35bd3f4d-44079037-ab21e16b SET [JI1943/MIR2] ID:c52a79f1-da8abfa2-c47c8813-3cbdb1a5-50b6d490 SET [JI1943/OBR2] ID:49191331-b4b07708-7e89c147-ce200efc-862d5240 SET [JS1952/MIR1] ID:b473ba96-11f607ca-b79b5f59-230adb5a-f86c8976 SET [JS1952/OBR1] ID:16e9c945-66d4c9ae-b796827f-4a598413-da10981b [KA1940/MIR1] @ 20190514 multiple matches: 3 FAIL [KA1940/MIR1] @ 20190514 no birth year 1940 [KA1940/OBR1] @ 20190513 multiple matches: 3 FAIL [KA1940/OBR1] @ 20190513 no birth year 1940 [KA1940/MIR2] @ 20210212 multiple matches: 2 FAIL [KA1940/MIR2] @ 20210212 no birth year 1940 [KA1940/OBR2] @ 20210209 multiple matches: 2 FAIL [KA1940/OBR2] @ 20210209 no birth year 1940 SET [MB1965/MIR] ID:b2bdb9c0-076fe14e-7d6481f1-14d4093f-7ca29b91 SET [MB1965/MIR1] ID:3fe308e8-48fd71e2-0638aba2-dbfc9e6f-4f7d7718 SET [MB1965/MIR2] ID:dc5d34f2-0fb785a6-d904ba2c-b765fbce-30161f8c SET [MI1943/MIR1] ID:36599b2d-35e85e38-5ccd4ce4-73b2fd77-a7dad7be SET [MI1943/OBR1] ID:00135c7f-9356e861-74c9704b-f133f38e-f42bf54a [MI1943/MIR2] @ 20210212 multiple matches: 2 FAIL [MI1943/MIR2] @ 20210212 no birth year 1943 [MI1943/OBR2] @ 20210209 multiple matches: 2 FAIL [MI1943/OBR2] @ 20210209 no birth year 1943 SET [MJ1963/MIR1] ID:7e643a55-34f441fc-de3d779a-9f6e29bf-6e354e21 SET [MJ1963/OBR1] ID:e619b089-31190797-09b7fa68-3b7ebce5-cb0e342e SET [MM/MIR] ID:137d9e53-0e77d03e-55f56fbf-55358d85-f473d2c5 SET [MM/MIR1] ID:3dd2760f-412cbfba-192c1d12-3832dc3c-321651a5 SET [MM1936/MIR1] ID:c511a074-bfa73799-5df11a3e-c2ad96e1-a4a8e6de SET [MM1936/OBR1] ID:f99216d5-3d3ef44b-2cee1efa-526e0901-b68349dc SET [MM1936/MIR2] ID:42bd91bd-20dd2d19-64a6ff77-7bce6317-4bab8aaf SET [MM1936/OBR2] ID:8eb39455-6fa76e34-c04349a6-7f3ad1cd-61f0a307 SET [MM/OBR] ID:07cb4e32-30da5d01-75d7067f-f393540f-432489e1 SET [MNG1940/OBR1] ID:a9d91056-1388e280-bd6d58df-1ee96555-87441107 SET [MNG1940/MIR1] ID:ad23f1a4-30388a48-9587d035-a5cfeb34-0e8d5d05 SET [MNG1940/MIR2] ID:a6df647d-5474750c-67b017d7-e37b85ec-d7e86f39 SET [MNG1940/OBR2] ID:842443a5-b97d0b03-dda3af69-16089e8b-70b6e87f SET [po1982022/MIR] ID:80bb7c25-6e4d4890-f6f3c46e-f0a7bdfd-2be580d2 SET [pred15052022/MIR] ID:1a759996-7bdd0109-c5e8f833-c6857dfe-84eaed66 SET [TT1998/MIR] ID:827fad2b-7a4b824f-c68d9e4a-7942961a-b9f1133f SET [VV1984/MIR] ID:484d95a5-fe38de02-d377e94b-74c1037d-201f8804 SET [VV1984/MIR1] ID:1c21ea83-b3721080-f272ac26-f5d5ef73-aa56e160
#get series for data with study set
def isCT(orthanc,sedata):
#base criteria - is CT and SeriesDescription contains AC
mtags=sedata['MainDicomTags']
if not mtags['Modality']=='CT':
return False
try:
if not mtags['SeriesDescription'].find('AC')==0:
return False
except KeyError:
pass
#backup - more than a single instance
n=len(sedata['Instances'])
if n==1:
return False
return True
def isMasterNM(orthanc,sedata):
mtags=sedata['MainDicomTags']
if not mtags['Modality']=='NM':
return False
n=len(sedata['Instances'])
if not n==1:
return False
idata=orthanc.getData('instances',sedata['Instances'][0])
imtags=idata['MainDicomTags']
iframes=int(imtags['NumberOfFrames'])
if iframes<500:
return False
#print(idata)
return True
def isCorrDataNM(orthanc,sedata):
mtags=sedata['MainDicomTags']
if not mtags['Modality']=='NM':
return False
n=len(sedata['Instances'])
if n==1:
return False
#idata=orthanc.getData('instances',sedata['Instances'][0])
#imtags=idata['MainDicomTags']
itype=orthanc.getDicomField(sedata['Instances'][0],'0028-0051')
if itype.find('SCAT')==-1:
return False
#print(itype)
return True
def setSeries(modifyRows=False):
db=connectDB('labkey-ukc')
orthanc=connectOrthanc('labkey-ukc')
project='dynamicSPECT/cardiacSPECT'
dataset='Imaging1'
ds=db.selectRows(project,'study',dataset,'')
for r in ds['rows']:
patientId=r['PatientId']
visit=r['visitCode']
sdate=r['imagingDate']
code=f'[{patientId}/{visit} @ {sdate}]'
if r['nmMasterOrthancId']:
print(f'SET {code}')
continue
if not r['studyOrthancId']:
print(f'FAIL {code}: no study id set, run assignFromDate()!')
continue
series=orthanc.getStudyData(r['studyOrthancId'])['Series']
for s in series:
sedata=orthanc.getSeriesData(s)
mtags=sedata['MainDicomTags']
#print('{} {}'.format(mtags['Modality'],mtags['SeriesDescription']))
if isCT(orthanc,sedata):
r['ctOrthancId']=s
continue
if isMasterNM(orthanc,sedata):
r['nmMasterOrthancId']=s
continue
if isCorrDataNM(orthanc,sedata):
r['nmCorrDataOrthancId']=s
continue
#print(sedata)
#break
print(f'{code}')
if r['ctOrthancId']:
x=r['ctOrthancId']
print(f'\tCT: OK ID: {x}')
else:
print(f'\tCT: FAIL')
if r['nmMasterOrthancId']:
x=r['nmMasterOrthancId']
print(f'\tNM(Raw) ID: {x}')
else:
print(f'\tNM(Raw) FAILED')
if r['nmCorrDataOrthancId']:
x=r['nmCorrDataOrthancId']
print(f'\tNM(Img) ID: {x}')
else:
print(f'\tNM(Img) FAILED')
if modifyRows:
ds=db.modifyRows('update',project,'study',dataset,[r])
#break
setSeries(True)
User: andrej studen CSRF: a675486ae1b1befbc6ebd792df3a8c17 SET [10KF/MIR @ 20190514] SET [10KF/OBR @ 20190513] FAIL [FJ1943/MIR1 @ 20190309]: no study id set, run assignFromDate()! FAIL [FJ1943/OBR1 @ 20190209]: no study id set, run assignFromDate()! SET [FJ1943/MIR2 @ 20210202] SET [FJ1943/OBR2 @ 20210203] [JA1960/OBR1 @ 20210421] CT: OK ID: b79ee29f-dc4aaa68-78f4ad43-e678e11e-a520fcaf NM(Raw) ID: 17187242-e96a62d6-0c34ea12-3b80d992-e4a0db30 NM(Img) ID: 4fe75631-dc32fbaf-c4f52623-faecfd73-f53ee029 User: andrej studen CSRF: d3796bb7537fd6b9462c460bcbd3a845 FAIL [JA1960/MIR1 @ 20210424]: no study id set, run assignFromDate()! [JA1960/OBR2 @ 20220215] CT: OK ID: cba7385d-7aaef4ed-f21155f5-db0e55b6-ac29dea3 NM(Raw) ID: 9e2e18d0-2799979f-d5794737-df61f83d-f0e8a8b4 NM(Img) ID: 70538040-5c662ab7-b11e2052-19e04c62-72b68967 User: andrej studen CSRF: 79cbd15f916c74e6ea58631348b4d08c [JA1960/MIR2 @ 20220217] CT: OK ID: 15ee88ea-35773b56-a6e864f7-c46f49a9-d1421f36 NM(Raw) ID: 0db18702-1dd7c0c2-866eade8-74f5ee30-79a12dcf NM(Img) ID: 7edd0445-ae06d9c5-268a1182-3a814255-1882fab3 User: andrej studen CSRF: c81de448540579af2ac305cb0b33431d [JD1971/MIR1 @ 20190903] CT: OK ID: 03d06718-724bfb17-3d181862-9d123117-e598f3ea NM(Raw) ID: 0de1d1d2-8710b71d-99cb9d3e-1c64c5db-5a2b495c NM(Img) ID: 690aa1c8-3db59555-b270e771-ba6c1992-e7c647c5 User: andrej studen CSRF: 0c096074f992403819bce555a2b22b65 [JD1971/OBR1 @ 20190902] CT: OK ID: afc725ba-c818c7b9-9843a39a-09905a44-e0b69f84 NM(Raw) ID: 6e346b85-2d5b0b13-ceedd23e-abaa46a6-5b4f6ce1 NM(Img) ID: 1a5192ca-23ebfcb5-3d2603c7-fade6633-7d427fb6 User: andrej studen CSRF: 85164cfa4c40f7f22f334cc37fd7242a [JD1971/MIR2 @ 20210219] CT: OK ID: d8f06cb7-89f01c5d-46a69d6b-ba8c653a-d0060e1a NM(Raw) ID: 01ef80c4-7ae0ab2c-230cb908-b8ddaf68-5b864a2b NM(Img) ID: 41e870de-06479edc-d5a43f4b-0b5440cd-79c4b6bf User: andrej studen CSRF: 8b992a30d78fd3c98a54e747251ccee7 [JD1971/OBR2 @ 20210216] CT: OK ID: 8acdda24-6d4cff97-eaaca89c-17c05b93-8be78bce NM(Raw) ID: 35b070a6-3f8b472c-cf186ca5-fcc35602-7ac7854c NM(Img) ID: eda3927f-eeced313-105b4088-7955765a-e0111caf User: andrej studen CSRF: 41b65d29b560745614cb4a1bbc8bfd02 [JD1973/MIR1 @ 20210423] CT: OK ID: 9367d757-0a93c89b-f29c2c44-a81cd459-25562726 NM(Raw) ID: 7d79ab8a-162aaad3-c85a0b83-213e4fcc-21d2815a NM(Img) ID: ecfd3162-665fa458-13889f24-4b10a77b-bbf6efa0 User: andrej studen CSRF: afb2b28b35aae2ae2b74b8a398fd4a62 [JD1973/OBR1 @ 20210421] CT: OK ID: 21f02bd0-7883466c-5cee4cf4-ac1762df-309fec00 NM(Raw) ID: b4f36691-ff2b4acf-4ed9b04f-60bf102f-2dfcc532 NM(Img) ID: 81b23560-456462a5-229f9508-3fbd7067-da170abd User: andrej studen CSRF: d0532d3451546a886e74edbe3ee0eea9 [JD1973/MIR2 @ 20220708] CT: OK ID: b5db5dcd-73ffb6a2-30e388d4-a8703df5-390c6e40 NM(Raw) ID: d2ad0b63-62409b0b-fd8a70b9-f71b805f-2f39f3fc NM(Img) ID: 3429be0f-f3824fd6-57426475-6bf47ed9-d75e4e0c User: andrej studen CSRF: 1e581bef379eee356c6d71654d57276f [JD1973/OBR2 @ 20220706] CT: OK ID: 7c79efa9-28523e0f-f897a8e9-63742b78-a26d0ff8 NM(Raw) ID: fa97be07-7a806101-44f7079d-e1a3381e-89854f27 NM(Img) ID: 39c7ae58-862bb23d-33c7e05e-d6587450-cabf15b2 User: andrej studen CSRF: 79875757c2656056293b51379e09b07d [JI1943/MIR1 @ 20200618] CT: OK ID: 683e9555-b9b6e5fd-d06f5521-5adf12d5-ed85ced2 NM(Raw) ID: f7b2bed3-c38a9600-e1bf5b01-cf2e4c70-4a4ab823 NM(Img) ID: af15224b-2dc57712-f324695c-a50547e2-34e72e62 User: andrej studen CSRF: 71c60846321c8033056406a1eb4d3d9f [JI1943/OBR1 @ 20200619] CT: OK ID: 9a78e8d8-df2fa3e7-02ba6d08-0fdbe51b-0e4246e9 NM(Raw) ID: a9caf516-a38c8fe1-90ea7ee2-52ce3de8-77615243 NM(Img) ID: 5bd63e93-651a5d1d-40076934-05cb0421-5c01d74d User: andrej studen CSRF: c0eec3718396480bb81e2379fe9244dc [JI1943/MIR2 @ 20210528] CT: OK ID: 773f9a42-dbdf8b4c-4ab0f808-b96be60d-a1084b63 NM(Raw) ID: 933a27de-057d0e80-eb78afdb-739d3d16-31c125b9 NM(Img) ID: 002ebf3c-3adb4ae0-728daeb5-7acce400-5362b1fa User: andrej studen CSRF: f3c4798a3ed8106e0339e88434bf30c8 [JI1943/OBR2 @ 20210526] CT: OK ID: 03ff48ce-2bb5a42e-73d6b709-3ac1a875-b521e3c0 NM(Raw) ID: 81a0661b-5e7c27d5-29c1288f-ca47451c-c83443ce NM(Img) ID: 056c3249-f132228b-68f39184-fd310fff-01cb4360 User: andrej studen CSRF: a2749828b4d77def4689100c17829549 [JS1952/MIR1 @ 20190514] CT: OK ID: 19f99b32-8d92b846-8865eeb2-7678b004-93bd4e76 NM(Raw) ID: 87e86b89-ee314eb1-a95228f5-c3587c3b-b8016f52 NM(Img) ID: 62bd627d-7e7b5824-b3b2bcb7-2493055f-1053d74e User: andrej studen CSRF: 2ce0ddc27763a76e44fb8393e6ced1ad [JS1952/OBR1 @ 20190513] CT: OK ID: b5b39140-58a11dbb-29f762ea-74eb5eee-babe1c29 NM(Raw) ID: 9cefe25d-4c8ea4eb-33b38501-3386729f-11a434fd NM(Img) ID: ea75ac15-b48d4c11-7088a758-95f5a5e3-e5cec172 User: andrej studen CSRF: c000d67775020e76aa21d2de55ddea11 FAIL [KA1940/MIR1 @ 20190514]: no study id set, run assignFromDate()! FAIL [KA1940/OBR1 @ 20190513]: no study id set, run assignFromDate()! FAIL [KA1940/MIR2 @ 20210212]: no study id set, run assignFromDate()! FAIL [KA1940/OBR2 @ 20210209]: no study id set, run assignFromDate()! SET [MB1965/MIR @ 20220512] SET [MB1965/MIR1 @ 20220819] SET [MB1965/MIR2 @ 20221129] [MI1943/MIR1 @ 20190326] CT: OK ID: 3cec3099-d6a5aa2c-80ceefa4-b2f24b5f-5914695d NM(Raw) ID: 1264c701-cf0be371-9c0639e0-9d3b1087-954bad3c NM(Img) ID: f4d20c35-856f0cbb-dd925c5b-869f392a-9cfd359e User: andrej studen CSRF: 583cdc2d38f1a2f1c54624e9f48a1a4b [MI1943/OBR1 @ 20190327] CT: OK ID: 3efeff50-bf7eb655-ee08824d-7b63792a-457fedd4 NM(Raw) ID: 0e722805-ecf04f38-ca9d0ac2-01e1d87e-cbea14ea NM(Img) ID: b6322734-d5efec5a-300525ab-975bc0b1-5718c7eb User: andrej studen CSRF: b8bd58a36daae5d165dd78e0d48f5f62 FAIL [MI1943/MIR2 @ 20210212]: no study id set, run assignFromDate()! FAIL [MI1943/OBR2 @ 20210209]: no study id set, run assignFromDate()! [MJ1963/MIR1 @ 20200304] CT: OK ID: 39aa62d1-dcbe7247-5cd23dac-6067bfc3-0e9e974e NM(Raw) ID: 17f28587-fcac56f2-a1747c7b-9e3e3a9d-b85ea454 NM(Img) ID: dad69a7e-96ab9c71-c653230f-ac6ca06f-6ebbcf70 User: andrej studen CSRF: 02f342665ba2523c5df64be20dfbb17a [MJ1963/OBR1 @ 20200305] CT: OK ID: 0047a1c3-6cdc3d79-8692a0cd-c3e23862-b0069561 NM(Raw) ID: fe979a39-696e2e65-3c012807-8ba9818a-b26523a7 NM(Img) ID: 133f8b65-8e1ca210-270c9259-b4244ad0-452fa07d User: andrej studen CSRF: d93fe40483a9f916bfe0946d40706e71 SET [MM/MIR @ 20220819] SET [MM/MIR1 @ 20221129] [MM1936/MIR1 @ 20190827] CT: OK ID: 74b2a919-5fc51491-34f4276c-7daae0cc-269dd4ac NM(Raw) ID: 4746b129-56061f7b-e5ecbe6c-9cbac5ba-fd6ee400 NM(Img) ID: c671017b-58898e0d-9aa6950e-7f31fbbb-9466a85a User: andrej studen CSRF: ba46f35b592cc78b0a851ee032028060 [MM1936/OBR1 @ 20190826] CT: OK ID: ff84df5d-695eb992-b80ab669-e5329506-cfadf3dd NM(Raw) ID: 173fd06d-ffc44f86-c47084b9-5888612b-ab9c430a NM(Img) ID: f5f31de2-968e183c-f4e6ef8d-59b09f8b-f55e6d24 User: andrej studen CSRF: b177ccb2d217743ad3fe57cbd3c2f6c9 [MM1936/MIR2 @ 20210521] CT: OK ID: f94eda1b-adff3b63-2fc2a467-b88f79fa-15925c64 NM(Raw) ID: 5a537e00-ca99bc11-6b0db820-fadfd1ab-76f3f712 NM(Img) ID: 7706d5ae-9c0ca196-6bf786f0-1fccd37b-e9463de6 User: andrej studen CSRF: 73a0e916d395710fc82c3742860227bc [MM1936/OBR2 @ 20210519] CT: OK ID: 61cb4866-fd57c584-9bffa6ad-30382fc8-7598b317 NM(Raw) ID: a39cc437-bb66f647-0f820a25-e5110ff0-41414aba NM(Img) ID: e42d465b-86a6222e-29ce1948-a22a6757-ed346ab5 User: andrej studen CSRF: 460b41c11fd660124a7de2f2d9c9eca2 SET [MM/OBR @ 20221206] [MNG1940/OBR1 @ 20210421] CT: OK ID: f32c172a-80b7f813-35ba3566-26d3acc2-82e016c8 NM(Raw) ID: 8b9e1175-e2cff1a3-1314ac58-50e8ba3d-59171f28 NM(Img) ID: 7be9bde7-6ee5f88f-3310c821-14733f77-346555b0 User: andrej studen CSRF: 5add02fab1cda2e6478b7037e1c76a6b [MNG1940/MIR1 @ 20210423] CT: OK ID: beb26f2d-67e874f6-8d4c2d07-0ea23e21-b68c437e NM(Raw) ID: 286de30e-663ca5d9-2507026e-345d2b82-0cff87cf NM(Img) ID: 3d26bdf4-96f7ae44-dd977c3b-f7721f77-271093df User: andrej studen CSRF: d3d8dc0fc56c658b20289e6b6aa50ec6 [MNG1940/MIR2 @ 20220217] CT: OK ID: 8edfbe5a-a4d171d2-9eae5b2b-bb3c92c7-e2fd3fc7 NM(Raw) ID: 945da723-e1b2eeca-1ff0af60-cd733123-94a1c135 NM(Img) ID: bf1c4f2d-72ce38bc-a77e0452-ca4b7079-a8dac61f User: andrej studen CSRF: 813eae5a892bb0669baa1cde2f490754 [MNG1940/OBR2 @ 20220215] CT: OK ID: b836c90f-85cab249-d7c5fdb0-e3475e53-1d069753 NM(Raw) ID: 0cc948ad-7856ba90-0c5f755b-8d58a5b8-62e32258 NM(Img) ID: b7b7764e-5290b3bd-79b18d47-4320e153-e44b0932 User: andrej studen CSRF: 073bad98ab82533d8232c3138ea4bff1 SET [po1982022/MIR @ 20220819] SET [pred15052022/MIR @ 20220512] SET [TT1998/MIR @ 20230830] SET [VV1984/MIR @ 20230515] SET [VV1984/MIR1 @ 20230830]
#get imagingDate from studyOrthancId
def getImagingDate():
db=connectDB('labkey-ukc')
orthanc=connectOrthanc('labkey-ukc')
project='/dynamicSPECT/cardiacSPECT'
dataset='Imaging1'
ds=db.selectRows(project,'study',dataset,'')
rows=ds['rows']
for r in rows:
sid=r['studyOrthancId']
patientId=r['PatientId']
if not sid:
print(f'No study id for {patientId}')
continue
sd=orthanc.getStudyData(r['studyOrthancId'])
r['imagingDate']=sd['MainDicomTags']['StudyDate']
db.modifyRows('update',project,'study',dataset,[r])
def setStudyDate():
db=connectDB('labkey-ukc')
orthanc=connectOrthanc('labkey-ukc')
project='/dynamicSPECT/cardiacSPECT'
dataset='Imaging1'
ds=db.selectRows(project,'study',dataset,[])
rows=ds['rows']
for r in rows:
dt=datetime.datetime.strptime(r['imagingDate'],'%Y%m%d')
r['studyDate']=dt.strftime('%Y/%m/%d')
db.modifyRows('update',project,'study',dataset,[r])
setStudyDate()User: andrej studen CSRF: eda92fe6acfc645dcc20e64451de2bcc User: andrej studen CSRF: ccdd6bfe993c84237648879c32922324 User: andrej studen CSRF: 1eefebcb86155da277327e320c6d855e User: andrej studen CSRF: 97ac1e100819769b7852e9a7dd3290fd User: andrej studen CSRF: ed40684a2b8537c23fc358ed4d900a47 User: andrej studen CSRF: 34ad147b1b7dd2dd3e61e67158a34afb User: andrej studen CSRF: 5f51b6f277e43102b44c97658b8a11c8 User: andrej studen CSRF: 8b66c1e79af33886680486734ab0b10b User: andrej studen CSRF: 0c4c51e3f4b05f46f5fe68b35a1d6e21 User: andrej studen CSRF: 73f023fe6494ee80f446212df52f6702 User: andrej studen CSRF: 479c20de89dc3d47e250677aab54db53 User: andrej studen CSRF: 375be6798203b87d56a61eafdcc2fdc4 User: andrej studen CSRF: 13553704c3885f2667711e1bb5bd8100 User: andrej studen CSRF: 84442ae1e529d6e74d730fe96342a64f
#set patientCode
db=connectDB('labkey-ukc')
project='/dynamicSPECT/cardiacSPECT'
dataset='Imaging1'
ds=db.selectRows(project,'study',dataset,'')
rows=ds['rows']
for r in rows:
r['patientCode']=r['PatientId']
db.modifyRows('update',project,'study',dataset,[r])User: andrej studen CSRF: ef76bf934ffbf0af9fc0547fc7871983 User: andrej studen CSRF: 816ac23d327ba77af1abb18b9c0ba3e1 User: andrej studen CSRF: 1be64b3e1b0d3ed0b6853d56ac70e6a5 User: andrej studen CSRF: d5b958584db13089e2731feb37334487 User: andrej studen CSRF: 9ecdad5e798ef004b999fce6727c4e0f User: andrej studen CSRF: 19850f8c5b0c4217d483bea59a6fe743 User: andrej studen CSRF: 3ecb54e610afb5605c92a7fa19fb3326 User: andrej studen CSRF: 602968a1373dac5c14d55af8dd1c475b User: andrej studen CSRF: 16eb98eddbaa6b58f4a5d733a270c013 User: andrej studen CSRF: 207b55bf76fcd1a88fb316cd832d88a4 User: andrej studen CSRF: ecf8895ef0da5c1f092a6ec3a64f7d9c User: andrej studen CSRF: 94735fb33035a678e5836a38f7cdcdb6 User: andrej studen CSRF: 9cbec531e64fed313135398a92341495 User: andrej studen CSRF: 2387d8b279dfa87b4a1d6cadf1db7d3f
#copy files from one orthanc instance to another
db=connectDB('merlin')
orthanc=connectOrthanc('merlin')
project='/dinamic_spect/Patients'
dataset='Imaging1'
ds=db.selectRows(project,'study',dataset,'')
src=configFile('merlin')
target=configFile('kclj')
path=['software','src','orthancInterface','scripts','moveDicom.sh']
path.insert(0,os.path.expanduser('~'))
script=os.path.join(*path)
for r in ds['rows']:
subprocess.run([script,src,target,r['studyOrthancId']])
User: andrej studen CSRF: 4f341fbc6f8b6681df54039307becbd7
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 9.8M 0 9.8M 0 0 1017k 0 --:--:-- 0:00:09 --:--:-- 2100k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0Downloaded study 992c0733-b219b554-7ffbb1eb-e29d0606-63a62c51 to /home/studen/temp/Study.zip
100 9.9M 100 23131 100 9.8M 3353 1468k 0:00:06 0:00:06 --:--:-- 1524k
AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored AlreadyStored
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 9262k 0 9262k 0 0 369k 0 --:--:-- 0:00:25 --:--:-- 1015k
Downloaded study 8de576d0-e88601c2-5317457b-47705c87-60c15eee to /home/studen/temp/Study.zip
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 9283k 100 21233 100 9262k 3544 1546k 0:00:05 0:00:05 --:--:-- 1745k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success
100 11.7M 0 11.7M 0 0 346k 0 --:--:-- 0:00:34 --:--:-- 37959
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0Downloaded study 137d9e53-0e77d03e-55f56fbf-55358d85-f473d2c5 to /home/studen/temp/Study.zip
100 11.7M 100 33199 100 11.7M 4014 1455k 0:00:08 0:00:08 --:--:-- 1347k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success
100 12.9M 0 12.9M 0 0 359k 0 --:--:-- 0:00:36 --:--:-- 2426k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0Downloaded study 3dd2760f-412cbfba-192c1d12-3832dc3c-321651a5 to /home/studen/temp/Study.zip
100 12.9M 100 35515 100 12.9M 3549 1326k 0:00:10 0:00:10 --:--:-- 307k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success
100 12.1M 0 12.1M 0 0 539k 0 --:--:-- 0:00:22 --:--:-- 123k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0Downloaded study 07cb4e32-30da5d01-75d7067f-f393540f-432489e1 to /home/studen/temp/Study.zip
100 12.1M 100 34743 100 12.1M 4214 1503k 0:00:08 0:00:08 --:--:-- 939k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success
100 11.7M 0 11.7M 0 0 857k 0 --:--:-- 0:00:14 --:--:-- 964k
Downloaded study 80bb7c25-6e4d4890-f6f3c46e-f0a7bdfd-2be580d2 to /home/studen/temp/Study.zip
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 11.7M 100 33199 100 11.7M 4160 1508k 0:00:07 0:00:07 --:--:-- 1091k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success
100 12.4M 0 12.4M 0 0 659k 0 --:--:-- 0:00:19 --:--:-- 2216k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0Downloaded study 1a759996-7bdd0109-c5e8f833-c6857dfe-84eaed66 to /home/studen/temp/Study.zip
100 12.4M 0 0 100 12.4M 0 1671k 0:00:07 0:00:07 --:--:-- 1762kSuccess Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success Success
100 12.5M 100 35515 100 12.4M 4102 1474k 0:00:08 0:00:08 --:--:-- 910k
#copy dataset from one instance to another
src=connectDB('merlin')
target=connectDB('kclj')
srcProject='dinamic_spect/Patients'
targetProject='dynamicSPECT/cardiacSPECT'
schema='study'
dataset='Imaging1'
def copyDatasetDesign(src,srcProject,target,targetProject,schema,dataset):
minProperties=['name','label','rangeURI','lookupSchema',
'lookupContainer','lookupQuery']
dsgn=target.getQueryDesign(targetProject,'study',dataset)
if 'exception' in dsgn:
print('Missing {} {}'.format(schema,dataset))
#impossible to create list copy them by hand
if schema=='lists':
print('create lists by list archive export')
return
design=src.getQueryDesign(srcProject,schema,dataset)
fields=[]
for f in design['fields']:
#skip Key
if f['name']=='Key':
continue
#use subselection
q={p:f[p] for p in minProperties}
fields.append(q)
print(target.addQuery(targetProject,schema,dataset,fields))
print('Created {}'.format(dataset))
def internalField(v):
if v.find('_')==0:
return True
if v=='lsid':
return True
return False
def copyDatasetData(src,srcProject,target,targetProject,schema,dataset):
ds=src.selectRows(srcProject,schema,dataset,[])
fVar=['PatientId','SequenceNum']
skipVar=['lsid']
for r in ds['rows']:
qfilter=[{'variable':x,'value':'{}'.format(r[x]),'oper':'eq'} for x in fVar]
ds1=target.selectRows(targetProject,schema,dataset,qfilter)
if len(ds1['rows'])>0:
outRow=ds1['rows'][0]
mode='update'
else:
mode='insert'
outRow={}
for x in r:
if internalField(x):
#print('{}/Skip'.format(x))
continue
#print('{}/Use'.format(x))
outRow[x]=r[x]
target.modifyRows(mode,targetProject,schema,dataset,[outRow])
#break
#copyDatasetDesign(src,srcProject,target,targetProject,schema,dataset)
copyDatasetData(src,srcProject,target,targetProject,schema,dataset)User: andrej studen CSRF: ad0e9a315e6fac8a19f892af1e550d39 User: andrej studen CSRF: e89f9c751f9ca44877fceac804e4909f User: andrej studen CSRF: f7b3b5f0ddf5198e98a29b7ba31072bd User: andrej studen CSRF: d34f232a12afc576f9d0477842f9d099 User: andrej studen CSRF: 16deee5f2eb2c59edb604416b8a71bab User: andrej studen CSRF: fab98bb2b2fc0bb9c7c356ed7d468963 User: andrej studen CSRF: 20974f8994412e7c209edb0c100b59bc User: andrej studen CSRF: 84cff63141f897248071e16692de5338 User: andrej studen CSRF: a80d3d28add7108dd4287c5fbf4b65b8
#check for converted NRRD files
def checkNRRD():
db=connectDB('labkey-ukc')
fb=connectFB('labkey-ukc')
project='dynamicSPECT/cardiacSPECT'
schema='study'
dataset='Imaging1'
ds=db.selectRows(project,schema,dataset,[])
for r in ds['rows']:
#print(r)
fDir='processedImages'
fDir=[fDir,r['PatientId'],r['visitCode']]
fNameCT='{}_{}_CT.nrrd'.format(r['PatientId'],r['visitCode'])
fNameSPECTCT='{}_{}_Volume19.nrrd'.format(r['PatientId'],r['visitCode'])
fRemoteDir=fb.buildPathURL(project,fDir)
fURL='/'.join([fRemoteDir,fName])
if fb.entryExists(fURL):
print(fName)
#row={x:r[x] for x in ['PatientId','visitCode']}
checkNRRD()
User: andrej studen CSRF: e8d8f790b143dd4457ee6213d8ea11e6 User: andrej studen CSRF: 8af4603306dd5888f96e038b676b86dc MB1965_MIR_CT.nrrd MB1965_MIR1_CT.nrrd MB1965_MIR2_CT.nrrd MM_MIR1_CT.nrrd TT1998_MIR_CT.nrrd VV1984_MIR_CT.nrrd VV1984_MIR1_CT.nrrd
#calculate k1 in units of ml/g*min
def convertToMinutes():
db=connectDB('labkey-ukc')
project='/dynamicSPECT/cardiacSPECT'
dataset='Summary'
ds=db.selectRows(project,'study',dataset,'')
rows=ds['rows']
for r in rows:
k1=r['mean']
k1p=60*r['mean']
r['k1']=k1p
db.modifyRows('update',project,'study',dataset,[r])
convertToMinutes()User: andrej studen CSRF: 2b647191df95dff06e7a0c2fca6d8cfc User: andrej studen CSRF: b9df37c5e367adc8640e4a3364df7273 User: andrej studen CSRF: c395eec2b1488cc7b67ff0f9a0eed82e User: andrej studen CSRF: 7856f86e340ca8ea9cff217ce2ec45ea User: andrej studen CSRF: f27049f4751cee7ae2d57cafbb903bc2 User: andrej studen CSRF: ac7532abb8da76c99052bb75c8eb01f7 User: andrej studen CSRF: 0f4d2fc6118e4a375b1448cb757cc448 User: andrej studen CSRF: e63ef87d0921b6688a9c36acc4d12033 User: andrej studen CSRF: 4777412ef946acc7496ae7bb12f9d843 User: andrej studen CSRF: 138efce81860aba8e2658ccd36f4f7bc User: andrej studen CSRF: 3c54b3e94ffe618ec1733ecdb5b32baa User: andrej studen CSRF: 0d9a9b94af06ff3dc2114845c7ce0fbb User: andrej studen CSRF: 4519a0e635665a62ed494cd109c99d36 User: andrej studen CSRF: 07ad2d764675b85ad2eaa3ea03c19405 User: andrej studen CSRF: d04f0a0d00aec42f3ce4d5e96d3a3639 User: andrej studen CSRF: a50021923bce897e16f5bd1540ac36de User: andrej studen CSRF: 0535c280d72a6aa7c35d9f0a6398a08a User: andrej studen CSRF: d8a4d2a69ff4255ab4d0aaf9bf40de06 User: andrej studen CSRF: 02e76facca72414a6c28222e65ed75db User: andrej studen CSRF: d65f663691b8f56bddb1e11dd0a6f1cf User: andrej studen CSRF: 4574afaa21f7a3cf2b95736fd5a09521 User: andrej studen CSRF: 3b6bca3ca5d0e5ea4917b9ac71cc5313 User: andrej studen CSRF: 5fd4f12846e075e935f62bb421829d62 User: andrej studen CSRF: 737cf34db94a96870325218f639a64f7 User: andrej studen CSRF: 1cc23ba392ff498f2d5bf4d67ffca0a9 User: andrej studen CSRF: 975ab9ea5665016c0e0ce49dcd65780c User: andrej studen CSRF: b6e8ec797131c9fe72726297a42fd2ea User: andrej studen CSRF: 612e0d5eba1a9e940b320696cccb8304 User: andrej studen CSRF: ba12deac50bf69b82cf055e1ac302631 User: andrej studen CSRF: 88b7fdb4814f4442fed7ab3bf3e7f8ae User: andrej studen CSRF: f95cc32b46243554e2e10812215cedb3 User: andrej studen CSRF: dd488484d5d7491dbdb657da60250edf User: andrej studen CSRF: d818269c6dec47ddbbfddd7a3e17cc6c User: andrej studen CSRF: 6b3a468a3d0e5d51ce0c005e369b787b User: andrej studen CSRF: b48ba7a9ab7ea5e261aead00857a39be User: andrej studen CSRF: 61b8cc1a60cc0618d2b4bf1267a0e02a User: andrej studen CSRF: 0b7d3ebc8876a169ef5fc1f92e12412c User: andrej studen CSRF: 8885784efb0b7730dd027c346ca8f6b3 User: andrej studen CSRF: a571c572ba07cf7cc94711b683da847a User: andrej studen CSRF: fc4e4f3db722b9051ced9a134666c439 User: andrej studen CSRF: 90698920c95287d2a20f3898dbf92a75 User: andrej studen CSRF: 403d971e220822a88029f870440efb48 User: andrej studen CSRF: 04b0b7d180538b9939add86ddd02c334 User: andrej studen CSRF: b6ea921009be3be82c0865286b7cc83b User: andrej studen CSRF: 66382f86201d2dbde8cfbea9198991c3 User: andrej studen CSRF: aa8ae1a1f9002224238cddf77b8e02ba User: andrej studen CSRF: 3ddc81c982fa767587710491547c58d8 User: andrej studen CSRF: b78c2f9e29dd8117ef3012c7a7bc7397 User: andrej studen CSRF: 0be6b61aac56c78fec2bd265415e398d
#get fit results
def getPar(fb,project,patientCode,visitCode,ic,ir):
rPath=['processedImages',patientCode,visitCode]
opts={'global':'','IVF':'_IVF'}
fs={x:f'{patientCode}_{visitCode}_{ic}_{ir}{opts[x]}_fitParFinal.txt' for x in opts}
remotePaths={x:fb.formatPathURL(project,'/'.join([*rPath,fs[x]])) for x in opts}
retVal={}
for x in opts:
if not fb.entryExists(remotePaths[x]):
print(f'[{x}] Could not load for {patientCode}/{visitCode} {ic} {ir}')
continue
buffer=fb.readFileToBuffer(remotePaths[x])
val=buffer.getvalue()
xval=val.decode(chardet.detect(val)['encoding'])
xval=re.sub('\n','',xval)
retVal[x]=[float(y) for y in xval.split('\t')]
return retVal
def clear(setup,dataset,qPar):
qFilter=[{'variable':x,'value':'{}'.format(qPar[x]),'oper':'eq'} for x in qPar]
ds=setup['db'].selectRows(setup['project'],'study',dataset,qFilter)
if len(ds['rows'])>0:
ds=setup['db'].modifyRows('delete',setup['project'],'study',dataset,ds['rows'])
def update(setup,dataset,qPar,row,val):
#qFilter=[{'variable':x,'value':'{}'.format(qPar[x]),'oper':'eq'} for x in qPar]
#ds=db.selectRows(project,'study',dataset,qFilter)
try:
debug=setup[dataset]['debug']
except KeyError:
debug=False
if debug:
print(f'qPar: {qPar}')
outRow={x:qPar[x] for x in qPar}
outRow['PatientId']=row['PatientId']
seqNumOffset=setup[dataset]['count']*setup[dataset]['factor']
outRow['SequenceNum']=row['SequenceNum']+seqNumOffset
outRow.update(val)
try:
setup[dataset]['outRows'].append(outRow)
if debug:
print('Adding')
except KeyError:
setup[dataset]['outRows']=[outRow]
if debug:
print('Setting')
setup[dataset]['count']=setup[dataset]['count']+1
c=setup[dataset]['count']
if debug:
x=setup[dataset]['debug']
s=outRow['SequenceNum']
sz=len(setup[dataset]['outRows'])
last=setup[dataset]['outRows'][0]
s1=last['SequenceNum']
print(f'{dataset} count {c} seqNum={s} sz={sz} seqNum(first)={s1}')
def upload(setup,dataset,last=False):
mode='insert'
rows=setup[dataset]['outRows']
n=len(rows)
print(f'Uploading {dataset} with {n} rows')
try:
x=setup[dataset]['debug']
for r in setup[dataset]['outRows']:
print('{} {}'.format(r['PatientId'],r['SequenceNum']))
except KeyError:
pass
if n==setup['modifyBatch'] or last:
x=setup['db'].modifyRows(mode,setup['project'],'study',dataset,rows)
x1=x.decode(chardet.detect(x)['encoding'])
xval=json.loads(x1)
try:
print(xval['exception'])
print(xval)
except KeyError:
pass
setup[dataset]['outRows']=[]
def setGlobalVal(par):
val={}
val['chi2']=par[0]
val['A']=par[1]
val['tau']=par[2]
val['alpha']=par[3]
val['dt']=par[4]
rTau=max(val['tau'],1/val['alpha'])
rAlpha=max(1/val['tau'],val['alpha'])
val['rTau']=rTau
val['rAlpha']=rAlpha
return val
def setCenterVal(par,i):
val={}
val['k1']=par[4*i+5]
val['BVF']=par[4*i+6]
val['k2']=par[4*i+7]
val['dt']=par[4*i+8]
return val
def extractFitParameters():
db=connectDB('labkey-ukc')
fb=connectFB('labkey-ukc')
project='/dynamicSPECT/cardiacSPECT'
dataset='Imaging1'
idFilter={'variable':'PatientId','value':'MB1965','oper':'eq'}
ds=db.selectRows(project,'study',dataset,[idFilter])
rows=ds['rows']
dataset='fitResults'
nc=[10,20,30]
nr=20
debug=True
#expect no more than 1000 entries per visit/id pair
setup={'db':db,'project':project,'modifyBatch':100}
datasets=['globalFitParameters','centerFitParameters']
setup['globalFitParameters']={'count':0,'factor':0.01}
setup['centerFitParameters']={'count':0,'factor':0.0001}
#setup['globalFitParameters']['debug']=True
for r in rows:
qVal=['patientCode','visitCode']
qPar={x:r[x] for x in qVal}
visitCode=r['visitCode']
patientCode=r['patientCode']
for d in datasets:
clear(setup,d,qPar)
setup[d]['count']=0
for ic in nc:
#print(f'[{ic}]')
for ir in range(nr):
#print(f'\t{ir}')
qPar.update({'nc':ic,'realizationId':ir})
dataset='globalFitParameters'
qpar=getPar(fb,project,patientCode,visitCode,ic,ir+1)
qval={x:setGlobalVal(qpar[x]) for x in qpar}
val=qval['global']
val['chi2IVF']=qval['IVF']['chi2']
update(setup,dataset,qPar,r,val)
for i in range(ic):
val=setCenterVal(qpar['IVF'],i)
val['file']=f'{patientCode}_{visitCode}_{ic}_{ir+1}_IVF_centers{i+1}.png'
dataset='centerFitParameters'
qPar1={x:qPar[x] for x in qPar}
qPar1['ic']=i
update(setup,dataset,qPar1,r,val)
# if debug:
# break
val=setGlobalVal(qpar['IVF'])
qPar.update({'nc':0,'realizationId':0})
update(setup,'globalFitParameters',qPar,r,val)
_tmp=[upload(setup,dataset,True) for dataset in datasets]
if debug:
break
extractFitParameters()User: andrej studen CSRF: 2fcf1c21f2bc0fd02e727cc980d41512 User: andrej studen CSRF: ec0ddef0d985b0887827a9c934628186 User: andrej studen CSRF: dc72cad653ea65355b7d9048d3d6914c User: andrej studen CSRF: b3061712c65aae314fa16540f3654af7 Uploading globalFitParameters with 61 rows User: andrej studen CSRF: 156e6545790e1a4be8ff209ab04fad51 Uploading centerFitParameters with 1200 rows User: andrej studen CSRF: 2b82e89d9f8ebfca7563d2473cb4f522