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@@ -30,6 +30,8 @@
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"import matplotlib.pyplot\n",
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"import subprocess\n",
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"import json\n",
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+ "import chardet\n",
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+ "import re\n",
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"\n",
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"import segmentation\n",
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"import importlib\n",
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@@ -58,6 +60,13 @@
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" net.getCSRF()\n",
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" return labkeyDatabaseBrowser.labkeyDB(net)\n",
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"\n",
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+ "def connectFB(server):\n",
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+ " fconfig=configFile(server)\n",
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+ " net=labkeyInterface.labkeyInterface()\n",
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+ " net.init(fconfig)\n",
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+ " net.getCSRF()\n",
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+ " return labkeyFileBrowser.labkeyFileBrowser(net)\n",
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+ "\n",
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"def connectOrthanc(server):\n",
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" fconfig=configFile(server)\n",
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" net=orthancInterface.orthancInterface()\n",
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@@ -72,11 +81,80 @@
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},
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{
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"cell_type": "code",
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- "execution_count": null,
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+ "execution_count": 17,
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"metadata": {},
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- "outputs": [],
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+ "outputs": [
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "User: andrej studen CSRF: 07c44a2191bd67a30f42f1696b4b3fdf\n",
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+ "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']\n",
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+ "SET [10KF/MIR] ID:992c0733-b219b554-7ffbb1eb-e29d0606-63a62c51\n",
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+ "SET [10KF/OBR] ID:8de576d0-e88601c2-5317457b-47705c87-60c15eee\n",
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+ "FAIL [FJ1943/MIR1] @ 20190309 study date not found\n",
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+ "FAIL [FJ1943/OBR1] @ 20190209 study date not found\n",
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+ "SET [FJ1943/MIR2] ID:79bcca93-9a5b01f7-516b7ea0-4e5ff2b1-7a1bdaac\n",
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+ "SET [FJ1943/OBR2] ID:4b1cde0a-72e63430-a9a00264-8861a4cb-a46377cd\n",
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+ "SET [JA1960/OBR1] ID:b6c889de-f8d38668-e7a15a74-c8530db3-08388687\n",
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+ "FAIL [JA1960/MIR1] @ 20210424 study date not found\n",
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+ "SET [JA1960/OBR2] ID:adcd3506-691a5541-220c8aa1-b0f796fb-fa2db1cd\n",
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+ "SET [JA1960/MIR2] ID:84791e18-eefcd3cd-4c16e1ff-eaf2b9b4-ee8051a0\n",
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+ "SET [JD1971/MIR1] ID:6b4eacd2-2fbf8ef0-ee0ee52b-5dc1e26c-0ae36a23\n",
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+ "SET [JD1971/OBR1] ID:18a061b9-db13bed9-90bb43ea-c7f044c4-a86cfd3e\n",
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+ "SET [JD1971/MIR2] ID:8b017f66-1598a87d-1b8a3c3f-fe9f1ed5-0344686a\n",
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+ "SET [JD1971/OBR2] ID:72a6e5cd-0d1cac70-0f38027c-5c1c7d8a-f6eba43b\n",
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+ "SET [JD1973/MIR1] ID:670e9d2a-c1feec4b-99757eaf-997f73e8-8df2742a\n",
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+ "SET [JD1973/OBR1] ID:96c75aa9-0a16ea6e-d080cd60-29ffddf5-ef3c3f05\n",
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+ "SET [JD1973/MIR2] ID:9ae9acd5-5063fedb-0e0d7a72-29f3a951-1ff5fb6d\n",
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+ "SET [JD1973/OBR2] ID:36a0503d-220a1996-fec9b6ff-29de8388-a3cf3788\n",
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+ "SET [JI1943/MIR1] ID:345ed9ec-ec584712-87154bb0-1e6cb5a8-065443eb\n",
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+ "SET [JI1943/OBR1] ID:fb51a384-24bf561a-35bd3f4d-44079037-ab21e16b\n",
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+ "SET [JI1943/MIR2] ID:c52a79f1-da8abfa2-c47c8813-3cbdb1a5-50b6d490\n",
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+ "SET [JI1943/OBR2] ID:49191331-b4b07708-7e89c147-ce200efc-862d5240\n",
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+ "SET [JS1952/MIR1] ID:b473ba96-11f607ca-b79b5f59-230adb5a-f86c8976\n",
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+ "SET [JS1952/OBR1] ID:16e9c945-66d4c9ae-b796827f-4a598413-da10981b\n",
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+ "\t [KA1940/MIR1] @ 20190514 multiple matches: 3\n",
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+ "FAIL [KA1940/MIR1] @ 20190514 no birth year 1940\n",
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+ "\t [KA1940/OBR1] @ 20190513 multiple matches: 3\n",
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+ "FAIL [KA1940/OBR1] @ 20190513 no birth year 1940\n",
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+ "\t [KA1940/MIR2] @ 20210212 multiple matches: 2\n",
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+ "FAIL [KA1940/MIR2] @ 20210212 no birth year 1940\n",
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+ "\t [KA1940/OBR2] @ 20210209 multiple matches: 2\n",
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+ "FAIL [KA1940/OBR2] @ 20210209 no birth year 1940\n",
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+ "SET [MB1965/MIR] ID:b2bdb9c0-076fe14e-7d6481f1-14d4093f-7ca29b91\n",
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+ "SET [MB1965/MIR1] ID:3fe308e8-48fd71e2-0638aba2-dbfc9e6f-4f7d7718\n",
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+ "SET [MB1965/MIR2] ID:dc5d34f2-0fb785a6-d904ba2c-b765fbce-30161f8c\n",
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+ "SET [MI1943/MIR1] ID:36599b2d-35e85e38-5ccd4ce4-73b2fd77-a7dad7be\n",
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+ "SET [MI1943/OBR1] ID:00135c7f-9356e861-74c9704b-f133f38e-f42bf54a\n",
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+ "\t [MI1943/MIR2] @ 20210212 multiple matches: 2\n",
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+ "FAIL [MI1943/MIR2] @ 20210212 no birth year 1943\n",
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+ "\t [MI1943/OBR2] @ 20210209 multiple matches: 2\n",
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+ "FAIL [MI1943/OBR2] @ 20210209 no birth year 1943\n",
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+ "SET [MJ1963/MIR1] ID:7e643a55-34f441fc-de3d779a-9f6e29bf-6e354e21\n",
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+ "SET [MJ1963/OBR1] ID:e619b089-31190797-09b7fa68-3b7ebce5-cb0e342e\n",
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+ "SET [MM/MIR] ID:137d9e53-0e77d03e-55f56fbf-55358d85-f473d2c5\n",
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+ "SET [MM/MIR1] ID:3dd2760f-412cbfba-192c1d12-3832dc3c-321651a5\n",
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+ "SET [MM1936/MIR1] ID:c511a074-bfa73799-5df11a3e-c2ad96e1-a4a8e6de\n",
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+ "SET [MM1936/OBR1] ID:f99216d5-3d3ef44b-2cee1efa-526e0901-b68349dc\n",
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+ "SET [MM1936/MIR2] ID:42bd91bd-20dd2d19-64a6ff77-7bce6317-4bab8aaf\n",
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+ "SET [MM1936/OBR2] ID:8eb39455-6fa76e34-c04349a6-7f3ad1cd-61f0a307\n",
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+ "SET [MM/OBR] ID:07cb4e32-30da5d01-75d7067f-f393540f-432489e1\n",
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+ "SET [MNG1940/OBR1] ID:a9d91056-1388e280-bd6d58df-1ee96555-87441107\n",
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+ "SET [MNG1940/MIR1] ID:ad23f1a4-30388a48-9587d035-a5cfeb34-0e8d5d05\n",
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+ "SET [MNG1940/MIR2] ID:a6df647d-5474750c-67b017d7-e37b85ec-d7e86f39\n",
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+ "SET [MNG1940/OBR2] ID:842443a5-b97d0b03-dda3af69-16089e8b-70b6e87f\n",
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+ "SET [po1982022/MIR] ID:80bb7c25-6e4d4890-f6f3c46e-f0a7bdfd-2be580d2\n",
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+ "SET [pred15052022/MIR] ID:1a759996-7bdd0109-c5e8f833-c6857dfe-84eaed66\n",
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+ "SET [TT1998/MIR] ID:827fad2b-7a4b824f-c68d9e4a-7942961a-b9f1133f\n",
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+ "SET [VV1984/MIR] ID:484d95a5-fe38de02-d377e94b-74c1037d-201f8804\n",
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+ "SET [VV1984/MIR1] ID:1c21ea83-b3721080-f272ac26-f5d5ef73-aa56e160\n"
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+ ]
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+ }
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+ ],
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"source": [
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"#figure out and set studyId from seriesId\n",
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+ "#below - assingOrthancId from date\n",
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"def assignFromSeriesId():\n",
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" db=connectDB('merlin')\n",
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" orthanc=connectOrthanc('merlin')\n",
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@@ -117,56 +195,250 @@
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" \n",
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" \n",
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" \n",
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- "def assignFromDate():\n",
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+ "def assignFromDate(modifyRows=False):\n",
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" db=connectDB('labkey-ukc')\n",
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" orthanc=connectOrthanc('labkey-ukc')\n",
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" project='dynamicSPECT/cardiacSPECT'\n",
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" dataset='Imaging1'\n",
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" oStudies=studyMap(orthanc)\n",
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" ds=db.selectRows(project,'study',dataset,'')\n",
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+ " print('Study date candidates: {}'.format(list(oStudies.keys())))\n",
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" for r in ds['rows']:\n",
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" sid=r['studyOrthancId']\n",
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" patientId=r['patientCode']\n",
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+ " visit=r['visitCode']\n",
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+ " if not patientId:\n",
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+ " patientId=r['PatientId']\n",
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+ " code=f'{patientId}/{visit}'\n",
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+ " \n",
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" if sid:\n",
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- " print(f'{patientId} ID:{sid}')\n",
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+ " print(f'SET [{code}] ID:{sid}')\n",
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" continue\n",
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" sdate=r['imagingDate']\n",
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- " studies=oStudies[sdate]\n",
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+ " try:\n",
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+ " studies=oStudies[sdate]\n",
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+ " except:\n",
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+ " print(f'FAIL [{code}] @ {sdate} study date not found'.format(patientId,sdate))\n",
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+ " continue\n",
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" if len(studies)==1:\n",
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" r['studyOrthancId']=studies[0]\n",
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- " ds=db.modifyRows('update',project,'study',dataset,[r])\n",
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+ " studyId=studies[0]\n",
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+ " print(f'OK [{code}] @ {sdate} found {studyId}')\n",
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+ " if modifyRows:\n",
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+ " ds=db.modifyRows('update',project,'study',dataset,[r])\n",
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" continue\n",
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+ " print(f'\\t [{code}] @ {sdate} multiple matches: {len(studies)}')\n",
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" xm=sortStudies(orthanc,studies,getBirthYear)\n",
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- " bdate=patientId[2:]\n",
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+ " #bdate=patientId[2:]\n",
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+ " #select only numeric glyphs\n",
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+ " bdate=re.sub(r'[^0-9]*','',patientId)\n",
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" #filter on bdate\n",
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- " xmPrime=xm[bdate]\n",
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+ " try:\n",
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+ " xmPrime=xm[bdate]\n",
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+ " except KeyError:\n",
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+ " print(f'FAIL [{code}] @ {sdate} no birth year {bdate}')\n",
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+ " continue\n",
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" #unique solution\n",
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" if len(xmPrime)==1:\n",
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+ " studyId=xmPrime[0]\n",
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+ " print(f'OK [{code}] @ {sdate} match birth year {bdate}: {studyId}')\n",
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" r['studyOrthancId']=xmPrime[0]\n",
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- " ds=db.modifyRows('update',project,'study',dataset,[r])\n",
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+ " if modifyRows:\n",
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+ " ds=db.modifyRows('update',project,'study',dataset,[r])\n",
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" continue\n",
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- " print(xm)\n",
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+ " #print(xm)\n",
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+ " print(f'FAIL [{code}] @ {sdate} birth year {bdate} multiple: {xmPrime}')\n",
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+ " \n",
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" \n",
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" \n",
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- "assignFromDate() "
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+ "assignFromDate(False) "
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]
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},
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{
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"cell_type": "code",
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- "execution_count": 5,
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+ "execution_count": 22,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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- "User: andrej studen CSRF: 7350f9dcc87c17afddc8c65618089763\n",
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- "User: andrej studen CSRF: 7ddb2a798e2815d2cc6344b560e9a8e1\n",
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- "User: andrej studen CSRF: 523db9b5e52a7a6c294b36d8e86b81d4\n"
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+ "User: andrej studen CSRF: a675486ae1b1befbc6ebd792df3a8c17\n",
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+ "SET [10KF/MIR @ 20190514]\n",
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+ "SET [10KF/OBR @ 20190513]\n",
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+ "FAIL [FJ1943/MIR1 @ 20190309]: no study id set, run assignFromDate()!\n",
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+ "FAIL [FJ1943/OBR1 @ 20190209]: no study id set, run assignFromDate()!\n",
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+ "SET [FJ1943/MIR2 @ 20210202]\n",
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+ "SET [FJ1943/OBR2 @ 20210203]\n",
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+ "[JA1960/OBR1 @ 20210421]\n",
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+ "\tCT: OK ID: b79ee29f-dc4aaa68-78f4ad43-e678e11e-a520fcaf\n",
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+ "\tNM(Raw) ID: 17187242-e96a62d6-0c34ea12-3b80d992-e4a0db30\n",
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+ "\tNM(Img) ID: 4fe75631-dc32fbaf-c4f52623-faecfd73-f53ee029\n",
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+ "User: andrej studen CSRF: d3796bb7537fd6b9462c460bcbd3a845\n",
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+ "FAIL [JA1960/MIR1 @ 20210424]: no study id set, run assignFromDate()!\n",
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+ "[JA1960/OBR2 @ 20220215]\n",
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+ "\tCT: OK ID: cba7385d-7aaef4ed-f21155f5-db0e55b6-ac29dea3\n",
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+ "\tNM(Raw) ID: 9e2e18d0-2799979f-d5794737-df61f83d-f0e8a8b4\n",
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+ "\tNM(Img) ID: 70538040-5c662ab7-b11e2052-19e04c62-72b68967\n",
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+ "User: andrej studen CSRF: 79cbd15f916c74e6ea58631348b4d08c\n",
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+ "[JA1960/MIR2 @ 20220217]\n",
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+ "\tCT: OK ID: 15ee88ea-35773b56-a6e864f7-c46f49a9-d1421f36\n",
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+ "\tNM(Raw) ID: 0db18702-1dd7c0c2-866eade8-74f5ee30-79a12dcf\n",
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+ "\tNM(Img) ID: 7edd0445-ae06d9c5-268a1182-3a814255-1882fab3\n",
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+ "User: andrej studen CSRF: c81de448540579af2ac305cb0b33431d\n",
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+ "[JD1971/MIR1 @ 20190903]\n",
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+ "\tCT: OK ID: 03d06718-724bfb17-3d181862-9d123117-e598f3ea\n",
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+ "\tNM(Raw) ID: 0de1d1d2-8710b71d-99cb9d3e-1c64c5db-5a2b495c\n",
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+ "\tNM(Img) ID: 690aa1c8-3db59555-b270e771-ba6c1992-e7c647c5\n",
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+ "User: andrej studen CSRF: 0c096074f992403819bce555a2b22b65\n",
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+ "[JD1971/OBR1 @ 20190902]\n",
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+ "\tCT: OK ID: afc725ba-c818c7b9-9843a39a-09905a44-e0b69f84\n",
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+ "\tNM(Raw) ID: 6e346b85-2d5b0b13-ceedd23e-abaa46a6-5b4f6ce1\n",
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+ "\tNM(Img) ID: 1a5192ca-23ebfcb5-3d2603c7-fade6633-7d427fb6\n",
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+ "User: andrej studen CSRF: 85164cfa4c40f7f22f334cc37fd7242a\n",
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+ "[JD1971/MIR2 @ 20210219]\n",
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+ "\tCT: OK ID: d8f06cb7-89f01c5d-46a69d6b-ba8c653a-d0060e1a\n",
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+ "\tNM(Raw) ID: 01ef80c4-7ae0ab2c-230cb908-b8ddaf68-5b864a2b\n",
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+ "\tNM(Img) ID: 41e870de-06479edc-d5a43f4b-0b5440cd-79c4b6bf\n",
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+ "User: andrej studen CSRF: 8b992a30d78fd3c98a54e747251ccee7\n",
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+ "[JD1971/OBR2 @ 20210216]\n",
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+ "\tCT: OK ID: 8acdda24-6d4cff97-eaaca89c-17c05b93-8be78bce\n",
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+ "\tNM(Raw) ID: 35b070a6-3f8b472c-cf186ca5-fcc35602-7ac7854c\n",
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+ "\tNM(Img) ID: eda3927f-eeced313-105b4088-7955765a-e0111caf\n",
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+ "User: andrej studen CSRF: 41b65d29b560745614cb4a1bbc8bfd02\n",
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+ "[JD1973/MIR1 @ 20210423]\n",
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+ "\tCT: OK ID: 9367d757-0a93c89b-f29c2c44-a81cd459-25562726\n",
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+ "\tNM(Raw) ID: 7d79ab8a-162aaad3-c85a0b83-213e4fcc-21d2815a\n",
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+ "\tNM(Img) ID: ecfd3162-665fa458-13889f24-4b10a77b-bbf6efa0\n",
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|
|
+ "User: andrej studen CSRF: afb2b28b35aae2ae2b74b8a398fd4a62\n",
|
|
|
+ "[JD1973/OBR1 @ 20210421]\n",
|
|
|
+ "\tCT: OK ID: 21f02bd0-7883466c-5cee4cf4-ac1762df-309fec00\n",
|
|
|
+ "\tNM(Raw) ID: b4f36691-ff2b4acf-4ed9b04f-60bf102f-2dfcc532\n",
|
|
|
+ "\tNM(Img) ID: 81b23560-456462a5-229f9508-3fbd7067-da170abd\n",
|
|
|
+ "User: andrej studen CSRF: d0532d3451546a886e74edbe3ee0eea9\n",
|
|
|
+ "[JD1973/MIR2 @ 20220708]\n",
|
|
|
+ "\tCT: OK ID: b5db5dcd-73ffb6a2-30e388d4-a8703df5-390c6e40\n",
|
|
|
+ "\tNM(Raw) ID: d2ad0b63-62409b0b-fd8a70b9-f71b805f-2f39f3fc\n",
|
|
|
+ "\tNM(Img) ID: 3429be0f-f3824fd6-57426475-6bf47ed9-d75e4e0c\n",
|
|
|
+ "User: andrej studen CSRF: 1e581bef379eee356c6d71654d57276f\n",
|
|
|
+ "[JD1973/OBR2 @ 20220706]\n",
|
|
|
+ "\tCT: OK ID: 7c79efa9-28523e0f-f897a8e9-63742b78-a26d0ff8\n",
|
|
|
+ "\tNM(Raw) ID: fa97be07-7a806101-44f7079d-e1a3381e-89854f27\n",
|
|
|
+ "\tNM(Img) ID: 39c7ae58-862bb23d-33c7e05e-d6587450-cabf15b2\n",
|
|
|
+ "User: andrej studen CSRF: 79875757c2656056293b51379e09b07d\n",
|
|
|
+ "[JI1943/MIR1 @ 20200618]\n",
|
|
|
+ "\tCT: OK ID: 683e9555-b9b6e5fd-d06f5521-5adf12d5-ed85ced2\n",
|
|
|
+ "\tNM(Raw) ID: f7b2bed3-c38a9600-e1bf5b01-cf2e4c70-4a4ab823\n",
|
|
|
+ "\tNM(Img) ID: af15224b-2dc57712-f324695c-a50547e2-34e72e62\n",
|
|
|
+ "User: andrej studen CSRF: 71c60846321c8033056406a1eb4d3d9f\n",
|
|
|
+ "[JI1943/OBR1 @ 20200619]\n",
|
|
|
+ "\tCT: OK ID: 9a78e8d8-df2fa3e7-02ba6d08-0fdbe51b-0e4246e9\n",
|
|
|
+ "\tNM(Raw) ID: a9caf516-a38c8fe1-90ea7ee2-52ce3de8-77615243\n",
|
|
|
+ "\tNM(Img) ID: 5bd63e93-651a5d1d-40076934-05cb0421-5c01d74d\n",
|
|
|
+ "User: andrej studen CSRF: c0eec3718396480bb81e2379fe9244dc\n",
|
|
|
+ "[JI1943/MIR2 @ 20210528]\n",
|
|
|
+ "\tCT: OK ID: 773f9a42-dbdf8b4c-4ab0f808-b96be60d-a1084b63\n",
|
|
|
+ "\tNM(Raw) ID: 933a27de-057d0e80-eb78afdb-739d3d16-31c125b9\n",
|
|
|
+ "\tNM(Img) ID: 002ebf3c-3adb4ae0-728daeb5-7acce400-5362b1fa\n",
|
|
|
+ "User: andrej studen CSRF: f3c4798a3ed8106e0339e88434bf30c8\n",
|
|
|
+ "[JI1943/OBR2 @ 20210526]\n",
|
|
|
+ "\tCT: OK ID: 03ff48ce-2bb5a42e-73d6b709-3ac1a875-b521e3c0\n",
|
|
|
+ "\tNM(Raw) ID: 81a0661b-5e7c27d5-29c1288f-ca47451c-c83443ce\n",
|
|
|
+ "\tNM(Img) ID: 056c3249-f132228b-68f39184-fd310fff-01cb4360\n",
|
|
|
+ "User: andrej studen CSRF: a2749828b4d77def4689100c17829549\n",
|
|
|
+ "[JS1952/MIR1 @ 20190514]\n",
|
|
|
+ "\tCT: OK ID: 19f99b32-8d92b846-8865eeb2-7678b004-93bd4e76\n",
|
|
|
+ "\tNM(Raw) ID: 87e86b89-ee314eb1-a95228f5-c3587c3b-b8016f52\n",
|
|
|
+ "\tNM(Img) ID: 62bd627d-7e7b5824-b3b2bcb7-2493055f-1053d74e\n",
|
|
|
+ "User: andrej studen CSRF: 2ce0ddc27763a76e44fb8393e6ced1ad\n",
|
|
|
+ "[JS1952/OBR1 @ 20190513]\n",
|
|
|
+ "\tCT: OK ID: b5b39140-58a11dbb-29f762ea-74eb5eee-babe1c29\n",
|
|
|
+ "\tNM(Raw) ID: 9cefe25d-4c8ea4eb-33b38501-3386729f-11a434fd\n",
|
|
|
+ "\tNM(Img) ID: ea75ac15-b48d4c11-7088a758-95f5a5e3-e5cec172\n",
|
|
|
+ "User: andrej studen CSRF: c000d67775020e76aa21d2de55ddea11\n",
|
|
|
+ "FAIL [KA1940/MIR1 @ 20190514]: no study id set, run assignFromDate()!\n",
|
|
|
+ "FAIL [KA1940/OBR1 @ 20190513]: no study id set, run assignFromDate()!\n",
|
|
|
+ "FAIL [KA1940/MIR2 @ 20210212]: no study id set, run assignFromDate()!\n",
|
|
|
+ "FAIL [KA1940/OBR2 @ 20210209]: no study id set, run assignFromDate()!\n",
|
|
|
+ "SET [MB1965/MIR @ 20220512]\n",
|
|
|
+ "SET [MB1965/MIR1 @ 20220819]\n",
|
|
|
+ "SET [MB1965/MIR2 @ 20221129]\n",
|
|
|
+ "[MI1943/MIR1 @ 20190326]\n",
|
|
|
+ "\tCT: OK ID: 3cec3099-d6a5aa2c-80ceefa4-b2f24b5f-5914695d\n",
|
|
|
+ "\tNM(Raw) ID: 1264c701-cf0be371-9c0639e0-9d3b1087-954bad3c\n",
|
|
|
+ "\tNM(Img) ID: f4d20c35-856f0cbb-dd925c5b-869f392a-9cfd359e\n",
|
|
|
+ "User: andrej studen CSRF: 583cdc2d38f1a2f1c54624e9f48a1a4b\n",
|
|
|
+ "[MI1943/OBR1 @ 20190327]\n",
|
|
|
+ "\tCT: OK ID: 3efeff50-bf7eb655-ee08824d-7b63792a-457fedd4\n",
|
|
|
+ "\tNM(Raw) ID: 0e722805-ecf04f38-ca9d0ac2-01e1d87e-cbea14ea\n",
|
|
|
+ "\tNM(Img) ID: b6322734-d5efec5a-300525ab-975bc0b1-5718c7eb\n",
|
|
|
+ "User: andrej studen CSRF: b8bd58a36daae5d165dd78e0d48f5f62\n",
|
|
|
+ "FAIL [MI1943/MIR2 @ 20210212]: no study id set, run assignFromDate()!\n",
|
|
|
+ "FAIL [MI1943/OBR2 @ 20210209]: no study id set, run assignFromDate()!\n",
|
|
|
+ "[MJ1963/MIR1 @ 20200304]\n",
|
|
|
+ "\tCT: OK ID: 39aa62d1-dcbe7247-5cd23dac-6067bfc3-0e9e974e\n",
|
|
|
+ "\tNM(Raw) ID: 17f28587-fcac56f2-a1747c7b-9e3e3a9d-b85ea454\n",
|
|
|
+ "\tNM(Img) ID: dad69a7e-96ab9c71-c653230f-ac6ca06f-6ebbcf70\n",
|
|
|
+ "User: andrej studen CSRF: 02f342665ba2523c5df64be20dfbb17a\n",
|
|
|
+ "[MJ1963/OBR1 @ 20200305]\n",
|
|
|
+ "\tCT: OK ID: 0047a1c3-6cdc3d79-8692a0cd-c3e23862-b0069561\n",
|
|
|
+ "\tNM(Raw) ID: fe979a39-696e2e65-3c012807-8ba9818a-b26523a7\n",
|
|
|
+ "\tNM(Img) ID: 133f8b65-8e1ca210-270c9259-b4244ad0-452fa07d\n",
|
|
|
+ "User: andrej studen CSRF: d93fe40483a9f916bfe0946d40706e71\n",
|
|
|
+ "SET [MM/MIR @ 20220819]\n",
|
|
|
+ "SET [MM/MIR1 @ 20221129]\n",
|
|
|
+ "[MM1936/MIR1 @ 20190827]\n",
|
|
|
+ "\tCT: OK ID: 74b2a919-5fc51491-34f4276c-7daae0cc-269dd4ac\n",
|
|
|
+ "\tNM(Raw) ID: 4746b129-56061f7b-e5ecbe6c-9cbac5ba-fd6ee400\n",
|
|
|
+ "\tNM(Img) ID: c671017b-58898e0d-9aa6950e-7f31fbbb-9466a85a\n",
|
|
|
+ "User: andrej studen CSRF: ba46f35b592cc78b0a851ee032028060\n",
|
|
|
+ "[MM1936/OBR1 @ 20190826]\n",
|
|
|
+ "\tCT: OK ID: ff84df5d-695eb992-b80ab669-e5329506-cfadf3dd\n",
|
|
|
+ "\tNM(Raw) ID: 173fd06d-ffc44f86-c47084b9-5888612b-ab9c430a\n",
|
|
|
+ "\tNM(Img) ID: f5f31de2-968e183c-f4e6ef8d-59b09f8b-f55e6d24\n",
|
|
|
+ "User: andrej studen CSRF: b177ccb2d217743ad3fe57cbd3c2f6c9\n",
|
|
|
+ "[MM1936/MIR2 @ 20210521]\n",
|
|
|
+ "\tCT: OK ID: f94eda1b-adff3b63-2fc2a467-b88f79fa-15925c64\n",
|
|
|
+ "\tNM(Raw) ID: 5a537e00-ca99bc11-6b0db820-fadfd1ab-76f3f712\n",
|
|
|
+ "\tNM(Img) ID: 7706d5ae-9c0ca196-6bf786f0-1fccd37b-e9463de6\n",
|
|
|
+ "User: andrej studen CSRF: 73a0e916d395710fc82c3742860227bc\n",
|
|
|
+ "[MM1936/OBR2 @ 20210519]\n",
|
|
|
+ "\tCT: OK ID: 61cb4866-fd57c584-9bffa6ad-30382fc8-7598b317\n",
|
|
|
+ "\tNM(Raw) ID: a39cc437-bb66f647-0f820a25-e5110ff0-41414aba\n",
|
|
|
+ "\tNM(Img) ID: e42d465b-86a6222e-29ce1948-a22a6757-ed346ab5\n",
|
|
|
+ "User: andrej studen CSRF: 460b41c11fd660124a7de2f2d9c9eca2\n",
|
|
|
+ "SET [MM/OBR @ 20221206]\n",
|
|
|
+ "[MNG1940/OBR1 @ 20210421]\n",
|
|
|
+ "\tCT: OK ID: f32c172a-80b7f813-35ba3566-26d3acc2-82e016c8\n",
|
|
|
+ "\tNM(Raw) ID: 8b9e1175-e2cff1a3-1314ac58-50e8ba3d-59171f28\n",
|
|
|
+ "\tNM(Img) ID: 7be9bde7-6ee5f88f-3310c821-14733f77-346555b0\n",
|
|
|
+ "User: andrej studen CSRF: 5add02fab1cda2e6478b7037e1c76a6b\n",
|
|
|
+ "[MNG1940/MIR1 @ 20210423]\n",
|
|
|
+ "\tCT: OK ID: beb26f2d-67e874f6-8d4c2d07-0ea23e21-b68c437e\n",
|
|
|
+ "\tNM(Raw) ID: 286de30e-663ca5d9-2507026e-345d2b82-0cff87cf\n",
|
|
|
+ "\tNM(Img) ID: 3d26bdf4-96f7ae44-dd977c3b-f7721f77-271093df\n",
|
|
|
+ "User: andrej studen CSRF: d3d8dc0fc56c658b20289e6b6aa50ec6\n",
|
|
|
+ "[MNG1940/MIR2 @ 20220217]\n",
|
|
|
+ "\tCT: OK ID: 8edfbe5a-a4d171d2-9eae5b2b-bb3c92c7-e2fd3fc7\n",
|
|
|
+ "\tNM(Raw) ID: 945da723-e1b2eeca-1ff0af60-cd733123-94a1c135\n",
|
|
|
+ "\tNM(Img) ID: bf1c4f2d-72ce38bc-a77e0452-ca4b7079-a8dac61f\n",
|
|
|
+ "User: andrej studen CSRF: 813eae5a892bb0669baa1cde2f490754\n",
|
|
|
+ "[MNG1940/OBR2 @ 20220215]\n",
|
|
|
+ "\tCT: OK ID: b836c90f-85cab249-d7c5fdb0-e3475e53-1d069753\n",
|
|
|
+ "\tNM(Raw) ID: 0cc948ad-7856ba90-0c5f755b-8d58a5b8-62e32258\n",
|
|
|
+ "\tNM(Img) ID: b7b7764e-5290b3bd-79b18d47-4320e153-e44b0932\n",
|
|
|
+ "User: andrej studen CSRF: 073bad98ab82533d8232c3138ea4bff1\n",
|
|
|
+ "SET [po1982022/MIR @ 20220819]\n",
|
|
|
+ "SET [pred15052022/MIR @ 20220512]\n",
|
|
|
+ "SET [TT1998/MIR @ 20230830]\n",
|
|
|
+ "SET [VV1984/MIR @ 20230515]\n",
|
|
|
+ "SET [VV1984/MIR1 @ 20230830]\n"
|
|
|
]
|
|
|
}
|
|
|
],
|
|
|
"source": [
|
|
|
+ "#get series for data with study set\n",
|
|
|
+ "\n",
|
|
|
"def isCT(orthanc,sedata):\n",
|
|
|
" #base criteria - is CT and SeriesDescription contains AC\n",
|
|
|
" mtags=sedata['MainDicomTags']\n",
|
|
|
@@ -214,14 +486,23 @@
|
|
|
" return True\n",
|
|
|
" \n",
|
|
|
"\n",
|
|
|
- "def getSeries():\n",
|
|
|
+ "def setSeries(modifyRows=False):\n",
|
|
|
" db=connectDB('labkey-ukc')\n",
|
|
|
" orthanc=connectOrthanc('labkey-ukc')\n",
|
|
|
" project='dynamicSPECT/cardiacSPECT'\n",
|
|
|
" dataset='Imaging1'\n",
|
|
|
" ds=db.selectRows(project,'study',dataset,'')\n",
|
|
|
" for r in ds['rows']:\n",
|
|
|
+ " patientId=r['PatientId']\n",
|
|
|
+ " visit=r['visitCode']\n",
|
|
|
+ " sdate=r['imagingDate']\n",
|
|
|
+ " code=f'[{patientId}/{visit} @ {sdate}]'\n",
|
|
|
+ " \n",
|
|
|
" if r['nmMasterOrthancId']:\n",
|
|
|
+ " print(f'SET {code}')\n",
|
|
|
+ " continue\n",
|
|
|
+ " if not r['studyOrthancId']:\n",
|
|
|
+ " print(f'FAIL {code}: no study id set, run assignFromDate()!')\n",
|
|
|
" continue\n",
|
|
|
" series=orthanc.getStudyData(r['studyOrthancId'])['Series']\n",
|
|
|
" for s in series:\n",
|
|
|
@@ -240,9 +521,27 @@
|
|
|
" \n",
|
|
|
" #print(sedata)\n",
|
|
|
" #break\n",
|
|
|
- " ds=db.modifyRows('update',project,'study',dataset,[r])\n",
|
|
|
+ " print(f'{code}')\n",
|
|
|
+ " if r['ctOrthancId']:\n",
|
|
|
+ " x=r['ctOrthancId']\n",
|
|
|
+ " print(f'\\tCT: OK ID: {x}')\n",
|
|
|
+ " else:\n",
|
|
|
+ " print(f'\\tCT: FAIL')\n",
|
|
|
+ " if r['nmMasterOrthancId']:\n",
|
|
|
+ " x=r['nmMasterOrthancId']\n",
|
|
|
+ " print(f'\\tNM(Raw) ID: {x}')\n",
|
|
|
+ " else:\n",
|
|
|
+ " print(f'\\tNM(Raw) FAILED')\n",
|
|
|
+ " if r['nmCorrDataOrthancId']:\n",
|
|
|
+ " x=r['nmCorrDataOrthancId']\n",
|
|
|
+ " print(f'\\tNM(Img) ID: {x}')\n",
|
|
|
+ " else:\n",
|
|
|
+ " print(f'\\tNM(Img) FAILED')\n",
|
|
|
+ " \n",
|
|
|
+ " if modifyRows:\n",
|
|
|
+ " ds=db.modifyRows('update',project,'study',dataset,[r])\n",
|
|
|
" #break\n",
|
|
|
- "getSeries() \n",
|
|
|
+ "setSeries(True) \n",
|
|
|
" "
|
|
|
]
|
|
|
},
|
|
|
@@ -704,6 +1003,317 @@
|
|
|
},
|
|
|
{
|
|
|
"cell_type": "code",
|
|
|
+ "execution_count": 10,
|
|
|
+ "metadata": {},
|
|
|
+ "outputs": [
|
|
|
+ {
|
|
|
+ "name": "stdout",
|
|
|
+ "output_type": "stream",
|
|
|
+ "text": [
|
|
|
+ "User: andrej studen CSRF: e8d8f790b143dd4457ee6213d8ea11e6\n",
|
|
|
+ "User: andrej studen CSRF: 8af4603306dd5888f96e038b676b86dc\n",
|
|
|
+ "MB1965_MIR_CT.nrrd\n",
|
|
|
+ "MB1965_MIR1_CT.nrrd\n",
|
|
|
+ "MB1965_MIR2_CT.nrrd\n",
|
|
|
+ "MM_MIR1_CT.nrrd\n",
|
|
|
+ "TT1998_MIR_CT.nrrd\n",
|
|
|
+ "VV1984_MIR_CT.nrrd\n",
|
|
|
+ "VV1984_MIR1_CT.nrrd\n"
|
|
|
+ ]
|
|
|
+ }
|
|
|
+ ],
|
|
|
+ "source": [
|
|
|
+ "#check for converted NRRD files\n",
|
|
|
+ "def checkNRRD():\n",
|
|
|
+ " db=connectDB('labkey-ukc')\n",
|
|
|
+ " fb=connectFB('labkey-ukc')\n",
|
|
|
+ " project='dynamicSPECT/cardiacSPECT'\n",
|
|
|
+ " schema='study'\n",
|
|
|
+ " dataset='Imaging1'\n",
|
|
|
+ " ds=db.selectRows(project,schema,dataset,[])\n",
|
|
|
+ " for r in ds['rows']:\n",
|
|
|
+ " #print(r)\n",
|
|
|
+ " fDir='processedImages'\n",
|
|
|
+ " fDir=[fDir,r['PatientId'],r['visitCode']]\n",
|
|
|
+ " fNameCT='{}_{}_CT.nrrd'.format(r['PatientId'],r['visitCode'])\n",
|
|
|
+ " fNameSPECTCT='{}_{}_Volume19.nrrd'.format(r['PatientId'],r['visitCode'])\n",
|
|
|
+ " \n",
|
|
|
+ " fRemoteDir=fb.buildPathURL(project,fDir)\n",
|
|
|
+ " fURL='/'.join([fRemoteDir,fName])\n",
|
|
|
+ " if fb.entryExists(fURL):\n",
|
|
|
+ " print(fName)\n",
|
|
|
+ " #row={x:r[x] for x in ['PatientId','visitCode']}\n",
|
|
|
+ " \n",
|
|
|
+ "\n",
|
|
|
+ "checkNRRD()\n"
|
|
|
+ ]
|
|
|
+ },
|
|
|
+ {
|
|
|
+ "cell_type": "code",
|
|
|
+ "execution_count": 2,
|
|
|
+ "metadata": {},
|
|
|
+ "outputs": [
|
|
|
+ {
|
|
|
+ "name": "stdout",
|
|
|
+ "output_type": "stream",
|
|
|
+ "text": [
|
|
|
+ "User: andrej studen CSRF: 2b647191df95dff06e7a0c2fca6d8cfc\n",
|
|
|
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+ ]
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+ }
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+ ],
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+ "source": [
|
|
|
+ "#calculate k1 in units of ml/g*min\n",
|
|
|
+ "def convertToMinutes():\n",
|
|
|
+ " db=connectDB('labkey-ukc')\n",
|
|
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+ " project='/dynamicSPECT/cardiacSPECT'\n",
|
|
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+ " dataset='Summary'\n",
|
|
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+ " ds=db.selectRows(project,'study',dataset,'')\n",
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|
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+ " rows=ds['rows']\n",
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|
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+ " for r in rows:\n",
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+ " k1=r['mean']\n",
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+ " k1p=60*r['mean']\n",
|
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+ " r['k1']=k1p\n",
|
|
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+ " db.modifyRows('update',project,'study',dataset,[r])\n",
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+ " \n",
|
|
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+ "convertToMinutes()"
|
|
|
+ ]
|
|
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+ },
|
|
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+ {
|
|
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+ "cell_type": "code",
|
|
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+ "execution_count": 14,
|
|
|
+ "metadata": {},
|
|
|
+ "outputs": [
|
|
|
+ {
|
|
|
+ "name": "stdout",
|
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+ "output_type": "stream",
|
|
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+ "text": [
|
|
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+ "User: andrej studen CSRF: 2fcf1c21f2bc0fd02e727cc980d41512\n",
|
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+ "User: andrej studen CSRF: ec0ddef0d985b0887827a9c934628186\n",
|
|
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+ "User: andrej studen CSRF: dc72cad653ea65355b7d9048d3d6914c\n",
|
|
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+ "User: andrej studen CSRF: b3061712c65aae314fa16540f3654af7\n",
|
|
|
+ "Uploading globalFitParameters with 61 rows\n",
|
|
|
+ "User: andrej studen CSRF: 156e6545790e1a4be8ff209ab04fad51\n",
|
|
|
+ "Uploading centerFitParameters with 1200 rows\n",
|
|
|
+ "User: andrej studen CSRF: 2b82e89d9f8ebfca7563d2473cb4f522\n"
|
|
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+ ]
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+ }
|
|
|
+ ],
|
|
|
+ "source": [
|
|
|
+ "#get fit results\n",
|
|
|
+ "\n",
|
|
|
+ "def getPar(fb,project,patientCode,visitCode,ic,ir):\n",
|
|
|
+ " rPath=['processedImages',patientCode,visitCode]\n",
|
|
|
+ " opts={'global':'','IVF':'_IVF'}\n",
|
|
|
+ " fs={x:f'{patientCode}_{visitCode}_{ic}_{ir}{opts[x]}_fitParFinal.txt' for x in opts}\n",
|
|
|
+ " remotePaths={x:fb.formatPathURL(project,'/'.join([*rPath,fs[x]])) for x in opts}\n",
|
|
|
+ " retVal={}\n",
|
|
|
+ " for x in opts:\n",
|
|
|
+ " if not fb.entryExists(remotePaths[x]):\n",
|
|
|
+ " print(f'[{x}] Could not load for {patientCode}/{visitCode} {ic} {ir}')\n",
|
|
|
+ " continue\n",
|
|
|
+ " \n",
|
|
|
+ " buffer=fb.readFileToBuffer(remotePaths[x])\n",
|
|
|
+ " val=buffer.getvalue()\n",
|
|
|
+ " xval=val.decode(chardet.detect(val)['encoding'])\n",
|
|
|
+ " xval=re.sub('\\n','',xval)\n",
|
|
|
+ " retVal[x]=[float(y) for y in xval.split('\\t')]\n",
|
|
|
+ " return retVal\n",
|
|
|
+ "\n",
|
|
|
+ "def clear(setup,dataset,qPar):\n",
|
|
|
+ " qFilter=[{'variable':x,'value':'{}'.format(qPar[x]),'oper':'eq'} for x in qPar]\n",
|
|
|
+ " ds=setup['db'].selectRows(setup['project'],'study',dataset,qFilter)\n",
|
|
|
+ " if len(ds['rows'])>0:\n",
|
|
|
+ " ds=setup['db'].modifyRows('delete',setup['project'],'study',dataset,ds['rows'])\n",
|
|
|
+ "\n",
|
|
|
+ "def update(setup,dataset,qPar,row,val):\n",
|
|
|
+ " #qFilter=[{'variable':x,'value':'{}'.format(qPar[x]),'oper':'eq'} for x in qPar]\n",
|
|
|
+ " #ds=db.selectRows(project,'study',dataset,qFilter)\n",
|
|
|
+ " \n",
|
|
|
+ " try:\n",
|
|
|
+ " debug=setup[dataset]['debug']\n",
|
|
|
+ " except KeyError:\n",
|
|
|
+ " debug=False\n",
|
|
|
+ " if debug:\n",
|
|
|
+ " print(f'qPar: {qPar}')\n",
|
|
|
+ " outRow={x:qPar[x] for x in qPar}\n",
|
|
|
+ " outRow['PatientId']=row['PatientId']\n",
|
|
|
+ " seqNumOffset=setup[dataset]['count']*setup[dataset]['factor']\n",
|
|
|
+ " outRow['SequenceNum']=row['SequenceNum']+seqNumOffset\n",
|
|
|
+ " outRow.update(val)\n",
|
|
|
+ " \n",
|
|
|
+ " try:\n",
|
|
|
+ " setup[dataset]['outRows'].append(outRow)\n",
|
|
|
+ " if debug:\n",
|
|
|
+ " print('Adding')\n",
|
|
|
+ " except KeyError:\n",
|
|
|
+ " setup[dataset]['outRows']=[outRow]\n",
|
|
|
+ " if debug:\n",
|
|
|
+ " print('Setting')\n",
|
|
|
+ " \n",
|
|
|
+ " setup[dataset]['count']=setup[dataset]['count']+1\n",
|
|
|
+ " c=setup[dataset]['count']\n",
|
|
|
+ " if debug:\n",
|
|
|
+ " x=setup[dataset]['debug']\n",
|
|
|
+ " s=outRow['SequenceNum']\n",
|
|
|
+ " sz=len(setup[dataset]['outRows'])\n",
|
|
|
+ " last=setup[dataset]['outRows'][0]\n",
|
|
|
+ " s1=last['SequenceNum']\n",
|
|
|
+ " print(f'{dataset} count {c} seqNum={s} sz={sz} seqNum(first)={s1}')\n",
|
|
|
+ "\n",
|
|
|
+ " \n",
|
|
|
+ "def upload(setup,dataset,last=False):\n",
|
|
|
+ " mode='insert'\n",
|
|
|
+ " rows=setup[dataset]['outRows']\n",
|
|
|
+ " n=len(rows)\n",
|
|
|
+ " print(f'Uploading {dataset} with {n} rows')\n",
|
|
|
+ " try:\n",
|
|
|
+ " x=setup[dataset]['debug']\n",
|
|
|
+ " for r in setup[dataset]['outRows']:\n",
|
|
|
+ " print('{} {}'.format(r['PatientId'],r['SequenceNum']))\n",
|
|
|
+ " except KeyError:\n",
|
|
|
+ " pass\n",
|
|
|
+ " if n==setup['modifyBatch'] or last:\n",
|
|
|
+ " x=setup['db'].modifyRows(mode,setup['project'],'study',dataset,rows)\n",
|
|
|
+ " x1=x.decode(chardet.detect(x)['encoding'])\n",
|
|
|
+ " xval=json.loads(x1)\n",
|
|
|
+ " try:\n",
|
|
|
+ " print(xval['exception'])\n",
|
|
|
+ " print(xval)\n",
|
|
|
+ " except KeyError:\n",
|
|
|
+ " pass\n",
|
|
|
+ " \n",
|
|
|
+ " setup[dataset]['outRows']=[]\n",
|
|
|
+ "\n",
|
|
|
+ "def setGlobalVal(par):\n",
|
|
|
+ " val={}\n",
|
|
|
+ " val['chi2']=par[0]\n",
|
|
|
+ " val['A']=par[1]\n",
|
|
|
+ " val['tau']=par[2]\n",
|
|
|
+ " val['alpha']=par[3]\n",
|
|
|
+ " val['dt']=par[4]\n",
|
|
|
+ " rTau=max(val['tau'],1/val['alpha'])\n",
|
|
|
+ " rAlpha=max(1/val['tau'],val['alpha'])\n",
|
|
|
+ " val['rTau']=rTau\n",
|
|
|
+ " val['rAlpha']=rAlpha\n",
|
|
|
+ " return val\n",
|
|
|
+ "\n",
|
|
|
+ "def setCenterVal(par,i):\n",
|
|
|
+ " val={}\n",
|
|
|
+ " val['k1']=par[4*i+5]\n",
|
|
|
+ " val['BVF']=par[4*i+6]\n",
|
|
|
+ " val['k2']=par[4*i+7]\n",
|
|
|
+ " val['dt']=par[4*i+8]\n",
|
|
|
+ " return val\n",
|
|
|
+ "\n",
|
|
|
+ "\n",
|
|
|
+ "def extractFitParameters():\n",
|
|
|
+ " db=connectDB('labkey-ukc')\n",
|
|
|
+ " fb=connectFB('labkey-ukc')\n",
|
|
|
+ " project='/dynamicSPECT/cardiacSPECT'\n",
|
|
|
+ " dataset='Imaging1'\n",
|
|
|
+ " idFilter={'variable':'PatientId','value':'MB1965','oper':'eq'}\n",
|
|
|
+ " ds=db.selectRows(project,'study',dataset,[idFilter])\n",
|
|
|
+ " rows=ds['rows']\n",
|
|
|
+ " dataset='fitResults'\n",
|
|
|
+ " nc=[10,20,30]\n",
|
|
|
+ " nr=20\n",
|
|
|
+ " debug=True\n",
|
|
|
+ " #expect no more than 1000 entries per visit/id pair\n",
|
|
|
+ " setup={'db':db,'project':project,'modifyBatch':100}\n",
|
|
|
+ " datasets=['globalFitParameters','centerFitParameters']\n",
|
|
|
+ " setup['globalFitParameters']={'count':0,'factor':0.01}\n",
|
|
|
+ " setup['centerFitParameters']={'count':0,'factor':0.0001}\n",
|
|
|
+ " #setup['globalFitParameters']['debug']=True\n",
|
|
|
+ " for r in rows:\n",
|
|
|
+ " qVal=['patientCode','visitCode']\n",
|
|
|
+ " qPar={x:r[x] for x in qVal}\n",
|
|
|
+ " visitCode=r['visitCode']\n",
|
|
|
+ " patientCode=r['patientCode']\n",
|
|
|
+ " for d in datasets:\n",
|
|
|
+ " clear(setup,d,qPar)\n",
|
|
|
+ " setup[d]['count']=0\n",
|
|
|
+ " for ic in nc:\n",
|
|
|
+ " #print(f'[{ic}]')\n",
|
|
|
+ " for ir in range(nr):\n",
|
|
|
+ " #print(f'\\t{ir}')\n",
|
|
|
+ " qPar.update({'nc':ic,'realizationId':ir})\n",
|
|
|
+ " \n",
|
|
|
+ " dataset='globalFitParameters'\n",
|
|
|
+ " \n",
|
|
|
+ " qpar=getPar(fb,project,patientCode,visitCode,ic,ir+1)\n",
|
|
|
+ " qval={x:setGlobalVal(qpar[x]) for x in qpar}\n",
|
|
|
+ " val=qval['global']\n",
|
|
|
+ " val['chi2IVF']=qval['IVF']['chi2']\n",
|
|
|
+ " update(setup,dataset,qPar,r,val)\n",
|
|
|
+ " for i in range(ic):\n",
|
|
|
+ " val=setCenterVal(qpar['IVF'],i)\n",
|
|
|
+ " val['file']=f'{patientCode}_{visitCode}_{ic}_{ir+1}_IVF_centers{i+1}.png'\n",
|
|
|
+ " dataset='centerFitParameters'\n",
|
|
|
+ " qPar1={x:qPar[x] for x in qPar}\n",
|
|
|
+ " qPar1['ic']=i\n",
|
|
|
+ " update(setup,dataset,qPar1,r,val)\n",
|
|
|
+ "# if debug:\n",
|
|
|
+ "# break\n",
|
|
|
+ " val=setGlobalVal(qpar['IVF'])\n",
|
|
|
+ " qPar.update({'nc':0,'realizationId':0})\n",
|
|
|
+ " update(setup,'globalFitParameters',qPar,r,val)\n",
|
|
|
+ " _tmp=[upload(setup,dataset,True) for dataset in datasets]\n",
|
|
|
+ " if debug:\n",
|
|
|
+ " break\n",
|
|
|
+ " \n",
|
|
|
+ "extractFitParameters()"
|
|
|
+ ]
|
|
|
+ },
|
|
|
+ {
|
|
|
+ "cell_type": "code",
|
|
|
"execution_count": null,
|
|
|
"metadata": {},
|
|
|
"outputs": [],
|
