pythonScripts/runStat.py

@@ -49,11 +49,16 @@ def main(parFile='../templates/statistics.json'):
 
         setup['SUVdataset']='SUVanalysis_SUVmax'
         suvMaxDone=checkData(setup,r) 
+
+        setup['SUVdataset']='SUVanalysis_liver1p5'
+        liver1p5Done=checkData(setup,r)
+
         
-        if liverDone and suvMaxDone:
+        if liverDone and suvMaxDone and liver1p5Done:
             print('Skipping {} {}'.format(r['ParticipantId'],r['visitCode']))
             continue
-
+        doneCode=f'({liverDone}/{liver1p5Done}/{suvMaxDone})'
+        print(f'Done: (liver/liver1p5/suvMax): {doneCode}')
         #PET
         for q in ['petResampled']:
             localPath=statUtils.getImage(setup,r,q)
@@ -95,6 +100,9 @@ def main(parFile='../templates/statistics.json'):
         liverThreshold={x:outputs[x].get(liverId,default)['SUVmean']
                 +2*outputs[x].get(liverId,default)['SUVSD'] 
                 for x in outputs}
+        liver1p5Threshold={x:outputs[x].get(liverId,default)['SUVmean']
+                +1.5*outputs[x].get(liverId,default)['SUVSD'] 
+                for x in outputs}
         lesionId=4
         bmId=3
         suvMax={x:numpy.max([outputs[x].get(lesionId,default)['SUVmax'],
@@ -103,28 +111,24 @@ def main(parFile='../templates/statistics.json'):
         suvMaxThreshold={x:0.41*suvMax[x] for x in suvMax}
     
 
-        print('thr[liver]={} thr(suvmax)={}'.format(liverThreshold,suvMaxThreshold))
+        print('thr[liver]={} thr[liver/1.5]={} thr(suvmax)={}'.format(liverThreshold,liver1p5Threshold,suvMaxThreshold))
        
-        #thresholds are by user
-        liverOutputs={}
-        for s in liverThreshold:
-            #update radiomics setting
-            setup['radiomics']['setting']['resegmentRange']=[liverThreshold[s]]
-            setup['radiomics']['setting']['resegmentShape']=True
-            liverOutputs[s]=getValuesForSegmentation(setup,r,pet,seg[s])
-            
-            _=[liverOutputs[s][y].update({'threshold':liverThreshold[s]}) for y in liverOutputs[s]]
-        setup['SUVdataset']='SUVanalysis_liver'
-        uploadData(setup,r,liverOutputs)
 
-        suvMaxOutputs={}
-        for s in suvMaxThreshold:
-            setup['radiomics']['setting']['resegmentRange']=[suvMaxThreshold[s]]
-            setup['radiomics']['setting']['resegmentShape']=True
-            suvMaxOutputs[s]=getValuesForSegmentation(setup,r,pet,seg[s])
-            _=[suvMaxOutputs[s][y].update({'threshold':suvMaxThreshold[s]}) for y in suvMaxOutputs[s]]
-        setup['SUVdataset']='SUVanalysis_SUVmax'
-        uploadData(setup,r,suvMaxOutputs)
+        if not liverDone:
+            setup['SUVdataset']='SUVanalysis_liver'
+            liverOutputs=thresholdAnalysis(setup,r,pet,seg,liverThreshold)
+            uploadData(setup,r,liverOutputs)
+
+        #also for threshold=1.5
+        if not liver1p5Done:
+            setup['SUVdataset']='SUVanalysis_liver1p5'
+            liver1p5Outputs=thresholdAnalysis(setup,r,pet,seg,liver1p5Threshold)
+            uploadData(setup,r,liver1p5Outputs)
+
+        if not suvMaxDone:
+            setup['SUVdataset']='SUVanalysis_SUVmax'
+            suvMaxOutputs=thresholdAnalysis(setup,r,pet,seg,suvMaxThreshold)
+            uploadData(setup,r,suvMaxOutputs)
 
         #skip threshold of 4
         doThreshold4=False
@@ -146,6 +150,20 @@ def main(parFile='../templates/statistics.json'):
         for x in segPaths:
             os.remove(segPaths[x])
 
+
+def thresholdAnalysis(setup,r,pet,seg,thrs):
+    #thresholds thrs are by participant and region
+    outputs={}
+    for s in thrs:
+        #update radiomics setting
+        setup['radiomics']['setting']['resegmentRange']=[thrs[s]]
+        setup['radiomics']['setting']['resegmentShape']=True
+        outputs[s]=getValuesForSegmentation(setup,r,pet,seg[s])
+            
+        _=[outputs[s][y].update({'threshold':thrs[s]}) for y in outputs[s]]
+    return outputs
+
+
 def getValues(setup,row,pet,seg):
 
     rFile='radiomics.json'

pythonScripts/statUtils.py

@@ -235,10 +235,10 @@ def updateDatasetRows(db,project,dataset,rows,filterVars=['ParticipantId','Seque
         else:
             mode='insert'
             resp=db.modifyRows('insert',project,'study',dataset,[r])
-        encoding=chardet.detect(resp)['encoding']
-        respJSON=json.loads(resp.decode(encoding))
+        #encoding=chardet.detect(resp)['encoding']
+        #respJSON=json.loads(resp.decode(encoding))
         try:
+            print(resp['exception'])
             print(f'Using mode={mode}')
-            print(respJSON['exception'])
         except KeyError:
             pass