Moving segmentation functions from notebook to package

pythonScripts/segmentation.py

@@ -0,0 +1,70 @@
+import numpy
+import config
+import SimpleITK
+import os
+import getData
+
+def guessPixelPosition(sx=-1,sy=-1,sz=-1):
+    #guess position of segments
+    if sx<0:
+        sx=12
+    if sy<0:
+        sy=28
+    if sz<0:
+        sz=32
+    rz=4
+    oz=0
+
+    slc=[sx,sy,sz]
+    p1=[sx,sy,sz]
+
+    #tip
+    fp={'0':[\
+            [sx,sy,sz],   
+            [sx-5,sy,sz],\
+            [sx-2,sy,sz-rz],\
+            [sx+3,sy,sz-rz],\
+            [sx-2,sy,sz+rz-1],\
+            [sx+3,sy,sz+rz]],\
+        '1':[\
+            [sx,sy,sz],  
+            [sx-5,sy,sz],\
+            [sx-1,sy-rz,sz],\
+            [sx-1,sy+rz-1,sz],\
+            [sx+3,sy-rz,sz],\
+            [sx+3,sy+rz,sz]],\
+        '2':[\
+            [sx,sy,sz],
+            [sx,sy+rz+oz,sz],\
+            [sx,sy+0.3*rz+oz,sz-rz],\
+            [sx,sy-0.3*rz+oz,sz-rz],\
+            [sx,sy-rz+oz,sz],\
+            [sx,sy-0.3*rz+oz,sz+rz],\
+            [sx,sy+0.3*rz+oz,sz+rz]]}
+    return fp
+
+    
+def getPatientNIM(r,setup):
+    locDir=config.getLocalDir(r,setup)
+    fileName=config.getNodeName(r,setup,'NM',19)+'.nrrd'
+    f=os.path.join(locDir,fileName)
+    im=SimpleITK.ReadImage(f)
+    nim=SimpleITK.GetArrayFromImage(im)
+    return nim
+
+def writeSegmentation(db,r,setup):
+    locDir=config.getLocalDir(r,setup)
+    fileName='{}_Segmentation.txt'.format(config.getCode(r,setup))
+    idFilter={'variable':'PatientId','value':config.getPatientId(r,setup),'oper':'eq'}
+    visitFilter={'variable':'visitName','value':config.getVisitId(r,setup),'oper':'eq'}
+    rows=getData.getSegmentation(db,setup,[idFilter,visitFilter])
+    v=numpy.zeros((len(rows),3))
+    for qr in rows:
+        region=int(qr['regionId'])
+        v[region,2]=float(qr['x'])
+        v[region,1]=float(qr['y'])
+        v[region,0]=float(qr['z'])
+    #for i in range(len(rows)):
+    #    print(v[i,:])
+    numpy.savetxt(os.path.join(locDir,fileName),v)
+