Moving plotSegmentation from segmentation.py to plotData to avoid matplotlib dependency in Slicer, through convertToNRRD.py which depends on segmentation.py

pythonScripts/plotData.py

@@ -4,6 +4,7 @@ import fitModel
 import numpy
 import functools
 import geometry
+import segmentation
 
 def plotIVF(t,ivf,samples,threshold,file0=None,file1=None):
     
@@ -170,3 +171,51 @@ def plotSamples(t,evalArray,file0=None,file1=None):
       matplotlib.pyplot.figure(f2.number)
       matplotlib.pyplot.savefig(file1)
 
+def plotSegmentation(r,setup,spect,vmax=1000,file0=None,fb=None):
+   fp={}
+   
+   for q in rows:
+      if q['regionId']==0:
+         slc=[q['x'],q['y'],q['z']]
+         slc=[int(x) for x in slc]
+      slices=q['sliceId'].split(';')
+      for s in slices:
+         try:
+            fp[s].append([float(x) for x in [q['x'],q['y'],q['z']]])
+         except KeyError:
+            fp[s]=[]
+            fp[s].append([float(x) for x in [q['x'],q['y'],q['z']]])
+
+   cut0=20
+   w0=20
+   cut1=20
+   w1=20
+   cut2=20
+   w2=20
+   vmin=0
+   nd=3
+   fig,ax=matplotlib.pyplot.subplots(3,2*nd+1,figsize=(20,12))
+   for i in numpy.arange(0,2*nd+1):
+      ax[0,i].set_xlabel('z')
+      ax[0,i].set_ylabel('x')
+      ax[0,i].imshow(spect[cut2:cut2+w2,slc[1]-nd+i,cut0:cut0+w0],cmap='gray_r',vmax=vmax,vmin=vmin)
+      ax[1,i].set_xlabel('x')
+      ax[1,i].set_ylabel('y')
+      ax[1,i].imshow(spect[cut2:cut2+w2,cut0:cut0+w0,slc[2]-nd+i].T,cmap='gray_r',vmax=vmax,vmin=vmin)
+      ax[2,i].set_xlabel('z')
+      ax[2,i].set_ylabel('y')
+      ax[2,i].imshow(spect[slc[0]-nd+i,cut1:cut1+w1,cut1:cut1+w1],cmap='gray_r',vmax=vmax,vmin=vmin)
+      if i==nd:
+         pt=fp['0']
+         ax[0,i].scatter([x[2]-cut0 for x in pt],[x[0]-cut2 for x in pt])
+         pt=fp['1']
+         ax[1,i].scatter([x[0]-cut2 for x in pt],[x[1]-cut0 for x in pt])
+         pt=fp['2']
+         ax[2,i].scatter([x[2]-cut1 for x in pt],[x[1]-cut1 for x in pt])
+
+         if i==0:
+            ax[0,i].text(2,2,pId,fontsize='large')
+   if file0:
+      fig.savefig(file0)
+
+

pythonScripts/segmentation.py

@@ -3,7 +3,6 @@ import config
 import SimpleITK
 import os
 import getData
-import matplotlib.pyplot
 
 def guessPixelPosition15(sx=-1,sy=-1,sz=-1):
     #guess position of segments
@@ -230,66 +229,6 @@ def loadSegmentation(db,fb,r,setup):
       return numpy.loadtxt(fName)
 
    
-def plotSegmentation(db,fb,r,setup,vmax=1000):    
-   copyFields=['PatientId','visitCode']
-   qFilter=[{'variable':x,'value':r[x],'oper':'eq'} for x in copyFields]
-   nim=getData.getPatientNIM(fb,r,setup)
-   rows=getData.getSegmentation(db,setup,qFilter)
-
-   if len(rows)==0:
-      pId=r['PatientId']
-      visitCode=r['visitCode']
-      print(f'Not found for id={pId}/{visitCode}')
-      return
-   
-   fp={}
-   
-   for q in rows:
-      if q['regionId']==0:
-         slc=[q['x'],q['y'],q['z']]
-         slc=[int(x) for x in slc]
-      slices=q['sliceId'].split(';')
-      for s in slices:
-         try:
-            fp[s].append([float(x) for x in [q['x'],q['y'],q['z']]])
-         except KeyError:
-            fp[s]=[]
-            fp[s].append([float(x) for x in [q['x'],q['y'],q['z']]])
-
-   cut0=20
-   w0=20
-   cut1=20
-   w1=20
-   cut2=20
-   w2=20
-   vmin=0
-   nd=3
-   fig,ax=matplotlib.pyplot.subplots(3,2*nd+1,figsize=(20,12))
-   for i in numpy.arange(0,2*nd+1):
-      ax[0,i].set_xlabel('z')
-      ax[0,i].set_ylabel('x')
-      ax[0,i].imshow(nim[cut2:cut2+w2,slc[1]-nd+i,cut0:cut0+w0],cmap='gray_r',vmax=vmax,vmin=vmin)
-      ax[1,i].set_xlabel('x')
-      ax[1,i].set_ylabel('y')
-      ax[1,i].imshow(nim[cut2:cut2+w2,cut0:cut0+w0,slc[2]-nd+i].T,cmap='gray_r',vmax=vmax,vmin=vmin)
-      ax[2,i].set_xlabel('z')
-      ax[2,i].set_ylabel('y')
-      ax[2,i].imshow(nim[slc[0]-nd+i,cut1:cut1+w1,cut1:cut1+w1],cmap='gray_r',vmax=vmax,vmin=vmin)
-      if i==nd:
-         pt=fp['0']
-         ax[0,i].scatter([x[2]-cut0 for x in pt],[x[0]-cut2 for x in pt])
-         pt=fp['1']
-         ax[1,i].scatter([x[0]-cut2 for x in pt],[x[1]-cut0 for x in pt])
-         pt=fp['2']
-         ax[2,i].scatter([x[2]-cut1 for x in pt],[x[1]-cut1 for x in pt])
-
-         if i==0:
-            ax[0,i].text(2,2,pId,fontsize='large')
-   name='{}_segmentation.png'.format(config.getCode(r,setup))
-   fPath=getData.getLocalPath(r,setup,name)
-   fig.savefig(fPath)
-   getData.copyToServer(fb,r,setup,[name])
-
 
 def getNRRDImage(r,setup,names=None):
    if names: