added normalized murray

py/krebs/analyzeBloodVolumeSimple.py

@@ -176,7 +176,7 @@ def boxplotFromData_rBV(data, pp, data2=None):
     aColor = violin2['cmedians'].get_color()
     aColor = aColor[0,0:3]
     red_patch = matplotlib.patches.Patch(color=aColor)
-    label = ['tumorCode', 'adaption']
+    label = ['Tumorcode', 'adaption']
     fake_handels = [blue_patch, red_patch]
     ax2.legend(fake_handels, label)
 #  else:
@@ -203,7 +203,7 @@ def boxplotFromData_s2v(data, pp, data2=None):
     aColor = violin2['cmedians'].get_color()
     aColor = aColor[0,0:3]
     red_patch = matplotlib.patches.Patch(color=aColor)
-    label = ['tumorCode', 'adaption']
+    label = ['Tumorcode', 'adaption']
     fake_handels = [blue_patch, red_patch]
     ax2.legend(fake_handels, label, loc='upper center')
   else:
@@ -242,11 +242,9 @@ def getDataFromFiles(filenames, groupname):
   parser = argparse.ArgumentParser(description='Plot/ Analyze rBV surface to volume.')
   parser.add_argument('grp_pattern1',help='Where to find the vessel group in the file')    
   parser.add_argument('--grp_pattern2',default=None, help='Where to find the vessel group in the file') 
-  parser.add_argument('vesselFileNames1', nargs='*', type=argparse.FileType('r'), default=sys.stdin, help='Vessel file to calculate')  
-
-  #parser.add_argument('--vesselFileNames2', nargs='*', type=argparse.FileType('r'), default=sys.stdin, help='Vessel file to calculate')  
-  #parser.add_argument('vesselFileNames2', nargs='+', type=argparse.FileType('r'), default=sys.stdin,help='Vessel file to calculate')  
 
+  ''' usage: use all file names here'''
+  parser.add_argument('vesselFileNames1', nargs='*', type=argparse.FileType('r'), default=sys.stdin, help='Vessel file to calculate')  
 
   goodArguments, otherArguments = parser.parse_known_args()
 

py/krebs/analyzeMurray.py

@@ -248,6 +248,35 @@ def DoSymetryMurrayForSingleFile(fn,pattern, pdfpages):
 #    ax2.grid()
 #    plt.savefig('murray_%s.png' % os.path.basename(afile.filename))
 
+def DoSymetryMurrayForSingleFileNorm(fn,pattern, pdfpages):
+
+  result_v, result_a = ku.get_Murray2(fn, pattern)
+  result_v = removeZeros(result_v)
+  result_a = removeZeros(result_a)
+
+  fig2, ax2 = plt.subplots(1,1)
+  ### histogramm deviation of daughters
+  hist_a, bin_edges_a = np.histogram((result_a[1,:]-result_a[0,:])/result_a[2,:], bins=50) #note. they are sorted in on c++ side
+  width_a = 0.45*(bin_edges_a[1]-bin_edges_a[0])
+  centers_a = (bin_edges_a[:-1]+bin_edges_a[1:])/2
+  ax2.bar(centers_a,hist_a/float(len(result_a[0,:])), align='center', width=width_a, color='red')
+  ax2.set_xlabel(r'$\frac{\|r^{daughter}_a- r^{daughter}_b\|}{\| r^{mother} \|}$',fontsize=18)
+  ax2.set_ylabel(r'probability',fontsize=18)
+
+  hist_v, bin_edges_v = np.histogram((result_v[1,:]-result_v[0,:])/result_v[2,:], bin_edges_a) #note. they are sorted in on c++ side
+  width_v = 0.45*(bin_edges_v[1]-bin_edges_v[0])
+  centers_v = (bin_edges_v[:-1]+bin_edges_v[1:])/2+width_a
+  ax2.bar(centers_v,hist_v/float(len(result_v[0,:])), align='center', width=width_v, color='blue')
+#  
+  ax2.legend(['arterial branch', 'venous branch'])
+  print('check norm: %f' % np.sum(hist_a/float(len(result_a[0,:]))))
+  #print('check norm: %f' % np.sum(hist_v/float(len(result_v[0,:]))))
+  #fig1.tight_layout()
+#  pdfpages.savefig(fig1) 
+  fig2.tight_layout()
+  pdfpages.savefig(fig2)
+
+
 def removeZeros(atwoarray):
     first_line = atwoarray[0,:]
     good_indeces_first_line = first_line>0
@@ -394,4 +423,8 @@ def DoGetMurray(filenames, pdfpages):
     outfilename='murray_symmetry_for_file_%s' % basename(filenames[0])
     with mpl_utils.PdfWriter(outfilename + '.pdf') as pdfpages:  
       DoSymetryMurrayForSingleFile(filenames[0],pattern, pdfpages)
+
+    outfilename='murray_symmetry_norm_for_file_%s' % basename(filenames[0])
+    with mpl_utils.PdfWriter(outfilename + '.pdf') as pdfpages:  
+      DoSymetryMurrayForSingleFileNorm(filenames[0],pattern, pdfpages)