some cleaning

Author: idhamari

CochleaSeg/CochleaSeg.py

@@ -20,15 +20,7 @@
 #-------------------------------------------------------------------------------------#
 #  Slicer 4.11.0                                                                      #
 #  Updated: 24.6.2019                                                                 #
-#-------------------------------------------------------------------------------------#
-#  - Add branches to github to support new Slicer versions                            #
-#  - Using VisSimCommon for shared functions.                                         #
-#  - Use transformation directly to transform the points.                             #
-#  - Add more support for windows and mac.                                            #
-#  - Logic functions are independent and can be called from external script.          #
-#  - test function can be used in external scripts. A demo example is provided        #
 #======================================================================================
-
 from __future__ import print_function
 import os, time, unittest, logging
 from shutil import copyfile
@@ -90,7 +82,6 @@ def __init__(self, parent):
   #end def init
 #end class CochleaSeg
 
-
 #===================================================================
 #                           Main Widget
 #===================================================================
@@ -281,21 +272,15 @@ def run(self, inputVolumeNode, inputFiducialNode, cochleaSide):
       Styp="Dv"
 
       # segmentation atlas model paths
-
-      modelPath      =   self.vsc.vtVars['modelPath']+ ",Mdl"+Styp +cochleaSide +"c"+self.vsc.vtVars['imgType']
-      modelPath      =   os.path.join(*modelPath.split(","))
-      modelSegPath   =   self.vsc.vtVars['modelPath']+ ",Mdl"+Styp +cochleaSide +"cS.seg"+self.vsc.vtVars['imgType']
-      modelSegPath   =   os.path.join(*modelSegPath.split(","))
-      modelImgStPath =   self.vsc.vtVars['modelPath']+ ",Mdl"+Styp +cochleaSide +"cSt.fcsv"
-      modelImgStPath   =   os.path.join(*modelImgStPath.split(","))
+      modelPath      =   os.path.join(self.vsc.vtVars['modelPath'] , "Mdl"+Styp +cochleaSide +"c"+self.vsc.vtVars['imgType'])
+      modelSegPath   =   os.path.join(self.vsc.vtVars['modelPath'] , "Mdl"+Styp +cochleaSide +"cS.seg"+self.vsc.vtVars['imgType'])
+      modelImgStPath =   os.path.join(self.vsc.vtVars['modelPath'] , "Mdl"+Styp +cochleaSide +"cSt.fcsv")
       # set the results paths:
       resTransPathOld  = os.path.join(self.vsc.vtVars['outputPath'] ,"TransformParameters.0.txt")
       resTransPath=resTransPathOld[0:-6]+'Pars.txt'
       resOldDefPath = os.path.join(self.vsc.vtVars['outputPath'] , "deformationField"+self.vsc.vtVars['imgType'])
       resDefPath    = os.path.join(self.vsc.vtVars['outputPath'] , inputVolumeNode.GetName()+"_dFld"+self.vsc.vtVars['imgType'])
-      inputImgName  = inputVolumeNode.GetStorageNode().GetFileName()
-      inputImgName  = os.path.basename(os.path.splitext(inputImgName)[0])
-
+      inputImgName  = os.path.basename(os.path.splitext(inputVolumeNode.GetStorageNode().GetFileName())[0])
       segNodeName   = inputVolumeNode.GetName() + "_S.Seg"
       stpNodeName   = inputVolumeNode.GetName() + "_StPts"
       transNodeName = inputVolumeNode.GetName() + "_Transform"

VisSimCommon/VisSimCommon.py

@@ -1,4 +1,3 @@
-
 #======================================================================================
 #  3D Slicer [1] common functions used by VisSim extensions                           #
 #                                                                                     #
@@ -238,8 +237,6 @@ def s2b(self,s):
         return s.lower() in ("yes", "true", "t", "1")
   #enddef
 
-        inputPointT = self.vsc.v2t(inputPoint) # "["+str(inputPoint[0])+","+str(inputPoint[1])+","+str(inputPoint[2])+"]"
-
   #convert a vector to text
   def v2t(self,v):
       return  "["+str(v[0])+","+str(v[1])+","+str(v[2])+"]"
@@ -322,7 +319,7 @@ def ptRAS2IJK(self,ptRAS,inputImg,i):
       ptIJK = ptIJKf.astype(np.int64)
       #print("RAS= " + str(ras)+ "   IJK= " + str(ptIJK))
       return  ptIJK
-
+  #enddef
 
   #------------------------------------------------------
   #         image2points
@@ -374,7 +371,7 @@ def image2points(self,inputImgNode):
         self.markupsNode.SetName(inputImgNode.GetName()+ "_StPts")
         return self.markupsNode
 
-#enddef
+  #enddef
 
 
   #-----------------------------------------------------------------------------------
@@ -525,6 +522,7 @@ def runCropping(self, inputVolume, pointT,croppingLengthT, samplingLengthT, hrCh
         # so we can remove these files later
         return inputCropPath
   #enddef
+
   #--------------------------------------------------------------------------------------------
   #                        run elastix
   #--------------------------------------------------------------------------------------------
@@ -800,7 +798,6 @@ def setItemChk(self,itemT, itemChk, itemName, nodes,):
           #endif
           #print("side selected is " + self.vtVars[itemT])
       #endif
-
    #enddef
 
   def setVtID(self,idx,inputVolumeNode , inputFiducialNode):
@@ -853,7 +850,8 @@ def setVtIDfromEdt(self,point,vtID):
         return isExternalCall
   #enddef
 
-  #this part need to be optimized
+  # Slicer4 Slicer5 conflict
+  # this part need to be optimized
   # reg =0: no registration, 1: fixed image, 2: moving image
   def locateItem(self, inputVolumeNode, inputPointEdt, reg, vtID):
       self.inputFiducialNodes = []
@@ -1162,8 +1160,7 @@ def dispSeg(self,inputVolumeNode, vtSegNode, view):
         v3DDWidgetV.zoomIn()
         v3DDWidgetV.zoomFactor =0.05 # back to default value
   #enddef
-
-
+#endclass 
 
 class VisSimCommonTest(ScriptedLoadableModuleLogic):