update slicer cochlea to add 9 measuerments

Author: idhamari

Screenshots/s2.png

@@ -105,7 +105,7 @@ def setGlobalVariables(self,vsExtension):
 
       if vsExtension == 0: #0=cochlea
          self.vtVars['othersWebLink']       = ("https://github.com/MedicalImageAnalysisTutorials/VisSimData/raw/master/VisSimToolsCochlea.zip")
-         self.OthersSHA256 = "3964baf33b2978c452a858f3647a7ac95e09d5dfb83a73faef88d027a75b03cb"
+         self.OthersSHA256 = "645e55b1f4ffcfdd5cf4722e89e51eb53a72a146986164a53c7d490c9a544881"
          self.vtVars['parsPath']            = os.path.join(self.vtVars['vissimPath'] ,   "pars","parCochSeg.txt")
          self.vtVars['parsNRPath']          = os.path.join(self.vtVars['vissimPath'] , "pars","parCochSegNR.txt")        
          self.vtVars['modelPath']           = os.path.join(self.vtVars['vissimPath'] , "models","modelCochlea")
@@ -125,7 +125,7 @@ def setGlobalVariables(self,vsExtension):
          self.vtVars['dispViewTxt']         = "Green"
          self.vtVars['dispViewID']          = "8" #Green, coronal view
          if (sys.platform == 'win32') or (platform.system()=='Windows'):
-           self.OthersSHA256                = '9a2ee6a67a190e438a18be811310cbf4eb26b6ad3e00243affa44cc0b26c4393'
+           self.OthersSHA256                = '645e55b1f4ffcfdd5cf4722e89e51eb53a72a146986164a53c7d490c9a544881'
       #Only for Cervical Spine
       elif vsExtension == 1: # Cervical Spine
          print("VisSimCommonLogic: initializing global variables:")
@@ -205,8 +205,7 @@ def checkVisSimTools(self,vtVars,vsExtension ):
                 os.remove(vissimZip)
                 # moved the folder: fix bug related to windows
                 # TODO: bug related to slicer, it works in python interactor but not in the extension
-                shutil.move(os.path.join(os.path.expanduser("~/"),"VisSimToolsCochlea","VisSimTools") , os.path.expanduser("~/") )                
-                os.rmdir(os.path.join(os.path.expanduser("~/"),"VisSimToolsCochlea"))
+                shutil.move(os.path.join(os.path.expanduser("~/"),"VisSimToolsCochlea") , os.path.join(os.path.expanduser("~/"),"VisSimTools") )                
                 print ("    done! ")
          except Exception as e:
                 print("      Error: can not download and extract VisSimTools ...")

Screenshots/s3.png

@@ -7,13 +7,12 @@
 (FixedImagePyramid "FixedRecursiveImagePyramid") 
 (MovingImagePyramid "MovingRecursiveImagePyramid") 
 (Interpolator "LinearInterpolator")
-(Optimizer "AdaptiveStochasticGradientDescent")
+(Optimizer "QuasiNewtonLBFGS")
 (Transform "EulerTransform")
 (Metric "AdvancedMattesMutualInformation")
 (NumberOfHistogramBins 16)
 (NumberOfResolutions 1)
 (MaximumNumberOfIterations 500)
-(MaximumStepLength 1.0)  
 (NumberOfSpatialSamples 3000)
 (NewSamplesEveryIteration "true")  
 (ImageSampler "RandomCoordinate")  

Screenshots/s4.png

@@ -0,0 +1,36 @@
+(FixedInternalImagePixelType  "short")
+(MovingInternalImagePixelType "short")
+(UseDirectionCosines "true")
+(Registration "MultiResolutionRegistration")
+(ResampleInterpolator "FinalBSplineInterpolator")
+(Resampler "DefaultResampler")
+(FixedImagePyramid "FixedRecursiveImagePyramid") 
+(MovingImagePyramid "MovingRecursiveImagePyramid") 
+(Interpolator "LinearInterpolator")
+(Optimizer "QuasiNewtonLBFGS")
+//(Transform "EulerTransform")
+(Transform "BSplineTransform")
+(Metric "AdvancedMattesMutualInformation")
+(NumberOfHistogramBins 16)
+(NumberOfResolutions 1)
+(MaximumNumberOfIterations 7)
+(MaximumStepLength 1.0)  
+(NumberOfSpatialSamples 3000)
+(NewSamplesEveryIteration "true")  
+(ImageSampler "RandomCoordinate")  
+(ErodeMask "false")
+(AutomaticScalesEstimation "true")  
+(AutomaticTransformInitialization "true")  
+(AutomaticTransformInitializationMethod "GeomteryTop")  
+(HowToCombineTransforms "Compose")  
+(RequiredRatioOfValidSamples 0.01) 
+(BSplineInterpolationOrder 3)
+(FinalBSplineInterpolationOrder 3)
+(DefaultPixelValue 0)
+(WriteResultImage "true")
+(ResultImagePixelType "short")
+(ResultImageFormat "nrrd")
+(WriteTransformParametersEachIteration "false")
+(WriteTransformParametersEachResolution  "false")
+(WriteResultImageAfterEachIteration "false")
+(WriteResultImageAfterEachResolution "false")