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idhamari
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fix a windows bug when running elastix
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‎README.md‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -17,13 +17,14 @@ This is a [3D Slicer](https://gaithub.com/Slicer/Slicer) plugin that uses [elast
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# Tested on
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* Slicer 5.0.3 [for windows](https://slicer-packages.kitware.com/api/v1/file/62d5d2ebe911182f1dc285b2/download) and [for linux](https://slicer-packages.kitware.com/api/v1/file/62cc52d2aa08d161a31c1af2/download). Tested on Windows 10 and Ubuntu 20.04
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* Slicer 5.6, Windows 10 and Ubuntu 20.04
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This project contains three modules:
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1. Cochlea image registration and fusion.
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2. Cochlea image segmentation and analysis.
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3. VisSimCommon for common functions.
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# How to use:
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‎VisSimCommon/VisSimCommon.py‎

Lines changed: 41 additions & 27 deletions
Original file line numberDiff line numberDiff line change
@@ -6,8 +6,8 @@
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# [1] https://www.slicer.org #
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# #
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#-------------------------------------------------------------------------------------#
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# Slicer 5.4.0 #
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# Updated: 18.11.2023 #
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# Slicer 5.6 #
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# Updated: 17.3.2024 #
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#-------------------------------------------------------------------------------------#
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#TODO: check Documentation/Nightly/Developers/Tutorials/MigrationGuide #
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#-------------------------------------------------------------------------------------#
@@ -25,7 +25,7 @@
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# Non Slicer libs
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from __future__ import print_function, unicode_literals
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import os, sys, time, re, shutil, math, unittest, logging, zipfile, platform, subprocess, hashlib
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import os, sys, glob, time, re, shutil, math, unittest, logging, zipfile, platform, subprocess, hashlib
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from shutil import copyfile
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from six.moves.urllib.request import urlretrieve
@@ -75,6 +75,14 @@ def tstSum(self, x,y):
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print("testing")
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return x+y
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# Get slicer lib path automatically
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def getSlicerLibPath(SlicerPath):
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# Search for directories that match the "Slicer-*" pattern within the lib directory
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slicer_dirs = glob.glob(os.path.join(os.path.join(SlicerPath, "lib"), "Slicer-*"))
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# Assuming there's only one Slicer directory per installation, take the first match
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return slicer_dirs[0]
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# vsExtension = 0: Cochlea, vsExtension = 1: Spine
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def setGlobalVariables(self,vsExtension):
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# define global variables as a dictonary
@@ -196,18 +204,16 @@ def checkVisSimTools(self,vtVars,vsExtension ):
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print(" Downloading VisSim Tools ... ")
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try:
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print(" Downloading VisSimTools others ...")
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vissimZip = os.path.expanduser("~/VisSimToolsTmp.zip")
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uFile = urlretrieve(othersWebLink,vissimZip)
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vissimZip = os.path.join(os.path.expanduser("~"),"VisSimToolsTmp.zip")
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print("vissimZip: ",vissimZip)
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uFile = urlretrieve(othersWebLink, vissimZip)
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print (" Extracting to user home ")
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zip_ref = zipfile.ZipFile(vissimZip, 'r')
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zip_ref.extractall(os.path.expanduser("~/"))
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zip_ref.extractall(os.path.expanduser("~"))
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zip_ref.close()
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#remove the downloaded zip file
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os.remove(vissimZip)
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# moved the folder: fix bug related to windows
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# TODO: bug related to slicer, it works in python interactor but not in the extension
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shutil.move(os.path.join(os.path.expanduser("~/"),"VisSimToolsCochlea") , os.path.join(os.path.expanduser("~/"),"VisSimTools") )
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print (" done! ")
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print (" Extracting to user home ... done! ")
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except Exception as e:
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print(" Error: can not download and extract VisSimTools ...")
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print(e)
@@ -463,18 +469,16 @@ def runCropping(self, inputVolume, pointT,croppingLengthT, samplingLengthT, hrCh
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SlicerBinPath=""
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ResampleBinPath=""
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## this produces error in windows
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#resamplingCommand = slicer.modules.resamplescalarvolume.path
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#os.system(resamplingCommand)
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#TODO: Get Slicer PATH
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SlicerPath = os.path.abspath(os.path.join(os.path.abspath(os.path.join(os.sys.executable, os.pardir)), os.pardir))
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SlicerBinPath = os.path.join(SlicerPath,"Slicer")
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ResampleBinPath = os.path.join(SlicerPath,"lib","Slicer-5.4" , "cli-modules","ResampleScalarVolume" )
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SlicerLibPath = VisSimCommonLogic.getSlicerLibPath(SlicerPath)
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#ResampleBinPath = os.path.join(SlicerPath,"lib","Slicer-5.4" , "cli-modules","ResampleScalarVolume" )
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ResampleBinPath = os.path.join(SlicerLibPath, "cli-modules","ResampleScalarVolume" )
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#ResampleBinPath = os.path.join(SlicerPath,"lib","Slicer-5.6" , "cli-modules","ResampleScalarVolume" )
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resamplingCommand = ResampleBinPath
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if sys.platform == 'win32':
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ResampleBinPath + ".exe"
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resamplingCommand = SlicerBinPath + " --launch " + ResampleBinPath
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else:
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#note: in windows, no need to use --launch
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resamplingCommand = ResampleBinPath
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resamplingCommand = f'"{SlicerBinPath}" --launch "{ResampleBinPath}"'
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print(resamplingCommand)
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si = None
@@ -511,15 +515,24 @@ def runCropping(self, inputVolume, pointT,croppingLengthT, samplingLengthT, hrCh
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def runElastix(self, elastixBinPath, fixed, moving, output, parameters, verbose, line):
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print ("************ Compute the Transform **********************")
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currentOS = sys.platform
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print(currentOS)
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Cmd = elastixBinPath + ' -f ' + fixed + ' -m ' + moving + ' -out ' + output + ' -p ' + parameters
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print("currentOS: ",currentOS)
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Cmd = elastixBinPath + " -f " +fixed+" -m "+ moving +" -out "+ output +" -p "+ parameters
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errStr="No error!"
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if currentOS in ["win32","msys","cygwin"]:
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print(" elastix is running in Windows :( !!!")
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print(Cmd)
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si = subprocess.STARTUPINFO()
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si.dwFlags |= subprocess.STARTF_USESHOWWINDOW
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cTI = subprocess.call(Cmd , shell = (sys.platform == currentOS) , startupinfo=si )
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print(" elastix is running in Windows :( !!!")
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Cmd = f'"{elastixBinPath}" -f "{fixed}" -m "{moving}" -out "{output}" -p "{parameters}"'
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526+
print(Cmd)
527+
Cmd = f'"{elastixBinPath}" -f "{fixed}" -m "{moving}" -out "{output}" -p "{parameters}"'
528+
si = subprocess.STARTUPINFO()
529+
si.dwFlags |= subprocess.STARTF_USESHOWWINDOW
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process = subprocess.Popen(Cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True, startupinfo=si)
531+
stdout, stderr = process.communicate()
532+
cTI = process.returncode
533+
# print(f"STDOUT: {stdout.decode()}")
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# print(f"STDERR: {stderr.decode()}")
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elif currentOS in ["linux","linux2"]:
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print(" elastix is running in Linux :) !!!")
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CmdList = Cmd.split()
@@ -553,12 +566,13 @@ def runElastix(self, elastixBinPath, fixed, moving, output, parameters, verbose,
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def runTransformix(self,transformixBinPath, img, output, parameters, verbose, line):
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print ("************ Apply transform **********************")
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currentOS = sys.platform
556-
Cmd = transformixBinPath + ' -tp ' + parameters + ' -in ' + img +' -out ' + output +' -def '+ ' all '
569+
Cmd = transformixBinPath + " -tp " + parameters + " -in " + img +" -out " + output + " -def all "
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557571
#if subprocess.mswindows:
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errStr="No error!"
559-
# if hasattr(subprocess, 'mswindows'):
560573
if currentOS in ["win32","msys","cygwin"]:
561574
print(" transformix is running in Windows :( !!!")
575+
Cmd = f'"{transformixBinPath}" -tp "{parameters}" -in "{img}" -out "{output}" -def all '
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print(Cmd)
563577
si = subprocess.STARTUPINFO()
564578
si.dwFlags |= subprocess.STARTF_USESHOWWINDOW

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