allow spaces in the subframe directory

processing/mc2FromMDOC.py

@@ -137,7 +137,7 @@ with open(os.path.join(mdocDir, inBaseName + "_alignFramesMC2.sh"), "w+") as scr
             doseWeightParams = ""
             
         scriptFile.write("echo Aligning frame stack %s \n" % (os.path.join(subframesDir, imageParams['filename']) ))
-        scriptFile.write("MotionCor2-cuda%i -InMrc %s -OutMrc %s -Patch %i %i -InFmMotion 1 -Iter 30 -Tilt %f -FtBin %i -PixSize %f%s%s\n\n" %(args.cudaVer, os.path.join(subframesDir, imageParams['filename']), os.path.join(alignedDir, imageParams['filename']), args.patchSize, args.patchSize,  imageParams['tiltangle'], args.binning,  imageParams['pixelspacing'], doseWeightParams, verboseString) )
+        scriptFile.write("MotionCor2-cuda%i -InMrc \"%s\" -OutMrc \"%s\" -Patch %i %i -InFmMotion 1 -Iter 30 -Tilt %f -FtBin %i -PixSize %f%s%s\n\n" %(args.cudaVer, os.path.join(subframesDir, imageParams['filename']), os.path.join(alignedDir, imageParams['filename']), args.patchSize, args.patchSize,  imageParams['tiltangle'], args.binning,  imageParams['pixelspacing'], doseWeightParams, verboseString) )
     scriptFile.write("echo Creating combined tilt series stack %s\n" % (inBaseName + "_mc2.mrc"))
     scriptFile.write("source /sw/apps/imod/current/imodenv\n")    
     scriptFile.write("newstack -fileinlist %s -output %s -tilt %s%s\n\n" % ( os.path.basename(stackFileName), inBaseName + "_mc2.mrc", os.path.basename(tiltFileName), verboseString ))