From 5056bd1364c8a9efeb9135d4b582ff4288d149fd Mon Sep 17 00:00:00 2001 From: Adrian Nievergelt Date: Fri, 5 Jul 2019 19:01:55 +0200 Subject: [PATCH] allow spaces in the subframe directory --- processing/mc2FromMDOC.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/processing/mc2FromMDOC.py b/processing/mc2FromMDOC.py index 5e0ee98..0ed1b84 100755 --- a/processing/mc2FromMDOC.py +++ b/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 )) -- 2.22.0