added group parameter to motioncor

processing/mc2FromMDOC.py

@@ -39,6 +39,8 @@ parser.add_argument('-v', '--verbose', action='store_true', help='Allow verbose
 parser.add_argument('-nl', '--noLog', action='store_true', help='Allow verbose output from motioncor2 during script run.')
 parser.add_argument('-kf', '--keepFrames', action='store_true', help='Keep temporary individual aligned frames.')
 parser.add_argument('-psf', '--pixelSizeFactor', nargs='?', type=float, default=1, help='Correction factor for pixel size, set to 0.5 for super resolution with binned mdoc.')
+parser.add_argument('-g', '--group', nargs='?', type=int, default=1, help='Group parameter to motioncor2. Default 1, set to 2 or 3 on very low signal input.')
+#parser.add_argument('-g', '--group', nargs='?', type=int, default=1, help='Group parameter to motioncor2. Default 1, set to 2 or 3 on very low signal input.')
 
 # parser.add_argument('-c', '--cutoff', nargs='?', type=float, default='1', help='The threshold of how many standard deviations above or below the a line must deviate before it is corrected')
 # parser.add_argument('-g', '--graph', action='store_true', help='Store a graph of the corrected and uncorrected line intensities for debug purposes.')
@@ -150,7 +152,7 @@ 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']*args.pixelSizeFactor, doseWeightParams, verboseString) )
+        scriptFile.write("MotionCor2-cuda%i -InMrc \"%s\" -OutMrc \"%s\" -Patch %i %i -InFmMotion 1 -Iter 30 -Tilt %f -Group %i -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.group, args.binning,  imageParams['pixelspacing']*args.pixelSizeFactor, 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 ))