added pixel size factor

processing/mc2FromMDOC.py

@@ -37,6 +37,7 @@ parser.add_argument('-b', '--binning', nargs='?', type=int, default=1, help='Out
 parser.add_argument('-dw', '--doseWeight', action='store_true', help='Do dose-weighting on alignment.')
 parser.add_argument('-v', '--verbose', 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('-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.')
@@ -104,8 +105,12 @@ if not subframesDir:
     print("No subframes found in current directory tree, terminating!")
     sys.exit()
 
-stackParams = sorted(stackParams, key = lambda i: i['tiltangle']) 
-inBaseName = re.search("(\w+)\..*", args.input).group(1)
+stackParams = sorted(stackParams, key = lambda i: i['tiltangle'])
+try:
+    inBaseName = re.search("([^\/]+)\.\w+.mdoc$", args.input).group(1)
+except:
+    print("Not a .mdoc file, skipping.")
+    sys.exit()
 stackFileName = os.path.join(mdocDir, inBaseName + ".stackFiles")
 tiltFileName = os.path.join(mdocDir, inBaseName + ".rawTlt")
 
@@ -137,7 +142,7 @@ 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']*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 ))