fix silencing

processing/mc2FromMDOC.py

@@ -103,13 +103,19 @@ stackFileName = os.path.join(mdocDir, inBaseName + ".stackFiles")
 tiltFileName = os.path.join(mdocDir, inBaseName + ".rawTlt")
 
 with open(stackFileName, "w+") as stackFile:
+    stackFile.write("%i\n" % ( len(stackParams) ))
     for imageParams in stackParams:
-        stackFile.write("%s\n" % (os.path.join(alignedDir, imageParams['filename']) ))
+        stackFile.write("%s\n0\n" % (os.path.join(alignedDir, imageParams['filename']) ))
 
 with open(tiltFileName, "w+") as tiltFile:
     for imageParams in stackParams:
         tiltFile.write("%f\n" % (imageParams['tiltangle']) )
 
+if args.verbose:
+    verboseString = ""
+else:
+    verboseString = " &>/dev/null"
+
 with open(os.path.join(mdocDir, inBaseName + "_alignFramesMC2.sh"), "w+") as scriptFile:
     scriptFile.write("#!/bin/bash\n\n")
     scriptFile.write("# Script file for motioncor2 alignment of tilt series created by mc2FromMDOC.py on %s by %s\n\n" % (datetime.today().strftime('%Y-%m-%d %H:%M'), getpass.getuser()) )                 
@@ -122,16 +128,12 @@ with open(os.path.join(mdocDir, inBaseName + "_alignFramesMC2.sh"), "w+") as scr
             doseWeightParams = " -Kv 300 -FmDose %f -InitDose %f" % (imageParams['frameDose'], imageParams['priorrecorddose'])
         else:
             doseWeightParams = ""
-        if args.verbose:
-            verboseString = ""
-        else:
-            verboseString = " &>/dev/null"
             
         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("echo Creating combined tilt series stack %s\n" % (inBaseName + "_mc2.mrc"))
-    scriptFile.write("imodenv")    
-    scriptFile.write("newstack -fileinlist %s -output %s -tilt %s\n\n" % ( os.path.basename(stackFileName), inBaseName + "_mc2.mrc", os.path.basename(tiltFileName) ))
+    scriptFile.write("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 ))
     
     if not args.keepFrames:
         scriptFile.write("echo Removing temporary aligned files.\n")