cuda version update adjustments

processing/mc2FromMDOC.py

@@ -34,7 +34,7 @@ parser.add_argument('-i', '--input', nargs='+', default='.', help='Input MDOC fi
 # parser.add_argument('-d', '--outDir', nargs='?', default='.', help='Optional output directory to write scripts to.')
 # parser.add_argument('-dp', '--dataPath', nargs='?', default='.', help='Optional override to use if the data is mounted in a different network base path.')
 # parser.add_argument('-cp', '--clusterPath', nargs='?', default='/projects/project-nieverge/', help='Destination path of the HPC filesystem data directory.')
-parser.add_argument('-cv', '--cudaVer', nargs='?', type=int, default=92, help='Override CUDA version. Default 92. Reduce to a lower value if MotionCor2 does not run properly with the installed graphics card.')
+parser.add_argument('-cv', '--cudaVer', nargs='?', type=int, default=0, help='Override CUDA version. Default 92. Reduce to a lower value if MotionCor2 does not run properly with the installed graphics card.')
 parser.add_argument('-ps', '--patchSize', nargs='?', type=int, default=3, help='Override local alignment patch count. Default 3.')
 parser.add_argument('-b', '--binning', nargs='?', type=int, default=1, help='Output binning. Default 1 (no binning).')
 parser.add_argument('-bfg', '--bFactorGlobal', nargs='?', type=int, default=800, help='Global bFactor. Default 800.')
@@ -210,9 +210,13 @@ for inputFile in args.input:
             else:
                 doseWeightParams = ""
 
+            if args.cudaVer is not 0:
+                cudaExtra = "-cuda" + str(args.cudaVer)
+            else:
+                cudaExtra = ""
             scriptFile.write("echo Aligning frame stack %s \n" % (os.path.join(sourceDir, imageParams['filename']) ))
-            scriptFile.write("MotionCor2-cuda%i -InMrc \"%s\" -OutMrc \"%s\" -Patch %i %i -Bft %i %i \
-             -InFmMotion 0 -Iter 10 -Tilt %f -Group %i -FtBin %i -PixSize %f%s %s\n\n" %(args.cudaVer,
+            scriptFile.write("MotionCor2%s -InMrc \"%s\" -OutMrc \"%s\" -Patch %i %i -Bft %i %i \
+             -InFmMotion 0 -Iter 10 -Tilt %f -Group %i -FtBin %i -PixSize %f%s %s\n\n" %(cudaExtra,
                                                                                          os.path.join(sourceDir, imageParams['filename']),
                                                                                          os.path.join(alignedDir, imageParams['filename']),
                                                                                          args.patchSize, args.patchSize,

subtomogramAveraging/multiplyMOTL.py

@@ -4,7 +4,7 @@
 
 import os,sys
 import argparse
-import matplotlib.pyplot as plt
+#import matplotlib.pyplot as plt
 import csv
 
 parser = argparse.ArgumentParser(description = "Takes a PEET motif list (MOTL) file and duplicates the motif descriptor lines a specified number of times.")