Commit 905812be authored by Adrian Nievergelt's avatar Adrian Nievergelt
Browse files

cuda version update adjustments

parent 8fbd5825
......@@ -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,
......
......@@ -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.")
......
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