'Align and weight projections, save them and reconstruct tomogram (optional). \n\
See http://pytom.org/doc/pytom/reconstructTomograms.html for documentation.',
authors='Gijs van der Schot',
options=options)
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
tiltSeriesName, tiltSeriesFormat, firstProj, lastProj, \
tltFile, prexgFile, preBin, referenceIndex, markerFileName, referenceMarkerIndex, expectedRotationAngle, handflip, \
projectionTargets, fineAlignFile, projBinning, lowpassFilter, \
volumeName, filetype, \
tomogramSizeX, tomogramSizeY, tomogramSizeZ, \
reconstructionCenterX, reconstructionCenterY, reconstructionCenterZ, \
numberProcesses, weightingType, projIndices, verbose, help = parse_script_options(sys.argv[1:], helper)
except Exception as e:
print(sys.version_info)
print(e)
sys.exit()
if help is True:
print(helper)
sys.exit()
# input parameters
#tiltSeriesName = tiltSeriesPath + tiltSeriesPrefix # "../projections/tomo01_sorted" # ending is supposed to be tiltSeriesName_index.em (or mrc)
if not tiltSeriesFormat:
tiltSeriesFormat = 'em'
if firstProj:
firstProj = int(firstProj) # 1 # index of first projection
else:
options=[
ScriptOption('-p', 'Projection prefix.', True, False),
ScriptOption('-a', 'Projection suffix.', True, False),
ScriptOption('-w', 'Apply weighting to the projections or not',
False, True),
ScriptOption('-f', 'Projection start index (int).', True, False),
ScriptOption('-t', 'Projection end index (int).', True, False),
ScriptOption('-s', 'Volume size.', True, False),
ScriptOption('-o', 'Output filename.', True, False),
ScriptOption(['-h', '--help'], 'Help.', False, True)
])
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
prefix, suffix, weighting, start_idx, end_idx, vol_size, output, b_help = parse_script_options(
sys.argv[1:], helper)
except Exception as e:
print(e)
sys.exit()
if b_help is True:
print(helper)
sys.exit()
# parse the argument
start_idx = int(start_idx)
end_idx = int(end_idx)
vol_size = [int(i) for i in vol_size.split(",")]
from pytom.reconstruction.reconstructionStructures import Projection, ProjectionList
projections = ProjectionList()
for i in range(start_idx, end_idx + 1):
arg=True,
optional=False),
ScriptOption(['-j', '--jobName'],
'Specify job.xml filename',
arg=True,
optional=False),
ScriptOption(['-h', '--help'], 'Help.', arg=False, optional=True)
])
if len(sys.argv) <= 2:
print(helper)
sys.exit()
try:
particleList, mask, numberClasses, endThreshold,wedge1,wedge2,symmetryN,symmetryAxisZ,symmetryAxisX,\
lowestFrequency,highestFrequency,destination,numberIterations,binning,\
pixelSize,diameter,jobName,help = parse_script_options(sys.argv[1:], helper)
except Exception as e:
print(e)
sys.exit()
if help is True:
print(helper)
sys.exit()
if not checkFileExists(particleList):
raise RuntimeError('ParticleList file ' + particleList +
' does not exist!')
if not checkFileExists(mask):
raise RuntimeError('Mask file ' + mask + ' does not exist!')
'Number of bins of histogram. Default is 10.', True,
True),
ScriptOption(['-p', '--gaussianPeak'],
'The correspondent index of the gaussian peak.', True,
False),
ScriptOption(['-c', '--numberParticles'],
'Number of particles up to CCC value.', True, True),
ScriptOption(['-i', '--imageFile'], 'Save plot to a image file.',
True, True),
ScriptOption(['-h', '--help'], 'Help.', False, True)
])
if len(sys.argv) == 1:
print helper
sys.exit()
try:
pl_filename, num_steps, peak_index, ccc_value, imageFile, help = parse_script_options(
sys.argv[1:], helper)
except Exception as e:
print e
sys.exit()
if help is True:
print helper
sys.exit()
# process the arguments
num_steps = int(num_steps)
if not num_steps:
num_steps = 10
peak_index = int(peak_index)
scores = []
helper = ScriptHelper(
sys.argv[0].split('/')[-1], # script name
description=
'Create a folder with specific folder structure, as used by the GUI.',
authors='GvdS',
options=[
ScriptOption(['-d'], 'Name of Folder.', True, False),
ScriptOption(['-h', '--help'], 'Help.', False, True)
])
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
dir_name, bHelp = parse_script_options(sys.argv[1:], helper)
except:
print(helper)
sys.exit()
if bHelp == True:
print(helper)
sys.exit()
if os.path.exists(dir_name):
raise Exception(
'Folder already exists. Please give non-existent foldername.')
create_project_filestructure(dir_name)
'Create a particle list from the EM files in a directory. Documentation is available at\n\
http://www.pytom.org/doc/pytom/genParticleList.html',
authors='Yuxiang Chen',
options=[
ScriptOption(['-d'], 'Directory', True, False),
ScriptOption(['-p'], 'Particle name prefix', True, True),
ScriptOption(['-w'], 'Wedge Angle (degree)', True, False),
ScriptOption(['-o'], 'Output particle list', True, False),
ScriptOption(['-h', '--help'], 'Help.', False, True)
])
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
dir_name, name_prefix, wedge_angle, output, bHelp = parse_script_options(
sys.argv[1:], helper)
except:
sys.exit()
if bHelp is True:
print(helper)
sys.exit()
if name_prefix is None:
name_prefix = ''
wedge_angle = float(wedge_angle)
w = SingleTiltWedge(wedge_angle)
pl = ParticleList()
all_files = os.listdir(dir_name)
for fname in all_files:
p = None
ScriptOption(['-h', '--help'], 'Help.', False, True)
]
#num_procs=20, num_procs_per_proc=1, tiltseriesname='sorted/sorted_aligned',
#markerfile='sorted/markerfile.em',targets='alignment', firstindex=1, lastindex=21, refindex=11, weightingtype=0, deploy=False
helper = ScriptHelper(
sys.argv[0].split('/')[-1],
description='BATCHSUBMISSION TILT ALIGNMENT: submits \n',
authors='Gijs van der Schot',
options=options)
if len(sys.argv) == 1:
print helper
sys.exit()
fnames_tomograms, projectfolder, numTomograms, num_procs, procPerTomo, tiltSeriesName, firstIndex, lastIndex, referenceIndex, markerFileName, projectionTargets, weightingType, deploy, help = parse_script_options(
sys.argv[1:], helper)
if not projectfolder:
projectfolder = '/home/gijsvds/ost_2/03_Tomographic_Reconstruction'
if not fnames_tomograms:
tomonames = sorted([
t for t in os.listdir(projectfolder) if len(t.split('_')[-1]) == 3
])
fnames_tomograms = '{}/names_tomograms.txt'.format(projectfolder)
out = open(fnames_tomograms, 'w')
for i in tomonames:
out.write(i + '\n')
out.close()
numTomograms = len(tomonames)
if not num_procs: num_procs = 20
if not procPerTomo: procPerTomo = 1
from pytom.tools.script_helper import ScriptHelper, ScriptOption
from pytom.tools.parse_script_options import parse_script_options
options = [
ScriptOption(['-p', '--particleList'], 'Particle List', True, False),
ScriptOption(['-h', '--help'], 'Help.', False, True)
]
helper = ScriptHelper(
sys.argv[0].split('/')[-1], # script name
description=
'Convert particle list to n particle list based on tomoname.',
authors='Gijs van der Schot',
options=options)
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
plName, help = parse_script_options(sys.argv[1:], helper)
except Exception as e:
print(e)
sys.exit()
if help is True:
print(helper)
sys.exit()
if not os.path.exists(plName):
sys.exit()
extractParticleListsByTomoNameFromXML(plName)
ScriptOption(['-h', '--help'], 'Help.', False, True)
]
helper = ScriptHelper(
sys.argv[0].split('/')[-1], # script name
description=
'Extract tilt images from mrcstack, and creation of meta data file.',
authors='Gijs van der Schot',
options=options)
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
filename, outname, num_cycles, help = parse_script_options(
sys.argv[1:], helper)
except Exception as e:
print(e)
sys.exit()
if help is True:
print(helper)
sys.exit()
if os.path.exists(filename):
data = read(filename)
else:
print(helper)
sys.exit()
if num_cycles is None:
authors='Yuxiang Chen',
options=[
ScriptOption(
'-d',
'Unbinned projection directory. Note the projections should be aligned but not weighted!',
True, False),
ScriptOption('-o', 'Output filename.', True, False),
ScriptOption('-i', 'Number of iterations to run.', True, True),
ScriptOption('-m', 'Meta file including tiltangles.', True, True),
ScriptOption(['-h', '--help'], 'Help.', False, True)
])
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
proj_dir, output_filename, iter, metafile, b_help = parse_script_options(
sys.argv[1:], helper)
except Exception as e:
print(e)
sys.exit()
if b_help is True:
print(helper)
sys.exit()
# parse the arguments
if not iter:
iter = 10
else:
iter = int(iter)
if metafile and os.path.exists(metafile):
metadata = loadstar(metafile, dtype=datatype)
ScriptOption(['-b', '--binningFactor'],
'Binning Factor for reconstruction.', True, False),
ScriptOption(['-h', '--help'], 'Help.', False, True)
]
helper = ScriptHelper(
sys.argv[0].split('/')[-1], # script name
description=
'Convert particle list to n particle list based on tomoname.',
authors='Gijs van der Schot',
options=options)
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
plName, logfile, binningFactor, help = parse_script_options(
sys.argv[1:], helper)
except Exception as e:
print(e)
sys.exit()
if help is True:
print(helper)
sys.exit()
if not binningFactor:
binningFactor = 8
else:
try:
binningFactor = int(binningFactor)
except:
print('Invalid binningFactor. Exit.')
'Binning factor of the particle list.', True, True),
ScriptOption(['-g', '--gpuID'], 'Which gpu do you want to use?',
True, True),
ScriptOption(['-m', '--metaFile'],
'Metafile containing tiltangles.', True, True),
ScriptOption(['-a', '--alignmentResultsFile'],
'Alignment ResultsFile', True, True),
ScriptOption([
'-s', '--sizeReconstruction'
], 'Size Reconstruction in pixels. Three numbers separated by a comma.',
True, True),
ScriptOption(['-v', '--verbose'], 'print intermediate output',
False, True)
])
try:
proj_dir, outdir, coordinateBinning, gpu, metafile, alignmentfile, size, verbose = ll = parse_script_options(
sys.argv[1:], helper)
except Exception as e:
print(e)
print(helper)
sys.exit()
coordinateBinning = int(coordinateBinning) if coordinateBinning else 1
metadata = loadstar(metafile, dtype=DATATYPE_METAFILE)
tilt_angles = metadata['TiltAngle']
size = [464, 464, 464] if size is None else list(map(int, size.split(',')))
patches = xp.zeros((size[0], size[1], len(tilt_angles)), dtype=xp.float32)
images = []
tt = time()
optional=False),
ScriptOption(['-c', '--cubeSize'],
'Cube size along each dimension.',
arg=True,
optional=False),
ScriptOption(['--help'],
'Print this help.',
arg=False,
optional=True)
])
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
volFilename, plFilename, cubeSize, help = parse_script_options(
sys.argv[1:], helper)
except:
sys.exit()
if help is True:
print(helper)
sys.exit()
cubeSize = int(cubeSize)
particleList = ParticleList()
try:
particleList.fromXMLFile(plFilename)
except:
from pytom.localization.structures import readParticleFile
particles = readParticleFile(plFilename)
ScriptOption(['-o', '--outputParticleList'],
'classified Particle List.', True, True),
ScriptOption(['-c', '--ccc'], 'constrained correlation matrix.',
True, True),
ScriptOption(['-e', '--neig'], 'number of eigenvectors.', True,
True),
ScriptOption(['-n', '--nclass'], 'number of classes.', True, True),
ScriptOption(['-a', '--average'], 'name for class averages.', True,
True),
ScriptOption(['-h', '--help'], 'Help.', False, True)
])
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
pl, cpl, ccc, neig, nclass, cName, help = parse_script_options(
sys.argv[1:], helper)
except Exception:
sys.exit()
if help is True:
print(helper)
sys.exit()
neig = int(neig)
nclass = int(nclass)
if not cName:
cName = 'class'
doClassification(pl=pl,
cpl=cpl,
ccc=ccc,
neig=neig,
nclass=nclass,
cName=cName)
False, True),
ScriptOption(['-n', '--normalize'],
'Normalize average. False by default.', False, True),
ScriptOption(['-h', '--help'], 'Help.', False, True)
]
helper = ScriptHelper(
sys.argv[0].split('/')[-1], # script name
description='Convert coordinate list to particle list.',
authors='Friedrich Foerster',
options=options)
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
plName, outname, cores, weighting, verbose, showProgressBar, createInfoVol, norm, help = dd = parse_script_options(
sys.argv[1:], helper)
except Exception as e:
print(e)
sys.exit()
if help is True:
print(helper)
sys.exit()
try:
cores = int(cores)
except:
cores = 1
if not os.path.exists(plName):
print('Please provide an existing particle list')
ScriptOption(['-o', '--outputVolumePath'],
'Path to output volume ',
arg=True,
optional=False),
ScriptOption(['-i', '--invertDensity'],
'Set if density should be negative',
arg=False,
optional=False),
ScriptOption(['-h', '--help'], 'Help.', arg=False, optional=True)
])
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
mmCIF, chain, pixelSize, cubeSize, volumePath, densityNegative, helpme = parse_script_options(
sys.argv[1:], helper)
except:
sys.exit()
if helpme is True:
print(helper)
sys.exit()
pass
volume = mmCIF2em(mmCIF,
float(pixelSize),
int(cubeSize),
chain=chain,
densityNegative=densityNegative)
volume.write(volumePath)
description='Calculate the correlation matrix, given the aligned particle list. The result will be written to the disk named correlation_matrix.csv.',
authors='Yuxiang Chen',
options= [ScriptOption(['-p'], 'Aligned particle list file.', True, False),
ScriptOption(['-m'], 'Mask.', True, False),
ScriptOption(['-f'], 'Frequency (after binning).', True, False),
ScriptOption(['-b'], 'Binning factor.', True, True),
ScriptOption(['-v'], 'Verbose mode.', False, True),
ScriptOption(['-o'], 'Output directory.', True, True),
ScriptOption(['--help'], 'Help info.', False, True)])
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
pl_filename, mask_filename, freq, binning, verbose, outdir, help = parse_script_options(sys.argv[1:], helper)
except Exception as e:
print(e)
sys.exit()
if help is True:
print(helper)
sys.exit()
if verbose:
from pytom.tools.timing import Timing
t = Timing()
t.start()
# construct the job
freq = int(freq)
'-g', '--createGraphics'
], 'Flag to turn on to create graphical reports of intermediate steps of '
'the particle polishing', False, True),
ScriptOption(
['-n', '--numberOfParticles'],
'To take a subset of the particlelist for debugging purposes',
True, True),
ScriptOption(['--metaFile'], 'Metafile containing tiltangles.',
True, True),
ScriptOption(['-v', '--verbose'], 'print intermediate output',
False, True)
])
try:
particleList, proj_dir, template, outdir, fsc_path, coordinateBinning, recOffset, max_shift, \
create_graphics, number_of_particles, metafile, verbose = ll = parse_script_options(sys.argv[1:], helper)
except Exception as e:
print(e)
print(helper)
sys.exit()
print(ll)
vol_size = read_size(template, 'x')
if vol_size % 2 != 0:
raise ValueError("The particle size has to be an even number.")
coordinateBinning = int(coordinateBinning) if coordinateBinning else 1
recOffset = list(map(int,
recOffset.split(','))) if recOffset else [0, 0, 0]
max_shift = int(max_shift) if max_shift else 6
create_graphics = True if create_graphics else False
sys.argv[0].split('/')[-1], # script name
description=
'Select the particle list for alignment according to the class list.',
authors='Yuxiang Chen',
options=[
ScriptOption('-p', 'Particle list.', True, False),
ScriptOption('-c', 'Class label file.', True, False),
ScriptOption('-o', 'Output particle list.', True, False),
ScriptOption('-t', 'True positive class.', True, True),
ScriptOption(['-h', '--help'], 'Help.', False, True)
])
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
pl_filename, class_label_filename, output, tp_label, help = parse_script_options(
sys.argv[1:], helper)
except Exception as e:
print(e)
sys.exit()
if help is True:
print(helper)
sys.exit()
if tp_label is None:
tp_label = 1
else:
tp_label = int(tp_label)
from pytom.basic.structures import ParticleList
pl = ParticleList(".")
pl.fromXMLFile(pl_filename)
ScriptOption(['-h', '--help'], 'Help.', False, True)
]
helper = ScriptHelper(
sys.argv[0].split('/')[-1], # script name
description=
'Extract tilt images from mrcstack, and creation of meta data file.',
authors='Gijs van der Schot',
options=options)
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
filename, outname, numSTD, smooth, num_cycles, mask, help = parse_script_options(
sys.argv[1:], helper)
except Exception as e:
print(e)
sys.exit()
if help is True:
print(helper)
sys.exit()
if os.path.exists(filename):
data = read(filename)
else:
print(helper)
sys.exit()
num_cycles = 2 if num_cycles is None else int(num_cycles)
['--scale'],
'Scale coordinates by a factor. Set > 1 to adjust to larger volumes. Use 2 if the localization tomo was 1x binned.',
arg=True,
optional=True),
ScriptOption(['--help'],
'Print this help.',
arg=False,
optional=True)
])
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
jobFilename, maskFile, resultFilename, orientFilename, maxNumParticle, sizeParticle, plFilename, particlePath, minScore, motlFilename, margin, write2disk, scale, help = parse_script_options(
sys.argv[1:], helper)
except:
sys.exit()
if help is True:
print(helper)
sys.exit()
if minScore == None:
minScore = -1
else:
minScore = float(minScore)
if write2disk == None:
write2disk = 0
if margin.__class__ == str:
margin = int(margin)
if particlePath is None:
ScriptOption(['--particleDiameter'], 'Particle diameter in Angstrom', arg=True,
optional=False),
ScriptOption(['-w', '--weighting'], 'Weight particles by exp of CC', arg=False,
optional=True),
ScriptOption(['-c', '--compound'], 'Use compound weighting in Fourier space',
arg=False, optional=True),
ScriptOption(['-j','--jobName'], 'Specify job.xml output filename', arg=True,
optional=False),
ScriptOption(['-h', '--help'], 'Help.', arg=False, optional=True)])
if len(sys.argv) <= 2:
print(helper)
sys.exit()
try:
results = parse_script_options(sys.argv[1:], helper)
particleList, reference, mask, isSphere, angShells, angleInc, scoreObject, \
symmetryN, symmetryAxisZ, symmetryAxisX,\
destination, numberIterations, binning,\
pixelSize, diameter, weighting, compound, jobName, help = results
except Exception as e:
print(e)
sys.exit()
if help is True:
print(helper)
sys.exit()
from pytom.alignment.GLocalSampling import GLocalSamplingJob, mainAlignmentLoop
from pytom.basic.structures import ParticleList, Reference, Mask, SampleInformation, PointSymmetry
from pytom.score.score import FLCFScore, nxcfScore
'Align and weight projections, save them and reconstruct tomogram (optional). \n\
See http://pytom.org/doc/pytom/reconstructTomograms.html for documentation.',
authors='Friedrich Foerster',
options=options)
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
tiltSeriesName, tiltSeriesFormat, firstProj, lastProj, projIndices,\
tltFile, prexgFile, preBin, referenceIndex, markerFileName, alignResultFile, referenceMarkerIndex, expectedRotationAngle, \
projectionTargets, fineAlignFile, projBinning, lowpassFilter, \
volumeName, filetype, \
tomogramSizeX, tomogramSizeY, tomogramSizeZ, \
reconstructionCenterX, reconstructionCenterY, reconstructionCenterZ, \
weightingType, noOutputImages, verbose, help = parse_script_options(sys.argv[1:], helper)
except Exception as e:
print(sys.version_info)
print(e)
print()
print(helper)
sys.exit()
if help is True:
print(helper)
sys.exit()
if (markerFileName is None) and (alignResultFile is None):
raise Exception(
'Please provide either a markerfile or an alignmentResults.txt file'
)
options = [ScriptOption(['-f','--FCSFile'], 'File with FSC values in single column', True, False),
ScriptOption(['-b','--boxSize'], 'Box size of average', True, False),
ScriptOption(['-p','--pixelSize'],'Pixel size of voxels in model.',True, False),
ScriptOption(['-o','--outputName'],'Save figure under this name.',True, True),
ScriptOption(['-s','--show'],'Show figure.',False, True),
ScriptOption(['-c','--FSCCutoff'],'Cut-off used to determine the resolution of your object from the FSC curve. Typical values are 0.5 or 0.143.', True, False),
ScriptOption(['-h', '--help'], 'Help.', False, True)]
helper = ScriptHelper(sys.argv[0].split('/')[-1], description='Convert coordinate list to particle list.',
authors='Gijs van der Schot', options=options)
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
FSCFile, boxsize, pixelsize, outname, show_image, cutoff, help = parse_script_options(sys.argv[1:], helper)
except Exception as e:
print(e)
sys.exit()
if help is True:
print(helper)
sys.exit()
if not boxsize: boxsize=0
if not os.path.exists(FSCFile):
print('FSC File does not exist')
sys.exit()
if not outname:
'Print this help.',
arg=False,
optional=True)
])
if len(sys.argv) == 1:
print(helper)
sys.exit()
particleList = None
projectionDirectory = None
aw = False
try:
tomogram, particleListXMLPath, prefix, logfile, projectionList, projectionDirectoryTemplate, aw, size, coordinateBinning, \
recOffset, projBinning, metafile, numProcesses, help= parse_script_options(sys.argv[1:], helper)
except Exception as e:
print(e)
sys.exit()
if help:
print(helper)
sys.exit()
size = [int(i) for i in size.split(",")]
if len(size) == 1:
tmp = size[0]
size.append(tmp)
size.append(tmp)
True, True),
ScriptOption(['-h', '--help'], 'Help.', False, True)
]
helper = ScriptHelper(
sys.argv[0].split('/')[-1], # script name
description='Update paramters in a particle list.',
authors='Gijs van der Schot',
options=options)
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
outname, XMLfnames, suffix, prefix, wedgeangles, rotate, shiftBin, help = parse_script_options(
sys.argv[1:], helper)
except Exception as e:
print(e)
sys.exit()
if help is True:
print(helper)
sys.exit()
fnames = []
if wedgeangles:
wedgeangles = wedgeangles.split(',')
if len(wedgeangles) % 2:
wedgeangles = wedgeangles + [wedgeangles[-1]]
else:
description='Convert em file to mrc.',
authors='Thomas Hrabe',
options=[
ScriptOption(['-f', '--file'], 'Filename', True, True),
ScriptOption(['-d', '--directory'], 'A directory of files.', True,
True),
ScriptOption(['-t', '--targetPath'], 'Path to new file.', True,
True),
ScriptOption(['-h', '--help'], 'Help.', False, True)
])
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
filename, directory, target, help = parse_script_options(
sys.argv[1:], helper)
except Exception as e:
print(e)
sys.exit()
if help is True:
print(helper)
sys.exit()
if filename:
#convert only one file
em2mrc(filename, target)
elif directory:
import os
fileList = os.listdir(directory)
for file in fileList:
helper = ScriptHelper(
sys.argv[0].split('/')[-1],
description='Subtomogram alignment by Fast Rotational Matching.',
authors='Yuxiang Chen',
options=[
ScriptOption(['-j'], 'Job xml file.', True, False),
ScriptOption(['-v'], 'Verbose mode.', False, True),
ScriptOption(['--help'], 'Help info.', False, True)
])
if len(sys.argv) == 1:
print(helper)
sys.exit()
if 1:
job_filename, verbose, bHelp = parse_script_options(
sys.argv[1:], helper)
else:
sys.exit()
if bHelp is True:
print(helper)
sys.exit()
# check the job
job = FRMJob()
job.fromXMLFile(job_filename)
job.check()
worker = FRMWorker()
if verbose:
]
helper = ScriptHelper(
sys.argv[0].split('/')[-1], # script name
description=
'Extract tilt images from mrcstack, and creation of meta data file.',
authors='Gijs van der Schot',
options=options)
# mpi.begin()
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
filename, outdir, prefix, origdir, mdoc, help = parse_script_options(
sys.argv[1:], helper)
except Exception as e:
print(e)
sys.exit()
if help is True:
print(helper)
sys.exit()
if mdoc is None: mdoc = False
else: mdoc = True
if os.path.exists(filename):
data = mrcfile.open(filename, permissive=True).data.copy()
print(data.shape)
else:
from pytom.tools.script_helper import ScriptHelper, ScriptOption
from pytom.tools.parse_script_options import parse_script_options
helper = ScriptHelper(
sys.argv[0].split('/')[-1], # script name
description='Mirror the volume.',
authors='Yuxiang Chen',
options=[
ScriptOption(['-v'], 'Input volume.', True, False),
ScriptOption(['-o'], 'Output volume.', True, True),
ScriptOption(['-h', '--help'], 'Help.', False, True)
])
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
input_filename, output_filename, help = parse_script_options(
sys.argv[1:], helper)
except Exception as e:
print(e)
sys.exit()
if help is True:
print(helper)
sys.exit()
# process the arguments
if output_filename is None:
output_filename = input_filename.split('.')[0] + '_mirror.em'
from pytom_volume import read, vol, mirrorVolume
v = read(input_filename)
res = vol(v)
mirrorVolume(v, res)
