averageClasses(particleListFilename=cpl, avName=cName)
if __name__ == '__main__':
import sys
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=
'Classification of particle list using CPCA. Documentation is available at\n\
http://www.pytom.org/doc/pytom/classification.html',
authors='Friedrich Foerster',
options=[
ScriptOption(['-p', '--particleList'], 'ParticleList', True, True),
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:
@author: yuxiangchen
'''
if __name__ == '__main__':
# parse command line arguments
import sys
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=
'Reconstruct a volume from its projections using weighted back projection.',
authors='Yuxiang Chen',
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)
import sys
from pytom.tools.script_helper import ScriptHelper, ScriptOption
from pytom.tools.parse_script_options import parse_script_options
from pytom.tools.files import checkFileExists, checkDirExists
helper = ScriptHelper(
sys.argv[0].split('/')[-1],
description=
'Create an EXMX alignment job. Documentation is available at\n \
http://www.pytom.org/doc/pytom/classification.html',
authors='Thomas Hrabe',
options=[
ScriptOption(
['-p', '--particleList'],
'Particle list : xml file storing information to all subvolumes',
arg=True,
optional=False),
ScriptOption(['-m', '--mask'],
'Mask : a mask ',
arg=True,
optional=False),
ScriptOption(['-c', '--classes'],
'Number of classes',
arg=True,
optional=False),
ScriptOption(['-t', '--endThreshold'],
'End threshold',
arg=True,
optional=False),
ScriptOption(['--wedge1'],
@author: yuxiangchen
'''
if __name__ == '__main__':
# parse command line arguments
import sys
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='Do the Gaussian fitting on the found particle list.',
authors='Yuxiang Chen',
options=[
ScriptOption(['-f', '--file'],
'Particle list after extracting candidates.', True,
False),
ScriptOption(['-n', '--numberBins'],
'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
@author: GvdS
'''
if __name__ == '__main__':
# parse command line arguments
import sys, os
from pytom.tools.script_helper import ScriptHelper, ScriptOption
from pytom.tools.parse_script_options import parse_script_options
from pytom.gui.guiFunctions import create_project_filestructure
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)
if __name__ == '__main__':
# parse command line arguments
import sys
from pytom.tools.script_helper import ScriptHelper, ScriptOption
from pytom.tools.parse_script_options import parse_script_options
from pytom.basic.structures import Particle, ParticleList, SingleTiltWedge
import os
helper = ScriptHelper(
sys.argv[0].split('/')[-1], # script name
description=
'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:
if __name__ == "__main__":
from pytom.tools.script_helper import ScriptHelper, ScriptOption
from pytom.tools.parse_script_options import parse_script_options
from pytom.gui.additional.reconstructionFunctions import alignWeightReconstruct
from pytom_volume import read
from pytom_numpy import vol2npy
import os
from multiprocessing import Process
import time
import sys
options = [
ScriptOption(
['--fileTomoFolders'],
'File with tomogram folder names (Relative to projectfolder)',
arg=True,
optional=False),
ScriptOption(
['--projectFolder'],
'base folder where all tomograms are located in. From this folder jobs will be submitted.',
arg=True,
optional=False),
ScriptOption(['--numberOfTomograms'],
'Number of tomograms.',
arg=True,
optional=False),
ScriptOption(['--numberProcesses'],
'Number of occupied CPU cores per node.',
arg=True,
optional=True),
print('writing {} failed.'.format(xmlfile))
print('No file written.')
pL = tree.xpath('Particle')
#print(os.path.basename(tomogram), len(pL))
return outfiles
if __name__ == '__main__':
import sys
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:
from pylab import *
from skimage.morphology import *
from scipy.ndimage.morphology import binary_fill_holes
from scipy.ndimage import label
from scipy.ndimage.filters import gaussian_filter
from scipy.ndimage import median_filter
if __name__ == '__main__':
import sys
from pytom.tools.script_helper import ScriptHelper, ScriptOption
from pytom.tools.parse_script_options import parse_script_options
from pytom.basic.structures import ParticleList
options = [
ScriptOption(['-f', '--fileName'], 'Filename of model.', True, False),
ScriptOption(['-o', '--outputName'], 'Filename of mask file.', True,
False),
ScriptOption(['-b', '--binaryDilationCycles'],
'Number of binary dilation cycles.', True, False),
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:
outfname = '.tempCM_particleList_{}_refMarkerIndex_{}.xml'.format(
pl_key, markerIndex)
outfname = os.path.join(directory, outfname)
outLists[markerIndex].toXMLFile(outfname)
xmlsCM.append([markerIndex, outfname])
return xmlsCM
if __name__ == '__main__':
import sys
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(['-l', '--logfileReconstruction'], 'Particle List', True,
False),
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)
module load imod/4.10.25
cd {}
ctfphaseflip -inp ../sorted/{}_sorted.st -o ctfCorrected.st -an ../sorted/{}_sorted.tlt -defF resultsCTFPlotter.defocus -defT 200 -iW 15 -pi 0.1724 -am 0.08 -cs 2.7 -vo 200 -AxisAngle 270
'''
if __name__ == '__main__':
import sys
import os
from pytom.tools.script_helper import ScriptHelper, ScriptOption
from pytom.tools.parse_script_options import parse_script_options
from pytom.basic.structures import ParticleList
options = [
ScriptOption(['-f', '--fileName'], 'Filename of project folders.',
True, False),
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:
import os
from pytom.gui.guiFunctions import datatype, loadstar
if __name__ == '__main__':
# parse command line arguments
import sys
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=
'Reconstruct the whole tomogram from projections using iterative NFFT method.',
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()
from pytom.tompy.reconstruction_functions import backProjectGPU
from pytom.tompy.io import write, read
from pytom_numpy import vol2npy
import numpy
import os
from time import time, sleep
from pytom.gui.guiFunctions import loadstar
from pytom.basic.datatypes import DATATYPE_METAFILE
helper = ScriptHelper(
sys.argv[0].split('/')[-1], # script name
description=
'Reconstruct a tomogram on a GPU based on a alignment Results alignment.',
authors='Gvds',
options=[
ScriptOption(['-p', '--projectionDirectory'],
'Projection Directory', True, False),
ScriptOption(['-o', '--outputDirectory'],
'Results are written to this directory', True, False),
ScriptOption(['-b', '--coordinateBinning'],
'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',
from pytom.tools.parse_script_options import parse_script_options
from pytom_volume import read, subvolume
from pytom.tools.ProgressBar import FixedProgBar
from pytom.basic.structures import ParticleList
from pytom.tools.files import checkDirExists
import os
helper = ScriptHelper(
sys.argv[0].split('/')[-1],
description=
'Cut particles out from a volume, given the particle list. Documentation is available at\n\
http://www.pytom.org/doc/pytom/cutParticles.html',
authors='Yuxiang Chen',
options=[
ScriptOption(['-v', '--volume'],
'Volume.',
arg=True,
optional=False),
ScriptOption(['-p', '--particleFile'],
'Particle list.',
arg=True,
optional=False),
ScriptOption(['-c', '--cubeSize'],
'Cube size along each dimension.',
arg=True,
optional=False),
ScriptOption(['--help'],
'Print this help.',
arg=False,
optional=True)
])
createInfoVolumes=False,
weighting=False,
norm=False,
setParticleNodesRatio=3,
cores=cores)
#evenAverage.getVolume().write('Even.em')
if __name__ == '__main__':
import sys
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(['-a', '--averageName'], 'Filename of output average.',
True, False),
ScriptOption(['-c', '--numberOfCores'],
'Number of Cores used for average calculation', True,
False),
ScriptOption(
['-w', '--weighting'],
'Weight particles by exp CC in average. False by default.', False,
True),
ScriptOption(['-v', '--verbose'],
'Print particle information. False by default.', False,
True),
ScriptOption(['-s', '--showProgressBar'],
'Show progress bar. False by default.', False, True),
ScriptOption([
if __name__ == '__main__':
# parse command line arguments
import sys
from pytom.tools.script_helper import ScriptHelper, ScriptOption
from pytom.tools.parse_script_options import parse_script_options
from pytom.basic.files import mmCIF2em
helper = ScriptHelper(
sys.argv[0].split('/')[-1], # script name
description='Compile a electron density from PDB file\n\
http://pytom.org/doc/pytom/files.html',
authors='Thomas Hrabe',
options=[
ScriptOption(['-m', '--mmCIFFile'],
'A mmCIF file',
arg=True,
optional=False),
ScriptOption(['-c', '--chain'], 'A Chain', arg=True,
optional=True),
ScriptOption(['-s', '--pixelSize'],
'Pixel size of output volume (in Angstrom)',
arg=True,
optional=True),
ScriptOption(['-v', '--volumeSize'],
'Volume length (size) in all dimensions',
arg=True,
optional=True),
ScriptOption(['-o', '--outputVolumePath'],
'Path to output volume ',
arg=True,
optional=False),
sub_job["Binning"] = job["Binning"]
self.send_job(sub_job, i)
if verbose:
print(self.node_name + ': distributed %d particles to node %d' % (len(sub_pairs), i))
if __name__ == '__main__':
# parse command line arguments
import sys
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],
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)
from pytom.tools.parse_script_options import parse_script_options
from pytom.tompy.mpi import MPI
from time import gmtime, strftime
from pytom.polishing.reconstruct_local_alignment import polish_particles
from pytom.tompy.io import read_size
from pytom.tompy.mpi import MPI
from pytom.reconstruction.reconstructionStructures import ProjectionList
import sys
helper = ScriptHelper(
sys.argv[0].split('/')[-1], # script name
description=
'Reconstruct a local alignment of particles based on a global alignment.',
authors='Douwe Schulte',
options=[
ScriptOption(['-p', '--particleList'], 'particleList', True,
False),
ScriptOption(['--projectionDirectory'], 'Projection Directory',
True, False),
ScriptOption([
'-t', '--template'
], 'The path to an averaged subtomogram, to use instead of many subtomograms',
True, False),
ScriptOption(['--outputDirectory'],
'Results are written to this directory', True, False),
ScriptOption([
'-f', '--FSCPath'
], "The path to an FSC file (.dat) to use as a filter for the cutouts.",
True, True),
ScriptOption(['-b', '--coordinateBinning'],
'Binning factor of the particle list.', True, True),
ScriptOption(
@author: yuxiangchen
'''
if __name__ == '__main__':
# parse command line arguments
import sys
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=
'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:
if outname is None:
return mask
else:
write(outname, mask.astype(float32))
return mask
if __name__ == '__main__':
import sys
from pytom.tools.script_helper import ScriptHelper, ScriptOption
from pytom.tools.parse_script_options import parse_script_options
from pytom.basic.structures import ParticleList
options = [
ScriptOption(['-f', '--fileName'], 'Filename of model.', True, False),
ScriptOption(['-o', '--outputName'], 'Filename of mask file.', True,
False),
ScriptOption([
'-n', '--numStd'
], 'The particle threshold is set to mean - stdev * numStd. Default value = 1',
True, True),
ScriptOption([
'-s', '--smooth'
], 'Smooth factor used to soften the edges of the mask (pixels). Default = 2',
True, True),
ScriptOption(['-c', '--numDilationCycles'],
'Number of binary dilation cycles. Default = 2', True,
True),
ScriptOption(['-m', '--mask'],
'Number of binary dilation cycles. Default = 2', True,
return particleList
if __name__ == '__main__':
import sys, os
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],
description='Extract candidate molecules from localization result.',
authors='Yuxiang Chen',
options=[
ScriptOption(['-j', '--jobFile'],
'Localization job XML file.',
arg=True,
optional=False),
ScriptOption(['-q', '--mask'],
'Mask file (mask.em).',
arg=True,
optional=True),
ScriptOption(['-r', '--result'],
'File with score coefficients (score.em).',
arg=True,
optional=False),
ScriptOption(['-o', '--orientation'],
'File with orientation indices (angles.em).',
arg=True,
optional=False),
ScriptOption(['-n', '--numberCandidates'],
'Number of candidates to extract.',
'''
if __name__ == '__main__':
# parse command line arguments
import sys
from pytom.tools.script_helper import ScriptHelper, ScriptOption
from pytom.tools.parse_script_options import parse_script_options
from pytom.tools.files import checkFileExists,checkDirExists
helper = ScriptHelper(sys.argv[0].split('/')[-1],
description='Create an GLocalSampling job. Documentation is available at\n\
http://www.pytom.org/doc/pytom/alignment.html',
authors='Friedrich Foerster',
options=[ScriptOption(['-p','--particleList'],
'Particle list : xml file storing information to all subvolumes',
arg=True, optional=False),
ScriptOption(['-r','--reference'],
'Reference : the initial reference - if none provided average of particle list',
arg=True, optional=True),
ScriptOption(['-m','--mask'], 'Mask : a mask ', arg=True, optional=False),
ScriptOption(['--SphericalMask'], 'Mask is spherical / speed up!', arg=False,
optional=True),
ScriptOption(['--angleShells'], '# angle shells used for angular refinement. Default= 3',
arg=True, optional=True),
ScriptOption(['--angleIncrement'], 'Angular increment for refinement. Default = 3',
arg=True, optional=True),
ScriptOption(['-s','--scoreObject'],
'Score Object, i.e., the scoring function. Options: FLCF, NXCF. Default = FLCF',
arg=True, optional=True),
ScriptOption(['--symmetry'], 'PointSymmetry : specify n-fold symmetry (n)',
@author: FF
"""
if __name__ == '__main__':
import sys
#from pytom.reconstruction.TiltAlignmentStructures import TiltAlignmentParameters, TiltSeries, TiltAlignment
from pytom.tools.script_helper import ScriptHelper, ScriptOption
from pytom.tools.parse_script_options import parse_script_options
from pytom.reconstruction.reconstructionFunctions import alignWeightReconstruct
import numpy
import os
options = [
ScriptOption(
['--tiltSeriesName'],
'Name tilt series - either prefix of sequential tilt series files \
expected as "tiltSeriesName_index.em/mrc" or full name of stack "tiltSeriesName.st"',
arg=True,
optional=False),
ScriptOption(
['--tiltSeriesFormat'],
'Format of tilt series (series of "em" or "mrc" images or "st" stack).',
arg=True,
optional=True),
ScriptOption(['--firstIndex'],
'Index of first projection.',
arg=True,
optional=True),
ScriptOption(['--lastIndex'],
'Index of last projection.',
arg=True,
optional=True),
ax.legend()
ax.set_yticks([ 0, 0.25, 0.5, 0.75, 1])
ax.set_yticklabels([0,0.25,0.5,0.75,1])
fig.tight_layout()
if outname:
savefig(outname)
if show_image:
show()
if __name__ == '__main__':
import sys
from pytom.tools.script_helper import ScriptHelper, ScriptOption
from pytom.tools.parse_script_options import parse_script_options
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)
from pytom.tools.files import checkFileExists, checkDirExists
from pytom.basic.files import read_em_header
from pytom.bin.createXMLsClosestMarker import *
from pytom.gui.guiFunctions import datatypeAR
helper = ScriptHelper(
sys.argv[0].split('/')[-1],
description=
'Reconstruct particles in a particle list. Documentation is available at\n\
http://www.pytom.org/doc/pytom/resonstructTomograms.html or\n\
http://www.pytom.org/doc/pytom/resonstructSubtomograms.html',
authors='Thomas Hrabe, FF',
options=[
ScriptOption(
['-t', '--tomogram'],
'Reconstruct a tomogram. Specify name of tomogam here. You do not need a particle list for that!',
arg=True,
optional=True),
ScriptOption(['-p', '--particleList'],
'XML particle list.',
arg=True,
optional=True),
ScriptOption(['-r', '--prefixFileName'],
'Prefix of files that are selected.',
arg=True,
optional=True),
ScriptOption(
['-l', '--logfileReconstruction'],
'Log files reconstruction, containing the positions of the markers.',
arg=True,
optional=True),
tempPL.toXMLFile(outnames[n])
if mirror:
mirrorParticleList(outnames[n],
outnames[n],
directory=tomogram_dir)
if __name__ == '__main__':
import sys
from pytom.tools.script_helper import ScriptHelper, ScriptOption
from pytom.tools.parse_script_options import parse_script_options
from pytom.basic.structures import ParticleList
options = [
ScriptOption(['-o', '--outputName'], 'Output name of xml', True,
False),
ScriptOption(['-f', '--fileName'], 'particleList filesname.', True,
False),
ScriptOption(
['-s', '--suffix'],
'Suffix placed behind last dirname before particle_??.em.', True,
True),
ScriptOption([
'-d', '--subtomoDirectory'
], 'Update directory of subtomogram reconstructions. If "particle_" is included in name, only dirname before prefix is considered',
True, True),
ScriptOption([
'-w', '--wedgeAngles'
], 'Wedge angles for all particles. if one angle is given, both angles are updated with this angle.',
True, True),
ScriptOption([
emfile.write(newFilename, 'mrc')
if __name__ == '__main__':
# parse command line arguments
import sys
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='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)
': distributed %d particles to node %d' %
(len(subPL), i))
if __name__ == '__main__':
# parse command line arguments
import sys
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],
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:
else:
outname = os.path.join(outdir, '{}{:02d}.mrc'.format(prefix, sliceId))
print(f'extracted {os.path.basename(outname)} into {outdir}')
# write(outname, data[:,:,sliceId], tilt_angle=tiltangle)
mrcfile.new(outname, dataSlice.astype('float32'), overwrite=True)
if __name__ == '__main__':
import sys
from pytom.tools.script_helper import ScriptHelper, ScriptOption
from pytom.tools.parse_script_options import parse_script_options
from pytom.basic.structures import ParticleList
options = [
ScriptOption(['-f', '--fileName'], 'Filename of mrc stack.', True,
False),
ScriptOption(['-t', '--targetDir'],
'Folder in which the output files are saved', True,
False),
ScriptOption(['-p', '--prefix'],
'Prefix to filename. Default name of file.', True, False),
ScriptOption(
['-o', '--origDir'],
'Directory from which images in the stack originate. '
'It will use the prefix "sorted" to select the output file names.',
True, False),
ScriptOption(['-m', '--mdoc'], 'Create truncated mdoc files.', False,
True),
ScriptOption(['-h', '--help'], 'Help.', False, True)
]
out.write('{:8.0f} {:8.0f} {:8.0f}\n'.format(x, y, z))
out.close()
if __name__ == '__main__':
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='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', '--target'], 'Path to output folder.', True,
True),
ScriptOption(['-s', '--size'], 'mdoc name.', True, True),
ScriptOption(['-p', '--postfix'], 'Prefix to filename.', True,
True),
ScriptOption(['-h', '--help'], 'Help.', False, True)
])
if len(sys.argv) == 1:
print(helper)
sys.exit()
try:
filename, directory, target, size, postfix, help = parse_script_options(