def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("-i", "--input", type=str, help="Particle star file")
parser.add_argument("-o",
"--output",
type=str,
help="Output directory",
default=None)
parser.add_argument("-cols",
"--columns",
type=str,
help="Columns to copy",
nargs='*',
default=None)
args = parser.parse_args()
# Prepare args dict
args_dict = {
'input': args.input,
'output': args.output,
'columns': args.columns
}
# Check if the input file exists
if args_dict['input'] is None or not os.path.isfile(args_dict['input']):
parser.print_help()
sys.exit('Input file does not exist!')
# Get the new column parameters
if args_dict['columns'] is not None:
new_column_parameters = util.parse_star_parameters(
args_dict['columns'])
else:
new_column_parameters = None
# Create an EM project object
new_project = em.Project(name='EMRenameColumns')
new_project.set_output_directory(args_dict['output'], project_root='.')
# Write parameters to args filename
args_filename = new_project.output_directory + '/args.yaml'
util.write_config_file(args_filename, args_dict)
# Read particles
new_project.read_particles(args_dict['input'])
print('Read particle star file {}'.format(args_dict['input']))
# Prepare input and output files
new_project.prepare_io_files_star()
# Add new columns
new_project.rename_columns(new_column_parameters)
# Write output files
new_project.write_output_files(write_ref_class_star=False)
def parse_barcode(ptcl_star):
'''
Parse barcode
'''
barcode_dict = {}
if 'rlnParticleName' in ptcl_star:
barcode_arr = ptcl_star['rlnParticleName'].strip().split(',')
# Get barcode dictionary
barcode_dict = util.parse_star_parameters(barcode_arr)
return barcode_dict
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("-i", "--input", type=str, help="Particle star file")
parser.add_argument("-o",
"--output",
type=str,
help="Output directory",
default=None)
parser.add_argument("-cols",
"--columns",
type=str,
help="Columns to copy",
nargs='*',
default=None)
parser.add_argument("-copytopriors",
"--copypriors",
type=str,
help="Copy offset and/or angle parameters to priors",
default=None,
choices=['angle', 'all', 'helix'])
parser.add_argument(
"-copytooffsets",
"--copyoffsets",
type=str,
help="Copy priors to angle and distance offset parameters",
default=None,
choices=['angle', 'all', 'helix'])
parser.add_argument("-reset-priors",
"--resetpriors",
action='store_true',
help="Delete prior offset and angle columngs")
parser.add_argument("-reset-offsets",
"--resetoffsets",
action='store_true',
help="Assign angle and origin offsets to 0")
parser.add_argument("-invert-psi",
"--invertpsi",
action='store_true',
help="Invert psi angle")
parser.add_argument("-invert-origin",
"--invertorigin",
action='store_true',
help="Invert originX and originY")
args = parser.parse_args()
# Prepare args dict
args_dict = {
'input': args.input,
'output': args.output,
'columns': args.columns,
'copypriors': args.copypriors,
'copyoffsets': args.copyoffsets,
'resetpriors': args.resetpriors,
'resetoffsets': args.resetoffsets,
'invertpsi': args.invertpsi,
'invertorigin': args.invertorigin
}
# Check if the input file exists
if args_dict['input'] is None or not os.path.isfile(args_dict['input']):
parser.print_help()
sys.exit('Input file does not exist!')
# Get the new column parameters
if args_dict['columns'] is not None:
new_column_parameters = util.parse_star_parameters(
args_dict['columns'])
else:
new_column_parameters = None
# Copy offsets to priors overwrites
if args_dict['copypriors'] == 'all':
new_column_parameters = {
'rlnOriginX': 'rlnOriginXPrior',
'rlnOriginY': 'rlnOriginYPrior',
'rlnAnglePsi': 'rlnAnglePsiPrior',
'rlnAngleRot': 'rlnAngleRotPrior',
'rlnAngleTilt': 'rlnAngleTiltPrior'
}
elif args_dict['copypriors'] == 'angle':
new_column_parameters = {
'rlnAnglePsi': 'rlnAnglePsiPrior',
'rlnAngleRot': 'rlnAngleRotPrior',
'rlnAngleTilt': 'rlnAngleTiltPrior'
}
elif args_dict['copypriors'] == 'helix':
new_column_parameters = {
'rlnOriginX': 'rlnOriginXPrior',
'rlnOriginY': 'rlnOriginYPrior',
'rlnAnglePsi': 'rlnAnglePsiPrior',
'rlnAngleTilt': 'rlnAngleTiltPrior'
}
# Copy priors to offsets overwrites
if args_dict['copyoffsets'] == 'all':
new_column_parameters = {
'rlnOriginXPrior': 'rlnOriginX',
'rlnOriginYPrior': 'rlnOriginY',
'rlnAnglePsiPrior': 'rlnAnglePsi',
'rlnAngleRotPrior': 'rlnAngleRot',
'rlnAngleTiltPrior': 'rlnAngleTilt'
}
elif args_dict['copyoffsets'] == 'angle':
new_column_parameters = {
'rlnAnglePsiPrior': 'rlnAnglePsi',
'rlnAngleRotPrior': 'rlnAngleRot',
'rlnAngleTiltPrior': 'rlnAngleTilt'
}
elif args_dict['copyoffsets'] == 'helix':
new_column_parameters = {
'rlnOriginXPrior': 'rlnOriginX',
'rlnOriginYPrior': 'rlnOriginY',
'rlnAnglePsiPrior': 'rlnAnglePsi',
'rlnAngleTiltPrior': 'rlnAngleTilt'
}
# Create an EM project object
new_project = em.Project(name='EMCopyColumns')
new_project.set_output_directory(args_dict['output'], project_root='.')
# Write parameters to args filename
args_filename = new_project.output_directory + '/args.yaml'
util.write_config_file(args_filename, args_dict)
# Read particles
new_project.read_particles(args_dict['input'])
print('Read particle star file {}'.format(args_dict['input']))
# Prepare input and output files
new_project.prepare_io_files_star()
# If reset priors option is ON
if args_dict['resetpriors']:
new_project.reset_priors()
# If reset offset option is on
if args_dict['resetoffsets']:
new_project.reset_offsets()
# If invert-psi option is on
if args_dict['invertpsi']:
new_project.invert_psi()
# If invert-origin
if args_dict['invertorigin']:
new_project.invert_origin()
# Add new columns
new_project.copy_columns(new_column_parameters)
# Write output files
new_project.write_output_files(write_ref_class_star=False)
def main():
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("-i", "--input", type=str, help="Particle star file")
parser.add_argument("-o", "--output", type=str, help="Output directory", default=None)
parser.add_argument("-cols", "--columns", type=str, nargs='*', default=['rlnDefocusU',
'rlnDefocusV',
'rlnDefocusAngle',
'rlnCtfFigureOfMerit',
'rlnFinalResolution',
'rlnMaxValueProbDistribution',
'rlnNrOfSignificantSamples',
'rlnLogLikeliContribution',
'rlnAngleRot',
'rlnAngleRotPrior',
'rlnAngleTilt',
'rlnAngleTiltPrior',
'rlnAnglePsi',
'rlnOriginX',
'rlnOriginY'])
parser.add_argument("-pairs", "--pairs", type=str, nargs='*', default=['rlnCtfFigureOfMerit:rlnFinalResolution',
'rlnAngleTilt:rlnAngleRot',
'rlnMaxValueProbDistribution:rlnNrOfSignificantSamples',
'rlnOriginX:rlnOriginY',
'rlnAngleRot:rlnAngleRotPrior',
'rlnAngleTilt:rlnAngleTiltPrior',
'rlnAnglePsi:rlnAnglePsiPrior'])
parser.add_argument("-diffs", "--diffs", type=str, nargs='*', default=['rlnOriginX:rlnOriginXPrior',
'rlnOriginY:rlnOriginYPrior',
'rlnAngleRot:rlnAngleRotPrior',
'rlnAngleTilt:rlnAngleTiltPrior',
'rlnAnglePsi:rlnAnglePsiPrior'])
parser.add_argument("-orientation", "--orientation", action='store_true', help="Plot orientation of the particles with respect to priors")
parser.add_argument("-nbins", "--nbins", type=int, default=30)
parser.add_argument("-fontsize", "--fontsize", type=int, default=5)
parser.add_argument("-format", "--format", type=str, default='svg', choices=['png','svg'])
parser.add_argument("-ref", "--reference", type=str, help="Reference star file", default=None)
parser.add_argument("-barcode", "--barcode", type=str, help="Barcode to select", nargs='*', default={})
parser.add_argument("-offsetrot", "--offsetrot", type=int, default=0)
args = parser.parse_args()
# Prepare args dict
args_dict = {'input': args.input,
'output': args.output,
'columns': args.columns,
'pairs': args.pairs,
'diffs': args.diffs,
'orientation': args.orientation,
'fontsize': args.fontsize,
'reference': args.reference,
'nbins': args.nbins,
'format': args.format,
'barcode': args.barcode,
'offsetrot': args.offsetrot}
# Get the new column parameters
if args_dict['barcode'] is not None:
barcode_parameters = util.parse_star_parameters(args_dict['barcode'])
else:
barcode_parameters = None
# Create an EM project object
new_project = em.ProjectPlot(name='EMPlot')
new_project.set_output_directory(args_dict['output'], project_root='.')
# Write parameters to args filename
args_filename = new_project.output_directory+'/args.yaml'
util.write_config_file(args_filename, args_dict)
# Read particles
new_project.read_particles(args_dict['input'])
print('Read particle star file {}'.format(args_dict['input']))
# Select based on the barcode
if barcode_parameters is not None:
new_project.select_by_barcode(args_dict['barcode'])
# Read particle mrc paths
new_project.read_ptcl_mrc_paths()
# Prepare io files
new_project.prepare_io_files(args_dict['format'])
# Set rotation angle offset
new_project.set_offsetrot(args_dict['offsetrot'])
# Set tick fontsizes
new_project.set_tick_fontsize(size=args_dict['fontsize'])
# Read references if it is provided
if args_dict['reference'] is not None and os.path.isfile(args_dict['reference']):
# Read particles
new_project.read_reference(args_dict['reference'])
print('Read reference star file {}'.format(args_dict['reference']))
# Run ptcl project
new_project.run_ptcl(args_dict['columns'], args_dict['pairs'], args_dict['diffs'], args_dict['orientation'], args_dict['nbins'])
# Write output files
new_project.write_output_files(args_dict['format'])
def main():
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("-i", "--input", type=str, help="Particle star file")
parser.add_argument("-o", "--output", type=str, help="Output directory", default=None)
parser.add_argument("-ref", "--reference", type=str, help="Reference class star file", default=None)
parser.add_argument("-newclassid", "--newclassid",
action='store_true', help="Create new class ids for the reference file")
parser.add_argument("-addcols", "--addcolumns",
type=str, help="Add new columns with same value for all particles", nargs='*', default=None)
parser.add_argument("-recenter", "--recenter", action='store_true', help="Recenter particles")
parser.add_argument("-offset", "--offset", nargs=2, type=float, default=[0, 0], help="Final offset")
parser.add_argument("-offsetcom", "--offsetcom", action='store_true', help="Set final offset from center-of-mass")
parser.add_argument("-apix", "--apix", type=float,
help="Micrograph pixel size", default=1.82)
parser.add_argument("-rotatepsi", "--rotatepsi", type=float, help="Rotate psi by angle", default=0)
parser.add_argument("-flipX", "--flipX", action='store_true', help='Modify star file for flip around X axis')
args = parser.parse_args()
# Prepare args dict
args_dict = {'input': args.input,
'output': args.output,
'reference': args.reference,
'addcolumns': args.addcolumns,
'recenter': args.recenter,
'newclassid': args.newclassid,
'apix': args.apix,
'offset': args.offset,
'offsetcom': args.offsetcom,
'rotatepsi': args.rotatepsi,
'flipX': args.flipX
}
# Check if the input file exists
if args_dict['input'] is None or not os.path.isfile(args_dict['input']):
parser.print_help()
sys.exit('Input file does not exist!')
# Get the new column parameters
if not args_dict['addcolumns'] is None:
new_column_parameters = util.parse_star_parameters(args_dict['addcolumns'])
else:
new_column_parameters = None
# Create an EM project object
new_project = em.Project(name='EMTransform')
new_project.set_output_directory(args_dict['output'], project_root='.')
# Set microgragraph pixel size
new_project.set_mic_apix(args_dict['apix'])
# Write parameters to args filename
args_filename = new_project.output_directory+'/args.yaml'
util.write_config_file(args_filename, args_dict)
# Read particles
new_project.read_particles(args_dict['input'])
print('Read particle star file {}'.format(args_dict['input']))
# Check if the input file exists
if args_dict['reference'] is not None and os.path.isfile(args_dict['reference']):
new_project.read_class_refs(args_dict['reference'], new_classids=args_dict['newclassid'])
print('Read class reference file {}'.format(args_dict['reference']))
# Prepare input and output files
new_project.prepare_io_files_star()
# Perform reference based particle star transformation
new_project.transform_particles(final_offset=args_dict['offset'], com_offset=args_dict['offsetcom'], rotate_psi=args_dict['rotatepsi'])
# Add new columns
new_project.add_columns(new_column_parameters)
# Recenter
if args_dict['recenter']:
new_project.read_particle_apix()
new_project.recenter_particles()
if args_dict['flipX']:
new_project.flipX_particles()
# Write output files
new_project.write_output_files()
