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 main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("-i", "--input", type=str, help="Particle star file")
parser.add_argument("-n",
"--numptcls",
type=int,
help="Number of ptcls in the subset",
default=100000)
parser.add_argument("-r",
"--randseed",
type=int,
help="Random seed",
default=1)
parser.add_argument("-o",
"--output",
type=str,
help="Output directory",
default=None)
args = parser.parse_args()
# Prepare args dict
args_dict = {
'input': args.input,
'numptcls': args.numptcls,
'randseed': args.randseed,
'output': args.output
}
# 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!')
# Create an EM project object
new_project = em.Project(name='EMSubset')
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.pick_random_set(args_dict['numptcls'], args_dict['randseed'])
# Write output files
new_project.write_output_files()
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")
parser.add_argument("-cols", "--columns", type=str, help="Columns to copy", nargs='+')
parser.add_argument("-comp", "--compare", type=str, help="Criteria to compare", choices=['img','mic'], default='img')
args = parser.parse_args()
# Prepare args dict
args_dict = {'input': args.input,
'output': args.output,
'reference': args.reference,
'columns': args.columns,
'compare': args.compare
}
# 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!')
# Check if the reference file exists
if args_dict['reference'] is None and not os.path.isfile(args_dict['reference']):
parser.print_help()
sys.exit('Reference file file does not exist!')
# Create an EM project object
new_project = em.Project(name='EMCopy')
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']))
new_project.read_class_refs(args_dict['reference'])
print('Read class reference file {}'.format(args_dict['reference']))
# Prepare input and output files
new_project.prepare_io_files_star()
# Add new columns
new_project.copy_from_ref(args_dict['columns'], args_dict['compare'])
# 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("-offsetrot",
"--offsetrot",
type=float,
help="Rotation offset",
default=0)
args = parser.parse_args()
# Prepare args dict
args_dict = {
'input': args.input,
'output': args.output,
'offsetrot': args.offsetrot
}
# 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!')
# Create an EM project object
new_project = em.Project(name='EMApplyBarcode')
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.apply_barcode(args_dict['offsetrot'])
# 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, nargs='+', help="Star file(s)")
parser.add_argument("-o", "--output", type=str, help="Output directory", default=None)
args = parser.parse_args()
# Prepare args dict
args_dict = {'input': args.input,
'output': args.output
}
# Check if the input file exists
if args_dict['input'] is None:
parser.print_help()
sys.exit('Input file does not exist!')
# Create an EM project object
new_project = em.Project(name='EMMergeStar')
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_particle_stars(args_dict['input'])
print('Read particle star files {}'.format(','.join(args_dict['input'])))
# Prepare input and output files
new_project.prepare_io_files_star()
# Write output files
new_project.write_output_files()
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("-i", "--input", type=str, help="Particle cs file")
parser.add_argument("-ref",
"--reference",
type=str,
help="Template cs file",
default=None)
parser.add_argument("-pass",
"--passthrough",
type=str,
help="Passthrough cs file from cryosparc",
default=None)
parser.add_argument("-o",
"--output",
type=str,
help="Output directory",
default=None)
parser.add_argument("-orig",
"--original",
type=str,
help="Original star file",
default=None)
parser.add_argument("-micpath",
"--micpath",
type=str,
help="Micrographs path",
default="Micrographs")
parser.add_argument("-projpath",
"--projpath",
type=str,
help="Cryosparc project path",
default="")
parser.add_argument("-delclass",
"--delclass",
type=int,
nargs='+',
help="Classes to delete",
default=[])
parser.add_argument("-delstr",
"--delstr",
type=str,
help="String to delete from Micrograph name",
default='')
parser.add_argument("-restore-offsets",
"--restoreoffsets",
action='store_true',
help="Restore offsets from original star file")
parser.add_argument("-merge-orig",
"--mergeoriginal",
action='store_true',
help="Merge with original star file")
args = parser.parse_args()
# Prepare args dict
args_dict = {
'input': args.input,
'reference': args.reference,
'passthrough': args.passthrough,
'output': args.output,
'original': args.original,
'micpath': args.micpath,
'projpath': args.projpath,
'delclass': args.delclass,
'delstr': args.delstr,
'restoreoffsets': args.restoreoffsets,
'mergeoriginal': args.mergeoriginal
}
# 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!')
# Create an EM project object
new_project = em.Project(name='EMcsparc2star')
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)
# Set cs files
new_project.set_cs_files(blob_cs_file=args_dict['input'],
passthrough_cs_file=args_dict['passthrough'],
original_star_file=args_dict['original'],
ref_class_cs_file=args_dict['reference'])
# Read cs files
new_project.read_cs_files()
# Prepare input and output files
new_project.prepare_io_files_cs()
# Conert cs to star
new_project.convert_cs2star(args_dict['micpath'], args_dict['projpath'],
args_dict['delclass'], args_dict['delstr'],
args_dict['restoreoffsets'],
args_dict['mergeoriginal'])
# Write output files
new_project.write_output_files()
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("-selbarcode",
"--selbarcode",
type=str,
help="Barcode to select",
nargs='*',
default={})
parser.add_argument("-delbarcode",
"--delbarcode",
type=str,
help="Barcode to delete",
nargs='*',
default={})
args = parser.parse_args()
# Prepare args dict
args_dict = {
'input': args.input,
'output': args.output,
'selbarcode': args.selbarcode,
'delbarcode': args.delbarcode
}
# 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!')
# Create an EM project object
new_project = em.Project(name='EMSelectBarcode')
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()
# Select barcode
new_project.select_by_barcode(args_dict['selbarcode'])
# Delete barcode
new_project.delete_by_barcode(args_dict['delbarcode'])
# 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("-copytopriors", "--copypriors", action='store_true', help="Copy offset and/or angle parameters to priors", default=True)
parser.add_argument("-copytooffsets", "--copyoffsets", action='store_true', help="Copy priors to angle and distance offset parameters")
parser.add_argument("-fliponly", "--fliponly", action='store_true', help="Set only flip ratio to 0")
parser.add_argument("-fliprot", "--fliprot", action='store_true', help="Set flip ratio to 0 and delete rlnAngleRotPrior")
args = parser.parse_args()
# Prepare args dict
args_dict = {'input': args.input,
'output': args.output,
'copypriors': args.copypriors,
'copyoffsets': args.copyoffsets,
'fliponly': args.fliponly,
'fliprot': args.fliprot
}
# 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!')
# Copy offsets to priors overwrites
if args_dict['copypriors']:
add_column_parameters = {'rlnAngleTilt':90,
'rlnAngleTiltPrior':90,
'rlnAnglePsiFlipRatio':0}
del_column_parameters = {'rlnAngleRotPrior':None}
copy_column_parameters = {'rlnOriginX': 'rlnOriginXPrior',
'rlnOriginY': 'rlnOriginYPrior',
'rlnAnglePsi': 'rlnAnglePsiPrior',
'rlnAngleTilt':'rlnAngleTiltPrior'}
if args_dict['copyoffsets']:
add_column_parameters = {}
del_column_parameters = {}
copy_column_parameters = {'rlnOriginXPrior': 'rlnOriginX',
'rlnOriginYPrior': 'rlnOriginY',
'rlnAnglePsiPrior': 'rlnAnglePsi',
'rlnAngleTiltPrior':'rlnAngleTilt'}
if args_dict['fliponly']:
add_column_parameters = {'rlnAnglePsiFlipRatio':0}
del_column_parameters = {}
copy_column_parameters = {}
if args_dict['fliprot']:
add_column_parameters = {'rlnAnglePsiFlipRatio':0}
del_column_parameters = {'rlnAngleRotPrior':None}
copy_column_parameters = {}
# Create an EM project object
new_project = em.Project(name='EMHelixReady')
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()
# Delete columns
new_project.delete_columns(del_column_parameters)
# Add new columns
new_project.add_columns(add_column_parameters)
# Add new columns
new_project.copy_columns(copy_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("-Zflip",
"--Zflip",
action='store_true',
help="Z-Flip particles in star file")
parser.add_argument("-tilt90",
"--tilt90",
action='store_true',
help="Set tilt of particles to 90-degree side")
parser.add_argument("-aligntopriors",
"--aligntopriors",
type=str,
nargs='*',
default=None)
args = parser.parse_args()
# Prepare args dict
args_dict = {
'input': args.input,
'Zflip': args.Zflip,
'tilt90': args.tilt90,
'output': args.output,
'aligntopriors': args.aligntopriors
}
# 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!')
# Create an EM project object
new_project = em.Project(name='EMRotate')
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()
# Make tilt angle around 90 degree
if args_dict['tilt90']:
new_project.tilt90_particles()
# Z-flip particles
if args_dict['Zflip']:
new_project.Zflip_particles()
# Align to priors
if args_dict['aligntopriors'] is not None:
new_project.align_to_priors(args_dict['aligntopriors'])
# Write output files
new_project.write_output_files()
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("-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()
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("-mic",
"--micrograph",
type=str,
help="Micrograph star file")
args = parser.parse_args()
# Prepare args dict
args_dict = {
'input': args.input,
'output': args.output,
'micrograph': args.micrograph
}
# 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!')
# Check if the reference file exists
if args_dict['micrograph'] is None and not os.path.isfile(
args_dict['micrograph']):
parser.print_help()
sys.exit('Micrographs file does not exist!')
# Create an EM project object
new_project = em.Project(name='EMClean')
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']))
# Read particle pixel size information
new_project.read_particle_apix()
new_project.read_micrographs(args_dict['micrograph'])
print('Read micrographs star file {}'.format(args_dict['micrograph']))
# Read micrograph pixel size information
new_project.read_mic_apix()
# Read micrograph header
new_project.read_mic_header()
# Prepare input and output files
new_project.prepare_io_files_star()
# Check particle positions
new_project.check_particle_pos()
# Delete outside particles
new_project.delete_outside_ptcls()
# Write output files
new_project.write_output_files()
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("-maxprob", "--maxprob", type=float, help="Maximum probability", default=None)
parser.add_argument("-maxclass", "--maxclass", type=int, help="Maximum number of classes assigned for a particle", default=None)
parser.add_argument("-tilt", "--tilt", type=float, nargs=2, help="Accepted range of tilt angles. [ min ,max]", default=[0, 360])
parser.add_argument("-dtilt", "--dtilt", type=float, nargs=2, help="Accepted range of diff-tilt angles. [ min ,max]", default=[0, 360])
parser.add_argument("-dpsi", "--dpsi", type=float, nargs=2, help="Accepted range of diff-psi angles. [ min ,max]", default=[0, 360])
parser.add_argument("-drot", "--drot", type=float, nargs=2, help="Accepted range of diff-rot angles. [ min ,max]", default=[0, 360])
parser.add_argument("-dalign", "--dalign", type=float, nargs=2, help="Accepted range of diff-align angles. [ min ,max]", default=[-1, 1])
args = parser.parse_args()
# Prepare args dict
args_dict = {'input': args.input,
'output': args.output,
'maxprob': args.maxprob,
'maxclass': args.maxclass,
'tilt': args.tilt,
'dtilt': args.dtilt,
'dpsi': args.dpsi,
'drot': args.drot,
'dalign': args.dalign}
# 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!')
# Create an EM project object
new_project = em.Project(name='EMFilter')
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()
# Determine pixel size from particle star file
new_project.read_particle_apix()
# Subtract class mrc from particle mrc
new_project.filter_ptcls(maxprob=args_dict['maxprob'],
maxclass=args_dict['maxclass'],
tilt_range=args_dict['tilt'],
dpsi_range=args_dict['dpsi'],
dtilt_range=args_dict['dtilt'],
drot_range=args_dict['drot'],
dalign_range=args_dict['dalign'])
# Write output files
new_project.write_output_files()
