def main(self):
self.define_parser()
args = self.parser.parse_args()
self.validate(args)
print("Performing rotation of particles from star file...")
md = MetaData(args.i)
new_particles = []
particles = self.get_particles(md)
new_particles.extend(
self.rotateParticles(particles, rotValue, tiltValue, psiValue,
xValue, yValue, zValue, md.version))
mdOut = MetaData()
if md.version == "3.1":
mdOut.version = "3.1"
mdOut.addDataTable("data_optics")
mdOut.addLabels("data_optics", md.getLabels("data_optics"))
mdOut.addData("data_optics", getattr(md, "data_optics"))
particleTableName = "data_particles"
else:
particleTableName = "data_"
mdOut.addDataTable(particleTableName)
mdOut.addLabels(particleTableName, md.getLabels(particleTableName))
mdOut.addData(particleTableName, new_particles)
mdOut.write(args.o)
print("New star file %s created. Have fun!" % args.o)
def main(self):
self.define_parser()
args = self.parser.parse_args()
self.validate(args)
md = MetaData(args.i)
print("Reading in input star file.....")
micrographs = self.get_micrographs(md)
print(
"Total %s micrographs in input star file. \nRenaming to micXXX convention."
% str(len(micrographs)))
self.renameMicrographs(micrographs, args.mic_dir)
mdOut = MetaData()
if md.version == "3.1":
mdOut.version = "3.1"
mdOut.addDataTable("data_optics")
mdOut.addLabels("data_optics", md.getLabels("data_optics"))
mdOut.addData("data_optics", getattr(md, "data_optics"))
particleTableName = "data_particles"
else:
particleTableName = "data_"
mdOut.addDataTable(particleTableName)
mdOut.addLabels(particleTableName, md.getLabels(particleTableName))
mdOut.addData(particleTableName, micrographs)
mdOut.write(args.o)
print("New star file %s created. Have fun!" % args.o)
def main(self):
self.define_parser()
args = self.parser.parse_args()
self.validate(args)
md = MetaData(args.i)
md.addLabels("data_particles", "rlnBeamTiltClass")
print("Reading in input star file.....")
particles = self.get_particles(md)
print(
"Total %s particles in input star file. \nAdding rlnBeamTiltClass."
% str(len(particles)))
self.addBeamTiltClass(particles)
mdOut = MetaData()
mdOut.addDataTable("data_")
mdOut.addLabels("data_", md.getLabels("data_"))
mdOut.addData("data_", particles)
mdOut.write(args.o)
print("New star file %s created. Have fun!" % args.o)
def main(self):
self.define_parser()
args = self.parser.parse_args()
self.validate(args)
print("Making orientation heatmap from star file...")
md = MetaData(args.i)
particles = self.get_particles(md)
new_particles = []
new_particles.extend(self.removePrefOrient(particles, args.sd))
mdOut = MetaData()
if md.version == "3.1":
mdOut.version = "3.1"
mdOut.addDataTable("data_optics")
mdOut.addLabels("data_optics", md.getLabels("data_optics"))
mdOut.addData("data_optics", getattr(md, "data_optics"))
particleTableName = "data_particles"
else:
particleTableName = "data_"
mdOut.addDataTable(particleTableName)
mdOut.addLabels(particleTableName, md.getLabels(particleTableName))
mdOut.addData(particleTableName, new_particles)
mdOut.write(args.o)
print("File %s was created..." % args.o)
print("Finished. Have fun!")
def main(self):
self.define_parser()
args = self.parser.parse_args()
self.validate(args)
print("Selecting particles/micrographs from star file...")
md = MetaData(args.i)
if md.version == "3.1":
ilabels = md.getLabels("data_particles")
else:
ilabels = md.getLabels("data_")
if ("rlnDefocusU" not in ilabels) or ("rlnDefocusV" not in ilabels):
self.error(
"No labels rlnDefocusU or rlnDefocusV found in Input file.")
if ("rlnFinalResolution" not in ilabels) and (args.res > 0):
print(
"No label rlnFinalResolution found in input file. Switching off resolution filtering..."
)
args.res = 0
mdOut = MetaData()
new_particles = []
particles = self.get_particles(md)
new_particles.extend(
self.selParticles(
particles,
args.astg,
args.res,
))
if md.version == "3.1":
mdOut.version = "3.1"
mdOut.addDataTable("data_optics")
mdOut.addLabels("data_optics", md.getLabels("data_optics"))
mdOut.addData("data_optics", getattr(md, "data_optics"))
particleTableName = "data_particles"
else:
particleTableName = "data_"
mdOut.addDataTable(particleTableName)
mdOut.addLabels(particleTableName, md.getLabels(particleTableName))
mdOut.addData(particleTableName, new_particles)
mdOut.write(args.o)
print("New star file %s created. Have fun!" % args.o)
def main(self):
self.define_parser()
args = self.parser.parse_args()
compValue, selValue, rangeHi, rangeLo, rangeSel = self.validate(args)
if args.sellb == "None":
print("Performing math on all particles from star file...")
else:
if rangeSel:
print(
"Performing math on particles where %s is in range <%s, %s>."
% (args.sellb, rangeLo, rangeHi))
else:
print("Performing math on particles where %s is %s %s." %
(args.sellb, args.selop, selValue))
md = MetaData(args.i)
if md.version == "3.1":
ilabels = md.getLabels("data_particles")
else:
ilabels = md.getLabels("data_")
if args.lb not in ilabels:
self.error("No label " + args.lb + " found in Input file.")
new_particles = []
particles = self.get_particles(md)
new_particles.extend(
self.mathParticles(particles, args.lb, args.op, compValue,
args.selop, args.sellb, selValue, rangeHi,
rangeLo, rangeSel))
mdOut = MetaData()
if md.version == "3.1":
mdOut.version = "3.1"
mdOut.addDataTable("data_optics")
mdOut.addLabels("data_optics", md.getLabels("data_optics"))
mdOut.addData("data_optics", getattr(md, "data_optics"))
particleTableName = "data_particles"
else:
particleTableName = "data_"
mdOut.addDataTable(particleTableName)
mdOut.addLabels(particleTableName, md.getLabels(particleTableName))
mdOut.addData(particleTableName, new_particles)
mdOut.write(args.o)
print("New star file %s created. Have fun!" % args.o)
def main(self):
self.define_parser()
args = self.parser.parse_args()
self.validate(args)
print("Binning correct input star file. Using binning factor %s." % str(args.bin_factor))
md = MetaData(args.i)
new_particles = []
particles = self.get_particles(md)
if (hasattr(particles[0], 'rlnOriginX')) and (hasattr(particles[0], 'rlnOriginY')):
correctOrigin = True
else:
print("Note: rlnOriginX or rlnOriginY not found in input star file. Not correcting for particle shift.")
correctOrigin = False
if hasattr(particles[0], 'rlnDetectorPixelSize'):
correctApix = True
else:
print("Note: rlnDetectorPixelSize not found in input star file. Not correcting for pixel size.")
correctApix = False
new_particles.extend(
self.binParticles(particles, args.bin_factor, correctOrigin, correctApix, args.suf_orig, args.suf_new))
mdOut = MetaData()
if md.version == "3.1":
mdOut.version = "3.1"
mdOut.addDataTable("data_optics")
mdOut.addLabels("data_optics", md.getLabels("data_optics"))
mdOut.addData("data_optics", getattr(md, "data_optics"))
particleTableName = "data_particles"
else:
particleTableName = "data_"
mdOut.addDataTable(particleTableName)
mdOut.addLabels(particleTableName, md.getLabels(particleTableName))
mdOut.addData(particleTableName, new_particles)
mdOut.write(args.o)
print("New star file %s created. Have fun!" % args.o)
def main(self):
self.define_parser()
args = self.parser.parse_args()
self.validate(args)
md = MetaData(args.i)
if md.version != "3.1":
self.error("Input file '%s' is not RELION 3.1 format." % args.i)
new_particles = []
print("Reading in input star file.....")
particles = self.get_particles(md)
optic_groups = self.get_optic_groups(md)
print("Total %s particles in input star file." % str(len(particles)))
print("Total %s optic groups found in input star file." %
str(len(optic_groups)))
new_particles.extend(self.rel30format(particles, optic_groups))
mdOut = MetaData()
particleTableName = "data_"
mdOut.addDataTable(particleTableName)
mdOut.addLabels(particleTableName, md.getLabels("data_particles"))
mdOut.addLabels(particleTableName, [
'rlnVoltage', 'rlnSphericalAberration', 'rlnAmplitudeContrast',
'rlnMagnification', 'rlnDetectorPixelSize', 'rlnOriginX',
'rlnOriginY', 'rlnBeamTiltClass'
])
mdOut.removeLabels(
"data_", ['rlnOpticsGroup', 'rlnOriginXAngst', 'rlnOriginYAngst'])
mdOut.addData(particleTableName, new_particles)
mdOut.write(args.o)
print("New star file %s in RELION 3.0 format created. Have fun!" %
args.o)
def main(self):
self.define_parser()
args = self.parser.parse_args()
self.validate(args)
print("Modifying star file to be compatible with helix refinement.")
md = MetaData(args.i)
if md.version == "3.1":
ilabels = md.getLabels("data_particles")
else:
ilabels = md.getLabels("data_")
if 'rlnAnglePsiFlipRatio' not in ilabels:
md.addLabels(['rlnAnglePsiFlipRatio'])
if 'rlnHelicalTubeID' not in ilabels:
md.addLabels(['rlnHelicalTubeID'])
if 'rlnHelicalTrackLength' not in ilabels:
md.addLabels(['rlnHelicalTrackLength'])
mdOut = MetaData()
if md.version == "3.1":
mdOut.version = "3.1"
mdOut.addDataTable("data_optics")
mdOut.addLabels("data_optics", md.getLabels("data_optics"))
mdOut.addData("data_optics", getattr(md, "data_optics"))
particleTableName = "data_particles"
else:
particleTableName = "data_"
mdOut.addDataTable(particleTableName)
mdOut.addLabels(particleTableName, md.getLabels(particleTableName))
particles = self.get_particles(md)
self.helixParticles(particles)
mdOut.addData(particleTableName, particles)
mdOut.write(args.o)
print("New star file %s created. Have fun!" % args.o)
def main(self):
self.define_parser()
args = self.parser.parse_args()
self.validate(args)
md = MetaData(args.i)
# create output star file
mdOut = MetaData()
mdOut.version = "3.1"
mdOut.addDataTable("data_optics")
mdOut.addLabels("data_optics", md.getLabels("data_optics"))
mdOut.addDataTable("data_particles")
mdOut.addLabels("data_particles", md.getLabels("data_particles"))
print("Reading in input star file.....")
particles = self.get_particles(md)
print(
"Total %s particles in input star file. \nAdding rlnOpticsGroup." %
str(len(particles)))
new_particles, opticsGroupsNames = self.addOpticGroupsToParticles(
particles, args.word_count)
# create new optics groups
opticGroup = md.data_optics[0]
opticsGroups = []
for opticGroupNr, opticGroupName in enumerate(opticsGroupsNames):
newOpticGroup = deepcopy(opticGroup)
newOpticGroup.rlnOpticsGroup = opticGroupNr + 1
newOpticGroup.rlnOpticsGroupName = "opticsGroup_" + str(
opticGroupName)
opticsGroups.append(newOpticGroup)
mdOut.addData("data_optics", opticsGroups)
mdOut.addData("data_particles", new_particles)
mdOut.write(args.o)
print("New star file %s created. Have fun!" % args.o)
def main(self):
self.define_parser()
args = self.parser.parse_args()
compValue, rangeHi, rangeLo, rangeSel, prctl_l, prctl_h = self.validate(
args)
if rangeSel:
print(
"Selecting particles particles where %s is in range <%s, %s>."
% (args.lb, rangeLo, rangeHi))
elif args.prctl_l == "-1" and args.prctl_h == "-1":
print("Selecting particles particles where %s is %s %s." %
(args.lb, args.op, compValue))
md = MetaData(args.i)
new_particles = []
particles = self.get_particles(md)
new_particles.extend(
self.selParticles(particles, args.lb, args.op, compValue, rangeHi,
rangeLo, rangeSel, prctl_l, prctl_h))
mdOut = MetaData()
if md.version == "3.1":
mdOut.version = "3.1"
mdOut.addDataTable("data_optics")
mdOut.addLabels("data_optics", md.getLabels("data_optics"))
mdOut.addData("data_optics", getattr(md, "data_optics"))
particleTableName = "data_particles"
else:
particleTableName = "data_"
mdOut.addDataTable(particleTableName)
mdOut.addLabels(particleTableName, md.getLabels(particleTableName))
mdOut.addData(particleTableName, new_particles)
mdOut.write(args.o)
print("New star file %s created. Have fun!" % args.o)
def main(self):
self.define_parser()
args = self.parser.parse_args()
self.validate(args)
md = MetaData(args.i)
new_particles = []
print("Reading in input star file.....")
particles = self.get_particles(md)
print(
"Total %s particles in input star file. \nSelecting random particles from their symmetry copies."
% str(len(particles)))
new_particles.extend(self.randParticles(particles))
mdOut = MetaData()
if md.version == "3.1":
mdOut.version = "3.1"
mdOut.addDataTable("data_optics")
mdOut.addLabels("data_optics", md.getLabels("data_optics"))
mdOut.addData("data_optics", getattr(md, "data_optics"))
particleTableName = "data_particles"
else:
particleTableName = "data_"
mdOut.addDataTable(particleTableName)
mdOut.addLabels(particleTableName, md.getLabels(particleTableName))
mdOut.addData(particleTableName, new_particles)
mdOut.write(args.o)
print("New star file %s created. Have fun!" % args.o)
def main(self):
self.define_parser()
args = self.parser.parse_args()
self.validate(args)
print("Selecting particles from star file...")
md = MetaData(args.i)
new_particles = []
particles = self.get_particles(md)
new_particles.extend(
self.selParticles(particles, args.rot_min, args.rot_max,
args.tilt_min, args.tilt_max, args.psi_min,
args.psi_max))
mdOut = MetaData()
if md.version == "3.1":
mdOut.version = "3.1"
mdOut.addDataTable("data_optics")
mdOut.addLabels("data_optics", md.getLabels("data_optics"))
mdOut.addData("data_optics", getattr(md, "data_optics"))
particleTableName = "data_particles"
else:
particleTableName = "data_"
mdOut.addDataTable(particleTableName)
mdOut.addLabels(particleTableName, md.getLabels(particleTableName))
mdOut.addData(particleTableName, new_particles)
mdOut.write(args.o)
print("New star file %s created. Have fun!" % args.o)
print(
"No particle star input file given. Please, define one by --istar")
sys.exit(2)
# read in particle star file
md = MetaData(args.istar)
particles = []
for particle in md:
particles.append(particle)
# create output star file
mdOut = MetaData()
mdOut.version = "3.1"
mdOut.addDataTable("data_optics")
mdOut.addLabels("data_optics", md.getLabels("data_optics"))
mdOut.addDataTable("data_particles")
mdOut.addLabels("data_particles", md.getLabels("data_particles"))
# create optics groups
opticGroup = md.data_optics[0]
opticsGroups = []
for opticGroupNr in range(max(pred_y)):
newOpticGroup = deepcopy(opticGroup)
newOpticGroup.rlnOpticsGroup = opticGroupNr + 1
newOpticGroup.rlnOpticsGroupName = "opticsGroup" + str(opticGroupNr +
1)
opticsGroups.append(newOpticGroup)
def main(self):
self.define_parser()
args = self.parser.parse_args()
self.validate(args)
print("Selecting particles from star file...")
md1 = MetaData(args.i1)
md2 = MetaData(args.i2)
if md1.version == "3.1":
i1labels = md1.getLabels("data_particles")
i2labels = md2.getLabels("data_particles")
else:
i1labels = md1.getLabels("data_")
i2labels = md2.getLabels("data_")
if args.col_lb in i1labels:
self.error("Column %s is already in Input1 star file. Please remove it first..." % args.col_lb)
if args.col_lb not in i2labels:
self.error("Column %s is not present in Input2 star file." % args.col_lb)
if args.comp_lb not in i1labels:
self.error("Column %s is not present in Input1 star file." % args.comp_lb)
if args.comp_lb not in i2labels:
self.error("Column %s is not present in Input2 star file." % args.comp_lb)
if LABELS[args.col_lb] == float:
# add label with default values 0.0
print("Adding label %s to Input1 data with default value 0.0." % args.col_lb)
dic = {args.col_lb: 0.0}
if LABELS[args.col_lb] == int:
# add label with default values 0
print("Adding label %s to Input1 data with default value 0." % args.col_lb)
dic = {args.col_lb: 0}
if LABELS[args.col_lb] == str:
# add label with default values "dummy"
print("Adding label %s to Input1 data with default value \"dummy\"" % args.col_lb)
dic = {args.col_lb: "dummy"}
if md1.version == "3.1":
md1.setLabels("data_particles", **dic)
else:
md1.setLabels("data_", **dic)
particles1 = self.get_particles(md1)
particles2 = self.get_particles(md2)
print(
"Assigning values for Input1 label %s where the %s of Input2 matches Input1" % (args.col_lb, args.comp_lb))
mdOut = MetaData()
if md1.version == "3.1":
mdOut.version = "3.1"
mdOut.addDataTable("data_optics")
mdOut.addLabels("data_optics", md1.getLabels("data_optics"))
mdOut.addData("data_optics", getattr(md1, "data_optics"))
particleTableName = "data_particles"
else:
particleTableName = "data_"
mdOut.addDataTable(particleTableName)
mdOut.addLabels(particleTableName, md1.getLabels(particleTableName))
mdOut.addData(particleTableName, self.assign_column(particles1, particles2, args.col_lb, args.comp_lb))
print("%s particles were processed..." % str((len(particles1) + len(particles2))))
mdOut.write(args.o)
print("New star file %s created. Have fun!" % args.o)
def main(self):
self.define_parser()
args = self.parser.parse_args()
self.validate(args)
print("Selecting particles from star file...")
md1 = MetaData(args.i1)
md2 = MetaData(args.i2)
# UNION
if args.op == "union":
# check if both stars contains same labels
if md1.version == "3.1":
i1labels = md1.getLabels("data_particles")
i2labels = md2.getLabels("data_particles")
else:
i1labels = md1.getLabels("data_")
i2labels = md2.getLabels("data_")
if len(i1labels) != len(i2labels):
if len(i1labels) > len(i2labels):
print("WARNING: Input2 does not contain all the labels of Input1.")
missingLabels = [Labels for Labels in i1labels if Labels not in i2labels]
for label in missingLabels:
if LABELS[label] == float:
# add label with default values 0.0
print("Adding label %s to Input2 data with default value 0.0." % label)
dic = {label: 0.0}
md2.setLabels("data_particles", **dic)
if LABELS[label] == int:
# add label with default values 0
print("Adding label %s to Input2 data with default value 0." % label)
dic = {label: 0}
md2.setLabels("data_particles", **dic)
if LABELS[label] == str:
# add label with default values "dummy"
print("Adding label %s to Input2 data with default value \"dummy\"" % label)
dic = {label: "dummy"}
md2.setLabels("data_particles", **dic)
if len(i1labels) < len(i2labels):
print("WARNING: Input1 does not contain all the labels of Input2.")
missingLabels = [Labels for Labels in i2labels if Labels not in i1labels]
for label in missingLabels:
if LABELS[label] == float:
# add label with default values 0.0
print("Adding label %s to Input1 data with default value 0.0." % label)
dic = {label: 0.0}
md1.setLabels("data_particles", **dic)
if LABELS[label] == int:
# add label with default values 0
print("Adding label %s to Input1 data with default value 0." % label)
dic = {label: 0}
md1.setLabels("data_particles", **dic)
if LABELS[label] == str:
# add label with default values "dummy"
print("Adding label %s to Input1 data with default value \"dummy\"" % label)
dic = {label: "dummy"}
md1.setLabels("data_particles", **dic)
mdOut = MetaData()
if md1.version == "3.1":
mdOut.version = "3.1"
mdOut.addDataTable("data_optics")
mdOut.addLabels("data_optics", md1.getLabels("data_optics"))
mdOut.addData("data_optics", getattr(md1, "data_optics"))
particleTableName = "data_particles"
else:
particleTableName = "data_"
mdOut.addDataTable(particleTableName)
mdOut.addLabels(particleTableName, md1.getLabels(particleTableName))
particles1 = self.get_particles(md1)
particles2 = self.get_particles(md2)
mdOut.addData(particleTableName, particles1)
mdOut.addData(particleTableName, particles2)
print("%s particles were selected..." % str((len(particles1) + len(particles2))))
# INTERSECT
if args.op == "intersect":
# create intersect unique values
if md1.version == "3.1":
i1labels = md1.getLabels("data_particles")
i2labels = md2.getLabels("data_particles")
else:
i1labels = md1.getLabels("data_")
i2labels = md2.getLabels("data_")
if (args.lb not in i1labels) or (args.lb not in i2labels):
self.error("No label %s found in Input1 or Input2 file." % args.lb)
particles1 = self.get_particles(md1)
particles2 = self.get_particles(md2)
intersectParticles = []
selectedValues = []
while len(particles2) > 0:
selectedParticle = particles2.pop(0)
if getattr(selectedParticle, args.lb) not in selectedValues:
selectedValues.append(getattr(selectedParticle, args.lb))
for particle in particles1:
if getattr(particle, args.lb) in selectedValues:
intersectParticles.append(particle)
mdOut = MetaData()
if md1.version == "3.1":
mdOut.version = "3.1"
mdOut.addDataTable("data_optics")
mdOut.addLabels("data_optics", md1.getLabels("data_optics"))
mdOut.addData("data_optics", getattr(md1, "data_optics"))
particleTableName = "data_particles"
else:
particleTableName = "data_"
mdOut.addDataTable(particleTableName)
mdOut.addLabels(particleTableName, md1.getLabels(particleTableName))
mdOut.addData(particleTableName, intersectParticles)
print("%s particles were selected..." % str(len(intersectParticles)))
# EXCEPT
if args.op == "except":
# create unique values for except
if md1.version == "3.1":
i1labels = md1.getLabels("data_particles")
i2labels = md2.getLabels("data_particles")
else:
i1labels = md1.getLabels("data_")
i2labels = md2.getLabels("data_")
if (args.lb not in i1labels) or (args.lb not in i2labels):
self.error("No label %s found in Input1 or Input2 file." % args.lb)
particles1 = self.get_particles(md1)
particles2 = self.get_particles(md2)
exceptParticles = []
selectedValues = []
while len(particles2) > 0:
selectedParticle = particles2.pop(0)
if getattr(selectedParticle, args.lb) not in selectedValues:
selectedValues.append(getattr(selectedParticle, args.lb))
for particle in particles1:
if getattr(particle, args.lb) not in selectedValues:
exceptParticles.append(particle)
mdOut = MetaData()
if md1.version == "3.1":
mdOut.version = "3.1"
mdOut.addDataTable("data_optics")
mdOut.addLabels("data_optics", md1.getLabels("data_optics"))
mdOut.addData("data_optics", getattr(md1, "data_optics"))
particleTableName = "data_particles"
else:
particleTableName = "data_"
mdOut.addDataTable(particleTableName)
mdOut.addLabels(particleTableName, md1.getLabels(particleTableName))
mdOut.addData(particleTableName, exceptParticles)
print("%s particles were selected..." % str(len(exceptParticles)))
mdOut.write(args.o)
print("New star file %s created. Have fun!" % args.o)
