def readSetOfCoordinates(outputDir, micSet, coordSet):
""" Read from Bsoft .star files.
Params:
outputDir: the directory where the .star files are.
micSet: the SetOfMicrographs to associate the .star, which
name should be the same of the micrographs.
coordSet: the SetOfCoordinates that will be populated.
"""
addBsoftLabelAliases()
boxSize = 0
for mic in micSet:
outputFile = join(outputDir, replaceBaseExt(mic.getFileName(), 'star'))
#scipionPosFile = join(outputDir, "scipion_" + replaceBaseExt(mic.getFileName(), 'pos'))
if exists(outputFile):
posMd = xmipp.MetaData(outputFile)
for objId in posMd:
coord = rowToCoordinate(rowFromMd(posMd, objId))
boxSize = 2 * posMd.getValue(xmipp.MDL_PICKING_PARTICLE_SIZE, objId)
coord.setMicrograph(mic)
coord.setX(coord.getX())
coord.setY(coord.getY())
coordSet.append(coord)
# Add an unique ID that will be propagated to particles
posMd.setValue(xmipp.MDL_ITEM_ID, long(coord.getObjId()), objId)
# if not posMd.isEmpty():
# posMd.write("particles@%s" % scipionPosFile)
#reading origin.x value and converting to particle size, can change, we take last value
coordSet.setBoxSize(boxSize)
def readSetOfCoordinates(outputDir, micSet, coordSet):
""" Read from Bsoft .star files.
Params:
outputDir: the directory where the .star files are.
micSet: the SetOfMicrographs to associate the .star, which
name should be the same of the micrographs.
coordSet: the SetOfCoordinates that will be populated.
"""
addBsoftLabelAliases()
boxSize = 0
for mic in micSet:
outputFile = join(outputDir, replaceBaseExt(mic.getFileName(), 'star'))
#scipionPosFile = join(outputDir, "scipion_" + replaceBaseExt(mic.getFileName(), 'pos'))
if exists(outputFile):
posMd = xmipp.MetaData(outputFile)
for objId in posMd:
coord = rowToCoordinate(rowFromMd(posMd, objId))
boxSize = 2 * posMd.getValue(xmipp.MDL_PICKING_PARTICLE_SIZE,
objId)
coord.setMicrograph(mic)
coord.setX(coord.getX())
coord.setY(coord.getY())
coordSet.append(coord)
# Add an unique ID that will be propagated to particles
posMd.setValue(xmipp.MDL_ITEM_ID, long(coord.getObjId()),
objId)
# if not posMd.isEmpty():
# posMd.write("particles@%s" % scipionPosFile)
#reading origin.x value and converting to particle size, can change, we take last value
coordSet.setBoxSize(boxSize)
def readCoordinates(part, fileName, coordsSet, outputDir):
from pyworkflow.em.packages.xmipp3.convert import (readPosCoordinates,
rowToCoordinate,
rowFromMd)
posMd = readPosCoordinates(fileName)
for objId in posMd:
coord = rowToCoordinate(rowFromMd(posMd, objId))
coord.setX(coord.getX())
coord.setY(coord.getY())
coord.setMicId(part.getObjId())
coord._subparticle = part
coordsSet.append(coord)
def readCoordinates(part, fileName, coordsSet, outputDir):
from pyworkflow.em.packages.xmipp3.convert import (readPosCoordinates,
rowToCoordinate,
rowFromMd)
posMd = readPosCoordinates(fileName)
for objId in posMd:
coord = rowToCoordinate(rowFromMd(posMd, objId))
coord.setX(coord.getX())
coord.setY(coord.getY())
coord.setMicId(part.getObjId())
coord._subparticle = part
coordsSet.append(coord)
def importCoordinates(self, fileName, addCoordinate):
posMd = readPosCoordinates(fileName)
for objId in posMd:
coord = rowToCoordinate(rowFromMd(posMd, objId))
addCoordinate(coord)
