def _updateClass(self, item):
classId = item.getObjId()
classRow = findRow(self.mdClasses, xmipp.MDL_REF2, classId)
representative = item.getRepresentative()
representative.setTransform(rowToAlignment(classRow, ALIGN_PROJ))
representative.setLocation(xmippToLocation(classRow.getValue(xmipp.MDL_IMAGE)))
setXmippAttributes(representative, classRow, xmipp.MDL_ANGLE_ROT)
setXmippAttributes(representative, classRow, xmipp.MDL_ANGLE_TILT)
setXmippAttributes(representative, classRow, xmipp.MDL_CLASS_COUNT)
self.averageSet.append(representative)
reprojection = Image()
reprojection.setLocation(xmippToLocation(classRow.getValue(xmipp.MDL_IMAGE1)))
item.reprojection = reprojection
def _updateClass(self, item):
classId = item.getObjId()
classRow = findRow(self.mdClasses, xmipp.MDL_REF2, classId)
representative = item.getRepresentative()
representative.setTransform(rowToAlignment(classRow, ALIGN_PROJ))
representative.setLocation(xmippToLocation(classRow.getValue(xmipp.MDL_IMAGE)))
setXmippAttributes(representative, classRow, xmipp.MDL_ANGLE_ROT)
setXmippAttributes(representative, classRow, xmipp.MDL_ANGLE_TILT)
setXmippAttributes(representative, classRow, xmipp.MDL_CLASS_COUNT)
self.averageSet.append(representative)
reprojection = Image()
reprojection.setLocation(xmippToLocation(classRow.getValue(xmipp.MDL_IMAGE1)))
item.reprojection = reprojection
def _updateItem(self, item, row):
""" Implement this function to do some
update actions over each single item
that will be stored in the output Set.
"""
# By default update the item location (index, filename)
# with the new binary data location (after preprocessing)
newFn = row.getValue(md.MDL_IMAGE)
newLoc = xmippToLocation(newFn)
item.setLocation(newLoc)
def _updateItem(self, item, row):
""" Implement this function to do some
update actions over each single item
that will be stored in the output Set.
"""
# By default update the item location (index, filename) with the new binary data location
newFn = row.getValue(xmipp.MDL_IMAGE)
newLoc = xmippToLocation(newFn)
item.setLocation(newLoc)
# Also remove alignment info
item.setTransform(None)
def _updateItem(self, item, row):
""" Implement this function to do some
update actions over each single item
that will be stored in the output Set.
"""
# By default update the item location (index, filename) with the new binary data location
newFn = row.getValue(md.MDL_IMAGE)
newLoc = xmippToLocation(newFn)
item.setLocation(newLoc)
# Also remove alignment info
item.setTransform(None)
def _loadClassesInfo(self, filename):
""" Read some information about the produced 2D classes
from the metadata file.
"""
self._classesInfo = {} # store classes info, indexed by class id
mdClasses = md.MetaData(filename)
for classNumber, row in enumerate(md.iterRows(mdClasses)):
index, fn = xmippToLocation(row.getValue(md.MDL_IMAGE))
# Store info indexed by id, we need to store the row.clone() since
# the same reference is used for iteration
self._classesInfo[classNumber+1] = (index, fn, row.clone())
def _loadClassesInfo(self, filename):
""" Read some information about the produced 2D classes
from the metadata file.
"""
self._classesInfo = {} # store classes info, indexed by class id
mdClasses = md.MetaData(filename)
for classNumber, row in enumerate(md.iterRows(mdClasses)):
index, fn = xmippToLocation(row.getValue(md.MDL_IMAGE))
# Store info indexed by id, we need to store the row.clone() since
# the same reference is used for iteration
self._classesInfo[classNumber + 1] = (index, fn, row.clone())
def readPartsFromMics(self, micList, outputParts):
""" Read the particles extract for the given list of micrographs
and update the outputParts set with new items.
"""
p = Particle()
for mic in micList:
# We need to make this dict because there is no ID in the .xmd file
coordDict = {}
for coord in self.coordDict[mic.getObjId()]:
pos = self._getPos(coord)
if pos in coordDict:
print(
"WARNING: Ignoring duplicated coordinate: %s, id=%s" %
(coord.getObjId(), pos))
coordDict[pos] = coord
added = set() # Keep track of added coords to avoid duplicates
for row in md.iterRows(self._getMicXmd(mic)):
pos = (row.getValue(md.MDL_XCOOR), row.getValue(md.MDL_YCOOR))
coord = coordDict.get(pos, None)
if coord is not None and coord.getObjId() not in added:
# scale the coordinates according to particles dimension.
coord.scale(self.getBoxScale())
p.copyObjId(coord)
p.setLocation(xmippToLocation(row.getValue(md.MDL_IMAGE)))
p.setCoordinate(coord)
p.setMicId(mic.getObjId())
p.setCTF(mic.getCTF())
# disabled particles (in metadata) should not add to the
# final set
if row.getValue(md.MDL_ENABLED) > 0:
outputParts.append(p)
added.add(coord.getObjId())
# Release the list of coordinates for this micrograph since it
# will not be longer needed
del self.coordDict[mic.getObjId()]
def _preprocessClass(self, classItem, classRow):
classItem.average = Particle()
classItem.average.setLocation(
xmippToLocation(classRow.getValue(xmipp.MDL_IMAGE2)))
def _preprocessClass(self, classItem, classRow):
classItem.average = Particle()
classItem.average.setLocation(xmippToLocation(classRow.getValue(xmipp.MDL_IMAGE2)))
def _updateLocation(self, item, row):
index, filename = xmippToLocation(row.getValue(md.MDL_IMAGE))
item.setLocation(index, filename)
def _updateLocation(self, item, row):
index, filename = xmippToLocation(row.getValue(md.MDL_IMAGE))
item.setLocation(index, filename)
