def rowToCoordinate(coordRow):
""" Create a Coordinate from a row of a meta """
# Check that all required labels are present in the row
if coordRow.containsAll(COOR_DICT):
coord = Coordinate()
rowToObject(coordRow, coord, COOR_DICT, extraLabels=COOR_EXTRA_LABELS)
# Gautomatch starts _rlnClassNumber at 0, but relion at 1
# so let's increment its value
if coord.hasAttribute('_rlnClassNumber'):
coord._rlnClassNumber.increment()
micName = None
if coordRow.hasLabel(md.RLN_MICROGRAPH_ID):
micId = int(coordRow.getValue(md.RLN_MICROGRAPH_ID))
coord.setMicId(micId)
# If RLN_MICROGRAPH_NAME is not present, use the id as a name
micName = micId
if coordRow.hasLabel(md.RLN_MICROGRAPH_NAME):
micName = coordRow.getValue(md.RLN_MICROGRAPH_NAME)
coord.setMicName(micName)
else:
coord = None
return coord
def getParticleList(start=1, end=3):
""" Mocks a Particle dict"""
newPartDict = {}
for index in range(start, end + 1):
part = Particle()
coord = Coordinate()
coord.setMicId(index)
coord.setMicName(getMicNameFromId(index))
part.setCoordinate(coord)
newPartDict[index] = part
return newPartDict