def createOutputStep(self):
micSet = self.getInputMicrographs()
ih = em.ImageHandler()
coordSet = self._createSetOfCoordinates(micSet)
if self.boxSize == 0:
coordSet.setBoxSize(self.inputReferences.get().getDim()[0])
else:
coordSet.setBoxSize(self.boxSize.get())
for mic in micSet:
fnCoords = pwutils.replaceBaseExt(mic.getFileName(), 'txt')
fn2parse = self._getExtraPath('pik_coord', fnCoords)
print fn2parse
xdim, _, _, _ = ih.getDimensions(mic)
#xdim, ydim, _ = em.getDimensions(micSet)
#print xdim, ydim
with open(fn2parse, "r") as source:
source.readline() # Skip first line
for line in source:
tokens = line.split()
coord = em.Coordinate()
coord.setPosition(xdim - int(tokens[3]), int(tokens[2]))
coord.setMicrograph(mic)
coordSet.append(coord)
self._defineOutputs(outputCoordinates=coordSet)
self._defineSourceRelation(micSet, coordSet)
def readCoordinates(mic, fileName, coordsSet):
if os.path.exists(fileName):
mdCoords = md.MetaData()
mdCoords.readPlain(fileName, "xcoor ycoor xSize ySize")
for row in md.iterRows(mdCoords):
coord = em.Coordinate(
x=row.getValue("xcoor") + row.getValue("xSize") / 2,
y=row.getValue("ycoor") + row.getValue("ySize") / 2)
coord.setMicrograph(mic)
coordsSet.append(coord)
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 = em.Coordinate()
rowToObject(coordRow, coord, COOR_DICT)
#FIXME: THE FOLLOWING IS NOT CLEAN
try:
coord.setMicId(int(coordRow.getValue(md.RLN_MICROGRAPH_NAME)))
except Exception:
pass
else:
coord = None
return coord
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 = em.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()
# FIXME: THE FOLLOWING IS NOT CLEAN
try:
coord.setMicId(int(coordRow.getValue(md.RLN_MICROGRAPH_NAME)))
except Exception:
pass
else:
coord = None
return coord
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 = em.Coordinate()
rowToObject(coordRow, coord, COOR_DICT, extraLabels=COOR_EXTRA_LABELS)
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