def _writeXmippPosFile(self, movie, coordinatesName, shiftX, shiftY):
""" Create an Xmipp coordinates files to be extracted
from the frames of the movie.
"""
coordSet = self.inputCoordinates.get()
# to support multiple access to db
coordToIter = SetOfCoordinates()
coordToIter.copy(coordSet)
coordSet.close()
mData = md.MetaData()
coordRow = XmippMdRow()
for coord in coordToIter.iterCoordinates(movie.getObjId()):
coord.shiftX(int(round(float(shiftX))))
coord.shiftY(int(round(float(shiftY))))
coordinateToRow(coord, coordRow)
coordRow.writeToMd(mData, mData.addObject())
coordToIter.close()
if mData.isEmpty():
return False
else:
self.info("Writing coordinates metadata: %s, with shifts: %s %s" %
(coordinatesName, shiftX, shiftY))
mData.write('particles@' + coordinatesName)
return True
def _writeXmippPosFile(self, movieId, movieName, coordinatesName, shiftX,
shiftY):
""" Create an Xmipp coordinates files to be extracted
from the frames of the movie.
"""
##### import em abre una nueva conexion?
#TODO ROB move this import to the header
from pyworkflow.em import SetOfCoordinates
inputCoords = self.inputCoordinates.get()
coordinates = SetOfCoordinates(filename=inputCoords.getFileName())
#####coordinates = self.inputCoordinates.get()
#####micrograph = coordinates.getMicrographs()[movieId]
####if micrograph is None:
#####raise Exception("Micrograph with id %d was not found in SetOfCoordinates!!!" % movieId)
mData = md.MetaData()
coordRow = XmippMdRow()
#### for coord in coordinates.iterCoordinates(micrograph):
for coord in coordinates.iterCoordinates(movieId):
coord.shiftX(int(round(float(shiftX))))
coord.shiftY(int(round(float(shiftY))))
coordinateToRow(coord, coordRow)
coordRow.writeToMd(mData, mData.addObject())
if mData.isEmpty():
return False
else:
self.info("Writing coordinates metadata: %s, with shifts: %s %s" %
(coordinatesName, shiftX, shiftY))
mData.write('particles@' + coordinatesName)
return True
def _writeXmippPosFile(self, movieId, movieName, coordinatesName, shiftX, shiftY):
""" Create an Xmipp coordinates files to be extracted
from the frames of the movie.
"""
##### import em abre una nueva conexion?
#TODO ROB move this import to the header
from pyworkflow.em import SetOfCoordinates
inputCoords = self.inputCoordinates.get()
coordinates = SetOfCoordinates(filename=inputCoords.getFileName())
#####coordinates = self.inputCoordinates.get()
#####micrograph = coordinates.getMicrographs()[movieId]
####if micrograph is None:
#####raise Exception("Micrograph with id %d was not found in SetOfCoordinates!!!" % movieId)
mData = md.MetaData()
coordRow = XmippMdRow()
#### for coord in coordinates.iterCoordinates(micrograph):
for coord in coordinates.iterCoordinates(movieId):
coord.shiftX( int(round(float(shiftX))))
coord.shiftY( int(round(float(shiftY))))
coordinateToRow(coord, coordRow)
coordRow.writeToMd(mData, mData.addObject())
if mData.isEmpty():
return False
else:
self.info("Writing coordinates metadata: %s, with shifts: %s %s" % (coordinatesName, shiftX, shiftY))
mData.write('particles@' + coordinatesName)
return True
def createOutputStep(self):
fnSqlite = self._getPath('modes.sqlite')
nmSet = SetOfNormalModes(filename=fnSqlite)
md = xmipp.MetaData(self._getPath('modes.xmd'))
row = XmippMdRow()
for objId in md:
row.readFromMd(md, objId)
nmSet.append(rowToMode(row))
inputPdb = self.inputStructure.get()
nmSet.setPdb(inputPdb)
self._defineOutputs(outputModes=nmSet)
self._defineSourceRelation(self.inputStructure, nmSet)
def createOutputStep(self):
fnSqlite = self._getPath('modes.sqlite')
nmSet = SetOfNormalModes(filename=fnSqlite)
md = xmipp.MetaData(self._getPath('modes.xmd'))
row = XmippMdRow()
for objId in md:
row.readFromMd(md, objId)
nmSet.append(rowToMode(row))
inputPdb = self.inputStructure.get()
nmSet.setPdb(inputPdb)
self._defineOutputs(outputModes=nmSet)
self._defineSourceRelation(self.inputStructure, nmSet)
def _writeXmippPosFile(self, movie, coordinatesName, shiftX, shiftY):
""" Create Xmipp coordinate files to be extracted
from the frames of the movie.
"""
coordSet = self.getCoords()
mData = md.MetaData()
coordRow = XmippMdRow()
for coord in coordSet.iterCoordinates(movie.getObjId()):
coord.shiftX( int(round(float(shiftX))))
coord.shiftY( int(round(float(shiftY))))
coordinateToRow(coord, coordRow)
coordRow.writeToMd(mData, mData.addObject())
self.info("Writing coordinates metadata: %s, with shifts: %s %s"
% (coordinatesName, shiftX, shiftY))
mData.write('particles@' + coordinatesName)
def _writeXmippPosFile(self, movie, coordinatesName, shiftX, shiftY):
""" Create Xmipp coordinate files to be extracted
from the frames of the movie.
"""
coordSet = self.getCoords()
mData = md.MetaData()
coordRow = XmippMdRow()
for coord in coordSet.iterCoordinates(movie.getObjId()):
coord.shiftX(int(round(float(shiftX))))
coord.shiftY(int(round(float(shiftY))))
coordinateToRow(coord, coordRow)
coordRow.writeToMd(mData, mData.addObject())
self.info("Writing coordinates metadata: %s, with shifts: %s %s" %
(coordinatesName, shiftX, shiftY))
mData.write('particles@' + coordinatesName)
def writeModesMetaData(self):
""" Iterate over the input SetOfNormalModes and write
the proper Xmipp metadata.
Take into account a possible selection of modes (This option is
just a shortcut for testing. The recommended
way is just create a subset from the GUI and use that as input)
"""
modeSelection = []
if self.modeList.empty():
modeSelection = []
else:
modeSelection = getListFromRangeString(self.modeList.get())
md = xmipp.MetaData()
inputModes = self.inputModes.get()
for mode in inputModes:
# If there is a mode selection, only
# take into account those selected
if not modeSelection or mode.getObjId() in modeSelection:
row = XmippMdRow()
modeToRow(mode, row)
row.writeToMd(md, md.addObject())
md.write(self.modesFn)
def writeModesMetaData(self):
""" Iterate over the input SetOfNormalModes and write
the proper Xmipp metadata.
Take into account a possible selection of modes (This option is
just a shortcut for testing. The recommended
way is just create a subset from the GUI and use that as input)
"""
modeSelection = []
if self.modeList.empty():
modeSelection = []
else:
modeSelection = getListFromRangeString(self.modeList.get())
mdModes = md.MetaData()
inputModes = self.inputModes.get()
for mode in inputModes:
# If there is a mode selection, only
# take into account those selected
if not modeSelection or mode.getObjId() in modeSelection:
row = XmippMdRow()
modeToRow(mode, row)
row.writeToMd(mdModes, mdModes.addObject())
mdModes.write(self.modesFn)