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 get2DCoordList(start=1, end=3):
""" Mocks a 2d coordinates dict"""
newCoordDict = {}
for index in range(start, end + 1):
coord = Coordinate()
newCoordDict[index] = coord
return newCoordDict
def _checkNewOutput(self):
if getattr(self, 'finished', False):
return
self.finished = self.streamClosed and self.checkedMics == self.processedMics
streamMode = Set.STREAM_CLOSED if self.finished else Set.STREAM_OPEN
newFiles = getFiles(self._getTmpPath())
if newFiles or self.finished: # when finished to close the output set
outSet = self._loadOutputSet(SetOfCoordinates,
'coordinates.sqlite')
for fnTmp in newFiles:
coords = np.loadtxt(fnTmp)
moveFile(fnTmp, self._getExtraPath())
if coords.size == 2: # special case with only one coordinate
coords = [coords]
for coord in coords:
newCoord = Coordinate()
micrographs = self.getMainInput().getMicrographs()
newCoord.setMicrograph(micrographs[self.getMicId(fnTmp)])
newCoord.setPosition(coord[0], coord[1])
outSet.append(newCoord)
firstTime = not self.hasAttribute(self.outputName)
self._updateOutputSet(self.outputName, outSet, streamMode)
if firstTime:
self.defineRelations(outSet)
outSet.close()
if self.finished: # Unlock createOutputStep if finished all jobs
outputStep = self._getFirstJoinStep()
if outputStep and outputStep.isWaiting():
outputStep.setStatus(STATUS_NEW)
def _createSetOfParts(self, nMics=10, nOptics=2, partsPerMic=10):
micSet = self._createSetOfMics(nMics, nOptics)
outputSqlite = self.getOutputPath('particles.sqlite')
cleanPath(outputSqlite)
print(">>> Writing to particles db: %s" % outputSqlite)
outputParts = SetOfParticles(filename=outputSqlite)
outputParts.setSamplingRate(1.234)
outputParts.setAcquisition(micSet.getAcquisition())
part = SetOfParticles.ITEM_TYPE()
coord = Coordinate()
for mic in micSet:
for i in range(1, partsPerMic + 1):
part.setLocation(i, mic.getFileName().replace('mrc', 'mrcs'))
coord.setPosition(x=np.random.randint(0, 1000),
y=np.random.randint(0, 1000))
coord.setMicrograph(mic)
part.setObjId(None)
part.setCoordinate(coord)
part.setAcquisition(mic.getAcquisition())
outputParts.append(part)
outputParts.write()
return outputParts
def basiccoordsFactory(self, iteration):
# newCoord = Coordinate(x=i, y=i)
# To avoid dict get
newCoord = Coordinate()
newCoord.setX(iteration)
newCoord.setY(iteration)
return newCoord
def rowToCoordinate(coordRow):
""" Create a Coordinate from a row of a metadata. """
# Check that all required labels are present in the row
if _containsAll(coordRow, COOR_DICT):
coord = Coordinate()
rowToObject(coordRow, coord,
COOR_DICT) # , extraLabels=COOR_EXTRA_LABELS)
# TODO: switch back on extra labels when
# sqlite mapper can tolerate dots in label names
else:
coord = None
return coord
def _fillParticles(self, outputParticles, outputCoords, inputParticles):
""" Create the SetOfParticles and SetOfCoordinates"""
myParticles = md.MetaData(self._getExtraPath('final_images.xmd'))
outputParticles.enableAppend()
outputCoords.enableAppend()
#Calculating the scale that relates the coordinates with the actual
# position in the mic
scale = inputParticles.getSamplingRate() / \
self.inputMics.get().getSamplingRate()
#Dictionary with the name and id of the inpt mics
micDictname = {}
micDictId = {}
for mic in self.inputMics.get():
micKey = mic.getMicName()
micDictname[micKey] = mic.clone()
micKey2 = mic.getObjId()
micDictId[micKey2] = mic.clone()
for row in md.iterRows(myParticles):
#To create the new particle
p = rowToParticle(row)
#To create the new coordinate
newCoord = Coordinate()
coord = p.getCoordinate()
if coord.getMicName() is not None:
micKey = coord.getMicName()
micDict = micDictname
else:
micKey = coord.getMicId()
micDict = micDictId
mic = micDict.get(micKey, None)
if mic is None:
print("Skipping particle, key %s not found" % micKey)
else:
newCoord.copyObjId(p)
x, y = coord.getPosition()
newCoord.setPosition(x * scale, y * scale)
newCoord.setMicrograph(mic)
outputCoords.append(newCoord)
p.setCoordinate(newCoord)
#Storing the new particle
outputParticles.append(p)
boxSize = inputParticles.getXDim() * scale
outputCoords.setBoxSize(boxSize)
def readSetOfCoordinates(coordinatesCsvFn, micSet, coordSet, scale):
""" Read coordinates produced by Topaz.
Coordinates are expected in a single csv file, with the following columns:
first: image_name (mic id)
second: x_coord
third: y_coord
forth: score
"""
csv = CsvCoordinateList(coordinatesCsvFn, score=True)
lastMicId = None
coord = Coordinate()
coord._topazScore = Float()
micDict = {}
# loop to generate a dictionary --> micBaseName : Micrograph
for mic in micSet:
micNew = mic.clone()
micDict[mic.getObjId()] = micNew
#loop the Topaz outputfile
for row in csv:
micId = int(row[0])
if micId != lastMicId:
mic = micDict[micId]
if mic is None:
print("Missing id: ", micId)
else:
coord.setMicrograph(mic)
lastMicId = micId
coord.setPosition(int(round(float(row[1]) * scale)),
int(round(float(row[2]) * scale)))
coord._topazScore.set(float(row[3]))
coord.setObjId(None)
coordSet.append(coord)
csv.close()
def readCoordinates(mic, fileName, coordsSet):
if exists(fileName):
md = emlib.MetaData()
md.readPlain(fileName, 'xcoor ycoor')
for objId in md:
x = md.getValue(emlib.MDL_XCOOR, objId)
y = md.getValue(emlib.MDL_YCOOR, objId)
coord = Coordinate()
coord.setPosition(x, y)
coord.setMicrograph(mic)
coordsSet.append(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
def readCoordinates(mic, fn, coordsSet):
""" Parse coords file and populate coordsSet.
:param mic: input micrograph object
:param fn: input file to parse
:param coordsSet: output set of coords
"""
if exists(fn):
with open(fn, 'r') as f:
for line in f:
values = line.strip().split()
# plt coords are in Imagic style
x = float(values[1])
y = float(mic.getYDim() - float(values[0]))
coord = Coordinate()
coord.setPosition(x, y)
coord.setMicrograph(mic)
coordsSet.append(coord)
def readCoordsFromMics(self, workingDir, micList, coordSet):
coordSet.setBoxSize(self.radius.get() * 2)
for mic in micList:
micFn = mic.getFileName()
micDir = self._getMicDir(micFn)
coordFile = os.path.join(micDir, self._getMicPosFn(micFn))
if os.path.exists(coordFile):
coordMd = md.MetaData()
coordMd.readPlain(coordFile, 'xcoor ycoor')
for objId in coordMd:
x = coordMd.getValue(md.MDL_XCOOR, objId)
y = coordMd.getValue(md.MDL_YCOOR, objId)
coord = Coordinate()
coord.setPosition(x, y)
coord.setMicrograph(mic)
coordSet.append(coord)
else:
print("Coordinate file '%s' not found. " % coordFile)
def createOutputStep(self):
input = self.input.get()
imgSetOut = self._createSetOfParticles()
imgSetOut.setSamplingRate(input.getSamplingRate())
imgSetOut.setAlignmentProj()
for i, subtomo in enumerate(input.iterItems()):
idx = subtomo.getObjId()
p = Particle()
p.setLocation(ih._convertToLocation((i+1, self._getExtraPath("projections.mrcs"))))
p._subtomogramID = String(idx)
if type(subtomo) == SubTomogram:
if subtomo.hasCoordinate3D():
coord = Coordinate()
coord.setX(subtomo.getCoordinate3D().getX(const.BOTTOM_LEFT_CORNER))
coord.setY(subtomo.getCoordinate3D().getY(const.BOTTOM_LEFT_CORNER))
p.setCoordinate(coord)
p.setClassId(subtomo.getClassId())
if subtomo.hasTransform():
transform = Transform()
transform.setMatrix(subtomo.getTransform().getMatrix())
p.setTransform(transform)
imgSetOut.append(p)
imgSetOut.setObjComment(self.getSummary(imgSetOut))
self._defineOutputs(outputParticles=imgSetOut)
self._defineSourceRelation(self.input, imgSetOut)
if self.radAvg.get():
avgFile = self._getExtraPath("average.xmp")
imgh = ih()
avgImage = imgh.computeAverage(imgSetOut)
avgImage.write(avgFile)
avg = Particle()
avg.setLocation(1, avgFile)
avg.copyInfo(imgSetOut)
self._defineOutputs(outputAverage=avg)
self._defineSourceRelation(self.input, avg)
def coordsFactory(iteration):
# newCoord = Coordinate(x=i, y=i)
# To avoid dict get
newCoord = Coordinate()
newCoord.setX(iteration)
newCoord.setY(iteration)
newCoord.extra1 = Integer(1)
newCoord.extra2 = Integer(1)
newCoord.extra3 = Integer(1)
newCoord.extra4 = Integer(1)
newCoord.extra5 = Integer(1)
newCoord.extra6 = Integer(1)
newCoord.extra7 = Integer(1)
newCoord.extra8 = Integer(1)
newCoord.extra9 = Integer(1)
newCoord.extra10 = Integer(1)
newCoord.extra11 = Integer(1)
newCoord.extra12 = Integer(1)
newCoord.extra13 = Integer(1)
newCoord.extra14 = Integer(1)
newCoord.extra15 = Integer(1)
newCoord.extra16 = Integer(1)
newCoord.extra17 = Integer(1)
newCoord.extra18 = Integer(1)
newCoord.extra19 = Integer(1)
newCoord.extra20 = Integer(1)
return newCoord
def particlesFactory(index):
newParticle = Particle(location=(1, self.particlesStk))
newParticle.setCoordinate(Coordinate(x=1, y=2))
newParticle.setAcquisition(Acquisition())
return newParticle