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 importCoordinates(self, fileName, addCoordinate):
print("In importCoordinates Appion with filename=%s" % fileName)
if exists(fileName):
mdata = md.MetaData()
mdata.readPlain(fileName, 'xcoor ycoor')
for objId in mdata:
x = mdata.getValue(md.MDL_XCOOR, objId)
y = mdata.getValue(md.MDL_YCOOR, objId)
coord = Coordinate()
coord.setPosition(x, y)
addCoordinate(coord)
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 _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 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 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()