def generateMicImage(self, input_file, output_file=None):
if not output_file:
output_file = os.path.splitext(input_file)[0] + '.png'
img = ImageHandler().createImage()
img.read(input_file)
pimg = getPILImage(img)
pwutils.makeFilePath(output_file)
pimg.save(output_file, "PNG")
def projectStep(self, start, end, samplingRate, threadNumber):
# Project
md = xmipp.MetaData(self._getInputParticlesSubsetFn(threadNumber))
##
projection = xmipp.Image()
projection.setDataType(xmipp.DT_DOUBLE)
##
for id in md:
rot = md.getValue(xmipp.MDL_ANGLE_ROT, id)
tilt = md.getValue(xmipp.MDL_ANGLE_TILT, id)
psi = md.getValue(xmipp.MDL_ANGLE_PSI, id)
##projection =self.vol.projectVolumeDouble(rot, tilt, psi)
self.fourierProjectVol.projectVolume(projection, rot, tilt, psi)
##
# Apply CTF
if self.projType == self.CORRECT_NONE:
pass
elif self.projType == self.CORRECT_FULL_CTF:
projection.applyCTF(md, samplingRate, id, False)
elif self.projType == self.CORRECT_PHASE_FLIP:
projection.applyCTF(md, samplingRate, id, True)
else:
raise Exception("ERROR: Unknown projection mode: %d" %
self.projType)
# Shift image
projection.applyGeo(md, id, True, False) #onlyapplyshist, wrap
ih = ImageHandler()
expProj = ih.read(md.getValue(xmipp.MDL_IMAGE, id))
expProj.convert2DataType(xmipp.DT_DOUBLE)
# Subtract from experimental and write result
projection.resetOrigin()
if self.normalize:
expProj = expProj.adjustAndSubtract(projection)
else:
expProj.inplaceSubtract(projection)
expProj.write(self._getProjGalleryIndexFn(id + start - 1))
def projectStep(self, start, end, samplingRate, threadNumber):
# Project
md = xmipp.MetaData(self._getInputParticlesSubsetFn(threadNumber))
##
projection = xmipp.Image()
projection.setDataType(xmipp.DT_DOUBLE)
##
for id in md:
rot = md.getValue(xmipp.MDL_ANGLE_ROT, id)
tilt = md.getValue(xmipp.MDL_ANGLE_TILT, id)
psi = md.getValue(xmipp.MDL_ANGLE_PSI, id)
##projection =self.vol.projectVolumeDouble(rot, tilt, psi)
self.fourierProjectVol.projectVolume(projection, rot, tilt, psi)
##
# Apply CTF
if self.projType == self.CORRECT_NONE:
pass
elif self.projType == self.CORRECT_FULL_CTF:
projection.applyCTF(md, samplingRate, id, False)
elif self.projType == self.CORRECT_PHASE_FLIP:
projection.applyCTF(md, samplingRate, id, True)
else:
raise Exception("ERROR: Unknown projection mode: %d" % self.projType)
# Shift image
projection.applyGeo(md,id,True,False)#onlyapplyshist, wrap
ih = ImageHandler()
expProj = ih.read(md.getValue(xmipp.MDL_IMAGE, id))
expProj.convert2DataType(xmipp.DT_DOUBLE)
# Subtract from experimental and write result
projection.resetOrigin()
if self.normalize:
expProj = expProj.adjustAndSubtract(projection)
else:
expProj.inplaceSubtract(projection)
expProj.write( self._getProjGalleryIndexFn(id+start-1))
def createOutputStep(self, particlesId, coordsId, boxSize):
""" Create the input file in STAR format as expected by Relion.
Params:
particlesId: use this parameters just to force redo of convert if
the input particles are changed.
"""
ih = ImageHandler()
outputStack = self._getPath('particles.mrcs')
outputImg = ih.createImage()
inputParticles = self._getInputParticles()
inputCoords = self.inputCoordinates.get()
outputSet = self._createSetOfParticles()
outputSet.copyInfo(inputParticles)
boxSize = self.boxSize.get()
b2 = int(round(boxSize / 2))
center = np.zeros((boxSize, boxSize))
ih = ImageHandler()
i = 0
outliers = 0
partIdExcluded = []
lastPartId = None
for coord in inputCoords.iterItems(
orderBy=['_subparticle._micId', '_micId', 'id']):
# The original particle id is stored in the sub-particle as micId
partId = coord._micId.get()
# Load the particle if it has changed from the last sub-particle
if partId != lastPartId:
particle = inputParticles[partId]
if particle is None:
partIdExcluded.append(partId)
self.info("WARNING: Missing particle with id %s from "
"input particles set" % partId)
else:
# Now load the particle image to extract later sub-particles
img = ih.read(particle)
x, y, _, _ = img.getDimensions()
data = img.getData()
lastPartId = partId
# If particle is not in inputParticles, subparticles will not be
# generated. Now, subtract from a subset of original particles is
# supported.
if not partId in partIdExcluded:
xpos = coord.getX()
ypos = coord.getY()
# Check that the sub-particle will not lay out of the particle
if (ypos - b2 < 0 or ypos + b2 > y or xpos - b2 < 0
or xpos + b2 > x):
outliers += 1
continue
# Crop the sub-particle data from the whole particle image
center[:, :] = data[ypos - b2:ypos + b2, xpos - b2:xpos + b2]
outputImg.setData(center)
i += 1
outputImg.write((i, outputStack))
subpart = coord._subparticle
subpart.setLocation(
(i, outputStack)) # Change path to new stack
subpart.setObjId(None) # Force to insert as a new item
outputSet.append(subpart)
if outliers:
self.info(
"WARNING: Discarded %s particles because laid out of the "
"particle (for a box size of %d" % (outliers, boxSize))
self._defineOutputs(outputParticles=outputSet)
self._defineSourceRelation(self.inputParticles, outputSet)
def createOutputStep(self, particlesId, coordsId, boxSize):
""" Create the input file in STAR format as expected by Relion.
Params:
particlesId: use this parameters just to force redo of convert if
the input particles are changed.
"""
ih = ImageHandler()
outputStack = self._getPath('particles.mrcs')
outputImg = ih.createImage()
inputParticles = self._getInputParticles()
inputCoords = self.inputCoordinates.get()
outputSet = self._createSetOfParticles()
outputSet.copyInfo(inputParticles)
boxSize = self.boxSize.get()
b2 = int(round(boxSize / 2))
center = np.zeros((boxSize, boxSize))
ih = ImageHandler()
i = 0
outliers = 0
partIdExcluded = []
lastPartId = None
for coord in inputCoords.iterItems(orderBy=['_subparticle._micId',
'_micId', 'id']):
# The original particle id is stored in the sub-particle as micId
partId = coord._micId.get()
# Load the particle if it has changed from the last sub-particle
if partId != lastPartId:
particle = inputParticles[partId]
if particle is None:
partIdExcluded.append(partId)
self.info("WARNING: Missing particle with id %s from "
"input particles set" % partId)
else:
# Now load the particle image to extract later sub-particles
img = ih.read(particle)
x, y, _, _ = img.getDimensions()
data = img.getData()
lastPartId = partId
# If particle is not in inputParticles, subparticles will not be
# generated. Now, subtract from a subset of original particles is
# supported.
if not partId in partIdExcluded:
xpos = coord.getX()
ypos = coord.getY()
# Check that the sub-particle will not lay out of the particle
if (ypos - b2 < 0 or ypos + b2 > y or
xpos - b2 < 0 or xpos + b2 > x):
outliers += 1
continue
# Crop the sub-particle data from the whole particle image
center[:, :] = data[ypos-b2:ypos+b2, xpos-b2:xpos+b2]
outputImg.setData(center)
i += 1
outputImg.write((i, outputStack))
subpart = coord._subparticle
subpart.setLocation((i, outputStack)) # Change path to new stack
subpart.setObjId(None) # Force to insert as a new item
outputSet.append(subpart)
if outliers:
self.info("WARNING: Discarded %s particles because laid out of the "
"particle (for a box size of %d" % (outliers, boxSize))
self._defineOutputs(outputParticles=outputSet)
self._defineSourceRelation(self.inputParticles, outputSet)
