def _itemSelected(self, obj):
index = obj.getIndex()
filename = ImageHandler.fixXmippVolumeFileName(obj)
if index:
filename = "%03d@%s" % (index, filename)
# self.image = xmipp.Image()
self.image = ImageHandler()._img
try:
self.image.readPreview(filename, self.dim)
if filename.endswith('.psd'):
self.image.convertPSD()
self.Z = self.image.getData()
except Exception, e:
from pyworkflow.gui.matplotlib_image import getPngData
self.Z = getPngData(findResource('no-image.png'))
dialog.showError("Input particles", "Error reading image <%s>"
% filename, self)
def _processMovie(self, movie):
movId = movie.getObjId()
x, y, n = movie.getDim()
iniFrame, lastFrame, _ = movie.getFramesRange()
frame0, frameN = self._getRange(movie)
boxSize = self.boxSize.get()
if movie.hasAlignment() and self.applyAlignment:
shiftX, shiftY = movie.getAlignment().getShifts() # lists.
else:
shiftX = [0] * (lastFrame - iniFrame + 1)
shiftY = shiftX
stkIndex = 0
movieStk = self._getMovieName(movie, '.stk')
movieMdFile = self._getMovieName(movie, '.xmd')
movieMd = md.MetaData()
frameMd = md.MetaData()
frameMdImages = md.MetaData()
frameRow = md.Row()
if self._hasCoordinates(movie):
imgh = ImageHandler()
for frame in range(frame0, frameN + 1):
indx = frame - iniFrame
frameName = self._getFnRelated('frameMic', movId, frame)
frameMdFile = self._getFnRelated('frameMdFile', movId, frame)
coordinatesName = self._getFnRelated('frameCoords', movId,
frame)
frameImages = self._getFnRelated('frameImages', movId, frame)
frameStk = self._getFnRelated('frameStk', movId, frame)
self._writeXmippPosFile(movie, coordinatesName, shiftX[indx],
shiftY[indx])
self.info("Writing frame: %s" % frameName)
# TODO: there is no need to write the frame and then operate
# the input of the first operation should be the movie
movieName = imgh.fixXmippVolumeFileName(movie)
imgh.convert((frame, movieName), frameName)
if self.doRemoveDust:
self.info("Removing Dust")
self._runNoDust(frameName)
self.info("Extracting particles")
args = '-i %(frameName)s --pos %(coordinatesName)s ' \
'-o %(frameImages)s --Xdim %(boxSize)d' % locals()
if self.doInvert:
args += " --invert"
if self.doBorders:
args += " --fillBorders"
args += " --downsampling %f " % self.getBoxScale()
self.runJob('xmipp_micrograph_scissor', args)
cleanPath(frameName)
self.info("Combining particles into one stack.")
frameMdImages.read(frameMdFile)
frameMd.read('particles@%s' % coordinatesName)
frameMd.merge(frameMdImages)
for objId in frameMd:
stkIndex += 1
frameRow.readFromMd(frameMd, objId)
location = xmippToLocation(frameRow.getValue(md.MDL_IMAGE))
newLocation = (stkIndex, movieStk)
imgh.convert(location, newLocation)
# Fix the name to be accessible from the Project directory
# so we know that the movie stack file will be moved
# to final particles folder
newImageName = '%d@%s' % newLocation
frameRow.setValue(md.MDL_IMAGE, newImageName)
frameRow.setValue(md.MDL_MICROGRAPH_ID, long(movId))
frameRow.setValue(md.MDL_MICROGRAPH, str(movId))
frameRow.setValue(md.MDL_FRAME_ID, long(frame))
frameRow.setValue(md.MDL_PARTICLE_ID,
frameRow.getValue(md.MDL_ITEM_ID))
frameRow.writeToMd(movieMd, movieMd.addObject())
movieMd.addItemId()
movieMd.write(movieMdFile)
cleanPath(frameStk)
if self.doNormalize:
numberOfFrames = frameN - frame0 + 1
self._runNormalize(movieStk, numberOfFrames)
def _processMovie(self, movie):
movId = movie.getObjId()
x, y, n = movie.getDim()
iniFrame, lastFrame, _ = movie.getFramesRange()
frame0, frameN = self._getRange(movie)
boxSize = self.boxSize.get()
if movie.hasAlignment() and self.applyAlignment:
shiftX, shiftY = movie.getAlignment().getShifts() # lists.
else:
shiftX = [0] * (lastFrame-iniFrame+1)
shiftY = shiftX
stkIndex = 0
movieStk = self._getMovieName(movie, '.stk')
movieMdFile = self._getMovieName(movie, '.xmd')
movieMd = md.MetaData()
frameMd = md.MetaData()
frameMdImages = md.MetaData()
frameRow = md.Row()
if self._hasCoordinates(movie):
imgh = ImageHandler()
for frame in range(frame0, frameN+1):
indx = frame-iniFrame
frameName = self._getFnRelated('frameMic',movId, frame)
frameMdFile = self._getFnRelated('frameMdFile',movId, frame)
coordinatesName = self._getFnRelated('frameCoords',movId, frame)
frameImages = self._getFnRelated('frameImages',movId, frame)
frameStk = self._getFnRelated('frameStk', movId, frame)
self._writeXmippPosFile(movie, coordinatesName,
shiftX[indx], shiftY[indx])
self.info("Writing frame: %s" % frameName)
# TODO: there is no need to write the frame and then operate
# the input of the first operation should be the movie
movieName = imgh.fixXmippVolumeFileName(movie)
imgh.convert((frame, movieName), frameName)
if self.doRemoveDust:
self.info("Removing Dust")
self._runNoDust(frameName)
self.info("Extracting particles")
args = '-i %(frameName)s --pos %(coordinatesName)s ' \
'-o %(frameImages)s --Xdim %(boxSize)d' % locals()
if self.doInvert:
args += " --invert"
if self.doBorders:
args += " --fillBorders"
args += " --downsampling %f " % self.getBoxScale()
self.runJob('xmipp_micrograph_scissor', args)
cleanPath(frameName)
self.info("Combining particles into one stack.")
frameMdImages.read(frameMdFile)
frameMd.read('particles@%s' % coordinatesName)
frameMd.merge(frameMdImages)
for objId in frameMd:
stkIndex += 1
frameRow.readFromMd(frameMd, objId)
location = xmippToLocation(frameRow.getValue(md.MDL_IMAGE))
newLocation = (stkIndex, movieStk)
imgh.convert(location, newLocation)
# Fix the name to be accessible from the Project directory
# so we know that the movie stack file will be moved
# to final particles folder
newImageName = '%d@%s' % newLocation
frameRow.setValue(md.MDL_IMAGE, newImageName)
frameRow.setValue(md.MDL_MICROGRAPH_ID, long(movId))
frameRow.setValue(md.MDL_MICROGRAPH, str(movId))
frameRow.setValue(md.MDL_FRAME_ID, long(frame))
frameRow.setValue(md.MDL_PARTICLE_ID,
frameRow.getValue(md.MDL_ITEM_ID))
frameRow.writeToMd(movieMd, movieMd.addObject())
movieMd.addItemId()
movieMd.write(movieMdFile)
cleanPath(frameStk)
if self.doNormalize:
numberOfFrames = frameN - frame0 + 1
self._runNormalize(movieStk, numberOfFrames)
