def _computeRightPreview(self):
""" This function should compute the right preview
using the self.lastObj that was selected
"""
xmippLib.gaussianFilter(self.rightImage,
ImageHandler.locationToXmipp(self.lastObj),
self.getFreqSigma(), self.dim)
def _computeRightPreview(self):
""" This function should compute the right preview
using the self.lastObj that was selected
"""
xmippLib.bandPassFilter(self.rightImage,
ImageHandler.locationToXmipp(self.lastObj),
self.getLowFreq(), self.getHighFreq(),
self.getFreqDecay(), self.dim)
def _loadPath(self, path):
self._tableName = None
# If path is a tuple, we will convert to the filename format
# as expected by Showj
if isinstance(path, tuple):
self._path = ImageHandler.locationToXmipp(path)
# Check if there is a table name with @ in path
# in that case split table name and path
# table names can never starts with a number
# this is considering an image inside an stack
elif isinstance(path, basestring):
if '@' in path and path[0] not in '0123456789':
self._tableName, self._path = path.split('@')
else:
self._path = path
else:
raise Exception("Invalid input path, "
"should be 'string' or 'tuple'")
def writeSetOfMicrographs(micSet, filename):
""" Simplified function borrowed from xmipp. """
mdata = md.MetaData()
for img in micSet:
objId = mdata.addObject()
imgRow = md.Row()
imgRow.setValue(md.MDL_ITEM_ID, long(objId))
index, fname = img.getLocation()
fn = ImageHandler.locationToXmipp((index, fname))
imgRow.setValue(md.MDL_MICROGRAPH, fn)
if img.isEnabled():
enabled = 1
else:
enabled = -1
imgRow.setValue(md.MDL_ENABLED, enabled)
imgRow.writeToMd(mdata, objId)
mdata.write('Micrographs@%s' % filename)
def _visualize(self, obj, **kwargs):
cls = type(obj)
if issubclass(cls, em.Volume):
fn = ImageHandler.locationToXmipp(obj)
self._addObjView(obj, fn, {
showj.RENDER: 'image',
showj.SAMPLINGRATE: obj.getSamplingRate()
})
elif issubclass(cls, em.Image):
fn = ImageHandler.locationToXmipp(obj)
self._addObjView(obj, fn)
elif issubclass(cls, em.SetOfPDBs):
fn = obj.getFileName()
labels = 'id _filename '
self._addObjView(
obj, fn, {
showj.ORDER: labels,
showj.VISIBLE: labels,
showj.MODE: showj.MODE_MD,
showj.RENDER: "no"
})
elif issubclass(cls, em.SetOfMovies):
fn = obj.getFileName()
# Enabled for the future has to be available
labels = ('id _filename _samplingRate _acquisition._dosePerFrame '
'_acquisition._doseInitial ')
moviesView = self._addObjView(
obj, fn, {
showj.ORDER: labels,
showj.VISIBLE: labels,
showj.MODE: showj.MODE_MD,
showj.RENDER: "no"
})
# For movies increase the JVM memory by 1 GB, just in case
moviesView.setMemory(showj.getJvmMaxMemory() + 1)
elif issubclass(cls, em.SetOfMicrographs):
self._views.append(
views.MicrographsView(self._project, obj, **kwargs))
elif issubclass(cls, em.MicrographsTiltPair):
labels = 'id enabled _untilted._filename _tilted._filename'
renderLabels = '_untilted._filename _tilted._filename'
self._addObjView(
obj, obj.getFileName(), {
showj.ORDER: labels,
showj.VISIBLE: labels,
showj.MODE: showj.MODE_MD,
showj.RENDER: renderLabels
})
elif issubclass(cls, em.ParticlesTiltPair):
labels = 'id enabled _untilted._filename _tilted._filename'
renderLabels = '_untilted._filename _tilted._filename'
self._addObjView(
obj, obj.getFileName(), {
showj.ORDER: labels,
showj.VISIBLE: labels,
showj.RENDER: renderLabels,
showj.MODE: showj.MODE_MD
})
elif issubclass(cls, em.SetOfCoordinates):
# FIXME: Remove dependency on xmipp3 plugin to visualize coordinates
xmipp3 = pwutils.importFromPlugin(
'xmipp3',
errorMsg="xmipp3 plugin is required "
"now to visualize coordinates.")
micSet = obj.getMicrographs(
) # accessing mics to provide metadata file
if micSet is None:
raise Exception(
'visualize: SetOfCoordinates has no micrographs set.')
mdFn = getattr(micSet, '_xmippMd', None)
if mdFn:
fn = mdFn.get()
else: # happens if protocol is not an xmipp one
fn = self._getTmpPath(micSet.getName() + '_micrographs.xmd')
xmipp3.convert.writeSetOfMicrographs(micSet, fn)
tmpDir = self._getTmpPath(obj.getName())
pwutils.cleanPath(tmpDir)
pwutils.makePath(tmpDir)
# FIXME: (JMRT) We are always writing the SetOfCoordinates and removing
# the tmpDir, we need to take into account if the user have pick
# some particles in the tmpDir and have not save them, that now
# will loose all picked particles.
# A possible solution could be to alert that changes have not been
# written during modification of tmpDir or create a new Xmipp picking
# protocol to continue picking later without loosing the coordinates.
xmipp3.convert.writeSetOfCoordinates(tmpDir, obj)
self._views.append(
views.CoordinatesObjectView(self._project,
fn,
tmpDir,
self.protocol,
inTmpFolder=True))
elif issubclass(cls, em.SetOfParticles):
fn = obj.getFileName()
labels = (
'id enabled _index _filename _xmipp_zScore _xmipp_cumulativeSSNR '
'_sampling _xmipp_scoreByVariance _xmipp_scoreEmptiness '
'_ctfModel._defocusU _ctfModel._defocusV _ctfModel._defocusAngle '
'_transform._matrix')
self._addObjView(
obj, fn, {
showj.ORDER: labels,
showj.VISIBLE: labels,
showj.SORT_BY: '_xmipp_zScore asc',
showj.RENDER: '_filename'
})
elif issubclass(cls, em.SetOfVolumes):
fn = obj.getFileName()
labels = 'id enabled comment _filename '
self._addObjView(
obj, fn, {
showj.MODE: showj.MODE_MD,
showj.ORDER: labels,
showj.VISIBLE: labels,
showj.RENDER: '_filename'
})
elif issubclass(cls, em.SetOfClasses2D):
self._views.append(
views.ClassesView(self._project, obj.strId(),
obj.getFileName(), **kwargs))
elif issubclass(cls, em.SetOfClasses3D):
self._views.append(
views.Classes3DView(self._project, obj.strId(),
obj.getFileName()))
elif issubclass(cls, em.SetOfImages):
self._views.append(
views.ObjectView(self._project, obj.strId(), obj.getFileName(),
**kwargs))
elif issubclass(cls, em.SetOfCTF):
self._views.append(views.CtfView(self._project, obj))
elif issubclass(cls, em.CoordinatesTiltPair):
# FIXME: Remove dependency on xmipp3 plugin to visualize coordinates
xmipp3 = pwutils.importFromPlugin(
'xmipp3',
errorMsg="xmipp3 plugin is required "
"now to visualize coordinates.")
tmpDir = self._getTmpPath(obj.getName())
pwutils.makePath(tmpDir)
mdFn = os.path.join(tmpDir, 'input_micrographs.xmd')
xmipp3.convert.writeSetOfMicrographsPairs(
obj.getUntilted().getMicrographs(),
obj.getTilted().getMicrographs(), mdFn)
parentProtId = obj.getObjParentId()
parentProt = self.getProject().mapper.selectById(parentProtId)
extraDir = parentProt._getExtraPath()
# extraDir = parentProt._getExtraPath()
# TODO: Review this if ever a non Xmipp CoordinatesTiltPair is available
xmipp3.convert.writeSetOfCoordinates(tmpDir, obj.getUntilted())
xmipp3.convert.writeSetOfCoordinates(tmpDir, obj.getTilted())
showj.launchTiltPairPickerGUI(mdFn, tmpDir, self.protocol)
elif issubclass(cls, em.ProtParticlePicking):
if obj.getOutputsSize() >= 1:
self._visualize(obj.getCoords())
elif issubclass(cls, em.ProtImportMovies):
movs = obj.outputMovies
self._visualize(movs)
gainFn = movs.getGain()
if gainFn is not None:
if os.path.exists(gainFn):
self._views.append(views.DataView(gainFn))
return self._views