def _showProjMatchLibAndImages(self, paramName=None):
from numpy import array, dot
#map stack position with ref number
imgAndClasses = []
mdIn = xmipp.MetaData()
mdOut = xmipp.MetaData()
mdTmp = xmipp.MetaData()
for ref3d in self._refsList:
for it in self._iterations:
convert_refno_to_stack_position = {}
file_name = self.protocol._getFileName('projectLibrarySampling', iter=it, ref=ref3d)
file_nameReferences = 'projectionDirections@' + file_name
if exists(file_name):
#last reference name
mdReferences = xmipp.MetaData(file_nameReferences)
mdReferencesSize = mdReferences.size()
for id in mdReferences:
convert_refno_to_stack_position[mdReferences.getValue(xmipp.MDL_NEIGHBOR,id)]=id
file_nameImages = "ctfGroup[0-9][0-9][0-9][0-9][0-9][0-9]@" + self.protocol._getFileName('docfileInputAnglesIters', iter=it)
mdTmp.read(file_nameImages)#query with ref3D
mdIn.importObjects(mdTmp, xmipp.MDValueEQ(xmipp.MDL_REF3D, ref3d))
mdOut.clear()
for i in mdIn:
id1 = mdOut.addObject()
mdOut.setValue(xmipp.MDL_IMAGE, mdIn.getValue(xmipp.MDL_IMAGE,i), id1)
psi = -1. * mdIn.getValue(xmipp.MDL_ANGLE_PSI, i)
flip = mdIn.getValue(xmipp.MDL_FLIP, i)
if(flip):
psi = -psi
eulerMatrix = xmipp.Euler_angles2matrix(0., 0., psi)
x = mdIn.getValue(xmipp.MDL_SHIFT_X, i)
y = mdIn.getValue(xmipp.MDL_SHIFT_Y, i)
shift = array([x, y, 0])
shiftOut = dot(eulerMatrix, shift)
[x,y,z] = shiftOut
if flip:
x = -x
mdOut.setValue(xmipp.MDL_ANGLE_PSI, psi, id1)
mdOut.setValue(xmipp.MDL_SHIFT_X, x, id1)
mdOut.setValue(xmipp.MDL_SHIFT_Y, y, id1)
mdOut.setValue(xmipp.MDL_FLIP, flip, id1)
ref2D = mdIn.getValue(xmipp.MDL_REF,i)
file_references = self.protocol._getFileName('projectLibraryStk', iter=it, ref=ref3d)
file_reference = xmipp.FileName()
file_reference.compose(convert_refno_to_stack_position[ref2D], file_references)
id2 = mdOut.addObject()
mdOut.setValue(xmipp.MDL_IMAGE, file_reference, id2)
mdOut.setValue(xmipp.MDL_ANGLE_PSI, 0., id2)
if mdOut.size() == 0:
print "Empty metadata"
else:
file_nameReferences = self.protocol._getFileName('projectLibrarySampling', iter=it, ref=ref3d)
sfn = createUniqueFileName(file_nameReferences)
file_nameReferences = 'projectionDirections@' + sfn
mdOut.write(file_nameReferences)
imgAndClasses.append(self.createDataView(file_nameReferences))
else:
print "File %s does not exist" % file_name
return imgAndClasses
def _showProjMatchLibAndImages(self, paramName=None):
from numpy import (array, dot)
#map stack position with ref number
imgAndClasses = []
mdIn = xmippLib.MetaData()
mdOut = xmippLib.MetaData()
mdTmp = xmippLib.MetaData()
for ref3d in self._refsList:
for it in self._iterations:
convert_refno_to_stack_position = {}
file_name = self.protocol._getFileName('projectLibrarySampling', iter=it, ref=ref3d)
file_nameReferences = 'projectionDirections@' + file_name
if exists(file_name):
#last reference name
mdReferences = xmippLib.MetaData(file_nameReferences)
mdReferencesSize = mdReferences.size()
for id in mdReferences:
convert_refno_to_stack_position[mdReferences.getValue(xmippLib.MDL_NEIGHBOR,id)]=id
file_nameImages = "ctfGroup[0-9][0-9][0-9][0-9][0-9][0-9]@" + self.protocol._getFileName('docfileInputAnglesIters', iter=it)
mdTmp.read(file_nameImages)#query with ref3D
mdIn.importObjects(mdTmp, xmippLib.MDValueEQ(xmippLib.MDL_REF3D, ref3d))
mdOut.clear()
for i in mdIn:
id1 = mdOut.addObject()
mdOut.setValue(xmippLib.MDL_IMAGE, mdIn.getValue(xmippLib.MDL_IMAGE,i), id1)
psi = -1. * mdIn.getValue(xmippLib.MDL_ANGLE_PSI, i)
flip = mdIn.getValue(xmippLib.MDL_FLIP, i)
if(flip):
psi = -psi
eulerMatrix = xmippLib.Euler_angles2matrix(0., 0., psi)
x = mdIn.getValue(xmippLib.MDL_SHIFT_X, i)
y = mdIn.getValue(xmippLib.MDL_SHIFT_Y, i)
shift = array([x, y, 0])
shiftOut = dot(eulerMatrix, shift)
[x,y,z] = shiftOut
if flip:
x = -x
mdOut.setValue(xmippLib.MDL_ANGLE_PSI, psi, id1)
mdOut.setValue(xmippLib.MDL_SHIFT_X, x, id1)
mdOut.setValue(xmippLib.MDL_SHIFT_Y, y, id1)
mdOut.setValue(xmippLib.MDL_FLIP, flip, id1)
ref2D = mdIn.getValue(xmippLib.MDL_REF,i)
file_references = self.protocol._getFileName('projectLibraryStk', iter=it, ref=ref3d)
file_reference = xmippLib.FileName()
file_reference.compose(convert_refno_to_stack_position[ref2D], file_references)
id2 = mdOut.addObject()
mdOut.setValue(xmippLib.MDL_IMAGE, file_reference, id2)
mdOut.setValue(xmippLib.MDL_ANGLE_PSI, 0., id2)
if mdOut.size() == 0:
print "Empty metadata"
else:
file_nameReferences = self.protocol._getFileName('projectLibrarySampling', iter=it, ref=ref3d)
sfn = createUniqueFileName(file_nameReferences)
file_nameReferences = 'projectionDirections@' + sfn
mdOut.write(file_nameReferences)
imgAndClasses.append(self.createDataView(file_nameReferences))
else:
print "File %s does not exist" % file_name
return imgAndClasses
def _showProjMatchLibAndClasses(self, paramName=None):
#map stack position with ref number
list = []
mdIn = emlib.MetaData()
mdOut = emlib.MetaData()
for ref3d in self._refsList:
for it in self._iterations:
convert_refno_to_stack_position = {}
file_name = self.protocol._getFileName(
'projectLibrarySampling', iter=it, ref=ref3d)
file_nameReferences = 'projectionDirections@' + file_name
if exists(file_name):
mdReferences = emlib.MetaData(file_nameReferences)
mdReferencesSize = mdReferences.size()
for id in mdReferences:
convert_refno_to_stack_position[mdReferences.getValue(
emlib.MDL_NEIGHBOR, id)] = id
file_nameAverages = self.protocol._getFileName(
'outClassesXmd', iter=it, ref=ref3d)
file_references = self.protocol._getFileName(
'projectLibraryStk', iter=it, ref=ref3d)
if exists(file_nameAverages):
mdIn.read(file_nameAverages)
mdOut.clear()
for i in mdIn:
ref2D = mdIn.getValue(emlib.MDL_REF, i)
file_reference = emlib.FileName()
file_reference.compose(
convert_refno_to_stack_position[ref2D],
file_references)
id1 = mdOut.addObject()
mdOut.setValue(emlib.MDL_IMAGE,
mdIn.getValue(emlib.MDL_IMAGE, i),
id1)
mdOut.setValue(emlib.MDL_IMAGE2, file_reference,
id1)
if mdOut.size() == 0:
print("Empty metadata: ", file_nameReferences)
else:
file_nameReferences = self.protocol._getFileName(
'projectLibrarySampling', iter=it, ref=ref3d)
sfn = createUniqueFileName(file_nameReferences)
file_nameReferences = 'projectionDirections@' + sfn
mdOut.merge(mdIn)
mdOut.write(file_nameReferences)
# ToDo: show the metadata in "metadata" form.
list.append(
self.createDataView(file_nameReferences))
else:
print("File %s does not exist" % file_name)
return list
def _showProjMatchLibrary(self, paramName=None):
#map stack position with ref number
list = []
mdIn = xmipp.MetaData()
mdOut = xmipp.MetaData()
cleanPattern(self.protocol._getTmpPath('references_library*'))
for ref3d in self._refsList:
for it in self._iterations:
convert_refno_to_stack_position = {}
file_name = self.protocol._getFileName(
'projectLibrarySampling', iter=it, ref=ref3d)
file_nameReferences = 'projectionDirections@' + file_name
#last reference name
if exists(file_name):
mdReferences = xmipp.MetaData(file_nameReferences)
mdReferencesSize = mdReferences.size()
for id in mdReferences:
convert_refno_to_stack_position[mdReferences.getValue(
xmipp.MDL_NEIGHBOR, id)] = id
file_nameAverages = self.protocol._getFileName(
'outClassesXmd', iter=it, ref=ref3d)
if exists(file_nameAverages):
#print "OutClassesXmd", OutClassesXmd
mdIn.read(file_nameAverages)
mdOut.clear()
for i in mdIn:
#id1=mdOut.addObject()
#mdOut.setValue(MDL_IMAGE,mdIn.getValue(MDL_IMAGE,i),id1)
ref2D = mdIn.getValue(xmipp.MDL_REF, i)
file_references = self.protocol._getFileName(
'projectLibraryStk', iter=it, ref=ref3d)
file_reference = xmipp.FileName()
file_reference.compose(
convert_refno_to_stack_position[ref2D],
file_references)
id2 = mdOut.addObject()
mdOut.setValue(xmipp.MDL_IMAGE, file_reference,
id2)
if mdOut.size() == 0:
print "Empty metadata: ", file_nameReferences
else:
file_nameReferences = self.protocol._getTmpPath(
'references_library.xmd')
sfn = createUniqueFileName(file_nameReferences)
file_nameReferences = 'projectionDirections@' + sfn
mdOut.write(file_nameReferences)
list.append(
self.createDataView(file_nameReferences))
else:
print "File %s does not exist" % file_name
return list
def _showProjMatchLibrary(self, paramName=None):
#map stack position with ref number
list = []
mdIn = xmipp.MetaData()
mdOut = xmipp.MetaData()
cleanPattern(self.protocol._getTmpPath('references_library*'))
for ref3d in self._refsList:
for it in self._iterations:
convert_refno_to_stack_position = {}
file_name = self.protocol._getFileName('projectLibrarySampling', iter=it, ref=ref3d)
file_nameReferences = 'projectionDirections@' + file_name
#last reference name
if exists(file_name):
mdReferences = xmipp.MetaData(file_nameReferences)
mdReferencesSize = mdReferences.size()
for id in mdReferences:
convert_refno_to_stack_position[mdReferences.getValue(xmipp.MDL_NEIGHBOR,id)]=id
file_nameAverages = self.protocol._getFileName('outClassesXmd', iter=it, ref=ref3d)
if exists(file_nameAverages):
#print "OutClassesXmd", OutClassesXmd
mdIn.read(file_nameAverages)
mdOut.clear()
for i in mdIn:
#id1=mdOut.addObject()
#mdOut.setValue(MDL_IMAGE,mdIn.getValue(MDL_IMAGE,i),id1)
ref2D = mdIn.getValue(xmipp.MDL_REF,i)
file_references = self.protocol._getFileName('projectLibraryStk', iter=it, ref=ref3d)
file_reference = xmipp.FileName()
file_reference.compose(convert_refno_to_stack_position[ref2D],file_references)
id2=mdOut.addObject()
mdOut.setValue(xmipp.MDL_IMAGE, file_reference, id2)
if mdOut.size() == 0:
print "Empty metadata: ", file_nameReferences
else:
file_nameReferences = self.protocol._getTmpPath('references_library.xmd')
sfn = createUniqueFileName(file_nameReferences)
file_nameReferences = 'projectionDirections@' + sfn
mdOut.write(file_nameReferences)
list.append(self.createDataView(file_nameReferences))
else:
print "File %s does not exist" % file_name
return list
