def createOutput(self):
# Check vol and pdb files
directory = self._getExtraPath()
for filename in sorted(os.listdir(directory)):
if filename.endswith(".mrc"):
volFileName = os.path.join(directory, filename)
vol = Volume()
vol.setFileName(volFileName)
# fix mrc header
ccp4header = Ccp4Header(volFileName, readHeader=True)
sampling = ccp4header.computeSampling()
origin = Transform()
shifts = ccp4header.getOrigin()
origin.setShiftsTuple(shifts)
vol.setOrigin(origin)
vol.setSamplingRate(sampling)
keyword = filename.split(".mrc")[0]
kwargs = {keyword: vol}
self._defineOutputs(**kwargs)
elif filename.endswith(".pdb") or filename.endswith(".cif"):
path = os.path.join(directory, filename)
pdb = AtomStruct()
pdb.setFileName(path)
keyword = filename.split(".pdb")[0].replace(".","_")
kwargs = {keyword: pdb}
self._defineOutputs(**kwargs)
def createOutputStep(self):
outVolFn = self._getExtraPath("inputVolumeAligned.mrc")
Ts = self.inputVolume.get().getSamplingRate()
self.runJob("xmipp_image_header",
"-i %s --sampling_rate %f" % (outVolFn, Ts))
outVol = Volume()
outVol.setLocation(outVolFn)
#set transformation matrix
fhInputTranMat = self._getExtraPath('transformation-matrix.txt')
transMatFromFile = np.loadtxt(fhInputTranMat)
transformationMat = np.reshape(transMatFromFile, (4, 4))
transform = Transform()
transform.setMatrix(transformationMat)
outVol.setTransform(transform)
outVol.setSamplingRate(Ts)
outputArgs = {'outputVolume': outVol}
self._defineOutputs(**outputArgs)
self._defineSourceRelation(self.inputVolume, outVol)
#particles....
outParticlesFn = self._getExtraPath('outputParticles.xmd')
outputParticles = self._createSetOfParticles()
outputParticles.copyInfo(self.inputParticles.get())
outputParticles.setAlignmentProj()
readSetOfParticles(outParticlesFn, outputParticles)
outputArgs = {'outputParticles': outputParticles}
self._defineOutputs(**outputArgs)
self._defineSourceRelation(self.inputParticles, outputParticles)
def createOutput(self):
""" Copy the PDB structure and register the output object.
"""
# Check vol and pdb files
directory = self._getExtraPath()
for filename in sorted(os.listdir(directory)):
if not filename.startswith("tmp"):
# files starting with "tmp" will not be converted in scipion objects
if filename.endswith(".mrc"):
volFileName = os.path.join(directory, filename)
vol = Volume()
vol.setFileName(volFileName)
# fix mrc header
ccp4header = Ccp4Header(volFileName, readHeader=True)
sampling = ccp4header.computeSampling()
origin = Transform()
shifts = ccp4header.getOrigin()
origin.setShiftsTuple(shifts)
vol.setOrigin(origin)
vol.setSamplingRate(sampling)
keyword = filename.split(".mrc")[0]
kwargs = {keyword: vol}
self._defineOutputs(**kwargs)
if filename.endswith(".pdb") or filename.endswith(".cif"):
path = os.path.join(directory, filename)
pdb = AtomStruct()
pdb.setFileName(path)
if filename.endswith(".cif"):
keyword = filename.split(".cif")[0].replace(".", "_")
else:
keyword = filename.split(".pdb")[0].replace(".", "_")
kwargs = {keyword: pdb}
self._defineOutputs(**kwargs)
def createOutputStep(self, tsObjId):
ts = self.inputSetOfTiltSeries.get()[tsObjId]
tsId = ts.getTsId()
extraPrefix = self._getExtraPath(tsId)
outputSetOfTomograms = self.getOutputSetOfTomograms()
newTomogram = Tomogram()
newTomogram.setLocation(os.path.join(extraPrefix, ts.getFirstItem().parseFileName(extension=".mrc")))
# Set tomogram origin
ih = ImageHandler()
xDim, yDim, zDim, _ = \
ih.getDimensions(os.path.join(extraPrefix, ts.getFirstItem().parseFileName(extension=".mrc")))
origin = Transform()
sr = self.inputSetOfTiltSeries.get().getSamplingRate()
origin.setShifts(xDim / -2. * sr,
yDim / -2. * sr,
zDim / -2 * sr)
newTomogram.setOrigin(origin)
# Set tomogram acquisition
acquisition = TomoAcquisition()
acquisition.setAngleMin(ts.getFirstItem().getTiltAngle())
acquisition.setAngleMax(ts[ts.getSize()].getTiltAngle())
acquisition.setStep(self.getAngleStepFromSeries(ts))
newTomogram.setAcquisition(acquisition)
outputSetOfTomograms.append(newTomogram)
outputSetOfTomograms.update(newTomogram)
outputSetOfTomograms.write()
self._store()
def _visualize(self, obj, **args):
""" Visualize any saved pdb and map if none were saved
show the input files.
"""
_inputVolFlag = False
_inputPDBFlag = False
directory = self.protocol._getExtraPath()
fnCmd = os.path.abspath(self.protocol._getTmpPath("chimera_output.cxc"))
f = open(fnCmd, 'w')
f.write('cd %s\n' % os.getcwd())
counter = 0
# Find all saved maps and pdbs from protocl. If none
# are found show the input files to the protocol
for filename in sorted(os.listdir(directory)):
if filename.endswith(".mrc"):
_inputVolFlag = True
counter += 1
volFileName = os.path.join(directory, filename)
vol = Volume()
vol.setFileName(volFileName)
# fix mrc header
ccp4header = Ccp4Header(volFileName, readHeader=True)
sampling = ccp4header.computeSampling()
origin = Transform()
shifts = ccp4header.getOrigin()
origin.setShiftsTuple(shifts)
f.write("open %s\n" % volFileName)
f.write("volume #%d style surface voxelSize %f\n"
"volume #%d origin %0.2f,%0.2f,%0.2f\n"
% (counter, sampling, counter, shifts[0], shifts[1], shifts[2]))
# Set volume to translucent
f.write("volume #%d transparency 0.5\n" % counter)
for filename in os.listdir(directory):
if filename.endswith(".pdb") or filename.endswith(".cif"):
_inputPDBFlag = True
path = os.path.join(directory, filename)
f.write("open %s\n" % path)
# If no pdbs or maps found use inputs to protocol
if not _inputVolFlag:
counter += 1
f.write("open %s \n" % os.path.abspath(self.protocol.inputVolume.get().getFileName()))
# Set volume to translucent
f.write("volume #%d transparency 0.5\n" % counter)
if not _inputPDBFlag:
f.write("open %s \n" % os.path.abspath(self.protocol.pdbFileToBeRefined.get().getFileName()))
f.close()
# run in the background
Chimera.runProgram(chimera.getProgram(), fnCmd + "&")
return []
def importSubTomogramsStep(self, pattern, samplingRate):
""" Copy images matching the filename pattern
Register other parameters.
"""
self.info("Using pattern: '%s'" % pattern)
# Create a Volume template object
subtomo = SubTomogram()
subtomo.setSamplingRate(samplingRate)
imgh = ImageHandler()
self.subtomoSet = self._createSetOfSubTomograms()
self.subtomoSet.setSamplingRate(samplingRate)
# if self.importCoordinates.get():
# self.coords = []
# for coord3D in self.importCoordinates.get().iterCoordinates():
# self.coords.append(coord3D.clone())
# self.subtomoSet.setCoordinates3D(self.importCoordinates)
self._parseAcquisitionData()
for fileName, fileId in self.iterFiles():
x, y, z, n = imgh.getDimensions(fileName)
if fileName.endswith('.map'):
fileName += ':mrc'
if fileName.endswith('.mrc') or fileName.endswith(':mrc'):
if z == 1 and n != 1:
zDim = n
n = 1
else:
zDim = z
else:
zDim = z
origin = Transform()
origin.setShifts(x / -2. * samplingRate, y / -2. * samplingRate,
zDim / -2. * samplingRate)
subtomo.setOrigin(origin) # read origin from form
newFileName = _getUniqueFileName(self.getPattern(), fileName)
# newFileName = abspath(self._getVolumeFileName(fileName))
if fileName.endswith(':mrc'):
fileName = fileName[:-4]
createAbsLink(fileName, self._getExtraPath(newFileName))
if n == 1:
self._addSubtomogram(subtomo, self._getExtraPath(fileName),
self._getExtraPath(newFileName))
else:
for index in range(1, n + 1):
self._addSubtomogram(subtomo,
self._getExtraPath(fileName),
self._getExtraPath(newFileName),
index=index)
def createOutput(self):
volume = Volume()
volume.setSamplingRate(self.sampling.get())
volume.setFileName(self._getVolName())
if self.vol:
origin = Transform()
origin.setShiftsTuple(self.shifts)
volume.setOrigin(origin)
self._defineOutputs(outputVolume=volume)
if self.inputPdbData == self.IMPORT_OBJ:
self._defineSourceRelation(self.pdbObj, volume)
def alignParticlesStep(self):
fhInputTranMat = self._getExtraPath('transformation-matrix.txt')
outParticlesFn = self._getExtraPath('outputParticles.xmd')
transMatFromFile = np.loadtxt(fhInputTranMat)
transformationMat = np.reshape(transMatFromFile, (4, 4))
transform = Transform()
transform.setMatrix(transformationMat)
resultMat = Transform()
outputParts = md.MetaData()
mdToAlign = md.MetaData(self.imgsInputFn)
for row in md.iterRows(mdToAlign):
inMat = rowToAlignment(row, ALIGN_PROJ)
partTransformMat = inMat.getMatrix()
partTransformMatrix = np.matrix(partTransformMat)
newTransformMatrix = np.matmul(transformationMat,
partTransformMatrix)
resultMat.setMatrix(newTransformMatrix)
rowOut = md.Row()
rowOut.copyFromRow(row)
alignmentToRow(resultMat, rowOut, ALIGN_PROJ)
rowOut.addToMd(outputParts)
outputParts.write(outParticlesFn)
cleanPath(self.imgsInputFn)
def generateOutputStackStep(self, tomoObjId):
tomo = self.inputSetOfTomograms.get()[tomoObjId]
tomoId = os.path.splitext(os.path.basename(tomo.getFileName()))[0]
extraPrefix = self._getExtraPath(tomoId)
outputProjectedSetOfTiltSeries = self.getOutputProjectedSetOfTiltSeries(
)
newTs = tomoObj.TiltSeries(tsId=tomoId)
newTs.copyInfo(tomo)
newTs.setTsId(tomoId)
# Add origin to output tilt-series
origin = Transform()
outputProjectedSetOfTiltSeries.append(newTs)
tiltAngleList = self.getTiltAngleList()
for index in range(self.getProjectionRange()):
newTi = tomoObj.TiltImage()
newTi.setTiltAngle(tiltAngleList[index])
newTi.setTsId(tomoId)
newTi.setLocation(
index + 1,
os.path.join(extraPrefix,
os.path.basename(tomo.getFileName())))
newTi.setSamplingRate(
self.inputSetOfTomograms.get().getSamplingRate())
newTs.append(newTi)
ih = ImageHandler()
x, y, z, _ = ih.getDimensions(newTs.getFirstItem().getFileName())
newTs.setDim((x, y, z))
# Set origin to output tilt-series
origin.setShifts(
x / -2. * self.inputSetOfTomograms.get().getSamplingRate(),
y / -2. * self.inputSetOfTomograms.get().getSamplingRate(), 0)
newTs.setOrigin(origin)
newTs.write(properties=False)
outputProjectedSetOfTiltSeries.update(newTs)
outputProjectedSetOfTiltSeries.updateDim()
outputProjectedSetOfTiltSeries.write()
self._store()
def createOutputStep(self):
vol1 = self.vol1.get()
volume = Volume()
volume.setSamplingRate(vol1.getSamplingRate())
if vol1.getFileName().endswith('mrc'):
origin = Transform()
ccp4header = headers.Ccp4Header(vol1.getFileName(), readHeader=True)
shifts = ccp4header.getOrigin()
origin.setShiftsTuple(shifts)
volume.setOrigin(origin)
volume.setFileName(self._getExtraPath("output_volume.mrc"))
filename = volume.getFileName()
if filename.endswith('.mrc') or filename.endswith('.map'):
volume.setFileName(filename + ':mrc')
self._defineOutputs(outputVolume=volume)
def _createCoordinate3D(self):
# Tomogram associated to Coordinate3D
self.Tomo = Tomogram()
self.Tomo.setSamplingRate(1)
self.Tomo.setLocation(self.TomogramPath)
x, y, z = self.Tomo.getDim()
origin = Transform()
origin.setShifts(x / -2., y / -2., z / -2.)
self.Tomo.setOrigin(origin)
# Coordinate3D
self.coord = Coordinate3D()
self.coord.setBoxSize(32)
self.coord.setVolume(self.Tomo)
self.coord.setPosition(0, 0, 0, const.BOTTOM_LEFT_CORNER)
self.coord.setMatrix(np.eye(4))
def createSetOfParticles(self, setPartSqliteName, partFn, doCtf=False):
# create a set of particles
self.partSet = SetOfParticles(filename=setPartSqliteName)
self.partSet.setAlignment(ALIGN_PROJ)
self.partSet.setAcquisition(
Acquisition(voltage=300,
sphericalAberration=2,
amplitudeContrast=0.1,
magnification=60000))
self.partSet.setSamplingRate(samplingRate)
self.partSet.setHasCTF(True)
aList = [np.array(m) for m in mList]
#defocus=15000 + 5000* random.random()
for i, a in enumerate(aList):
p = Particle()
if doCtf:
defocusU = defocusList[i] #+500.
defocusV = defocusList[i]
ctf = CTFModel(defocusU=defocusU,
defocusV=defocusV,
defocusAngle=defocusAngle[i])
ctf.standardize()
p.setCTF(ctf)
p.setLocation(i + 1, partFn)
p.setTransform(Transform(a))
self.partSet.append(p)
self.partSet.write()
def createOutputStep(self):
vol = Volume()
vol.setLocation(self._getOutputVol())
sampling = self.inputVolumes.get().getSamplingRate()
vol.setSamplingRate(sampling)
#
ccp4header = Ccp4Header(self._getOutputVol(), readHeader=True)
t = Transform()
x, y, z = ccp4header.getOrigin() # origin output vol
# coordinates
t.setShifts(x, y, z)
vol.setOrigin(t)
#
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self.inputVolumes, self.outputVolume)
def createOutputStep(self):
Ts = self.inputReference.get().getSamplingRate()
vols = []
idx = 1
for vol in self._iterInputVolumes():
outVol = Volume()
fnOutVol = self._getExtraPath("vol%02d.mrc" % idx)
outVol.setLocation(fnOutVol)
outVol.setObjComment(vol.getObjComment())
#set transformation matrix
fhInputTranMat = self._getExtraPath(
'transformation-matrix_vol%06d.txt' % idx)
transMatFromFile = np.loadtxt(fhInputTranMat)
transformationMat = np.reshape(transMatFromFile, (4, 4))
transform = Transform()
transform.setMatrix(transformationMat)
outVol.setTransform(transform)
vols.append(outVol)
# Set the sampling rate in the mrc header
self.runJob("xmipp_image_header",
"-i %s --sampling_rate %f" % (fnOutVol, Ts))
idx += 1
if len(vols) > 1:
volSet = self._createSetOfVolumes()
volSet.setSamplingRate(Ts)
for vol in vols:
volSet.append(vol)
outputArgs = {'outputVolumes': volSet}
else:
vols[0].setSamplingRate(Ts)
outputArgs = {'outputVolume': vols[0]}
self._defineOutputs(**outputArgs)
if len(vols) > 1:
for pointer in self.inputVolumes:
self._defineSourceRelation(pointer,
outputArgs['outputVolumes'])
else:
for pointer in self.inputVolumes:
self._defineSourceRelation(pointer, outputArgs['outputVolume'])
def createOutputStep(self):
""" Copy the PDB structure and register the output object.
"""
# Check vol and pdb files
directory = self._getExtraPath()
for filename in sorted(os.listdir(directory)):
if filename.endswith(".mrc"):
volFileName = os.path.join(directory, filename)
vol = Volume()
vol.setFileName(volFileName)
# fix mrc header
ccp4header = Ccp4Header(volFileName, readHeader=True)
sampling = ccp4header.computeSampling()
origin = Transform()
shifts = ccp4header.getOrigin()
origin.setShiftsTuple(shifts)
vol.setOrigin(origin)
vol.setSamplingRate(sampling)
keyword = filename.split(".mrc")[0]
kwargs = {keyword: vol}
self._defineOutputs(**kwargs)
if filename.endswith(".pdb") or filename.endswith(".cif"):
path = os.path.join(directory, filename)
pdb = AtomStruct()
pdb.setFileName(path)
if filename.endswith(".cif"):
keyword = filename.split(".cif")[0].replace(".", "_")
else:
keyword = filename.split(".pdb")[0].replace(".", "_")
kwargs = {keyword: pdb}
self._defineOutputs(**kwargs)
# upodate config file flag enablebundle
# so scipionwrite is disabled
config = configparser.ConfigParser()
config.read(self._getExtraPath(CHIMERA_CONFIG_FILE))
config.set('chimerax', 'enablebundle', 'False')
with open(self._getExtraPath(CHIMERA_CONFIG_FILE), 'w') as configfile:
config.write(configfile)
def importTomogramsStep(self, pattern, samplingRate):
""" Copy images matching the filename pattern
Register other parameters.
"""
self.info("Using pattern: '%s'" % pattern)
# Create a Volume template object
tomo = Tomogram()
tomo.setSamplingRate(samplingRate)
imgh = ImageHandler()
tomoSet = self._createSetOfTomograms()
tomoSet.setSamplingRate(samplingRate)
self._parseAcquisitionData()
for fileName, fileId in self.iterFiles():
x, y, z, n = imgh.getDimensions(fileName)
if fileName.endswith('.mrc') or fileName.endswith('.map'):
fileName += ':mrc'
if z == 1 and n != 1:
zDim = n
n = 1
else:
zDim = z
else:
zDim = z
origin = Transform()
if self.setOrigCoord.get():
origin.setShiftsTuple(self._getOrigCoord())
else:
origin.setShifts(x / -2. * samplingRate,
y / -2. * samplingRate,
zDim / -2. * samplingRate)
tomo.setOrigin(origin) # read origin from form
newFileName = _getUniqueFileName(self.getPattern(),
fileName.split(':')[0])
tsId = removeExt(newFileName)
tomo.setTsId(tsId)
if fileName.endswith(':mrc'):
fileName = fileName[:-4]
createAbsLink(fileName, abspath(self._getExtraPath(newFileName)))
tomo.setAcquisition(self._extractAcquisitionParameters(fileName))
if n == 1: # One volume per file
tomo.cleanObjId()
tomo.setFileName(self._getExtraPath(newFileName))
tomoSet.append(tomo)
else: # A stack of volumes per file (not common)
for index in range(1, n + 1):
tomo.cleanObjId()
tomo.setLocation(index, self._getExtraPath(newFileName))
tomoSet.append(tomo)
self._defineOutputs(outputTomograms=tomoSet)
def rowToAlignment(alignmentRow, samplingRate):
""" Return an Transform object representing the Alignment
from a given parFile row.
:param alignmentRow: input row object
:param samplingRate: input pixel size
:return Transform object
"""
angles = np.zeros(3)
shifts = np.zeros(3)
alignment = Transform()
# PSI THETA PHI SHX SHY
angles[0] = float(alignmentRow.get('PSI'))
angles[1] = float(alignmentRow.get('THETA'))
angles[2] = float(alignmentRow.get('PHI'))
# shifts are converted from Angstroms to px
shifts[0] = float(alignmentRow.get('SHX')) / samplingRate
shifts[1] = float(alignmentRow.get('SHY')) / samplingRate
M = matrixFromGeometry(shifts, angles)
alignment.setMatrix(M)
return alignment
def createOutputStep(self):
inputVol = self.inputStructure.get()
samplingRate = inputVol.getSamplingRate()
volume = Volume()
volume.setFileName(self._getExtraPath("pseudoatoms_approximation.vol"))
volume.setSamplingRate(samplingRate)
x, y, z = volume.getDim()
xv, yv, zv = inputVol.getOrigin(force=True).getShifts()
t = Transform()
t.setShifts((x / 2. * samplingRate) - xv, (y / 2. * samplingRate) - yv,
(z / 2. * samplingRate) - zv)
volume.setOrigin(inputVol.getOrigin())
self._defineOutputs(outputVolume=volume)
self._defineSourceRelation(self.inputStructure.get(), volume)
pdb = AtomStruct(self._getPath('pseudoatoms.pdb'), pseudoatoms=True)
pdb.setVolume(volume)
pdb.setOrigin(t)
self.createChimeraScript(inputVol, pdb)
self._defineOutputs(outputPdb=pdb)
self._defineSourceRelation(self.inputStructure, pdb)
def _testInv(matrix):
matrix = np.array(matrix)
a = Transform(matrix)
row1 = md.Row()
convert.alignmentToRow(a, row1, alignType=ALIGN_2D)
row2 = None
row3 = md.Row()
convert.alignmentToRow(a, row3, alignType=ALIGN_PROJ)
return row1, row2, row3
def rowToAlignment(alignmentRow, alignType):
"""
is2D == True-> matrix is 2D (2D images alignment)
otherwise matrix is 3D (3D volume alignment or projection)
invTransform == True -> for xmipp implies projection
"""
is2D = alignType == ALIGN_2D
inverseTransform = True # alignType == em.ALIGN_PROJ
alignment = Transform()
angles = numpy.zeros(3)
shifts = numpy.zeros(3)
angles[2] = alignmentRow.get('ANGLE_PSI')
shifts[0] = alignmentRow.get('SHIFTX')
shifts[1] = alignmentRow.get('SHIFTY')
if not is2D:
angles[0] = alignmentRow.get('ANGLE_PHI')
angles[1] = alignmentRow.get('ANGLE_THE')
M = matrixFromGeometry(shifts, angles, inverseTransform)
alignment.setMatrix(M)
return alignment
def createOutputStep(self):
input = self.input.get()
imgSetOut = self._createSetOfParticles()
imgSetOut.setSamplingRate(input.getSamplingRate())
imgSetOut.setAlignmentProj()
for i, subtomo in enumerate(input.iterItems()):
idx = subtomo.getObjId()
p = Particle()
p.setLocation(ih._convertToLocation((i+1, self._getExtraPath("projections.mrcs"))))
p._subtomogramID = String(idx)
if type(subtomo) == SubTomogram:
if subtomo.hasCoordinate3D():
coord = Coordinate()
coord.setX(subtomo.getCoordinate3D().getX(const.BOTTOM_LEFT_CORNER))
coord.setY(subtomo.getCoordinate3D().getY(const.BOTTOM_LEFT_CORNER))
p.setCoordinate(coord)
p.setClassId(subtomo.getClassId())
if subtomo.hasTransform():
transform = Transform()
transform.setMatrix(subtomo.getTransform().getMatrix())
p.setTransform(transform)
imgSetOut.append(p)
imgSetOut.setObjComment(self.getSummary(imgSetOut))
self._defineOutputs(outputParticles=imgSetOut)
self._defineSourceRelation(self.input, imgSetOut)
if self.radAvg.get():
avgFile = self._getExtraPath("average.xmp")
imgh = ih()
avgImage = imgh.computeAverage(imgSetOut)
avgImage.write(avgFile)
avg = Particle()
avg.setLocation(1, avgFile)
avg.copyInfo(imgSetOut)
self._defineOutputs(outputAverage=avg)
self._defineSourceRelation(self.input, avg)
def createOutputStep(self):
outSubtomos = self._createSetOfSubTomograms()
outSubtomos.setSamplingRate(self.second_subtomos.getSamplingRate())
outSubtomos.setCoordinates3D(self.second_subtomos.getCoordinates3D())
# if self.second_subtomos.getAcquisition() is not None:
# acquisition = TomoAcquisition()
# acquisition.setAngleMin(self.second_subtomos.getFirstItem().getAcquisition().getAngleMin())
# acquisition.setAngleMax(self.second_subtomos.getFirstItem().getAcquisition().getAngleMax())
# acquisition.setStep(self.second_subtomos.getFirstItem().getAcquisition().getStep())
# outSubtomos.setAcquisition(acquisition)
for ids, inSubtomo in enumerate(self.second_subtomos.iterItems()):
subtomogram = SubTomogram()
subtomogram.setObjId(self.second_matrices[ids][0])
subtomogram.setLocation(inSubtomo.getLocation())
subtomogram.setCoordinate3D(inSubtomo.getCoordinate3D())
subtomogram.setTransform(Transform(self.second_matrices[ids][1]))
subtomogram.setVolName(inSubtomo.getVolName())
outSubtomos.append(subtomogram)
self._defineOutputs(outputSetOfSubtomogram=outSubtomos)
self._defineSourceRelation(self.firstAverage, outSubtomos)
self._defineSourceRelation(self.secondAverage, outSubtomos)
def setParticleTransform(self, particle, row):
""" Set the transform values from the row. """
if ((self._alignType == ALIGN_NONE)
or not row.hasAnyColumn(self.ALIGNMENT_LABELS)):
self.setParticleTransform = self.__setParticleTransformNone
else:
# Ensure the Transform object exists
self._angles = np.zeros(3)
self._shifts = np.zeros(3)
particle.setTransform(Transform())
if self._alignType == ALIGN_2D:
self.setParticleTransform = self.__setParticleTransform2D
elif self._alignType == ALIGN_PROJ:
self.setParticleTransform = self.__setParticleTransformProj
else:
raise TypeError("Unexpected alignment type: %s" %
self._alignType)
# Call again the modified function
self.setParticleTransform(particle, row)
def launchTest(self, fileKey, mList, alignType=None, **kwargs):
""" Helper function to launch similar alignment tests
given the EMX transformation matrix.
Params:
fileKey: the file where to grab the input stack images.
mList: the matrix list of transformations
(should be the same length of the stack of images)
"""
print("\n")
print("*" * 80)
print("* Launching test: ", fileKey)
print("*" * 80)
is2D = alignType == ALIGN_2D
if fileKey == 'alignShiftRotExp':
# relion requires mrcs stacks
origFn = self.dataset.getFile(fileKey)
stackFn = replaceExt(origFn, ".mrcs")
createLink(origFn, stackFn)
else:
stackFn = self.dataset.getFile(fileKey)
partFn1 = self.getOutputPath(fileKey + "_particles1.sqlite")
mdFn = self.getOutputPath(fileKey + "_particles.star")
partFn2 = self.getOutputPath(fileKey + "_particles2.sqlite")
if self.IS_ALIGNMENT:
outputFn = self.getOutputPath(fileKey + "_output.mrcs")
outputFnRelion = self.getOutputPath(fileKey + "_output")
goldFn = self.dataset.getFile(fileKey + '_Gold_output_relion.mrcs')
else:
outputFn = self.getOutputPath(fileKey + "_output.vol")
goldFn = self.dataset.getFile("reconstruction/gold/" + fileKey +
'_Gold_rln_output.vol')
if PRINT_FILES:
print("BINARY DATA: ", stackFn)
print("SET1: ", partFn1)
print(" MD: ", mdFn)
print("SET2: ", partFn2)
print("OUTPUT: ", outputFn)
print("GOLD: ", goldFn)
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
partSet = SetOfParticles(filename=partFn1)
else:
partSet = SetOfVolumes(filename=partFn1)
partSet.setAlignment(alignType)
acq = Acquisition(voltage=300,
sphericalAberration=2,
amplitudeContrast=0.1,
magnification=60000)
og = OpticsGroups.create(rlnMtfFileName="mtfFile1.star",
rlnImageSize=128)
partSet.setSamplingRate(1.0)
partSet.setAcquisition(acq)
og.toImages(partSet)
# Populate the SetOfParticles with images
# taken from images.mrc file
# and setting the previous alignment parameters
aList = [np.array(m) for m in mList]
for i, a in enumerate(aList):
p = Particle()
p.setLocation(i + 1, stackFn)
p.setTransform(Transform(a))
partSet.append(p)
# Write out the .sqlite file and check that are correctly aligned
print("Partset", partFn1)
partSet.printAll()
partSet.write()
# Convert to a Xmipp metadata and also check that the images are
# aligned correctly
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
starWriter = convert.createWriter()
starWriter.writeSetOfParticles(partSet, mdFn, alignType=alignType)
partSet2 = SetOfParticles(filename=partFn2)
else:
convert.writeSetOfVolumes(partSet, mdFn, alignType=alignType)
partSet2 = SetOfVolumes(filename=partFn2)
# Let's create now another SetOfImages reading back the written
# Xmipp metadata and check one more time.
partSet2.copyInfo(partSet)
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
convert.readSetOfParticles(mdFn, partSet2, alignType=alignType)
else:
convert.readSetOfParticles(mdFn,
partSet2,
rowToFunc=convert.rowToVolume,
alignType=alignType)
partSet2.write()
if PRINT_MATRIX:
for i, img in enumerate(partSet2):
m1 = aList[i]
m2 = img.getTransform().getMatrix()
print("-" * 5)
print(img.getFileName(), img.getIndex())
print('m1:\n', m1, convert.geometryFromMatrix(m1, False))
print('m2:\n', m2, convert.geometryFromMatrix(m2, False))
self.assertTrue(np.allclose(m1, m2, rtol=1e-2))
# Launch apply transformation and check result images
runRelionProgram(self.CMD % locals())
if SHOW_IMAGES:
runRelionProgram('scipion show %(outputFn)s' % locals())
if os.path.exists(goldFn):
self.assertTrue(
ImageHandler().compareData(goldFn, outputFn, tolerance=0.001),
"Different data files:\n>%s\n<%s" % (goldFn, outputFn))
if CLEAN_IMAGES:
cleanPath(outputFn)
def _visualize(self, obj, **args):
# THe input map or pdb may be a parameter from the protocol
# or from the parent protocol.
dim = 150.
sampling = 1.
_inputVol = None
directory = self.protocol._getExtraPath()
try:
try:
if self.protocol.inputVolume.get() is not None:
_inputVol = self.protocol.inputVolume.get()
elif self.protocol.pdbFileToBeRefined.get().getVolume(
) is not None:
_inputVol = self.protocol.pdbFileToBeRefined.get(
).getVolume()
elif self.protocol.inputVolumes[0] is not None:
_inputVol = self.protocol.inputVolumes[0].get()
except:
output3DMapList = []
for filename in sorted(os.listdir(directory)):
if filename.endswith(".mrc"):
output3DMapList.append(filename.split('.')[0])
output3DMap = str(output3DMapList[0])
if len(output3DMap) > 0:
_inputVol = self.protocol.output3DMap
except:
# TODO: I do not know if we still need this part
# Remark that inputProtocol does not longer exist, it has been replaced by inputProtocolDict
# Compare with the previous code, specially the alternative directory
for item in list(self.protocol.inputProtocolDict().values()):
if item.hasAttribute(
'inputVolume') and item.inputVolume.get() is not None:
_inputVol = item.inputVolume.get()
break
elif item.hasAttribute('pdbFileToBeRefined') and \
item.pdbFileToBeRefined.get().getVolume() is not None:
_inputVol = item.pdbFileToBeRefined.get().getVolume()
break
# directory = item._getExtraPath()
if _inputVol is not None:
dim = _inputVol.getDim()[0]
sampling = _inputVol.getSamplingRate()
bildFileName = self.protocol._getTmpPath("axis_output.bild")
Chimera.createCoordinateAxisFile(dim,
bildFileName=bildFileName,
sampling=sampling)
fnCmd = self.protocol._getTmpPath("chimera_output.cxc")
f = open(fnCmd, 'w')
# change to workingDir
# If we do not use cd and the project name has an space
# the protocol fails even if we pass absolute paths
f.write('cd %s\n' % os.getcwd())
f.write("open %s\n" % bildFileName)
f.write("cofr 0,0,0\n") # set center of coordinates
inputVolFileName = ''
counter = 2
if _inputVol is not None:
# In case we have PDBs only, _inputVol is None:
self.visInputVolume(f, _inputVol, counter)
else:
counter = 1
if (self.protocol.hasAttribute("inputVolume2") and\
self.protocol.inputVolume2.get() is not None):
counter += 1
_inputVol2 = self.protocol.inputVolume2.get()
self.visInputVolume(f, _inputVol2, counter)
for filename in sorted(os.listdir(directory)):
if filename.endswith(".mrc") and filename != inputVolFileName:
counter += 1
volFileName = os.path.join(directory, filename)
vol = Volume()
vol.setFileName(volFileName)
# fix mrc header
ccp4header = Ccp4Header(volFileName, readHeader=True)
sampling = ccp4header.computeSampling()
origin = Transform()
shifts = ccp4header.getOrigin()
origin.setShiftsTuple(shifts)
f.write("open %s\n" % volFileName)
f.write("volume #%d style surface voxelSize %f\n"
"volume #%d origin %0.2f,%0.2f,%0.2f\n" %
(counter, sampling, counter, shifts[0], shifts[1],
shifts[2]))
f.write("volume #%d level %0.3f\n" % (counter, 0.001))
for filename in os.listdir(directory):
if filename.endswith(".pdb") or filename.endswith(".cif"):
path = os.path.join(directory, filename)
# f.write("open %s\n" % os.path.abspath(path))
f.write("open %s\n" % path)
f.close()
# run in the background
Chimera.runProgram(Chimera.getProgram(), fnCmd + "&")
return []
def extractunitCell(self, sym, offset=0, cropZ=False):
# FlexProtConvertToPseudoAtoms = Domain.importFromPlugin("continuousflex.protocols",
# "FlexProtConvertToPseudoAtoms",
# doRaise=True)
# NMA_MASK_THRE = Domain.importFromPlugin("continuousflex.protocols.pdb.protocol_pseudoatoms_base",
# "NMA_MASK_THRE",
# doRaise=True)
""" extract unit cell from icosahedral phantom
using xmipp_i2 symmetry
"""
# create phantom (3D map)
_samplingRate = 1.34
_, outputFile1 = mkstemp(suffix=".mrc")
command = "xmipp_phantom_create "
args = " -i %s" % self.filename[sym]
args += " -o %s" % outputFile1
runJob(None, command, args, env=Plugin.getEnviron())
ccp4header = Ccp4Header(outputFile1, readHeader=True)
x, y, z = ccp4header.getDims()
t = Transform()
if cropZ:
_, outputFile2 = mkstemp(suffix=".mrc")
args = "-i %s -o %s" % (outputFile1, outputFile2)
args += " --corners "
args += " %d " % (-x / 2.)
args += " %d " % (-y / 2.)
args += " %d " % (0.)
args += " %d " % (+x / 2.)
args += " %d " % (+y / 2.)
args += " %d " % (+z / 2.)
runJob(None,
"xmipp_transform_window",
args,
env=Plugin.getEnviron())
t.setShifts(0, 0, 0)
outputFile = outputFile2
ccp4header = Ccp4Header(outputFile2, readHeader=True)
else:
t.setShifts(0, 0, 0)
outputFile = outputFile1
ccp4header.setSampling(_samplingRate)
ccp4header.setOrigin(t.getShifts())
ccp4header.writeHeader()
# import volume
if cropZ:
args = {
'filesPath': outputFile,
'filesPattern': '',
'samplingRate': _samplingRate,
'copyFiles': True,
'setOrigCoord': True,
'x': 90. * _samplingRate,
'y': 90. * _samplingRate,
'z': 0.
# x, y, z in Angstroms
}
else:
args = {
'filesPath': outputFile,
'filesPattern': '',
'samplingRate': _samplingRate,
'copyFiles': True,
'setDefaultOrigin': False,
}
prot = self.newProtocol(ProtImportVolumes, **args)
prot.setObjLabel('import volume(%s)' % XMIPP_SYM_NAME[sym])
self.launchProtocol(prot)
# execute protocol extract unitCell
args = {
'inputVolumes': prot.outputVolume,
'symmetryGroup': sym,
'symmetryOrder': self.symOrder,
'innerRadius': self.innerRadius,
'outerRadius': self.outerRadius,
'expandFactor': .2,
'offset': offset
}
prot = self.newProtocol(XmippProtExtractUnit, **args)
prot.setObjLabel('extract unit cell')
self.launchProtocol(prot)
# check results
ih = ImageHandler()
xdim, ydim, zdim, ndim = \
ih.getDimensions(prot.outputVolume.getFileName())
self.assertTrue(abs(xdim - self.box[sym][0]) < 2)
self.assertTrue(abs(ydim - self.box[sym][1]) < 2)
self.assertTrue(abs(zdim - self.box[sym][2]) < 2)
# create pdb fileoutput
# args = {'inputStructure': prot.outputVolume,
# 'maskMode': NMA_MASK_THRE,
# 'maskThreshold': 0.5,
# 'pseudoAtomRadius': 1.5
# }
# prot = self.newProtocol(FlexProtConvertToPseudoAtoms, **args)
# prot.setObjLabel('get pdb')
# self.launchProtocol(prot)
# check results
# filenamePdb = prot._getPath('pseudoatoms.pdb')
# self.assertTrue(os.path.isfile(filenamePdb))
# delete temporary files
os.remove(self.filename[sym])
os.remove(outputFile)
def _updateItem(self, item, index):
item.setLocation(index, self._getFileName('particlesAligned'))
item.setTransform(Transform())
def test_forward_backwards(self):
"""convert transformation matrix to xmipp and back"""
mList = [
[
[0.71461016, 0.63371837, -0.29619813, 1.], # a1
[-0.61309201, 0.77128059, 0.17101008, 2.],
[0.33682409, 0.059391174, 0.93969262, 3.],
[0, 0, 0, 1.]
],
[
[0., 0., -1., 0.], # a2
[0., 1., 0., 0.],
[1., 0., 0., 0.],
[0., 0., 0., 1.]
],
[
[0., 1., 0., 0.], # a3
[0., 0., 1., 0.],
[1., 0., 0., 0.],
[0., 0., 0., 1.]
],
[
[0.22612257, 0.82379508, -0.51983678, 0.], # a4
[-0.88564873, 0.39606407, 0.24240388, 0.],
[0.40557978, 0.40557978, 0.81915206, 0.],
[0., 0., 0., 1.]
],
[
[-0.78850311, -0.24329656, -0.56486255, 0.], # a5
[0.22753462, -0.96866286, 0.099600501, 0.],
[-0.57139379, -0.049990479, 0.81915206, 0.],
[0., 0., 0., 1.]
],
[
[1.0, 0.0, 0.0, 0.0], # a6
[0.0, 1.0, 0.0, 0.0],
[0.0, 0.0, 1.0, 0.0],
[0.0, 0.0, 0.0, 1.0]
],
[
[0., 0., -1., 0.], # a7
[-1., 0., 0., 0.],
[0., 1., 0., 0.],
[0., 0., 0., 1.]
]
]
aList = [np.array(m) for m in mList]
rowa = md.Row()
rowb = md.Row()
labelList = [
md.RLN_ORIENT_ROT, md.RLN_ORIENT_TILT, md.RLN_ORIENT_PSI,
md.RLN_ORIENT_ORIGIN_X, md.RLN_ORIENT_ORIGIN_Y,
md.RLN_ORIENT_ORIGIN_Z
]
for i, a in enumerate(aList):
a = Transform(aList[i])
convert.alignmentToRow(a, rowa, ALIGN_PROJ)
b = convert.rowToAlignment(rowa, ALIGN_PROJ)
convert.alignmentToRow(b, rowb, ALIGN_PROJ)
# same two matrices
self.assertTrue(
np.allclose(a.getMatrix(), b.getMatrix(), rtol=1e-2))
for label in labelList:
auxBtilt = rowb.getValue(label)
auxAtilt = rowa.getValue(label)
# same two rows
self.assertAlmostEqual(auxBtilt, auxAtilt, places=3)
b = convert.rowToAlignment(rowa, ALIGN_PROJ)
convert.alignmentToRow(b, rowb, ALIGN_PROJ)
aMatrix = a.getMatrix()
# aMatrix[0,:] *= -1; aMatrix[2,:] *= -1;
# same two matrices with flip
print("\naMatrix: \n", aMatrix, "\nbMatrix: \n", b.getMatrix())
self.assertTrue(np.allclose(aMatrix, b.getMatrix(), rtol=1e-2))
def realignStep(self):
inputMdName = self._getExtraPath('inputClasses.xmd')
writeSetOfClasses2D(self.inputClasses.get(), inputMdName,
writeParticles=True)
centeredStackName = self._getExtraPath('centeredStack.stk')
self._params = {'input': inputMdName,
'output': centeredStackName}
args = ('-i %(input)s -o %(output)s --save_metadata_transform')
self.runJob("xmipp_transform_center_image", args % self._params,
numberOfMpi=1)
centeredMdName = centeredStackName.replace('stk', 'xmd')
centeredMd = md.MetaData(centeredMdName)
centeredStack = md.MetaData(centeredStackName)
listName = []
listTransform=[]
for rowStk in md.iterRows(centeredStack):
listName.append(rowStk.getValue(md.MDL_IMAGE))
for rowMd in md.iterRows(centeredMd):
listTransform.append(rowToAlignment(rowMd, ALIGN_2D))
mdNewClasses = md.MetaData()
for i, row in enumerate(md.iterRows(inputMdName)):
newRow = md.Row()
newRow.setValue(md.MDL_IMAGE, listName[i])
refNum = row.getValue(md.MDL_REF)
newRow.setValue(md.MDL_REF, refNum)
classCount = row.getValue(md.MDL_CLASS_COUNT)
newRow.setValue(md.MDL_CLASS_COUNT, classCount)
newRow.addToMd(mdNewClasses)
mdNewClasses.write('classes@' + self._getExtraPath('final_classes.xmd'),
MD_APPEND)
mdImages = md.MetaData()
i=0
mdBlocks = md.getBlocksInMetaDataFile(inputMdName)
resultMat = Transform()
for block in mdBlocks:
if block.startswith('class00'):
newMat = listTransform[i]
newMatrix = newMat.getMatrix()
mdClass = md.MetaData(block + "@" + inputMdName)
mdNewClass = md.MetaData()
i+=1
for rowIn in md.iterRows(mdClass):
#To create the transformation matrix (and its parameters)
# for the realigned particles
if rowIn.getValue(md.MDL_ANGLE_PSI)!=0:
flag_psi=True
if rowIn.getValue(md.MDL_ANGLE_ROT)!=0:
flag_psi=False
inMat = rowToAlignment(rowIn, ALIGN_2D)
inMatrix = inMat.getMatrix()
resultMatrix = np.dot(newMatrix,inMatrix)
resultMat.setMatrix(resultMatrix)
rowOut=md.Row()
rowOut.copyFromRow(rowIn)
alignmentToRow(resultMat, rowOut, ALIGN_2D)
if flag_psi==False:
newAngle = rowOut.getValue(md.MDL_ANGLE_PSI)
rowOut.setValue(md.MDL_ANGLE_PSI, 0.)
rowOut.setValue(md.MDL_ANGLE_ROT, newAngle)
#To create the new coordinates for the realigned particles
inPoint = np.array([[0.],[0.],[0.],[1.]])
invResultMat = np.linalg.inv(resultMatrix)
centerPoint = np.dot(invResultMat,inPoint)
rowOut.setValue(md.MDL_XCOOR, rowOut.getValue(
md.MDL_XCOOR)+int(centerPoint[0]))
rowOut.setValue(md.MDL_YCOOR, rowOut.getValue(
md.MDL_YCOOR)+int(centerPoint[1]))
rowOut.addToMd(mdNewClass)
mdNewClass.write(block + "@" + self._getExtraPath(
'final_classes.xmd'), MD_APPEND)
mdImages.unionAll(mdNewClass)
mdImages.write(self._getExtraPath('final_images.xmd'))
