def getTomoSetFromStar(prot, starFile):
samplingRate = prot.pixelSize.get()
imgh = ImageHandler()
tomoTable = Table()
tomoTable.read(starFile)
tomoList = [row.get(TOMO_NAME, FILE_NOT_FOUND) for row in tomoTable]
prot.tomoList = List(tomoList)
tomoNamesUnique = list(set(tomoList))
# Create a Volume template object
tomo = Tomogram()
tomo.setSamplingRate(samplingRate)
for fileName in tomoNamesUnique:
x, y, z, n = imgh.getDimensions(fileName)
if fileName.endswith('.mrc') or fileName.endswith('.map'):
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)
tomo.setOrigin(origin) # read origin from form
for index in range(1, n + 1):
tomo.cleanObjId()
tomo.setLocation(index, fileName)
tomo.setAcquisition(TomoAcquisition(**prot.acquisitionParams))
prot.tomoSet.append(tomo)
def _relionTomoStar2Subtomograms(prot, outputSubTomogramsSet, tomoTable, invert):
ih = ImageHandler()
samplingRate = outputSubTomogramsSet.getSamplingRate()
for row, inSubtomo in zip(tomoTable, prot.inputSubtomos.get()):
subtomo = SubTomogram()
coordinate3d = Coordinate3D()
transform = Transform()
origin = Transform()
volname = row.get(TOMO_NAME, FILE_NOT_FOUND)
subtomoFn = row.get(SUBTOMO_NAME, FILE_NOT_FOUND)
subtomo.setVolName(managePath4Sqlite(volname))
subtomo.setTransform(transform)
subtomo.setAcquisition(TomoAcquisition())
subtomo.setClassId(row.get('rlnClassNumber', 0))
subtomo.setSamplingRate(samplingRate)
subtomo.setCoordinate3D(coordinate3d) # Needed to get later the tomogram pointer via getCoordinate3D()
x = row.get(COORD_X, 0)
y = row.get(COORD_Y, 0)
z = row.get(COORD_Z, 0)
tiltPrior = row.get(TILT_PRIOR, 0)
psiPrior = row.get(PSI_PRIOR, 0)
# ctf3d = row.get(CTF_MISSING_WEDGE, FILE_NOT_FOUND)
coordinate3d = subtomo.getCoordinate3D()
coordinate3d.setX(float(x), BOTTOM_LEFT_CORNER)
coordinate3d.setY(float(y), BOTTOM_LEFT_CORNER)
coordinate3d.setZ(float(z), BOTTOM_LEFT_CORNER)
coordinate3d._3dcftMrcFile = inSubtomo.getCoordinate3D()._3dcftMrcFile # Used for the ctf3d in Relion 3.0 (tomo)
M = _getTransformMatrix(row, invert)
transform.setMatrix(M)
subtomo.setCoordinate3D(coordinate3d)
subtomo._tiltPriorAngle = Float(tiltPrior)
subtomo._psiPriorAngle = Float(psiPrior)
# Set the origin and the dimensions of the current subtomogram
x, y, z, n = ih.getDimensions(subtomoFn)
zDim, _ = manageIhDims(subtomoFn, z, n)
origin.setShifts(x / -2. * samplingRate, y / -2. * samplingRate, zDim / -2. * samplingRate)
subtomo.setOrigin(origin)
subtomo.setFileName(managePath4Sqlite(subtomoFn))
# if subtomo is in a vesicle
if 'tid_' in subtomoFn:
vesicleId = subtomoFn.split('tid_')[1]
vesicleId = vesicleId[0]
scoor = subtomo.getCoordinate3D()
scoor.setGroupId(vesicleId)
subtomo.setCoordinate3D(scoor)
# Add current subtomogram to the output set
outputSubTomogramsSet.append(subtomo)
def updateSubTomogram(subTomogram, index):
particleParams = particlesParams.get(index)
if not particleParams:
print("Could not get params for particle %d" % index)
setattr(subTomogram, "_appendItem", False)
else:
setattr(subTomogram, 'coverage', Float(particleParams["coverage"]))
setattr(subTomogram, 'score', Float(particleParams["score"]))
# Create 4x4 matrix from 4x3 e2spt_sgd align matrix and append row [0,0,0,1]
am = particleParams["alignMatrix"]
angles = numpy.array([am[0:3], am[4:7], am[8:11], [0, 0, 0]])
samplingRate = outputSetOfSubTomograms.getSamplingRate()
shift = numpy.array([am[3] * samplingRate, am[7] * samplingRate, am[11] * samplingRate, 1])
matrix = numpy.column_stack((angles, shift.T))
subTomogram.setTransform(Transform(matrix))
def rowToAlignment(alignmentList, alignType):
"""
is2D == True-> matrix is 2D (2D images alignment)
otherwise matrix is 3D (3D volume alignment or projection)
invTransform == True -> for xmipp implies projection
"""
# use all angles in 2D since we might have mirrors
# is2D = alignType == em.ALIGN_2D
inverseTransform = alignType == emcts.ALIGN_PROJ
alignment = Transform()
angles = numpy.zeros(3)
shifts = numpy.zeros(3)
shifts[0] = alignmentList[3]
shifts[1] = alignmentList[4]
shifts[2] = 0
angles[0] = alignmentList[0]
angles[1] = alignmentList[1]
angles[2] = alignmentList[2]
matrix = matrixFromGeometry(shifts, angles, inverseTransform)
alignment.setMatrix(matrix)
return alignment
def importVolumesStep(self, pattern, samplingRate, setOrigCoord=False):
""" Copy images matching the filename pattern
Register other parameters.
"""
volSet = self._createSetOfVolumes()
vol = emobj.Volume()
if self.importFrom == self.IMPORT_FROM_FILES:
self.info("Using pattern: '%s'" % pattern)
# Create a Volume template object
vol.setSamplingRate(samplingRate)
imgh = emlib.image.ImageHandler()
volSet.setSamplingRate(samplingRate)
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 = emobj.Transform()
if setOrigCoord:
origin.setShiftsTuple(self._getOrigCoord())
else:
origin.setShifts(x / -2. * samplingRate,
y / -2. * samplingRate,
zDim / -2. * samplingRate)
vol.setOrigin(origin) # read origin from form
if self.copyFiles or setOrigCoord:
newFileName = abspath(
self._getVolumeFileName(fileName, "mrc"))
emconv.Ccp4Header.fixFile(fileName, newFileName,
origin.getShifts(), samplingRate,
emconv.Ccp4Header.ORIGIN)
if self.setHalfMaps.get():
newFileName1 = abspath(
self._getVolumeFileName(self.half1map.get(),
"mrc"))
emconv.Ccp4Header.fixFile(self.half1map.get(),
newFileName1,
origin.getShifts(),
samplingRate,
emconv.Ccp4Header.ORIGIN)
newFileName2 = abspath(
self._getVolumeFileName(self.half2map.get(),
"mrc"))
emconv.Ccp4Header.fixFile(self.half2map.get(),
newFileName2,
origin.getShifts(),
samplingRate,
emconv.Ccp4Header.ORIGIN)
vol.setHalfMaps(
[relpath(newFileName1),
relpath(newFileName2)])
else:
newFileName = abspath(self._getVolumeFileName(fileName))
if fileName.endswith(':mrc'):
fileName = fileName[:-4]
pwutils.createAbsLink(fileName, newFileName)
if self.setHalfMaps.get():
pwutils.createAbsLink(
self.half1map.get(),
abspath(
self._getVolumeFileName(self.half1map.get())))
pwutils.createAbsLink(
self.half2map.get(),
abspath(
self._getVolumeFileName(self.half2map.get())))
vol.setHalfMaps([
relpath(
self._getVolumeFileName(self.half1map.get())),
relpath(
self._getVolumeFileName(self.half2map.get()))
])
# Make newFileName relative
# https://github.com/I2PC/scipion/issues/1935
newFileName = relpath(newFileName)
if n == 1:
vol.cleanObjId()
vol.setFileName(newFileName)
volSet.append(vol)
else:
for index in range(1, n + 1):
vol.cleanObjId()
vol.setLocation(index, newFileName)
volSet.append(vol)
else: # import from EMDB
self.info("Downloading map with ID = %s" % self.emdbId)
try:
localFileName, sampling, origin = \
fetch_emdb_map(self.emdbId,
self._getExtraPath(),
self._getTmpPath())
except Exception as e:
print(e)
return
# open volume and fill sampling and origin
vol.setSamplingRate(sampling)
vol.setFileName(localFileName)
from pwem.objects.data import Transform
originMat = Transform()
originMat.setShifts(origin[0], origin[1], origin[2])
vol.setOrigin(originMat)
if volSet.getSize() > 1:
self._defineOutputs(outputVolumes=volSet)
else:
self._defineOutputs(outputVolume=vol)
def createPhantomsStep(self):
mwfilter = self.mwfilter.get()
rotmin = self.rotmin.get()
rotmax = self.rotmax.get()
tiltmin = self.tiltmin.get()
tiltmax = self.tiltmax.get()
psimin = self.psimin.get()
psimax = self.psimax.get()
fnVol = self._getExtraPath("phantom000.vol")
if self.option.get() == 0:
inputVol = self.inputVolume.get()
fnInVol = inputVol.getLocation()[1]
dim = inputVol.getDim()
if mwfilter:
mwangle = self.mwangle.get()
self.runJob(
"xmipp_transform_filter",
" --fourier wedge -%d %d 0 0 0 -i %s -o %s" %
(mwangle, mwangle, fnInVol, fnVol))
else:
self.runJob("xmipp_image_convert",
" -i %s -o %s" % (fnInVol, fnVol))
else:
desc = self.create.get()
fnDescr = self._getExtraPath("phantom.descr")
fhDescr = open(fnDescr, 'w')
fhDescr.write(desc)
fhDescr.close()
dim = [desc.split()[0], desc.split()[1], desc.split()[2]]
self.runJob("xmipp_phantom_create",
" -i %s -o %s" % (fnDescr, fnVol))
if mwfilter:
mwangle = self.mwangle.get()
self.runJob(
"xmipp_transform_filter",
" --fourier wedge -%d %d 0 0 0 -i %s -o %s" %
(mwangle, mwangle, fnVol, fnVol))
self.outputSet = self._createSetOfSubTomograms(
self._getOutputSuffix(SetOfSubTomograms))
self.outputSet.setDim(dim)
self.outputSet.setSamplingRate(self.sampling.get())
coordsBool = self.coords.get()
if coordsBool:
tomos = self.tomos.get()
tomo = tomos.getFirstItem()
tomoDim = tomo.getDim()
self.coords = self._createSetOfCoordinates3D(tomos)
subtomobase = SubTomogram()
acq = TomoAcquisition()
subtomobase.setAcquisition(acq)
subtomobase.setLocation(fnVol)
subtomobase.setSamplingRate(self.sampling.get())
transformBase = Transform()
transformBase.setMatrix(np.identity(4))
subtomobase.setTransform(transformBase)
if coordsBool:
coor = Coordinate3D()
coor.setVolume(tomo)
coor.setX(np.random.randint(0, tomoDim[0]),
const.BOTTOM_LEFT_CORNER)
coor.setY(np.random.randint(0, tomoDim[1]),
const.BOTTOM_LEFT_CORNER)
coor.setZ(np.random.randint(0, tomoDim[2]),
const.BOTTOM_LEFT_CORNER)
subtomobase.setCoordinate3D(coor)
subtomobase.setVolName(tomo.getFileName())
self.coords.append(coor)
self.coords.setBoxSize(subtomobase.getDim()[0])
self.outputSet.append(subtomobase)
for i in range(int(self.nsubtomos.get()) - 1):
fnPhantomi = self._getExtraPath("phantom%03d.vol" % int(i + 1))
rot = np.random.randint(rotmin, rotmax)
tilt = np.random.randint(tiltmin, tiltmax)
psi = np.random.randint(psimin, psimax)
self.runJob(
"xmipp_transform_geometry",
" -i %s -o %s --rotate_volume euler %d %d %d " %
(fnVol, fnPhantomi, rot, tilt, psi))
if mwfilter:
self.runJob(
"xmipp_transform_filter",
" --fourier wedge -%d %d 0 0 0 -i %s -o %s" %
(mwangle, mwangle, fnPhantomi, fnPhantomi))
subtomo = SubTomogram()
subtomo.setAcquisition(acq)
subtomo.setLocation(fnPhantomi)
subtomo.setSamplingRate(self.sampling.get())
A = euler_matrix(np.deg2rad(psi), np.deg2rad(tilt),
np.deg2rad(rot), 'szyz')
transform = Transform()
transform.setMatrix(A)
subtomo.setTransform(transform)
if coordsBool:
coor = Coordinate3D()
coor.setVolume(tomo)
coor.setX(np.random.randint(0, tomoDim[0]),
const.BOTTOM_LEFT_CORNER)
coor.setY(np.random.randint(0, tomoDim[1]),
const.BOTTOM_LEFT_CORNER)
coor.setZ(np.random.randint(0, tomoDim[2]),
const.BOTTOM_LEFT_CORNER)
subtomo.setCoordinate3D(coor)
subtomo.setVolName(tomo.getFileName())
self.coords.append(coor)
self.outputSet.append(subtomo)
if coordsBool:
self.outputSet.setCoordinates3D(self.coords)