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 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)