# *
# * Authors: Scipion Team
# *
# * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion-users@lists.sourceforge.net'
# *
# **************************************************************************
from os import symlink
from emtable import Table
from pwem.emlib.image import ImageHandler
import pyworkflow.utils as pwutils
from pwem.objects import Transform
from pyworkflow.object import Float
from pyworkflow.utils import removeBaseExt
from reliontomo.constants import FILE_NOT_FOUND, COORD_X, COORD_Y, COORD_Z, SUBTOMO_NAME, \
TILT_PRIOR, PSI_PRIOR, TOMO_NAME_30, CTF_MISSING_WEDGE, \
CLASS_NUMBER, MRC, PARTICLES_TABLE
from reliontomo.convert.convertBase import WriterTomo, getTransformInfoFromCoordOrSubtomo, ReaderTomo, \
getTransformMatrixFromRow
from reliontomo.utils import getAbsPath, _gen2LevelBaseName
from scipion.install.funcs import mkdir
from os.path import join
from tomo.constants import BOTTOM_LEFT_CORNER
from tomo.objects import SubTomogram, Coordinate3D, TomoAcquisition
[docs]class Writer(WriterTomo):
""" Helper class to convert from Scipion SetOfImages subclasses
with star file format previous to Relion>3.1, but providing the same
interface as the new Writer class.
"""
def __init__(self, **kwargs):
super().__init__(**kwargs)
[docs] def subtomograms2Star(self, subtomoSet, subtomosStar):
currentTomo = ''
ih = ImageHandler()
tomoTable = Table(columns=self.starHeaders)
tmpDir = pwutils.getParentFolder(subtomosStar)
for subtomo in subtomoSet:
if pwutils.getExt(subtomo.getFileName().replace(':' + MRC, '')) != '.' + MRC:
mrcDir = join(tmpDir, pwutils.removeBaseExt(subtomo.getVolName()))
if currentTomo != subtomo.getVolName():
mkdir(mrcDir)
mrcFile = join(mrcDir, pwutils.replaceBaseExt(subtomo.getFileName(), MRC))
ih.convert(subtomo.getFileName(), mrcFile)
angles, shifts = getTransformInfoFromCoordOrSubtomo(subtomo)
magn = subtomo.getAcquisition().getMagnification()
ctfFile = getattr(subtomo.getCoordinate3D(), '_3dcftMrcFile', None)
if ctfFile:
ctfFile = ctfFile.get()
rlnMicrographName = subtomo.getVolName()
rlnCoordinateX = subtomo.getCoordinate3D().getX(BOTTOM_LEFT_CORNER)
rlnCoordinateY = subtomo.getCoordinate3D().getY(BOTTOM_LEFT_CORNER)
rlnCoordinateZ = subtomo.getCoordinate3D().getZ(BOTTOM_LEFT_CORNER)
rlnImageName = subtomo.getFileName().replace(':' + MRC, '')
rlnCtfImage = ctfFile if ctfFile else FILE_NOT_FOUND
rlnMagnification = magn if magn else 10000 #64000
rlnDetectorPixelSize = subtomo.getSamplingRate()
rlnAngleRot = angles[0]
rlnAngleTilt = angles[1]
rlnAnglePsi = angles[2]
rlnOriginX = shifts[0]
rlnOriginY = shifts[1]
rlnOriginZ = shifts[2]
rlnTiltPrior = subtomo._tiltPriorAngle.get() if hasattr(subtomo, '_tiltPriorAngle') else rlnAngleTilt
rlnPsiPrior = subtomo._psiPriorAngle.get() if hasattr(subtomo, '_psiPriorAngle') else rlnAnglePsi
# Add row to the table which will be used to generate the STAR file
fieldsToAdd = [rlnMicrographName,
rlnCoordinateX,
rlnCoordinateY,
rlnCoordinateZ,
rlnImageName,
rlnCtfImage,
rlnMagnification,
rlnDetectorPixelSize,
rlnAngleRot,
rlnAngleTilt,
rlnTiltPrior,
rlnAnglePsi,
rlnPsiPrior,
rlnOriginX,
rlnOriginY,
rlnOriginZ]
if self.isPyseg:
fieldsToAdd = [rlnMicrographName,
rlnCoordinateX,
rlnCoordinateY,
rlnCoordinateZ,
rlnImageName,
rlnCtfImage,
rlnAngleRot,
rlnAngleTilt,
rlnAnglePsi,
rlnOriginX,
rlnOriginY,
rlnOriginZ]
tomoTable.addRow(*fieldsToAdd)
# Write the STAR file
tomoTable.write(subtomosStar)
[docs]class Reader(ReaderTomo):
def __init__(self, starFile, **kwargs):
super().__init__(starFile)
[docs] def read(self, tableName=None):
try:
self.dataTable.read(self.starFile, tableName=tableName)
except Exception:
# If the particles table isn't present in the introduced star, it means that it isn't a
# coordinates/particles star, which means that we are in relion4, in which there are other star files for
# tomography, like tomograms or pseudosubtomograms
self.dataTable.read(self.starFile)
[docs] @staticmethod
def gen3dCoordFromStarRow(row, precedentsSet, precedentIdList, scaleFactor):
coordinate3d = Coordinate3D()
tomoId = removeBaseExt(row.get(TOMO_NAME_30))
x = float(row.get(COORD_X, 0))
y = float(row.get(COORD_Y, 0))
z = float(row.get(COORD_Z, 0))
volId = precedentIdList.index(tomoId) + 1 # Set indices begin in 1
coordinate3d.setVolume(precedentsSet[volId])
coordinate3d.setVolId(volId)
ctf3d = row.get(CTF_MISSING_WEDGE, FILE_NOT_FOUND)
coordinate3d.setTomoId(tomoId)
coordinate3d.setX(x * scaleFactor, BOTTOM_LEFT_CORNER)
coordinate3d.setY(y * scaleFactor, BOTTOM_LEFT_CORNER)
coordinate3d.setZ(z * scaleFactor, BOTTOM_LEFT_CORNER)
coordinate3d._3dcftMrcFile = ctf3d # Used for the ctf3d generation in Relion
coordinate3d.setMatrix(getTransformMatrixFromRow(row))
return coordinate3d
[docs] def starFile2Coords3D(self, coordsSet, precedentsSet, scaleFactor):
self.read(tableName=PARTICLES_TABLE)
precedentIdList = [tomo.getTsId() for tomo in precedentsSet]
for row in self.dataTable:
coordsSet.append(self.gen3dCoordFromStarRow(row, precedentsSet, precedentIdList, scaleFactor))
[docs] def starFile2Subtomograms(self, subtomoSet, coordSet, linkedSubtomosDir, starFilePath):
self.read(tableName=PARTICLES_TABLE)
samplingRate = subtomoSet.getSamplingRate()
for row, coordinate3d in zip(self.dataTable, coordSet):
subtomo = SubTomogram()
transform = Transform()
origin = Transform()
# Files
tomoName = row.get(TOMO_NAME_30, FILE_NOT_FOUND)
subtomoName = row.get(SUBTOMO_NAME, FILE_NOT_FOUND)
linkedSubtomoName = join(linkedSubtomosDir, _gen2LevelBaseName(subtomoName))
symlink(getAbsPath(starFilePath, subtomoName), linkedSubtomoName) # Link the subtomos to the extra folder
# Subtomograms
tiltPrior = row.get(TILT_PRIOR, 0)
psiPrior = row.get(PSI_PRIOR, 0)
transform.setMatrix(coordinate3d.getMatrix())
subtomo.setVolName(tomoName)
subtomo.setFileName(linkedSubtomoName)
subtomo.setCoordinate3D(coordinate3d)
subtomo.setVolId(coordinate3d.getVolId())
subtomo.setTransform(transform)
subtomo.setAcquisition(TomoAcquisition())
subtomo.setClassId(row.get(CLASS_NUMBER, 0))
subtomo.setSamplingRate(samplingRate)
subtomo._tiltPriorAngle = Float(tiltPrior)
subtomo._psiPriorAngle = Float(psiPrior)
subtomo.setOrigin(origin)
# Add current subtomogram to the output set
subtomoSet.append(subtomo)
# Set the set of coordinates which corresponds to the current set of subtomograms
subtomoSet.setCoordinates3D(coordSet)