Source code for tomo.convert.convert

# **************************************************************************
# *
# * Authors:     David Herreros Calero (dherreros@cnb.csic.es) [1]
# *
# * [1] 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 3 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@cnb.csic.es'
# *
# **************************************************************************
import numpy as np
from pwem.emlib.metadata import (MetaData, MDL_XCOOR, MDL_YCOOR, MDL_ZCOOR)
import pyworkflow.utils as pwutils

import tomo.constants as const

[docs]class TomoImport: def __init__(self, protocol): self.protocol = protocol self.copyOrLink = protocol.getCopyOrLink()
[docs] def importCoordinates3D(self, fileName, addCoordinate): from tomo.objects import Coordinate3D if pwutils.exists(fileName): ext = pwutils.getExt(fileName) if ext == ".txt": md = MetaData() md.readPlain(fileName, "xcoor ycoor zcoor") for objId in md: x = md.getValue(MDL_XCOOR, objId) y = md.getValue(MDL_YCOOR, objId) z = md.getValue(MDL_ZCOOR, objId) coord = Coordinate3D() addCoordinate(coord, x, y, z) else: raise Exception('Unknown extension "%s" to import Eman coordinates' % ext)
[docs]def getMeshVolFileName(volId): return 'Meshes_Vol%d.txt' % volId
[docs]def setOfMeshes2Files(meshes, path): def writeFile(): fnInputCoor = getMeshVolFileName(currentVolId) pathInputCoor = pwutils.join(path, fnInputCoor) np.savetxt(pathInputCoor, np.asarray(coords), fmt='%d', delimiter=",") currentVolId = None coords = [] for coor in meshes.iterCoordinates(orderBy="_volId"): if coor.getVolId() != currentVolId: if currentVolId != None: writeFile() currentVolId = coor.getVolId() coords = [] coords.append([coor.getX(const.BOTTOM_LEFT_CORNER), coor.getY(const.BOTTOM_LEFT_CORNER), coor.getZ(const.BOTTOM_LEFT_CORNER), coor.getGroupId()]) if coords: writeFile()