# **************************************************************************
# *
# * 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 is not 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()