# **************************************************************************
# *
# * Authors: Airen Zaldivar (azaldivar@cnb.csic.es) [1]
# * Authors: Grigory Sharov (gsharov@mrc-lmb.cam.ac.uk) [2]
# *
# * [1] Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# * [2] MRC Laboratory of Molecular Biology (MRC-LMB)
# *
# * 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 os
import pyworkflow.utils as pwutils
from pwem.objects.data import Coordinate, CTFModel
from pwem.objects.data_tiltpairs import Angles
from pwem.emlib.metadata import (MetaData, MDL_XCOOR, MDL_YCOOR, MDL_ZCOOR,
MDL_PICKING_PARTICLE_SIZE)
# from .convert import loadJson, readCTFModel, readSetOfParticles
from .convert import loadJson, readCTFModel
import tomo.constants as const
[docs]class EmanTomoImport:
def __init__(self, protocol, lstFile=''):
self.protocol = protocol
self._lstFile = lstFile
self.copyOrLink = protocol.getCopyOrLink()
[docs] def importAngles(self, fileName, addAngles):
if pwutils.exists(fileName):
ext = pwutils.getExt(fileName)
if ext == ".json":
fnBase = pwutils.replaceBaseExt(fileName, 'hdf')
keyName = 'tiltparams_micrographs/' + fnBase.replace('_info', '')
jsonAngDict = loadJson(fileName)
if keyName in jsonAngDict:
angles = jsonAngDict[keyName]
tilt, y2, y = angles[:3] # y2=tilted, y=gamma(untilted)
ang = Angles()
# TODO: check this conversion
ang.setAngles(y, y2, tilt)
addAngles(ang)
else:
raise Exception('Unknown extension "%s" to import Eman tilt pair angles' % ext)
# def importCoordinates(self, fileName, addCoordinate):
# if pwutils.exists(fileName):
# ext = pwutils.getExt(fileName)
#
# if ext == ".json":
# jsonPosDict = loadJson(fileName)
# boxes = []
#
# if "boxes" in jsonPosDict:
# boxes = jsonPosDict["boxes"]
# elif "boxes_rct" in jsonPosDict:
# boxes = jsonPosDict["boxes_rct"]
# if boxes:
# for box in boxes:
# x, y = box[:2]
# coord = Coordinate()
# coord.setPosition(x, y)
# addCoordinate(coord)
#
# elif ext == ".box":
# md = MetaData()
# md.readPlain(fileName, "xcoor ycoor particleSize")
# size = md.getValue(MDL_PICKING_PARTICLE_SIZE, md.firstObject())
# if size is None:
# print(">>> WARNING: Error parsing coordinate file: %s" % fileName)
# print(" Skipping this file.")
# else:
# half = size / 2
# for objId in md:
# x = md.getValue(MDL_XCOOR, objId)
# y = md.getValue(MDL_YCOOR, objId)
# coord = Coordinate()
# coord.setPosition(x + half, y + half)
# addCoordinate(coord)
# else:
# raise Exception('Unknown extension "%s" to import Eman coordinates' % ext)
[docs] def importCoordinates3D(self, fileName, addCoordinate):
from tomo.objects import Coordinate3D
if pwutils.exists(fileName):
ext = pwutils.getExt(fileName)
if ext == ".json":
jsonPosDict = loadJson(fileName)
boxes = []
if "boxes_3d" in jsonPosDict:
boxes = jsonPosDict["boxes_3d"]
if boxes:
for box in boxes:
x, y, z = box[:3]
coord = Coordinate3D()
addCoordinate(coord, x, y, z)
else:
raise Exception('Unknown extension "%s" to import Eman coordinates' % ext)
[docs] def getBoxSize(self, coordFile):
""" Try to infer the box size from the given coordinate file.
In the case of .box files, the size is the 3rd column
In the case of .json files, we will look for file
e2boxercache/base.json
"""
if coordFile.endswith('.box'):
md = MetaData()
md.readPlain(coordFile, "xcoor ycoor particleSize")
return md.getValue(MDL_PICKING_PARTICLE_SIZE, md.firstObject())
elif coordFile.endswith('.json'):
infoDir = os.path.dirname(coordFile)
# Still go one level up of info dir
jsonBase = pwutils.join(os.path.dirname(infoDir), 'e2boxercache', 'base.json')
jsonBase2 = pwutils.join(infoDir, 'project.json')
if pwutils.exists(jsonBase):
jsonDict = loadJson(jsonBase)
if 'box_size' in jsonDict:
return int(jsonDict["box_size"])
elif pwutils.exists(jsonBase2):
jsonDict = loadJson(jsonBase2)
if 'global.boxsize' in jsonDict:
return int(jsonDict["global.boxsize"])
return None
[docs] def importCTF(self, mic, fileName):
ctf = CTFModel()
ctf.setMicrograph(mic)
readCTFModel(ctf, fileName)
return ctf
# def importParticles(self):
# """ Import particles from 'imageSet.lst' file. """
# partSet = self.protocol._createSetOfParticles()
# partSet.setObjComment('Particles imported from EMAN lst file:\n%s' % self._lstFile)
# self.protocol.setSamplingRate(partSet)
# partSet.setIsPhaseFlipped(self.protocol.haveDataBeenPhaseFlipped.get())
# self.protocol.fillAcquisition(partSet.getAcquisition())
#
# direc = self.protocol._getExtraPath()
# readSetOfParticles(self._lstFile, partSet, self.copyOrLink, direc)
# # Register the output set of particles
# self.protocol._defineOutputs(outputParticles=partSet)
# def validateParticles(self):
# errors = []
# return errors