Source code for emxlib.convert.dataimport

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin ( [1]
# *              Roberto Marabini ( [2]
# *
# * [1] SciLifeLab, Stockholm University
# * [2] Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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# * the Free Software Foundation; either version 2 of the License, or
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# * This program is distributed in the hope that it will be useful,
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from os.path import join, dirname, exists
from collections import OrderedDict

from pwem.constants import ALIGN_NONE

import emxlib.utils as utils
from emxlib.constants import *

[docs]class EmxImport(): """ Import micrographs, coordinates or particles from EMX file. EMX is a joint initiative for data exchange format between different EM software packages. """ def __init__(self, protocol, emxFile, alignType=ALIGN_NONE): self.protocol = protocol self._emxFile = emxFile self.copyOrLink = protocol.getCopyOrLink() self.alignType = alignType def _loadEmxInfo(self): """ Load the EMX file and get some information about the type of objects contained and the binary data. """ emxData = utils.EmxData() emxDir = dirname(self._emxFile) self.classElement = None self.binaryFile = None self.object = None self.objDict = {} # store the first object of each class for classElement in utils.CLASSLIST: obj = emxData.readFirstObject(classElement, self._emxFile) if obj is not None: self.objDict[classElement] = obj #is the binary file of this type binaryFile = join(emxDir, obj.get(utils.FILENAME)) if exists(binaryFile): self.object = obj self.binaryFile = binaryFile self.classElement = classElement
[docs] def loadAcquisitionInfo(self): """ Try to read acquistion from input file. """ acquisitionDict = OrderedDict() if exists(self._emxFile): self._loadEmxInfo() for k, v in PARAM_DICT.items(): # Read from the EMX files the values and fill acquisition if self.object.get(v) is not None: acquisitionDict[k] = self.object.get(v) return acquisitionDict
#--------------------------- STEPS functions --------------------------------------------
[docs] def importData(self): """ Import micrographs, coordinates and particles from EMX file. If the file contains information about the CTF, it will be also taken into account. """ prot = self.protocol acquisition = prot.getAcquisition() from .convert import importData #emxFile=self._getRelPathExecutionDir(emxFile) importData(prot, self._emxFile, prot._getExtraPath(), acquisition, prot.samplingRate.get(), self.copyOrLink, self.alignType)
[docs] def importMicrographs(self): self.importData()
[docs] def importParticles(self): self.importData()
#--------------------------- INFO functions --------------------------------------------
[docs] def validate(self, objectClassName): """ Do some validation about the input EMX file. Params: objectClassName: it could be either (MICROGRAPHS or PARTICLES) """ emxFile = self._emxFile errors = [] # Check that input EMX file exist if not exists(emxFile): errors.append("Input EMX file doesn't exists:\n*%s*" % emxFile) else: self._loadEmxInfo() if self.object is None: errors.append("Cannot find any object in EMX file:\n*%s*" % emxFile) else: if self.binaryFile is None: errors.append("Cannot find binary data *%s* associated with EMX metadata file.\n" % self.binaryFile) if objectClassName not in self.objDict: errors.append("EMX object *%s* not found in EMX file:\n*%s*" % emxFile) if self.alignType != ALIGN_NONE: f = open(emxFile) if not 'transformationMatrix' in errors.append("Align type different from None, but no transformation matrix found in file %s*" % emxFile) f.close() return errors
[docs] def validateMicrographs(self): return self.validate(utils.MICROGRAPH)
[docs] def validateParticles(self): return self.validate(utils.PARTICLE)