Source code for emxlib.protocols.protocol_export

# **************************************************************************
# *
# * 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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# * This program is distributed in the hope that it will be useful,
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# * GNU General Public License for more details.
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# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
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# *  All comments concerning this program package may be sent to the
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import os

import pyworkflow.protocol.params as params
from pwem import RELATION_CTF
from pwem.protocols import EMProtocol
from pyworkflow.utils import join, exists

from emxlib.constants import *
from emxlib.convert import exportData

[docs]class ProtEmxExport(EMProtocol): """ Export micrographs, coordinates or particles to EMX format. EMX is a joint initiative for data exchange format between different EM software packages. """ _label = 'emx export' _exportTypes = ['Micrographs', 'Coordinates', 'Particles', 'Averages'] def __init__(self, **kwargs): EMProtocol.__init__(self, **kwargs) # We need to trace the changes of 'inputType' to # dynamically modify the property of pointerClass # of the 'inputSets' parameter def onChangeInputType(): inputText = self.getEnumText('inputType') pointerClass = 'SetOf' + inputText self.getParam('inputSet').setPointerClass(pointerClass) self.inputType.trace(onChangeInputType) # --------------------------- DEFINE param functions ------------------ def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputType', params.EnumParam, choices=self._exportTypes, default=2, # Particles label='Input type:', help='Select the type of objects that you want to export.') form.addParam('inputSet', params.PointerParam, pointerClass='SetOfMicrographs,SetOfCoordinates,SetOfParticles', label="Set to export", important=True, help="Select the micrographs, coordinates or particles " "set to be exported to EMX.") form.addParam('outputStack', params.EnumParam, default=STACK_SINGLE, choices=['single stack', 'one stack per micrograph'], condition='inputType==2', # for Particles display=params.EnumParam.DISPLAY_LIST, label="Output images", help="Select how you want to export the particles binary file.\n" "*single stack*: write all particles into a single stack.\n" "*one stack per micrograph*: create one stack with particles" " beloging to the same micrograph.") form.addParam('ctfEstimation', params.RelationParam, allowsNull=True, condition='inputType==0', # for Micrographs relationName=RELATION_CTF, attributeName='getInputSet', label='Include CTF from', help='You can select a CTF estimation associated with these ' 'micrographs to be included in the EMX file') form.addParam('outputPrefix', params.StringParam, default='data', label='EMX files prefix', help='Select how do you want to name the EMX files. ' 'For example, if you use "data" as prefix, two ' 'files will be generated:\n' '_data.emx_ and _data.mrc_')
[docs] def getInputSet(self): return self.inputSet.get()
# --------------------------- INSERT steps functions ---------------------- def _insertAllSteps(self): self._insertFunctionStep('exportDataStep', self.inputSet.get().getObjId()) # --------------------------- STEPS functions -----------------------------
[docs] def exportDataStep(self, micsId): """ Export micrographs to EMX file. micsId is only passed to force redone of this step if micrographs change. """ emxDir = self._getPath('emxData') xmlFile = self.outputPrefix.get() + '.emx' if self.outputStack == STACK_SINGLE: binaryFile = self.outputPrefix.get() + '.mrc' else: binaryFile = None # None for binary file means to output one # stack per micrograph exportData(emxDir, self.inputSet.get(), ctfSet=self.ctfEstimation.get(), xmlFile=xmlFile, binaryFile=binaryFile)
# --------------------------- INFO functions ------------------------------ def _validate(self): errors = [] return errors def _summary(self): summary = [] fname = os.path.abspath(join(self._getPath('emxData'), self.outputPrefix.get() + '.emx')) if exists(fname): summary.append('Exported %s to %s' % ( self._exportTypes[self.inputType.get()], fname)) return summary def _methods(self): return self._summary()