Source code for pwem.protocols.protocol_origin_sampling_volume

# -*- coding: utf-8 -*-
# **************************************************************************
# *
# * Authors:     Roberto Marabini (roberto@cnb.csic.es)
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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# * This program is free software; you can redistribute it and/or modify
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# * the Free Software Foundation; either version 3 of the License, or
# * (at your option) any later version.
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# * 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.
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# * 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
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# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
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import os

import pyworkflow.protocol.params as params
from pyworkflow import VERSION_3_0

from pwem.convert import Ccp4Header
from pwem.protocols import EMProtocol
import pwem.objects as emobj
import pyworkflow.utils as pwutils
from os.path import basename


[docs]class ProtOrigSampling(EMProtocol): """ Modify the origin and sampling values assigned to a 3D map """ _label = 'assign Orig & Sampling' _program = "" _lastUpdateVersion = VERSION_3_0 def __init__(self, **kwargs): EMProtocol.__init__(self, **kwargs) # --------------------------- DEFINE param functions ---------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('inVolume', params.PointerParam, label="Input Volume", important=True, pointerClass='Volume', help='A new object volume will be created with the assigned sampling rate and origin. ' 'No new binary file will be created') form.addParam('copyFiles', params.BooleanParam, label="Copy volume", help="Option Yes:\nA new volume file will be copied " "otherwise a link to the input volume is made\n", expertLevel=params.LEVEL_ADVANCED, default=False) form.addParam('setSampling', params.BooleanParam, label="Set sampling rate", help="Option Yes:\nA new volume object will be created with " "the given SamplingRate. " "This sampling rate will NOT be set in the map file header.\n\n", default=False) form.addParam('samplingRate', params.FloatParam, condition='setSampling', label=pwutils.Message.LABEL_SAMP_RATE) form.addParam('setOrigCoord', params.BooleanParam, label="Set origin", help="Option Yes:\nA new volume object will be created with " "the given ORIGIN of coordinates. " "This ORIGIN will NOT be set in the map file header.\n\n", default=False) line = form.addLine("Coordinates (Å)", help="A wizard will suggest you possible " "coordinates for the ORIGIN. In MRC volume " "files, the ORIGIN coordinates will be " "obtained from the file header.\n " "In case you prefer set your own ORIGIN " "coordinates, write them here. You have to " "provide the map center coordinates in " "Å (pixels x sampling).\n", condition='setOrigCoord') line.addParam('x', params.FloatParam, label="x", default=0., help="offset along x axis (Å)") line.addParam('y', params.FloatParam, label=" y", default=0., help="offset along y axis (Å)") line.addParam('z', params.FloatParam, label=" z", default=0., help="offset along z axis (Å)") # --------------------------- INSERT steps functions ---------------------- def _insertAllSteps(self): self._insertFunctionStep('assignStep') # --------------------------- STEPS functions -----------------------------
[docs] def assignStep(self): # Create a Volume object self.inVol = self.inVolume.get() self.outVol = emobj.Volume() self.outVol.copy(self.inVol) # Set sampling Rate (or copy from input) if self.setSampling.get(): samplingRate = self.samplingRate.get() else: samplingRate = self.inVol.getSamplingRate() self.outVol.setSamplingRate(samplingRate) # set Origin if self.setOrigCoord.get(): origin = emobj.Transform() origin.setShifts(self.x.get(), self.y.get(), self.z.get()) else: origin = self.inVol.getOrigin() self.outVol.setOrigin(origin) # Files system stuff fileName = os.path.abspath(self.inVol.getFileName()) fileName = fileName.replace(':mrc', '') # copy or link if self.copyFiles: imgBase = pwutils.replaceBaseExt(fileName, "mrc") imgDst = self._getExtraPath(imgBase) Ccp4Header.fixFile(fileName,imgDst, origin.getShifts(), sampling=samplingRate) else: imgBase = basename(fileName) imgDst = self._getExtraPath(imgBase) pwutils.createAbsLink(fileName, imgDst) self.outVol.setLocation(imgDst) # save self._defineOutputs(outputVolume=self.outVol) self._defineSourceRelation(self.inVol, self.outVol)
# --------------------------- INFO functions ------------------------------ def _validate(self): message = [] # message.append("You must set a path to export.") # Nothing to append return message def _summary(self): # volume copy or linked message = [] if self.setSampling.get(): message.append("New Sampling: %f\n" % self.samplingRate) if self.setOrigCoord.get(): message.append("New Origin: %f %f %f\n" % (self.x, self.y, self.z)) return message def _methods(self): return [] # --------------------------- UTILS functions ---------------------------------
[docs] def getFnPath(self, label='volume'): return os.path.join(self.filesPath.get(), self._getFileName(label))