Source code for relion.protocols.protocol_crop_resize

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# *
# * Authors:     Grigory Sharov (
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# * MRC Laboratory of Molecular Biology (MRC-LMB)
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# * This program is free software; you can redistribute it and/or modify
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import pyworkflow.protocol.params as params
import pyworkflow.utils as pwutils
from pyworkflow.constants import PROD
from pwem.protocols import ProtPreprocessVolumes
from pwem.emlib.image import ImageHandler
from pwem.objects import Volume

[docs]class ProtRelionResizeVolume(ProtPreprocessVolumes): """ This protocol rescales/resizes 3D volumes using relion_image_handler. """ _label = 'crop/resize volumes' _devStatus = PROD def __init__(self, **kwargs): ProtPreprocessVolumes.__init__(self, **kwargs) def _createFilenameTemplates(self): """ Centralize how the protocol files are called. """ myDict = { 'input_vol': self._getTmpPath('volume_%(volId)03d.mrc'), 'output_vol': self._getExtraPath('volume_rescaled_%(volId)03d.mrc') } self._updateFilenamesDict(myDict) # --------------------------- DEFINE param functions ---------------------- def _defineParams(self, form): form.addSection(label=pwutils.Message.LABEL_INPUT) form.addParam('inputVolumes', params.PointerParam, important=True, label=pwutils.Message.LABEL_INPUT_VOLS, pointerClass='Volume, SetOfVolumes', help='Can be a Volume or a SetOfVolumes.') form.addParam('doRescale', params.BooleanParam, default=False, label='Rescale volumes?') form.addParam('rescaleSamplingRate', params.FloatParam, default=1.0, condition='doRescale', label='New sampling rate (Å/px)') form.addParam('doResize', params.BooleanParam, default=False, label='Resize volumes to a new box?') form.addParam('resizeSize', params.IntParam, default=0, condition='doResize', label='New box size (px)', help='Provide even box size.') form.addParallelSection(threads=0, mpi=0) # --------------------------- INSERT steps functions ---------------------- def _insertAllSteps(self): self._createFilenameTemplates() self._insertFunctionStep('convertInputStep') self._insertFunctionStep('resizeVolumesStep') self._insertFunctionStep('createOutputStep') # --------------------------- STEPS functions -----------------------------
[docs] def convertInputStep(self): vols = self.inputVolumes.get() self.convertedVols = [] if isinstance(vols, Volume): fn = self._convertVol(vols, 1) self.convertedVols.append(fn) else: for i, vol in enumerate(vols): fn = self._convertVol(vol, i) self.convertedVols.append(fn)
[docs] def resizeVolumesStep(self): argDict = {' --angpix': self.inputVolumes.get().getSamplingRate()} if self.doRescale: argDict[' --rescale_angpix'] = self.rescaleSamplingRate.get() if self.doResize: argDict[' --new_box'] = self.resizeSize.get() for i, fn in enumerate(self.convertedVols): argDict[' --i'] = fn argDict[' --o'] = self._getFileName('output_vol', volId=i+1) args = ' '.join(['%s %s' % (k, v) for k, v in argDict.items()]) self.runJob("relion_image_handler", "".join(args))
[docs] def createOutputStep(self): volInput = self.inputVolumes.get() if isinstance(volInput, Volume): # Create the output with the same class as the input, that should # be Volume or a subclass of Volume e.g. VolumeMask volClass = volInput.getClass() vol = volClass() vol.copyInfo(volInput) vol.setLocation(self._getFileName('output_vol', volId=1)) vol.setSamplingRate(self._getNewSampling()) self._defineOutputs(outputVol=vol) else: volumes = self._createSetOfVolumes() volumes.copyInfo(volInput) volumes.setSamplingRate(self._getNewSampling()) for i, obj in enumerate(volInput.iterItems()): vol = obj vol.setLocation(self._getFileName('output_vol', volId=i+1)) vol.setSamplingRate(self._getNewSampling()) volumes.append(vol) self._defineOutputs(outputVol=volumes) self._defineTransformRelation(self.inputVolumes, self.outputVol)
# --------------------------- INFO functions ------------------------------ def _validate(self): errors = [] if not self.doRescale and not self.doResize: errors.append("You have to select at least one option!") if self.doResize: if not self.resizeSize.get() % 2 == 0: errors.append("Only even box sizes are allowed!") return errors def _summary(self): messages = [] if self.doRescale: messages.append("- Rescaled volumes to pixel size of %0.3f" % self.rescaleSamplingRate.get()) if self.doResize: messages.append("- Resized volumes to box size of %d" % self.resizeSize.get()) return messages # -------------------------- UTILS functions ------------------------------ def _convertVol(self, vol, index): ih = ImageHandler() fn = vol.getFileName() if not fn.endswith('.mrc'): newFn = self._getFileName('input_vol', volId=index) ih.convert(fn, newFn) return newFn return fn def _getNewSampling(self): if self.doRescale: return self.rescaleSamplingRate.get() else: return self.inputVolumes.get().getSamplingRate()