Source code for xmipp3.protocols.protocol_preprocess.protocol_movie_resize

# **************************************************************************
# *
# * Authors:     Amaya Jimenez (ajimenez@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
# * it under the terms of the GNU General Public License as published by
# * 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,
# * 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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# **************************************************************************

from os.path import exists

from pyworkflow import VERSION_1_2
from pyworkflow.utils.properties import Message
from pyworkflow.protocol.params import (PointerParam, FloatParam, EnumParam,
                                       IntParam)
from pyworkflow.object import Set
import pyworkflow.protocol.constants as cons
from pyworkflow.protocol.constants import STEPS_PARALLEL

from pwem.protocols import EMProtocol, ProtProcessMovies
from pwem.objects import SetOfMovies, Movie


RESIZE_SAMPLINGRATE = 0
RESIZE_DIMENSIONS = 1
RESIZE_FACTOR = 2


[docs]class XmippProtMovieResize(ProtProcessMovies): """ Resize a set of movies. Only downsampling is allowed. """ _label = 'movie resize' _lastUpdateVersion = VERSION_1_2 def __init__(self, **args): EMProtocol.__init__(self, **args) self.stepsExecutionMode = STEPS_PARALLEL # --------------------------- DEFINE param functions ---------------------- def _defineParams(self, form): form.addSection(label=Message.LABEL_INPUT) form.addParam('inputMovies', PointerParam, pointerClass='SetOfMovies', label=Message.LABEL_INPUT_MOVS, help='Select a set of movies to be resized.') form.addParam('resizeOption', EnumParam, choices=['Sampling Rate', 'Dimensions', 'Factor'], default=RESIZE_SAMPLINGRATE, label="Resize option", display=EnumParam.DISPLAY_COMBO, help='Select an option to resize the images: \n ' '_Sampling Rate_: Set the desire sampling rate ' 'to resize. \n' '_Dimensions_: Set the output dimensions. \n' '_Factor_: Set a resize factor to resize. \n ') form.addParam('resizeSamplingRate', FloatParam, default=4.0, condition='resizeOption==%d' % RESIZE_SAMPLINGRATE, label='Resize sampling rate (A/px)', help='Set the new output sampling rate.') form.addParam('resizeDim', IntParam, default=1024, condition='resizeOption==%d' % RESIZE_DIMENSIONS, label='New image size (px)', help='Size in pixels of the particle images ' '<x> <y=x> <z=x>.') form.addParam('resizeFactor', FloatParam, default=2.0, condition='resizeOption==%d' % RESIZE_FACTOR, label='Downsampling factor', help='New size is the old one x resize factor.') form.addParallelSection(threads=1, mpi=1) # ------------------------ INSERT STEPS functions -------------------------- def _insertNewMoviesSteps(self, insertedDict, inputMovies): """ Insert steps to process new movies (from streaming) Params: insertedDict: contains already processed movies inputMovies: input movies set to be check """ deps = [] # For each movie insert the step to process it for idx, movie in enumerate(self.inputMovies.get()): if movie.getObjId() not in insertedDict: stepId = self._insertMovieStep(movie) deps.append(stepId) insertedDict[movie.getObjId()] = stepId return deps # --------------------------- STEPS functions ------------------------------ def _processMovie(self, movie): movieId = movie.getObjId() fnMovie = movie.getFileName() dim, _, numMov = self.inputMovies.get().getDim() samplingRate = self.inputMovies.get().getSamplingRate() if self.resizeOption==RESIZE_FACTOR: factor = self.resizeFactor.get() newDim = int(dim/factor) self.newSamplingRate = samplingRate*factor if self.resizeOption==RESIZE_DIMENSIONS: newDim = self.resizeDim.get() self.newSamplingRate = float(samplingRate)*(float(dim)/float( newDim)) if self.resizeOption==RESIZE_SAMPLINGRATE: self.newSamplingRate = self.resizeSamplingRate.get() factor = self.newSamplingRate/samplingRate newDim = int(dim/factor) args = "-i %s -o %s --fourier %d %d %d" % \ (fnMovie, self._getPath("movie_%06d_resize.mrcs" % movieId), newDim, newDim, numMov) self.runJob("xmipp_image_resize", args, numberOfMpi=1) # -------------- Methods for Streaming --------------------
[docs] def createOutputStep(self): # Do nothing now, the output should be ready. pass
def _checkNewOutput(self): if getattr(self, 'finished', False): return # Load previously done items (from text file) doneList = self._readDoneList() # Check for newly done items newDone = [m.clone() for m in self.listOfMovies if int(m.getObjId()) not in doneList and self._isMovieDone(m)] allDone = len(doneList) + len(newDone) # We have finished when there is not more input movies (stream closed) # and the number of processed movies is equal to the number of inputs self.finished = self.streamClosed and allDone == len(self.listOfMovies) streamMode = Set.STREAM_CLOSED if self.finished else Set.STREAM_OPEN if newDone: self._writeDoneList(newDone) elif not self.finished: # If we are not finished and no new output have been produced # it does not make sense to proceed and updated the outputs # so we exit from the function here return imageSet = self._loadOutputSet(SetOfMovies, 'movies.sqlite') for movie in newDone: imgOut = Movie() imgOut.setObjId(movie.getObjId()) imgOut.setFileName(self._getPath( "movie_%06d_resize.mrcs" % movie.getObjId())) imgOut.setAcquisition(movie.getAcquisition()) imgOut.setSamplingRate(self.newSamplingRate) imgOut.setFramesRange(self.inputMovies.get().getFramesRange()) imageSet.append(imgOut) self._updateOutputSet('outputMovies', imageSet, streamMode) if self.finished: # Unlock createOutputStep if finished all jobs outputStep = self._getFirstJoinStep() if outputStep and outputStep.isWaiting(): outputStep.setStatus(cons.STATUS_NEW) # --------------------------- UTILS functions ------------------------------ def _loadOutputSet(self, SetClass, baseName): """ Load the output set if it exists or create a new one. """ setFile = self._getPath(baseName) if exists(setFile): outputSet = SetClass(filename=setFile) outputSet.loadAllProperties() outputSet.enableAppend() else: outputSet = SetClass(filename=setFile) outputSet.setStreamState(outputSet.STREAM_OPEN) inputMovies = self.inputMovies.get() outputSet.copyInfo(inputMovies) outputSet.setSamplingRate(self.newSamplingRate) return outputSet def _updateOutputSet(self, outputName, outputSet, state=Set.STREAM_OPEN): outputSet.setStreamState(state) if self.hasAttribute(outputName): outputSet.write() # Write to commit changes outputAttr = getattr(self, outputName) # Copy the properties to the object contained in the protcol outputAttr.copy(outputSet, copyId=False) # Persist changes self._store(outputAttr) else: # Here the defineOutputs function will call the write() method self._defineOutputs(**{outputName: outputSet}) self._store(outputSet) # Close set database to avoid locking it outputSet.close() # --------------------------- INFO functions ------------------------------- def _summary(self): if not hasattr(self, 'outputMovies'): summary = ["No summary information yet."] else: xIn, yIn, zIn = self.inputMovies.get().getDim() xOut, yOut, zOut = self.outputMovies.getDim() summary = ["%d input movies of size %dx%dx%d resized to %d " "output movies of size %dx%dx%d." %(self.inputMovies.get().getSize(), xIn, yIn, zIn, self.outputMovies.getSize(), xOut, yOut, zOut)] return summary
[docs] def validate(self): """ Try to find errors on define params. """ errors = [] dim, _, numMov = self.inputMovies.get().getDim() samplingRate = self.inputMovies.get().getSamplingRate() if self.resizeOption == RESIZE_FACTOR: if self.resizeFactor.get()<1.0: errors.append('Please provide a resizeFactor higher than 1, ' 'only downsampling is allowed.') if self.resizeOption == RESIZE_DIMENSIONS: if self.resizeDim.get() > dim: errors.append('Please provide a resizeDim higher than the ' 'size of the input set, only downsampling is ' 'allowed.') if self.resizeOption == RESIZE_SAMPLINGRATE: if self.resizeSamplingRate.get() <= samplingRate: errors.append('Please provide a resizeSamplingRate higher ' 'than the original one, only downsampling is ' 'allowed.') return errors