Source code for relion.protocols.protocol_compress_movies

# ******************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
# *
# * [1] SciLifeLab, Stockholm University
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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
# *  e-mail address 'scipion@cnb.csic.es'
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import os

import pyworkflow.protocol.params as params
import pyworkflow.utils as pwutils
from pyworkflow.constants import PROD
from pwem.protocols import ProtAlignMovies
from pwem.objects import MovieAlignment
from pyworkflow.protocol import STEPS_PARALLEL

import relion


[docs]class ProtRelionCompressMovies(ProtAlignMovies): """ Using *relion_convert_to_tiff* to compress a set of movies. """ _label = 'compress movies' _devStatus = PROD OP_COMPRESS = 0 OP_ESTIMATE = 1 def __init__(self, **kwargs): ProtAlignMovies.__init__(self, **kwargs) self.stepsExecutionMode = STEPS_PARALLEL def _getConvertExtension(self, filename): """ Check whether it is needed to convert to .mrc or not """ ext = pwutils.getExt(filename).lower() return None if ext in ['.mrc', '.mrcs', '.tiff', '.tif'] else 'mrc' # -------------------------- DEFINE param functions ----------------------- def _defineAlignmentParams(self, form): form.addParam('inputGainProt', params.PointerParam, allowsNull=True, pointerClass='ProtRelionCompressEstimateGain', label='Input gain (Optional)', help='Provide as input a compress estimate protocol ' 'from where the estimated gain file will be taken.') group = form.addGroup("TIFF Options") group.addParam('compression', params.EnumParam, default=1, choices=['none', 'auto', 'zip', 'lzw'], label='Compression type') group.addParam('deflateLevel', params.IntParam, default=6, label='Deflate level', help="deflate level. 1 (fast) " "to 9 (slowest but best compression)") form.addParallelSection(threads=4, mpi=1) # --------------------------- STEPS functions ------------------------------- def _convertInputStep(self): self.info("Relion version:") self.runJob("relion_convert_to_tiff --version", "", numberOfMpi=1) self.info("Detected version from config: %s" % relion.Plugin.getActiveVersion()) # Create a local link to the input gain file if necessary inputGain = self.getInputGain() if inputGain: tmpGain = self._getTmpPath('gain_estimate.bin') pwutils.createLink(inputGain, tmpGain) pwutils.createLink(inputGain.replace('.bin', '_reliablity.bin'), tmpGain.replace('.bin', '_reliablity.bin')) ProtAlignMovies._convertInputStep(self) def _processMovie(self, movie): fn = movie.getAttributeValue('_originalFileName', movie.getFileName()) baseName = os.path.basename(fn) compression = self.getEnumText('compression') pwutils.createLink(fn, self._getTmpPath(baseName)) args = "--i %s --o ../extra/ " % baseName args += "--compression %s " % compression # TODO: Check if deflateLevel is only valid for zip (deflate) if compression == 'zip': # deflate args += "--deflate_level %d" % self.deflateLevel if self.getInputGain(): args += "--gain gain_estimate.bin " self.runJob('relion_convert_to_tiff', args, cwd=self._getTmpPath()) # --------------------------- INFO functions ------------------------------ def _summary(self): summary = [] return summary def _citations(self): return ['Zivanov2019'] def _validate(self): # Check base validation before the specific ones for Motioncor errors = ProtAlignMovies._validate(self) return errors # ------------------------ Extra BASE functions --------------------------- def _getRelPath(self, baseName, refPath): return os.path.relpath(self._getExtraPath(baseName), refPath) def _getNameExt(self, movie, postFix, ext, extra=False): fn = self._getMovieRoot(movie) + postFix + '.' + ext return self._getExtraPath(fn) if extra else fn def _createOutputMovies(self): return True def _createOutputMicrographs(self): return False def _createOutputWeightedMicrographs(self): return False def _savePsSum(self): return self.getAttributeValue('savePSsum', False) def _createOutputMovie(self, movie): n = movie.getNumberOfFrames() newMovie = movie.clone() movieName = pwutils.replaceBaseExt(movie.getFileName(), 'tif') newMovie.setFileName(self._getExtraPath(movieName)) newMovie.setAlignment(MovieAlignment(first=1, last=n, xshifts=[0]*n, yshifts=[0]*n)) return newMovie
[docs] def getInputGain(self): inputGainProt = self.inputGainProt.get() if inputGainProt is not None: inputGain = inputGainProt.getOutputGain() if os.path.exists(inputGain): return inputGain return None