Source code for pwem.protocols.protocol_import.masks

# **************************************************************************
# *
# * Authors:     Laura del Cano (ldelcano@cnb.csic.es)
# *              Ignacio Foche (ifoche@cnb.csic.es)
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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# *  All comments concerning this program package may be sent to the
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"""
In this module are protocol related to EM imports of Masks...
"""

from os.path import exists, basename

import pyworkflow.protocol.params as params
import pyworkflow.utils as pwutils

from pwem.objects import Mask, VolumeMask
from pwem.emlib.image import ImageHandler

from .base import ProtImport


[docs]class ProtImportMask(ProtImport): """ Class for import masks from existing files. """ _label = 'import mask' # --------------------------- DEFINE param functions ---------------------- def _defineParams(self, form): form.addSection(label='Import') form.addParam('maskPath', params.PathParam, label="Mask path", help="Select the file path of the mask\n") form.addParam('samplingRate', params.FloatParam, default=1., label=pwutils.properties.Message.LABEL_SAMP_RATE) def _insertAllSteps(self): self._insertFunctionStep('importMaskStep', self.maskPath.get(), self.samplingRate.get()) # --------------------------- STEPS functions -----------------------------
[docs] def importMaskStep(self, path, samplingRate): """ Copy mask from maskPath. """ self.info("Using mask path: '%s'" % path) # Copy the image file into the project dst = self._getExtraPath(basename(path)) pwutils.copyFile(path, dst) # Retrieve image dimensions imgh = ImageHandler() _, _, z, n = imgh.getDimensions(dst) # Create a 2D or 3D Mask, consider the case of n>1 # as the case of some volume maps in mrc format if z > 1 or n > 1: mask = VolumeMask() else: mask = Mask() mask.setFileName(dst) mask.setSamplingRate(samplingRate) self._defineOutputs(outputMask=mask)
# --------------------------- INFO functions ------------------------------ def _validate(self): errors = [] if not self.maskPath.hasValue(): errors.append("Mask path cannot be empty.") elif not exists(self.maskPath.get()): errors.append("Mask not found at *%s*" % self.maskPath.get()) if not self.samplingRate.hasValue(): errors.append("Sampling rate cannot be empty.") return errors def _summary(self): summary = ['Mask file imported from *%s*' % self.maskPath.get()] return summary