Source code for tomo.protocols.protocol_base

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
# *
# * [1] SciLifeLab, Stockholm University
# *
# * 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
# * (at your option) any later version.
# *
# * 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.
# *
# * 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
# *
# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************

import pyworkflow as pw
from pyworkflow.protocol.params import (PointerParam, EnumParam, PathParam,
                                        FloatParam, StringParam,
                                        BooleanParam, LEVEL_ADVANCED)
from pyworkflow.mapper.sqlite_db import SqliteDb
from pyworkflow.utils.properties import Message
from pwem.protocols import ProtImport, EMProtocol, ProtImportFiles

import tomo.objects


[docs]class ProtTomoBase: def _createSet(self, SetClass, template, suffix, **kwargs): """ Create a set and set the filename using the suffix. If the file exists, it will be delete. """ setFn = self._getPath(template % suffix) # Close the connection to the database if # it is open before deleting the file pw.utils.cleanPath(setFn) SqliteDb.closeConnection(setFn) setObj = SetClass(filename=setFn, **kwargs) return setObj def _createSetOfTiltSeriesM(self, suffix=''): return self._createSet(tomo.objects.SetOfTiltSeriesM, 'tiltseriesM%s.sqlite', suffix) def _createSetOfTiltSeries(self, suffix=''): self._ouputSuffix = '' return self._createSet(tomo.objects.SetOfTiltSeries, 'tiltseries%s.sqlite', suffix) def _createSetOfCoordinates3D(self, volSet, suffix=''): coord3DSet = self._createSet(tomo.objects.SetOfCoordinates3D, 'coordinates%s.sqlite', suffix, indexes=['_volId']) coord3DSet.setPrecedents(volSet) return coord3DSet def _createSetOfTomograms(self, suffix=''): return self._createSet(tomo.objects.SetOfTomograms, 'tomograms%s.sqlite', suffix) def _createSetOfSubTomograms(self, suffix=''): return self._createSet(tomo.objects.SetOfSubTomograms, 'subtomograms%s.sqlite', suffix) def _createSetOfAverageSubTomograms(self, suffix=''): return self._createSet(tomo.objects.SetOfAverageSubTomograms, 'avgSubtomograms%s.sqlite', suffix) def _createSetOfClassesSubTomograms(self, subTomograms, suffix=''): classes = self._createSet(tomo.objects.SetOfClassesSubTomograms, 'subtomogramClasses%s.sqlite', suffix) classes.setImages(subTomograms) return classes def _createSetOfLandmarkModels(self, suffix=''): return self._createSet(tomo.objects.SetOfLandmarkModels, 'setOfLandmarks%s.sqlite', suffix) def _createSetOfMeshes(self, volSet, suffix=''): meshSet = self._createSet(tomo.objects.SetOfMeshes, 'meshes%s.sqlite', suffix) meshSet.setPrecedents(volSet) return meshSet def _getOutputSuffix(self, cls): """ Get the name to be used for a new output. For example: output3DCoordinates7. It should take into account previous outputs and number with a higher value. """ maxCounter = -1 for attrName, _ in self.iterOutputAttributes(cls): suffix = attrName.replace(self.OUTPUT_PREFIX, '') try: counter = int(suffix) except: counter = 1 # when there is not number assume 1 maxCounter = max(counter, maxCounter) return str(maxCounter+1) if maxCounter > 0 else '' # empty if not output
[docs]class ProtTomoPicking(ProtImport, ProtTomoBase): OUTPUT_PREFIX = 'output3DCoordinates' """ Base class for Tomogram boxing protocols. """ def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputTomograms', PointerParam, label="Input Tomograms", important=True, pointerClass='SetOfTomograms', help='Select the Tomogram to be used during picking.') def _summary(self): summary = [] if self.isFinished(): summary.append("Output 3D Coordinates not ready yet.") if self.getOutputsSize() >= 1: for key, output in self.iterOutputAttributes(): summary.append("*%s:* \n %s " % (key, output.getSummary())) else: summary.append(Message.TEXT_NO_OUTPUT_CO) return summary
[docs]class ProtTomoImportFiles(ProtImportFiles, ProtTomoBase): def _defineParams(self, form): self._defineImportParams(form) self._defineAcquisitionParams(form) def _defineImportParams(self, form): """ Override to add options related to the different types of import that are allowed by each protocol. """ importChoices = self._getImportChoices() form.addSection(label='Import') if len(importChoices) > 1: # not only from files form.addParam('importFrom', EnumParam, choices=importChoices, default=self._getDefaultChoice(), label='Import from', help='Select the type of import.') else: form.addHidden('importFrom', EnumParam, choices=importChoices, default=self.IMPORT_FROM_FILES, label='Import from', help='Select the type of import.') form.addParam('filesPath', PathParam, label="Files directory", help="Directory with the files you want to import.\n\n" "The path can also contain wildcards to select" "from several folders. \n\n" "Examples:\n" " ~/Tomograms/data/day??_tomograms/\n" "Each '?' represents one unknown character\n\n" " ~/Tomograms/data/day*_tomograms/\n" "'*' represents any number of unknown characters\n\n" " ~/Tomograms/data/day#_tomograms/\n" "'#' represents one digit that will be used as " "tomogram ID\n\n" "NOTE: wildcard characters ('*', '?', '#') " "cannot appear in the actual path.)") form.addParam('filesPattern', StringParam, label='Pattern', help="Pattern of the files to be imported.\n\n" "The pattern can contain standard wildcards such as\n" "*, ?, etc, or special ones like ### to mark some\n" "digits in the filename as ID.\n\n" "NOTE: wildcards and special characters " "('*', '?', '#', ':', '%') cannot appear in the " "actual path.") form.addParam('copyFiles', BooleanParam, default=False, expertLevel=LEVEL_ADVANCED, label="Copy files?", help="By default the files are not copied into the " "project to avoid data duplication and to save " "disk space. Instead of copying, symbolic links are " "created pointing to original files. This approach " "has the drawback that if the project is moved to " "another computer, the links need to be restored.") def _defineAcquisitionParams(self, form): """ Override to add options related to acquisition info. """ form.addParam('samplingRate', FloatParam, label=Message.LABEL_SAMP_RATE) def _validate(self): pass
[docs]class ProtTomoSubtomogramAveraging(EMProtocol, ProtTomoBase): """ Base class for subtomogram averaging protocols. """ pass
[docs]class ProtTomoImportAcquisition: MANUAL_IMPORT = 0 FROM_FILE_IMPORT = 1 def _defineParams(self, form): """ Override to add options related to acquisition info. """ importAcquisitionChoices = ['Manual', 'From file'] form.addSection(label='Acquisition Info') form.addParam('importAcquisitionFrom', EnumParam, choices=importAcquisitionChoices, default=self._getDefaultChoice(), label='Import from', help='Select the type of import.') form.addParam('acquisitionData', PathParam, label="Acquisition parameters file", help="File with the acquisition parameters for every " "subtomogram to import. File must be in plain format." " The file must contain a row per file to be imported " "and have the following parameters in order: \n" "\n" "'File_name AcquisitionAngleMin AcquisitionAngleMax Step AngleAxis1 AngleAxis2' \n" "\n" "An example would be: \n" "subtomo1.em -40 40 3 25 30 \n" "subtomo2.em -45 50 2 15 15 \n", condition="importAcquisitionFrom == %d" % self.FROM_FILE_IMPORT) form.addParam('acquisitionAngleMax', FloatParam, allowsNull=True, default=90, label='Acquisition angle max', condition="importAcquisitionFrom == %d" % self.MANUAL_IMPORT, help='Enter the positive limit of the acquisition angle') form.addParam('acquisitionAngleMin', FloatParam, allowsNull=True, default=-90, condition="importAcquisitionFrom == %d" % self.MANUAL_IMPORT, label='Acquisition angle min', help='Enter the negative limit of the acquisition angle') form.addParam('step', FloatParam, allowsNull=True, condition="importAcquisitionFrom == %d" % self.MANUAL_IMPORT, label='Step', help='Enter the step size for the import') form.addParam('angleAxis1', FloatParam, allowsNull=True, condition="importAcquisitionFrom == %d" % self.MANUAL_IMPORT, label='Angle axis 1', help='Enter the angle axis 1') form.addParam('angleAxis2', FloatParam, allowsNull=True, condition="importAcquisitionFrom == %d" % self.MANUAL_IMPORT, label='Angle Axis 2', help='Enter the angle axis 2') def _parseAcquisitionData(self): if self.importAcquisitionFrom.get() == self.MANUAL_IMPORT: self.acquisitionParameters = { 'angleMin': self.acquisitionAngleMin.get(), 'angleMax': self.acquisitionAngleMax.get(), 'step': self.step.get(), 'angleAxis1': self.angleAxis1.get(), 'angleAxis2': self.angleAxis2.get() } else: params = open(self.acquisitionData.get(), "r") self.acquisitionParameters = {} for line in params.readlines(): param = line.split() try: self.acquisitionParameters.update({param[0]: { 'angleMin': float(param[1]), 'angleMax': float(param[2]), 'step': int(param[3]), 'angleAxis1': float(param[4]), 'angleAxis2': float(param[5]) }}) except Exception as e: print('Wrong acquisition data file format', e) def _extractAcquisitionParameters(self, fileName): if self.importAcquisitionFrom.get() == self.FROM_FILE_IMPORT: onlyName = fileName.split('/')[-1] acquisitionParams = self.acquisitionParameters[onlyName] else: acquisitionParams = self.acquisitionParameters return tomo.objects.TomoAcquisition(**acquisitionParams) def _summary(self, summary, setOfObject): for obj in setOfObject: if obj.hasAcquisition(): summary.append(u"File: %s" % obj.getFileName()) summary.append(u"Acquisition angle max: *%0.2f*" % obj.getAcquisition().getAngleMax()) summary.append(u"Acquisition angle min: *%0.2f*" % obj.getAcquisition().getAngleMin()) if obj.getAcquisition().getStep(): summary.append(u"Step: *%d*" % obj.getAcquisition().getStep()) if obj.getAcquisition().getAngleAxis1(): summary.append(u"Angle axis 1: *%0.2f*" % obj.getAcquisition().getAngleAxis1()) if obj.getAcquisition().getAngleAxis2(): summary.append(u"Angle axis 2: *%0.2f*" % obj.getAcquisition().getAngleAxis2())