Source code for pwem.viewers.viewer_base

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin ( [1]
# *
# * [1] SciLifeLab, Stockholm University
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# * This program is free software: you can redistribute it and/or modify
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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
# * 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, see <>.
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import os

import pyworkflow.viewer as pwviewer
import pyworkflow.utils as pwutils
import pyworkflow.object as pwobj

# FIXME: rename data by objects
import pwem.objects as emobj
import pwem.emlib.metadata as md
from pwem.viewers import ObjectView

[docs]class EmProtocolViewer(pwviewer.ProtocolViewer): """ Subclass of ProtocolViewer that have specific functions for EM data visualization. """
[docs] def objectView(self, filenameOrObject, **kwargs): """ This is a wrapper around the ObjectView constructor, just to avoid passing the project and protocol, since both are know here in the ProtocolViewer. Params: filenameOrObject: This parameter can be either a filename or an object that has 'getFileName' method. **kwargs: Can receive extra keyword-arguments that will be passed to the ObjectView constructor """ fn = None if isinstance(filenameOrObject, str): # If the input is a string filename, we should take the object id # from the protocol. This assumes that self.protocol have been # previously set fn = filenameOrObject strId = self.getProtocolId() elif isinstance(filenameOrObject, pwobj.Object): if filenameOrObject.getObjId() is None: strId = self.getProtocolId() else: strId = filenameOrObject.strId() if hasattr(filenameOrObject, 'getLocation'): # In this case fn will be a location tuple that will be # correctly handled by the showj DataView fn = filenameOrObject.getLocation() elif hasattr(filenameOrObject, 'getFileName'): # If the input is an object, we can take the id from it fn = filenameOrObject.getFileName() if fn is None: raise Exception("Incorrect input object, it should be 'string' or " "'Object' (with 'getLocation' or 'getFileName' " "methods).") return ObjectView(self._project, strId, fn, **kwargs)
[docs] def createVolumesSqlite(self, files, path, samplingRate, updateItemCallback=None): pwutils.cleanPath(path) volSet = emobj.SetOfVolumes(filename=path) volSet.setSamplingRate(samplingRate) for volFn in files: vol = emobj.Volume() vol.setFileName(volFn) if updateItemCallback: updateItemCallback(vol) volSet.append(vol) volSet.write() volSet.close() return volSet
[docs] def createAngDistributionSqlite(self, sqliteFn, numberOfParticles, itemDataIterator): if not os.path.exists(sqliteFn): # List of list of 3 elements containing angleTilt, anglePsi, weight projectionList = [] def getCloseProjection(angleRot, angleTilt): """ Get an existing projection close to angleRot, angleTilt. Return None if not found close enough. """ for projection in projectionList: if (abs(projection[0] - angleRot) <= 0.5 and abs(projection[1] - angleTilt) <= 0.5): return projection return None weight = 1. / numberOfParticles for angleRot, angleTilt in itemDataIterator: projection = getCloseProjection(angleRot, angleTilt) if projection is None: projectionList.append([angleRot, angleTilt, weight]) else: projection[2] = projection[2] + weight mdProj = md.MetaData() for projection in projectionList: mdRow = md.Row() mdRow.setValue(md.MDL_ANGLE_ROT, projection[0]) mdRow.setValue(md.MDL_ANGLE_TILT, projection[1]) mdRow.setValue(md.MDL_WEIGHT, projection[2]) mdRow.writeToMd(mdProj, mdProj.addObject()) mdProj.write(sqliteFn)