# **************************************************************************
# *
# * 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 3 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, see <https://www.gnu.org/licenses/>.
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
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
print("RELION-ROT\tRELION-TILT")
for angleRot, angleTilt in itemDataIterator:
print("%s\t%s" % (angleRot, angleTilt))
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)