# **************************************************************************
# *
# * 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, 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 os
from pwem.objects import SetOfMicrographs
from pwem.protocols import EMProtocol
from pyworkflow.constants import PROD
import pyworkflow.utils as pwutils
import pyworkflow.protocol.params as params
import relion.convert as convert
[docs]class ProtRelionExportCtf(EMProtocol):
""" Export a SetOfCTF to a Relion STAR file. """
_label = 'export ctf'
_devStatus = PROD
CTF_STAR_FILE = 'micrographs_ctf_%06d.star'
# -------------------------- DEFINE param functions -----------------------
def _defineParams(self, form):
form.addSection(label='Input')
form.addParam('inputCTF', params.PointerParam,
pointerClass="SetOfCTF",
label='Input CTF',
help='Select set of CTF that you want to export.')
form.addParam('micrographSource', params.EnumParam,
choices=['used for CTF estimation', 'other'],
default=0, important=True,
display=params.EnumParam.DISPLAY_HLIST,
label='Micrographs source',
help='By default the micrograph used to create the'
'exported STAR files are those used for the CTF '
'estimation. You can selected *other* to use a '
'different set of micrographs (e.g., dose weighted)')
form.addParam('inputMicrographs', params.PointerParam,
pointerClass='SetOfMicrographs',
condition='micrographSource == 1',
important=True, label='Input micrographs',
help='Select the SetOfMicrographs from which to extract.')
form.addParallelSection(threads=0, mpi=0)
# -------------------------- INSERT steps functions -----------------------
def _insertAllSteps(self):
self._insertFunctionStep('writeCtfStarStep')
[docs] def writeCtfStarStep(self):
pwutils.cleanPath(self._getExportPath())
pwutils.makePath(self._getExportPath())
inputCTF = self.inputCTF.get()
if self.micrographSource == 0: # same as CTF estimation
ctfMicSet = inputCTF.getMicrographs()
else:
ctfMicSet = self.inputMicrographs.get()
micSet = SetOfMicrographs(filename=':memory:')
psd = inputCTF.getFirstItem().getPsdFile()
hasPsd = psd and os.path.exists(psd)
if hasPsd:
psdPath = self._getExportPath('PSD')
pwutils.makePath(psdPath)
print("Writing PSD files to %s" % psdPath)
for ctf in inputCTF:
# Get the corresponding micrograph
mic = ctfMicSet[ctf.getObjId()]
if mic is None:
print("Skipping CTF id: %s, it is missing from input "
"micrographs. " % ctf.getObjId())
continue
micFn = mic.getFileName()
if not os.path.exists(micFn):
print("Skipping micrograph %s, it does not exists. " % micFn)
continue
mic2 = mic.clone()
mic2.setCTF(ctf)
if hasPsd:
psdFile = ctf.getPsdFile()
newPsdFile = os.path.join(psdPath,
'%s_psd.mrc' % pwutils.removeExt(mic.getMicName()))
if not os.path.exists(psdFile):
print("PSD file %s does not exits" % psdFile)
print("Skipping micrograph %s" % micFn)
continue
pwutils.copyFile(psdFile, newPsdFile)
# PSD path is relative to Export dir
newPsdFile = os.path.relpath(newPsdFile, self._getExportPath())
ctf.setPsdFile(newPsdFile)
else:
# remove pointer to non-existing psd file
ctf.setPsdFile(None)
micSet.append(mic2)
print("Writing set: %s to: %s" % (inputCTF, self._getStarFile()))
micDir = self._getExportPath('Micrographs')
pwutils.makePath(micDir)
starWriter = convert.createWriter(rootDir=self._getExportPath(),
outputDir=micDir,
useBaseName=True)
starWriter.writeSetOfMicrographs(micSet, self._getStarFile())
# -------------------------- INFO functions -------------------------------
def _summary(self):
summary = []
if os.path.exists(self._getStarFile()):
summary.append("Output is written to: \n%s\n" %
os.path.abspath(self._getExportPath()))
summary.append("Pixel size: *%0.3f*" % self._getPixelSize())
else:
summary.append("No output generated yet.")
return summary
# --------------------------- UTILS functions -----------------------------
def _getExportPath(self, *paths):
return os.path.join(self._getPath('Export'), *paths)
def _getStarFile(self):
return self._getExportPath(self.CTF_STAR_FILE % self.getObjId())
def _getPixelSize(self):
if self.micrographSource == 0: # same as CTF estimation
ctfMicSet = self.inputCTF.get().getMicrographs()
else:
ctfMicSet = self.inputMicrographs.get()
return ctfMicSet.getSamplingRate()