# **************************************************************************
# *
# * Authors: David Herreros Calero (dherreros@cnb.csic.es) [1]
# *
# * [1] Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * 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'
# *
# **************************************************************************
from pwem.protocols import EMProtocol
from pyworkflow import BETA
import pyworkflow.utils as pwutils
from pyworkflow.protocol.params import PointerParam, IntParam
from pyworkflow.utils.properties import Message
from tomo.protocols import ProtTomoBase
import emantomo
[docs]class EmanProtTomoResize(ProtTomoBase, EMProtocol):
""" Tomogram resize using e2proc3d """
_label = 'resize tomos'
_devStatus = BETA
def __init__(self, **kwargs):
EMProtocol.__init__(self, **kwargs)
# --------------------------- DEFINE param functions ----------------------
def _defineParams(self, form):
form.addSection(label='Input')
form.addParam('inputTomograms', PointerParam,
pointerClass='SetOfTomograms',
label="Input tomograms", important=True,
help='Select the tomograms to be resized')
form.addParam('xDim', IntParam, important=True, label="New X dimension",
help='Select the new X dimension for the Tomogram')
form.addParam('yDim', IntParam, important=True, label="New Y dimension",
help='Select the new Y dimension for the Tomogram')
form.addParam('zDim', IntParam, important=True, label="New Z dimension",
help='Select the new Z dimension for the Tomogram')
# --------------------------- STEPS functions -----------------------------
def _insertAllSteps(self):
self._insertFunctionStep(self.resizeTomograms)
self._insertFunctionStep(self.createOutputStep)
[docs] def resizeTomograms(self):
program = emantomo.Plugin.getProgram("e2proc3d.py")
xDim = self.xDim.get()
yDim = self.yDim.get()
zDim = self.zDim.get()
for tomo in self.inputTomograms.get().iterItems():
tomo_file = tomo.getFileName()
out_file = self._getExtraPath(pwutils.removeBaseExt(tomo_file) + ".mrc")
args = "%s %s --process normalize --clip %d,%d,%d" \
% (tomo_file, out_file, xDim, yDim, zDim)
pwutils.runJob(None, program, args, env=emantomo.Plugin.getEnviron())
[docs] def createOutputStep(self):
input_tomos = self.inputTomograms.get()
sr = input_tomos.getSamplingRate()
out_tomos = self._createSetOfTomograms()
out_tomos.copyInfo(input_tomos)
out_tomos.setSamplingRate(sr)
for tomo in input_tomos.iterItems():
out_tomo = tomo.clone()
tomo_file = self._getExtraPath(pwutils.removeBaseExt(tomo.getFileName()) + ".mrc")
out_tomo.setFileName(tomo_file)
out_tomo.setSamplingRate(sr)
out_tomos.append(out_tomo)
self._defineOutputs(resizedTomograms=out_tomos)
self._defineSourceRelation(self.inputTomograms, out_tomos)
# --------------------------- INFO functions -----------------------------
def _methods(self):
methodsMsgs = []
methodsMsgs.append("Tomogram resizing by e2proc3d.")
return methodsMsgs
def _summary(self):
summary = []
if self.getOutputsSize() < 1:
summary.append(Message.TEXT_NO_OUTPUT_CO)
else:
summary.append("A total of %d Tomograms were resized to dimensions (%d,%d,%d)"
% (self.resizedTomograms.getSize(), self.xDim.get(),
self.yDim.get(), self.zDim.get()))
return summary