# -*- coding: utf-8 -*-
# **************************************************************************
# *
# * Authors: Estrella Fernandez Gimenez (me.fernandez@cnb.csic.es)
# *
# * BCU, 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.objects.data import Volume
from pwem.protocols import EMProtocol
from pyworkflow.protocol.params import FloatParam, TextParam
[docs]class XmippProtPhantom(EMProtocol):
""" Create phantom volume from a feature description file using xmipp_phantom_create """
_label = 'phantom volume'
# --------------------------- DEFINE param functions ------------------------
def _defineParams(self, form):
form.addSection(label='Input')
form.addParam('desc', TextParam, label='Create phantom',
default='40 40 40 0\ncyl + 1 0 0 0 15 15 2 0 0 0\nsph + 1 0 0 5 2\ncyl + 1 0 0 -5 2 2 10 0 90 0\n'
'sph + 1 0 -5 5 2',
help="create a phantom description: x y z backgroundValue geometry(cyl, sph...) +(superimpose) "
"desnsityValue origin radius height rot tilt psi. See more information in "
"https://web.archive.org/web/20180813105422/http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/FileFormats#Phantom_metadata_file")
form.addParam('sampling', FloatParam, label='Sampling rate', default=4)
# --------------------------- INSERT steps functions --------------------------------------------
def _insertAllSteps(self):
self._insertFunctionStep('createPhantomsStep')
self._insertFunctionStep('createOutputStep')
# --------------------------- STEPS functions --------------------------------------------
[docs] def createPhantomsStep(self):
desc = self.desc.get()
fnDescr = self._getExtraPath("phantom.descr")
fhDescr = open(fnDescr, 'w')
fhDescr.write(desc)
fhDescr.close()
self.runJob("xmipp_phantom_create", " -i %s -o %s" % (fnDescr, self._getExtraPath("phantom.vol")))
[docs] def createOutputStep(self):
outputVol = Volume()
outputVol.setLocation(self._getExtraPath("phantom.vol"))
outputVol.setSamplingRate(self.sampling.get())
self._defineOutputs(outputVolume=outputVol)
# --------------------------- INFO functions --------------------------------------------
def _summary(self):
summary = []
if not hasattr(self, 'outputVolume'):
summary.append("Output phantom not ready yet.")
else:
summary.append("Phantoms created")
return summary