# **************************************************************************
# *
# * Authors: Roberto Marabini (roberto@cnb.csic.es)
# *
# * 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'
# *
# **************************************************************************
import os
from pyworkflow.protocol.constants import STEPS_PARALLEL
from pyworkflow.protocol.params import IntParam
from pyworkflow import VERSION_1_1
from pwem.objects import Image
from pwem.protocols import ProtProcessParticles
import pwem.emlib.metadata as md
from pwem.emlib import *
from xmipp3.convert import xmippToLocation
[docs]class XmippProtWriteTestP(ProtProcessParticles):
"""
using mpi write data to a large file (python level)
"""
_label = None
_lastUpdateVersion = VERSION_1_1
def __init__(self, *args, **kwargs):
ProtProcessParticles.__init__(self, *args, **kwargs)
self.stepsExecutionMode = STEPS_PARALLEL
#--------------------------- DEFINE param functions --------------------------------------------
def _defineParams(self, form):
form.addSection(label='Size is important')
form.addParam('xDim', IntParam, default=128,label='X dimension')
form.addParam('yDim', IntParam, default=128,label='Y dimension')
form.addParam('nframes', IntParam, default=1024,label='Number of frames')
form.addParallelSection(threads=1, mpi=4)
#--------------------------- INSERT steps functions --------------------------------------------
def _insertAllSteps(self):
stepId = self._insertFunctionStep('createReferenceStep')
pre=[]
for counter in range(self.nframes.get(),0,-1):
wid = self._insertFunctionStep('testWriteStep', counter, prerequisites=[stepId] )
pre.append(wid)
self._insertFunctionStep('testWriteValidate', prerequisites=pre)
[docs] def createReferenceStep(self):
img = Image()
img.setDataType(DT_FLOAT)
img.resize(self.xDim.get(), self.yDim.get())
img.initConstant(1.)
img.write(self._getExtraPath("reference.mrc"))
img.write('%d@%s' % (self.nframes, self._getExtraPath('kk.mrcs')))
[docs] def testWriteStep(self, counter):
params = ' -i reference.mrc '
params += ' -o %d@kk.mrcs' %counter
params += ' --mult %d' % counter
#change to directory
nproc = self.numberOfMpi.get()
#nT=self.numberOfThreads.get()
self.runJob('xmipp_image_operate', params, numberOfMpi=1,
cwd=self._getExtraPath())
[docs] def testWriteValidate(self):
img = Image()
for counter in range(self.nframes.get(),0,-1):
img.read("%d@%s"%(counter,os.path.join(self._getExtraPath(),"kk.mrcs")))
mean, dev, min, max = img.computeStats()
if (min == max) and (min == counter) and (dev == 0):
print("frame %d ok" % counter)
else:
print("frame %d no OK mean dev, min max" % counter, mean,dev,min,max)
break
#--------------------------- INFO functions --------------------------------------------
def _validate(self):
pass
def _summary(self):
pass
def _methods(self):
messages = []
return messages
def _citations(self):
return ['Vargas2014a']
#--------------------------- UTILS functions --------------------------------------------
def _updateLocation(self, item, row):
index, filename = xmippToLocation(row.getValue(md.MDL_IMAGE))
item.setLocation(index, filename)