# **************************************************************************
# * Authors: Mohamad Harastani (mohamad.harastani@upmc.fr)
# *
# * 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 ProtAnalysis3D
import xmipp3.convert
import pwem.emlib.metadata as md
import pyworkflow.protocol.params as params
from pyworkflow.utils.path import makePath, copyFile
from os.path import basename, isfile
from .utilities.spider_files3 import save_volume, open_volume
from pyworkflow.utils import replaceBaseExt
import numpy as np
from pwem.utils import runProgram
from pwem.emlib.image import ImageHandler
# TODO: return the matching histograms once conflics with pillow are solved
#from skimage.exposure import match_histograms
[docs]class FlexProtHistogramMatch(ProtAnalysis3D):
""" Protocol for volume histogram matching. """
_label = 'histogram matching'
# --------------------------- DEFINE param functions --------------------------------------------
def _defineParams(self, form):
form.addSection(label='Input')
form.addParam('inputVolumes', params.PointerParam,
pointerClass='SetOfVolumes,Volume',
label="Input volume(s)", important=True,
help='Select a volume of a set of volumes')
form.addParam('reference', params.PointerParam,
pointerClass='Volume',
label="Reference volume", important=True,
help='Select a reference volume')
# --------------------------- INSERT steps functions --------------------------------------------
def _insertAllSteps(self):
# Define some outputs filenames
self.imgsFn = self._getExtraPath('volumes.xmd')
makePath(self._getExtraPath() + '/histogram_matched')
self._insertFunctionStep('convertInputStep')
self._insertFunctionStep('doHistogramMatchingStep')
self._insertFunctionStep('createOutputStep')
# --------------------------- STEPS functions --------------------------------------------
[docs] def doHistogramMatchingStep(self):
# looping on all images and performing mwr
reference = self.reference.get().getFileName()
# xmipp convert to spider format just in case:
params = '-i ' + reference + ' -o ' + self._getExtraPath('reference.spi')
runProgram('xmipp_image_convert', params)
ref = ImageHandler().read(self._getExtraPath('reference.spi')).getData()
ref = np.squeeze(ref)
mdImgs = md.MetaData(self._getExtraPath('input.xmd'))
for objId in mdImgs:
imgPath = mdImgs.getValue(md.MDL_IMAGE, objId)
index, fname = xmipp3.convert.xmippToLocation(imgPath)
new_imgPath = self._getExtraPath() + '/histogram_matched/'
if index: # case of stack
new_imgPath += str(index).zfill(6) + '.spi'
else:
new_imgPath += basename(replaceBaseExt(basename(imgPath), 'spi'))
# Get a copy of the volume converted to spider format
temp_path = self._getTmpPath('temp.spi')
# params = '-i ' + imgPath + ' -o ' + new_imgPath + ' --type vol'
params = '-i ' + imgPath + ' -o ' + temp_path + ' --type vol'
runProgram('xmipp_image_convert', params)
# perform the mwr:
# in case the file exists (continuing or injecting)
if (isfile(new_imgPath)):
continue
else:
v = ImageHandler().read(temp_path).getData()
v = np.squeeze(v)
# TODO: return mathcing histograms
#map = match_histograms(v, ref)
#save_volume(np.float32(map), new_imgPath)
# update the name in the metadata file
mdImgs.setValue(md.MDL_IMAGE, new_imgPath, objId)
mdImgs.write(self.imgsFn)
[docs] def createOutputStep(self):
partSet = self._createSetOfVolumes('histogram_matched')
xmipp3.convert.readSetOfVolumes(self._getExtraPath('volumes.xmd'), partSet)
partSet.setSamplingRate(self.inputVolumes.get().getSamplingRate())
self._defineOutputs(HistogramMatched=partSet)
# --------------------------- INFO functions --------------------------------------------
def _summary(self):
summary = []
return summary
def _citations(self):
return ['']
def _methods(self):
pass
# --------------------------- UTILS functions --------------------------------------------
def _printWarnings(self, *lines):
""" Print some warning lines to 'warnings.xmd',
the function should be called inside the working dir."""
fWarn = open("warnings.xmd", 'w')
for l in lines:
print >> fWarn, l
fWarn.close()