# -*- coding: utf-8 -*-
# **************************************************************************
# *
#* Authors: Erney Ramirez-Aportela, eramirez@cnb.csic.es
# * Jose Luis Vilas, jlvilas@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'
# *
# **************************************************************************
from pyworkflow import VERSION_1_1
from pyworkflow.protocol.params import (PointerParam, FloatParam,
LEVEL_ADVANCED)
from pwem.protocols import ProtAnalysis3D
from pwem.emlib.image import ImageHandler
from pyworkflow.utils import getExt
from pwem.objects import Volume
import numpy as np
import os
import pwem.emlib.metadata as md
from pwem.emlib.metadata import (MDL_COST, MDL_ITER, MDL_SCALE)
from ntpath import dirname
from os.path import exists
LOCALDEBLUR_METHOD_URL='https://github.com/I2PC/scipion/wiki/XmippProtLocSharp'
[docs]class XmippProtLocSharp(ProtAnalysis3D):
"""
Given a resolution map the protocol calculate the sharpened map.
"""
_label = 'localdeblur sharpening'
_lastUpdateVersion = VERSION_1_1
def __init__(self, **args):
ProtAnalysis3D.__init__(self, **args)
# --------------------------- DEFINE param functions ----------------------
def _defineParams(self, form):
form.addSection(label='Input')
form.addParam('inputVolume', PointerParam, pointerClass='Volume',
label="Input Map", important=True,
help='Select a volume for sharpening.')
form.addParam('resolutionVolume', PointerParam, pointerClass='Volume',
label="Resolution Map", important=True,
help='Select a local resolution map.'
' LocalDeblur has been specially designed to work with'
' resolution maps obtained with MonoRes,'
' however resolution map from ResMap and BlocRes are also accepted.')
form.addParam('const', FloatParam, default=1,
expertLevel=LEVEL_ADVANCED,
label="lambda",
help='Regularization Param.'
'The method determines this parameter automatically.'
' This parameter is directly related to the convergence.'
' Increasing it would accelerate the convergence,'
' however it presents the risk of falling into local minima.')
form.addParam('K', FloatParam, default=0.025,
expertLevel=LEVEL_ADVANCED,
label="K",
help='K = 0.025 works well for all tested cases.'
' K should be in the 0.01-0.05 range.'
' For maps with FSC resolution lower than 6Å,'
' K = 0.01 can be a good alternative.')
form.addParallelSection(threads = 4, mpi = 0)
# --------------------------- INSERT steps functions --------------------------------------------
def _createFilenameTemplates(self):
""" Centralize how files are called """
myDict= {
'BINARY_MASK': self._getTmpPath('binaryMask.mrc'),
'OUTPUT_RESOLUTION_FILE': self._getTmpPath('monoresResolutionMap.mrc'),
'METADATA_PARAMS_SHARPENING': self._getTmpPath('params.xmd'),
}
self._updateFilenamesDict(myDict)
def _insertAllSteps(self):
self.iteration = 0
self._createFilenameTemplates()
self._insertFunctionStep('convertInputStep')
self._insertFunctionStep('checkBackgroundStep')
self._insertFunctionStep('createMaskStep')
self._insertFunctionStep('sharpeningAndMonoResStep')
self._insertFunctionStep('createOutputStep')
[docs] def checkBackgroundStep(self):
initRes=self.resolutionVolume.get().getFileName()
img = ImageHandler().read(initRes)
imgData = img.getData()
max_value = np.amax(imgData)
min_value = np.amin(imgData)
# print("minvalue %s y maxvalue %s" % (min_value, max_value))
if (min_value > 0.01):
params = ' -i %s' % self.resFn
params += ' -o %s' % self.resFn
params += ' --select above %f' % (max_value-1)
params += ' --substitute value 0'
self.runJob('xmipp_transform_threshold', params)
[docs] def createMaskStep(self):
params = ' -i %s' % self.resFn
params += ' -o %s' % self._getFileName('BINARY_MASK')
params += ' --select below %f' % 0.1
params += ' --substitute binarize'
self.runJob('xmipp_transform_threshold', params)
[docs] def MonoResStep(self, iter):
sampling = self.inputVolume.get().getSamplingRate()
if (iter == 1):
resFile = self.resolutionVolume.get().getFileName()
else:
resFile = self._getFileName('OUTPUT_RESOLUTION_FILE')
pathres=dirname(resFile)
img = ImageHandler().read(resFile)
imgData = img.getData()
max_res = np.amax(imgData)
significance = 0.95
mtd = md.MetaData()
if exists(os.path.join(pathres,'mask_data.xmd')):
mtd.read(os.path.join(pathres,'mask_data.xmd'))
radius = mtd.getValue(MDL_SCALE,1)
else:
xdim, _ydim, _zdim = self.inputVolume.get().getDim()
radius = xdim*0.5
params = ' --vol %s' % self._getExtraPath('sharpenedMap_'+str(iter)+'.mrc')
params += ' --mask %s' % self._getFileName('BINARY_MASK')
params += ' --sampling_rate %f' % sampling
params += ' --minRes %f' % (2*sampling)
params += ' --maxRes %f' % max_res
params += ' --step %f' % 0.25
params += ' -o %s' % self._getTmpPath()
params += ' --significance %f' % significance
params += ' --threads %i' % self.numberOfThreads.get()
self.runJob('xmipp_resolution_monogenic_signal', params)
[docs] def sharpenStep(self, iter):
sampling = self.inputVolume.get().getSamplingRate()
#params = ' --vol %s' % self.volFn
if (iter == 1):
params = ' --resolution_map %s' % self.resFn
else:
params = ' --resolution_map %s' % self._getFileName(
'OUTPUT_RESOLUTION_FILE')
params += ' --sampling %f' % sampling
params += ' -n %i' % self.numberOfThreads.get()
params += ' -k %f' % self.K
params += ' --md %s' % self._getFileName('METADATA_PARAMS_SHARPENING')
if (iter == 1 and self.const!=1):
params += ' -l %f' % self.const
if (iter == 1):
invol = ' --vol %s' % self.volFn
else:
invol = ' --vol %s' % self._getExtraPath('sharpenedMap_'+str(iter-1)+'.mrc')
params +=invol
self.runJob("xmipp_volume_local_sharpening -o %s"
%(self._getExtraPath('sharpenedMap_'+str(iter)+'.mrc')), params)
self.runJob("xmipp_image_header -i %s -s %f"
%(self._getExtraPath('sharpenedMap_'+str(iter)+'.mrc'), sampling), "")
[docs] def sharpeningAndMonoResStep(self):
last_Niters = -1
last_lambda_sharpening = 1e38
nextIter = True
while nextIter is True:
self.iteration = self.iteration + 1
# print("iteration")
print('\n====================\n'
'Iteration %s' % (self.iteration))
self.sharpenStep(self.iteration)
mtd = md.MetaData()
mtd.read(self._getFileName('METADATA_PARAMS_SHARPENING'))
lambda_sharpening = mtd.getValue(MDL_COST,1)
Niters = mtd.getValue(MDL_ITER,1)
# if (Niters == last_Niters):
# nextIter = False
# break
if (abs(lambda_sharpening - last_lambda_sharpening)<= 0.2):
nextIter = False
break
last_Niters = Niters
last_lambda_sharpening = lambda_sharpening
self.MonoResStep(self.iteration)
imageFile = self._getFileName('OUTPUT_RESOLUTION_FILE')
img = ImageHandler().read(imageFile)
imgData = img.getData()
max_res = np.amax(imgData)
min_res = 2*self.inputVolume.get().getSamplingRate()
if (max_res-min_res<0.75):
nextIter = False
break
os.rename(self._getExtraPath('sharpenedMap_' + str(self.iteration) + '.mrc'),
self._getExtraPath('sharpenedMap_last.mrc'))
resFile = self.resolutionVolume.get().getFileName()
pathres=dirname(resFile)
if not exists(self._getFileName('OUTPUT_RESOLUTION_FILE')):
print('\n====================\n'
' WARNING---This is not the ideal case because resolution map has been imported.'
' The ideal case is to calculate it previously'
' in the same project using MonoRes.'
'\n====================\n')
[docs] def createOutputStep(self):
volumesSet = self._createSetOfVolumes()
volumesSet.setSamplingRate(self.inputVolume.get().getSamplingRate())
for i in range(self.iteration):
vol = Volume()
vol.setOrigin(self.inputVolume.get().getOrigin(True))
if (self.iteration > (i + 1)):
vol.setLocation(i, self._getExtraPath('sharpenedMap_%d.mrc' % (i + 1)))
vol.setObjComment("Sharpened Map, \n Epoch %d" % (i + 1))
else:
vol.setLocation(i, self._getExtraPath('sharpenedMap_last.mrc'))
vol.setObjComment("Sharpened Map, \n Epoch last")
volumesSet.append(vol)
self._defineOutputs(outputVolumes=volumesSet)
self._defineSourceRelation(self.inputVolume, volumesSet)
# --------------------------- INFO functions ------------------------------
def _methods(self):
messages = []
if hasattr(self, 'sharpened_map'):
messages.append(
'Information about the method/article in ' + LOCALDEBLUR_METHOD_URL)
return messages
def _summary(self):
summary = []
summary.append("LocalDeblur Map")
return summary
def _citations(self):
return ['Ramirez-Aportela 2018']