# -*- coding: utf-8 -*-
# **************************************************************************
# *
# * Authors: Scipion Team
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# * National Center of Biotechnology, CSIC, Spain
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# * 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
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# * All comments concerning this program package may be sent to the
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from collections import OrderedDict
from os.path import basename, join, abspath
import xml.etree.ElementTree as ET
from pwem.protocols import EMProtocol
from pyworkflow import BETA
from pyworkflow.protocol import FloatParam, NumericListParam, EnumParam, PointerParam
from pyworkflow.utils import Message, makePath, removeBaseExt, copyFile
from scipion.constants import PYTHON
from tomo.protocols import ProtTomoBase
from tomo.protocols.protocol_base import ProtTomoImportAcquisition
from pyseg import Plugin
from pyseg.constants import FILS_SCRIPT, FILS_SOURCES, FILS_TARGETS, MEMBRANE, \
MEMBRANE_OUTER_SURROUNDINGS, PRESEG_AREAS_LIST
from pyseg.utils import encodePresegArea
TH_MODE_IN = 0
TH_MODE_OUT = 1
# Fils sources xml fields
SEG_LABEL_S = 'segLabelS'
MIN_EUC_DIST_S = 'minEucDistS'
MAX_EUC_DIST_S = 'maxEucDistS'
EUC_RANGE_S = 'eucRangeS'
MIN_GEO_DIST_S = 'minGeoDistS'
MAX_GEO_DIST_S = 'maxGeoDistS'
GEO_RANGE_S = 'geoDistRangeS'
MIN_GEO_LEN_S = 'minGeoLenS'
MAX_GEO_LEN_S = 'maxGeoLenS'
GEO_LEN_RANGE_S = 'geoLenRangeS'
MIN_FIL_SINU_S = 'minSinuS'
MAX_FIL_SINU_S = 'maxSinuS'
SINU_RANGE_S = 'sinurangeS'
# Fils targets xml fields
SEG_LABEL_T = 'segLabelT'
MIN_EUC_DIST_T = 'minEucDistT'
MAX_EUC_DIST_T = 'maxEucDistT'
EUC_RANGE_T = 'eucRangeT'
MIN_GEO_DIST_T = 'minGeoDistT'
MAX_GEO_DIST_T = 'maxGeoDistT'
GEO_RANGE_T = 'geoDistRangeT'
MIN_GEO_LEN_T = 'minGeoLenT'
MAX_GEO_LEN_T = 'maxGeoLenT'
GEO_LEN_RANGE_T = 'geoLenRangeT'
MIN_FIL_SINU_T = 'minSinuT'
MAX_FIL_SINU_T = 'maxSinuT'
SINU_RANGE_T = 'sinurangeT'
[docs]class ProtPySegFils(EMProtocol, ProtTomoBase, ProtTomoImportAcquisition):
"""filter a MbGraphMCF (Mean Cumulative Function) object by extracting a filament network"""
_label = 'fils'
_devStatus = BETA
_xmlSources = None
_xmlTargets = None
# -------------------------- DEFINE param functions ----------------------
def _defineParams(self, form):
""" Define the input parameters that will be used.
Params:
form: this is the form to be populated with sections and params.
"""
# You need a params to belong to a section:
form.addSection(label=Message.LABEL_INPUT)
form.addParam('inGraphsProt', PointerParam,
pointerClass='ProtPySegGraphs',
label='Graphs',
important=True,
allowsNull=False,
help='Pointer to graphs protocol.')
form.addSection(label='Sources')
self._defineFilsXMLParams(form, self._getXMLSourcesDefaultVals())
form.addSection(label='Targets')
self._defineFilsXMLParams(form, self._getXMLTargetsDefaultVals(), isSources=False)
form.addSection(label='Refinement')
group = form.addGroup('Graph thresholding')
group.addParam('thMode', EnumParam,
default=TH_MODE_IN,
choices=['in', 'out'],
label='Orientation with respect to the membrane/filament',
display=EnumParam.DISPLAY_HLIST)
group = form.addGroup('Filament geometry refinement')
group.addParam('gRgEud', NumericListParam,
label='Euclidean distance of vertices source-target (nm)',
default='1 1000',
allowsNull=False,
help='Euclidean distance between source and target vertices in nm.')
group.addParam('gRgLen', NumericListParam,
label='Geodesic distance of vertices source-target (nm)',
default='1 1000',
allowsNull=False,
help='Geodesic distance trough the graph between source and target vertices in nm.')
group.addParam('gRgSin', NumericListParam,
label='Filament sinuosity',
default='0 1000',
allowsNull=False,
help='Filament sinuosity, geodesic/euclidean distances ratio.')
@staticmethod
def _defineFilsXMLParams(form, d, isSources=True):
"""d is a disctionary with the default values"""
sectionName = 'Sources - ' if isSources else 'Targets - '
paramList = list(d.keys())
valList = list(d.values())
form.addParam(paramList[0], EnumParam,
choices=PRESEG_AREAS_LIST,
label='Filament area',
default=valList[0],
allowsNull=False,
help='Source or destination (depending if you are in the Sources or Targets tab) '
'area for the filament calculation.')
group = form.addGroup('%sEuclidean distance to membrane (nm)' % sectionName)
group.addParam(paramList[1], FloatParam,
label='Min',
default=valList[1],
allowsNull=False)
group.addParam(paramList[2], FloatParam,
label='Max',
default=valList[2],
allowsNull=False)
group.addParam(paramList[3], EnumParam,
default=valList[3],
choices=['[min, max]', '[-inf, min] U [max, +inf]'],
label='range',
display=EnumParam.DISPLAY_HLIST)
group = form.addGroup('%sGeodesic distance to membrane (nm)' % sectionName)
group.addParam(paramList[4], FloatParam,
label='Min',
default=valList[4],
allowsNull=False)
group.addParam(paramList[5], FloatParam,
label='Max',
default=valList[5],
allowsNull=False)
group.addParam(paramList[6], EnumParam,
default=valList[6],
choices=['[min, max]', '[-inf, min] U [max, +inf]'],
label='range',
display=EnumParam.DISPLAY_HLIST)
group = form.addGroup('%sGeodesic length to membrane (nm)' % sectionName)
group.addParam(paramList[7], FloatParam,
label='Min',
default=valList[7],
allowsNull=False)
group.addParam(paramList[8], FloatParam,
label='Max',
default=valList[8],
allowsNull=False)
group.addParam(paramList[9], EnumParam,
default=valList[9],
choices=['[min, max]', '[-inf, min] U [max, +inf]'],
label='range',
display=EnumParam.DISPLAY_HLIST)
group = form.addGroup('%sFilament sinuosity' % sectionName)
group.addParam(paramList[10], FloatParam,
label='Min',
default=valList[10],
allowsNull=False)
group.addParam(paramList[11], FloatParam,
label='Max',
default=valList[11],
allowsNull=False)
group.addParam(paramList[12], EnumParam,
default=valList[12],
choices=['[min, max]', '[-inf, min] U [max, +inf]'],
label='range',
display=EnumParam.DISPLAY_HLIST)
def _insertAllSteps(self):
self._insertFunctionStep(self.pysegFils)
[docs] def pysegFils(self):
# Generate output dir
outDir = self._getExtraPath()
makePath(outDir)
# Generate sources xml
self._createFilsXmlFile(Plugin.getHome(FILS_SOURCES), outDir)
# Generate targets xml
self._createFilsXmlFile(Plugin.getHome(FILS_TARGETS), outDir, isSource=False)
# Script called
Plugin.runPySeg(self, PYTHON, self._getFilsCommand(outDir))
# --------------------------- INFO functions -----------------------------------
def _summary(self):
""" Summarize what the protocol has done"""
summary = []
if self.isFinished():
summary.append('*Filaments calculation*:\n\t- Source = %s\n\t- Target = %s\n' %
(PRESEG_AREAS_LIST[int(self.segLabelS.get())], PRESEG_AREAS_LIST[int(self.segLabelT.get())]))
return summary
# --------------------------- UTIL functions -----------------------------------
def _getFilsCommand(self, outDir):
filsCmd = ' '
filsCmd += '%s ' % Plugin.getHome(FILS_SCRIPT)
filsCmd += '--inStar %s ' % self._getGraphsStarFile()
filsCmd += '--outDir %s ' % outDir
filsCmd += '--inSources %s ' % abspath(self._xmlSources)
filsCmd += '--inTargets %s ' % abspath(self._xmlTargets)
filsCmd += '--thMode %s ' % self._parseThModeSelection()
filsCmd += '--gRgLen %s ' % self.gRgLen.get()
filsCmd += '--gRgSin %s ' % self.gRgSin.get()
filsCmd += '--gRgEud %s ' % self.gRgEud.get()
return filsCmd
def _getGraphsStarFile(self):
prot = self.inGraphsProt.get()
return prot._getExtraPath(removeBaseExt(prot._getPreSegStarFile()) + '_mb_graph.star')
def _parseThModeSelection(self):
if self.thMode.get() == TH_MODE_IN:
return 'in'
else:
return 'out'
@staticmethod
def _getXMLSourcesDefaultVals():
d = OrderedDict()
d[SEG_LABEL_S] = MEMBRANE
d[MIN_EUC_DIST_S] = 0
d[MAX_EUC_DIST_S] = 15
d[EUC_RANGE_S] = 0
d[MIN_GEO_DIST_S] = 0
d[MAX_GEO_DIST_S] = float('inf')
d[GEO_RANGE_S] = 0
d[MIN_GEO_LEN_S] = 0
d[MAX_GEO_LEN_S] = 45
d[GEO_LEN_RANGE_S] = 0
d[MIN_FIL_SINU_S] = 0
d[MAX_FIL_SINU_S] = 3
d[SINU_RANGE_S] = 0
return d
@staticmethod
def _getXMLTargetsDefaultVals():
d = OrderedDict()
d[SEG_LABEL_T] = MEMBRANE_OUTER_SURROUNDINGS
d[MIN_EUC_DIST_T] = 0
d[MAX_EUC_DIST_T] = 15
d[EUC_RANGE_T] = 0
d[MIN_GEO_DIST_T] = 0
d[MAX_GEO_DIST_T] = float('inf')
d[GEO_RANGE_T] = 0
d[MIN_GEO_LEN_T] = 0
d[MAX_GEO_LEN_T] = 45
d[GEO_LEN_RANGE_T] = 0
d[MIN_FIL_SINU_T] = 0
d[MAX_FIL_SINU_T] = 3
d[SINU_RANGE_T] = 0
return d
def _createFilsXmlFile(self, templateFile, outDir, isSource=True):
EUCLIDEAN_DIST = 'eu_dst'
GEODESIC_DIST = 'geo_dst'
GEODESIC_LEN = 'geo_len'
FIL_SINU = 'sin'
# Copy the template xml to extra
filename = join(outDir, basename(templateFile))
copyFile(templateFile, filename)
# Prepare the data to be read as expected by the xml file
geomDict = OrderedDict()
if isSource:
self._xmlSources = filename
segLabel = encodePresegArea(self.segLabelS.get())
geomDict[EUCLIDEAN_DIST] = [MIN_EUC_DIST_S, MAX_EUC_DIST_S, EUC_RANGE_S]
geomDict[GEODESIC_DIST] = [MIN_GEO_DIST_S, MAX_GEO_DIST_S, GEO_RANGE_S]
geomDict[GEODESIC_LEN] = [MIN_GEO_LEN_S, MAX_GEO_LEN_S, GEO_LEN_RANGE_S]
geomDict[FIL_SINU] = [MIN_FIL_SINU_S, MAX_FIL_SINU_S, SINU_RANGE_S]
else:
self._xmlTargets = filename
segLabel = encodePresegArea(self.segLabelT.get())
geomDict[EUCLIDEAN_DIST] = [MIN_EUC_DIST_T, MAX_EUC_DIST_T, EUC_RANGE_T]
geomDict[GEODESIC_DIST] = [MIN_GEO_DIST_T, MAX_GEO_DIST_T, GEO_RANGE_T]
geomDict[GEODESIC_LEN] = [MIN_GEO_LEN_T, MAX_GEO_LEN_T, GEO_LEN_RANGE_T]
geomDict[FIL_SINU] = [MIN_FIL_SINU_T, MAX_FIL_SINU_T, SINU_RANGE_S]
# Edit the corresponding fields
xmlTree = ET.parse(filename)
rootElement = xmlTree.getroot()
mb_slice = rootElement.findall("mb_slice")
mb_slice = mb_slice[0]
mb_slice.find('side').text = str(segLabel)
for key, valList in geomDict.items():
for el in mb_slice.findall(key):
if el.attrib['id'] == 'low':
el.text = str(getattr(self, valList[0]).get())
elif el.attrib['id'] == 'high':
el.text = str(getattr(self, valList[1]).get())
elif el.attrib['id'] == 'sign':
el.text = self._decodeRangeValue(getattr(self, valList[2]).get())
# Write the modified xml file.
xmlTree.write(filename, encoding='UTF-8', xml_declaration=True)
@staticmethod
def _decodeRangeValue(val):
"""Decode the range values and represent them as expected by pySeg"""
# Choices are:
# 0 --> [min, max], expected as '+'
# 1 --> [-inf, min] U [max, +inf]'], expected as any other thing
return '+' if val == 0 else '-'