# This software and supporting documentation are distributed by
# Institut Federatif de Recherche 49
# CEA/NeuroSpin, Batiment 145,
# 91191 Gif-sur-Yvette cedex
# France
#
# This software is governed by the CeCILL license version 2 under
# French law and abiding by the rules of distribution of free software.
# You can use, modify and/or redistribute the software under the
# terms of the CeCILL license version 2 as circulated by CEA, CNRS
# and INRIA at the following URL "http://www.cecill.info".
#
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# modify and redistribute granted by the license, users are provided only
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# software by the user in light of its specific status of free software,
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# The fact that you are presently reading this means that you have had
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from __future__ import absolute_import
import os
import shutil
from brainvisa.processes import *
from brainvisa import anatomist
from brainvisa.processing.qtgui.neuroProcessesGUI import mainThreadActions
from soma.qt_gui.qtThread import MainThreadLife
import threading
import os
name = 'Label volume editor'
roles = ('editor',)
userLevel = 0
def validation():
anatomist.validation()
signature = Signature(
'label_volume', WriteDiskItem('Label volume',
'Aims writable volume formats'),
'support_volume', ReadDiskItem('Raw T1 MRI',
'Anatomist volume formats',
exactType=True),
'pipeline_mask_nomenclature', ReadDiskItem('Nomenclature', 'Hierarchy'),
'background_label', OpenChoice('minimum'),
)
def initialization(self):
self.linkParameters('support_volume', 'label_volume', self.linkSupportVolume)
self.pipeline_mask_nomenclature = self.signature['pipeline_mask_nomenclature'].findValue(
{"filename_variable": "pipeline_masks"}, requiredAttributes={"filename_variable": "pipeline_masks"})
self.setOptional('pipeline_mask_nomenclature')
self.setOptional('support_volume')
def linkSupportVolume(self, *args):
"""Find a T1 that is guaranteed to be from the same acquisition."""
label_vol_attrs = self.label_volume.hierarchyAttributes()
required_attrs = {
'center': label_vol_attrs.get('center'),
'subject': label_vol_attrs.get('subject'),
'acquisition': label_vol_attrs.get('acquisition'),
}
if 'normalization' in label_vol_attrs:
required_attrs['normalization'] = label_vol_attrs['normalization']
if None in required_attrs.values():
# Give up: findValue could match anything, including images from a
# different subject
return None
wdi = self.signature['support_volume']
return wdi.findValue(self.label_volume,
requiredAttributes=required_attrs)
def add_save_button(self, win):
if neuroConfig.anatomistImplementation == 'socket':
return None # cannot add buttons via socket API
from soma.wip.application.api import findIconFile
from soma.qt_gui.qt_backend import QtGui, QtCore
toolbar = win.findChild(QtGui.QToolBar, 'mutations')
if toolbar is None:
toolbar = win.findChild(QtGui.QToolBar)
if toolbar is None:
toolbar = win.addToolBar('BV toolbar')
if win.toolBarsVisible():
toolbar.show()
if toolbar is not None:
toolbar.addSeparator()
icon = QtGui.QIcon(findIconFile('save.png'))
ac = QtGui.QAction(icon,
win.tr('Save ROI', 'QAWindow'), win.getInternalRep())
toolbar.addAction(ac)
data = self.data.ref()
ac.triggered.connect(data.save_roi)
data.win_deleted = False
win.getInternalRep().destroyed.connect(data.close_and_save)
return ac
# def remove_save_button(self, win, ac):
# if neuroConfig.anatomistImplementation == 'socket':
# return None # cannot add buttons via socket API
# from soma.wip.application.api import findIconFile
# from soma.qt_gui.qt_backend import QtGui, QtCore
# toolbar = win.findChild( QtGui.QToolBar, 'mutations' )
# if toolbar is None:
# toolbar = win.findChild( QtGui.QToolBar )
# if toolbar is None:
# toolbar = win.addToolBar( 'BV toolbar' )
# if win.toolBarsVisible():
# toolbar.show()
# if toolbar is not None:
# import sip
# sip.transferbacck(ac)
class EditData:
glob_lock = threading.RLock()
edited_data = set()
def __del__(self):
self.close_and_save(self.window)
def close_and_save(self, win):
self.save_roi()
self.win_deleted = True
if self.label_volume is not None:
with self.glob_lock:
self.edited_data.remove(self.label_volume.fullPath())
self.label_volume = None
self.tmpdir = None
self.context = None
self.voigraph = None
self.window = None
self.fgraphbase = None
self.finalgraph = None
self.voigraphnum = None
self.ana_objects = None
def save_roi(self, message=None):
data = self
if self.win_deleted:
return # nothing to do
context = data.context
if not isinstance(message, str) or not message:
message = 'Save ROI {0} ?'.format(data.label_volume)
modified = (os.stat(data.label_volume.fullPath()).st_mtime
!= data.m_date)
if modified:
message += '
WARNING: the file ' \
'has been modified after it has been loaded, thus saving it ' \
'may overwrite other modifications !'
rep = context.ask(message, "OK", "Cancel", modal=0)
if rep != 1:
data.voigraphnum.save(data.voigraph)
a = anatomist.Anatomist()
a.sync()
# make sure that anatomist has finished to process previous
# commands
# a.getInfo()
context.system('AimsGraphConvert',
'-i', data.voigraph,
'-o', data.finalgraph,
'--volume')
if self.background_label != 'minimum':
val = self.background_label
else:
val = 0
context.system('AimsReplaceLevel', '-i',
os.path.join(
data.fgraphbase + '.data', 'roi_Volume'), '-o',
data.label_volume, '-g', -1, '-n', val)
shutil.rmtree(os.path.join(self.fgraphbase + '.data'))
os.unlink(self.finalgraph)
# update loaded date
data.m_date = os.stat(data.label_volume.fullPath()).st_mtime
def execution(self, context):
data = EditData()
already_edited = False
with data.glob_lock:
if self.label_volume.fullPath() in data.edited_data:
already_edited = True
data.edited_data.add(self.label_volume.fullPath())
if already_edited:
raise RuntimeError(
'The file {0} is already edited in another editor in the same '
'BrainVisa/Anatomist session.'.format(
self.label_volume.fullPath()))
self.data = MainThreadLife(data)
data.m_date = os.stat(self.label_volume.fullPath()).st_mtime
a = anatomist.Anatomist()
ana_objects = []
if self.pipeline_mask_nomenclature is not None:
hie = a.loadObject(self.pipeline_mask_nomenclature)
ana_objects.append(hie)
if self.background_label != 'minimum':
mask = context.temporary('GIS image', 'Label Volume')
context.write('not min')
context.system('AimsReplaceLevel', '-i', self.label_volume, '-o', mask,
'-g', int(self.background_label), '-g', -
32767, '-n', -32767, '-n',
-32766)
else:
mask = self.label_volume
if self.support_volume:
vol = self.support_volume
else:
vol = mask
tmpdir = context.temporary('directory')
voigraphname = os.path.basename(self.label_volume.fullName())
voigraph = os.path.join(tmpdir.fullPath(), '{0}.arg'.format(voigraphname))
fgraphbase = os.path.join(tmpdir.fullPath(),
'finalgraph_{0}'.format(voigraphname))
finalgraph = fgraphbase + '.arg'
context.system('AimsGraphConvert',
'-i', mask.fullPath(),
'-o', voigraph,
'--bucket')
imagenum = a.loadObject(vol)
ana_objects.append(imagenum)
voigraphnum = a.loadObject(voigraph)
ref = imagenum.referential
if ref != a.centralRef:
voigraphnum.assignReferential(ref)
windownum = a.createWindow('Axial')
windownum.assignReferential(ref)
else:
windownum = a.createWindow('Axial')
a.addObjects(objects=[voigraphnum, imagenum], windows=[windownum])
voigraphnum.setMaterial(a.Material(diffuse=[0.8, 0.8, 0.8, 0.5]))
# selects the graph
children = voigraphnum.children
windownum.group.addToSelection(children)
if len(children) > 1:
windownum.group.unSelect(children[1:])
del children
a.execute('SetControl', windows=[windownum], control='PaintControl')
windownum.showToolbox(True)
data.tmpdir = tmpdir
data.label_volume = self.label_volume
data.context = context
data.voigraph = voigraph
data.window = windownum
data.fgraphbase = fgraphbase
data.finalgraph = finalgraph
data.voigraphnum = voigraphnum
data.background_label = self.background_label
data.ana_objects = ana_objects
data.win_deleted = False
ac = mainThreadActions().call(self.add_save_button, windownum)
res = self.data
del self.data
return res