#! /bin/env python
# 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".
#
# As a counterpart to the access to the source code and rights to copy,
# modify and redistribute granted by the license, users are provided only
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# economic rights, and the successive licensors have only limited
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# software by the user in light of its specific status of free software,
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import sys, os, weakref, gc, operator
from PyQt4.QtCore import Qt, QPoint, SIGNAL
from PyQt4.QtGui import QSplitter, QListWidget, QTextEdit, QApplication
import anatomist.direct.api as anatomist
from soma import aims
import matplotlib, numpy
matplotlib.use('Qt4Agg')
import pylab
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
class MeasuresWindow( QSplitter ):
def __init__( self, fileName, roiIterator=None, parent=None,
anatomistInstance=None ):
QSplitter.__init__( self, Qt.Horizontal, parent )
if anatomistInstance is None:
# initialize Anatomist
self.anatomist = anatomist.Anatomist()
else:
self.anatomist = anatomistInstance
# open an axial window
self.aWindow = self.anatomist.createWindow( 'Axial', no_decoration=True )
self.aWindow.setParent( self )
if roiIterator is not None:
self.roiList = QListWidget( self )
self.maskIterators = []
# Iterate on each region
while roiIterator.isValid():
self.roiList.addItem( roiIterator.regionName() )
maskIterator = roiIterator.maskIterator().get()
maskIterator.bucket = None
self.maskIterators.append( maskIterator )
roiIterator.next()
self.selectedBucket = None
self.connect( self.roiList, SIGNAL( 'currentRowChanged( int )' ), self.regionSelected )
else:
self.roiList = None
self.infoSplitter = QSplitter( Qt.Vertical, self )
self.info = QTextEdit( self.infoSplitter )
self.info.setReadOnly( True )
self.matplotFigure = Figure()
self.matplotAxes = self.matplotFigure.add_subplot(111)
# We want the axes cleared every time plot() is called
self.matplotAxes.hold(False)
self.matplotCanvas = FigureCanvas( self.matplotFigure )
self.matplotCanvas.setParent( self.infoSplitter )
self.matplotCanvas.updateGeometry()
self.anatomist.onCursorNotifier.add( self.clicked2 )
self.resize( 800, 600 )
# Read the image
dir, base = os.path.split( fileName )
if dir:
self.setWindowTitle( base + ' (' + dir + ')' )
else:
self.setWindowTitle( base )
# load any volume as a aims.Volume_* object
r = aims.Reader( {'Volume' : 'AimsData'} )
self.volume = r.read( fileName )
self.interpolator = aims.aims.getLinearInterpolator( self.volume ).get()
# convert the AimsData volume to Anatomist API
avol = self.anatomist.toAObject( self.volume )
# put volume in window
self.aWindow.addObjects( avol )
self._ignoreClicked = False
voxelSize = self.volume.header()[ 'voxel_size' ]
tmp = self.volume.header()[ 'volume_dimension' ]
volumeSize = [ int(i) for i in tmp ]
volumeCenter = [v*s/2 for v,s in zip( volumeSize, voxelSize )]
self.clicked( volumeCenter )
infoHeight = self.info.sizeHint().height()
self.infoSplitter.setSizes( [ infoHeight, self.height() - infoHeight ] )
def clicked2( self, eventName, eventParameters ):
self.clicked( eventParameters[ 'position' ], eventParameters[ 'window' ] )
def clicked( self, posMM, aWindow=None ):
posMM = [float(i) for i in posMM]
if self._ignoreClicked: return
text = '\n'
text += 'Coordinate millimeters: %.2f, %.2f, %.2f, %.2f' % tuple( posMM ) + '
\n'
voxelSize = self.volume.header()[ 'voxel_size' ]
posVoxel = [int(round(i/j)) for i,j in zip(posMM,voxelSize)]
text += 'Coordinate voxels: %d, %d, %d, %d' % tuple( posVoxel ) + '
\n'
tmp = self.volume.header()[ 'volume_dimension' ]
volumeSize = [int(i) for i in tmp]
if not [None for i in posVoxel if i < 0] and \
not [None for i,j in zip(posVoxel, volumeSize) if i >= j]:
text += 'Voxel value: ' + str( self.volume.value( *posVoxel ) ) + '
\n'
if volumeSize[ 3 ] > 1:
indices = numpy.arange( volumeSize[ 3 ] )
# Extract values as numarray structure
values = self.interpolator.values( posVoxel[0] * voxelSize[0],
posVoxel[1] * voxelSize[1],
posVoxel[2] * voxelSize[2] )
self.matplotAxes.plot( indices, numpy.array( values ) )
self.matplotCanvas.draw()
text += ''
self.info.setText( text )
def regionSelected( self ):
index = self.roiList.currentRow()
if index >= 0:
text = '\n'
text += '' + unicode( self.roiList.item( index ).text() ) + '
\n'
maskIterator = self.maskIterators[ index ]
if maskIterator.bucket is None:
roiCenter = aims.Point3df(0, 0, 0)
bucket = aims.BucketMap_VOID()
bucket.setSizeXYZT( *maskIterator.voxelSize().items() + (1,) )
maskIterator.restart()
valid = 0
invalid = 0
sum = None
# Iterate on each point of a region
while maskIterator.isValid():
bucket[ 0 ][ maskIterator.value() ] = 1
p = maskIterator.valueMillimeters()
roiCenter += p
# Check if the point is in the image limit
if self.interpolator.isValid( p ):
values = self.interpolator.values( p )
if sum is None:
sum = values
else:
sum = [s+v for s,v in zip(sum,values)]
valid += 1
else:
invalid += 1
maskIterator.next()
text += 'valid points: ' + str( valid ) + '
\n'
text += 'invalid points: ' + str( invalid ) + '
\n'
if valid:
means = [s / float( valid ) for s in sum]
mean = reduce( operator.add, means ) / len( means )
else:
means = []
mean = 'N/A'
text += 'mean: ' + str( mean ) + '
\n'
text += ''
maskIterator.text = text
# convert the BucketMap to Anatomist API
maskIterator.bucket = self.anatomist.toAObject( bucket )
maskIterator.bucket.setName( str( self.roiList.item( index ).text() ) )
maskIterator.bucket.setChanged()
count = valid + invalid
if count:
maskIterator.roiCenter = [c/count for c in roiCenter.items()]
else:
maskIterator.roiCenter = None
maskIterator.means = means
# put bucket in window
self.info.setText( maskIterator.text )
self.aWindow.addObjects( [ maskIterator.bucket ] )
# Set selected color to bucket
maskIterator.bucket.setMaterial( self.anatomist.Material(
diffuse = [ 1, 0, 0, 0.5 ],
lighting = 0,
face_culling = 1,
) )
# Set unselected color to previously selected bucket
if self.selectedBucket is not None:
self.selectedBucket.setMaterial( self.anatomist.Material( diffuse=[0,0.8,0.8,0.8] ) )
self.selectedBucket = maskIterator.bucket
if maskIterator.roiCenter is not None:
self._ignoreClicked = True
self.aWindow.moveLinkedCursor( maskIterator.roiCenter )
self._ignoreClicked = False
if len( maskIterator.means ) > 1:
indices = numpy.arange( len( maskIterator.means ) )
self.matplotAxes.plot( indices, numpy.array( maskIterator.means ) )
self.matplotCanvas.draw()
if __name__ == '__main__':
qApp = QApplication( sys.argv )
if len( sys.argv ) == 3:
roiIterator = aims.aims.getRoiIterator( sys.argv[ 2 ] ).get()
w = MeasuresWindow( sys.argv[ 1 ], roiIterator=roiIterator )
else:
w = MeasuresWindow( sys.argv[ 1 ] )
w.show()
anatomist.Anatomist().getControlWindow().hide()
qApp.exec_()