def __init__(self, anato=None, app=None):
# UI init
QtGui.QWidget.__init__(self)
self.ui = uic.loadUi("electrodeEditor.ui", self)
self.setWindowTitle('Electrode editor')
# Init of variables
self.app = app
self.cylinders = {}
self.displayed = {}
#self.elementIndex = 1
self.currentColorHue = 0
self.typeColors = {}
# Linking UI elements to functions
self.connect(self.exitButton, QtCore.SIGNAL('clicked()'), self.quit)
self.connect(self.openButton, QtCore.SIGNAL('clicked()'), self.open)
self.connect(self.saveButton, QtCore.SIGNAL('clicked()'), self.save)
self.connect(self.addButton, QtCore.SIGNAL('clicked()'),
self.addCylinder)
self.connect(self.updateButton, QtCore.SIGNAL('clicked()'),
self.updateCylinder)
self.connect(self.deleteButton, QtCore.SIGNAL('clicked()'),
self.deleteCylinder)
self.connect(self.axisCombo,
QtCore.SIGNAL('currentIndexChanged(QString)'),
self.axisChanged)
#self.connect(self.typeCombo, QtCore.SIGNAL('currentIndexChanged(QString)'), self.updateName)
self.cylinderList.sortItems(QtCore.Qt.AscendingOrder)
self.connect(
self.cylinderList,
QtCore.SIGNAL(
"currentItemChanged(QListWidgetItem*,QListWidgetItem*)"),
self.cylinderListClick) #itemClicked
# Anatomist windows
if anato is None:
self.a = anatomist.Anatomist('-b')
else:
self.a = anato
layout = QtGui.QHBoxLayout(self.anatomistBox)
self.axWindow = self.a.createWindow('Axial', no_decoration=True)
self.sagWindow = self.a.createWindow('Sagittal', no_decoration=True)
self.corWindow = self.a.createWindow('Coronal', no_decoration=True)
self.wins = [self.axWindow, self.sagWindow, self.corWindow]
[w.setHasCursor(0) for w in self.wins]
self.sagWindow.setParent(self.anatomistBox)
self.axWindow.setParent(self.anatomistBox)
self.corWindow.setParent(self.anatomistBox)
layout.addWidget(self.sagWindow.getInternalRep())
layout.addWidget(self.axWindow.getInternalRep())
layout.addWidget(self.corWindow.getInternalRep())
def changeDisplay(self, index, object):
'''
Changes display on user's demand
index : int between 0 and 3
object : object to display
'''
a = ana.Anatomist('-b')
views = ['Axial', 'Sagittal', 'Coronal', '3D']
new_view = views[index]
self.disableButton(index)
self.createNewWindow(new_view)
a.addObjects(object, self.new_awindow)
def showPopup(self, object):
'''
Defines the dimensions of the popup which is a QWidget
QWidget is added to self.popups in order to keep the widget
but beeing able to replace the object inside
'''
a = ana.Anatomist('-b')
self.layout.addWidget(self.window)
self.popups.append(self.popup_window)
index = len(self.popups) - 1
self.popups[index].setWindowTitle(object.name)
#Create empty view (Axial, Sagittal,...)
self.createNewWindow()
self.setObject(object)
#Add object into view
a.addObjects(object, self.new_awindow)
self.popups[index].show()
def createNewWindow(self, wintype='Axial'):
'''
Opens a new window in the vertical layout
Function is nearly the same as createWindow in AnaSimpleViewer2
Default display each time a new popup opens is 'Axial' view
'''
a = ana.Anatomist('-b')
w = a.createWindow(wintype, no_decoration=True, options={'hidden': 1})
w.setAcceptDrops(False)
#Set wanted view button checked and others unchecked
views = ['Axial', 'Sagittal', 'Coronal', '3D']
index = views.index(wintype)
self.disableButton(index)
#Delete object if there is already one
if self.newViewLay.itemAt(0):
self.newViewLay.itemAt(0).widget().deleteLater()
x = 0
y = 0
i = 0
if not hasattr(self, '_winlayouts'):
self._winlayouts = [[0, 0], [0, 0]]
else:
freeslot = False
for y in (0, 1):
for x in (0, 1):
i = i + 1
if not self._winlayouts[x][y]:
freeslot = True
break
if freeslot:
break
self.newViewLay.addWidget(w.getInternalRep())
self.new_awindow = w
self._winlayouts[x][y] = 1
if wintype == '3D':
a.execute('SetControl', windows=[w], control='LeftSimple3DControl')
a.execute('Camera',
windows=[self.new_awindow],
view_quaternion=[0.404603, 0.143829, 0.316813, 0.845718])
else:
a.execute('SetControl', windows=[w], control='Simple2DControl')
a.assignReferential(a.mniTemplateRef, w)
# force redrawing in MNI orientation
# (there should be a better way to do so...)
if wintype == 'Axial':
w.muteAxial()
print('MUTEAXIAL', w.muteAxial)
elif wintype == 'Coronal':
w.muteCoronal()
elif wintype == 'Sagittal':
w.muteSagittal()
elif wintype == 'Oblique':
w.muteOblique()
# set a black background
a.execute('WindowConfig',
windows=[w],
light={'background': [0., 0., 0., 1.]},
view_size=(500, 600))
def csvMapGraph(options,
agraphs=None,
window=None,
displayProp=None,
palette=None,
propPrefix=None,
csvfilename=None,
filterCol=None,
filterExpr=None,
min=None,
max=None):
'''csvMapGraph( options, agraphs=None, window=None, displayProp=None,
palette=None, propPrefix=None, csvfilename=None )
read a CSV-like file, extract numeric figures on sulci from it and map it
on a sulci graph displayed in anatomist.
Paramters:
options: command-line parsing options of siCsvMapGraph (see the help of this
command)
agraphs: existing anatomist graph(s) on which to map data. If not specified, a
graph is read from the options.graphname parameter.
window: existing anatomist window in which the sulci graph will be displayed.
If not specified, a new window will be opened.
displayProp: when several data are read at the same time, specifies which
one will be currently displayed. If not specified, the first data column
will be used.
palette: color palette to apply to the graph display. May be either an
anatomist palette object, or a parameters dictionary, corresponding to the
parameters of the SetObjectPalette command (see
http://brainvisa.info/doc/anatomist-4.0/html/fr/programmation/commands.html#SetObjectPalette)
propPrefix: data read from the CSV file are stored in the graph nodes as
properties. The prefix is used in the properties names. If not specified,
'csv' is used
csvfilename: if specified, overrides options.csvfilename for convenience
Return values: aobjects, awindows
'''
if csvfilename is None:
csvfilename = options.csvfilename
if csvfilename is None:
parseOpts([sys.argv[0], '-h'])
sys.exit(1)
# read
ft = sigraph.FoldLabelsTranslator(options.transfile)
sigraph.si().setLabelsTranslPath(options.transfile)
labels, sulci_data, mode = read_csv(csvfilename,
options.columns,
operator=options.operator,
filterCol=filterCol,
filterExpr=filterExpr)
if options.summarycsvfilename:
write_summary_csv(options.summarycsvfilename, labels, sulci_data, mode)
# graph
if not options.graphname: return
from soma import aims
graphs = []
if agraphs:
if isinstance(agraphs, anatomist.Anatomist.AGraph):
agraphs = [agraphs]
graphs = [x.graph() for x in agraphs]
else:
r = aims.Reader(options={'subobjectsfilter': 1})
graphs = [r.read(f) for f in options.graphname]
for g in graphs:
ft.translate(g, options.label_attribute, options.label_attribute)
# mesh
for mfile in options.meshname:
m = aims.read(mfile)
else:
m = None
if propPrefix is None:
propPrefix = 'csv'
for g in graphs:
for v in g.vertices():
if v.getSyntax() != 'fold': continue
if mode in ('sulci', 'label', 'name'):
try:
l = v[options.label_attribute]
data = getdata(sulci_data, v[options.label_attribute])
except exceptions.KeyError:
continue
elif mode == 'nodes':
try:
data = getdata(sulci_data, str(int(v['index'])))
except exceptions.KeyError:
continue
for i, h in enumerate(labels):
v[propPrefix + '_mean_' + h] = data[0][i]
if options.log and data[0][i] != 0:
v[propPrefix + '_log_mean_' + h] = numpy.log(data[0][i])
elif options.log10 and data[0][i] != 0:
v[propPrefix + '_log_mean_' + h] = numpy.log10(data[0][i])
# add only no-null std
if data[1][i]: v[propPrefix + '_std_' + h] = data[1][i]
v[propPrefix + '_sum_' + h] = data[2][i]
a = anatomist.Anatomist()
aobjects = []
if not agraphs:
agraphs = [a.toAObject(g) for g in graphs]
aobjects = agraphs
if displayProp is None:
displayProp = propPrefix + '_mean_' + labels[0]
for ag in agraphs:
ag.setColorMode(ag.PropertyMap)
ag.setColorProperty(displayProp)
#modified to get the palette as imput argument
palette = a.getPalette(palette)
if palette is not None:
if isinstance(palette, a.APalette):
#modified to get min and max values as imputs
ag.setPalette(palette,
minVal=min,
maxVal=max,
absoluteMode=True)
#ag.setPalette( palette )
else: # dict
a.execute('SetObjectPalette', objects=[ag], **palette)
ag.notifyObservers()
if m:
am = a.toAObject(m)
aobjects.append(am)
if window is not None:
win = window
wins = []
else:
win = a.createWindow(wintype='3D')
wins = [win]
win.setHasCursor(0)
win.addObjects(aobjects, add_graph_nodes=True)
return aobjects, wins