.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/anaevensimplerviewer.py"
.. LINE NUMBERS ARE GIVEN BELOW.
.. only:: html
.. note::
:class: sphx-glr-download-link-note
:ref:`Go to the end <sphx_glr_download_auto_examples_anaevensimplerviewer.py>`
to download the full example code
.. rst-class:: sphx-glr-example-title
.. _sphx_glr_auto_examples_anaevensimplerviewer.py:
Build a custom simplified viewer based on Anatomist
===================================================
An even simplified version of the anasimpleviewer application, which may also
be used as a programming example. Its code is in the “bin/â€â€ directory of the
binary packages.
.. .. figure:: ../images/anaevensimplerviewer.png
.. GENERATED FROM PYTHON SOURCE LINES 45-391
.. image-sg:: /auto_examples/images/sphx_glr_anaevensimplerviewer_001.png
:alt: anaevensimplerviewer
:srcset: /auto_examples/images/sphx_glr_anaevensimplerviewer_001.png
:class: sphx-glr-single-img
.. rst-class:: sphx-glr-script-out
.. code-block:: none
config.setitem: setAutomaticReferential : 1
config.setitem: windowSizeFactor : 1.0
Exiting
|
.. code-block:: default
import anatomist.direct.api as ana
from soma import aims
from soma.aims import colormaphints
import sys
import os
from soma.qt_gui import qt_backend
from soma.qt_gui.qt_backend import Qt, loadUi
import six
from six.moves import zip
def findChild(x, y): return Qt.QObject.findChild(x, Qt.QObject, y)
close_qt = False
if 'sphinx_gallery' in sys.modules \
or ('IPython' in sys.modules
and Qt.QApplication.instance() is None):
run_qt = False
close_qt = True
elif Qt.QApplication.instance() is None:
run_qt = True
else:
run_qt = False
# start the Anatomist engine, in batch mode (no main window)
a = ana.Anatomist('-b')
# load the anasimpleviewer GUI
uifile = 'anasimpleviewer-qt4.ui'
anasimpleviewerdir = os.path.join(six.text_type(a.anatomistSharedPath()),
'anasimpleviewer')
cwd = os.getcwd()
# PyQt4 uic doesn' seem to allow specifying the directory when looking for
# icon files: we have no other choice than globally changing the working
# directory
os.chdir(anasimpleviewerdir)
awin = loadUi(os.path.join(anasimpleviewerdir, uifile))
os.chdir(cwd)
# global variables: lists of windows, objects, a fusion2d with a number of
# volumes in it
awindows = []
aobjects = []
fusion2d = []
# vieww: parent block widget for anatomist windows
vieww = findChild(awin, 'windows')
viewgridlay = Qt.QGridLayout(vieww)
nviews = 0
# This class holds methods for menu/actions callbacks, and utility functions
# like load/view objects, remove/delete, etc.
class AnaSimpleViewer(Qt.QObject):
def __init__(self):
Qt.QObject.__init__(self)
self.filedialogdir = '.'
def createWindow(self, wintype='Axial'):
'''Opens a new window in the windows grid layout.
The new window will be set in MNI referential, and have no
menu/toolbars.
'''
global vieww, nviews
x = nviews % 2
y = nviews // 2
nviews += 1
w = a.createWindow(wintype, no_decoration=True, options={'hidden': 1})
w.setAcceptDrops(False)
viewgridlay.addWidget(w.getInternalRep(), x, y)
# keep it in anasimpleviewer list of windows
awindows.append(w)
a.assignReferential(a.mniTemplateRef, w)
# force redrawing in MNI orientation
# (there should be a better way to do so...)
if wintype == 'Axial':
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.]})
def loadObject(self, fname):
'''Load an object and display it in all anasimpleviewer windows
'''
obj = a.loadObject(fname)
self.registerObject(obj)
def registerObject(self, obj):
'''Register an object in anasimpleviewer objects list, and display it
'''
findChild(awin, 'objectslist').addItem(obj.name)
# keep it in the global list
aobjects.append(obj)
if obj.objectType == 'VOLUME':
# volume are checked for possible adequate colormaps
hints = colormaphints.checkVolume(
ana.cpp.AObjectConverter.aims(obj))
obj.attributed()['colormaphints'] = hints
bb = obj.boundingbox()
# create the 4 windows if they don't exist
if len(awindows) == 0:
self.createWindow('Coronal')
self.createWindow('Axial')
self.createWindow('Sagittal')
self.createWindow('3D')
# set a cool angle of view for 3D
a.execute('Camera', windows=[awindows[-1]],
view_quaternion=[0.404603, 0.143829, 0.316813, 0.845718])
# view obj in these views
self.addObject(obj)
# set the cursot at the center of the object (actually, overcome a bug
# in anatomist...)
position = (aims.Point3df(bb[1][:3]) - bb[0][:3]) / 2.
t = a.getTransformation(obj.getReferential(),
awindows[0].getReferential())
if t:
position = t.transform(position)
a.execute('LinkedCursor', window=awindows[0], position=position)
def addVolume(self, obj, opts={}):
'''Display a volume in all windows.
If several volumes are displayed, a Fusion2D will be built to wrap all
of them.
'''
global fusion2d
if obj in fusion2d:
return
if len(fusion2d) == 0:
# only one object
fusion2d = [None, obj]
else:
# several objects: fusion them
fusobjs = fusion2d[1:] + [obj]
f2d = a.fusionObjects(fusobjs, method='Fusion2DMethod')
if fusion2d[0] is not None:
# destroy the previous fusion
a.deleteObjects(fusion2d[0])
else:
a.removeObjects(fusion2d[1], awindows)
fusion2d = [f2d] + fusobjs
# repalette( fusobjs )
obj = f2d
if obj.objectType == 'VOLUME':
# choose a good colormap for a single volume
if 'volume_contents_likelihoods' in \
obj.attributed()['colormaphints']:
cmap = colormaphints.chooseColormaps(
(obj.attributed()['colormaphints'], ))
obj.setPalette(cmap[0])
else:
# choose good colormaps for the current set of volumes
hints = [x.attributed()['colormaphints'] for x in obj.children]
children = [x for x, y in zip(obj.children, hints)
if 'volume_contents_likelihoods' in y]
hints = [x for x in hints
if 'volume_contents_likelihoods' in x]
cmaps = colormaphints.chooseColormaps(hints)
for x, y in zip(children, cmaps):
x.setPalette(y)
a.addObjects(obj, awindows, **opts)
def removeVolume(self, obj, opts={}):
'''Hides a volume from views (low-level function: use removeObject)
'''
global fusion2d
if obj in fusion2d:
fusobjs = [o for o in fusion2d[1:] if o != obj]
if len(fusobjs) >= 2:
f2d = a.fusionObjects(fusobjs, method='Fusion2DMethod')
else:
f2d = None
if fusion2d[0] is not None:
a.deleteObjects(fusion2d[0])
else:
a.removeObjects(fusion2d[1], awindows)
if len(fusobjs) == 0:
fusion2d = []
else:
fusion2d = [f2d] + fusobjs
# repalette( fusobjs )
if f2d:
obj = f2d
elif len(fusobjs) == 1:
obj = fusobjs[0]
else:
return
a.addObjects(obj, awindows, **opts)
def addObject(self, obj):
'''Display an object in all windows
'''
opts = {}
if obj.objectType == 'VOLUME':
# volumes have a specific function since several volumes have to be
# fusionned, and a volume rendering may occur
self.addVolume(obj, opts)
return
elif obj.objectType == 'GRAPH':
opts['add_graph_nodes'] = 1
a.addObjects(obj, awindows, **opts)
def removeObject(self, obj):
'''Hides an object from views
'''
if obj.objectType == 'VOLUME':
self.removeVolume(obj)
else:
a.removeObjects(obj, awindows, remove_children=True)
def fileOpen(self):
'''File browser + load object(s)
'''
fdialog = Qt.QFileDialog()
fdialog.setDirectory(self.filedialogdir)
fdialog.setFileMode(fdialog.ExistingFiles)
res = fdialog.exec_()
if res:
fnames = fdialog.selectedFiles()
self.filedialogdir = fdialog.directory()
for fname in fnames:
self.loadObject(six.text_type(fname))
def selectedObjects(self):
'''list of objects selected in the list box on the upper left panel
'''
olist = findChild(awin, 'objectslist')
sobjs = []
for o in olist.selectedItems():
sobjs.append(six.text_type(o.text()).strip('\0'))
return [o for o in aobjects if o.name in sobjs]
def editAdd(self):
'''Display selected objects'''
objs = self.selectedObjects()
for o in objs:
self.addObject(o)
def editRemove(self):
'''Hide selected objects'''
objs = self.selectedObjects()
for o in objs:
self.removeObject(o)
def editDelete(self):
'''Delete selected objects'''
objs = self.selectedObjects()
for o in objs:
self.removeObject(o)
olist = findChild(awin, 'objectslist')
for o in objs:
olist.takeItem(olist.row(olist.findItems(o.name,
Qt.Qt.MatchExactly)[0]))
global aobjects
aobjects = [o for o in aobjects if o not in objs]
a.deleteObjects(objs)
def closeAll(self):
'''Exit'''
print("Exiting")
global vieww, awindows, fusion2d, aobjects, anasimple
global awin, viewgridlay
# remove windows from their parent to prevent them to be brutally
# deleted by Qt.
w = None # ensure there is a w variable before the "del" later
for w in awindows:
w.hide()
viewgridlay.removeWidget(w.internalRep._get())
w.setParent(None)
del w
del viewgridlay, vieww
del anasimple
del awindows, fusion2d, aobjects
awin.close()
del awin
a = ana.Anatomist()
a.close()
# instantiate the machine
anasimple = AnaSimpleViewer()
# connect GUI actions callbacks
findChild(awin, 'fileOpenAction').triggered.connect(anasimple.fileOpen)
findChild(awin, 'fileExitAction').triggered.connect(anasimple.closeAll)
findChild(awin, 'editAddAction').triggered.connect(anasimple.editAdd)
findChild(awin, 'editRemoveAction').triggered.connect(anasimple.editRemove)
findChild(awin, 'editDeleteAction').triggered.connect(anasimple.editDelete)
# display on the whole screen
awin.showMaximized()
# tweak: override some user config options
a.config()['setAutomaticReferential'] = 1
a.config()['windowSizeFactor'] = 1.
# run Qt
if __name__ == '__main__':
if run_qt:
Qt.QApplication.instance().exec_()
elif 'sphinx_gallery' in sys.modules:
# load a data
awin.showNormal()
awin.resize(1000, 700) # control the size of the snapshot
anasimple.loadObject('irm.ima')
# these 2 events ensure things are actually drawn
Qt.QApplication.instance().processEvents()
Qt.QApplication.instance().processEvents()
# snapshot the whole widget
if Qt.QT_VERSION >= 0x050000:
ws = awin.grab() # Qt5 only
else:
ws = Qt.QPixmap.grabWidget(awin) # Qt4 only
# openGl areas are not rendered in the snapshot, we have to make them
# by hand
p = Qt.QPainter(ws)
for w in awindows:
s = w.snapshotImage()
# draw the GL rendering into the image (pixmap)
p.drawImage(w.mapTo(awin, Qt.QPoint(0, 0)), s)
del w, s, p
# snapshot to matplotlib
import matplotlib
# backend = matplotlib.get_backend()
matplotlib.use('agg', force=True) # force agg
from matplotlib import pyplot
im = qt_backend.qimage_to_np(ws)
plot = pyplot.imshow(im)
axes = pyplot.gcf().axes
axes[0].get_xaxis().set_visible(False)
axes[0].get_yaxis().set_visible(False)
pyplot.show(block=False)
# matplotlib.use(backend, force=True) # restore backend
if close_qt:
anasimple.closeAll()
.. rst-class:: sphx-glr-timing
**Total running time of the script:** (0 minutes 1.374 seconds)
.. _sphx_glr_download_auto_examples_anaevensimplerviewer.py:
.. only:: html
.. container:: sphx-glr-footer sphx-glr-footer-example
.. container:: sphx-glr-download sphx-glr-download-python
:download:`Download Python source code: anaevensimplerviewer.py <anaevensimplerviewer.py>`
.. container:: sphx-glr-download sphx-glr-download-jupyter
:download:`Download Jupyter notebook: anaevensimplerviewer.ipynb <anaevensimplerviewer.ipynb>`
.. only:: html
.. rst-class:: sphx-glr-signature
`Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_