def test_save_and_remove(self):
"""Test methods save, reload and remove."""
# Define the ROI object and save it :
roi_custom = RoiObj('mist_roi', vol=vol, labels=label, index=roi_index,
hdr=hdr)
roi_custom.save()
# Test reloading roi from name only :
roi_sec = RoiObj('mist_roi')
roi_sec.remove()
def test_save_and_remove_tmp(self):
"""Test methods save, reload and remove for tmp files."""
# Define the ROI object and save it :
roi_custom = RoiObj('tmp_roi', vol=vol, labels=label, index=roi_index,
hdr=hdr)
roi_custom.save(tmpfile=True)
# Test reloading roi from name only :
RoiObj('tmp_roi')
clean_tmp()
def test_save_and_remove_tmp(self):
"""Test methods save, reload and remove for tmp files."""
# Define the ROI object and save it :
roi_custom = RoiObj('tmp_roi',
vol=vol,
labels=label,
index=roi_index,
hdr=hdr)
roi_custom.save(tmpfile=True)
# Test reloading roi from name only :
RoiObj('tmp_roi')
clean_tmp()
def test_save_and_remove(self):
"""Test methods save, reload and remove."""
# Define the ROI object and save it :
roi_custom = RoiObj('mist_roi',
vol=vol,
labels=label,
index=roi_index,
hdr=hdr)
roi_custom.save()
# Test reloading roi from name only :
roi_sec = RoiObj('mist_roi')
roi_sec.remove()
class Visuals(object):
"""Initialize Engram objects.
Initialize sources / connectivity / areas / colorbar / projections.
Organize them at diffrent levels and make the link with the graphical
user interface (if no object is detected, the corresponding panel in the
GUI has to be deactivate).
"""
def __init__(self, canvas, **kwargs):
"""Init."""
# Create a root node :
self._vbNode = scene.Node(name='Engram')
self._vbNode.transform = vist.STTransform(scale=[self._gl_scale] * 3)
logger.debug("Engram rescaled " + str([self._gl_scale] * 3))
PROFILER("Root node", level=1)
# ========================= SOURCES =========================
self.sources = CombineSources(kwargs.get('source_obj', None))
if self.sources.name is None:
self._obj_type_lst.model().item(4).setEnabled(False)
# Disable menu :
self.menuDispSources.setChecked(False)
self.menuTransform.setEnabled(False)
self.sources.parent = self._vbNode
PROFILER("Sources object", level=1)
# ========================= CONNECTIVITY =========================
self.connect = CombineConnect(kwargs.get('connect_obj', None))
if self.connect.name is None:
self._obj_type_lst.model().item(5).setEnabled(False)
self.menuDispConnect.setEnabled(False)
self.connect.parent = self._vbNode
PROFILER("Connect object", level=1)
# ========================= TIME-SERIES =========================
self.tseries = CombineTimeSeries(kwargs.get('time_series_obj', None))
if self.tseries.name is None:
self._obj_type_lst.model().item(6).setEnabled(False)
self.tseries.parent = self._vbNode
PROFILER("Time-series object", level=1)
# ========================= PICTURES =========================
self.pic = CombinePictures(kwargs.get('picture_obj', None))
if self.pic.name is None:
self._obj_type_lst.model().item(7).setEnabled(False)
self.pic.parent = self._vbNode
PROFILER("Pictures object", level=1)
# ========================= VECTORS =========================
self.vectors = CombineVectors(kwargs.get('vector_obj', None))
if self.vectors.name is None:
self._obj_type_lst.model().item(8).setEnabled(False)
self.vectors.parent = self._vbNode
PROFILER("Vectors object", level=1)
# ========================= VOLUME =========================
# ----------------- Volume -----------------
if kwargs.get('vol_obj', None) is None:
self.volume = VolumeObj('brodmann')
self.volume.visible_obj = False
else:
self.volume = kwargs.get('vol_obj')
if self.volume.name not in self.volume.list():
self.volume.save(tmpfile=True)
self.volume.parent = self._vbNode
PROFILER("Volume object", level=1)
# ----------------- ROI -----------------
if kwargs.get('roi_obj', None) is None:
self.roi = RoiObj('brodmann')
self.roi.visible_obj = False
else:
self.roi = kwargs.get('roi_obj')
if self.roi.name not in self.roi.list():
self.roi.save(tmpfile=True)
self.roi.parent = self._vbNode
PROFILER("ROI object", level=1)
# ----------------- Cross-sections -----------------
if kwargs.get('cross_sec_obj', None) is None:
self.cross_sec = CrossSecObj('brodmann')
else:
self.cross_sec = kwargs.get('cross_sec_obj')
if self.cross_sec.name not in self.cross_sec.list():
self.cross_sec.save(tmpfile=True)
self.cross_sec.visible_obj = False
self.cross_sec.text_size = 2.
self.cross_sec.parent = self._csView.wc.scene
self._csView.camera = self.cross_sec._get_camera()
self.cross_sec.set_shortcuts_to_canvas(self._csView)
PROFILER("Cross-sections object", level=1)
# ========================= ENGRAM =========================
if kwargs.get('engram_obj', None) is None:
self.atlas = BrainObj('B1')
else:
self.atlas = kwargs['engram_obj']
if self.atlas.name not in self.atlas.list():
self.atlas.save(tmpfile=True)
self.atlas.scale = self._gl_scale
self.atlas.parent = self._vbNode
PROFILER("Engram object", level=1)
class Visuals(object):
"""Initialize Brain objects.
Initialize sources / connectivity / areas / colorbar / projections.
Organize them at diffrent levels and make the link with the graphical
user interface (if no object is detected, the corresponding panel in the
GUI has to be deactivate).
"""
def __init__(self, canvas, **kwargs):
"""Init."""
# Create a root node :
self._vbNode = scene.Node(name='Brain')
self._vbNode.transform = vist.STTransform(scale=[self._gl_scale] * 3)
logger.debug("Brain rescaled " + str([self._gl_scale] * 3))
PROFILER("Root node", level=1)
# ========================= SOURCES =========================
self.sources = CombineSources(kwargs.get('source_obj', None))
if self.sources.name is None:
self._obj_type_lst.model().item(4).setEnabled(False)
# Disable menu :
self.menuDispSources.setChecked(False)
self.menuTransform.setEnabled(False)
self.sources.parent = self._vbNode
PROFILER("Sources object", level=1)
# ========================= CONNECTIVITY =========================
self.connect = CombineConnect(kwargs.get('connect_obj', None))
if self.connect.name is None:
self._obj_type_lst.model().item(5).setEnabled(False)
self.menuDispConnect.setEnabled(False)
self.connect.parent = self._vbNode
PROFILER("Connect object", level=1)
# ========================= TIME-SERIES =========================
self.tseries = CombineTimeSeries(kwargs.get('time_series_obj', None))
if self.tseries.name is None:
self._obj_type_lst.model().item(6).setEnabled(False)
self.tseries.parent = self._vbNode
PROFILER("Time-series object", level=1)
# ========================= PICTURES =========================
self.pic = CombinePictures(kwargs.get('picture_obj', None))
if self.pic.name is None:
self._obj_type_lst.model().item(7).setEnabled(False)
self.pic.parent = self._vbNode
PROFILER("Pictures object", level=1)
# ========================= VECTORS =========================
self.vectors = CombineVectors(kwargs.get('vector_obj', None))
if self.vectors.name is None:
self._obj_type_lst.model().item(8).setEnabled(False)
self.vectors.parent = self._vbNode
PROFILER("Vectors object", level=1)
# ========================= VOLUME =========================
# ----------------- Volume -----------------
if kwargs.get('vol_obj', None) is None:
self.volume = VolumeObj('brodmann')
self.volume.visible_obj = False
else:
self.volume = kwargs.get('vol_obj')
if self.volume.name not in self.volume.list():
self.volume.save(tmpfile=True)
self.volume.parent = self._vbNode
PROFILER("Volume object", level=1)
# ----------------- ROI -----------------
if kwargs.get('roi_obj', None) is None:
self.roi = RoiObj('brodmann')
self.roi.visible_obj = False
else:
self.roi = kwargs.get('roi_obj')
if self.roi.name not in self.roi.list():
self.roi.save(tmpfile=True)
self.roi.parent = self._vbNode
PROFILER("ROI object", level=1)
# ----------------- Cross-sections -----------------
if kwargs.get('cross_sec_obj', None) is None:
self.cross_sec = CrossSecObj('brodmann')
else:
self.cross_sec = kwargs.get('cross_sec_obj')
if self.cross_sec.name not in self.cross_sec.list():
self.cross_sec.save(tmpfile=True)
self.cross_sec.visible_obj = False
self.cross_sec.text_size = 2.
self.cross_sec.parent = self._csView.wc.scene
self._csView.camera = self.cross_sec._get_camera()
self.cross_sec.set_shortcuts_to_canvas(self._csView)
PROFILER("Cross-sections object", level=1)
# ========================= BRAIN =========================
if kwargs.get('brain_obj', None) is None:
self.atlas = BrainObj('B1')
else:
self.atlas = kwargs['brain_obj']
if self.atlas.name not in self.atlas.list():
self.atlas.save(tmpfile=True)
self.atlas.scale = self._gl_scale
self.atlas.parent = self._vbNode
PROFILER("Brain object", level=1)