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)