more WIP

Author: mayofaulkner

needles2/needles_viewer.py

@@ -0,0 +1,75 @@
+from iblviewer.atlas_controller import AtlasController
+import vedo
+from iblviewer.atlas_model import AtlasModel, AtlasUIModel, CameraModel
+from iblviewer.slicer_model import SlicerModel
+
+from iblviewer.atlas_view import AtlasView
+from iblviewer.volume_view import VolumeView
+from iblviewer.slicer_view import SlicerView
+import iblviewer.utils as utils
+
+from ipyvtk_simple.viewer import ViewInteractiveWidget
+
+
+class NeedlesViewer(AtlasController):
+    def __init__(self):
+        super(NeedlesViewer, self).__init__()
+
+    def initialize(self, plot, resolution=25, mapping='Allen', num_windows=1, render=False):
+        vedo.settings.allowInteraction = False
+        self.plot = plot
+        self.plot_window_id = 0
+        self.model = AtlasModel()
+        self.model.initialize(resolution)
+        self.model.load_allen_volume(mapping)
+        self.model.initialize_slicers()
+
+        self.view = AtlasView(self.plot, self.model)
+        self.view.initialize()
+        self.view.volume = VolumeView(self.plot, self.model.volume, self.model)
+
+        #pn = SlicerModel.NAME_XYZ_POSITIVE
+        nn = SlicerModel.NAME_XYZ_NEGATIVE
+
+        #pxs_model = self.model.find_model(pn[0], self.model.slicers)
+        #self.px_slicer = SlicerView(self.plot, self.view.volume, pxs_model, self.model)
+        #pys_model = self.model.find_model(pn[1], self.model.slicers)
+        #self.py_slicer = SlicerView(self.plot, self.view.volume, pys_model, self.model)
+        #pzs_model = self.model.find_model(pn[2], self.model.slicers)
+        #self.pz_slicer = SlicerView(self.plot, self.view.volume, pzs_model, self.model)
+
+        nxs_model = self.model.find_model(nn[0], self.model.slicers)
+        self.nx_slicer = SlicerView(self.plot, self.view.volume, nxs_model, self.model)
+        nys_model = self.model.find_model(nn[1], self.model.slicers)
+        self.ny_slicer = SlicerView(self.plot, self.view.volume, nys_model, self.model)
+        nzs_model = self.model.find_model(nn[2], self.model.slicers)
+        self.nz_slicer = SlicerView(self.plot, self.view.volume, nzs_model, self.model)
+
+        self.slicers = [self.nx_slicer, self.ny_slicer, self.nz_slicer]
+
+        vedo.settings.defaultFont = self.model.ui.font
+        self.initialize_embed_ui(slicer_target=self.view.volume)
+
+        self.plot.show(interactive=False)
+        self.handle_transfer_function_update()
+        # By default, the atlas volume is our target
+        self.model.camera.target = self.view.volume.actor
+        # We start with a sagittal view
+        self.set_left_view()
+
+        self.render()
+
+    def initialize_embed_ui(self, slicer_target=None):
+        s_kw = self.model.ui.slider_config
+        d = self.view.volume.model.dimensions
+        if d is None:
+            return
+
+        #self.add_slider('px', self.update_px_slicer, 0, int(d[0]), 0, pos=(0.05, 0.065, 0.12),
+        #                title='+X', **s_kw)
+        #self.add_slider('py', self.update_py_slicer, 0, int(d[1]), 0, pos=(0.2, 0.065, 0.12),
+        #                title='+Y', **s_kw)
+        #self.add_slider('pz', self.update_pz_slicer, 0, int(d[2]), 0, pos=(0.35, 0.065, 0.12),
+        #                title='+Z', **s_kw)
+
+

needles2/run_needles2.py

@@ -10,6 +10,13 @@
 from ibllib.atlas import AllenAtlas, regions
 import qt
 
+from PyQt5 import Qt
+import vedo
+from vtk.qt.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
+from oneibl.one import ONE
+#one = ONE()
+from ibllib.pipes.histology import coverage
+from needles2.needles_viewer import NeedlesViewer
 
 class MainWindow(QtWidgets.QMainWindow):
 
@@ -38,6 +45,19 @@ def __init__(self):
 
         self.atlas = AllenAtlas(25)
         main_layout = QtWidgets.QGridLayout()
+        self.frame = Qt.QFrame()
+        self.vl = Qt.QVBoxLayout()
+        self.vtkWidget = QVTKRenderWindowInteractor(self.frame)
+        self.vl.addWidget(self.vtkWidget)
+        self.plt = vedo.Plotter(qtWidget=self.vtkWidget, N=1)
+        self.la = NeedlesViewer()
+        self.la.initialize(self.plt)
+        print(self.la)
+        self.la2 = NeedlesViewer()
+        self.la2.initialize(self.plt)
+        self.frame.setLayout(self.vl)
+
+
         self.coronal = SliceView(self, self.atlas, waxis=0, haxis=2, daxis=1)
         self.sagittal = SliceView(self, self.atlas, waxis=1, haxis=2, daxis=0)
         self.top = TopView(self, self.atlas)
@@ -61,6 +81,12 @@ def __init__(self):
         images = ['Image', 'Annotation']
         self.add_menu_bar(self.img_menu, self.img_group, images, callback=self.change_image)
 
+        # Add menu bar for coverage
+        self.coverage_menu = menu_bar.addMenu('Coverage')
+        self.coverage_group = QtGui.QActionGroup(self.coverage_menu)
+        self.coverage_group.setExclusive(True)
+        self.add_menu_bar(self.img_menu, self.img_group, ['Coverage'], callback=self.change_image)
+
         self.region_list = QtGui.QStandardItemModel()
         self.region_combobox = QtWidgets.QComboBox()
         # Add line edit and completer to be able to search for subject
@@ -70,23 +96,24 @@ def __init__(self):
         self.region_combobox.setCompleter(region_completer)
         self.region_combobox.setModel(self.region_list)
         self.region_combobox.completer().setModel(self.region_list)
-        data = self.atlas.regions.name[self.atlas._get_mapping(mapping=self.get_mapping())]
-        self.populate_lists(data, self.region_list, self.region_combobox)
-
         self.region_combobox.activated.connect(self.on_region_selected)
+        self.change_mapping()
+
 
+        offset = self.atlas.bc.lim(0)[0]
+        self.la.update_slicer(self.la.nx_slicer, self.top.line_sagittal.value()*1e6 + offset*1e6)
 
         main_layout.addWidget(self.region_combobox)
         main_layout.addWidget(self.top)
         main_layout.addWidget(self.coronal)
         main_layout.addWidget(self.sagittal)
+        main_layout.addWidget(self.frame)
         main_widget.setLayout(main_layout)
 
         # initialise
         self.set_slice(self.coronal)
         self.set_slice(self.sagittal)
-# menu bar for mapping
-# menu bar for image type
+
 
     def populate_lists(self, data, list_name, combobox):
         """
@@ -104,7 +131,7 @@ def populate_lists(self, data, list_name, combobox):
             item.setEditable(False)
             list_name.appendRow(item)
 
-        # This makes sure the drop down menu is wide enough to showw full length of string
+        # This makes sure the drop down menu is wide enough to show full length of string
         min_width = combobox.fontMetrics().width(max(data, key=len))
         min_width += combobox.view().autoScrollMargin()
         min_width += combobox.style().pixelMetric(QtGui.QStyle.PM_ScrollBarExtent)
@@ -114,7 +141,8 @@ def populate_lists(self, data, list_name, combobox):
         combobox.setCurrentIndex(0)
 
     def change_mapping(self):
-        data = self.atlas.regions.name[self.atlas._get_mapping(mapping=self.get_mapping())]
+        data = np.unique(self.atlas.regions.name[self.atlas._get_mapping(
+            mapping=self.get_mapping())])
         self.populate_lists(data, self.region_list, self.region_combobox)
         self._refresh()
 
@@ -128,6 +156,14 @@ def change_image(self):
                                           self.img_group.checkedAction().text())
         self._refresh()
 
+    def add_coverage(self):
+        traj = one.alyx.rest('trajectories', 'list', provenance='Ephys aligned histology track')
+        self.coverage = coverage(traj, self.atlas)
+        self.coronal.ctrl.add_volume_layer(self.coronal.fig_slice, self.coverage)
+        self.sagittal.ctrl.add_volume_layer(self.sagittal.fig_slice, self.coverage)
+        self._refresh()
+
+
     def add_menu_bar(self, menu, group, items, callback=None, default=None):
         if not default:
             default = items[0]
@@ -176,9 +212,13 @@ def _refresh(self):
 
     def _refresh_coronal(self):
         self.set_slice(self.coronal, self.top.line_coronal.value())
+        offset = self.atlas.bc.lim(1)[1]
+        self.la.update_slicer(self.la.ny_slicer,  (self.top.line_coronal.value()*1e6 + offset*16))
 
     def _refresh_sagittal(self):
         self.set_slice(self.sagittal, self.top.line_sagittal.value())
+        offset = self.atlas.bc.lim(0)[0]
+        self.la.update_slicer(self.la.nx_slicer, self.top.line_sagittal.value()*1e6 + offset*1e6)
 
     def _refresh_locked_region(self, region):
         region_values = np.zeros_like(self.atlas.regions.id)
@@ -197,6 +237,7 @@ def _refresh_locked_region(self, region):
         self._refresh()
         self.set_selected_region(region)
         # need to set the drop down to the selected region
+        self.la.reveal_regions(region_idx)
 
     def _reset_region(self, name):
         region_values = np.zeros_like(self.atlas.regions.id)
@@ -282,13 +323,13 @@ def __init__(self, qmain: MainWindow, atlas: AllenAtlas, waxis, haxis, daxis):
         label_layout.addWidget(self.label_ix)
         label_layout.addWidget(self.label_iy)
         label_layout.addWidget(self.label_v)
-        label_layout.addWidget(self.label_region)
+        #label_layout.addWidget(self.label_region)
         label_layout.addWidget(self.label_acronym)
         label_group.setLayout(label_layout)
 
 
-        main_layout.addWidget(self.fig_slice)
-        main_layout.addWidget(label_group)
+        main_layout.addWidget(self.fig_slice, 0, 0)
+        main_layout.addWidget(label_group, 0, 1)
         self.setLayout(main_layout)
 
         # init the image display
@@ -332,7 +373,7 @@ def mouseMoveEvent(self, scenepos):
             self.label_acronym.setText("")
             self.qmain._reset_region('non_locked')
         else:
-            self.label_region.setText(region['name'][0])
+            #self.label_region.setText(region['name'][0])
             self.label_acronym.setText(region['acronym'][0])
 
             if region['acronym'][0] != 'void':
@@ -414,6 +455,15 @@ def add_mask_layer(self, fig, name='locked', cmap='Blues'):
             'volume': 'value', 'region_values': np.zeros_like(self.atlas.regions.id),
             'mode': 'clip'})
 
+    def add_volume_layer(self, fig, volume, name='coverage', cmap='viridis'):
+        colormap = matplotlib.cm.get_cmap(cmap)
+        colormap._init()
+        # The last one is [0, 0, 0, 0] so remove this
+        lut = (colormap._lut * 255).view(np.ndarray)[:-1]
+        lut = np.insert(lut, 0, [0, 0, 0, 0], axis=0)
+        self.add_image_layer(fig, name=name, pg_kwargs={'lut': lut, 'opacity': 0.8}, slice_kwargs={
+            'volume': 'volume', 'region_values': volume, 'mode': 'clip'})
+
     def change_base_layer(self, fig, image='Image'):
         base_layer = self.get_image_layer(name='base')
         if image == 'Image':