brain regions aggregation mappings

Author: oliche

atlasview/atlasview.py

@@ -59,9 +59,13 @@ def __init__(self, **kwargs):
         self.line_sagittal.sigDragged.connect(self._refresh_sagittal)
         self.plotItem_topview.addItem(self.line_coronal)
         self.plotItem_topview.addItem(self.line_sagittal)
-        # connect signals and slots
+        # connect signals and slots: mouse moved
         s = self.plotItem_topview.getViewBox().scene()
         self.proxy = pg.SignalProxy(s.sigMouseMoved, rateLimit=60, slot=self.mouseMoveEvent)
+        # combobox for the atlas remapping choices
+        self.comboBox_mappings.addItems(self.ctrl.atlas.regions.mappings.keys())
+        self.comboBox_mappings.currentIndexChanged.connect(self._refresh)
+        # slider for transparency between image and labels
         self.slider_alpha.sliderMoved.connect(self.slider_alpha_move)
         self.ctrl.set_top()
 
@@ -119,10 +123,12 @@ def _refresh(self):
         self._refresh_coronal()
 
     def _refresh_coronal(self):
-        self.ctrl.set_slice(self.ctrl.fig_coronal, self.line_coronal.value())
+        self.ctrl.set_slice(self.ctrl.fig_coronal, self.line_coronal.value(),
+                            mapping=self.comboBox_mappings.currentText())
 
     def _refresh_sagittal(self):
-        self.ctrl.set_slice(self.ctrl.fig_sagittal, self.line_sagittal.value())
+        self.ctrl.set_slice(self.ctrl.fig_sagittal, self.line_sagittal.value(),
+                            mapping=self.comboBox_mappings.currentText())
 
 
 class SliceView(QtWidgets.QWidget):
@@ -255,10 +261,10 @@ class ControllerTopView(PgImageController):
     """
     TopView ControllerTopView
     """
-    def __init__(self, qmain: TopView, res: int = 25, volume='image'):
+    def __init__(self, qmain: TopView, res: int = 25, volume='image', brainmap='Allen'):
         super(ControllerTopView, self).__init__(qmain)
         self.volume = volume
-        self.atlas = AllenAtlas(res)
+        self.atlas = AllenAtlas(res, brainmap=brainmap)
         self.fig_top = self.qwidget = qmain
         # Setup Coronal slice: width: ml, height: dv, depth: ap
         self.fig_coronal = SliceView(qmain, waxis=0, haxis=2, daxis=1)
@@ -271,7 +277,7 @@ def __init__(self, qmain: TopView, res: int = 25, volume='image'):
         self.set_slice(self.fig_sagittal)
         self.fig_sagittal.show()
 
-    def set_slice(self, fig, coord=0):
+    def set_slice(self, fig, coord=0, mapping="Allen"):
         waxis, haxis, daxis = (fig.ctrl.waxis, fig.ctrl.haxis, fig.ctrl.daxis)
         # construct the transform matrix image 2 ibl coordinates
         dw = self.atlas.bc.dxyz[waxis]
@@ -281,7 +287,7 @@ def set_slice(self, fig, coord=0):
         # the ImageLayer object carries slice kwargs and pyqtgraph ImageSet kwargs
         # reversed order so the self.im is set with the base layer
         for layer in reversed(fig.ctrl.image_layers):
-            _slice = self.atlas.slice(coord, axis=daxis, **layer.slice_kwargs)
+            _slice = self.atlas.slice(coord, axis=daxis, mapping=mapping, **layer.slice_kwargs)
             fig.ctrl.set_image(layer.image_item, _slice, dw, dh, wl[0], hl[0], **layer.pg_kwargs)
         fig.ctrl.slice_coord = coord
 
@@ -354,10 +360,10 @@ class ImageLayer:
     slice_kwargs: dict = field(default_factory=lambda: {'volume': 'image', 'mode': 'clip'})
 
 
-def view(res=25, title=None, volume='image', levels=None):
+def view(res=25, title=None, brainmap='Allen'):
     """
     """
     qt.create_app()
-    av = TopView._get_or_create(title=title, res=res)
+    av = TopView._get_or_create(title=title, res=res, brainmap=brainmap)
     av.show()
     return av

atlasview/topview.ui

@@ -32,7 +32,7 @@
       <property name="frameShadow">
        <enum>QFrame::Raised</enum>
       </property>
-      <widget class="QLabel" name="label">
+      <widget class="QLabel" name="label_slider_annotation">
        <property name="geometry">
         <rect>
          <x>20</x>
@@ -61,7 +61,7 @@
         <enum>Qt::Vertical</enum>
        </property>
       </widget>
-      <widget class="QLabel" name="label_2">
+      <widget class="QLabel" name="label_slider_image">
        <property name="geometry">
         <rect>
          <x>10</x>
@@ -74,6 +74,29 @@
         <string>Image</string>
        </property>
       </widget>
+      <widget class="QComboBox" name="comboBox_mappings">
+       <property name="geometry">
+        <rect>
+         <x>0</x>
+         <y>350</y>
+         <width>93</width>
+         <height>27</height>
+        </rect>
+       </property>
+      </widget>
+      <widget class="QLabel" name="label_cb_mappings">
+       <property name="geometry">
+        <rect>
+         <x>10</x>
+         <y>330</y>
+         <width>67</width>
+         <height>17</height>
+        </rect>
+       </property>
+       <property name="text">
+        <string>Mapping</string>
+       </property>
+      </widget>
      </widget>
     </item>
    </layout>
@@ -84,7 +107,7 @@
      <x>0</x>
      <y>0</y>
      <width>435</width>
-     <height>22</height>
+     <height>24</height>
     </rect>
    </property>
   </widget>