Add human example script and some other fixes

brainglobe_heatmap/heatmaps.py

@@ -51,7 +51,7 @@ def check_values(values: dict, atlas: Atlas) -> Tuple[float, float]:
 class heatmap:
     def __init__(
         self,
-        values: Dict[str, float],
+        values: Dict,
         position: Union[list, tuple, np.ndarray],
         orientation: Union[str, tuple] = "frontal",
         hemisphere: str = "both",
@@ -253,40 +253,3 @@ def plot(
         plt.show()
 
         return f
-
-
-if __name__ == "__main__":
-    values = dict(  # scalar values for each region
-        TH=1,
-        RSP=0.2,
-        AI=0.4,
-        SS=-3,
-        MO=2.6,
-        PVZ=-4,
-        LZ=-3,
-        VIS=2,
-        AUD=0.3,
-        RHP=-0.2,
-        STR=0.5,
-        CB=0.5,
-        FRP=-1.7,
-        HIP=3,
-        PA=-4,
-    )
-
-    heatmap(
-        values,
-        position=None,
-        # or 'sagittal', or 'horizontal' or a tuple (x,y,z)
-        orientation=(
-            1,
-            1,
-            0,
-        ),
-        # thickness of the slices used for rendering (in microns)
-        thickness=250,
-        title="frontal",
-        vmin=-5,
-        vmax=3,
-        format="3D",
-    ).show()

examples/heatmap_human_brain.py

@@ -0,0 +1,19 @@
+"""
+This example shows how to generate a heatmap with the `allen_human_500um`
+human brain atlas.
+
+N.B. the physical scales are very different to e.g. the small animal atlases.
+"""
+
+import brainglobe_heatmap as bgh
+
+values = dict(SFG=1, PrCG=2, Ca=4, Pu=10)  # scalar values for each region
+
+
+scene = bgh.heatmap(
+    values,
+    position=(100000, 100000, 100000),
+    thickness=1000,
+    atlas_name="allen_human_500um",
+    format="2D",
+).show()