Merge pull request #68 from brainglobe/expose-check-latest

Expose check_latest parameter

Author: alessandrofelder

brainglobe_heatmap/heatmaps.py

@@ -66,8 +66,53 @@ def __init__(
         zoom: Optional[float] = None,
         atlas_name: Optional[str] = None,
         label_regions: Optional[bool] = False,
+        check_latest: bool = True,
         **kwargs,
     ):
+        """
+        Creates a heatmap visualization of the provided values in 3D or 2D
+        using brainrender or matplotlib in the specified atlas.
+
+        Parameters
+        ----------
+        values : dict
+            Dictionary with brain regions acronyms as keys and
+            magnitudes as the values.
+        position : list, tuple, np.ndarray, float
+            Position of the plane in the atlas.
+        orientation : str or tuple, optional
+            Orientation of the plane in the atlas. Either, "frontal",
+            "sagittal", "horizontal" or a tuple with the normal vector.
+            Default is "frontal".
+        hemisphere : str, optional
+            Hemisphere to display the heatmap. Default is "both".
+        title : str, optional
+            Title of the heatmap. Default is None.
+        cmap : str, optional
+            Colormap to use for the heatmap. Default is "Reds".
+        vmin : float, optional
+            Minimum value for the colormap. Default is None.
+        vmax : float, optional
+            Maximum value for the colormap. Default is None.
+        format : str, optional
+            Format of the heatmap visualization.
+            "3D" for brainrender or "2D" for matplotlib. Default is "3D".
+        thickness : float, optional
+            Thickness of the slicing plane in the brainrender scene.
+            Default is 10.
+        interactive : bool, optional
+            If True, the brainrender scene is interactive. Default is True.
+        zoom : float, optional
+            Zoom level for the brainrender scene. Default is None.
+        atlas_name : str, optional
+            Name of the atlas to use for the heatmap.
+            If None allen_mouse_25um is used. Default is None.
+        label_regions : bool, optional
+            If True, labels the regions on the colorbar (only valid in 2D).
+            Default is False.
+        check_latest : bool, optional
+            Check for the latest version of the atlas. Default is True.
+        """
         # store arguments
         self.values = values
         self.format = format
@@ -83,6 +128,7 @@ def __init__(
             atlas_name=atlas_name,
             title=title,
             title_color=grey_darker,
+            check_latest=check_latest,
             **kwargs,
         )
 

brainglobe_heatmap/slicer.py

@@ -147,14 +147,15 @@ def get_structures_slice_coords(
     position: Union[list, tuple, np.ndarray],
     orientation: Union[str, tuple] = "frontal",
     atlas_name: Optional[str] = None,
+    check_latest: bool = True,
 ) -> Dict[str, List[np.ndarray]]:
     """
     Given a list of region name and a set of plane parameters,
     it returns the coordinates of the plane/regions'
     intersection in the plane's coordinates
     """
 
-    scene = Scene(atlas_name=atlas_name)
+    scene = Scene(atlas_name=atlas_name, check_latest=check_latest)
     if len(regions) == 1:
         regions_actors = [scene.add_brain_region(*regions)]
     else:

pyproject.toml

@@ -6,7 +6,7 @@ readme = "README.md"
 requires-python = ">=3.10"
 dynamic = ["version"]
 
-dependencies = ["brainrender>=2.1.11", "matplotlib", "numpy", "myterial", "rich"]
+dependencies = ["brainrender>=2.1.16", "matplotlib", "numpy", "myterial", "rich"]
 
 license = { text = "MIT" }