From 7952179eea287731c5de6c2d435c5bc72d4c6755 Mon Sep 17 00:00:00 2001
From: Adam Tyson <code@adamltyson.com>
Date: Thu, 12 Sep 2024 10:27:35 +0100
Subject: [PATCH] Add a new example visualising brainmapper cells in specific
 brain regions. (#382)

* update description to reflect new brainmapper widget

* Add new example plotting cells from brainmapper only in specific regions

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update examples/brainmapper.py

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
---
 examples/brainmapper.py         |  9 +++--
 examples/brainmapper_regions.py | 69 +++++++++++++++++++++++++++++++++
 2 files changed, 75 insertions(+), 3 deletions(-)
 create mode 100644 examples/brainmapper_regions.py

diff --git a/examples/brainmapper.py b/examples/brainmapper.py
index c8891a00..376a401b 100644
--- a/examples/brainmapper.py
+++ b/examples/brainmapper.py
@@ -1,9 +1,12 @@
 """
-Visualise the output from brainmapper. Cells transformed to atlas space can
-be found at brainmapper_output/points/points.npy.
+Visualise the output from brainmapper.
+Cells transformed to atlas space can be found at
+brainmapper_output/points/points.npy or exported by the brainmapper
+napari widget
 
 For more details on brainmapper, please see:
-https://brainglobe.info/documentation/brainglobe-workflows/brainmapper/index.html
+- https://brainglobe.info/documentation/brainglobe-workflows/brainmapper/index.html
+- https://brainglobe.info/documentation/brainglobe-utils/transform-widget.html
 """
 
 from pathlib import Path
diff --git a/examples/brainmapper_regions.py b/examples/brainmapper_regions.py
new file mode 100644
index 00000000..f8528389
--- /dev/null
+++ b/examples/brainmapper_regions.py
@@ -0,0 +1,69 @@
+"""
+Visualise the output from brainmapper in some specific brain regions.
+Cells transformed to atlas space can be found at
+brainmapper_output/points/points.npy or exported by the brainmapper napari
+widget
+
+For more details on brainmapper, please see:
+- https://brainglobe.info/documentation/brainglobe-workflows/brainmapper/index.html
+- https://brainglobe.info/documentation/brainglobe-utils/transform-widget.html
+"""
+
+from pathlib import Path
+
+from myterial import orange
+from rich import print
+
+from brainrender.scene import Scene
+from brainrender.actors import Points
+from brainrender import settings
+
+import numpy as np
+
+settings.SHADER_STYLE = "plastic"
+settings.SHOW_AXES = False
+
+cells_path = Path(__file__).parent.parent / "resources" / "points.npy"
+
+# Define regions of interest (easier to define all at the
+# terminal/finest level of the hierarchy)
+regions = ["VISp1", "VISp4", "VISp5"]
+
+print(f"[{orange}]Running example: {Path(__file__).name}")
+
+
+def get_cells_in_regions(scene, cells_path, regions):
+    cells = np.load(cells_path)
+    new_cells = []
+
+    for cell in cells:
+        if (
+            scene.atlas.structure_from_coords(
+                cell, as_acronym=True, microns=True
+            )
+            in regions
+        ):
+            if cell[0] > 0:
+                new_cells.append(cell)
+
+    new_cells = np.asarray(new_cells)
+
+    return new_cells
+
+
+# Create a brainrender scene
+scene = Scene(title=f"brainmapper cells in {regions}", inset=False)
+
+cells_points = get_cells_in_regions(scene, cells_path, regions)
+
+# Create points actor
+cells = Points(cells_points, radius=45, colors="palegoldenrod", alpha=0.8)
+
+# Add specific regions
+for region in regions:
+    scene.add_brain_region(region, color="mediumseagreen", alpha=0.2)
+
+# Add cells
+scene.add(cells)
+
+scene.render()