From 9793868e156efecf73754eb550eafce5627ca259 Mon Sep 17 00:00:00 2001
From: sfmig <33267254+sfmig@users.noreply.github.com>
Date: Fri, 31 May 2024 17:24:56 +0100
Subject: [PATCH 1/2] add simple benchmark

---
 benchmarks/benchmarks/brainglobe_atlasapi.py  | 19 +++++++++++++++++++
 .../brainglobe_atlasapi/__init__.py           |  0
 .../brainglobe_atlasapi/create_mouse_atlas.py | 10 ++++++++++
 3 files changed, 29 insertions(+)
 create mode 100644 benchmarks/benchmarks/brainglobe_atlasapi.py
 create mode 100644 brainglobe_workflows/brainglobe_atlasapi/__init__.py
 create mode 100644 brainglobe_workflows/brainglobe_atlasapi/create_mouse_atlas.py

diff --git a/benchmarks/benchmarks/brainglobe_atlasapi.py b/benchmarks/benchmarks/brainglobe_atlasapi.py
new file mode 100644
index 00000000..43443ec9
--- /dev/null
+++ b/benchmarks/benchmarks/brainglobe_atlasapi.py
@@ -0,0 +1,19 @@
+from brainglobe_workflows.brainglobe_atlasapi.create_mouse_atlas import (
+    create_mouse_atlas,
+)
+
+
+class TimeBenchmark:
+    # Timing attributes
+    timeout = 3600  # default: 60 s
+    version = (
+        None  # benchmark version. Default:None (i.e. hash of source code)
+    )
+    warmup_time = 0.1  # seconds
+    rounds = 2
+    repeat = 0
+    sample_time = 0.01  # default: 10 ms = 0.01 s;
+    min_run_count = 2  # default:2
+
+    def time_create_mouse_atlas(self):
+        create_mouse_atlas()
diff --git a/brainglobe_workflows/brainglobe_atlasapi/__init__.py b/brainglobe_workflows/brainglobe_atlasapi/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/brainglobe_workflows/brainglobe_atlasapi/create_mouse_atlas.py b/brainglobe_workflows/brainglobe_atlasapi/create_mouse_atlas.py
new file mode 100644
index 00000000..980e6a31
--- /dev/null
+++ b/brainglobe_workflows/brainglobe_atlasapi/create_mouse_atlas.py
@@ -0,0 +1,10 @@
+from brainglobe_atlasapi import BrainGlobeAtlas
+
+
+def create_mouse_atlas():
+    atlas = BrainGlobeAtlas("allen_mouse_100um")
+    print(atlas.atlas_name)
+
+
+if __name__ == "__main__":
+    create_mouse_atlas()

From b86a6b8bc6cc6a31b269551cd5e58fc834d80750 Mon Sep 17 00:00:00 2001
From: sfmig <33267254+sfmig@users.noreply.github.com>
Date: Fri, 31 May 2024 17:54:21 +0100
Subject: [PATCH 2/2] Try with config file

---
 benchmarks/benchmarks/brainglobe_atlasapi.py  | 35 ++++++++++++++-----
 .../brainglobe_atlasapi/create_mouse_atlas.py |  6 ++--
 .../configs/brainglobe_atlasapi_large.json    |  3 ++
 .../configs/brainglobe_atlasapi_small.json    |  3 ++
 4 files changed, 35 insertions(+), 12 deletions(-)
 create mode 100644 brainglobe_workflows/configs/brainglobe_atlasapi_large.json
 create mode 100644 brainglobe_workflows/configs/brainglobe_atlasapi_small.json

diff --git a/benchmarks/benchmarks/brainglobe_atlasapi.py b/benchmarks/benchmarks/brainglobe_atlasapi.py
index 43443ec9..288dc344 100644
--- a/benchmarks/benchmarks/brainglobe_atlasapi.py
+++ b/benchmarks/benchmarks/brainglobe_atlasapi.py
@@ -1,3 +1,7 @@
+import json
+import os
+from pathlib import Path
+
 from brainglobe_workflows.brainglobe_atlasapi.create_mouse_atlas import (
     create_mouse_atlas,
 )
@@ -6,14 +10,27 @@
 class TimeBenchmark:
     # Timing attributes
     timeout = 3600  # default: 60 s
-    version = (
-        None  # benchmark version. Default:None (i.e. hash of source code)
-    )
-    warmup_time = 0.1  # seconds
-    rounds = 2
-    repeat = 0
-    sample_time = 0.01  # default: 10 ms = 0.01 s;
-    min_run_count = 2  # default:2
+
+    def setup(self):
+        # read input config: environment variable if it exists, else default
+        input_config_path = os.getenv(
+            "ATLAS_CONFIG_PATH",
+            default=str(
+                Path(__file__).parents[2]
+                / "brainglobe_workflows"
+                / "configs"
+                / "brainglobe_atlasapi_small.json"
+            ),
+        )
+
+        assert Path(input_config_path).exists()
+
+        # read as dict
+        with open(input_config_path) as cfg:
+            config_dict = json.load(cfg)
+
+        # pass dict to class
+        self.config = config_dict
 
     def time_create_mouse_atlas(self):
-        create_mouse_atlas()
+        create_mouse_atlas(**self.config)
diff --git a/brainglobe_workflows/brainglobe_atlasapi/create_mouse_atlas.py b/brainglobe_workflows/brainglobe_atlasapi/create_mouse_atlas.py
index 980e6a31..a52f96b3 100644
--- a/brainglobe_workflows/brainglobe_atlasapi/create_mouse_atlas.py
+++ b/brainglobe_workflows/brainglobe_atlasapi/create_mouse_atlas.py
@@ -1,10 +1,10 @@
 from brainglobe_atlasapi import BrainGlobeAtlas
 
 
-def create_mouse_atlas():
-    atlas = BrainGlobeAtlas("allen_mouse_100um")
+def create_mouse_atlas(atlas_name):
+    atlas = BrainGlobeAtlas(atlas_name)
     print(atlas.atlas_name)
 
 
 if __name__ == "__main__":
-    create_mouse_atlas()
+    create_mouse_atlas("allen_mouse_100um")
diff --git a/brainglobe_workflows/configs/brainglobe_atlasapi_large.json b/brainglobe_workflows/configs/brainglobe_atlasapi_large.json
new file mode 100644
index 00000000..a999d569
--- /dev/null
+++ b/brainglobe_workflows/configs/brainglobe_atlasapi_large.json
@@ -0,0 +1,3 @@
+{
+    "atlas_name": "allen_mouse_10um"
+}
diff --git a/brainglobe_workflows/configs/brainglobe_atlasapi_small.json b/brainglobe_workflows/configs/brainglobe_atlasapi_small.json
new file mode 100644
index 00000000..a41a627a
--- /dev/null
+++ b/brainglobe_workflows/configs/brainglobe_atlasapi_small.json
@@ -0,0 +1,3 @@
+{
+    "atlas_name": "allen_mouse_100um"
+}