testing and fixing outdated atlas generation scripts (#249)

* first commit, quick fixes of old syntax to try running it on the HPC * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * humanatlas.py: from brainio import brainio has to be installed manually * fixing azba_zfish issue: replace smoothLaplacian with smooth in mesh_utils.py * fixing kim_developmental_ccf_mouse.py issue: pandas syntax and df handling * fixing allen_cord.py: updating source URL * adding packages to dependencies * removing unnecessary comments --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
brainglobe · Mar 1, 2024 · 3c8a581 · 3c8a581
1 parent c733fe9
commit 3c8a581
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Showing 6 changed files with 14 additions and 13 deletions.
diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/admba_3d_dev_mouse.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/admba_3d_dev_mouse.py
@@ -226,9 +226,7 @@ def create_atlas(
     if isinstance(working_dir, str):
         working_dir = Path(working_dir)
     # Generated atlas path:
-    working_dir = (
-        working_dir / "brainglobe_workingdir" / atlas_config.atlas_name
-    )
+    working_dir = working_dir / "admba_3d_dev_mouse" / atlas_config.atlas_name
     working_dir.mkdir(exist_ok=True, parents=True)
 
     download_dir_path = working_dir / "downloads"

diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/allen_cord.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/allen_cord.py
@@ -221,10 +221,7 @@ def create_atlas(working_dir):
     ORIENTATION = "asr"
     RESOLUTION = (20, 10, 10)
     ROOT_ID = 250
-    ATLAS_FILE_URL = (
-        "https://md-datasets-cache-zipfiles-prod.s3.eu-west-1."
-        "amazonaws.com/4rrggzv5d5-1.zip"
-    )
+    ATLAS_FILE_URL = "https://prod-dcd-datasets-cache-zipfiles.s3.eu-west-1.amazonaws.com/4rrggzv5d5-1.zip"
     ATLAS_PACKAGER = "MetaCell LLC, Ltd."
 
     download_dir_path = working_dir / "downloads"

diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/kim_developmental_ccf_mouse.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/kim_developmental_ccf_mouse.py
@@ -133,8 +133,10 @@ def create_atlas(
     df = pd.read_csv(structures_file)
     clean_up_df_entries(df)
 
-    df.loc[len(df)] = ["root", ROOT_ID, "root", ROOT_ID]
-    df.append(["root", ROOT_ID, "root", ROOT_ID])
+    new_row = pd.DataFrame(
+        [["root", ROOT_ID, "root", ROOT_ID]], columns=df.columns
+    )
+    df = pd.concat([df, new_row], ignore_index=True)
 
     id_dict = dict(zip(df["ID"], df["Parent ID"]))
 

diff --git a/brainglobe_atlasapi/atlas_generation/mesh_utils.py b/brainglobe_atlasapi/atlas_generation/mesh_utils.py
@@ -158,10 +158,10 @@ def extract_mesh_from_mask(
         mesh = mesh.extractLargestRegion()
 
     # decimate
-    mesh.decimate(decimate_fraction, method="pro")
+    mesh.decimate_pro(decimate_fraction)
 
     if smooth:
-        mesh.smoothLaplacian()
+        mesh.smooth()
 
     if obj_filepath is not None:
         write(mesh, str(obj_filepath))

diff --git a/brainglobe_atlasapi/atlas_generation/volume_utils.py b/brainglobe_atlasapi/atlas_generation/volume_utils.py
@@ -14,7 +14,7 @@
 
 import os
 
-import imio
+import brainglobe_utils.image_io as image_io
 import numpy as np
 
 
@@ -85,7 +85,7 @@ def load_labelled_volume(data, vmin=0, alpha=1, **kwargs):
             raise FileNotFoundError(f"Volume data file {data} not found")
 
         try:
-            data = imio.load_any(data)
+            data = image_io.load_any(data)
         except Exception as e:
             raise ValueError(
                 f"Could not load volume data from file: {data} - {e}"

diff --git a/pyproject.toml b/pyproject.toml
@@ -37,6 +37,10 @@ dependencies = [
     "treelib",
     "vedo",
     "xmltodict",
+    "scikit-image",
+    "brainio",
+    "brainglobe-utils",
+
 ]
 dynamic = ["version"]