From f0128e7302e06d739dc8a32c918af2278a73ab01 Mon Sep 17 00:00:00 2001
From: Viktor Plattner <plattnerviktor@gmail.com>
Date: Mon, 20 Jan 2025 09:01:01 +0000
Subject: [PATCH 01/14] first commit, refactoring wrapup and validation

---
 .../atlas_generation/validate_atlases.py      | 34 ++++++++++---
 .../atlas_generation/wrapup.py                | 49 +++++++++++++++++++
 2 files changed, 77 insertions(+), 6 deletions(-)

diff --git a/brainglobe_atlasapi/atlas_generation/validate_atlases.py b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
index cf4183e2..d76129d1 100644
--- a/brainglobe_atlasapi/atlas_generation/validate_atlases.py
+++ b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
@@ -15,14 +15,22 @@
 )
 from brainglobe_atlasapi.update_atlases import update_atlas
 
+from brainglobe_atlasapi.config import DEFAULT_WORKDIR
 
 def validate_atlas_files(atlas: BrainGlobeAtlas):
     """Checks if basic files exist in the atlas folder"""
 
+    # atlas_path = (
+    #     Path(get_brainglobe_dir())
+    #     / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
+    # )
+
     atlas_path = (
-        Path(get_brainglobe_dir())
-        / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
+        Path(DEFAULT_WORKDIR
+             / f"{atlas.metadata['name']}"
+             / f"{atlas.atlas_name}_v{atlas.metadata['version']}")
     )
+
     assert atlas_path.is_dir(), f"Atlas path {atlas_path} not found"
     expected_files = [
         "annotation.tiff",
@@ -150,10 +158,17 @@ def catch_missing_mesh_files(atlas: BrainGlobeAtlas):
 
     ids_from_bg_atlas_api = list(atlas.structures.keys())
 
+    # atlas_path = (
+    #     Path(get_brainglobe_dir())
+    #     / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
+    # )
+
     atlas_path = (
-        Path(get_brainglobe_dir())
-        / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
+        Path(DEFAULT_WORKDIR
+             / f"{atlas.metadata['name']}"
+             / f"{atlas.atlas_name}_v{atlas.metadata['version']}")
     )
+
     obj_path = Path(atlas_path / "meshes")
 
     ids_from_mesh_files = [
@@ -182,10 +197,17 @@ def catch_missing_structures(atlas: BrainGlobeAtlas):
 
     ids_from_bg_atlas_api = list(atlas.structures.keys())
 
+    # atlas_path = (
+    #     Path(get_brainglobe_dir())
+    #     / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
+    # )
+
     atlas_path = (
-        Path(get_brainglobe_dir())
-        / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
+        Path(DEFAULT_WORKDIR
+             / f"{atlas.metadata['name']}"
+             / f"{atlas.atlas_name}_v{atlas.metadata['version']}")
     )
+
     obj_path = Path(atlas_path / "meshes")
 
     ids_from_mesh_files = [
diff --git a/brainglobe_atlasapi/atlas_generation/wrapup.py b/brainglobe_atlasapi/atlas_generation/wrapup.py
index fc86fe1d..62a41065 100644
--- a/brainglobe_atlasapi/atlas_generation/wrapup.py
+++ b/brainglobe_atlasapi/atlas_generation/wrapup.py
@@ -24,6 +24,19 @@
 )
 from brainglobe_atlasapi.utils import atlas_name_from_repr
 
+from brainglobe_atlasapi import BrainGlobeAtlas
+from brainglobe_atlasapi.atlas_generation.validate_atlases import (
+    validate_atlas_files,
+    validate_mesh_matches_image_extents,
+    open_for_visual_check,
+    validate_checksum,
+    validate_image_dimensions,
+    validate_additional_references,
+    catch_missing_structures,
+    catch_missing_mesh_files
+)
+
+
 # This should be changed every time we make changes in the atlas
 # structure:
 ATLAS_VERSION = brainglobe_atlasapi.atlas_generation.__version__
@@ -129,6 +142,11 @@ def wrapup_atlas_from_data(
     atlas_dir_name = atlas_name_from_repr(
         atlas_name, resolution[0], ATLAS_VERSION, atlas_minor_version
     )
+
+    atlas_name_for_validation = atlas_name_from_repr(
+        atlas_name, resolution[0]
+    )
+
     dest_dir = Path(working_dir) / atlas_dir_name
 
     # exist_ok would be more permissive but error-prone here as there might
@@ -231,6 +249,36 @@ def wrapup_atlas_from_data(
         additional_metadata=additional_metadata,
     )
 
+    atlas_to_validate = BrainGlobeAtlas(
+        atlas_name=atlas_name_for_validation,
+        brainglobe_dir=working_dir,
+        check_latest=False
+    )
+
+    # Run validation functions
+    print(f"Running atlas validation on {atlas_dir_name}")
+
+    validation_results = {}
+
+    for func in [
+        validate_atlas_files,
+        validate_mesh_matches_image_extents,
+        open_for_visual_check,
+        validate_checksum,
+        validate_image_dimensions,
+        validate_additional_references,
+        catch_missing_structures,
+        catch_missing_mesh_files
+    ]:
+        try:
+            func(atlas_to_validate)
+            validation_results[func.__name__] = "Pass"
+        except AssertionError as e:
+            print(f"Validation failed: {e}")
+            validation_results[func.__name__] = f"Fail: {str(e)}"
+
+    print("Validation complete")
+
     # Compress if required:
     if compress:
         output_filename = dest_dir.parent / f"{dest_dir.name}.tar.gz"
@@ -240,6 +288,7 @@ def wrapup_atlas_from_data(
 
     # Cleanup if required:
     if cleanup_files:
+        print(f"Cleaning up atlas data at: {dest_dir}")
         # Clean temporary directory and remove it:
         shutil.rmtree(dest_dir)
 

From 85b9e8b236c84d174e47a31e97de1eae5a65e6c4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 20 Jan 2025 14:43:05 +0000
Subject: [PATCH 02/14] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../atlas_generation/validate_atlases.py      | 28 +++++++++----------
 .../atlas_generation/wrapup.py                | 25 +++++++----------
 2 files changed, 23 insertions(+), 30 deletions(-)

diff --git a/brainglobe_atlasapi/atlas_generation/validate_atlases.py b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
index d76129d1..5e1b83f9 100644
--- a/brainglobe_atlasapi/atlas_generation/validate_atlases.py
+++ b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
@@ -7,15 +7,13 @@
 import numpy as np
 
 from brainglobe_atlasapi import BrainGlobeAtlas
-from brainglobe_atlasapi.config import get_brainglobe_dir
+from brainglobe_atlasapi.config import DEFAULT_WORKDIR, get_brainglobe_dir
 from brainglobe_atlasapi.list_atlases import (
     get_all_atlases_lastversions,
     get_atlases_lastversions,
-    get_local_atlas_version,
 )
 from brainglobe_atlasapi.update_atlases import update_atlas
 
-from brainglobe_atlasapi.config import DEFAULT_WORKDIR
 
 def validate_atlas_files(atlas: BrainGlobeAtlas):
     """Checks if basic files exist in the atlas folder"""
@@ -25,10 +23,10 @@ def validate_atlas_files(atlas: BrainGlobeAtlas):
     #     / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
     # )
 
-    atlas_path = (
-        Path(DEFAULT_WORKDIR
-             / f"{atlas.metadata['name']}"
-             / f"{atlas.atlas_name}_v{atlas.metadata['version']}")
+    atlas_path = Path(
+        DEFAULT_WORKDIR
+        / f"{atlas.metadata['name']}"
+        / f"{atlas.atlas_name}_v{atlas.metadata['version']}"
     )
 
     assert atlas_path.is_dir(), f"Atlas path {atlas_path} not found"
@@ -163,10 +161,10 @@ def catch_missing_mesh_files(atlas: BrainGlobeAtlas):
     #     / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
     # )
 
-    atlas_path = (
-        Path(DEFAULT_WORKDIR
-             / f"{atlas.metadata['name']}"
-             / f"{atlas.atlas_name}_v{atlas.metadata['version']}")
+    atlas_path = Path(
+        DEFAULT_WORKDIR
+        / f"{atlas.metadata['name']}"
+        / f"{atlas.atlas_name}_v{atlas.metadata['version']}"
     )
 
     obj_path = Path(atlas_path / "meshes")
@@ -202,10 +200,10 @@ def catch_missing_structures(atlas: BrainGlobeAtlas):
     #     / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
     # )
 
-    atlas_path = (
-        Path(DEFAULT_WORKDIR
-             / f"{atlas.metadata['name']}"
-             / f"{atlas.atlas_name}_v{atlas.metadata['version']}")
+    atlas_path = Path(
+        DEFAULT_WORKDIR
+        / f"{atlas.metadata['name']}"
+        / f"{atlas.atlas_name}_v{atlas.metadata['version']}"
     )
 
     obj_path = Path(atlas_path / "meshes")
diff --git a/brainglobe_atlasapi/atlas_generation/wrapup.py b/brainglobe_atlasapi/atlas_generation/wrapup.py
index 62a41065..d0d1f166 100644
--- a/brainglobe_atlasapi/atlas_generation/wrapup.py
+++ b/brainglobe_atlasapi/atlas_generation/wrapup.py
@@ -8,7 +8,7 @@
 import tifffile
 
 import brainglobe_atlasapi.atlas_generation
-from brainglobe_atlasapi import descriptors
+from brainglobe_atlasapi import BrainGlobeAtlas, descriptors
 from brainglobe_atlasapi.atlas_generation.metadata_utils import (
     create_metadata_files,
     generate_metadata_dict,
@@ -22,20 +22,17 @@
 from brainglobe_atlasapi.atlas_generation.structures import (
     check_struct_consistency,
 )
-from brainglobe_atlasapi.utils import atlas_name_from_repr
-
-from brainglobe_atlasapi import BrainGlobeAtlas
 from brainglobe_atlasapi.atlas_generation.validate_atlases import (
-    validate_atlas_files,
-    validate_mesh_matches_image_extents,
+    catch_missing_mesh_files,
+    catch_missing_structures,
     open_for_visual_check,
+    validate_additional_references,
+    validate_atlas_files,
     validate_checksum,
     validate_image_dimensions,
-    validate_additional_references,
-    catch_missing_structures,
-    catch_missing_mesh_files
+    validate_mesh_matches_image_extents,
 )
-
+from brainglobe_atlasapi.utils import atlas_name_from_repr
 
 # This should be changed every time we make changes in the atlas
 # structure:
@@ -143,9 +140,7 @@ def wrapup_atlas_from_data(
         atlas_name, resolution[0], ATLAS_VERSION, atlas_minor_version
     )
 
-    atlas_name_for_validation = atlas_name_from_repr(
-        atlas_name, resolution[0]
-    )
+    atlas_name_for_validation = atlas_name_from_repr(atlas_name, resolution[0])
 
     dest_dir = Path(working_dir) / atlas_dir_name
 
@@ -252,7 +247,7 @@ def wrapup_atlas_from_data(
     atlas_to_validate = BrainGlobeAtlas(
         atlas_name=atlas_name_for_validation,
         brainglobe_dir=working_dir,
-        check_latest=False
+        check_latest=False,
     )
 
     # Run validation functions
@@ -268,7 +263,7 @@ def wrapup_atlas_from_data(
         validate_image_dimensions,
         validate_additional_references,
         catch_missing_structures,
-        catch_missing_mesh_files
+        catch_missing_mesh_files,
     ]:
         try:
             func(atlas_to_validate)

From 31b518bf5cf9ade91f98788076f72e71c85d0acb Mon Sep 17 00:00:00 2001
From: Viktor Plattner <plattnerviktor@gmail.com>
Date: Mon, 20 Jan 2025 16:25:58 +0000
Subject: [PATCH 03/14] adding custom_atlas_path argument to validation
 functions

---
 .../atlas_generation/validate_atlases.py      | 66 +++++++++----------
 .../atlas_generation/wrapup.py                | 36 +++++-----
 2 files changed, 52 insertions(+), 50 deletions(-)

diff --git a/brainglobe_atlasapi/atlas_generation/validate_atlases.py b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
index d76129d1..be108edb 100644
--- a/brainglobe_atlasapi/atlas_generation/validate_atlases.py
+++ b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
@@ -17,19 +17,19 @@
 
 from brainglobe_atlasapi.config import DEFAULT_WORKDIR
 
-def validate_atlas_files(atlas: BrainGlobeAtlas):
+def validate_atlas_files(atlas: BrainGlobeAtlas, custom_atlas_path: Path = None):
     """Checks if basic files exist in the atlas folder"""
 
-    # atlas_path = (
-    #     Path(get_brainglobe_dir())
-    #     / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
-    # )
-
-    atlas_path = (
-        Path(DEFAULT_WORKDIR
-             / f"{atlas.metadata['name']}"
-             / f"{atlas.atlas_name}_v{atlas.metadata['version']}")
-    )
+    if custom_atlas_path is None:
+        atlas_path = (
+                Path(get_brainglobe_dir())
+                / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
+        )
+    else:
+        atlas_path = (
+            Path(custom_atlas_path
+                 / f"{atlas.atlas_name}_v{atlas.metadata['version']}")
+        )
 
     assert atlas_path.is_dir(), f"Atlas path {atlas_path} not found"
     expected_files = [
@@ -151,23 +151,23 @@ def validate_additional_references(atlas: BrainGlobeAtlas):
     return True
 
 
-def catch_missing_mesh_files(atlas: BrainGlobeAtlas):
+def catch_missing_mesh_files(atlas: BrainGlobeAtlas, custom_atlas_path: Path = None):
     """
     Checks if all the structures in the atlas have a corresponding mesh file
     """
 
     ids_from_bg_atlas_api = list(atlas.structures.keys())
 
-    # atlas_path = (
-    #     Path(get_brainglobe_dir())
-    #     / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
-    # )
-
-    atlas_path = (
-        Path(DEFAULT_WORKDIR
-             / f"{atlas.metadata['name']}"
-             / f"{atlas.atlas_name}_v{atlas.metadata['version']}")
-    )
+    if custom_atlas_path is None:
+        atlas_path = (
+                Path(get_brainglobe_dir())
+                / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
+        )
+    else:
+        atlas_path = (
+            Path(custom_atlas_path
+                 / f"{atlas.atlas_name}_v{atlas.metadata['version']}")
+        )
 
     obj_path = Path(atlas_path / "meshes")
 
@@ -189,7 +189,7 @@ def catch_missing_mesh_files(atlas: BrainGlobeAtlas):
         )
 
 
-def catch_missing_structures(atlas: BrainGlobeAtlas):
+def catch_missing_structures(atlas: BrainGlobeAtlas, custom_atlas_path: Path = None):
     """
     Checks if all the mesh files in the atlas folder
     are listed as a structure in the atlas.
@@ -197,16 +197,16 @@ def catch_missing_structures(atlas: BrainGlobeAtlas):
 
     ids_from_bg_atlas_api = list(atlas.structures.keys())
 
-    # atlas_path = (
-    #     Path(get_brainglobe_dir())
-    #     / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
-    # )
-
-    atlas_path = (
-        Path(DEFAULT_WORKDIR
-             / f"{atlas.metadata['name']}"
-             / f"{atlas.atlas_name}_v{atlas.metadata['version']}")
-    )
+    if custom_atlas_path is None:
+        atlas_path = (
+                Path(get_brainglobe_dir())
+                / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
+        )
+    else:
+        atlas_path = (
+            Path(custom_atlas_path
+                 / f"{atlas.atlas_name}_v{atlas.metadata['version']}")
+        )
 
     obj_path = Path(atlas_path / "meshes")
 
diff --git a/brainglobe_atlasapi/atlas_generation/wrapup.py b/brainglobe_atlasapi/atlas_generation/wrapup.py
index 62a41065..417af263 100644
--- a/brainglobe_atlasapi/atlas_generation/wrapup.py
+++ b/brainglobe_atlasapi/atlas_generation/wrapup.py
@@ -143,10 +143,6 @@ def wrapup_atlas_from_data(
         atlas_name, resolution[0], ATLAS_VERSION, atlas_minor_version
     )
 
-    atlas_name_for_validation = atlas_name_from_repr(
-        atlas_name, resolution[0]
-    )
-
     dest_dir = Path(working_dir) / atlas_dir_name
 
     # exist_ok would be more permissive but error-prone here as there might
@@ -249,6 +245,11 @@ def wrapup_atlas_from_data(
         additional_metadata=additional_metadata,
     )
 
+    atlas_name_for_validation = atlas_name_from_repr(
+        atlas_name, resolution[0]
+    )
+
+    # creating BrainGlobe object from local folder (working_dir)
     atlas_to_validate = BrainGlobeAtlas(
         atlas_name=atlas_name_for_validation,
         brainglobe_dir=working_dir,
@@ -260,25 +261,26 @@ def wrapup_atlas_from_data(
 
     validation_results = {}
 
-    for func in [
-        validate_atlas_files,
-        validate_mesh_matches_image_extents,
-        open_for_visual_check,
-        validate_checksum,
-        validate_image_dimensions,
-        validate_additional_references,
-        catch_missing_structures,
-        catch_missing_mesh_files
-    ]:
+    functions = [
+        (validate_atlas_files, atlas_to_validate, working_dir),
+        (catch_missing_structures, atlas_to_validate, working_dir),
+        (catch_missing_mesh_files, atlas_to_validate, working_dir),
+        (validate_mesh_matches_image_extents, atlas_to_validate),
+        (open_for_visual_check, atlas_to_validate),
+        (validate_checksum, atlas_to_validate),
+        (validate_image_dimensions, atlas_to_validate),
+        (validate_additional_references, atlas_to_validate)
+    ]
+
+    for func, *args in functions:
         try:
-            func(atlas_to_validate)
+            func(*args)
             validation_results[func.__name__] = "Pass"
+            print(f"{atlas_dir_name} passed {func.__name__}")
         except AssertionError as e:
             print(f"Validation failed: {e}")
             validation_results[func.__name__] = f"Fail: {str(e)}"
 
-    print("Validation complete")
-
     # Compress if required:
     if compress:
         output_filename = dest_dir.parent / f"{dest_dir.name}.tar.gz"

From ba6a9aa51c3c73c12688f41c3807ba3240dc027c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 20 Jan 2025 16:35:43 +0000
Subject: [PATCH 04/14] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../atlas_generation/validate_atlases.py      | 43 +++++++++++--------
 .../atlas_generation/wrapup.py                | 25 +++++------
 2 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/brainglobe_atlasapi/atlas_generation/validate_atlases.py b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
index be108edb..a3de8500 100644
--- a/brainglobe_atlasapi/atlas_generation/validate_atlases.py
+++ b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
@@ -15,20 +15,21 @@
 )
 from brainglobe_atlasapi.update_atlases import update_atlas
 
-from brainglobe_atlasapi.config import DEFAULT_WORKDIR
 
-def validate_atlas_files(atlas: BrainGlobeAtlas, custom_atlas_path: Path = None):
+def validate_atlas_files(
+    atlas: BrainGlobeAtlas, custom_atlas_path: Path = None
+):
     """Checks if basic files exist in the atlas folder"""
 
     if custom_atlas_path is None:
         atlas_path = (
-                Path(get_brainglobe_dir())
-                / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
+            Path(get_brainglobe_dir())
+            / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
         )
     else:
-        atlas_path = (
-            Path(custom_atlas_path
-                 / f"{atlas.atlas_name}_v{atlas.metadata['version']}")
+        atlas_path = Path(
+            custom_atlas_path
+            / f"{atlas.atlas_name}_v{atlas.metadata['version']}"
         )
 
     assert atlas_path.is_dir(), f"Atlas path {atlas_path} not found"
@@ -151,7 +152,9 @@ def validate_additional_references(atlas: BrainGlobeAtlas):
     return True
 
 
-def catch_missing_mesh_files(atlas: BrainGlobeAtlas, custom_atlas_path: Path = None):
+def catch_missing_mesh_files(
+    atlas: BrainGlobeAtlas, custom_atlas_path: Path = None
+):
     """
     Checks if all the structures in the atlas have a corresponding mesh file
     """
@@ -160,13 +163,13 @@ def catch_missing_mesh_files(atlas: BrainGlobeAtlas, custom_atlas_path: Path = N
 
     if custom_atlas_path is None:
         atlas_path = (
-                Path(get_brainglobe_dir())
-                / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
+            Path(get_brainglobe_dir())
+            / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
         )
     else:
-        atlas_path = (
-            Path(custom_atlas_path
-                 / f"{atlas.atlas_name}_v{atlas.metadata['version']}")
+        atlas_path = Path(
+            custom_atlas_path
+            / f"{atlas.atlas_name}_v{atlas.metadata['version']}"
         )
 
     obj_path = Path(atlas_path / "meshes")
@@ -189,7 +192,9 @@ def catch_missing_mesh_files(atlas: BrainGlobeAtlas, custom_atlas_path: Path = N
         )
 
 
-def catch_missing_structures(atlas: BrainGlobeAtlas, custom_atlas_path: Path = None):
+def catch_missing_structures(
+    atlas: BrainGlobeAtlas, custom_atlas_path: Path = None
+):
     """
     Checks if all the mesh files in the atlas folder
     are listed as a structure in the atlas.
@@ -199,13 +204,13 @@ def catch_missing_structures(atlas: BrainGlobeAtlas, custom_atlas_path: Path = N
 
     if custom_atlas_path is None:
         atlas_path = (
-                Path(get_brainglobe_dir())
-                / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
+            Path(get_brainglobe_dir())
+            / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
         )
     else:
-        atlas_path = (
-            Path(custom_atlas_path
-                 / f"{atlas.atlas_name}_v{atlas.metadata['version']}")
+        atlas_path = Path(
+            custom_atlas_path
+            / f"{atlas.atlas_name}_v{atlas.metadata['version']}"
         )
 
     obj_path = Path(atlas_path / "meshes")
diff --git a/brainglobe_atlasapi/atlas_generation/wrapup.py b/brainglobe_atlasapi/atlas_generation/wrapup.py
index 417af263..5b1a8a82 100644
--- a/brainglobe_atlasapi/atlas_generation/wrapup.py
+++ b/brainglobe_atlasapi/atlas_generation/wrapup.py
@@ -8,7 +8,7 @@
 import tifffile
 
 import brainglobe_atlasapi.atlas_generation
-from brainglobe_atlasapi import descriptors
+from brainglobe_atlasapi import BrainGlobeAtlas, descriptors
 from brainglobe_atlasapi.atlas_generation.metadata_utils import (
     create_metadata_files,
     generate_metadata_dict,
@@ -22,20 +22,17 @@
 from brainglobe_atlasapi.atlas_generation.structures import (
     check_struct_consistency,
 )
-from brainglobe_atlasapi.utils import atlas_name_from_repr
-
-from brainglobe_atlasapi import BrainGlobeAtlas
 from brainglobe_atlasapi.atlas_generation.validate_atlases import (
-    validate_atlas_files,
-    validate_mesh_matches_image_extents,
+    catch_missing_mesh_files,
+    catch_missing_structures,
     open_for_visual_check,
+    validate_additional_references,
+    validate_atlas_files,
     validate_checksum,
     validate_image_dimensions,
-    validate_additional_references,
-    catch_missing_structures,
-    catch_missing_mesh_files
+    validate_mesh_matches_image_extents,
 )
-
+from brainglobe_atlasapi.utils import atlas_name_from_repr
 
 # This should be changed every time we make changes in the atlas
 # structure:
@@ -245,15 +242,13 @@ def wrapup_atlas_from_data(
         additional_metadata=additional_metadata,
     )
 
-    atlas_name_for_validation = atlas_name_from_repr(
-        atlas_name, resolution[0]
-    )
+    atlas_name_for_validation = atlas_name_from_repr(atlas_name, resolution[0])
 
     # creating BrainGlobe object from local folder (working_dir)
     atlas_to_validate = BrainGlobeAtlas(
         atlas_name=atlas_name_for_validation,
         brainglobe_dir=working_dir,
-        check_latest=False
+        check_latest=False,
     )
 
     # Run validation functions
@@ -269,7 +264,7 @@ def wrapup_atlas_from_data(
         (open_for_visual_check, atlas_to_validate),
         (validate_checksum, atlas_to_validate),
         (validate_image_dimensions, atlas_to_validate),
-        (validate_additional_references, atlas_to_validate)
+        (validate_additional_references, atlas_to_validate),
     ]
 
     for func, *args in functions:

From 41b9d283afb6d9de874b2d491e33c0e013a1c643 Mon Sep 17 00:00:00 2001
From: Viktor Plattner <plattnerviktor@gmail.com>
Date: Mon, 20 Jan 2025 17:22:08 +0000
Subject: [PATCH 05/14] updating docstrings

---
 .../atlas_generation/validate_atlases.py      | 28 ++++++++++++++-----
 1 file changed, 21 insertions(+), 7 deletions(-)

diff --git a/brainglobe_atlasapi/atlas_generation/validate_atlases.py b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
index a3de8500..59f73294 100644
--- a/brainglobe_atlasapi/atlas_generation/validate_atlases.py
+++ b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
@@ -19,12 +19,18 @@
 def validate_atlas_files(
     atlas: BrainGlobeAtlas, custom_atlas_path: Path = None
 ):
-    """Checks if basic files exist in the atlas folder"""
+    """
+    Checks if basic files exist in the atlas folder
+
+    custom_atlas_path is used when the function is called as part of
+    the wrapup function in the atlas packaging script. The expected
+    input is working_dir
+    """
 
     if custom_atlas_path is None:
         atlas_path = (
-            Path(get_brainglobe_dir())
-            / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
+            Path(get_brainglobe_dir()) / f"{atlas.atlas_name}_v"
+            f"{get_local_atlas_version(atlas.atlas_name)}"
         )
     else:
         atlas_path = Path(
@@ -157,14 +163,18 @@ def catch_missing_mesh_files(
 ):
     """
     Checks if all the structures in the atlas have a corresponding mesh file
+
+    custom_atlas_path is used when the function is called as part of
+    the wrapup function in the atlas packaging script. The expected
+    input is working_dir
     """
 
     ids_from_bg_atlas_api = list(atlas.structures.keys())
 
     if custom_atlas_path is None:
         atlas_path = (
-            Path(get_brainglobe_dir())
-            / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
+            Path(get_brainglobe_dir()) / f"{atlas.atlas_name}_v"
+            f"{get_local_atlas_version(atlas.atlas_name)}"
         )
     else:
         atlas_path = Path(
@@ -198,14 +208,18 @@ def catch_missing_structures(
     """
     Checks if all the mesh files in the atlas folder
     are listed as a structure in the atlas.
+
+    custom_atlas_path is used when the function is called as part of
+    the wrapup function in the atlas packaging script. The expected
+    input is working_dir
     """
 
     ids_from_bg_atlas_api = list(atlas.structures.keys())
 
     if custom_atlas_path is None:
         atlas_path = (
-            Path(get_brainglobe_dir())
-            / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
+            Path(get_brainglobe_dir()) / f"{atlas.atlas_name}_v"
+            f"{get_local_atlas_version(atlas.atlas_name)}"
         )
     else:
         atlas_path = Path(

From c6ea6b302884728e5d80cc2eeb07551aa36edf19 Mon Sep 17 00:00:00 2001
From: Viktor Plattner <plattnerviktor@gmail.com>
Date: Mon, 20 Jan 2025 17:23:28 +0000
Subject: [PATCH 06/14] updating validation messages

---
 brainglobe_atlasapi/atlas_generation/wrapup.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/brainglobe_atlasapi/atlas_generation/wrapup.py b/brainglobe_atlasapi/atlas_generation/wrapup.py
index 5b1a8a82..92cdc20f 100644
--- a/brainglobe_atlasapi/atlas_generation/wrapup.py
+++ b/brainglobe_atlasapi/atlas_generation/wrapup.py
@@ -271,9 +271,9 @@ def wrapup_atlas_from_data(
         try:
             func(*args)
             validation_results[func.__name__] = "Pass"
-            print(f"{atlas_dir_name} passed {func.__name__}")
+            print(f"passed {func.__name__}")
         except AssertionError as e:
-            print(f"Validation failed: {e}")
+            print(f"failed {func.__name__}: {e}")
             validation_results[func.__name__] = f"Fail: {str(e)}"
 
     # Compress if required:

From 76873203034c72022657e0ad0eff8988c90b620b Mon Sep 17 00:00:00 2001
From: Viktor Plattner <plattnerviktor@gmail.com>
Date: Thu, 23 Jan 2025 18:48:59 +0000
Subject: [PATCH 07/14] simplifying atlas path

---
 .../atlas_generation/validate_atlases.py          | 15 +++------------
 brainglobe_atlasapi/atlas_generation/wrapup.py    | 14 +++++++++++---
 2 files changed, 14 insertions(+), 15 deletions(-)

diff --git a/brainglobe_atlasapi/atlas_generation/validate_atlases.py b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
index 59f73294..7638018a 100644
--- a/brainglobe_atlasapi/atlas_generation/validate_atlases.py
+++ b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
@@ -33,10 +33,7 @@ def validate_atlas_files(
             f"{get_local_atlas_version(atlas.atlas_name)}"
         )
     else:
-        atlas_path = Path(
-            custom_atlas_path
-            / f"{atlas.atlas_name}_v{atlas.metadata['version']}"
-        )
+        atlas_path = custom_atlas_path
 
     assert atlas_path.is_dir(), f"Atlas path {atlas_path} not found"
     expected_files = [
@@ -177,10 +174,7 @@ def catch_missing_mesh_files(
             f"{get_local_atlas_version(atlas.atlas_name)}"
         )
     else:
-        atlas_path = Path(
-            custom_atlas_path
-            / f"{atlas.atlas_name}_v{atlas.metadata['version']}"
-        )
+        atlas_path = custom_atlas_path
 
     obj_path = Path(atlas_path / "meshes")
 
@@ -222,10 +216,7 @@ def catch_missing_structures(
             f"{get_local_atlas_version(atlas.atlas_name)}"
         )
     else:
-        atlas_path = Path(
-            custom_atlas_path
-            / f"{atlas.atlas_name}_v{atlas.metadata['version']}"
-        )
+        atlas_path = custom_atlas_path
 
     obj_path = Path(atlas_path / "meshes")
 
diff --git a/brainglobe_atlasapi/atlas_generation/wrapup.py b/brainglobe_atlasapi/atlas_generation/wrapup.py
index 92cdc20f..5aa38d5c 100644
--- a/brainglobe_atlasapi/atlas_generation/wrapup.py
+++ b/brainglobe_atlasapi/atlas_generation/wrapup.py
@@ -257,9 +257,17 @@ def wrapup_atlas_from_data(
     validation_results = {}
 
     functions = [
-        (validate_atlas_files, atlas_to_validate, working_dir),
-        (catch_missing_structures, atlas_to_validate, working_dir),
-        (catch_missing_mesh_files, atlas_to_validate, working_dir),
+        (validate_atlas_files, atlas_to_validate, atlas_to_validate.root_dir),
+        (
+            catch_missing_structures,
+            atlas_to_validate,
+            atlas_to_validate.root_dir,
+        ),
+        (
+            catch_missing_mesh_files,
+            atlas_to_validate,
+            atlas_to_validate.root_dir,
+        ),
         (validate_mesh_matches_image_extents, atlas_to_validate),
         (open_for_visual_check, atlas_to_validate),
         (validate_checksum, atlas_to_validate),

From 5676c35189f46916becb67111c9111ef2077bc45 Mon Sep 17 00:00:00 2001
From: Viktor Plattner <plattnerviktor@gmail.com>
Date: Thu, 23 Jan 2025 19:16:14 +0000
Subject: [PATCH 08/14] simplifying validation print output, adding helper
 function to check if all validations passed

---
 .../atlas_generation/wrapup.py                | 28 +++++++++++++++++--
 1 file changed, 26 insertions(+), 2 deletions(-)

diff --git a/brainglobe_atlasapi/atlas_generation/wrapup.py b/brainglobe_atlasapi/atlas_generation/wrapup.py
index 5aa38d5c..d0364944 100644
--- a/brainglobe_atlasapi/atlas_generation/wrapup.py
+++ b/brainglobe_atlasapi/atlas_generation/wrapup.py
@@ -279,11 +279,35 @@ def wrapup_atlas_from_data(
         try:
             func(*args)
             validation_results[func.__name__] = "Pass"
-            print(f"passed {func.__name__}")
         except AssertionError as e:
-            print(f"failed {func.__name__}: {e}")
             validation_results[func.__name__] = f"Fail: {str(e)}"
 
+    def _check_validations(validation_results):
+        # Helper function to check if all validations passed
+        all_passed = all(
+            result == "Pass" for result in validation_results.values()
+        )
+
+        if all_passed:
+            print("This atlas is valid")
+        else:
+            failed_functions = [
+                func
+                for func, result in validation_results.items()
+                if result != "Pass"
+            ]
+            error_messages = [
+                result.split(": ")[1]
+                for result in validation_results.values()
+                if result != "Pass"
+            ]
+
+            print("These validation functions have failed:")
+            for func, error in zip(failed_functions, error_messages):
+                print(f"- {func}: {error}")
+
+    _check_validations(validation_results)
+
     # Compress if required:
     if compress:
         output_filename = dest_dir.parent / f"{dest_dir.name}.tar.gz"

From 1fa55e8b81268abbbd6c0de60211be56ae5df2a7 Mon Sep 17 00:00:00 2001
From: Viktor Plattner <plattnerviktor@gmail.com>
Date: Fri, 7 Feb 2025 12:58:18 +0000
Subject: [PATCH 09/14] replacing custom_atlas_path by atlas.root_dir

---
 .../atlas_generation/validate_atlases.py      | 37 +++----------------
 .../atlas_generation/wrapup.py                | 14 ++-----
 2 files changed, 9 insertions(+), 42 deletions(-)

diff --git a/brainglobe_atlasapi/atlas_generation/validate_atlases.py b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
index 7638018a..17d1adf1 100644
--- a/brainglobe_atlasapi/atlas_generation/validate_atlases.py
+++ b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
@@ -11,14 +11,11 @@
 from brainglobe_atlasapi.list_atlases import (
     get_all_atlases_lastversions,
     get_atlases_lastversions,
-    get_local_atlas_version,
 )
 from brainglobe_atlasapi.update_atlases import update_atlas
 
 
-def validate_atlas_files(
-    atlas: BrainGlobeAtlas, custom_atlas_path: Path = None
-):
+def validate_atlas_files(atlas: BrainGlobeAtlas):
     """
     Checks if basic files exist in the atlas folder
 
@@ -27,13 +24,7 @@ def validate_atlas_files(
     input is working_dir
     """
 
-    if custom_atlas_path is None:
-        atlas_path = (
-            Path(get_brainglobe_dir()) / f"{atlas.atlas_name}_v"
-            f"{get_local_atlas_version(atlas.atlas_name)}"
-        )
-    else:
-        atlas_path = custom_atlas_path
+    atlas_path = atlas.root_dir
 
     assert atlas_path.is_dir(), f"Atlas path {atlas_path} not found"
     expected_files = [
@@ -155,9 +146,7 @@ def validate_additional_references(atlas: BrainGlobeAtlas):
     return True
 
 
-def catch_missing_mesh_files(
-    atlas: BrainGlobeAtlas, custom_atlas_path: Path = None
-):
+def catch_missing_mesh_files(atlas: BrainGlobeAtlas):
     """
     Checks if all the structures in the atlas have a corresponding mesh file
 
@@ -168,13 +157,7 @@ def catch_missing_mesh_files(
 
     ids_from_bg_atlas_api = list(atlas.structures.keys())
 
-    if custom_atlas_path is None:
-        atlas_path = (
-            Path(get_brainglobe_dir()) / f"{atlas.atlas_name}_v"
-            f"{get_local_atlas_version(atlas.atlas_name)}"
-        )
-    else:
-        atlas_path = custom_atlas_path
+    atlas_path = atlas.root_dir
 
     obj_path = Path(atlas_path / "meshes")
 
@@ -196,9 +179,7 @@ def catch_missing_mesh_files(
         )
 
 
-def catch_missing_structures(
-    atlas: BrainGlobeAtlas, custom_atlas_path: Path = None
-):
+def catch_missing_structures(atlas: BrainGlobeAtlas):
     """
     Checks if all the mesh files in the atlas folder
     are listed as a structure in the atlas.
@@ -210,13 +191,7 @@ def catch_missing_structures(
 
     ids_from_bg_atlas_api = list(atlas.structures.keys())
 
-    if custom_atlas_path is None:
-        atlas_path = (
-            Path(get_brainglobe_dir()) / f"{atlas.atlas_name}_v"
-            f"{get_local_atlas_version(atlas.atlas_name)}"
-        )
-    else:
-        atlas_path = custom_atlas_path
+    atlas_path = atlas.root_dir
 
     obj_path = Path(atlas_path / "meshes")
 
diff --git a/brainglobe_atlasapi/atlas_generation/wrapup.py b/brainglobe_atlasapi/atlas_generation/wrapup.py
index d0364944..06002024 100644
--- a/brainglobe_atlasapi/atlas_generation/wrapup.py
+++ b/brainglobe_atlasapi/atlas_generation/wrapup.py
@@ -257,17 +257,9 @@ def wrapup_atlas_from_data(
     validation_results = {}
 
     functions = [
-        (validate_atlas_files, atlas_to_validate, atlas_to_validate.root_dir),
-        (
-            catch_missing_structures,
-            atlas_to_validate,
-            atlas_to_validate.root_dir,
-        ),
-        (
-            catch_missing_mesh_files,
-            atlas_to_validate,
-            atlas_to_validate.root_dir,
-        ),
+        (validate_atlas_files, atlas_to_validate),
+        (catch_missing_structures, atlas_to_validate),
+        (catch_missing_mesh_files, atlas_to_validate),
         (validate_mesh_matches_image_extents, atlas_to_validate),
         (open_for_visual_check, atlas_to_validate),
         (validate_checksum, atlas_to_validate),

From ed011a24f0a43e75191f1f5852f42760954467c3 Mon Sep 17 00:00:00 2001
From: Viktor Plattner <plattnerviktor@gmail.com>
Date: Fri, 7 Feb 2025 13:35:47 +0000
Subject: [PATCH 10/14] adding new validation functions from main

---
 brainglobe_atlasapi/atlas_generation/validate_atlases.py | 5 +++++
 brainglobe_atlasapi/atlas_generation/wrapup.py           | 6 ++++++
 2 files changed, 11 insertions(+)

diff --git a/brainglobe_atlasapi/atlas_generation/validate_atlases.py b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
index 04b25138..38f438e2 100644
--- a/brainglobe_atlasapi/atlas_generation/validate_atlases.py
+++ b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
@@ -259,6 +259,8 @@ def get_all_validation_functions():
     return [
         validate_atlas_files,
         validate_mesh_matches_image_extents,
+        open_for_visual_check,
+        validate_checksum,
         validate_image_dimensions,
         validate_additional_references,
         catch_missing_mesh_files,
@@ -305,6 +307,9 @@ def validate_atlas(atlas_name, version, validation_functions):
         validate_additional_references,
         catch_missing_mesh_files,
         catch_missing_structures,
+        validate_reference_image_pixels,
+        validate_annotation_symmetry,
+        validate_atlas_name,
     ]
 
     valid_atlases = []
diff --git a/brainglobe_atlasapi/atlas_generation/wrapup.py b/brainglobe_atlasapi/atlas_generation/wrapup.py
index 06002024..1b04dab0 100644
--- a/brainglobe_atlasapi/atlas_generation/wrapup.py
+++ b/brainglobe_atlasapi/atlas_generation/wrapup.py
@@ -27,10 +27,13 @@
     catch_missing_structures,
     open_for_visual_check,
     validate_additional_references,
+    validate_annotation_symmetry,
     validate_atlas_files,
+    validate_atlas_name,
     validate_checksum,
     validate_image_dimensions,
     validate_mesh_matches_image_extents,
+    validate_reference_image_pixels,
 )
 from brainglobe_atlasapi.utils import atlas_name_from_repr
 
@@ -265,6 +268,9 @@ def wrapup_atlas_from_data(
         (validate_checksum, atlas_to_validate),
         (validate_image_dimensions, atlas_to_validate),
         (validate_additional_references, atlas_to_validate),
+        (validate_reference_image_pixels, atlas_to_validate),
+        (validate_annotation_symmetry, atlas_to_validate),
+        (validate_atlas_name, atlas_to_validate),
     ]
 
     for func, *args in functions:

From e13b34e11818d23e15e1064fe08c32a670d2bb0a Mon Sep 17 00:00:00 2001
From: viktorpm <50667179+viktorpm@users.noreply.github.com>
Date: Tue, 11 Feb 2025 13:20:22 +0000
Subject: [PATCH 11/14] Update
 brainglobe_atlasapi/atlas_generation/validate_atlases.py

Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com>
---
 brainglobe_atlasapi/atlas_generation/validate_atlases.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/brainglobe_atlasapi/atlas_generation/validate_atlases.py b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
index 38f438e2..3b5d9553 100644
--- a/brainglobe_atlasapi/atlas_generation/validate_atlases.py
+++ b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
@@ -185,10 +185,6 @@ def catch_missing_structures(atlas: BrainGlobeAtlas):
     """
     Checks if all the mesh files in the atlas folder
     are listed as a structure in the atlas.
-
-    custom_atlas_path is used when the function is called as part of
-    the wrapup function in the atlas packaging script. The expected
-    input is working_dir
     """
 
     ids_from_bg_atlas_api = list(atlas.structures.keys())

From 607816b371357fb5ef08bf27567d6f1411ba6846 Mon Sep 17 00:00:00 2001
From: viktorpm <50667179+viktorpm@users.noreply.github.com>
Date: Tue, 11 Feb 2025 13:22:02 +0000
Subject: [PATCH 12/14] Update brainglobe_atlasapi/atlas_generation/wrapup.py

Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com>
---
 brainglobe_atlasapi/atlas_generation/wrapup.py | 14 +-------------
 1 file changed, 1 insertion(+), 13 deletions(-)

diff --git a/brainglobe_atlasapi/atlas_generation/wrapup.py b/brainglobe_atlasapi/atlas_generation/wrapup.py
index 1b04dab0..76c0b3c5 100644
--- a/brainglobe_atlasapi/atlas_generation/wrapup.py
+++ b/brainglobe_atlasapi/atlas_generation/wrapup.py
@@ -22,19 +22,7 @@
 from brainglobe_atlasapi.atlas_generation.structures import (
     check_struct_consistency,
 )
-from brainglobe_atlasapi.atlas_generation.validate_atlases import (
-    catch_missing_mesh_files,
-    catch_missing_structures,
-    open_for_visual_check,
-    validate_additional_references,
-    validate_annotation_symmetry,
-    validate_atlas_files,
-    validate_atlas_name,
-    validate_checksum,
-    validate_image_dimensions,
-    validate_mesh_matches_image_extents,
-    validate_reference_image_pixels,
-)
+from brainglobe_atlasapi.atlas_generation.validate_atlases import get_all_validation_functions
 from brainglobe_atlasapi.utils import atlas_name_from_repr
 
 # This should be changed every time we make changes in the atlas

From 057bd97efa41da1f8e3cc2cb0778f115e2f674f4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 11 Feb 2025 13:22:10 +0000
Subject: [PATCH 13/14] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 brainglobe_atlasapi/atlas_generation/wrapup.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/brainglobe_atlasapi/atlas_generation/wrapup.py b/brainglobe_atlasapi/atlas_generation/wrapup.py
index 76c0b3c5..7d2598c5 100644
--- a/brainglobe_atlasapi/atlas_generation/wrapup.py
+++ b/brainglobe_atlasapi/atlas_generation/wrapup.py
@@ -22,7 +22,6 @@
 from brainglobe_atlasapi.atlas_generation.structures import (
     check_struct_consistency,
 )
-from brainglobe_atlasapi.atlas_generation.validate_atlases import get_all_validation_functions
 from brainglobe_atlasapi.utils import atlas_name_from_repr
 
 # This should be changed every time we make changes in the atlas

From 932f6c1f9d49bad3dcde218f5036d8757828ff3b Mon Sep 17 00:00:00 2001
From: Viktor Plattner <plattnerviktor@gmail.com>
Date: Tue, 11 Feb 2025 13:47:11 +0000
Subject: [PATCH 14/14] Refactor atlas validation to use
 `get_all_validation_functions()`

- Replaced hardcoded list of validation functions in `wrapup.py` with `get_all_validation_functions()` for better maintainability.
- Modified `validate_atlases.py` to return `True` instead of `pass` for unimplemented validation functions.
---
 .../atlas_generation/validate_atlases.py      |  4 ++--
 .../atlas_generation/wrapup.py                | 21 +++++--------------
 2 files changed, 7 insertions(+), 18 deletions(-)

diff --git a/brainglobe_atlasapi/atlas_generation/validate_atlases.py b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
index 3b5d9553..908fd789 100644
--- a/brainglobe_atlasapi/atlas_generation/validate_atlases.py
+++ b/brainglobe_atlasapi/atlas_generation/validate_atlases.py
@@ -107,12 +107,12 @@ def validate_mesh_matches_image_extents(atlas: BrainGlobeAtlas):
 
 def open_for_visual_check(atlas: BrainGlobeAtlas):
     # implement visual checks later
-    pass
+    return True
 
 
 def validate_checksum(atlas: BrainGlobeAtlas):
     # implement later
-    pass
+    return True
 
 
 def validate_image_dimensions(atlas: BrainGlobeAtlas):
diff --git a/brainglobe_atlasapi/atlas_generation/wrapup.py b/brainglobe_atlasapi/atlas_generation/wrapup.py
index 7d2598c5..ab6e096b 100644
--- a/brainglobe_atlasapi/atlas_generation/wrapup.py
+++ b/brainglobe_atlasapi/atlas_generation/wrapup.py
@@ -22,6 +22,9 @@
 from brainglobe_atlasapi.atlas_generation.structures import (
     check_struct_consistency,
 )
+from brainglobe_atlasapi.atlas_generation.validate_atlases import (
+    get_all_validation_functions,
+)
 from brainglobe_atlasapi.utils import atlas_name_from_repr
 
 # This should be changed every time we make changes in the atlas
@@ -246,23 +249,9 @@ def wrapup_atlas_from_data(
 
     validation_results = {}
 
-    functions = [
-        (validate_atlas_files, atlas_to_validate),
-        (catch_missing_structures, atlas_to_validate),
-        (catch_missing_mesh_files, atlas_to_validate),
-        (validate_mesh_matches_image_extents, atlas_to_validate),
-        (open_for_visual_check, atlas_to_validate),
-        (validate_checksum, atlas_to_validate),
-        (validate_image_dimensions, atlas_to_validate),
-        (validate_additional_references, atlas_to_validate),
-        (validate_reference_image_pixels, atlas_to_validate),
-        (validate_annotation_symmetry, atlas_to_validate),
-        (validate_atlas_name, atlas_to_validate),
-    ]
-
-    for func, *args in functions:
+    for func in get_all_validation_functions():
         try:
-            func(*args)
+            func(atlas_to_validate)
             validation_results[func.__name__] = "Pass"
         except AssertionError as e:
             validation_results[func.__name__] = f"Fail: {str(e)}"