From cd65de70bc388ef0b0e178e0d04109f1917e5f3a Mon Sep 17 00:00:00 2001
From: Adam Tyson <code@adamltyson.com>
Date: Fri, 12 Jul 2024 15:05:45 +0100
Subject: [PATCH] Remove template script

---
 .../atlas_scripts/template_script.py          | 75 -------------------
 1 file changed, 75 deletions(-)
 delete mode 100644 brainglobe_atlasapi/atlas_generation/atlas_scripts/template_script.py

diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/template_script.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/template_script.py
deleted file mode 100644
index 9b9229a7..00000000
--- a/brainglobe_atlasapi/atlas_generation/atlas_scripts/template_script.py
+++ /dev/null
@@ -1,75 +0,0 @@
-"""Template script for the generation of an atlas. Note that the script
-has to be renamed to match the name of the atlas (e.g. allen_mouse.py)
-"""
-
-__version__ = "0"  # will be used to set minor version of the atlas
-
-from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data
-
-
-def create_atlas(working_dir, resolution):
-    """Function to generate source data for an atlas.
-
-    Parameters
-    ----------
-    working_dir : Path object
-        Path where atlas will be created.
-    resolution :
-        Resolution of the atlas, in um.
-
-    Returns
-    -------
-    Path object
-        Path to the final compressed atlas file.
-
-    """
-
-    ATLAS_NAME = ""
-    SPECIES = ""
-    ATLAS_LINK = ""
-    CITATION = ""
-    ORIENTATION = ""
-
-    # do stuff to create the atlas
-    template_volume = None  # volume with reference
-    annotated_volume = None  # volume with structures annotations
-    structures_list = None  # list of valid structure dictionaries
-    meshes_dict = None  # dictionary of files with region meshes
-    root_id = None  # id of the root structure
-
-    # Put here additional reference stacks
-    # (different genotypes, filtered volumes, etc)
-    additional_references = dict()
-
-    output_filename = wrapup_atlas_from_data(
-        atlas_name=ATLAS_NAME,
-        atlas_minor_version=__version__,
-        citation=CITATION,
-        atlas_link=ATLAS_LINK,
-        species=SPECIES,
-        resolution=(resolution,) * 3,  # if isotropic - highly recommended
-        orientation=ORIENTATION,
-        root_id=root_id,
-        reference_stack=template_volume,
-        annotation_stack=annotated_volume,
-        structures_list=structures_list,
-        meshes_dict=meshes_dict,
-        working_dir=working_dir,
-        additional_references=additional_references,
-        hemispheres_stack=None,
-        cleanup_files=False,
-        compress=True,
-    )
-
-    return output_filename
-
-
-# To test stuff locally:
-if __name__ == "__main__":
-    resolution = 100  # some resolution, in microns
-
-    # Generated atlas path:
-    bg_root_dir = "/path/to/some/dir"
-    bg_root_dir.mkdir(exist_ok=True)
-
-    create_atlas(bg_root_dir, resolution)