Restructuring code: metadata on top

brainglobe_atlasapi/atlas_generation/atlas_scripts/allen_cord.py

@@ -1,6 +1,4 @@
-__version__ = "1"
-__atlas__ = "allen_cord"
-
+### Import
 import json
 import multiprocessing as mp
 import time
@@ -14,8 +12,6 @@
 from loguru import logger
 from rich.progress import track
 
-# import sys
-# sys.path.append("./")
 from brainglobe_atlasapi import utils
 from brainglobe_atlasapi.atlas_generation.mesh_utils import (
     Region,
@@ -26,9 +22,23 @@
 from brainglobe_atlasapi.config import DEFAULT_WORKDIR
 from brainglobe_atlasapi.structure_tree_util import get_structures_tree
 
+### Settings
 PARALLEL = True
 TEST = False
 
+### Metadata
+__version__ = "1"
+
+ATLAS_NAME = "allen_cord"
+SPECIES = "Mus musculus"
+ATLAS_LINK = "https://data.mendeley.com/datasets/4rrggzv5d5/1"
+CITATION = "Fiederling et al. 2021, https://doi.org/10.1101/2021.05.06.443008"
+ORIENTATION = "asr"
+RESOLUTION = (20, 10, 10)
+ROOT_ID = 250
+ATLAS_FILE_URL = "https://prod-dcd-datasets-cache-zipfiles.s3.eu-west-1.amazonaws.com/4rrggzv5d5-1.zip"
+ATLAS_PACKAGER = "MetaCell LLC, Ltd."
+
 
 def download_atlas_files(download_dir_path: Path, atlas_file_url: str) -> Path:
     utils.check_internet_connection()
@@ -41,7 +51,7 @@ def download_atlas_files(download_dir_path: Path, atlas_file_url: str) -> Path:
         processor=pooch.Unzip(extract_dir="."),
     )
 
-    atlas_files_dir = download_dir_path / "SC_P56_Atlas_1bg0x10x20_v5_2020"
+    atlas_files_dir = download_dir_path / "SC_P56_Atlas_10x10x20_v5_2020"
 
     return atlas_files_dir
 
@@ -208,17 +218,17 @@ def create_mesh_dict(structures, meshes_dir_path):
 
 
 def create_atlas(working_dir):
-    ATLAS_NAME = "allen_cord"
-    SPECIES = "Mus musculus"
-    ATLAS_LINK = "https://data.mendeley.com/datasets/4rrggzv5d5/1"
-    CITATION = (
-        "Fiederling et al. 2021, https://doi.org/10.1101/2021.05.06.443008"
-    )
-    ORIENTATION = "asr"
-    RESOLUTION = (20, 10, 10)
-    ROOT_ID = 250
-    ATLAS_FILE_URL = "https://prod-dcd-datasets-cache-zipfiles.s3.eu-west-1.amazonaws.com/4rrggzv5d5-1.zip"
-    ATLAS_PACKAGER = "MetaCell LLC, Ltd."
+    # ATLAS_NAME = "allen_cord"
+    # SPECIES = "Mus musculus"
+    # ATLAS_LINK = "https://data.mendeley.com/datasets/4rrggzv5d5/1"
+    # CITATION = (
+    #     "Fiederling et al. 2021, https://doi.org/10.1101/2021.05.06.443008"
+    # )
+    # ORIENTATION = "asr"
+    # RESOLUTION = (20, 10, 10)
+    # ROOT_ID = 250
+    # 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"
     download_dir_path.mkdir(exist_ok=True)
@@ -288,7 +298,7 @@ def create_atlas(working_dir):
 
 if __name__ == "__main__":
     # Generated atlas path:
-    bg_root_dir = DEFAULT_WORKDIR / __atlas__
+    bg_root_dir = DEFAULT_WORKDIR / ATLAS_NAME
     bg_root_dir.mkdir(exist_ok=True, parents=True)
 
     # generate atlas

brainglobe_atlasapi/atlas_generation/atlas_scripts/allen_mouse.py

@@ -1,7 +1,4 @@
-__version__ = "2"
-__atlas__ = "allen_mouse"
-
-
+### Import
 from allensdk.api.queries.ontologies_api import OntologiesApi
 from allensdk.api.queries.reference_space_api import ReferenceSpaceApi
 from allensdk.core.reference_space_cache import ReferenceSpaceCache
@@ -12,14 +9,18 @@
 from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data
 from brainglobe_atlasapi.config import DEFAULT_WORKDIR
 
+### Metadata
+__version__ = "2"
+
+ATLAS_NAME = "allen_mouse"
+SPECIES = "Mus musculus"
+ATLAS_LINK = "http://www.brain-map.org"
+CITATION = "Wang et al 2020, https://doi.org/10.1016/j.cell.2020.04.007"
+ORIENTATION = "asr"
+RES_UM = 25
+
 
 def create_atlas(working_dir, resolution):
-    # Specify information about the atlas:
-    ATLAS_NAME = "allen_mouse"
-    SPECIES = "Mus musculus"
-    ATLAS_LINK = "http://www.brain-map.org"
-    CITATION = "Wang et al 2020, https://doi.org/10.1016/j.cell.2020.04.007"
-    ORIENTATION = "asr"
 
     # Temporary folder for nrrd files download:
     download_dir_path = working_dir / "downloading_path"
@@ -108,9 +109,8 @@ def create_atlas(working_dir, resolution):
 
 
 if __name__ == "__main__":
-    RES_UM = 25
     # Generated atlas path:
-    bg_root_dir = DEFAULT_WORKDIR / __atlas__
+    bg_root_dir = DEFAULT_WORKDIR / ATLAS_NAME
     bg_root_dir.mkdir(exist_ok=True)
 
     create_atlas(bg_root_dir, RES_UM)

brainglobe_atlasapi/atlas_generation/atlas_scripts/allen_mouse_bluebrain_barrels.py

@@ -1,7 +1,4 @@
-__version__ = "0"
-__atlas__ = "allen_mouse_bluebrain_barrels"
-
-
+### Import
 import json
 import time
 
@@ -25,18 +22,21 @@
 from brainglobe_atlasapi.config import DEFAULT_WORKDIR
 from brainglobe_atlasapi.structure_tree_util import get_structures_tree
 
+### Metadata
+__version__ = "0"
+
+ATLAS_NAME = "allen_mouse_bluebrain_barrels"
+SPECIES = "Mus musculus"
+ATLAS_LINK = "http://www.brain-map.org"
+CITATION = "Bolaños-Puchet S., Teska A., et al. (2024).  https://doi.org/10.1162/imag_a_00209"
+ATLAS_PACKAGER = "Axel Bisi"
+ORIENTATION = "asr"
+ROOT_ID = 997
+RES_UM = 25
 
-def create_atlas(working_dir, resolution):
-    # Specify information about the atlas:
-    ATLAS_NAME = "allen_mouse_bluebrain_barrels"
-    SPECIES = "Mus musculus"
-    ATLAS_LINK = "http://www.brain-map.org"
-    CITATION = "Bolaños-Puchet S., Teska A., et al. (2024).  https://doi.org/10.1162/imag_a_00209"
-    ATLAS_PACKAGER = "Axel Bisi"
-    ORIENTATION = "asr"
 
+def create_atlas(working_dir, resolution):
     # Parameters for mesh creation:
-    ROOT_ID = 997
     CLOSING_N_ITERS = 2
     DECIMATE_FRACTION = 0.3
     SMOOTH = True
@@ -368,9 +368,8 @@ def recurse(sub_d):
 
 
 if __name__ == "__main__":
-    RES_UM = 25
     # Generated atlas path:
-    bg_root_dir = DEFAULT_WORKDIR / __atlas__
+    bg_root_dir = DEFAULT_WORKDIR / ATLAS_NAME
     bg_root_dir.mkdir(exist_ok=True)
 
     create_atlas(bg_root_dir, RES_UM)

brainglobe_atlasapi/atlas_generation/atlas_scripts/azba_zfish.py

@@ -5,9 +5,7 @@
 @author: Kailyn Fields, [email protected]
 """
 
-__version__ = "2"
-__atlas__ = "azba_zfish"
-
+### Import
 import csv
 import time
 
@@ -24,18 +22,22 @@
 from brainglobe_atlasapi.config import DEFAULT_WORKDIR
 from brainglobe_atlasapi.structure_tree_util import get_structures_tree
 
+### Metadata
+__version__ = "2"
+
+ATLAS_NAME = "azba_zfish"
+SPECIES = "Danio rerio"
+ATLAS_LINK = "http://www.azba.wayne.edu"
+CITATION = "Kenney et al. 2021, https://doi.org/10.7554/elife.69988"
+ATLAS_FILE_URL = "http://www.azba.wayne.edu/2021-08-22_AZBA.tar.gz"
+ORIENTATION = "las"
+ROOT_ID = 9999
+ATLAS_PACKAGER = "Kailyn Fields, [email protected]"
+ADDITIONAL_METADATA = {}
+RESOLUTION = 4
+
 
 def create_atlas(working_dir, resolution):
-    # metadata
-    ATLAS_NAME = "azba_zfish"
-    SPECIES = "Danio rerio"
-    ATLAS_LINK = "http://www.azba.wayne.edu"
-    CITATION = "Kenney et al. 2021, https://doi.org/10.7554/elife.69988"
-    ATLAS_FILE_URL = "http://www.azba.wayne.edu/2021-08-22_AZBA.tar.gz"
-    ORIENTATION = "las"
-    ROOT_ID = 9999
-    ATLAS_PACKAGER = "Kailyn Fields, [email protected]"
-    ADDITIONAL_METADATA = {}
 
     working_dir = working_dir
     download_path = working_dir / "downloads"
@@ -203,8 +205,6 @@ def create_atlas(working_dir, resolution):
 
 
 if __name__ == "__main__":
-    resolution = 4
-
     # generated atlas path
-    bg_root_dir = DEFAULT_WORKDIR / __atlas__
-    create_atlas(bg_root_dir, resolution)
+    bg_root_dir = DEFAULT_WORKDIR / ATLAS_NAME
+    create_atlas(bg_root_dir, RESOLUTION)

brainglobe_atlasapi/atlas_generation/atlas_scripts/cavefish_atlas.py

@@ -1,8 +1,7 @@
 __version__ = "0"
-__atlas__ = "sju_cavefish"
 
+### Import
 import csv
-import glob as glob
 import time
 from pathlib import Path
 
@@ -22,18 +21,20 @@
 from brainglobe_atlasapi.config import DEFAULT_WORKDIR
 from brainglobe_atlasapi.structure_tree_util import get_structures_tree
 
+### Metadata
+ATLAS_NAME = "sju_cavefish"
+SPECIES = "Astyanax mexicanus"
+ATLAS_LINK = "https://a-cavefishneuroevoluti.vev.site/lab-website"
+CITATION = "Kozol et al. 2023, https://doi.org/10.7554/eLife.80777"
+ATLAS_FILE_URL = "https://cdn.vev.design/private/30dLuULhwBhk45Fm8dHoSpD6uG12/35s9sm-asty-atlas.zip"
+ORIENTATION = "sla"
+ROOT_ID = 999
+ATLAS_PACKAGER = "Robert Kozol, [email protected]"
+ADDITIONAL_METADATA = {}
+RESOLUTION = 2, 2, 2
 
-def create_atlas(working_dir, resolution):
-    ATLAS_NAME = "sju_cavefish"
-    SPECIES = "Astyanax mexicanus"
-    ATLAS_LINK = "https://a-cavefishneuroevoluti.vev.site/lab-website"
-    CITATION = "Kozol et al. 2023, https://doi.org/10.7554/eLife.80777"
-    ATLAS_FILE_URL = "https://cdn.vev.design/private/30dLuULhwBhk45Fm8dHoSpD6uG12/35s9sm-asty-atlas.zip"
-    ORIENTATION = "sla"
-    ROOT_ID = 999
-    ATLAS_PACKAGER = "Robert Kozol, [email protected]"
-    ADDITIONAL_METADATA = {}
 
+def create_atlas(working_dir, resolution):
     # setup folder for downloading
 
     download_dir_path = working_dir / "downloads"
@@ -208,9 +209,8 @@ def create_atlas(working_dir, resolution):
 
 
 if __name__ == "__main__":
-    res = 2, 2, 2
     home = str(Path.home())
-    bg_root_dir = DEFAULT_WORKDIR / __atlas__
+    bg_root_dir = DEFAULT_WORKDIR / ATLAS_NAME
     bg_root_dir.mkdir(exist_ok=True, parents=True)
 
-    create_atlas(bg_root_dir, res)
+    create_atlas(bg_root_dir, RESOLUTION)

brainglobe_atlasapi/atlas_generation/atlas_scripts/example_mouse.py

@@ -1,7 +1,6 @@
 __version__ = "2"
-__atlas__ = "example_mouse"
-
 
+### Import
 from allensdk.api.queries.ontologies_api import OntologiesApi
 from allensdk.api.queries.reference_space_api import ReferenceSpaceApi
 from allensdk.core.reference_space_cache import ReferenceSpaceCache
@@ -11,16 +10,16 @@
 from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data
 from brainglobe_atlasapi.config import DEFAULT_WORKDIR
 
+### Metadata
+RES_UM = 100  # 100
+ATLAS_NAME = "example_mouse"
+SPECIES = "Mus musculus"
+ATLAS_LINK = "http://www.brain-map.org"
+CITATION = "Wang et al 2020, https://doi.org/10.1016/j.cell.2020.04.007"
+ORIENTATION = "asr"
 
-def create_atlas(working_dir, resolution):
-    # Specify information about the atlas:
-    RES_UM = resolution  # 100
-    ATLAS_NAME = "example_mouse"
-    SPECIES = "Mus musculus"
-    ATLAS_LINK = "http://www.brain-map.org"
-    CITATION = "Wang et al 2020, https://doi.org/10.1016/j.cell.2020.04.007"
-    ORIENTATION = "asr"
 
+def create_atlas(working_dir, resolution):
     # Temporary folder for nrrd files download:
     download_dir_path = working_dir / "downloading_path"
     download_dir_path.mkdir(exist_ok=True)
@@ -30,7 +29,7 @@ def create_atlas(working_dir, resolution):
     spacecache = ReferenceSpaceCache(
         manifest=download_dir_path / "manifest.json",
         # downloaded files are stored relative to here
-        resolution=RES_UM,
+        resolution=resolution,
         reference_space_key="annotation/ccf_2017",
         # use the latest version of the CCF
     )
@@ -91,7 +90,7 @@ def create_atlas(working_dir, resolution):
         citation=CITATION,
         atlas_link=ATLAS_LINK,
         species=SPECIES,
-        resolution=(RES_UM,) * 3,
+        resolution=(resolution,) * 3,
         orientation=ORIENTATION,
         root_id=997,
         reference_stack=template_volume,
@@ -109,7 +108,7 @@ def create_atlas(working_dir, resolution):
 
 if __name__ == "__main__":
     # Generated atlas path:
-    bg_root_dir = DEFAULT_WORKDIR / __atlas__
+    bg_root_dir = DEFAULT_WORKDIR / ATLAS_NAME
     bg_root_dir.mkdir(exist_ok=True)
 
-    # create_atlas(working_dir, 100)
+    create_atlas(bg_root_dir, RES_UM)