list atlases

brainatlas_api/list_atlases.py

@@ -0,0 +1,65 @@
+from pathlib import Path
+from rich.table import Table
+from rich import print as rprint
+
+from brainatlas_api import config
+from brainatlas_api.bg_atlas import (
+    BrainGlobeAtlas,
+    FishAtlas,
+    RatAtlas,
+    AllenBrain25Um,
+    AllenHumanBrain500Um,
+)
+
+
+"""
+    Some functionality to list all available and downloaded brainglobe atlases
+"""
+
+
+def list_atlases():
+    # Parse config
+    conf = config.read_config()
+    brainglobe_dir = Path(conf["default_dirs"]["brainglobe_dir"])
+
+    # ----------------------------- Get local atlases ---------------------------- #
+    atlases = {}
+    for elem in brainglobe_dir.iterdir():
+        if elem.is_dir():
+            atlases[elem.name] = dict(
+                downloaded=True,
+                local=str(elem),
+                online=BrainGlobeAtlas._remote_url_base.format(elem.name),
+            )
+
+    # ---------------------- Get atlases not yet downloaded ---------------------- #
+    for atlas in [FishAtlas, RatAtlas, AllenBrain25Um, AllenHumanBrain500Um]:
+        name = f"{atlas.atlas_name}_v{atlas.version}"
+        if name not in atlases.keys():
+            atlases[str(name)] = dict(
+                downloaded=False,
+                local="[red]---[/red]",
+                online=BrainGlobeAtlas._remote_url_base.format(name),
+            )
+
+    # -------------------------------- print table ------------------------------- #
+    table = Table(
+        show_header=True,
+        header_style="bold green",
+        title="\n\nBrainglobe Atlases",
+    )
+    table.add_column("Name")
+    table.add_column("Downloaded")
+    table.add_column("Local path")
+    table.add_column("Online path", style="dim")
+
+    for atlas, info in atlases.items():
+        if info["downloaded"]:
+            downloaded = "[green]:heavy_check_mark:[/green]"
+        else:
+            downloaded = "[red]---[/red]"
+        table.add_row(
+            "[b]" + atlas + "[/b]", downloaded, info["local"], info["online"]
+        )
+
+    rprint(table)

setup.py

@@ -30,7 +30,8 @@
     python_requires=">=3.6, <3.8",
     entry_points={
         "console_scripts": [
-            "brainatlas_config = brainatlas_api.config:cli_modify_config"
+            "brainatlas_config = brainatlas_api.config:cli_modify_config",
+            "brainatlas_list_atlases = brainatlas_api.list_atlases:list_atlases",
         ]
     },
     packages=find_namespace_packages(exclude=("atlas_gen", "docs", "tests*")),