list atlases (#40)

* list atlases

* added test

* test fix

* auto detect available atlases

* test_get_atlas_from_name

* added rich to requirements.txt

brainatlas_api/__init__.py

@@ -0,0 +1,20 @@
+from brainatlas_api import bg_atlas
+from brainatlas_api.list_atlases import list_atlases
+
+available_atlases = [
+    cls for cls in map(bg_atlas.__dict__.get, bg_atlas.__all__)
+]
+
+
+def get_atlas_class_from_name(name):
+    names = [
+        f"{atlas.atlas_name}_v{atlas.version}" for atlas in available_atlases
+    ]
+    atlases = {n: a for n, a in zip(names, available_atlases)}
+
+    if name in atlases.keys():
+        return atlases[name]
+    else:
+        print(f"Could not find atlas with name {name}. Available atlases:\n")
+        list_atlases()
+        return None

brainatlas_api/bg_atlas.py

@@ -8,6 +8,8 @@
 
 COMPRESSED_FILENAME = "atlas.tar.gz"
 
+__all__ = ["FishAtlas", "RatAtlas", "AllenBrain25Um", "AllenHumanBrain500Um"]
+
 
 class BrainGlobeAtlas(core.Atlas):
     """Add download functionalities to Atlas class.

brainatlas_api/list_atlases.py

@@ -0,0 +1,64 @@
+from pathlib import Path
+from rich.table import Table
+from rich import print as rprint
+
+from brainatlas_api import config
+from brainatlas_api import bg_atlas
+
+
+"""
+    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=bg_atlas.BrainGlobeAtlas._remote_url_base.format(
+                    elem.name
+                ),
+            )
+
+    # ---------------------- Get atlases not yet downloaded ---------------------- #
+    available_atlases = [
+        cls for cls in map(bg_atlas.__dict__.get, bg_atlas.__all__)
+    ]
+    for atlas in available_atlases:
+        name = f"{atlas.atlas_name}_v{atlas.version}"
+        if name not in atlases.keys():
+            atlases[str(name)] = dict(
+                downloaded=False,
+                local="[red]---[/red]",
+                online=atlas._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)

requirements.txt

@@ -5,4 +5,5 @@ treelib
 pandas
 requests
 meshio
-click
+click
+rich

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*")),

tests/test_list_atlases.py

@@ -0,0 +1,15 @@
+import brainatlas_api
+
+
+def test_list_atlases():
+    brainatlas_api.list_atlases()
+
+
+def test_get_atlas_from_name():
+    a1 = brainatlas_api.get_atlas_class_from_name("allen_mouse_25um_v0.2")
+    a2 = brainatlas_api.get_atlas_class_from_name("xxxx")
+
+    if a1 is None:
+        raise ValueError
+    if a2 is not None:
+        raise ValueError