Merge branch 'main' into latest

src/cellmap_models/pytorch/cellpose/__init__.py

@@ -1,6 +1,7 @@
 from .add_model import add_model
 from .load_model import load_model
 from .get_model import get_model
+from .download_checkpoint import download_checkpoint
 
 models_dict = {
     "jrc_mus-epididymis-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-epididymis-1_nuc_cp",

src/cellmap_models/pytorch/cellpose/download_checkpoint.py

@@ -0,0 +1,30 @@
+from pathlib import Path
+from cellmap_models import download_url_to_file
+
+
+def download_checkpoint(checkpoint_name: str, checkpoint_path: Path):
+    """
+    download models checkpoint from GitHub release resources.
+
+    Args:
+        checkpoint_name (str): Name of the checkpoint file.
+        local_folder (Path): Local path to save the checkpoint.
+    return:
+        checkpoint_path (Path): Path to the downloaded checkpoint.
+    """
+    from . import models_dict, models_list  # avoid circular import
+
+    # Make sure the checkpoint exists
+    if checkpoint_name not in models_list:
+        raise ValueError(
+            f"Checkpoint {checkpoint_name} not found. Available checkpoints: {models_list}"
+        )
+
+    if not checkpoint_path.exists():
+        url = models_dict[checkpoint_name]
+        print(f"Downloading {checkpoint_name} from {url}")
+        download_url_to_file(url, checkpoint_path)
+    else:
+        print(f"Checkpoint {checkpoint_name} found at {checkpoint_path}")
+
+    return checkpoint_path

src/cellmap_models/pytorch/cosem/__init__.py

@@ -1,4 +1,5 @@
 from .load_model import load_model
+from .download_checkpoint import download_checkpoint
 
 models_dict = {
     "setup04/1820500": "https://janelia-cosem-networks.s3.amazonaws.com/v0003.2-pytorch/cosem_models/cosem_models/setup04/1820500",

src/cellmap_models/pytorch/cosem/download_checkpoint.py

@@ -0,0 +1,30 @@
+from pathlib import Path
+from cellmap_models import download_url_to_file
+
+
+def download_checkpoint(checkpoint_name: str, checkpoint_path: Path):
+    """
+    download models checkpoint from s3 bucket.
+
+    Args:
+        checkpoint_name (str): Name of the checkpoint file.
+        local_folder (Path): Local path to save the checkpoint.
+    return:
+        checkpoint_path (Path): Path to the downloaded checkpoint.
+    """
+    from . import models_dict, models_list  # avoid circular import
+
+    # Make sure the checkpoint exists
+    if checkpoint_name not in models_list:
+        raise ValueError(
+            f"Checkpoint {checkpoint_name} not found. Available checkpoints: {models_list}"
+        )
+
+    if not checkpoint_path.exists():
+        url = models_dict[checkpoint_name]
+        print(f"Downloading {checkpoint_name} from {url}")
+        download_url_to_file(url, checkpoint_path)
+    else:
+        print(f"Checkpoint {checkpoint_name} found at {checkpoint_path}")
+
+    return checkpoint_path