From 947b6692d5f64d46fde624faadda1dcd97b32ee0 Mon Sep 17 00:00:00 2001
From: Marwan Zouinkhi <zouinkhi.marwan@gmail.com>
Date: Sat, 16 Mar 2024 19:05:08 -0400
Subject: [PATCH 1/8] download checkpoints

---
 .../pytorch/cosem/load_checkpoint.py          | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100755 src/cellmap_models/pytorch/cosem/load_checkpoint.py

diff --git a/src/cellmap_models/pytorch/cosem/load_checkpoint.py b/src/cellmap_models/pytorch/cosem/load_checkpoint.py
new file mode 100755
index 0000000..081a1c4
--- /dev/null
+++ b/src/cellmap_models/pytorch/cosem/load_checkpoint.py
@@ -0,0 +1,34 @@
+from pathlib import Path
+from cellmap_models import download_url_to_file
+
+
+
+def download_checkpoint(checkpoint_name: str,local_folder: Path):
+    """
+    download models checkpoint from s3 bucket.
+
+    Args:
+        checkpoint_name (str): Name of the checkpoint file.
+        local_folder (Path): Local folder to save the checkpoint.
+    return:
+        checkpoint_path (Path): Path to the downloaded checkpoint.
+    """
+    from . import models_dict, models_list, model_names  # 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}"
+        )
+    
+    checkpoint_path = Path(
+        local_folder/ Path(checkpoint_name.replace(".", "_"))
+    ).with_suffix(".pth")
+    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

From 636c416bbf0ebb80766ca4c5c73e38c6b7d53446 Mon Sep 17 00:00:00 2001
From: Marwan Zouinkhi <zouinkhi.marwan@gmail.com>
Date: Sat, 16 Mar 2024 19:05:53 -0400
Subject: [PATCH 2/8] init

---
 src/cellmap_models/pytorch/cosem/__init__.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/cellmap_models/pytorch/cosem/__init__.py b/src/cellmap_models/pytorch/cosem/__init__.py
index 9109bd7..a840f5a 100755
--- a/src/cellmap_models/pytorch/cosem/__init__.py
+++ b/src/cellmap_models/pytorch/cosem/__init__.py
@@ -1,4 +1,5 @@
 from .load_model import load_model
+from .load_checkpoint import download_checkpoint
 
 models_dict = {
     "setup04/1820500": "https://janelia-cosem-networks.s3.amazonaws.com/v0003.2-pytorch/cosem_models/cosem_models/setup04/1820500",

From bf1acfaf95036d72e7a305a2d1381d8eabd09bb6 Mon Sep 17 00:00:00 2001
From: Marwan Zouinkhi <zouinkhi.marwan@gmail.com>
Date: Sun, 17 Mar 2024 11:46:49 -0400
Subject: [PATCH 3/8] :art: Format Python code with psf/black

---
 src/cellmap_models/pytorch/cosem/load_checkpoint.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/cellmap_models/pytorch/cosem/load_checkpoint.py b/src/cellmap_models/pytorch/cosem/load_checkpoint.py
index 081a1c4..51f19d4 100755
--- a/src/cellmap_models/pytorch/cosem/load_checkpoint.py
+++ b/src/cellmap_models/pytorch/cosem/load_checkpoint.py
@@ -2,8 +2,7 @@
 from cellmap_models import download_url_to_file
 
 
-
-def download_checkpoint(checkpoint_name: str,local_folder: Path):
+def download_checkpoint(checkpoint_name: str, local_folder: Path):
     """
     download models checkpoint from s3 bucket.
 
@@ -13,16 +12,16 @@ def download_checkpoint(checkpoint_name: str,local_folder: Path):
     return:
         checkpoint_path (Path): Path to the downloaded checkpoint.
     """
-    from . import models_dict, models_list, model_names  # avoid circular import
+    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}"
         )
-    
+
     checkpoint_path = Path(
-        local_folder/ Path(checkpoint_name.replace(".", "_"))
+        local_folder / Path(checkpoint_name.replace(".", "_"))
     ).with_suffix(".pth")
     if not checkpoint_path.exists():
         url = models_dict[checkpoint_name]

From 40b9b57b86333d12502927f846c737af4dcaa392 Mon Sep 17 00:00:00 2001
From: Marwan Zouinkhi <zouinkhi.marwan@gmail.com>
Date: Sun, 17 Mar 2024 12:25:48 -0400
Subject: [PATCH 4/8] use checkpoint path instead of folder

---
 src/cellmap_models/pytorch/cosem/load_checkpoint.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/cellmap_models/pytorch/cosem/load_checkpoint.py b/src/cellmap_models/pytorch/cosem/load_checkpoint.py
index 51f19d4..74d4e18 100755
--- a/src/cellmap_models/pytorch/cosem/load_checkpoint.py
+++ b/src/cellmap_models/pytorch/cosem/load_checkpoint.py
@@ -2,7 +2,7 @@
 from cellmap_models import download_url_to_file
 
 
-def download_checkpoint(checkpoint_name: str, local_folder: Path):
+def download_checkpoint(checkpoint_name: str, checkpoint_path: Path):
     """
     download models checkpoint from s3 bucket.
 
@@ -20,9 +20,6 @@ def download_checkpoint(checkpoint_name: str, local_folder: Path):
             f"Checkpoint {checkpoint_name} not found. Available checkpoints: {models_list}"
         )
 
-    checkpoint_path = Path(
-        local_folder / Path(checkpoint_name.replace(".", "_"))
-    ).with_suffix(".pth")
     if not checkpoint_path.exists():
         url = models_dict[checkpoint_name]
         print(f"Downloading {checkpoint_name} from {url}")

From 599b7ecd1fcf1b5ab9da1cf6a529210e55bc2eea Mon Sep 17 00:00:00 2001
From: Marwan Zouinkhi <zouinkhi.marwan@gmail.com>
Date: Sun, 17 Mar 2024 12:26:42 -0400
Subject: [PATCH 5/8] fix typo

---
 src/cellmap_models/pytorch/cosem/load_checkpoint.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cellmap_models/pytorch/cosem/load_checkpoint.py b/src/cellmap_models/pytorch/cosem/load_checkpoint.py
index 74d4e18..ea406bd 100755
--- a/src/cellmap_models/pytorch/cosem/load_checkpoint.py
+++ b/src/cellmap_models/pytorch/cosem/load_checkpoint.py
@@ -8,7 +8,7 @@ def download_checkpoint(checkpoint_name: str, checkpoint_path: Path):
 
     Args:
         checkpoint_name (str): Name of the checkpoint file.
-        local_folder (Path): Local folder to save the checkpoint.
+        local_folder (Path): Local path to save the checkpoint.
     return:
         checkpoint_path (Path): Path to the downloaded checkpoint.
     """

From d85f13a2aa6da2bf88917b532d2bd9fb72c3e260 Mon Sep 17 00:00:00 2001
From: Marwan Zouinkhi <zouinkhi.marwan@gmail.com>
Date: Mon, 18 Mar 2024 11:34:57 -0400
Subject: [PATCH 6/8] support cellpose checkpoint download

---
 .../pytorch/cellpose/__init__.py              |   1 +
 .../download_checkpoint.py}                   |   0
 src/cellmap_models/pytorch/cosem/.DS_Store    | Bin 6148 -> 0 bytes
 .../pytorch/cosem/download_checkpoint.py      |  30 ++++++++++++++++++
 4 files changed, 31 insertions(+)
 rename src/cellmap_models/pytorch/{cosem/load_checkpoint.py => cellpose/download_checkpoint.py} (100%)
 delete mode 100644 src/cellmap_models/pytorch/cosem/.DS_Store
 create mode 100755 src/cellmap_models/pytorch/cosem/download_checkpoint.py

diff --git a/src/cellmap_models/pytorch/cellpose/__init__.py b/src/cellmap_models/pytorch/cellpose/__init__.py
index 6e0bc43..97a9ec5 100644
--- a/src/cellmap_models/pytorch/cellpose/__init__.py
+++ b/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",
diff --git a/src/cellmap_models/pytorch/cosem/load_checkpoint.py b/src/cellmap_models/pytorch/cellpose/download_checkpoint.py
similarity index 100%
rename from src/cellmap_models/pytorch/cosem/load_checkpoint.py
rename to src/cellmap_models/pytorch/cellpose/download_checkpoint.py
diff --git a/src/cellmap_models/pytorch/cosem/.DS_Store b/src/cellmap_models/pytorch/cosem/.DS_Store
deleted file mode 100644
index 4ffd9ab8a762c1c5e58847836a3488df19be85e6..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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diff --git a/src/cellmap_models/pytorch/cosem/download_checkpoint.py b/src/cellmap_models/pytorch/cosem/download_checkpoint.py
new file mode 100755
index 0000000..ea406bd
--- /dev/null
+++ b/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

From d0989c3eae86ba83014a6ddead5c97c5c9818add Mon Sep 17 00:00:00 2001
From: Marwan Zouinkhi <zouinkhi.marwan@gmail.com>
Date: Mon, 18 Mar 2024 11:37:21 -0400
Subject: [PATCH 7/8] fix init

---
 src/cellmap_models/pytorch/cosem/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cellmap_models/pytorch/cosem/__init__.py b/src/cellmap_models/pytorch/cosem/__init__.py
index a840f5a..785743c 100755
--- a/src/cellmap_models/pytorch/cosem/__init__.py
+++ b/src/cellmap_models/pytorch/cosem/__init__.py
@@ -1,5 +1,5 @@
 from .load_model import load_model
-from .load_checkpoint import download_checkpoint
+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",

From 84be8fe195d5d9c3575a4823a031ab9cb7a20e74 Mon Sep 17 00:00:00 2001
From: Jeff Rhoades <37990507+rhoadesScholar@users.noreply.github.com>
Date: Mon, 18 Mar 2024 13:34:45 -0400
Subject: [PATCH 8/8] Update download_checkpoint.py

---
 src/cellmap_models/pytorch/cellpose/download_checkpoint.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cellmap_models/pytorch/cellpose/download_checkpoint.py b/src/cellmap_models/pytorch/cellpose/download_checkpoint.py
index ea406bd..df850d7 100755
--- a/src/cellmap_models/pytorch/cellpose/download_checkpoint.py
+++ b/src/cellmap_models/pytorch/cellpose/download_checkpoint.py
@@ -4,7 +4,7 @@
 
 def download_checkpoint(checkpoint_name: str, checkpoint_path: Path):
     """
-    download models checkpoint from s3 bucket.
+    download models checkpoint from GitHub release resources.
 
     Args:
         checkpoint_name (str): Name of the checkpoint file.