Merge pull request #1108 from computational-cell-analytics/dev

New release

Author: constantinpape

micro_sam/__version__.py

@@ -1 +1 @@
-__version__ = "1.6.1"
+__version__ = "1.6.2"

micro_sam/sam_annotator/_state.py

@@ -116,7 +116,7 @@ def progress_bar_factory(model_type):
                 checkpoint_path=checkpoint_path, return_state=True,
                 progress_bar_factory=None if use_cli else progress_bar_factory,
             )
-            if prefer_decoder and "decoder_state" in state:
+            if prefer_decoder and "decoder_state" in state and model_type != "vit_b_medical_imaging":
                 self.decoder = get_decoder(
                     image_encoder=self.predictor.model.image_encoder,
                     decoder_state=state["decoder_state"],

micro_sam/util.py

@@ -117,7 +117,7 @@ def models():
         "vit_l_histopathology": "xxh128:b591833c89754271023e901281dee3f2",
         "vit_h_histopathology": "xxh128:bd1856dafc156a43fb3aa705f1a6e92e",
         # Medical Imaging models:
-        "vit_b_medical_imaging": "xxh128:5be672f1458263a9edc9fd40d7f56ac1",
+        "vit_b_medical_imaging": "xxh128:40169f1e3c03a4b67bff58249c176d92",
     }
     # Additional decoders for instance segmentation.
     decoder_registry = {
@@ -133,6 +133,8 @@ def models():
         "vit_b_histopathology_decoder": "xxh128:6a66194dcb6e36199cbee2214ecf7213",
         "vit_l_histopathology_decoder": "xxh128:46aab7765d4400e039772d5a50b55c04",
         "vit_h_histopathology_decoder": "xxh128:3ed9f87e46ad5e16935bd8d722c8dc47",
+        # Medical Imaging models:
+        "vit_b_medical_imaging_decoder": "xxh128:9e498b12f526f119b96c88be76e3b2ed",
     }
     registry = {**encoder_registry, **decoder_registry}
 
@@ -150,7 +152,7 @@ def models():
         "vit_b_histopathology": "https://owncloud.gwdg.de/index.php/s/sBB4H8CTmIoBZsQ/download",
         "vit_l_histopathology": "https://owncloud.gwdg.de/index.php/s/IZgnn1cpBq2PHod/download",
         "vit_h_histopathology": "https://owncloud.gwdg.de/index.php/s/L7AcvVz7DoWJ2RZ/download",
-        "vit_b_medical_imaging": "https://owncloud.gwdg.de/index.php/s/AB69HGhj8wuozXQ/download",
+        "vit_b_medical_imaging": "https://owncloud.gwdg.de/index.php/s/f5Ol4FrjPQWfjUF/download",
     }
 
     decoder_urls = {
@@ -163,6 +165,7 @@ def models():
         "vit_b_histopathology_decoder": "https://owncloud.gwdg.de/index.php/s/KO9AWqynI7SFOBj/download",
         "vit_l_histopathology_decoder": "https://owncloud.gwdg.de/index.php/s/oIs6VSmkOp7XrKF/download",
         "vit_h_histopathology_decoder": "https://owncloud.gwdg.de/index.php/s/1qAKxy5H0jgwZvM/download",
+        "vit_b_medical_imaging_decoder": "https://owncloud.gwdg.de/index.php/s/ahd3ZhZl2e0RIwz/download",
     }
     urls = {**encoder_urls, **decoder_urls}
 
@@ -1312,16 +1315,44 @@ def micro_sam_info():
         )
     )
 
+    # Creating a cache directory when users' run `micro_sam.info`.
+    cache_dir = get_cache_directory()
+    os.makedirs(cache_dir, exist_ok=True)
+
     # The cache directory panel.
     console.print(
-        Panel(f"[bold #009E73]Cache Directory:[/bold #009E73]\n{get_cache_directory()}", title="Cache Directory")
+        Panel(f"[bold #009E73]Cache Directory:[/bold #009E73]\n{cache_dir}", title="Cache Directory")
     )
 
-    # The available models panel.
-    available_models = list(get_model_names())
-    # We filter out the decoder models.
-    available_models = [m for m in available_models if not m.endswith("_decoder")]
+    # We have a simple versioning logic here (which is what I'll follow here for mapping model versions).
+    available_models = []
+    for model_name, model_path in models().urls.items():  # We filter out the decoder models.
+        if model_name.endswith("decoder"):
+            continue
+
+        if "https://dl.fbaipublicfiles.com/segment_anything/" in model_path:  # Valid v1 SAM models.
+            available_models.append(model_name)
+
+        if "https://owncloud.gwdg.de/" in model_path:  # Our own hosted models (in their v1 mode quite often)
+            if model_name == "vit_t":  # MobileSAM model.
+                available_models.append(model_name)
+            else:
+                available_models.append(f"{model_name} (v1)")
+
+        # Now for our models, the BioImageIO ModelZoo upload structure is such that:
+        # '/1/files' corresponds to v2 models.
+        # '/1.1/files' corresponds to v3 models.
+        # '/1.2/files' corresponds to v4 models.
+        if "/1/files" in model_path:
+            available_models.append(f"{model_name} (v2)")
+        if "/1.1/files" in model_path:
+            available_models.append(f"{model_name} (v3)")
+        if "/1.2/files" in model_path:
+            available_models.append(f"{model_name} (v4)")
+
     model_list = "\n".join(available_models)
+
+    # The available models panel.
     console.print(
         Panel(f"[bold #D55E00]Available Models:[/bold #D55E00]\n{model_list}", title="List of Supported Models")
     )