Upstream dev with master (#624)

* Update modelzoo urls (#619) * Update installation.md (#617) * Bump to 101 (#620) * Update docs (#621) * Add progressbar to pooch download (#623) --------- Co-authored-by: Constantin Pape <[email protected]>
computational-cell-analytics · May 31, 2024 · 3488933 · 3488933
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diff --git a/README.md b/README.md
@@ -53,6 +53,10 @@ Compared to these we support more applications (2d, 3d and tracking), and provid
 
 ## Release Overview
 
+**New in version 1.0.1**
+
+Use stable URL for model downloads and fix issues in state precomputation for automatic segmentation.
+
 **New in version 1.0.0**
 
 This release mainly fixes issues with the previous release and marks the napari user interface as stable.

diff --git a/doc/installation.md b/doc/installation.md
@@ -7,7 +7,7 @@ There are three ways to install `micro_sam`:
 
 You can find more information on the installation and how to troubleshoot it in [the FAQ section](#installation-questions).
 
-We do *not* recommend installing `micro-sam` with pip.
+We do **not** recommend installing `micro-sam` with pip.
 
 ## From mamba
 
@@ -19,11 +19,11 @@ You can follow the instructions [here](https://mamba.readthedocs.io/en/latest/in
 
 `micro_sam` can be installed in an existing environment via:
 ```bash
-$ mamba install -c conda-forge micro_sam
+$ mamba install -c pytorch -c conda-forge micro_sam
 ```
 or you can create a new environment (here called `micro-sam`) via:
 ```bash
-$ mamba create -c conda-forge -n micro-sam micro_sam
+$ mamba create -c pytorch -c conda-forge -n micro-sam micro_sam
 ```
 if you want to use the GPU you need to install PyTorch from the `pytorch` channel instead of `conda-forge`. For example:
 ```bash
@@ -73,8 +73,8 @@ $ pip install -e .
 ## From installer
 
 We also provide installers for Linux and Windows:
-- [Linux](https://owncloud.gwdg.de/index.php/s/nrNBuHr9ncJqid6)
-- [Windows](https://owncloud.gwdg.de/index.php/s/kZmpAIBDmUSu4e9)
+- [Linux](https://owncloud.gwdg.de/index.php/s/nvLwlrHE4DkYcWl)
+- [Windows](https://owncloud.gwdg.de/index.php/s/feIs9069IrURmbt)
 <!---
 - [Mac](https://owncloud.gwdg.de/index.php/s/7YupGgACw9SHy2P)
 -->
@@ -113,3 +113,7 @@ https://www.makeuseof.com/how-to-disable-gatekeeper-mac/
 
 TODO detailed instruction
 -->
+
+### Easybuild installation
+
+There is also an easy-build recipe for `micro_sam` under development. You can find more information [here](https://github.com/easybuilders/easybuild-easyconfigs/pull/20636).
diff --git a/micro_sam/__version__.py b/micro_sam/__version__.py
@@ -1 +1 @@
-__version__ = "1.0.0post0"
+__version__ = "1.0.1"
diff --git a/micro_sam/util.py b/micro_sam/util.py
@@ -124,27 +124,26 @@ def models():
     }
     registry = {**encoder_registry, **decoder_registry}
 
-    # Note: the modelzoo urls should be updated at some point to not point at 'staged' but 'published'.
     encoder_urls = {
         "vit_l": "https://dl.fbaipublicfiles.com/segment_anything/sam_vit_l_0b3195.pth",
         "vit_h": "https://dl.fbaipublicfiles.com/segment_anything/sam_vit_h_4b8939.pth",
         "vit_b": "https://dl.fbaipublicfiles.com/segment_anything/sam_vit_b_01ec64.pth",
         "vit_t": "https://owncloud.gwdg.de/index.php/s/TuDzuwVDHd1ZDnQ/download",
-        "vit_l_lm": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/idealistic-rat/staged/1/files/vit_l.pt",
-        "vit_b_lm": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/diplomatic-bug/staged/1/files/vit_b.pt",
-        "vit_t_lm": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/faithful-chicken/staged/1/files/vit_t.pt",
-        "vit_l_em_organelles": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/humorous-crab/staged/1/files/vit_l.pt",
-        "vit_b_em_organelles": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/noisy-ox/staged/1/files/vit_b.pt",
-        "vit_t_em_organelles": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/greedy-whale/staged/1/files/vit_t.pt",
+        "vit_l_lm": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/idealistic-rat/1/files/vit_l.pt",
+        "vit_b_lm": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/diplomatic-bug/1/files/vit_b.pt",
+        "vit_t_lm": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/faithful-chicken/1/files/vit_t.pt",
+        "vit_l_em_organelles": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/humorous-crab/1/files/vit_l.pt",
+        "vit_b_em_organelles": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/noisy-ox/1/files/vit_b.pt",
+        "vit_t_em_organelles": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/greedy-whale/1/files/vit_t.pt",
     }
 
     decoder_urls = {
-        "vit_l_lm_decoder": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/idealistic-rat/staged/1/files/vit_l_decoder.pt",
-        "vit_b_lm_decoder": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/diplomatic-bug/staged/1/files/vit_b_decoder.pt",
-        "vit_t_lm_decoder": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/faithful-chicken/staged/1/files/vit_t_decoder.pt",
-        "vit_l_em_organelles_decoder": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/humorous-crab/staged/1/files/vit_l_decoder.pt",
-        "vit_b_em_organelles_decoder": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/noisy-ox/staged/1/files/vit_b_decoder.pt",
-        "vit_t_em_organelles_decoder": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/greedy-whale/staged/1/files/vit_t_decoder.pt",
+        "vit_l_lm_decoder": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/idealistic-rat/1/files/vit_l_decoder.pt",
+        "vit_b_lm_decoder": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/diplomatic-bug/1/files/vit_b_decoder.pt",
+        "vit_t_lm_decoder": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/faithful-chicken/1/files/vit_t_decoder.pt",
+        "vit_l_em_organelles_decoder": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/humorous-crab/1/files/vit_l_decoder.pt",
+        "vit_b_em_organelles_decoder": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/noisy-ox/1/files/vit_b_decoder.pt",
+        "vit_t_em_organelles_decoder": "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/greedy-whale/1/files/vit_t_decoder.pt",
     }
     urls = {**encoder_urls, **decoder_urls}
 
@@ -317,13 +316,13 @@ def get_sam_model(
     # URL from the model_type. If the model_type is invalid pooch will raise an error.
     if checkpoint_path is None:
         model_registry = models()
-        checkpoint_path = model_registry.fetch(model_type)
+        checkpoint_path = model_registry.fetch(model_type, progressbar=True)
         model_hash = model_registry.registry[model_type]
 
         # If we have a custom model then we may also have a decoder checkpoint.
         # Download it here, so that we can add it to the state.
         decoder_name = f"{model_type}_decoder"
-        decoder_path = model_registry.fetch(decoder_name) if decoder_name in model_registry.registry else None
+        decoder_path = model_registry.fetch(decoder_name, progressbar=True) if decoder_name in model_registry.registry else None
 
     # checkpoint_path has been passed, we use it instead of downloading a model.
     else: