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Add suggestion to transfer downloaded checkpoints and rename filenames #758

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Oct 24, 2024
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Add suggestion to transfer downloaded checkpoints and rename filenames #758

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Add suggestion to transfer and rename checkpoints
anwai98 Oct 21, 2024
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anwai98 Oct 21, 2024
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17 changes: 17 additions & 0 deletions doc/faq.md
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Expand Up @@ -53,6 +53,23 @@ The PyPI page for `micro-sam` exists only so that the [napari-hub](https://www.n
### 7. I get the following error: `importError: cannot import name 'UNETR' from 'torch_em.model'`.
It's possible that you have an older version of `torch-em` installed. Similar errors could often be raised from other libraries, the reasons being: a) Outdated packages installed, or b) Some non-existent module being called. If the source of such error is from `micro_sam`, then `a)` is most likely the reason . We recommend installing the latest version following the [installation instructions](https://github.com/constantinpape/torch-em?tab=readme-ov-file#installation).

### 8. My system does not support internet connection. Where should I put the model checkpoints for the `micro-sam` models?
We recommend transferring the model checkpoints to the system-level cache directory (you can find yours by running the following in terminal: `python -c "from micro_sam import util; print(util.microsam_cachedir())`). Once you have identified the cache directory, you need to create an additional `models` directory inside the `micro-sam` cache directory (if not present already) and move the model checkpoints there. At last, you **must** rename the transferred checkpoints as per the respective [key values](https://github.com/computational-cell-analytics/micro-sam/blob/master/micro_sam/util.py#L87) in the url dictionaries located in the `micro_sam.util.models` function (below mentioned is an example for Linux users).

```bash
# Download and transfer the model checkpoints for 'vit_b_lm' and `vit_b_lm_decoder`.
# Next, verify the cache directory.
> python -c "from micro_sam import util; print(util.microsam_cachedir())"
/home/anwai/.cache/micro_sam

# Create 'models' folder in the cache directory
> mkdir /home/anwai/.cache/micro_sam/models

# Move the checkpoints to the models directory and rename them
# The following steps transfer and rename the checkpoints to the desired filenames.
> mv vit_b.pt /home/anwai/.cache/micro_sam/models/vit_b_lm
> mv vit_b_decoder.pt /home/anwai/.cache/micro_sam/models/vit_b_lm_decoder
```

## Usage questions

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