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Update Environment Variable Table #303

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Mar 18, 2024
Merged

Update Environment Variable Table #303

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d8f11f6
updated env variable table
nkaenzig Mar 18, 2024
132fe21
fixed sentence in dataset docs
nkaenzig Mar 18, 2024
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3 changes: 1 addition & 2 deletions docs/datasets/bach.md
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Expand Up @@ -43,8 +43,7 @@ ICAR2018_BACH_Challenge

## Download and preprocessing

The `BACH` dataset class supports download the data no runtime with the initialized argument
`download: bool = True`.
The `BACH` dataset class supports downloading the data during runtime by setting the init argument `download=True`.

*Note that in the provided `BACH`-config files the download argument is set to `false`. To enable automatic download you will need to open the config and set `download: true`.*

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3 changes: 1 addition & 2 deletions docs/datasets/crc.md
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Expand Up @@ -67,8 +67,7 @@ CRC-VAL-HE-7K # All images used for validation

## Download and preprocessing

The `CRC` dataset class supports download the data no runtime with the initialized argument
`download: bool = True`.
The `CRC` dataset class supports downloading the data during runtime by setting the init argument `download=True`.

*Note that in the provided `CRC`-config files the download argument is set to `false`. To enable automatic download you will need to open the config and set `download: true`.*

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3 changes: 1 addition & 2 deletions docs/datasets/patch_camelyon.md
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Expand Up @@ -45,8 +45,7 @@ The PatchCamelyon data from [zenodo](https://zenodo.org/records/2546921) is orga


## Download and preprocessing
The dataset class `PatchCamelyon` supports download the data no runtime with the initialized argument
`download: bool = True`.
The dataset class `PatchCamelyon` supports downloading the data during runtime by setting the init argument `download=True`.

*Note that in the provided `PatchCamelyon`-config files the download argument is set to `false`. To enable automatic download you will need to open the config and set `download: true`.*

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37 changes: 18 additions & 19 deletions docs/user-guide/getting-started/how_to_use.md
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Expand Up @@ -41,22 +41,21 @@ To get a better understanding, inspect some of the provided [config files](https

To customize runs, without the need of creating custom config-files, you can overwrite the config-parameters listed below by setting them as environment variables.

| | |
|-------------------------|---------------------------|
| `OUTPUT_ROOT` | the directory to store logging outputs and recorded results |
| `MONITOR_METRIC` | the metric to monitor for early stopping and model checkpoint loading |
| `EMBEDDINGS_ROOT` | the directory to store the computed embeddings |
| `IN_FEATURES` | the input feature dimension (embedding) |
| `REPO_OR_DIR` | github repo with format, e.g. "facebookresearch/dino:main" |
| `DINO_BACKBONE` | Backbone model architecture if a facebookresearch/dino FM is evaluated |
| `PRETRAINED` | whether to load FM-backbone weights from a pretrained model |
| `FORCE_RELOAD` | whether to force a fresh download of the github repo unconditionally |
| `CHECKPOINT_PATH` | Path to the FM-checkpoint to be evaluated |
| `N_RUNS` | Number of `fit` runs to perform in a session, defaults to 5 |
| `MAX_STEPS` | Maximum number of training steps (if early stopping is not triggered) |
| `BATCH_SIZE` | Batch size for a training step |
| `LR_VALUE` | Learning rate for training the decoder |
| `NUM_CLASSES` | Number of classes for classification tasks |
| `PREDICT_BATCH_SIZE` | Batch size for a predict step |
| `MONITOR_METRIC` | Metric to be monitored for early stopping |
| `MONITOR_METRIC_MODE` | "min" or "max", depending on the `MONITOR_METRIC` used |
| | Type | Description |
|-------------------------|-------|-------------|
| `OUTPUT_ROOT` | str | The directory to store logging outputs and evaluation results |
| `EMBEDDINGS_ROOT` | str | The directory to store the computed embeddings |
| `CHECKPOINT_PATH` | str | Path to the FM-checkpoint to be evaluated |
| `IN_FEATURES` | int | The input feature dimension (embedding) |
| `NUM_CLASSES` | int | Number of classes for classification tasks |
| `N_RUNS` | int | Number of `fit` runs to perform in a session, defaults to 5 |
| `MAX_STEPS` | int | Maximum number of training steps (if early stopping is not triggered) |
| `BATCH_SIZE` | int | Batch size for a training step |
| `PREDICT_BATCH_SIZE` | int | Batch size for a predict step |
| `LR_VALUE` | float | Learning rate for training the decoder |
| `MONITOR_METRIC` | str | The metric to monitor for early stopping and final model checkpoint loading |
| `MONITOR_METRIC_MODE` | str | "min" or "max", depending on the `MONITOR_METRIC` used |
| `REPO_OR_DIR` | str | GitHub repo with format containing model implementation, e.g. "facebookresearch/dino:main" |
| `DINO_BACKBONE` | str | Backbone model architecture if a facebookresearch/dino FM is evaluated |
| `FORCE_RELOAD` | bool | Whether to force a fresh download of the github repo unconditionally |
| `PRETRAINED` | bool | Whether to load FM-backbone weights from a pretrained model |