# cellclass train


Train a model using an ROI dataset or resume from saved state.


``` bash
cellclass train [OPTIONS] DATASET.NPZ | STATE.JSON
```


<span class="gd-details-chevron" aria-hidden="true"></span>Full --help output


    Usage: cellclass train [OPTIONS] dataset.npz | state.json

      Train a model using an ROI dataset or resume from saved state.

    Options:
      --size INTEGER                  Number of images to use.
      --data-seed INTEGER             [default: 42]
      -d, --device TEXT               [default: cuda]
      -s, --state TEXT                [default: training.json]
      --model [densenet121|densenet161|densenet169|densenet201|squeezenet1_0|shufflenet2x1_0|shufflenet2x1_5|shufflenet2x2_0|efficientnetb3|efficientnetb4|efficientnetb3s|efficientnetb4s|resenext50_32x4d|alexnet|alexnet_att|googlenet|googlenet_att|simplegooglenet|simplegooglenet_att|simplegooglenet_ch_att|simplegooglenet_ch_sp_att]
      -n, --name TEXT                 [default: model.pt]
      --existing [overwrite|load|error]
      --weights TEXT                  [default: DEFAULT]
      --freeze-weights / --no-freeze-weights
      --epochs INTEGER                [default: 2000]
      --batch-size INTEGER            [default: 32]
      --num-workers INTEGER           [default: 0]
      --seed INTEGER                  [default: 3735928559]
      --validation-size FLOAT         [default: 0.2]
      --lr FLOAT                      [default: 0.0001]
      --lr-scheduler [step|plateau]
      --lr-gamma FLOAT                [default: 0.1]
      --lr-step INTEGER               [default: 5]
      --lr-factor FLOAT               [default: 0.1]
      --lr-patience INTEGER           [default: 2]
      --patience INTEGER              [default: 10]
      --delta FLOAT                   [default: 0.0]
      --rel-delta FLOAT               [default: 0.0001]
      --weight-decay FLOAT            [default: 0.0001]
      --flip INTEGER                  [default: 1]
      --rotate INTEGER                [default: 180]
      --translate FLOAT               [default: 0.1]
      --loss-function [focal_loss|cross_entropy]
      --focal-gamma FLOAT             [default: 2.0]
      --loss-weights / --no-loss-weights
      --dropout FLOAT                 [default: 0.4]
      --testing-size FLOAT            [default: 0.2]
      --testing-interval INTEGER      [default: 5]
      --log-level INTEGER             [default: 20]
      --cudnn-benchmark / --no-cudnn-benchmark
      --pin-memory / --no-pin-memory
      --wandb / --no-wandb
      --entity TEXT                   Weights and Biases team/entity.
      --project TEXT                  [default: cellclass]
      --run-name TEXT                 Weights and Biases run display name.
      --tags TEXT                     Weights and Biases tags.
      --wandb-id TEXT                 Weights and Biases run ID.
      --help                          Show this message and exit.


# Arguments


`DATASET.NPZ | STATE.JSON: FILE`  
Required.


# Options


`--size: INTEGER = 0`  
Number of images to use.

`--data-seed: INTEGER = 42`  
 

`-d, --device: TEXT = cuda`  
 

`-s, --state: TEXT = training.json`  
 

`--model: CHOICE = densenet121`  
 

`-n, --name: TEXT = model.pt`  
 

`--existing: CHOICE = error`  
 

`--weights: TEXT = DEFAULT`  
 

`--freeze-weights, --no-freeze-weights`  
 

`--epochs: INTEGER = 2000`  
 

`--batch-size: INTEGER = 32`  
 

`--num-workers: INTEGER = 0`  
 

`--seed: INTEGER = 3735928559`  
 

`--validation-size: FLOAT = 0.2`  
 

`--lr: FLOAT = 0.0001`  
 

`--lr-scheduler: CHOICE = step`  
 

`--lr-gamma: FLOAT = 0.1`  
 

`--lr-step: INTEGER = 5`  
 

`--lr-factor: FLOAT = 0.1`  
 

`--lr-patience: INTEGER = 2`  
 

`--patience: INTEGER = 10`  
 

`--delta: FLOAT = 0.0`  
 

`--rel-delta: FLOAT = 0.0001`  
 

`--weight-decay: FLOAT = 0.0001`  
 

`--flip: INTEGER = 1`  
 

`--rotate: INTEGER = 180`  
 

`--translate: FLOAT = 0.1`  
 

`--loss-function: CHOICE = focal_loss`  
 

`--focal-gamma: FLOAT = 2.0`  
 

`--loss-weights, --no-loss-weights`  
 

`--dropout: FLOAT = 0.4`  
 

`--testing-size: FLOAT = 0.2`  
 

`--testing-interval: INTEGER = 5`  
 

`--log-level: INTEGER = 20`  
 

`--cudnn-benchmark, --no-cudnn-benchmark`  
 

`--pin-memory, --no-pin-memory`  
 

`--wandb, --no-wandb`  
 

`--entity: TEXT`  
Weights and Biases team/entity.

`--project: TEXT = cellclass`  
 

`--run-name: TEXT`  
Weights and Biases run display name.

`--tags: TEXT`  
Weights and Biases tags.

`--wandb-id: TEXT`  
Weights and Biases run ID.