Training Custom Models • petrographer

This vignette explains the current petrographer training workflow at a high level. It covers:

preparing and validating a dataset
deciding whether to train detection or segmentation
choosing between local and HPC execution
understanding the artifacts produced by training

For a runnable end-to-end template, see inst/notebooks/templates/train_model.qmd.

Choose a Training Task

petrographer supports two RF-DETR training paths:

Detection: bounding boxes with SAHI-based sliced inference at predict time
Segmentation: instance masks with direct morphology analysis

Use detection when you mainly need counts, locations, and class labels. Use segmentation when you need mask-derived measurements such as area, eccentricity, circularity, or orientation.

Prepare the Dataset

Training expects a COCO-style dataset with train/ and valid/ splits.

library(petrographer)

validate_dataset("data/processed/my_dataset")

Expected structure:

my_dataset/
├── train/
│   ├── _annotations.coco.json
│   └── *.jpg / *.png
└── valid/
    ├── _annotations.coco.json
    └── *.jpg / *.png

Optional: Slice Large Images

If the source images are very large or contain many small objects, slicing can make training more stable and improve downstream detection performance.

slice_dataset(
  input_dir = "data/raw/large_images",
  output_dir = "data/processed/my_dataset_sliced",
  slice_size = 1024,
  overlap = 0.2
)

This is usually most helpful for detection workflows. Segmentation currently trains on the prepared dataset the same way, but prediction does not yet use SAHI slicing for RF-DETR segmentation models.

Optional: Pin the Dataset

Pinning makes the training data reproducible and lets the resulting model record the exact dataset id/version used during training.

pin_dataset(
  data_dir = "data/processed/my_dataset",
  dataset_id = "my_dataset_v1"
)

list_datasets()

Start Training

The main entry point is train_model(). You can supply either a raw dataset directory or a previously pinned dataset_id.

Detection Example

detector_id <- train_model(
  dataset_id = "my_dataset_v1",
  model_id = "my_detector_v1",
  model_variant = "small",
  epochs = 50,
  batch_size = 2,
  device = "cuda"
)

Segmentation Example

segmenter_id <- train_model(
  dataset_id = "my_dataset_v1",
  model_id = "my_segmenter_v1",
  model_variant = "seg_small",
  epochs = 50,
  batch_size = 4,
  device = "cuda"
)

Local vs HPC Training

Training mode is auto-detected:

if hipergator::hpg_configure() has been set up, train_model() uses the HPC path
otherwise it runs locally

That means the user-facing training call stays the same in both environments.

Local Training

Local training is the simplest option. It is appropriate when:

your dataset is modest in size
you have a suitable local GPU
you are iterating on setup or parameters

HPC Training

HPC training is useful when:

models need longer wall time than you want to spend locally
datasets are large
you want to run multiple experiments or model variants

Example configuration:

library(hipergator)

hpg_configure(
  host = "hpg",
  base_dir = "/blue/mygroup/myusername/petrographer"
)

Once configured, the same train_model() call will submit through the HPC path instead of running locally.

Choose a Model Variant

Detection variants:

nano
small
medium
large

Segmentation variants:

seg_nano
seg_small
seg_medium
seg_large
seg_xlarge
seg_2xlarge
seg_preview

In general:

smaller variants train faster and use less memory
larger variants can improve accuracy but require more time and VRAM

nano / small are good starting points for detection. seg_nano / seg_small are good starting points for segmentation.

What Training Produces

Successful training pins a model to the local model board and writes:

checkpoint_best_total.pth
manifest.json
training_summary.json
RF-DETR artifacts such as metrics.csv, hparams.yaml, log.txt, or results.json when available

The stable package contract is:

manifest.json for model/task/category/artifact metadata
training_summary.json for normalized training history and final metrics

Evaluate and Inspect the Result

Load the trained model:

model <- from_pretrained("my_detector_v1", board = "local", device = "cpu")
model

Inspect normalized training outputs:

eval_result <- evaluate_training(model_id = "my_detector_v1")
eval_result$summary

Detection Validation

Detection models can be evaluated with SAHI + COCO metrics:

sahi_eval <- evaluate_model_sahi(
  model = model,
  annotation_json = "data/processed/my_dataset/valid/_annotations.coco.json",
  image_dir = "data/processed/my_dataset/valid",
  use_slicing = TRUE,
  slice_size = 640,
  overlap = 0.2,
  max_dets = 300
)

sahi_eval$summary

Segmentation Validation

Segmentation currently does not use the SAHI evaluation path. Instead, the main downstream value is prediction plus morphology analysis.

seg_model <- from_pretrained("my_segmenter_v1", board = "local", device = "cpu")

seg_batch <- analyze_segmentation_dir(
  input_dir = "data/processed/my_dataset/valid",
  model = seg_model,
  output_dir = "results/segmentation_batch"
)

seg_batch$summary
seg_batch$population_stats

Maintainership and Publishing

Every successful training run is pinned locally. Maintainers can copy a completed local pin to a shared board with pin_model() and then refresh the destination board manifest with pins::write_board_manifest().

See inst/notebooks/templates/model_from_pretrained.qmd for the maintainer publishing workflow.

Troubleshooting

CUDA out of memory

lower batch_size
start with a smaller variant
consider detection before segmentation if masks are not strictly required

Training is slow

make sure you are not accidentally training on CPU
use a smaller variant for initial iteration
prefer HPC for long or repeated runs

Predictions are unlabeled or mislabeled

confirm the dataset categories are correct before training
inspect model$manifest$categories after loading

Need a runnable example

use inst/notebooks/templates/train_model.qmd as the executable template
use the ops/ notebooks only for maintainer or library-building workflows