Habitat segmentation (CLI / YAML)

Bookmark for habit get-habitat. Python walk-throughs: Two-step habitat analysis, One-step habitat analysis, Direct-pooling habitat analysis. Atomic op(subject): Atomic operators. Strategy table: Habitat analysis.

Before you start: Before you start. Data layout: Load data. Demo tree:

demo_data/preprocessed/

Demo commands (one physical line each):

habit check-config --config config/habitat/config_habitat_two_step.yaml
habit get-habitat --config config/habitat/config_habitat_two_step.yaml
habit view demo_data/preprocessed/images/subj001/LAP/WATER__WATER__Ax_Dyn_LAVA_Flex+C_Series0009.nrrd demo_data/results/habitat_two_step/subj001_habitats.nrrd

Other shipped YAMLs (same command):

habit get-habitat --config config/habitat/config_habitat_one_step_raw_concat_train.yaml
habit get-habitat --config config/habitat/config_habitat_direct_pooling.yaml

★ fields when you copy a YAML: data_dir / data.source, out_dir, and modality names in feature_construction. Schema: Habitat Segmentation Configuration. Spec names: Habitat Spec component catalog.

Success: *_habitats.nrrd under out_dir. Next CLI step: Feature extraction (CLI / YAML).