Package index • fmridataset

Frames

The canonical observation-by-feature container, its accessors, lazy views, explanation, binding, and coercion.

fmri_frame(): Construct a spatially typed annotated matrix
assays() assay() active_assay() observation_axis() observations() features() observation_ids() obs_blocks() feature_blocks() dim(<fmri_frame>) nrow.fmri_frame() ncol.fmri_frame() dim(<fmri_view>) nrow.fmri_view() ncol.fmri_view(): Frame accessors
aligned_assay_set(): Construct a strictly aligned assay set
filter_obs(): Filter frame observations using scalar metadata
select_features(): Select frame features using feature metadata
bind_observations(): Bind frames along observations
explain(): Explain a frame without reading numerical values
spatial_map(): Recover a spatial map for one observation
block_apply(): Apply a function to bounded feature blocks
collect_assay(): Collect one frame assay under an explicit memory budget
as_fmri_frame(): Coerce an object to the canonical frame protocol
validate_frame_schema() compare_frame_schema() validate_against_schema() frame_schema_digest(): Validate and compare canonical frame schemas
frame_schema(): Compute the canonical metadata-only frame schema

Axes, identity, and metadata

Axis frames, blocks, durable ID policy, typed metadata records, typed tables, and the identity contract.

axis_frame() axis_data() axis_blocks() axis_ids(): Construct an annotated axis
axis_block() axis_block_data() block_components() block_component_ids(): Construct an axis-aligned multivariate block
axis_id_policy() ids_are_durable(): Inspect axis ID durability
feature_axis(): Construct a spatial feature axis
unaligned_record(): Construct a typed unaligned metadata record
validate_unaligned_record(): Validate a typed unaligned metadata record
auxiliary_table(): Construct a typed auxiliary table
validate_auxiliary_table() table_data() table_key() table_role(): Validate and inspect a typed auxiliary table
identity_descriptor(): Inspect typed identity domains
canonicalization_contract(): Identity and canonicalization contract
canonical_bytes() canonical_sha256(): Encode and hash canonical R values

Temporal contract

temporal_schema() has_temporal_schema() as_sampling_frame(): The observation-axis temporal contract

Feature spaces

Volume, surface, parcel, basis, composite, and index spaces, their generics, and spatial compatibility.

n_features() feature_ids() native_shape() feature_data() space_digest() restrict_space() vectorize_space() reconstruct_space() adjacency() same_space() assert_same_space() compatible_space() assert_compatible_space(): Feature-space contract
index_space(): Construct a generic indexed feature space
volume_space(): Construct a packed volumetric feature space
surface_space(): Construct a packed cortical surface feature space
surface_space_from_neurosurf(): Adapt a neurosurf geometry to a surface feature space
parent_space() parcel_membership() parcel_aggregation(): Inspect parent-linked feature spaces and parcel-space operators
parcel_space(): Construct a parent-linked parcel feature space
parcel_space_from_atlas(): Build a parcel space from a neuroatlas atlas
basis_analysis() basis_synthesis() basis_projection_info(): Inspect basis-space operators
basis_space(): Construct a linear basis feature space
basis_space_from_decoder(): Construct a basis space from a synthesis dictionary
basis_space_from_fmrilatent(): Adapt fmrilatent spatial loadings to a basis feature space
composite_parts() composite_part_names() composite_part(): Inspect composite feature-space parts
composite_space(): Construct an ordered composite feature space
space(): Feature-space accessor
nifti_source_space(): Recover the spatial domain of a NIfTI source

Feature maps and provenance

validate_feature_map() feature_map_source_space() feature_map_target_space() feature_map_operator() feature_map_digest(): Validate and inspect feature maps
feature_map(): Describe an explicit transformation between feature spaces
feature_map_from_target(): Derive the canonical map owned by a parent-linked target space
feature_mapped_source(): Construct a lazy source transformed through a feature map
map_features(): Lazily transform a frame into a new feature domain
provenance_graph() validate_provenance_graph() provenance_records() provenance_tips() provenance_digest() append_provenance(): Construct and inspect an immutable provenance graph
provenance_record(): Create a content-addressed provenance record
as_provenance_graph(): Coerce serializable lineage to a provenance graph

Entities, relations, hierarchy, and validity

entities() entity() entity_names(): Access entities from a frame or registry
entity_key() entity_ids() entity_data() entity_blocks(): Entity-frame accessors
entity_feature_validity(): Describe compressed entity-by-feature validity
entity_frame(): Construct a keyed entity frame
entity_registry() validate_entity_registry(): Construct and validate an entity registry
entity_registry_digest(): Compute a stable entity-registry digest
hierarchy_ids() hierarchy_groups() hierarchy_levels() hierarchy_relations() hierarchy_complete(): Access derived hierarchy index data
key_relation(): Describe a symbolic foreign-key relation
relations() relation() relation_names(): Access frame relations
relation_registry(): Construct a relation registry
relation_registry_digest(): Compute a stable relation-registry digest
sparse_relation(): Describe an explicit sparse or many-to-many relation
validate_relation_registry(): Validate a relation registry
hierarchy_digest(): Compute the deterministic digest of a hierarchy index
hierarchy_index(): Derive stable observation hierarchy indices
validate_mask_bank() n_masks() mask_values() mask_bank_digest(): Validate and inspect a mask bank
mask_bank(): Construct a deduplicated, bit-packed bank of feature masks
apply_feature_validity(): Apply one validity relation lazily to frame assays
validate_entity_feature_validity() validity_entity() validity_entity_ids() validity_mask_bank() validity_space() validity_matrix(): Validate and inspect entity-feature validity
observation_validity(): Resolve validity onto frame observations
validity_coverage(): Summarize feature coverage without imposing an analysis policy
validity_masked_source(): Lazily mask invalid observation-feature cells with missing values
event_data() event_key(): Event-table accessors
event_table(): Construct a keyed event table
study_links() study_link() study_tables() study_table() events(): Study link and table accessors
validate_event_table(): Validate a keyed event table

Collections and studies

fmri_collection(): Construct a collection of semantically equivalent fMRI frames
collection_frames() collection_frame() collection_ids(): Access frames in an fMRI collection
collection_space_data() collection_common_space(): Summarize collection feature spaces
collection_digest(): Compute a deterministic collection digest
validate_fmri_collection(): Validate an fMRI collection
fmri_study(): Construct a linked fMRI study
study_frames() study_frame() study_ids(): Study representation accessors
study_links() study_link() study_tables() study_table() events(): Study link and table accessors
study_digest(): Compute a deterministic study digest
study_from_fds_manifest(): Reconstruct a study from semantic and physical components
validate_fmri_study(): Validate a study
frame_link(): Describe a typed link between study representations
compose_frame_links(): Compose source-to-target frame links
upgrade_frame_link(): Upgrade a provisional frame-link descriptor
filter_entities(): Filter every study representation through one shared entity selection

Array sources and bounded execution

The serializable ArraySource protocol, in-memory, NIfTI, sharded, and Zarr sources, realization budgets, block planning, and spatial execution.

as_array_source() source_shape() source_dtype() source_chunks() source_capabilities() source_fingerprint() source_open() source_read() source_read_native() source_close() source_realization_cost(): Serializable numerical array sources
counting_source() source_counts() reset_source_counts(): Developer tool: instrument an array source
source_descriptor() validate_array_source(): Inspect and validate an array-source contract
source_error(): Build the structured conditions an array source may signal
source_view(): Construct a lazy view over an array source
memory_source(): Construct an in-memory array source
nifti_array_source(): Construct a pushdown-aware NIfTI array source
zarr_array_source(): Construct an experimental Zarr array source
row_bound_source(): Bind compatible sources along observations
row_sharded_source(): Construct a manifest-backed row-sharded source
append_source_shards(): Append immutable source shards
shard_manifest(): Inspect a row-sharded source manifest
locate_source_rows(): Resolve logical observation rows to shards
content_hash(): Compute a numerical content hash of an array source
content_hash_contract(): Content-hash contract
as_delarr(): Convert an array source to a lazy delarr array
plan_blocks(): Plan bounded observation-by-feature blocks
block_manifest(): Inspect a frame block plan
execute_block_plan(): Execute a bounded frame block plan
execute_spatial(): Stream an operation over spatial maps
execution_path(): Select a matrix or spatial execution path
collect_spatial_maps(): Collect spatial maps through native or reconstructed reads

Persistence and import

FDS manifests, HDF5 persistence through fmristore, and the BIDS on-ramp.

write_frame() open_frame(): Persist and reopen an fmri frame
fds_frame_bindings(): Extract physical array bindings from a frame
fds_frame_manifest() validate_fds_manifest(): Construct and validate an FDS v1 frame manifest
fds_manifest_digest(): Compute a canonical FDS manifest digest
fds_schema() fds_schema_version(): FDS logical schema identity
fds_study_bindings(): Extract shared study-level physical bindings
fds_study_manifest() validate_fds_study_manifest(): Construct and validate an FDS v2 study manifest
fds_study_manifest_digest(): Compute a canonical FDS study-manifest digest
fds_study_representations(): Extract canonical study representations for persistence
frame_from_fds_manifest(): Reconstruct a frame from an FDS manifest and physical sources
upgrade_fds_study_manifest(): Upgrade a provisional FDS study manifest
read_bids_bold(): Read one subject's preprocessed BIDS BOLD data as an fmri_frame

Conformance tools

Developer-only instruments for certifying zero-I/O, lifecycle, and failure laws.

counting_source() source_counts() reset_source_counts(): Developer tool: instrument an array source
fault_source(): Developer tool: inject deterministic source failures