| # DRMHB conversion and evaluation examples |
|
|
| Use Python 3.12 and `vibframe-anndata==0.3.0`. Run from the repository root. |
| These examples explicitly request complete annotations; the package itself |
| keeps ground-truth import disabled by default. |
|
|
| ```bash |
| python -m pip install -r examples/requirements.txt |
| python examples/01_create_featureless_anndata.py data/DRMHB-compact.vibframe.zip derived/DRMHB-compact.v0.3.0.raw.h5ad |
| python examples/02_inspect_anndata.py derived/DRMHB-compact.v0.3.0.raw.h5ad --waveform-details |
| python examples/03_add_features.py derived/DRMHB-compact.v0.3.0.raw.h5ad derived/DRMHB-compact.v0.3.0.features.h5ad |
| ``` |
|
|
| ## 01 — Import once |
|
|
| Accepts a ZIP or extracted VibFrame. The base is featureless: `X` has zero |
| columns; raw waveforms, spectra, tachometers, identities and metadata remain |
| available for later features. The default is `float32`, 8 MiB raw blocks, |
| `scope=all`, strict missing truth and unchanged uncompressed raw HDF5 arrays. |
|
|
| `--ground-truth-scope snapshot` selects the legacy footprint; `none` (or |
| `--without-ground-truth`) excludes evaluation labels. `--max-sidecar-mib 512` |
| limits original encoded sidecars, not total memory. `--block-size-mib` and |
| `--dtype` are explicit. Existing destinations require `--overwrite`; inputs |
| cannot be used as outputs. |
|
|
| No feature is computed from `trends.parquet` or from construction/diagnostic |
| labels. The published dataset itself contains no scalar trends. |
|
|
| ## 02 — Inspect without loading multi-GiB raw signals |
|
|
| The inspector uses `h5py` group metadata, small `obs`/`var`/package metadata and |
| public ground-truth accessors. It never calls `anndata.read_h5ad(backed="r")` |
| as a blanket out-of-core solution: that mode does not make all `obsm`/`uns` |
| objects lazy. `--waveform-details` expands annotations only. `--verify-hashes` |
| reads one original annotation file at a time and checks its SHA-256. |
|
|
| ## 03 — Add the reference features |
|
|
| The thirteen feature requests remain the same as in the published EDA: |
| velocity/acceleration RMS, subsynchronous/1X/low-harmonic bands, 1X/2X/BPFO/BPFI |
| amplitudes, VPF-family RMS, and waveform RMS/crest factor/kurtosis. |
|
|
| For the current 2.6.0 fleet they materialized 468 machine/source-scoped columns. |
| Each machine populates its relevant descriptors; structural NaNs are not zeros. |
| The EDA constructs a common logical descriptor matrix without averaging different |
| machines. Preserve `var` units, processing mode, point and algorithm/options |
| when aligning columns. Do not match columns by short display name alone. |
|
|
| `--block-rows 256` controls feature block size. `--features-config FILE.yaml` |
| accepts an alternative package feature configuration. The original VibFrame |
| is not reopened. Dimension counts and original-annotation manifest identities |
| are compared before and after feature generation. |
|
|
| ## 04 — Upgrade existing H5ADs |
|
|
| ```bash |
| python examples/04_add_complete_ground_truth.py \ |
| derived/DRMHB-compact.v0.3.0.no-truth.h5ad data/DRMHB-compact.vibframe.zip \ |
| derived/DRMHB-compact.v0.3.0.enriched.h5ad |
| ``` |
|
|
| Uses `add_ground_truth_to_h5ad`. It preserves signals and features and creates a |
| transactional disk copy. Supply the matching source set and retain `obs.source`, |
| `obs.machine` and integer `obs.snap_t`. Roughly one extra H5AD of free disk is |
| needed temporarily. Source-name/path collisions must not be repaired by guessing. |
| Legacy capture-time companions are not populated retrospectively: reimport raw |
| signals to obtain those arrays. Per-waveform crop offsets remain available from |
| original and aligned waveform truth. |
|
|
| ## 05 — Read originals and DiagGT |
|
|
| ```bash |
| python examples/05_read_evaluation.py derived/DRMHB-compact.v0.3.0.features.h5ad |
| python examples/05_read_evaluation.py derived/DRMHB-compact.v0.3.0.features.h5ad \ |
| --path ground-truth/observations.parquet |
| python examples/05_read_evaluation.py derived/DRMHB-compact.v0.3.0.features.h5ad \ |
| --export derived/recovered-evaluation |
| ``` |
|
|
| Use the exact path from the printed inventory; the layout is not assumed. |
| Use `--source SOURCE_ID` when a relative path occurs in several sources. |
| `read_evaluation_table()` returns Arrow types; `read_evaluation_json()` returns |
| parsed JSON; `read_evaluation_file()` returns the exact original bytes. |
| Export refuses overwrites and retains dataset-wide originals, even for a sliced |
| AnnData. No implicit DiagGT interval-to-snapshot labelling is performed. |
|
|
| ## Complete information and model input |
|
|
| `obsm['ground_truth']` and `obsm['waveform_ground_truth']` follow `obs_names`. |
| The byte archive in `uns['vibframe_evaluation']` is dataset-wide. `snap_t` is the |
| snapshot key in integer microseconds UTC; raw capture `t` may include a crop |
| offset. Waveform bindings include source/machine/point and supplied mode identity. |
| Unknown sidecars/fields are retained instead of silently discarded. |
|
|
| For normality learning, fit scaling, missing-value rules and models only on |
| calibration. Set thresholds on normal holdout. Evaluate on the future stream |
| using timestamps. Faults, severities, OOD, nuisance and latent physical state |
| are targets/audit fields, not automatic inputs. Declare explicitly any use of |
| regime or RPM. Keep a separately generated controls dataset in a separate H5AD; |
| controls are in `data/DRMHB-compact-controls.vibframe.zip`, separate from the |
| current longitudinal ZIP. Use a distinct output basename for their H5AD. |
|
|
| ## Resources and verification |
|
|
| No raw compression settings or VibFrame bytes are changed. The current complete 0.3.0 base and feature H5ADs measure 8.169 and |
| 8.265 GiB respectively; both retain 97 original files (26,874,052 bytes). |
| Verify local derivatives with `python tools/audit_dataset.py --deep`. Metadata decoding also consumes RAM, so the raw block size and |
| 512 MiB encoded-sidecar budget are not process-memory caps. |
|
|
| For a quick end-to-end check using the smaller controls ZIP: |
|
|
| ```bash |
| python examples/01_create_featureless_anndata.py \ |
| data/DRMHB-compact-controls.vibframe.zip derived/DRMHB-compact-controls.v0.3.0.raw.h5ad |
| python examples/02_inspect_anndata.py \ |
| derived/DRMHB-compact-controls.v0.3.0.raw.h5ad --verify-hashes |
| python examples/03_add_features.py \ |
| derived/DRMHB-compact-controls.v0.3.0.raw.h5ad \ |
| derived/DRMHB-compact-controls.v0.3.0.features.h5ad |
| python examples/05_read_evaluation.py \ |
| derived/DRMHB-compact-controls.v0.3.0.features.h5ad |
| ``` |
|
|
| To exercise example 04, first create an H5AD with `--without-ground-truth` |
| from that same controls ZIP, then pass it and the ZIP to example 04. These |
| commands validate the conversion workflow without regenerating the campaign. |
|
|
| Package documentation: https://413hq.github.io/vibframe-anndata-docs/0.3.0/ |
| Ground truth guide: https://413hq.github.io/vibframe-anndata-docs/0.3.0/guides/ground-truth/ |
|
|
