generated: '2026-08-25'
method: derived
source: >-
  packages/mobilion-systems-packages.yml (public headers in
  https://github.com/MOBILionSystems/MOBILion_MBI_SDK/tree/main/include) and the SDK README data-model
  and common-tasks sections
note: >-
  Derived from the SDK's published C++ headers and README, not from an OpenAPI — MOBILion ships no
  network contract. The graph below describes the MBI file format's object model as the SDK exposes it.
root: MBIFile
entities:
- name: MBIFile
  header: MBIFile.h
  description: >-
    top-level handle on one .mbi file (HDF5 container). Construction does not read the file; Init()
    does. Close() releases it and, since 1.13.0, resets IsInitialized().
  summaries: [GetAcquisitionTimestamp, GetExperimentType, GetIonPolarity, GetRetentionTimes,
    GetFrameMSLevels, GetFrameCollisionEnergies, GetScanCounts, GetFrameTIC,
    GetAverageIMSamplingPeriod, GetMaxNumScansPerFrame, GetNumFrames, GetVersion]
- name: Frame
  header: MBIFrame.h
  description: >-
    one point in retention time, holding a sparse 2-D array of int32 ion counts indexed by
    (ion-mobility arrival-time bin, TOF sample index). Rows are arrival-time bins; columns are TOF
    sample indices.
  accessors: [GetFrameDataAsCSRArray, GetFrameDataAsCOOArray, GetFrameDataAsCSRComponents,
    GetFrameIMMSSpectrumAsCSR, GetFrameIMMSSpectrumAsCOO, GetNonZeroScanIndices, GetMassSpectrum,
    GetScanDataMzIndexedSparse, GetScanDataToFIndexedSparse, GetScanDataMzIndexedDense,
    GetScanDataToFIndexedDense, GetScanSummationToFIndexedDense, GetMaxPointsInScan,
    GetCollisionEnergy, IsCollisionEnergyValid, GetCalibration]
- name: MassSpectrum
  header: MBIFrame.h
  description: one arrival-time bin of a frame — a scan. Carries indices, mz, intensities, nnz.
- name: CSRArray / COOArray
  header: MBISparse.h
  description: >-
    sparse containers over int32 ion counts. Both carry nRows, nColumns, nnz, isZeroPadded and Sum().
    CSR is data/indices/indptr; COO is data/rowIndices/columnIndices.
- name: CSRIMMSSpectrum / COOIMMSSpectrum
  header: MBISparse.h
  description: the corresponding sparse array plus a calibrated mz vector.
- name: TofCalibration
  header: MBICalibration.h
  description: TOF sample index <-> m/z conversion (MzToIndex, IndexToMz, scalar and vectorized).
- name: EyeOnCcsCalibration
  header: MBICalibration.h
  description: >-
    arrival time <-> collision cross section, charge-aware since 1.13.0. Since 1.13.0 it is
    independent of the parent MBIFile's lifetime and may be used after Close().
  methods: [ArrivalTimeToCCS, CCSToArrivalTime, GetCCSCoefficients, SetCCSCoefficients, GetGasMass,
    ReductionFactor]
- name: NonReducedEyeOnCcsCalibration
  header: MBICalibration.h
  description: >-
    derives from EyeOnCcsCalibration; overrides ReductionFactor to return 1/Z (charge scaling only,
    no reduced-mass adjustment). Used when the stored gas mass is 0.
- name: Metadata / GlobalMetadata / FrameMetadata
  header: MBIMetadata.h
  description: >-
    key-addressed metadata. Key names are constants in MBIAttr::GlobalKey (MBIConstants.h). ReadAll()
    returns the whole map.
- name: ScanDefinition
  header: MBIScanDefinition.h
  description: >-
    CE ramps and isolation windows. The vendor states this is groundwork for future DIA support and is
    not required for current data.
- name: MBIFileHDF5Adapter
  header: MBIFileHDF5Adapter.h
  description: low-level HDF5 adapter; not normally called directly.
relationships:
- from: MBIFile
  to: Frame
  type: has_many
  via: GetFrame(index) — 1-based, 1..GetNumFrames()
- from: MBIFile
  to: TofCalibration
  type: has_one
  via: GetCalibration()
- from: MBIFile
  to: EyeOnCcsCalibration
  type: has_one
  via: GetEyeOnCCSCalibrationOwned() — present only when HasCCSCalibration()
- from: MBIFile
  to: GlobalMetadata
  type: has_one
  via: GetGlobalMetaData()
- from: MBIFile
  to: FrameMetadata
  type: has_many
  via: GetFrameMetadata(frameIndex)
- from: Frame
  to: MassSpectrum
  type: has_many
  via: GetMassSpectrum(scanIndex) over GetNonZeroScanIndices()
- from: Frame
  to: TofCalibration
  type: has_one
  via: Frame::GetCalibration() — the calibration in effect for that frame
- from: Frame
  to: CSRArray
  type: has_one
  via: GetFrameDataAsCSRArray()
- from: CSRIMMSSpectrum
  to: CSRArray
  type: extends
  via: adds a calibrated mz vector
- from: NonReducedEyeOnCcsCalibration
  to: EyeOnCcsCalibration
  type: extends
  via: overrides ReductionFactor
enums:
  experiment_type: [MS1, AIF, SIFF_MAF, MIFF_MAF]
container_format: HDF5