ms: bitbucket.org/proteinspector/ms/unthermo Index | Files | Directories

package unthermo

import "bitbucket.org/proteinspector/ms/unthermo"

Package unthermo is a library that can read Thermo RAW files. It only deals with version 57 and above (fairly recent machines).

Index

Package Files

reader.go

type AuditTag Uses

type AuditTag struct {
    Time     uint64   //8 bytes Windows 64-bit timestamp
    Tag1     audittag //50 bytes
    Tag2     audittag
    Unknown1 uint32 //4 bytes
}

type AutoSamplerInfo Uses

type AutoSamplerInfo struct {
    Preamble AutoSamplerPreamble
    Text     PascalString
}

AutoSamplerInfo comes from the sampling device

func (*AutoSamplerInfo) Read Uses

func (data *AutoSamplerInfo) Read(r io.Reader, v Version)

type AutoSamplerPreamble Uses

type AutoSamplerPreamble struct {
    Unknown1      uint32
    Unknown2      uint32
    NumberOfWells uint32
    Unknown3      uint32
    Unknown4      uint32
    Unknown15     uint32
}

type CDataPacket Uses

type CDataPacket struct {
    Value float64
    Time  float64
}

CDataPackets are the data from Chromatography machines

func (*CDataPacket) Read Uses

func (data *CDataPacket) Read(r io.Reader, v Version)

type CDataPackets Uses

type CDataPackets []CDataPacket

func (CDataPackets) Read Uses

func (data CDataPackets) Read(r io.Reader, v Version)

type CIndexEntries Uses

type CIndexEntries []CIndexEntry

func (CIndexEntries) Read Uses

func (data CIndexEntries) Read(r io.Reader, v Version)

type CIndexEntry Uses

type CIndexEntry struct {
    Offset32 uint32
    Index    uint32
    Event    uint16
    Unknown1 uint16
    Unknown2 uint32
    Unknown3 uint32
    Unknown4 uint32
    Unknown5 float64
    Time     float64
    Unknown6 float64
    Unknown7 float64
    Value    float64

    Offset uint64
}

func (*CIndexEntry) Read Uses

func (data *CIndexEntry) Read(r io.Reader, v Version)

func (CIndexEntry) Size Uses

func (data CIndexEntry) Size(v Version) uint64

type CentroidedPeak Uses

type CentroidedPeak struct {
    Mz        float32
    Abundance float32
}

A peak itself

type File Uses

type File struct {
    // contains filtered or unexported fields
}

File is an in-memory representation of the Thermo RAW file

func Open Uses

func Open(fn string) (file File, err error)

Open opens the supplied filename and reads the indices from the RAW file in memory. Multiple files may be read concurrently.

func (*File) AllScans Uses

func (rf *File) AllScans(fun func(scan ms.Scan))

AllScans is a convenience function that runs over all spectra in the raw file

On every encountered MS Scan, the function fun is called

func (*File) Chromatography Uses

func (rf *File) Chromatography(instr int) (cdata CDataPackets)

Experimental: read out chromatography data from a connected instrument

func (*File) Close Uses

func (rf *File) Close() error

Close closes the RAW file

func (*File) NScans Uses

func (rf *File) NScans() int

NScans returns the number of scans in the index

func (*File) Scan Uses

func (rf *File) Scan(sn int) (scan ms.Scan)

Scan returns the scan at the scan number in argument

type FileHeader Uses

type FileHeader struct {
    Magic      uint16    //2 bytes
    Signature  signature //18 bytes
    Unknown1   uint32    //4 bytes
    Unknown2   uint32    //4 bytes
    Unknown3   uint32    //4 bytes
    Unknown4   uint32    //4 bytes
    Version    Version   //4 bytes
    AuditStart AuditTag  //112 bytes
    AuditEnd   AuditTag  //112 bytes
    Unknown5   uint32    //4 bytes
    Unknown6   [60]byte  //60 bytes
    Tag        headertag //1028 bytes
}

The Thermo fileheaders most valuable piece of info is the file version. It determines the reading strategy for some data structures that changed over time

func (*FileHeader) Read Uses

func (data *FileHeader) Read(r io.Reader, v Version)

type FractionCollector Uses

type FractionCollector struct {
    Lowmz  float64
    Highmz float64
}

type InfoPreamble Uses

type InfoPreamble struct {
    Methodfilepresent uint32
    Year              uint16
    Month             uint16
    Weekday           uint16
    Day               uint16
    Hour              uint16
    Minute            uint16
    Second            uint16
    Millisecond       uint16

    Unknown1        uint32
    DataAddr32      uint32
    NControllers    uint32
    NControllers2   uint32
    Unknown2        uint32
    Unknown3        uint32
    RunHeaderAddr32 []uint32
    Unknown4        []uint32
    Unknown5        []uint32
    Padding1        [764]byte //760 bytes, 756 bytes in v57

    DataAddr      uint64
    Unknown6      uint64
    RunHeaderAddr []uint64
    Unknown7      []uint64
    Padding2      [1032]byte //1024 bytes, 1008 bytes in v64
}

type InjectionData Uses

type InjectionData struct {
    Unknown1                    uint32
    Rownumber                   uint32
    Unknown2                    uint32
    Vial                        [6]uint16 //utf-16
    Injectionvolume             float64
    SampleWeight                float64
    SampleVolume                float64
    InternationalStandardAmount float64
    Dilutionfactor              float64
}

type PacketHeader Uses

type PacketHeader struct {
    Unknown1           uint32
    ProfileSize        uint32
    PeaklistSize       uint32
    Layout             uint32
    DescriptorListSize uint32
    UnknownStreamSize  uint32
    TripletStreamSize  uint32
    Unknown2           uint32
    Lowmz              float32
    Highmz             float32
}

A Header containing info about how many peaks/profile points were registered

type PascalString Uses

type PascalString struct {
    Length int32
    Text   []uint16
}

func (PascalString) String Uses

func (t PascalString) String() string

type PeakDescriptor Uses

type PeakDescriptor struct {
    Index  uint16
    Flags  uint8
    Charge uint8
}

A struct containing more info about the peaks

type PeakList Uses

type PeakList struct {
    Count uint32
    Peaks []CentroidedPeak
}

The data structure holding the peaks

type Profile Uses

type Profile struct {
    FirstValue float64
    Step       float64
    PeakCount  uint32
    Nbins      uint32
    Chunks     []ProfileChunk
}

The structure containing the profile-mode points

type ProfileChunk Uses

type ProfileChunk struct {
    Firstbin uint32
    Nbins    uint32
    Fudge    float32
    Signal   []float32
}

Profile points are collected in chunks with adjacent signal points

type RawFileInfo Uses

type RawFileInfo struct {
    Preamble InfoPreamble
    Heading1 PascalString
    Heading2 PascalString
    Heading3 PascalString
    Heading4 PascalString
    Heading5 PascalString
    Unknown1 PascalString
}

RawFileInfo contains the addresses of the different RunHeaders, (header of the data that each connected instrument produced) also the acquisition date

func (*RawFileInfo) Read Uses

func (data *RawFileInfo) Read(r io.Reader, v Version)

type Reaction Uses

type Reaction struct {
    Precursormz float64
    Unknown1    float64
    Energy      float64
    Unknown2    uint32
    Unknown3    uint32
}

type RunHeader Uses

type RunHeader struct {
    SampleInfo        SampleInfo
    Filename1         filename
    Filename2         filename
    Filename3         filename
    Filename4         filename
    Filename5         filename
    Filename6         filename
    Unknown1          float64
    Unknown2          float64
    Filename7         filename
    Filename8         filename
    Filename9         filename
    Filename10        filename
    Filename11        filename
    Filename12        filename
    Filename13        filename
    ScantrailerAddr32 uint32
    ScanparamsAddr32  uint32
    Unknown3          uint32
    Unknown4          uint32
    Nsegs             uint32
    Unknown5          uint32
    Unknown6          uint32
    OwnAddr32         uint32
    Unknown7          uint32
    Unknown8          uint32

    ScanindexAddr   uint64
    DataAddr        uint64
    InstlogAddr     uint64
    ErrorlogAddr    uint64
    Unknown9        uint64
    ScantrailerAddr uint64
    ScanparamsAddr  uint64
    Unknown10       uint32
    Unknown11       uint32
    OwnAddr         uint64

    Unknown12 uint32
    Unknown13 uint32
    Unknown14 uint32
    Unknown15 uint32
    Unknown16 uint32
    Unknown17 uint32
    Unknown18 uint32
    Unknown19 uint32
    Unknown20 uint32
    Unknown21 uint32
    Unknown22 uint32
    Unknown23 uint32
    Unknown24 uint32
    Unknown25 uint32
    Unknown26 uint32
    Unknown27 uint32
    Unknown28 uint32
    Unknown29 uint32
    Unknown30 uint32
    Unknown31 uint32
    Unknown32 uint32
    Unknown33 uint32
    Unknown34 uint32
    Unknown35 uint32

    Unknown36 [8]byte
    Unknown37 uint32
    Device    PascalString
    Model     PascalString
    SN        PascalString
    SWVer     PascalString
    Tag1      PascalString
    Tag2      PascalString
    Tag3      PascalString
    Tag4      PascalString
}

RunHeaders contain all data addresses for data that a certain machine connected to the Mass Spectrometer (including the MS itself) has acquired. Also SN data is available

func (*RunHeader) Read Uses

func (data *RunHeader) Read(r io.Reader, v Version)

type SampleInfo Uses

type SampleInfo struct {
    Unknown1        uint32
    Unknown2        uint32
    FirstScanNumber uint32
    LastScanNumber  uint32
    InstlogLength   uint32
    Unknown3        uint32
    Unknown4        uint32
    ScanindexAddr   uint32 //unused in 64-bit versions
    DataAddr        uint32
    InstlogAddr     uint32
    ErrorlogAddr    uint32
    Unknown5        uint32
    MaxSignal       float64
    Lowmz           float64
    Highmz          float64
    Starttime       float64
    Endtime         float64
    Unknown6        [56]byte
    Tag1            [44]uint16
    Tag2            [20]uint16
    Tag3            [160]uint16
}

SampleInfo contains some other info

type ScanDataPacket Uses

type ScanDataPacket struct {
    Header         PacketHeader
    Profile        Profile
    PeakList       PeakList
    DescriptorList []PeakDescriptor
    Unknown        []float32
    Triplets       []float32
}

An MS scan packet, containing Centroid Peak or Profile intensities

func (*ScanDataPacket) Read Uses

func (data *ScanDataPacket) Read(r io.Reader, v Version)

type ScanDataPackets Uses

type ScanDataPackets []ScanDataPacket

func (ScanDataPackets) Read Uses

func (data ScanDataPackets) Read(r io.Reader, v Version)

type ScanEvent Uses

type ScanEvent struct {
    Preamble [132]uint8 //128 bytes from v63 on, 120 in v62, 80 in v57, 41 below that
    //Preamble[6] == ms-level
    //Preamble[40] == analyzer
    Nprecursors uint32

    Reaction []Reaction

    Unknown1 [13]uint32
    MZrange  [3]FractionCollector
    Nparam   uint32

    Unknown2 [4]float64
    A        float64
    B        float64
    C        float64
}

ScanEvents are encoded headers of the MS scans, their Preamble contain the MS level, type of ionization etc. Events themselves contain range, and conversion parameters from Hz to m/z

func (ScanEvent) Convert Uses

func (data ScanEvent) Convert(v float64) float64

Convert Hz values to m/z

func (*ScanEvent) Read Uses

func (data *ScanEvent) Read(r io.Reader, v Version)

type ScanEvents Uses

type ScanEvents []ScanEvent

func (ScanEvents) Read Uses

func (data ScanEvents) Read(r io.Reader, v Version)

type ScanIndex Uses

type ScanIndex []ScanIndexEntry

func (ScanIndex) Read Uses

func (data ScanIndex) Read(r io.Reader, v Version)

type ScanIndexEntry Uses

type ScanIndexEntry struct {
    Offset32       uint32
    Index          uint32
    Scanevent      uint16
    Scansegment    uint16
    Next           uint32
    Unknown1       uint32
    DataPacketSize uint32
    Time           float64
    Totalcurrent   float64
    Baseintensity  float64
    Basemz         float64
    Lowmz          float64
    Highmz         float64
    Offset         uint64
    Unknown2       uint32
    Unknown3       uint32
}

func (*ScanIndexEntry) Read Uses

func (data *ScanIndexEntry) Read(r io.Reader, v Version)

func (ScanIndexEntry) Size Uses

func (data ScanIndexEntry) Size(v Version) uint64

type SequencerRow Uses

type SequencerRow struct {
    Injection  InjectionData
    Unknown1   PascalString
    Unknown2   PascalString
    ID         PascalString
    Comment    PascalString
    Userlabel1 PascalString
    Userlabel2 PascalString
    Userlabel3 PascalString
    Userlabel4 PascalString
    Userlabel5 PascalString
    Instmethod PascalString
    Procmethod PascalString
    Filename   PascalString
    Path       PascalString

    Vial     PascalString
    Unknown3 PascalString
    Unknown4 PascalString
    Unknown5 uint32

    Unknown6  PascalString
    Unknown7  PascalString
    Unknown8  PascalString
    Unknown9  PascalString
    Unknown10 PascalString
    Unknown11 PascalString
    Unknown12 PascalString
    Unknown13 PascalString
    Unknown14 PascalString
    Unknown15 PascalString
    Unknown16 PascalString
    Unknown17 PascalString
    Unknown18 PascalString
    Unknown19 PascalString
    Unknown20 PascalString
}

SequencerRow contains more information about what the autosampler did

func (*SequencerRow) Read Uses

func (data *SequencerRow) Read(r io.Reader, v Version)

type TrailerLength Uses

type TrailerLength uint32

I currently have no idea what TrailerLength is

func (*TrailerLength) Read Uses

func (data *TrailerLength) Read(r io.Reader, v Version)

type Version Uses

type Version uint32

Directories

PathSynopsis
toolsA set of tools using the unthermo library

Package unthermo imports 8 packages (graph) and is imported by 1 packages. Updated 2016-11-18. Refresh now. Tools for package owners.