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Read 'Shimadzu' LCD 2D data

Source: R/read_shimadzu_lcd.R
read_sz_lcd_2d.Rd

Reads 2D PDA data stream from 'Shimadzu' .lcd files.

Usage

read_sz_lcd_2d(
  path,
  format_out = "data.frame",
  data_format = "wide",
  read_metadata = TRUE,
  metadata_format = "shimadzu_lcd",
  scale = TRUE
)

Arguments

path

Path to 'Shimadzu' .lcd 2D data file.

format_out

Matrix or data.frame.

data_format

Either wide (default) or long.

read_metadata

Logical. Whether to attach metadata.

metadata_format

Format to output metadata. Either chromconverter or raw.

scale

Whether to scale the data by the calibration factor and the value factor, converting the encoded integers into the unit reported by 'Lab Solutions' (e.g. mV).

Value

One or more 2D chromatograms from the chromatogram streams in matrix or data.frame format, according to the value of format_out. If multiple chromatograms are found, they will be returned as a list of matrices or data.frames. The chromatograms will be returned in wide or long format according to the value of data_format`.

Details

A parser to read chromatogram data streams from 'Shimadzu' .lcd files. LCD files are encoded as 'Microsoft' OLE documents. The parser relies on the olefile package in Python to unpack the files. The chromatogram data is encoded in streams titled LSS Raw Data:Chromatogram Ch<#>. The chromatogram data streams begin with a 24-byte header.

The 24 byte header consists of the following fields:

  • 4 bytes: segment label (17234).

  • 4 bytes: Little-endian integer specifying the sampling rate (in milliseconds).

  • 4 bytes: Little-endian integer specifying the number of values in the file.

  • 4 bytes: Little-endian integer specifying the total number of bytes in the file.

  • 8 bytes of 00s

Each segment is divided into multiple sub-segments, which begin and end with an integer specifying the length of the sub-segment in bytes. All known values in this data stream are little-endian and the data are delta-encoded. The first hexadecimal digit of each value is a sign digit specifying the number of bytes in the delta and whether the value is positive or negative. The sign digit represents the number of hexadecimal digits used to encode each value. Even numbered sign digits correspond to positive deltas, whereas odd numbers indicate negative deltas. Positive values are encoded as little-endian integers, while negative values are encoded as two's complements. The value at each position is derived by subtracting the delta at each position from the previous value.

See also

Other 'Shimadzu' parsers: read_shimadzu(), read_shimadzu_gcd(), read_shimadzu_lcd(), read_shimadzu_qgd(), read_sz_lcd_3d(), read_sz_tables()

Author

Ethan Bass

Examples

if (FALSE) { # \dontrun{
read_sz_lcd_2d("path/to/file.lcd")
} # }