read_shimadzu_lcd: Shimadzu LCD parser

In ethanbass/chromConverter: Chromatographic File Converter

Shimadzu LCD parser

Description

Read 3D PDA or 2D chromatogram streams from 'Shimadzu' LCD files.

Usage

read_shimadzu_lcd(
  path,
  what,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  scale = TRUE,
  collapse = TRUE
)

Arguments

path	Path to LCD file.
what	What stream to get: current options are pda, chromatograms (chroms), tic, or peak lists (peak_table). If a stream is not specified, the function will default to pda if the PDA stream is present.
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 value factor. Defaults to TRUE.
collapse	Logical. Whether to collapse lists that only contain a single element.

Details

A parser to read data 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 PDA data is encoded in a stream called PDA 3D Raw Data:3D Raw Data. The PDA data stream contains a segment for each retention time, beginning 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 along the time axis for 2D streams or along the spectral axis (?) for PDA streams.

• 4 bytes: Little-endian integer specifying the number of values in the file (for 2D data) or the number of wavelength values in each segment (for 3D data).

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

• 8 bytes of 00.

For 3D data, Each time point is divided into two sub-segments, which begin and end with an integer specifying the length of the sub-segment in bytes. 2D data are structured similarly but with more segments. All known values in this the LCD data streams 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.

Value

A chromatogram or list of chromatograms in the format specified by data_format and format_out. If data_format is wide, the chromatogram(s) will be returned with retention times as rows and a single column for the intensity. If long format is requested, two columns will be returned: one for the retention time and one for the intensity. The format_out argument determines whether chromatograms are returned as a matrix, data.frame, or data.table. Metadata can be attached to the chromatogram as attributes if read_metadata is TRUE.

Note

My parsing of the date-time format seems to be a little off, since the acquisition times diverge slightly from the ASCII file.

Author(s)

Ethan Bass

ethanbass/chromConverter documentation built on Jan. 14, 2025, 2:11 a.m.