Read the integration results 'LabSolutions' stored alongside the raw data
in a 'Shimadzu' OLE container (.lcd or .gcd), one table per channel.
Value
A named list with one peak table per channel, named for the stream
it was read from. A table that cannot be parsed is returned as NA with a
message, so one bad channel does not lose the others.
Details
Each table lives in its own stream, a short header followed by one
fixed-length record per peak. Only chromatographic tables are read: streams
named PT- plus the channel (PT-LC.1.1.DET.1.CH#1, matching that
channel's channel_id metadata), or Peak Table- plus a number
(Peak Table-100). The tables a mass spectrometry run produces
(Mass Peak Table, Compound Peak Table, Ident Peak Table) have layouts
of their own and are skipped.
There are two layouts. V0 has no magic number and opens with an 8-byte
header: the peak count as a uint32, then four unparsed bytes. V1 opens
with the magic number 56 45 52 31 (VER1), the peak count as a uint32,
and twelve further unparsed bytes, for a 20-byte header.
In every file seen so far the layout follows the stream name: PT- streams,
under LSS Data Processing, are V1, and Peak Table- streams, under
LC Data Processing, are V0. The parser still dispatches on the magic
number rather than on the name of the stream, since the name is the weaker
signal.
Retention, initial and final times are stored in milliseconds and converted to minutes, as elsewhere in the package. All values are little-endian.
A V0 record is 280 bytes:
| Offset | Type | Field |
| 0–3 | uint32 | Unparsed (peak number?) |
| 4–7 | uint32 | Retention time (R.time) |
| 8–15 | double | Area |
| 16–23 | double | Unparsed |
| 24–31 | double | Height |
| 32–39 | double | Unparsed |
| 40–55 | uint32 x 4 | Unparsed |
| 56–59 | uint32 | Start of the peak (I.time) |
| 60–63 | uint32 | End of the peak (F.time) |
| 64–67 | uint32 | Area/height ratio x 1000 (AH) |
| 68–215 | Unparsed | |
| 216–223 | double | Theoretical plates (Plate.no) |
| 224–231 | double | Plate height (Plate.ht) |
| 232–239 | double | Tailing factor |
| 240–247 | double | Resolution |
| 248–255 | double | Separation factor |
| 256–279 | Unparsed |
A V1 record is longer and its length is not fixed by the format: it is
derived as (stream size - 20) / peak count. The first 728 bytes are the
part this parser reads, and any remainder is skipped.
| Offset | Type | Field |
| 0–3 | uint32 | Unparsed (peak number?) |
| 4–7 | uint32 | Retention time (R.time) |
| 8–15 | double | Area |
| 16–23 | double | Unparsed |
| 24–31 | double | Height |
| 32–39 | double | Unparsed |
| 40–55 | uint32 x 4 | Unparsed |
| 56–59 | uint32 | Start of the peak (I.time) |
| 60–63 | uint32 | End of the peak (F.time) |
| 64–71 | double | Area/height ratio (AH) |
| 72–175 | Unparsed | |
| 176–183 | double | Concentration (Conc) |
| 184–187 | int32 | Compound identifier (ID), 0 for an unidentified peak |
| 188–239 | Unparsed | |
| 240–247 | double | Retention factor (k) |
| 248–255 | double | Theoretical plates (Plate.no) |
| 256–375 | Unparsed, with an unidentified double at 312 | |
| 376–383 | double | Plate height (Plate.ht) |
| 384–503 | Unparsed, with an unidentified double at 440 | |
| 504–511 | double | Tailing factor |
| 512–519 | double | Resolution |
| 520–639 | Unparsed, with unidentified doubles at 568 and 632 | |
| 640–647 | double | Separation factor |
| 648–711 | Unparsed | |
| 712–719 | double | Concentration, percent |
| 720–727 | double | Concentration, normalized |
Two things the tables above do not show. AH is a scaled integer in V0 but
a double in V1, so the same field has to be decoded differently in each.
The V1 values are also spaced rather than packed: seven doubles lie exactly
64 bytes apart — Plate.no (248), Plate.ht (376) and the tailing factor
(504), with unidentified values at 312, 440, 568 and 632 — while k
(240), the resolution (512) and the separation factor (640) each sit 8 bytes
to one side of that grid, paired with the value on it. Each derived quantity
therefore seems to occupy a 64-byte slot and use only the first eight bytes
of it. The field names are this package's reading of the format rather than
the vendor's own.
A V0 record is not always 280 bytes: the Peak Table-100 streams under
LC Data Processing hold 544-byte records whose first 256 bytes follow the
table above, with the retention factor (k) as a double at 208. As for
V1, the record length is derived as (stream size - 8) / peak count and
any remainder beyond 280 bytes is skipped. A table whose records are
shorter than 280 bytes, or do not divide the stream evenly, is rejected.
See also
Other 'Shimadzu' parsers:
read_shimadzu(),
read_shimadzu_gcd(),
read_shimadzu_lcd(),
read_shimadzu_method(),
read_shimadzu_qgd(),
read_sz_lcd_2d(),
read_sz_lcd_3d()