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isoread_isodat.R
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isoread_isodat.R
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# isodat file information common to multiple file types =====
# extract the datetime of the run
extract_isodat_datetime <- function(ds) {
# find date time
ds$binary <- ds$binary %>%
set_binary_file_error_prefix("cannot recover run datetime") %>%
move_to_C_block("CTimeObject") %>%
move_to_next_pattern(re_null(4), re_block("x-000")) %>%
capture_n_data("date", "integer", 1, sensible = c(0,1000*365*24*3600)) # 1000 years as sensible limit
# store as POSIXct (converting seconds from CTimeObject) - use system time zone
ds$file_info$file_datetime <- as_datetime(ds$binary$data$date, tz = Sys.timezone())
return(ds)
}
# extract resistor information
extract_isodat_resistors <- function(ds) {
# move to resistor information
ds$binary <- ds$binary %>%
set_binary_file_error_prefix("cannot recover resistors") %>%
move_to_C_block("CEvalIntegrationUnitHWInfo")
# cap depends on dxf vs did
if (iso_is_continuous_flow(ds)) {
ds$binary <- cap_at_next_C_block(ds$binary, "CConfiguration")
} else if (iso_is_dual_inlet(ds)) {
ds$binary <- cap_at_next_C_block(ds$binary, "CGasConfiguration")
}
# find resistors
R_pre_re <- re_combine(re_or(re_text("/"), re_text("-"), re_text(","), re_text("."), size = 2),
re_block("fef-0"), re_block("fef-0"), re_null(4), re_block("x-000"))
R_post_re <- re_combine(re_block("x-000"))
positions <- find_next_patterns(ds$binary, R_pre_re, re_direct(".{20}", label = ".{20}"), R_post_re)
resistors <- list()
for (pos in positions) {
ds$binary <- ds$binary %>%
move_to_pos(pos + R_pre_re$size) %>%
capture_n_data("mass", "double", n = 1) %>%
capture_n_data("cup", "integer", n = 1) %>%
capture_n_data("R.Ohm", "double", n = 1)
resistors <- c(resistors, list(ds$binary$data[c("cup", "R.Ohm", "mass")]))
}
ds$method_info$resistors <- bind_rows(resistors)
if (nrow(ds$method_info$resistors) > 0) {
ds$method_info$resistors$cup <- ds$method_info$resistors$cup + 1L # re-index from 1 instead of 0
ds$method_info$resistors$mass <- as.character(ds$method_info$resistors$mass) # resistors as character
resistor_masses <- ds$method_info$resistors$mass
} else {
resistor_masses <- c()
}
# if mass data is read, double check that it's the right number of resistors
if (ds$read_options$raw_data && nrow(ds$raw_data) > 0) {
mass_column_pattern <- "^[vi](\\d+)\\.(.*)$"
masses <- ds$raw_data %>%
names() %>%
str_subset(mass_column_pattern) %>%
{ if(length(.) == 0) return (NULL) else
str_match(., mass_column_pattern) %>% { .[,2] }
}
if (!setequal(masses, resistor_masses)) {
ds <- register_warning(
ds, func = "extract_isodat_resistors",
details = sprintf("masses found for resistors (%s) do not match those found for the raw data (%s)",
resistor_masses %>% { if (length(.) > 0) str_c(., collapse = ",") else "none" },
masses %>% { if (length(.) > 0) str_c(., collapse = ",") else "none" }))
}
}
return(ds)
}
# extract the reference deltas and ratios for isodat files
extract_isodat_reference_values <- function(ds, cap_at_fun = NULL) {
# get secondar standard values
ds$binary <- ds$binary %>%
set_binary_file_error_prefix("cannot recover references") %>%
move_to_C_block("CSecondaryStandardMethodPart", reset_cap = TRUE)
# run cap at function if provided
if (!is.null(cap_at_fun)) {
ds$binary <- cap_at_fun(ds$binary)
}
# instrument reference name reg exps
instrument_pre1 <- re_combine(re_block("etx"), re_or(re_text("/"), re_text(","), re_text("-"), re_text(".")), re_block("fef-0"), re_block("fef-x"))
instrument_pre2 <- re_combine(re_null(4), re_block("stx"), re_block("nl"), re_text("Instrument"))
instrument_post2 <- re_combine(re_null(4), re_direct("[^\\x00]{2}", label = "[^00]{2}"), re_block("etx"))
# capture reference names
capture_ref_names <- function(pos) {
bin <- ds$binary %>%
move_to_pos(pos) %>%
move_to_next_pattern(instrument_pre1, max_gap = 0) %>%
capture_data("ref_name", "text", instrument_pre2, move_past_dots = TRUE)
instrument_post1 <- re_combine(re_block("etx"), re_block("fef-x"), re_text(bin$data$ref_name), re_block("fef-x"))
# check for gas configuration name
if(!is.null(pos <- find_next_pattern(bin, re_combine(instrument_post1, re_block("text"), instrument_post2), max_gap = 0))) {
bin <- bin %>%
move_to_pos(pos) %>%
move_to_next_pattern(instrument_post1, max_gap = 0) %>%
capture_data("config", "text", instrument_post2)
} else {
bin$data$config <- ""
}
# store information
tibble(name = bin$data$ref_name, config = bin$data$config, pos = bin$pos)
}
# run refs capture
start_pos <- find_next_patterns(
ds$binary, re_combine(instrument_pre1, re_block("text"), instrument_pre2))
if (length(start_pos) == 0) {
stop("could not find reference names at position ", ds$binary$pos,
", no match for search ",
instrument_pre1$label, "<NAME>", instrument_pre2$label, call. = FALSE)
}
refs <- tibble(
start_pos = start_pos,
data = map(.data$start_pos, capture_ref_names)
) %>% unnest(.data$data)
### deltas
# get reference delta values
ds$binary <- ds$binary %>%
set_binary_file_error_prefix("cannot recover reference delta values") %>%
move_to_C_block("CSecondaryStandardMethodPart", reset_cap = FALSE)
# find delta values
delta_re <- re_combine(re_null(4), re_block("x-000"), re_block("fef-x"), re_text("Delta "))
positions <- find_next_patterns(ds$binary, delta_re)
# capture delta values
capture_delta_values <- function(pos) {
bin <- ds$binary %>%
move_to_pos(pos) %>%
capture_data("delta_code", "text", re_block("fef-x"), move_past_dots = TRUE) %>%
capture_data("delta_name", "text", re_block("fef-x"), move_past_dots = TRUE) %>%
capture_data("delta_format", "text", re_block("fef-x"), move_past_dots = TRUE) %>%
capture_data("gas", "text", re_block("fef-0"), re_block("fef-x"), move_past_dots = TRUE) %>%
#capture_data("delta_units", "text", re_block("fef-x"), move_past_dots = TRUE) %>%
move_to_next_pattern(re_block("x-000"), re_block("x-000")) %>%
capture_n_data("delta_value", "double", 1) %>%
move_to_next_pattern(re_block("stx"), re_block("fef-x")) %>%
capture_data("reference", "text", re_null(12),
re_direct("([^\\x00]{2})?", label = "[^00]{2}"), re_block("x-000"))
# return as data frame
dplyr::as_tibble(
bin$data[c("gas", "delta_code", "delta_name", "delta_value", "delta_format", "reference")]
) %>% mutate(
standard = refs$name[max(which(bin$pos > refs$pos))]
#config = refs$config[max(which(bin$pos > refs$pos))], # not actually used, usually the same as the $gas
)
}
# run delta capture
deltas <- tibble(
pos = positions + delta_re$size,
data = map(.data$pos, capture_delta_values)
) %>% unnest(.data$data) %>%
# delta_code is very isodat specific and not stored in final, delta_format does not really hold additional information
select(.data$standard, .data$gas, .data$delta_name, .data$delta_value, .data$reference)
### ratios
# get reference delta values
ds$binary <- ds$binary %>%
set_binary_file_error_prefix("cannot recover reference ratio values") %>%
move_to_C_block("CSecondaryStandardMethodPart", reset_cap = FALSE)
# find ratios
ratio_re <- re_combine(re_null(4), re_block("x-000"), re_block("fef-x"), re_text("Ratio "))
positions <- find_next_patterns(ds$binary, ratio_re)
# capture ratio values
capture_ratio_values <- function(pos) {
bin <- ds$binary %>%
move_to_pos(pos) %>%
capture_data("ratio_code", "text", re_block("fef-x"), move_past_dots = TRUE) %>%
capture_data("ratio_name", "text", re_block("fef-x"), move_past_dots = TRUE) %>%
capture_data("ratio_format", "text", re_block("fef-0"), re_block("fef-x"), move_past_dots = TRUE) %>%
capture_data("element", "text", re_block("fef-x"), move_past_dots = TRUE) %>%
move_to_next_pattern(re_block("x-000"), re_block("x-000")) %>% ###
capture_n_data("ratio_value", "double", 1)
# return as data frame
dplyr::as_tibble(bin$data[c("ratio_code", "element", "ratio_name", "ratio_value", "ratio_format")]) %>%
mutate(
reference = refs$name[max(which(bin$pos > refs$pos))]
)
}
# run ratio capture
if (length(positions) > 0) {
ratios <- tibble(
pos = positions + ratio_re$size,
data = map(.data$pos, capture_ratio_values)
) %>%
unnest(.data$data) %>%
select(.data$reference, .data$element, .data$ratio_name, .data$ratio_value)
} else {
# no ratios defined
ratios <- tibble(reference = character(0), element = character(0),
ratio_name = character(0), ratio_value = numeric(0))
}
# store information
ds$method_info$standards <- unique(deltas)
ds$method_info$reference_ratios <- unique(ratios)
return(ds)
}
# extracts the sequence line information for isodat files
extract_isodat_sequence_line_info <- function(ds) {
# find sequence line information
ds$binary <- ds$binary %>%
set_binary_file_error_prefix("cannot process sequence line info") %>%
move_to_C_block_range("CParsedEvaluationString", "CBinary") %>%
move_to_next_pattern(re_text("Sequence Line Information"))
seq_line_info <- list()
re_end_of_info <- re_combine(
re_null(4),
re_or(re_combine(re_not_null(2), re_block("etx")),
re_block("C-block")))
caps <- find_next_patterns(ds$binary, re_end_of_info)
if (length(caps) == 0) stop("could not any data", call. = FALSE)
positions <- c(ds$binary$pos, head(caps, -1))
# note: fef-x block seems to be used in .dxf, nl in .did
re_val_var_break <- re_or(re_block("fef-x"), re_block("nl"))
re_val_var_break$size <- 4
# loop through all
for (i in 1:length(positions)) {
# capture value
ds$binary <- ds$binary %>%
move_to_pos(positions[i], reset_cap = TRUE) %>%
cap_at_pos(caps[i]) %>%
move_to_next_pattern(re_or(re_text("/"), re_text(".")), re_block("fef-x")) %>%
capture_data("value", "text", re_val_var_break, data_bytes_max = 500, move_past_dots = TRUE)
# capture info name
info_length <- (ds$binary$max_pos - ds$binary$pos)/2
if (info_length %% 1 > 0)
stop("length of sequence info for value '", ds$binary$data$value, "' is not an integer (", info_length, ")", call. = FALSE)
ds$binary <- ds$binary %>%
capture_n_data("info", "text", (ds$binary$max_pos - ds$binary$pos)/2)
# store info
if (!is.null(ds$binary$data$info))
ds$file_info[[ds$binary$data$info]] <- ds$binary$data$value
}
return(ds)
}
# extract sequence line info from old isodat files (.cf and .caf)
extract_isodat_old_sequence_line_info <- function(ds) {
# find sequence line information
ds$binary <- ds$binary %>%
set_binary_file_error_prefix("cannot process sequence line info") %>%
move_to_C_block("CSequenceLineInformationGridStorage") %>%
move_to_next_pattern(re_direct("\xff{12}", label = "ff{12}"))
# block delimiter
cap_pos <- find_next_pattern(
ds$binary,
re_direct("\x86{3}\\x00\x96{3}\\x00\xCB{3}\\x00\xB2{3}\\x00\xD7{3}\\x00\xDD{3}\\x00",
label = "86{3}0096{3}00cb{3}00b2{3}00d7{3}00dd{3}00")
)
if (!is.null(cap_pos)) {
ds$binary <- ds$binary %>% cap_at_pos(cap_pos)
} else op_error(ds$binary, "cannot find binary delimiter for end of Sequence Information")
# first line marker
line_re <- re_combine(
re_block("x-000"), re_direct(".{2,8}", label = ".{2,8}"),
re_block("fef-x"), re_text("Line"))
ds$binary <- ds$binary %>%
move_to_next_pattern(line_re, move_to_end = FALSE) %>%
capture_n_data("info_marker", "raw", 4)
# regular expressions
re_entry_start <- re_control(ds$binary$data$info_marker)
label_pre_re <- re_combine(re_direct(".{2,8}", size = 8, label = ".{2,8}"), re_block("fef-x"))
# NOTE: all of these seem to be valid end blocks for text segements in this part of the file, any way to make this simpler?
label_post_re <- re_or(
re_combine(re_null(7), re_direct("\xff\\x00{3}", label = "ff00{3}")),
re_combine(re_block("x-000"), re_block("fef-x")),
re_combine(re_null(4), re_block("fef-x")),
re_combine(re_null(4), re_block("x-000")),
re_combine(re_null(4), re_direct("\xff{3}\\x00", size = 4, label = "ff{3}00")))
# extract information
positions <- find_next_patterns(ds$binary, re_entry_start)
label <- value <- NULL # global vars
labels <- list(list(label = "Line", label_marker = NA_character_))
values <- list()
reached_values <- FALSE
for (pos in positions) {
ds$binary <- ds$binary %>% move_to_pos(pos + re_entry_start$size)
if (!is.null(find_next_pattern(ds$binary, label_pre_re, max_gap = 0))) {
ds$binary <- ds$binary %>%
move_to_next_pattern(label_pre_re) %>%
{ move_to_pos(., .$pos - 1) } %>%
capture_n_data("marker", "raw", 1) %>%
capture_data("text", "text", label_post_re)
text <- ds$binary$data$text
marker <- as.character(ds$binary$data$marker)
} else {
text <- marker <- NA_character_
}
# check for values
if (!reached_values && marker %in% c("01", "02")) {
# NOTE: is there any better way to detect where the value starts??
reached_values <- TRUE
}
# add to values/labels
if (is.null(text)) text <- NA_character_
if (reached_values)
values <- c(values, list(list(value = text, value_marker = marker)))
else
labels <- c(labels, list(list(label = text, label_marker = marker)))
}
if (length(values) != length(labels)) {
if(default(debug)) {
print(bind_rows(labels))
print(bind_rows(values))
}
stop(sprintf("unequal number of file info labels (%d) and file info values (%d)",
length(labels), length(values)), call. = FALSE)
}
# store file info
file_info <- left_join(
bind_rows(labels) %>% mutate(n = 1:n()),
bind_rows(values) %>% mutate(n = 1:n()),
by = "n"
)
# transfer to
if (nrow(file_info) > 0) {
ds$file_info <-
dplyr::mutate(
ds$file_info,
!!!rlang::set_names(file_info$value, file_info$label)
)
}
return(ds)
}
# extracts the measurement information for isodat files
extract_isodat_measurement_info <- function(ds) {
# find measurement info
ds$binary <- ds$binary %>%
set_binary_file_error_prefix("cannot process measurement info") %>%
move_to_C_block_range("CMeasurmentInfos", "CMeasurmentErrors") %>%
move_to_next_C_block("CISLScriptMessageData")
isl_info_msgs <- c()
while(!is.null(find_next_pattern(ds$binary, re_text("CUserInfo")))) {
ds$binary <- ds$binary %>%
move_to_next_pattern(re_block("x-000"), re_block("fef-x")) %>%
capture_data("info", "text", re_block("fef-x"), re_text("CUserInfo"), move_past_dots = TRUE)
isl_info_msgs <- c(isl_info_msgs, ds$binary$data$info)
}
# store all in one information set
ds$file_info$measurement_info <- list(isl_info_msgs)
return(ds)
}
# extract H3 factor info
extract_H3_factor_info <- function(ds) {
# H3 factor (if available)
if ("CH3FactorResult" %in% ds$binary$C_blocks$block) {
# extract H3 factor value (note H3 stability is not present)
ds$binary <- ds$binary %>%
set_binary_file_error_prefix("cannot extract H3 factor") %>%
move_to_C_block("CH3FactorResult") %>%
move_to_next_pattern(re_text("H3 Factor")) %>%
move_to_next_pattern(re_block("x-000")) %>%
capture_n_data("H3_factor", "double", 1)
# this is a text field for compatibility with other file formats
ds$file_info$`H3 Factor` <- as.character(ds$binary$data$H3_factor)
}
return(ds)
}
# extract MS integration time
extract_MS_integration_time_info <- function(ds) {
ds$binary <- ds$binary %>%
set_binary_file_error_prefix("cannot extract MS integration time") %>%
move_to_C_block("CActionPeakCenter", move_to_end = FALSE) %>%
skip_pos(-5) %>%
capture_n_data("ms_integration_time", "integer", 1, sensible = c(0L, 3600000L))
# store ms integration time (should this be text for compatibility with other formats?)
ds$file_info$MS_integration_time.s <- ds$binary$data$ms_integration_time/1000
return(ds)
}
# extract vendor computed data table for continuous flow files
extract_isodat_continuous_flow_vendor_data_table <- function(ds, cap_at_fun = NULL) {
# find vendor data table
ds$binary <- ds$binary %>%
set_binary_file_error_prefix("cannot process vendor identified peaks") %>%
move_to_C_block("CGCPeakList")
# run cap at function if provided
if (!is.null(cap_at_fun)) {
ds$binary <- cap_at_fun(ds$binary)
}
### basic peak info
# find basic peak information (Rts, amplitude, bg) - this information is stored separatedly from the rest of the table
rt_pre_re <- re_combine(
re_null(18),
re_direct("(\\x00|[\x01-\x1f])\\x00{3}", size = 4, label = "00|[01-1f]00{3}"),
re_block("x-000"))
rt_re <- re_combine(rt_pre_re, re_direct("..\\x00{2}", label = "..00{2}"), re_block("x-000"))
positions <- find_next_patterns(ds$binary, rt_re)
rts <- list()
for (pos in positions) {
ds$binary <- ds$binary %>%
move_to_pos(pos + rt_pre_re$size) %>%
capture_n_data("mass", "integer", 1) %>%
move_to_next_pattern(re_block("x-000"), max_gap = 0) %>%
capture_n_data("peak", "integer", 1) %>%
skip_pos(4) %>% # random xx00 follows
capture_n_data("start", "double", 1) %>%
capture_n_data("bg", "double", 1) %>%
skip_pos(4) %>%
capture_n_data("rt", "double", 1) %>%
capture_n_data("amp", "double", 1) %>%
skip_pos(4) %>%
capture_n_data("end", "double", 1)
# NOTE: after this there is another unknown value similar to 'bg', then the rIntensity, then the Intensity (but we get those from the data table too)
rts <- c(rts, list(c(ini = pos, pos = ds$binary$pos, ds$binary$data[c("mass", "peak", "start", "rt", "end", "amp", "bg")])))
}
# NOTE: the retention time is only ALMOST repeated each time, if there are significant
# chromatographic shifts (as is alwayst he case for H2), these will in fact NOT quite be
# identical. Isodat seems to report only the major ion (first ion here) so we are doing the same
rts_df <- dplyr::bind_rows(rts)
if (nrow(rts_df) == 0 || !"mass" %in% names(rts_df) || !any(rts_df$mass > 0)) {
return(ds) # no vendor data table entries found
}
# filter out false matches
rts_df <- dplyr::filter(rts_df, .data$mass > 0)
# retention times
peaks <- rts_df %>%
select(.data$peak, Start = .data$start, Rt = .data$rt, End = .data$end) %>%
distinct(.data$peak, .keep_all = TRUE) %>%
# add in amplitudes
left_join(
rts_df %>%
select(.data$peak, Ampl = .data$mass, .data$amp) %>%
spread(.data$Ampl, .data$amp, sep = " "),
by = "peak"
) %>%
# add in backgrounds
left_join (
rts_df %>%
select(.data$peak, BGD = .data$mass, .data$bg) %>%
spread(.data$BGD, .data$bg, sep = " "),
by = "peak"
) %>%
rename(`Nr.` = .data$peak)
### rest of data table
extracted_dt <- extract_isodat_main_vendor_data_table(ds, C_block = "CGCPeakList", cap_at_fun = cap_at_fun)
if (nrow(extracted_dt$cell_values) == 0L) {
stop("could not find any vendor table data", call. = FALSE)
}
# store vendor data table
data_table <- full_join(peaks, mutate(extracted_dt$cell_values, .check = TRUE), by = "Nr.")
if (any(is.na(data_table$Start) | any(is.na(data_table$.check)))) {
ds <- register_warning(ds, details = "vendor data table has unexpected empty cells, process vendor table with care")
}
ds$vendor_data_table <- select(data_table, -.data$.check)
# safe information on the column units
attr(ds$vendor_data_table, "units") <-
bind_rows(
dplyr::select(extracted_dt$columns, .data$column, .data$units),
tibble::tibble(column = c("Start", "Rt", "End"), units = "[s]"),
tibble::tibble(column = peaks %>% select(starts_with("Ampl"), starts_with("BGD")) %>% names(), units = "[mV]")
) %>%
mutate(units = ifelse(units == " ", "", units))
# FIXME: do this directly
ds$vendor_data_table <- convert_df_units_attr_to_implicit_units(ds$vendor_data_table)
return(ds)
}
# extract the main (recurring portion of the vendor data table)
# @param C_block which C_block to start at
# @param col_include regexp to decide which columns to include (all by default)
# @param skip_row_check function to check whether to skip a row based on the most recent column and column value
# @note: doing this in a for loop actually turned out faster than with apply, epecially with the skip_row parameter
extract_isodat_main_vendor_data_table <- function(ds, C_block, cap_at_fun = NULL, col_include = "*",
skip_row_check = function(column, value) FALSE) {
# main data table
ds$binary <- ds$binary %>%
set_binary_file_error_prefix("cannot process vendor data table") %>%
move_to_C_block(C_block, reset_cap = FALSE) %>% # important to NOT reset position cap
move_to_next_C_block("CEvalDataIntTransferPart")
# run cap at function if provided
if (!is.null(cap_at_fun)) {
ds$binary <- cap_at_fun(ds$binary)
}
# find columns and row data for the whole data table
pre_column_re <- re_combine(
re_or(re_text("/"), re_text("-"), re_text(","), re_text("."), size = 2),
re_block("fef-0"), re_block("fef-0"), re_null(4), re_block("x-000"), re_block("fef-x"))
positions <- find_next_patterns(ds$binary, pre_column_re)
# collection variables
columns <- list()
rows <- list()
rows_i <- 0
skip_row <- FALSE
for(pos in positions) {
# get column name
ds$binary <- ds$binary %>%
move_to_pos(pos + pre_column_re$size) %>%
# skip ID column since it is not unique in peak jumping files
move_to_next_pattern(re_block("fef-x"))
# capture column
ds$binary <- ds$binary %>%
capture_data("column", "raw", re_block("fef-x"), move_past_dots = TRUE, ignore_trailing_zeros = FALSE)
# check for columns starting with delta symbol, replace with d instead of delta symbol
if (identical(ds$binary$data$column[1:2], as.raw(c(180, 03))))
ds$binary$data$column[1:2] <- as.raw(c(100, 00))
col <- parse_raw_data(ds$binary$data$column, "text")
# skip columns that don't fit the include criteria right away
if (!grepl(col_include, col)) next #skip
# check for new row
if (length(columns) == 0 || col == names(columns)[1]) {
rows_i <- rows_i + 1
rows[[rows_i]] <- list()
skip_row <- FALSE
}
# check whether still in row skip
if (skip_row) next # skip
# check if have a proper units next
if (is.null(find_next_pattern(ds$binary, re_block("text"), re_block("fef-x"), max_gap = 0))) {
# this is something else, not a proper units block
next # skip
}
# get column formatting
ds$binary <- ds$binary %>%
# retrieve format (!not always the same)
capture_data("format", "text", re_block("fef-x"), move_past_dots = TRUE)
# skip data columns without propre formatting infromation right away
if(ds$binary$data$format %in% c("", " ") || nchar(ds$binary$data$format) > 4) {
next # skip
}
# store information about new column if not already stored
if (!col %in% names(columns)) {
ds$binary <- ds$binary %>%
# skip what looks like it might be the gas configuration and an unknown piece of information
move_to_next_pattern(re_block("text0"), re_block("fef-x"), re_block("text0"), re_block("fef-x")) %>%
capture_data("units", "raw", re_block("fef-x"), move_past_dots = TRUE, ignore_trailing_zeros = FALSE) # retrieve units
# process isodat units
ds$binary$data$units <- process_isodat_units(ds$binary$data$units)
# data format
type <-
if (ds$binary$data$format == "%s") { "text"
} else if (ds$binary$data$format %in% c("%u", "%d")) { "integer"
} else if (str_detect(ds$binary$data$format, "\\%[0-9.]*f")) { "double"
} else { op_error(ds$binary,
sprintf("could not process data table column format '%s' for column '%s'",
ds$binary$data$format, col))
}
# store
new_col <- c(list(pos = ds$binary$pos, type = type, column = col), ds$binary$data[c("format", "units")])
columns[[col]] <- new_col
} else if (ds$binary$data$format != columns[[col]]$format) {
# double check formatting
op_error(ds$binary,
sprintf("mismatched data column format for column '%s', found '%s' but expected '%s'",
col, ds$binary$data$format, columns[[col]]$format))
}
# capture data
if (columns[[col]]$type == "text") {
ds$binary <-
ds$binary %>% move_to_next_pattern(
re_block("x-000"), re_direct("\\x00{4,6}", label = "00{4,6}"),
re_block("x-000"), re_block("x-000")) %>%
capture_data("value", "text", re_null(2), re_direct("..", label = ".."), re_block("etx"))
} else {
ds$binary <-
ds$binary %>% move_to_next_pattern(re_block("x-000"), re_block("x-000")) %>%
capture_data("value", columns[[col]]$type, re_block("x-000"),
data_bytes_min = 4) # read at least one number
# sanity checks
if (is.nan(ds$binary$data$value)) {
ds$binary$data$value <- NA # safety to catch things that are not valid numbers at all
} else if (length(ds$binary$data$value) > 1) {
op_error(ds$binary, sprintf("expected one value for cell '%s' but found %d", col, length(ds$binary$data$value)))
} else if (ds$binary$data$value != 0 && (abs(ds$binary$data$value) < 1e-100 || abs(ds$binary$data$value) > 1e100)) {
op_error(ds$binary, sprintf("found cell value '%s' for cell '%s' which is not a sensible numeric value", str_c(ds$binary$data$value), col))
}
}
# check whether row should be skipped
skip_row <- do.call(skip_row_check, args = list(col, ds$binary$data$value))
if (skip_row) {
rows[[rows_i]] <- NULL
} else {
rows[[rows_i]][[col]] <- ds$binary$data$value
}
}
cols <- bind_rows(columns)
cells <- bind_rows(rows)
return(list(columns = cols, cell_values = cells))
}
# utils ========
# process isodat raw units into text units
# replaces permil symbol with "permil" for ASCII compatibility
# standardizes "per mil" to "permil"
process_isodat_units <- function(raw_units) {
# raw vectors
raw_permil <- as.raw(c(0x30, 0x20))
text_permil <- as.raw(c(0x70, 0x00, 0x65, 0x00, 0x72, 0x00, 0x6d, 0x00, 0x69, 0x00, 0x6c, 0x00))
if (length(raw_units) > 1) {
# replace permil symbol (which is non-ASCII)
raw_units <-
tibble(
pos1 = raw_units,
pos2 = c(raw_units[-1], as.raw(0x00)),
idx = 1:length(.data$pos1)
) %>%
mutate(
is_permil = purrr::map2_lgl(.data$pos1, .data$pos2, ~ identical(c(.x, .y), raw_permil)),
pos1 = purrr::map2(.data$pos1, .data$is_permil, ~ {
if(.y) text_permil
else .x
})
) %>%
filter(
!.data$idx %in% (.data$idx[.data$is_permil] + 1L)
) %>%
dplyr::pull(.data$pos1) %>%
unlist()
}
# convert to text units
text_units <- parse_raw_data(raw_units, "text")
# standardize the units
text_units <- stringr::str_replace_all(text_units, "per mil", "permil")
return(text_units)
}
# ALTERNATIVE - too slow! ========
# alternative implementation
# @note: cleaner but slower than extract_isodat_main_vendor_data_table
# @note: either make faster or deprecate!
# @note: does not support the newer include and skip row parameters
extract_isodat_main_vendor_data_table2 <- function(ds, C_block, cap_at_fun = NULL) {
# main data table
ds$binary <- ds$binary %>%
set_binary_file_error_prefix("cannot process vendor data table") %>%
move_to_C_block(C_block, reset_cap = TRUE) %>%
move_to_next_C_block("CEvalDataIntTransferPart")
# run cap at function if provided
if (!is.null(cap_at_fun)) {
ds$binary <- cap_at_fun(ds$binary)
}
columns <- extract_isodat_main_vendor_data_table_cells(ds)
cell_values <- extract_isodat_main_vendor_data_table_cell_values(ds, columns)
return(list(columns = columns, cell_values = cell_values))
}
# extract the main (recurring) portion of the vendor data table
# @note part of extract_isodat_main_vendor_data_table2
# @note too slow (slower than the loop in this case)
extract_isodat_main_vendor_data_table_cells <- function(ds) {
# find columns and row data for the whole data table
pre_column_re <- re_combine(
re_or(re_text("/"), re_text("-"), size = 2),
re_block("fef-0"), re_block("fef-0"), re_null(4), re_block("x-000"), re_block("fef-x"))
positions <- find_next_patterns(ds$binary, pre_column_re)
# capture the table cells
# NOTES: this is the SLOWEST part taking ~4s for 300 entries (the actual column/format capture)
# is there a way to optimize this further?
# - lapply instead of map?
# - otimizing the capture data operations?
capture_table_cell <- function(pos, bin) {
bin <- bin %>%
move_to_pos(pos) %>%
move_to_next_pattern(re_block("fef-x")) %>% # skip ID column since it is not unique in peak jumping files
capture_data("column", "raw", re_block("fef-x"), move_past_dots = TRUE) %>%
capture_data("format", "text", re_block("fef-x"), move_past_dots = TRUE) # retrieve format (!not always the same)
# skip data columns without formatting infromation right away
if(bin$data$format %in% c("", " ")) return(tibble())
# check for columns starting with delta symbol, replace with d instead of delta symbol
if (identical(bin$data$column[1:2], as.raw(c(180, 03))))
bin$data$column[1:2] <- as.raw(c(100, 00))
col <- bin$data$column <- parse_raw_data(bin$data$column, "text")
# return column information
tibble(column = col, format = bin$data$format, continue_pos = bin$pos)
}
# capture the table cell details
# NOTES: very quick
capture_table_cell_units <- function(pos, bin) {
bin <- bin %>%
move_to_pos(pos) %>%
# skip what looks like it might be the gas configuration and an unknown piece of information
move_to_next_pattern(re_block("text0"), re_block("fef-x"), re_block("text0"), re_block("fef-x")) %>%
capture_data("units", "raw", re_block("fef-x"), move_past_dots = TRUE, ignore_trailing_zeros = FALSE) # retrieve units
# process isodat units
units <- process_isodat_units(bin$data$units)
return(units)
}
# cells (NOTE: lapply is faster than map+unnest in this situation)
cells <-
# retrieve cell information
lapply(positions + pre_column_re$size, capture_table_cell, bin = ds$binary) %>%
bind_rows() %>%
# row numbers
mutate(row = cumsum(.data$column == .data$column[1])) %>%
# nest by column and expand column details
nest(data = c(-.data$column)) %>%
mutate(
n_formats = map_int(.data$data, ~length(unique(.x$format))),
column_format = map_chr(.data$data, ~.x$format[1]),
units = map_chr(.data$data, ~capture_table_cell_units(min(.x$continue_pos), bin = ds$binary)),
type =
dplyr::case_when(
.data$column_format == "%s" ~ "text",
.data$column_format %in% c("%u", "%d") ~ "integer",
str_detect(.data$column_format, "\\%[0-9.]+f") ~ "double",
TRUE ~ NA_character_
)
)
# safety check: to make sure all columns have the same format specification
if (!all(ok <- cells$n_formats == 1)) {
formats <- map_chr(cells$data[!ok], ~collapse(unique(.x$format), ", "))
problems <- glue("column {cells$column[!ok]} has multiple formats '{formats}'")
op_error(ds$binary, glue("mismatched data column formats:\n{collapse(problems, '\n')}"))
}
# safety check: to make sure all formats are resolved
if (!all(ok <- !is.na(cells$type))) {
problems <- glue("column {cells$column[!ok]} has unknown format '{cells$column_format[!ok]}'")
op_error(ds$binary, glue("unknown column formats:\n{collapse(problems, '\n')}"))
}
return(cells)
}
# extract the cell values
# extract the main (recurring) portion of the vendor data table
# @note part of extract_isodat_main_vendor_data_table2
extract_isodat_main_vendor_data_table_cell_values <- function(ds, cells) {
# global vars
data <- column <- continue_pos <- type <- NULL
# capture cell value
# NOTES: adds about 1s to a 300 cell table)
capture_table_cell_value <- function(pos, type) {
# capture data
bin <- ds$binary %>% move_to_pos(pos)
if (type == "text") {
bin <-
bin %>% move_to_next_pattern(
re_block("x-000"), re_direct("\\x00{4,6}", label = "00{4,6}"),
re_block("x-000"), re_block("x-000")) %>%
capture_data("value", "text", re_null(2), re_direct("..", label = ".."), re_block("etx"))
} else {
bin <-
bin %>% move_to_next_pattern(re_block("x-000"), re_block("x-000")) %>%
capture_data("value", type, re_block("x-000"),
data_bytes_min = 4) # read at least one number
# sanity checks
if (length(bin$data$value) > 1) {
op_error(ds$binary, sprintf("expected one cell value but found %d", length(bin$data$value)))
} else if (bin$data$value != 0 && (abs(bin$data$value) < 1e-100 || abs(bin$data$value) > 1e100)) {
op_error(ds$binary, sprintf("found cell value '%s' which is not a sensible numeric value", str_c(ds$binary$data$value)))
}
}
return(bin$data$value)
}
# get cell values
cells %>%
unnest(data) %>%
select(column, continue_pos, type, row) %>%
nest(-row) %>%
mutate(
data = map(data, function(row) {
# note: have to do it this way (by row instead of in long format) to keep correct data types for each column
mapply(function(x,y,z) list(capture_table_cell_value(y, z)), row$column, row$continue_pos, row$type)
})
) %>%
{ bind_rows(.$data) }
}