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Merge pull request #61 from spectral-cockpit/opt-55-simplify-create-d…
…ataset New key-value mapping to simplify header decoding (& fix CI code check)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,180 +1,186 @@ | ||
| #' assign the classes to the dataset list | ||
| #' @param data_list list of the header information for each block | ||
| create_dataset <- function(data_list) { | ||
| block_type <- data_list$block_type | ||
| text_type <- data_list$text_type | ||
| channel_type <- data_list$channel_type | ||
| additional_type <- data_list$additional_type | ||
|
|
||
| # select read_class and block_type_name | ||
| # TODO: if there is a simpler method, happy to change! | ||
| if (block_type == 0) { | ||
| read_class <- "text" | ||
|
|
||
|
|
||
| if (text_type == 8) { | ||
| read_class <- "parameter" | ||
| block_type_name <- "info_block" | ||
| } else if (text_type == 104) { | ||
| block_type_name <- "history" | ||
| } else if (text_type == 152) { | ||
| block_type_name <- "curve_fit" | ||
| } else if (text_type == 168) { | ||
| block_type_name <- "signature" | ||
| } else if (text_type == 240) { | ||
| block_type_name <- "integration_method" | ||
| } else { | ||
| block_type_name <- "text_information" | ||
| } | ||
| } else if (block_type == 7) { | ||
| read_class <- "data" | ||
|
|
||
| if (channel_type == 4) { | ||
| block_type_name <- "sc_sample" | ||
| } else if (channel_type == 8) { | ||
| block_type_name <- "ig_sample" | ||
| } else if (channel_type == 12) { | ||
| block_type_name <- "ph_sample" | ||
| } | ||
| } else if (block_type == 11) { | ||
| read_class <- "data" | ||
|
|
||
| if (channel_type == 4) { | ||
| block_type_name <- "sc_ref" | ||
| } else if (channel_type == 8) { | ||
| block_type_name <- "ig_ref" | ||
| } else { | ||
| stop("There is a new block type, open an issue.") | ||
| } | ||
| } else if (block_type == 15) { | ||
| if (channel_type == 16) { | ||
| if (text_type == 112) { | ||
| read_class <- "parameter" | ||
| block_type_name <- "quant_report_ab" | ||
| } else if (text_type == 104) { | ||
| read_class <- "parameter" | ||
| block_type_name <- "me_test_report_ab" | ||
| } else { | ||
| read_class <- "data" | ||
| if (additional_type == 64) { | ||
| block_type_name <- "ab_no_atm_comp" | ||
| } else if (additional_type == 0) { | ||
| block_type_name <- "ab" | ||
| } else { | ||
| stop("There is a new block type, open an issue.") | ||
| } | ||
| } | ||
| } else if (channel_type == 48) { | ||
| if (text_type == 112) { | ||
| read_class <- "parameter" | ||
| block_type_name <- "quant_report_refl" | ||
| } else if (text_type == 104) { | ||
| read_class <- "parameter" | ||
| block_type_name <- "me_test_report_refl" | ||
| } else { | ||
| read_class <- "data" | ||
| if (additional_type == 64) { | ||
| block_type_name <- "refl_no_atm_comp" | ||
| } else if (additional_type == 0) { | ||
| block_type_name <- "refl" | ||
| } else { | ||
| stop("There is a new block type, open an issue.") | ||
| } | ||
| } | ||
| } else if (channel_type == 88) { | ||
| read_class <- "data" | ||
| block_type_name <- "match" | ||
| } else if (channel_type == 216) { | ||
| read_class <- "data" | ||
| block_type_name <- "match_2_chn" | ||
| } else { | ||
| stop("There is a new block type, open an issue.") | ||
| } | ||
| } else if (block_type == 23) { | ||
| read_class <- "parameter" | ||
|
|
||
| if (channel_type == 4) { | ||
| block_type_name <- "sc_sample_data_param" | ||
| } else if (channel_type == 8) { | ||
| block_type_name <- "ig_sample_data_param" | ||
| } else if (channel_type == 12) { | ||
| block_type_name <- "ph_sample_data_param" | ||
| } else { | ||
| stop("There is a new block type, open an issue.") | ||
| } | ||
| } else if (block_type == 27) { | ||
| read_class <- "parameter" | ||
|
|
||
| if (channel_type == 4) { | ||
| block_type_name <- "sc_ref_data_param" | ||
| } else if (channel_type == 8) { | ||
| block_type_name <- "ig_ref_data_param" | ||
| } else { | ||
| stop("There is a new block type, open an issue.") | ||
| } | ||
| } else { | ||
| read_class <- "parameter" | ||
|
|
||
| if (block_type == 31) { | ||
| if (channel_type == 16) { | ||
| if (additional_type == 64) { | ||
| block_type_name <- "ab_no_atm_comp_data_param" | ||
| } else if (additional_type == 0) { | ||
| block_type_name <- "ab_data_param" | ||
| } else { | ||
| stop("There is a new block type, open an issue.") | ||
| } | ||
| } else if (channel_type == 48) { | ||
| if (additional_type == 64) { | ||
| block_type_name <- "refl_no_atm_comp_data_param" | ||
| } else if (additional_type == 0) { | ||
| block_type_name <- "refl_data_param" | ||
| } else { | ||
| stop("There is a new block type, open an issue.") | ||
| } | ||
| } else if (channel_type == 88) { | ||
| block_type_name <- "match_data_param" | ||
| } else if (channel_type == 216) { | ||
| block_type_name <- "match_2_chn_data_param" | ||
| } else { | ||
| stop("There is a new block type, open an issue.") | ||
| } | ||
| } else if (block_type == 32) { | ||
| block_type_name <- "instrument" | ||
| } else if (block_type == 40) { | ||
| block_type_name <- "instrument_ref" | ||
| } else if (block_type == 48) { | ||
| block_type_name <- "acquisition" | ||
| } else if (block_type == 56) { | ||
| block_type_name <- "acquisition_ref" | ||
| } else if (block_type == 64) { | ||
| block_type_name <- "fourier_transformation" | ||
| } else if (block_type == 72) { | ||
| block_type_name <- "fourier_transformation_ref" | ||
| } else if (block_type == 96) { | ||
| block_type_name <- "optics" | ||
| } else if (block_type == 104) { | ||
| block_type_name <- "optics_ref" | ||
| } else if (block_type == 160) { | ||
| block_type_name <- "sample" | ||
| } else if (block_type == 176) { | ||
| if (additional_type == 64) { | ||
| block_type_name <- "lab_and_process_param_raw" | ||
| } else if (additional_type == 0) { | ||
| block_type_name <- "lab_and_process_param_processed" | ||
| } else { | ||
| stop("There is a new block type, open an issue.") | ||
| } | ||
| } else { | ||
| stop("block not known") | ||
| #' @param header_data list of the header information for each block | ||
| create_dataset <- function(header_data) { | ||
| block_type <- as.character(header_data$block_type) | ||
| text_type <- as.character(header_data$text_type) | ||
| channel_type <- as.character(header_data$channel_type) | ||
| additional_type <- as.character(header_data$additional_type) | ||
|
|
||
| # define compoosite key for chunk | ||
| composite_key <- paste( | ||
| paste0("b", block_type), paste0("c", channel_type), | ||
| paste0("t", text_type), paste0("a", additional_type), | ||
| sep = "-" | ||
| ) | ||
|
|
||
| # nolint start | ||
|
|
||
| # keys ("<block>-<text>-<channel>-<additional_type>") : | ||
| # values (read_class, block_type_name) | ||
| # general mapping rules for codes (keys): | ||
| # - additional type = 64 => default, no macro processing | ||
| # - additional type = 0 => extra processing, found atmospheric compensation | ||
| key_value_map <- list( | ||
| # block code 0, channel code 0 ------------------------------------------------------------ | ||
| # additional information and/or OPUS processing macros | ||
| "b0-c0-t0-a(0|64)" = c(read_class = "text", block_type_name = "text_information"), | ||
| "b0-c0-t8-a0" = c(read_class = "parameter", block_type_name = "info_block"), | ||
| "b0-c0-t104-a64" = c(read_class = "text", block_type_name = "history"), | ||
| "b0-c0-t152-a(0|64)" = c(read_class = "text", block_type_name = "curve_fit"), | ||
| "b0-c0-t168-a(0|64)" = c(read_class = "text", block_type_name = "signature"), | ||
| "b0-c0-t240-a(0|64)" = c(read_class = "text", block_type_name = "integration_method"), | ||
| # guess general text | ||
| "b0-c0-t\\d+-a(0|64)" = c(read_class = "text", block_type_name = "text_information"), | ||
|
|
||
| # block code 7 ----------------------------------------------------------------------------- | ||
| # spectrum types of sample | ||
| "b7-c4-t0-a(0|64)" = c(read_class = "data", block_type_name = "sc_sample"), | ||
| "b7-c8-t0-a(0|64)" = c(read_class = "data", block_type_name = "ig_sample"), | ||
| "b7-c12-t0-a(0|64)" = c(read_class = "data", block_type_name = "ph_sample"), | ||
|
|
||
| # block code 11 ---------------------------------------------------------------------------- | ||
| # spectrum types of reference (background) | ||
| "b11-c4-t0-a(0|64)" = c(read_class = "data", block_type_name = "sc_ref"), | ||
| "b11-c8-t0-a(0|64)" = c(read_class = "data", block_type_name = "ig_ref"), | ||
| "b11-c12-t0-a(0|64)" = c(read_class = "data", block_type_name = "ph_ref"), | ||
| # block code 15 ----------------------------------------------------------------------------- | ||
| # spectrum report blocs | ||
| # channel code 15: save (apparent) absorbance | ||
| "b15-c16-t112-a0" = c(read_class = "parameter", block_type_name = "quant_report_ab"), | ||
| "b15-c16-t104-a1" = c(read_class = "parameter", block_type_name = "me_test_report_ab"), | ||
| "b15-c16-t0-a64" = c(read_class = "data", block_type_name = "ab_no_atm_comp"), | ||
| "b15-c16-t0-a0" = c(read_class = "data", block_type_name = "ab"), | ||
| # channel code 48: save reflectance (settings | ||
| "b15-c48-t112-a0" = c(read_class = "parameter", block_type_name = "quant_report_refl"), | ||
| "b15-c48-t104-a1" = c(read_class = "parameter", block_type_name = "me_test_report_refl"), # check "a1" | ||
| "b15-c48-t0-a64" = c(read_class = "data", block_type_name = "refl_no_atm_comp"), | ||
| "b15-c48-t0-a0" = c(read_class = "data", block_type_name = "refl"), | ||
| # channel code 88 and 216: spectra matching | ||
| "b15-c88-t0-a(0|64)" = c(read_class = "data", block_type_name = "match"), | ||
| "b15-c216-t0-a(0|64)" = c(read_class = "data", block_type_name = "match_2_chn"), | ||
|
|
||
| # block code 23 ----------------------------------------------------------------------------- | ||
| # data parameters (metadata) for spectrum types of sample | ||
| "b23-c4-t0-a(0|64)" = c(read_class = "parameter", block_type_name = "sc_sample_data_param"), | ||
| "b23-c8-t0-a(0|64)" = c(read_class = "parameter", block_type_name = "ig_sample_data_param"), | ||
| "b23-c12-t0-a(0|64)" = c(read_class = "parameter", block_type_name = "ph_sample_data_param"), | ||
|
|
||
| # block code 27 ----------------------------------------------------------------------------- | ||
| # data parameters (metadata) for spectrum types of reference (background) | ||
| "b27-c4-t0-a(0|64)" = c(read_class = "parameter", block_type_name = "sc_ref_data_param"), | ||
| "b27-c8-t0-a(0|64)" = c(read_class = "parameter", block_type_name = "ig_ref_data_param"), | ||
| "b27-c12-t0-a(0|64)" = c(read_class = "parameter", block_type_name = "ph_ref_data_param"), | ||
|
|
||
| # block code 31 ----------------------------------------------------------------------------- | ||
| # data parameters (metadata) when spectra (normalized single channels) saved in apparent absorbance | ||
| "b31-c16-t0-a64" = c(read_class = "parameter", block_type_name = "ab_no_atm_comp_data_param"), | ||
| "b31-c16-t0-a0" = c(read_class = "parameter", block_type_name = "ab_data_param"), | ||
|
|
||
| # data parameters (metadata) when spectra (normalized single channels) saved in reflectance | ||
| "b31-c48-t0-a64" = c(read_class = "parameter", block_type_name = "refl_no_atm_comp_data_param"), | ||
| "b31-c48-t0-a0" = c(read_class = "parameter", block_type_name = "refl_data_param"), | ||
|
|
||
| # data parameters (metadata) for spectra matching | ||
| "b31-c88-t0-a(0|64)" = c(read_class = "parameter", block_type_name = "match_data_param"), | ||
| "b31-c216-t0-a(0|64)" = c(read_class = "parameter", block_type_name = "match_2_chn_data_param"), | ||
|
|
||
| ## General metadata blocks | ||
|
|
||
| # block code 32 ----------------------------------------------------------------------------- | ||
| "b32-c0-t0-a(0|64)" = c(read_class = "parameter", block_type_name = "instrument"), | ||
|
|
||
| # block code 40 ----------------------------------------------------------------------------- | ||
| "b40-c0-t0-a(0|64)" = c(read_class = "parameter", block_type_name = "instrument_ref"), | ||
|
|
||
| # block code 48 ----------------------------------------------------------------------------- | ||
| "b48-c0-t0-a(0|64)" = c(read_class = "parameter", block_type_name = "acquisition"), | ||
|
|
||
| # block code 56 ----------------------------------------------------------------------------- | ||
| "b56-c0-t0-a(0|64)" = c(read_class = "parameter", block_type_name = "acquisition_ref"), | ||
|
|
||
| # block code 64 ----------------------------------------------------------------------------- | ||
| "b64-c0-t0-a(0|64)" = c(read_class = "parameter", block_type_name = "fourier_transformation"), | ||
|
|
||
| # block code 72 ----------------------------------------------------------------------------- | ||
| "b72-c0-t0-a(0|64)" = c(read_class = "parameter", block_type_name = "fourier_transformation_ref"), | ||
|
|
||
| # block code 96 ----------------------------------------------------------------------------- | ||
| "b96-c0-t0-a(0|64)" = c(read_class = "parameter", block_type_name = "optics"), | ||
|
|
||
| # block code 104 ----------------------------------------------------------------------------- | ||
| "b104-c0-t0-a(0|64)" = c(read_class = "parameter", block_type_name = "optics_ref"), | ||
|
|
||
| # block code 160 ----------------------------------------------------------------------------- | ||
| "b160-c0-t0-a(0|64)" = c(read_class = "parameter", block_type_name = "sample"), | ||
|
|
||
| # block code 176 ----------------------------------------------------------------------------- | ||
| "b176-c0-t0-a64" = c(read_class = "parameter", block_type_name = "lab_and_process_param_raw"), | ||
| "b176-c0-t0-a0" = c(read_class = "parameter", block_type_name = "lab_and_process_param_processed") | ||
| ) | ||
|
|
||
| # nolint end | ||
|
|
||
| # check key names for matching composite key | ||
| key_names <- names(key_value_map) | ||
| is_match <- unlist(lapply(key_names, function(pat) grepl(pat, composite_key))) | ||
| key_value_match <- key_value_map[is_match] | ||
| nm_matches <- names(key_value_match) | ||
| # because of "b0-c0-t\\d+-a(0|64)" regex | ||
| is_match_guess <- grepl("\\\\d\\+", nm_matches) | ||
|
|
||
| if (length(key_value_match) == 1L) { | ||
| if (any(is_match_guess)) { | ||
| message(paste( | ||
| "Guessing header entry for block type 0 to be text information:\n", | ||
| "* Composite key :=", composite_key | ||
| )) | ||
| } | ||
| } else if (length(key_value_match) > 1L) { | ||
| # in block code 0, the less specific guess ("b0-c0-t\\d+-a(0|64)") | ||
| # has to be removed | ||
| key_value_match[is_match_guess] <- NULL | ||
| } else if (length(key_value_match) == 0L) { | ||
| # inform about details and what to do for improving {opusreader2} | ||
| stop_proactively(composite_key) | ||
| } | ||
|
|
||
| key_value_match_vec <- key_value_match[[1]] | ||
| read_class <- unname(key_value_match_vec["read_class"]) | ||
| block_type_name <- unname(key_value_match_vec["block_type_name"]) | ||
|
|
||
| # create a dataset | ||
| ds <- structure( | ||
| c(data_list, list(block_type_name = block_type_name)), | ||
| c(header_data, list(block_type_name = block_type_name)), | ||
| class = c(read_class) | ||
| ) | ||
|
|
||
| return(ds) | ||
| } | ||
|
|
||
| stop_proactively <- function(composite_key) { | ||
| stop( | ||
| paste( | ||
| "Unknown header entry.\n The following 'composite key' is not yet", | ||
| "mapped in the {opusreader2} key-value map of the header:\n", | ||
| "*", paste0('"', composite_key, '"'), "\nWe encourage your contribution", | ||
| "to feature this new OPUS block by opening a new issue on | ||
| https://github.com/spectral-cockpit/opusreader2/issues", | ||
| "\nPlease\n", | ||
| "1. report reproducibly, using short code with {opusreader2} | ||
| (recommended: https://reprex.tidyverse.org)", "\n", | ||
| "2. describe briefly\n", | ||
| " a) Bruker instrument used\n", | ||
| " b) equipment\n", | ||
| " c) measurement mode and spectral blocks saved (OPUS settings)\n", | ||
| " d) OPUS software version\n", | ||
| " e) your general workflow for spectroscopic diagnostics\n", | ||
| "3. provide an example OPUS binary file uploaded for public access\n", | ||
| " on GitHub (best in issue)\n", | ||
| "4. to facilitate widespread support of Bruker devices in open source\n", | ||
| " based infrastructure, show the data blocks as print screens in the\n", | ||
| " Bruker OPUS software (right-click in Viewer). Please upload the\n", | ||
| " contents of all OPUS blocks in individual screenshots." | ||
| ), | ||
| call. = FALSE | ||
| ) | ||
| } |
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