calculate inv_k0 in initiaize sampe + document

R/aaa-class-GCIMSChromatogram.R

@@ -5,6 +5,7 @@
 #' or the aggregation of several chromatograms.
 #'
 #' @slot retention_time A numeric vector with retention times
+#' @slot retention_index A numeric vector with retention indexes
 #' @slot intensity A numeric vector with the corresponding intensities
 #' @slot baseline A numeric vector of the same length as `intensity` with the corresponding baseline,
 #' or `NULL` if not set. Use [estimateBaseline()] to estimate it, [baseline()] to directly access it.
@@ -20,6 +21,7 @@ methods::setClass(
   Class = "GCIMSChromatogram",
   slots = c(
     retention_time = "numeric",
+    retention_index = "numericOrNULL",
     intensity = "numeric",
     baseline = "numericOrNULL",
     drift_time_idx = "integer",
@@ -32,12 +34,13 @@ methods::setClass(
 
 methods::setMethod(
   "initialize", "GCIMSChromatogram",
-  function(.Object, retention_time, intensity, drift_time_idx = NA_integer_,
+  function(.Object, retention_time, retention_index = NULL, intensity, drift_time_idx = NA_integer_,
            drift_time_ms = NA_real_, description = "", baseline = NULL,
            peaks = NULL, peaks_debug_info = NULL) {
     stopifnot(length(retention_time) == length(intensity))
     stopifnot(is.null(baseline) || length(retention_time) == length(baseline))
     .Object@retention_time <- retention_time
+    .Object@retention_index <- retention_index
     .Object@drift_time_idx <- as.integer(drift_time_idx)
     .Object@drift_time_ms <- drift_time_ms
     .Object@intensity <- intensity
@@ -52,6 +55,7 @@ methods::setMethod(
 #' Create a [GCIMSChromatogram-class] object
 #'
 #' @param retention_time A numeric vector with retention times
+#' @param retention_index A numeric vector with retention indexes
 #' @param intensity A numeric vector with the corresponding intensities
 #' @param baseline A numeric vector of the same length as `intensity` with the corresponding baseline,
 #' or `NULL` if not set. Use [estimateBaseline()] to estimate it, [baseline()] to directly access it.
@@ -69,10 +73,10 @@ methods::setMethod(
 #' @export
 #' @family GCIMSChromatogram
 GCIMSChromatogram <- function(
-    retention_time, intensity, drift_time_idx = NA_integer_,
+    retention_time, retention_index = NULL, intensity, drift_time_idx = NA_integer_,
     drift_time_ms = NA_real_, description = "",
     baseline = NULL, peaks = NULL, peaks_debug_info = NULL) {
-  methods::new("GCIMSChromatogram", retention_time, intensity, drift_time_idx,
+  methods::new("GCIMSChromatogram", retention_time, retention_index, intensity, drift_time_idx,
                drift_time_ms, description, baseline = NULL, peaks = NULL,
                peaks_debug_info = NULL)
 }

R/aaa-class-GCIMSSample.R

@@ -71,7 +71,7 @@ methods::setClass(
   )
 )
 
-.CURRENT_GCIMSSAMPLE_CLASS_VERSION <- numeric_version("0.0.4")
+.CURRENT_GCIMSSAMPLE_CLASS_VERSION <- numeric_version("0.1.1")
 
 methods::setMethod(
   "initialize", "GCIMSSample",
@@ -114,6 +114,17 @@ methods::setMethod(
       }
     }
 
+    #Calculate inv_k0 if possible
+    if (exists("drift_tube_length") & exists("params")){
+      ims_temp_k <- params$`Temp 1 setpoint`$value + 273.15
+      pressure_ims <- mean(as.numeric(strsplit(strsplit(params$`Pressure Ambient`$value, "\"")[[1]][2]," ")[[1]]))
+      drift_tube_length_cm <- drift_tube_length / 10
+      .Object@inverse_reduced_mobility <- get_inv_k0(drift_time,
+                                                     drift_tube_length_cm,
+                                                     pressure_ims,
+                                                     params$`nom Drift Potential Difference`$value,
+                                                     ims_temp_k)
+    }
     .Object@class_version <- .CURRENT_GCIMSSAMPLE_CLASS_VERSION
     .Object@drift_time <- drift_time
     .Object@retention_time <- retention_time

R/utils-io-mea.R

@@ -202,21 +202,9 @@ read_mea <- function(filename) {
     description <- tools::file_path_sans_ext(basename(filename), compression = TRUE)
   }
 
-  #Calculate inv_k0
-  ims_temp_k <- params$`Temp 1 setpoint`$value + 273.15
-  pressure_ims <- mean(as.numeric(strsplit(strsplit(params$`Pressure Ambient`$value, "\"")[[1]][2]," ")[[1]]))
-  drift_tube_length_cm <- drift_tube_length / 10
-  inv_k0 <- get_inv_k0(drift_time,
-                       drift_tube_length_cm,
-                       pressure_ims,
-                       params$`nom Drift Potential Difference`$value,
-                       ims_temp_k)
-
   GCIMSSample(
     drift_time = drift_time,
     retention_time = ret_time,
-    inverse_reduced_mobility = inv_k0,
-    retention_index = NULL,
     data = data,
     gc_column = gc_column,
     drift_tube_length = drift_tube_length,