add inv_k0 and ri slots and get k0 function

R/aaa-class-GCIMSDataset.R

@@ -79,6 +79,10 @@ GCIMSDataset <- R6::R6Class("GCIMSDataset",
     dt_ref = NULL, # numeric or NULL
     #' @field rt_ref A numeric retention time of reference
     rt_ref = NULL, # numeric or NULL
+    #' @field inv_k0_ref A numeric inverse reduced mobility reference
+    inv_k0_ref = NULL,
+    #' @field ri_ref A numeric retention index reference
+    ri_ref = NULL,
     #' @field userData A list to store arbitrary data in the dataset
     userData = list(), # list
     # Methods:
@@ -297,6 +301,18 @@ GCIMSDataset <- R6::R6Class("GCIMSDataset",
       invisible(self)
     },
     #' @description
+    #' Sets an action to extract the reference inverse reduced mobility
+    #' @return GCIMSDataset with inverse reduced mobility calculated
+    extract_inv_k0 = function() {
+      delayed_op <- DelayedOperation(
+        name = "extract_inv_k0",
+        fun_extract = .extract_inv_k0,
+        fun_aggregate = .extract_inv_k0_fun_aggregate
+      )
+      self$appendDelayedOp(delayed_op)
+      self
+    },
+    #' @description
     #' Whether the dataset is saved on disk or stored in RAM
     #' @return `TRUE` if on disk, `FALSE` otherwise
     is_on_disk = function() {

R/aaa-class-GCIMSSample.R

@@ -12,6 +12,8 @@
 #'
 #' @slot drift_time numeric. (required)
 #' @slot retention_time numeric. (required)
+#' @slot inverse_reduced_mobility 1/K0 (calculated from drift_time)
+#' @slot retention_index numeric. (calculated from retention_time and references)
 #' @slot data matrix A matrix with drift time in the rows and retention time
 #'  in columns. (required)
 #' @slot gc_column character. (optional) The type of chromatographic column used
@@ -51,6 +53,8 @@ methods::setClass(
   slots = c(
     drift_time = "numeric",
     retention_time = "numeric",
+    inverse_reduced_mobility = "numericOrNULL",
+    retention_index = "numericOrNULL",
     data = "matrix", # [dt, rt]
     gc_column = "character",
     drift_gas = "character",

R/inv_k0.R

@@ -0,0 +1,31 @@
+get_inv_k0 <- function(drift_time,
+                       drift_tube_length_cm,
+                       pressure_ims,
+                       voltage_ims,
+                       ims_temp_k){
+  k0 <- (0.0027315 * (drift_tube_length_cm ^ 2) * pressure_ims) /
+    (voltage_ims * (drift_time / 1000) * ims_temp_k)
+  inv_k0 <- 1 / k0
+}
+
+
+.extract_inv_k0 <- function(object) {
+  inv_k0 <- object@inverse_reduced_mobility
+  data.frame(
+    inv_k0_min = inv_k0[1],
+    inv_k0_max = inv_k0[length(inv_k0)],
+    inv_k0_step = stats::median(diff(inv_k0))
+  )
+}
+
+.extract_inv_k0_fun_aggregate <- function(object, extracted_objects) {
+  inv_k0_samples <- dplyr::bind_rows(extracted_objects, .id = "SampleID")
+
+  max_inv_k0_min <- max(inv_k0_samples$inv_k0_min)
+  min_inv_k0_max <- min(inv_k0_samples$inv_k0_max)
+  min_inv_k0_step <- min(inv_k0_samples$inv_k0_step)
+  max_inv_k0_length <- floor(round((min_inv_k0_max - max_inv_k0_min)/min_inv_k0_step, digits = 8)) + 1L
+  inv_k0_ref <- seq(from = max_inv_k0_min, to = min_inv_k0_max, length.out = max_inv_k0_length)
+
+  object$inv_k0_ref <- inv_k0_ref
+}

R/utils-io-mea.R

@@ -202,9 +202,21 @@ 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,