Enhance run support

Actually run should be placed after task field, but for historical reasons it is placed at the last column. Here workaround it by using `relocate()`.

Signed-off-by: Liang Zhang <psychelzh@outlook.com>

R/constants.R

@@ -76,33 +76,55 @@ params_fmri_tasks <- tibble::tribble(
   "1", "movie", 2,
   "2", "rest", 2,
   "2", "wm", 3,
-  "2", "movie", 2,
-  "0", "latent", 0
+  "2", "movie", 2
+) |>
+  tidyr::uncount(runs, .id = "run_id")
+# Note: sesion: 0 = all sessions, run_id: 0 = all runs
+params_fmri_special <- dplyr::bind_rows(
+  tibble::tibble(
+    session = "0",
+    task = "latent",
+    run_id = c(0, 1)
+  ),
+  tibble::tibble(
+    session = "0",
+    task = c("rest", "movie"),
+    run_id = 0
+  )
 )
+
 params_conmat <- tibble::tibble(
   xcpd = c(
     "gsr", # with global signal regression
     "no_gsr" # no global signal regression
   ),
   atlas = "4S256Parcels"
-)
+) |>
+  dplyr::filter(xcpd == "gsr")
 config_fmri <- tidyr::expand_grid(
   params_fmri_tasks,
   params_conmat
-) |>
-  dplyr::filter(xcpd == "gsr")
+)
 config_fc <- dplyr::bind_rows(
+  config_fmri,
   config_fmri |>
-    dplyr::mutate(run = "full") |>
-    dplyr::select(-runs),
-  config_fmri |>
-    tidyr::uncount(runs, .id = "run") |>
-    dplyr::mutate(run = paste("run", run, sep = "")),
-  config_fmri |>
-    dplyr::filter(task == "wm") |>
-    dplyr::mutate(run = "run12") |>
-    dplyr::select(-runs)
-)
+    dplyr::distinct(dplyr::pick(!run_id)) |>
+    dplyr::mutate(
+      run_id = ifelse(task == "wm", list(c(0, 12)), list(0))
+    ) |>
+    tidyr::unnest(run_id),
+  tidyr::expand_grid(params_fmri_special, params_conmat)
+) |>
+  dplyr::mutate(
+    run = ifelse(
+      run_id == 0,
+      "full",
+      sprintf("run%d", run_id)
+    ),
+    .keep = "unused",
+    # backward compatibility
+    .after = dplyr::last_col()
+  )
 
 # used in CPM modeling building
 hypers_cpm <- dplyr::bind_rows(

R/prepare_data_neural.R

@@ -1,5 +1,5 @@
 # functional connectivity data preparation ----
-prepare_meta_time_series <- function(xcpd, session, task, atlas) {
+prepare_meta_time_series <- function(xcpd, session, task, atlas, run) {
   path_xcpd <- fs::path(
     Sys.getenv("ROOT_BIDS_DERIV"),
     sprintf("xcpd_%s", xcpd)
@@ -10,6 +10,7 @@ prepare_meta_time_series <- function(xcpd, session, task, atlas) {
     session = session,
     task = task,
     atlas = atlas,
+    run = run,
     suffix = "timeseries",
     extension = "tsv"
   )

_scripts/prepare_neural.R

@@ -6,20 +6,20 @@ tar_option_set(
   controller = setup_crew_controller("fc")
 )
 setup_parallel_plan()
-config_meta <- config_fmri |>
-  dplyr::select(!runs) |>
+
+config_fc_calc <- config_fc |>
   tidyr::unite("name_suffix", everything(), remove = FALSE) |>
   dplyr::mutate(
+    session = lapply(session, \(x) if (x == "0") character() else x),
+    run = lapply(run, parse_digits),
     meta_time_series = rlang::syms(
-      sprintf("meta_time_series_%s", name_suffix)
-    )
+      paste0("meta_time_series_", name_suffix)
+    ),
+    fc = rlang::syms(paste0("fc_", name_suffix))
   )
-config_fc_calc <- config_fc |>
-  dplyr::left_join(config_meta, by = c("xcpd", "session", "task", "atlas")) |>
-  dplyr::mutate(fc = rlang::syms(sprintf("fc_%s_%s", name_suffix, run)))
 
 targets_fd <- tarchetypes::tar_map(
-  dplyr::filter(params_fmri_tasks, task != "latent"),
+  dplyr::distinct(params_fmri_tasks, session, task),
   names = !runs,
   tar_target(
     meta_data_motion,
@@ -34,15 +34,17 @@ targets_fd <- tarchetypes::tar_map(
 list(
   # prepare functional connectivity (FC) data ----
   tarchetypes::tar_eval(
-    tar_target(
-      meta_time_series,
-      prepare_meta_time_series(xcpd, session, task, atlas)
+    list(
+      tar_target(
+        meta_time_series,
+        prepare_meta_time_series(xcpd, session, task, atlas, run)
+      ),
+      tar_target(
+        fc,
+        prepare_data_fc(meta_time_series)
+      )
     ),
-    dplyr::filter(config_meta, task != "latent")
-  ),
-  tarchetypes::tar_eval(
-    tar_target(fc, prepare_data_fc(meta_time_series)),
-    dplyr::filter(config_fc_calc, run == "full" & task != "latent")
+    dplyr::filter(config_fc_calc, task != "latent")
   ),
   tarchetypes::tar_eval(
     tar_target(
@@ -54,23 +56,16 @@ list(
       dplyr::filter(task == "latent") |>
       dplyr::left_join(
         config_fc_calc |>
-          dplyr::filter(run == "full" & task != "latent") |>
+          dplyr::filter(task != "latent") |>
           dplyr::summarise(
             call_list_fc = list(
               as.call(c(quote(list), fc))
             ),
-            .by = xcpd
+            .by = c(xcpd, run)
           ),
-        by = "xcpd"
+        by = c("xcpd", "run")
       )
   ),
-  tarchetypes::tar_eval(
-    tar_target(
-      fc,
-      prepare_data_fc(meta_time_series, .data[["run"]] %in% parse_digits(run))
-    ),
-    dplyr::filter(config_fc_calc, grepl("^run\\d+$", run))
-  ),
   # extract mean frame-wise displacement (FD) ----
   targets_fd,
   tarchetypes::tar_combine(