Merge pull request #30 from mandymejia/4.3

4.3

R/make_xifti_components.R

@@ -82,11 +82,25 @@ make_cortex <- function(
         idx_string <- paste("-column", paste(idx, collapse=" -column "))
       }
       cortex_original <- cortex
-      cortex <- file.path(
-        tempdir(), 
-        # [TO DO] more elegant naming?
-        gsub("\\.gii$", ".selected_idx\\.func\\.gii", basename(cortex_original))
-      )
+
+      # Name for new GIFTI file
+      if (endsWith(cortex, ".func.gii")) {
+        cortex <- file.path(
+          tempdir(), 
+          gsub("\\.func\\.gii$", "\\.sel_idx\\.func\\.gii", basename(cortex_original))
+        )
+      } else if (endsWith(cortex, ".label.gii")) {
+        cortex <- file.path(
+          tempdir(), 
+          gsub("\\.label\\.gii$", "\\.sel_idx\\.label\\.gii", basename(cortex_original))
+        )
+      } else {
+        # Guess func.
+        # [TO DO] warn user?
+        cortex <- file.path(
+          tempdir(), paste0(basename(cortex_original), ".func.gii")
+        ) 
+      }
 
       run_wb_cmd(paste(
         "-metric-merge", cortex, "-metric", cortex_original, idx_string

R/read_cifti_flat.R

@@ -14,7 +14,8 @@
 #'  and then reading it in. Should the GIFTI file be kept? If \code{FALSE}
 #'  (default), write it in a temporary directory regardless of \code{write_dir}.
 #' @param gifti_fname File path of GIFTI-format data to save the CIFTI as. 
-#'  Default: the CIFTI_fname but with the extension replaced with "flat.gii".
+#'  Should end with ".func.gii". Default: the CIFTI_fname but with the extension
+#'  replaced with ".func.gii".
 #' @inheritParams idx_Param
 #' @param write_dir The directory in which to save the GIFTI, if it is being 
 #'  kept. If \code{NULL} (default), use the current working directory.
@@ -39,14 +40,23 @@ read_cifti_flat <- function(
     stop("`", cifti_fname, "` is not an existing file.") 
   }
 
-  # Get the components of the CIFTI file path.
+  # Get the components of the CIFTI and GIFTI file paths.
   bname_cifti <- basename(cifti_fname)
-  extn_cifti <- get_cifti_extn(bname_cifti)  # "dtseries.nii" or "dscalar.nii"
+  extn_cii <- get_cifti_extn(bname_cifti)
+  extn_cii <- paste0(".", extn_cii) # e.g. ".dtseries.nii"
+  is_label = FALSE# extn_cii == ".dlabel.nii"
+  extn_gii <- ifelse(is_label, ".label.gii", ".func.gii")
+  extn_gii2 <- gsub(".", "\\.", extn_gii, fixed=TRUE)
+  extn_cii2 <- paste0(gsub(".", "\\.", extn_cii, fixed=TRUE), "$")
 
   # If gifti_fname is not provided, use the CIFTI_fname but replace the 
   #   extension with "flat.gii".
   if (is.null(gifti_fname)) {
-    gifti_fname <- gsub(extn_cifti, "flat.gii", bname_cifti, fixed=TRUE)
+    if (grepl(bname_cifti, extn_cii2)) {
+      gifti_fname <- gsub(extn_cii2, extn_gii2, bname_cifti)
+    } else {
+      gifti_fname <- paste0(bname_cifti, extn_gii)
+    }
   }
   if (!keep) { write_dir <- tempdir() }
   gifti_fname <- format_path(gifti_fname, write_dir, mode=2)
@@ -74,7 +84,10 @@ read_cifti_flat <- function(
     gifti_fname_original <- gifti_fname
     gifti_fname <- file.path(
       tempdir(), 
-      gsub("\\.gii$", ".selected_idx\\.gii", basename(gifti_fname_original))
+      gsub(
+        paste0(extn_gii2, "$"), paste0("\\.sel_idx", extn_gii2), 
+        basename(gifti_fname_original)
+      )
     )
 
     run_wb_cmd(paste(

R/read_xifti2.R

@@ -95,7 +95,10 @@ read_xifti2 <- function(
     if (!is.null(cortexL)) {
       x <- resample_gifti(
         cortexL, 
-        paste0("resamp", cifti_component_suffix("cortexL")),
+        paste0(
+          "resamp", 
+          cifti_component_suffix("cortexL", ifelse(grepl("label\\.gii$", cortexL), "label", "func"))
+        ),
         hemisphere="left", resamp_res=resamp_res, 
         ROIcortex_original_fname=cortexL_mwall, 
         read_dir=read_dir, write_dir=tdir
@@ -107,7 +110,10 @@ read_xifti2 <- function(
     if (!is.null(cortexR)) {
       x <- resample_gifti(
         cortexR, 
-        paste0("resamp", cifti_component_suffix("cortexR")),
+        paste0(
+          "resamp", 
+          cifti_component_suffix("cortexR", ifelse(grepl("label\\.gii$", cortexR), "label", "func"))
+        ),
         hemisphere="right", resamp_res=resamp_res, 
         ROIcortex_original_fname=cortexR_mwall, 
         read_dir=read_dir, write_dir=tdir
@@ -118,19 +124,17 @@ read_xifti2 <- function(
     ## Left surface.
     if (!is.null(surfL)) {
       surfL <- resample_gifti(
-        surfL, 
-        paste0("surf_resamp", cifti_component_suffix("cortexL")),
-        hemisphere="left", file_type="surf", resamp_res=resamp_res,
+        surfL, paste0("resamp", cifti_component_suffix("cortexL", "surf")),
+        hemisphere="left", file_type="surface", resamp_res=resamp_res,
         read_dir=read_dir, write_dir=tdir
       )
     }
 
     ## Right surface.
     if (!is.null(surfR)) {
       surfR <- resample_gifti(
-        surfR, 
-        paste0("surf_resamp", cifti_component_suffix("cortexR")),
-        hemisphere="left", file_type="surf", resamp_res=resamp_res,
+        surfR, paste0("resamp", cifti_component_suffix("cortexR", "surf")),
+        hemisphere="right", file_type="surface", resamp_res=resamp_res,
         read_dir=read_dir, write_dir=tdir
       )
     }

cran-comments.md

@@ -26,3 +26,7 @@ Passes all the tests in `tests/run_ciftiTools_tests.R`
 ## Submission revision
 
 The previous submission was rejected because the tarball was over 5 MB. It has been reduced to 3.25 MB.
+
+## Submission revision 2
+
+The previous submission (0.4.1) was cancelled manually.

tests/testthat/test-misc.R

@@ -179,10 +179,10 @@ test_that("Miscellaneous functions are working", {
     if (!grepl("dlabel", cii_fname)) {
       # Smooth metric GIFTI
       fnames_sep <- separate_cifti(cii_fname, write_dir=tdir)
-      smooth_gifti(fnames_sep[1], file.path(tdir, "sm.metric.gii"), hemisphere="left")
+      smooth_gifti(fnames_sep[1], file.path(tdir, "sm.func.gii"), hemisphere="left")
       smg1 <- gifti::readgii(
         smooth_gifti(
-          fnames_sep[3], file.path(tdir, "sm.metric.gii"),
+          fnames_sep[3], file.path(tdir, "sm.func.gii"),
           ROI_fname=fnames_sep[4], hemisphere="right"
         )
       )

vignettes/ciftiTools_vignette.Rmd

@@ -36,7 +36,7 @@ library(ciftiTools)
 Next, we indicate where to find the Connectome Workbench. This can be the full path to the Connectome Workbench executable file, or the path to its containing folder, in which case `ciftiTools` will locate the full path. Here, we will use the latter:
 
 ```{r}
-# Replace '/Applications/workbench' with the actual path to 
+# Replace '../../workbench' with the actual path to 
 #   the Connectome Workbench folder on your computer.
 #   If successful, the full path to the Workbench executable will be printed.
 ciftiTools.setOption('wb_path', '../../workbench')