Merge branch 'develop'

dfsp-spirit · Jan 23, 2023 · fe1ddfc · fe1ddfc
2 parents f6ab0aa + d96e968
commit fe1ddfc
Show file tree

Hide file tree

Showing 8 changed files with 227 additions and 25 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -78,7 +78,13 @@ jobs:
         if: runner.os != 'Windows'
         run: export RGL_USE_NULL=true
 
-      - name: Install dependencies
+
+      - name: Install curl on Windows
+        if: runner.os == 'Windows'
+        run: install.packages("curl")
+        shell: Rscript {0}
+
+        name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")

diff --git a/R/cbar.R b/R/cbar.R
@@ -1,6 +1,6 @@
 # colorbar functions
 
-#' @title Draw coloredbar into background of current plot.
+#' @title Draw colorebar into background of current plot.
 #'
 #' @description Requires a rgl 3d visualisation to be open that already contains a rendered object. Uses \code{\link{bgplot3d}} to add a colorbar in the background of the plot using \code{\link[fields]{image.plot}}. Experimental.
 #'
@@ -18,6 +18,7 @@
 #' @importFrom fields image.plot
 #' @keywords internal
 draw.colorbar <- function(coloredmeshes, horizontal=FALSE, ...) {
+
     if(! is.list(coloredmeshes)) {
         stop("Parameter 'coloredmeshes' must be a list.");
     }
@@ -55,7 +56,20 @@ draw.colorbar <- function(coloredmeshes, horizontal=FALSE, ...) {
         }
         num_col = ifelse(is.null(makecmap_options$n), 100L, makecmap_options$n);
 
-        rgl::bgplot3d({op = graphics::par(mar = rep(0.1, 4)); plot.new(); fields::image.plot(add=T, legend.only = TRUE, zlim = zlim, col = makecmap_options$colFn(num_col), horizontal = horizontal, ...); graphics::par(op);});
+        # Check whether to plot in log10 scale.
+        if('base' %in% names(makecmap_options)) {
+            num_ticks_default = 5L;
+            if (as.integer(makecmap_options$base) == 10L) {
+                ticks = squash::prettyLog(combined_data_range, n=num_ticks_default);
+            } else {
+                stop(sprintf(" - Invalid 'base' value in 'makecmap_options', only 10 is supported for log 10 scale. (Do not set it at all for linear scale.)\n"));
+            }
+            axis.args = list('at'=log(ticks), 'labels'=ticks);
+            rgl::bgplot3d({op = graphics::par(mar = rep(0.1, 4)); plot.new(); fields::image.plot(add=T, legend.only = TRUE, zlim = log(zlim), axis.args=axis.args, col = makecmap_options$colFn(num_col), horizontal = horizontal, ...); graphics::par(op);});
+        } else {
+            # Plot linear scale.
+            rgl::bgplot3d({op = graphics::par(mar = rep(0.1, 4)); plot.new(); fields::image.plot(add=T, legend.only = TRUE, zlim = zlim, col = makecmap_options$colFn(num_col), horizontal = horizontal, ...); graphics::par(op);});
+        }
     } else {
         warning("Requested to draw colorbar, but meshes do not contain the required metadata. Skipping.");
     }
@@ -78,6 +92,8 @@ draw.colorbar <- function(coloredmeshes, horizontal=FALSE, ...) {
 #'
 #' @param trim_png logical, whether to trim the output PNG image using image magick, i.e., remove everything but the foreground. Ignored unless an output PNG image is actually written (see 'png_options') and the 'magick' package is installed.
 #'
+#' @param log_break: logical, scalar int, or vector of ints. Whether to use log10 scale for plotting the cbar. If logical and TRUE, uses log scale with default number (=5) ticks auto-computed from the data. If a single integer N, uses N ticks auto-computed from the data instead. If a numeric vector, uses the supplied values in the vector as ticks, note that they must be on a `log(data)` scale. If the 'makecmap_options' stored in the passed 'coloredmeshes' contain a 'base' value of 10, log 10 is assumed (with the default 5 ticks), even if this parameter is left at its default value, logical FALSE.
+#'
 #' @note If you increase the output resolution of the colorbar (using 'png_options'), you will have to increase the font sizes as well (using 'image.plot_extra_options'), otherwise the axis and legend labels will be hard to read.
 #'
 #' @examples
@@ -104,15 +120,15 @@ draw.colorbar <- function(coloredmeshes, horizontal=FALSE, ...) {
 #' @importFrom grDevices png pdf dev.off
 #' @importFrom utils modifyList
 #' @export
-coloredmesh.plot.colorbar.separate <- function(coloredmeshes, show=FALSE, image.plot_extra_options = list(horizontal=FALSE, 'legend.cex'=1.8, 'legend.width'=2, 'legend.mar' = 12, 'axis.args'=list('cex.axis'=5.0)), png_options=list('filename'='fsbrain_cbar.png', 'width'=1400, 'height'=1400, 'bg'='#FFFFFF00'), silent=FALSE, trim_png=TRUE) {
+coloredmesh.plot.colorbar.separate <- function(coloredmeshes, show=FALSE, image.plot_extra_options = list(horizontal=FALSE, 'legend.cex'=1.8, 'legend.width'=2, 'legend.mar' = 12, 'axis.args'=list('cex.axis'=5.0)), png_options=list('filename'='fsbrain_cbar.png', 'width'=1400, 'height'=1400, 'bg'='#FFFFFF00'), silent=FALSE, trim_png=TRUE, log_breaks=FALSE) {
 
     if(length(coloredmeshes) < 1) {
         message("Requested to draw separate colorbar, but mesh list is empty. Skipping.");
         return(invisible(NULL));
     }
 
-
     makecmap_options = coloredmeshes.get.md(coloredmeshes, 'makecmap_options');
+    print(makecmap_options);
     if(is.null(makecmap_options)) {
         warning("Requested to draw colorbar, but meshes contain no 'makecmap_options' metadata, falling back to defaults.");
         makecmap_options = mkco.seq();
@@ -145,6 +161,38 @@ coloredmesh.plot.colorbar.separate <- function(coloredmeshes, show=FALSE, image.
 
     image.plot_options_internal = list(legend.only=TRUE, zlim = zlim, col = makecmap_options$colFn(num_col), add=TRUE, graphics.reset=TRUE);
     image.plot_options = modifyList(image.plot_options_internal, image.plot_extra_options);
+
+    # Enable plotting log-scale color bar.
+    # NOTE: Use 'area' instead of 'thickness' as PVD when testing this with the code from the example, thickness has a min of 0 (won't work with log).
+    if((is.logical(log_breaks) && log_breaks) ||  is.numeric(log_breaks) || 'base' %in% names(makecmap_options)) {
+        num_ticks_default = 5L;
+        if(is.logical(log_breaks) && log_breaks) {
+            log_breaks = num_ticks_default;  # If simply 'True', use default number of breaks = 5.
+        }
+
+        if(is.numeric(log_breaks) && length(log_breaks) == 1L) { # If a single number, treat it as the *number* of ticks to create.
+            num_break_labels = as.integer(log_breaks);
+            ticks = squash::prettyLog(combined_data_range, n=num_break_labels);
+        } else if(is.numeric(log_breaks) && length(log_breaks) > 1L) {  # If a vector, treat the values in there as the desired ticks.
+            ticks = log_breaks;
+        } else {
+            if (as.integer(makecmap_options$base) == 10L) {
+                ticks = squash::prettyLog(combined_data_range, n=num_ticks_default);
+            } else {
+                stop(sprintf(" - Invalid 'base' value in 'makecmap_options', only 10 is supported for log 10 scale. (Do not set it at all for linear scale.)"));
+            }
+
+        }
+
+        tick_axis_args = list('at'=log(ticks), 'labels'=ticks)
+        if ("axis.args" %in% names(image.plot_options)) {
+            image.plot_options$axis.args = modifyList(image.plot_options$axis.args, tick_axis_args);
+        } else {
+            image.plot_options$axis.args = tick_axis_args;
+        }
+        image.plot_options$zlim = log(image.plot_options$zlim);
+    }
+
     if(show) {
         plot.new();
         do.call(fields::image.plot, image.plot_options);

diff --git a/R/optdata.R b/R/optdata.R
@@ -244,7 +244,9 @@ download_fsaverage <- function(accept_freesurfer_license=FALSE) {
                                     c(base_path_fsaverage, 'surf', 'lh.curv'),
                                     c(base_path_fsaverage, 'surf', 'rh.curv'),
                                     c(base_path_fsaverage, 'ext', 'FreeSurferColorLUT.txt'),
-                                    c(base_path_fsaverage, 'LICENSE')
+                                    c(base_path_fsaverage, 'LICENSE'),
+                                    c(base_path_fsaverage, 'surf', 'lh.sphere'),
+                                    c(base_path_fsaverage, 'surf', 'rh.sphere')
     );
 
 
@@ -265,7 +267,9 @@ download_fsaverage <- function(accept_freesurfer_license=FALSE) {
                 '3e81598a5ac0546443ec37d0ac477c80',
                 '76ad91d2488de081392313ad5a87fafb',
                 'a3735566ef949bd4d7ed303837cc5e77',  # color LUT
-                'b39610adfe02fdce2ad9d30797c567b3'    # LICENSE
+                'b39610adfe02fdce2ad9d30797c567b3',  # LICENSE
+                '9bcc318b66c4da5e479b33e9451ec5e1',
+                '9bcc318b66c4da5e479b33e9451ec5e1' # rh.sphere
     );
 
 
@@ -287,7 +291,9 @@ download_fsaverage <- function(accept_freesurfer_license=FALSE) {
                                    'surf/lh.curv',
                                    'surf/rh.curv',
                                    'ext/FreeSurferColorLUT.txt',
-                                   'LICENSE'
+                                   'LICENSE',
+                                   'surf/lh.sphere',
+                                   'surf/rh.sphere'
     );
     ext_urls = paste(ext_url_subject_part_fsaverage, ext_url_parts_each_subject, sep='');
     base_url = 'http://rcmd.org/projects/nitestdata/';

diff --git a/README.md b/README.md
@@ -95,10 +95,14 @@ The documentation can be accessed from within an R session after you have loaded
   * [basic fsbrain example notebook](https://htmlpreview.github.io/?https://github.com/dfsp-spirit/fsbrain/blob/develop/web/Rmd_web_examples/examples.html): Live visualization of subject data
   * [advanced fsbrain example notebook](https://htmlpreview.github.io/?https://github.com/dfsp-spirit/fsbrain/blob/develop/web/Rmd_web_examples/examples_adv.html): Plotting group data
   * [export API fsbrain example notebook](https://htmlpreview.github.io/?https://github.com/dfsp-spirit/fsbrain/blob/develop/web/Rmd_web_examples/examples_export.html): Exporting publication-ready plots
-* A detailed vignette with explanations and examples for the functions of the package is included, run `browseVignettes("fsbrain")` to see the vignettes. You can also open the vignette directly:
-  * learn how to load and visualize surface-based neuroimaging data and results: `vignette("fsbrain")` [read online at CRAN](https://cran.r-project.org/web/packages/fsbrain/vignettes/fsbrain.html)
-  * learn how to load and visualize volume-based neuroimaging data and results: `vignette("fsbrain_vol")` [read online at CRAN](https://cran.r-project.org/web/packages/fsbrain/vignettes/fsbrain_vol.html)
-  * read the fsbrain FAQ: `vignette("fsbrain_faq")` [read online at CRAN](https://cran.r-project.org/web/packages/fsbrain/vignettes/fsbrain_faq.html)
+
+
+* Detailed vignettes with explanations and examples for the functions of the package is included, run `browseVignettes("fsbrain")` to see the vignettes. You can also open the vignette directly:
+  * How to load and visualize surface-based neuroimaging data: `vignette("fsbrain")` or: [read online at CRAN](https://cran.r-project.org/web/packages/fsbrain/vignettes/fsbrain.html)
+  * How to load and visualize volume-based neuroimaging data: `vignette("fsbrain_vol")` or: [read online at CRAN](https://cran.r-project.org/web/packages/fsbrain/vignettes/fsbrain_vol.html)
+  * The fsbrain FAQ: `vignette("fsbrain_faq")` or: [read online at CRAN](https://cran.r-project.org/web/packages/fsbrain/vignettes/fsbrain_faq.html)
+
+
 * Help for a specific function can be accessed in the usual R manner: `?<function>`, where you replace `<function>` with a function name. Like this: `?group.morph.native`.
 * Run `example(<function>)` to see a live demo that uses the function `<function>`. Like this: `example(group.morph.native)`.
 * The [unit tests](./tests/testthat/) that come with this package are essentially a list of examples that illustrate how to use the functions.

diff --git a/docker/README_DEV_DOCKER.md b/docker/README_DEV_DOCKER.md
@@ -23,7 +23,7 @@ To create a new version of the image on docker.io, one needs to build the new im
 1) login to docker.io:
 
 ```
-sudo docker login -u "dfspspirit" --password-stdin docker.io
+docker login -u "dfspspirit"  docker.io
 ```
 
 2) tag the image with the dockerhub user/repo and a version,  e.g.:

diff --git a/docker/fsbrain0.5.3/R4.1.0/Dockerfile b/docker/fsbrain0.5.3/R4.1.0/Dockerfile
@@ -0,0 +1,67 @@
+# Docker build for distributing an fsbrain container.
+# This file is part of fsbrain, https://github.com/dfsp-spirit/fsbrain
+#
+# See the very bottom of this script for info on how to run it.
+
+FROM rocker/r-ver:4.1.0
+
+# Shell setup:
+WORKDIR /root
+
+##### Install tools and system dependencies #####
+RUN apt-get update && apt-get install -y apt-utils
+RUN apt-get update && apt-get install -y \
+  build-essential \
+  git \
+  libcurl4-openssl-dev \
+  libfreetype6-dev \
+  libgfortran4 \
+  libgl1-mesa-dev \
+  libglu1-mesa-dev \
+  libmagick++-dev \
+  libssh-dev \
+  libx11-dev \
+  libxml2-dev \
+  mesa-common-dev \
+  xvfb \
+  libtk8.6 \
+  libfontconfig1-dev \
+  libharfbuzz-dev \
+  libfribidi-dev \
+  && rm -rf /var/lib/apt/lists/*
+
+##### Install required R packages #####
+
+## Get fsbrain dependencies.
+RUN R -e "install.packages('devtools', repos = 'http://cran.rstudio.com/')"
+
+## We want freesurferformats with all optional dependencies for full file format support.
+RUN R -e "devtools::install_version('freesurferformats', version = '0.1.17', dependencies=TRUE, repos = 'http://cran.rstudio.com')"
+
+RUN R -e "install.packages('rgl', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('viridis', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('RColorBrewer', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('misc3d', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('igraph', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('magick', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('Rvcg', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('pracma', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('reshape', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('squash', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('data.table', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('methods', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('fields', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('pkgfilecache', repos = 'http://cran.rstudio.com/')"
+
+## Now get fsbrain
+RUN R -e "devtools::install_version('fsbrain', version = '0.5.3', dependencies=TRUE, repos = 'http://cran.rstudio.com')"
+
+## Create folders for mapping. You should write output to /home/output in the R session.
+RUN mkdir /home/input
+RUN mkdir /home/output
+
+## Run R in xvfb with 2k resolution.
+CMD cd /home/input \
+  && xvfb-run --server-args="-screen 0, 2560x1440x24" R
+
+## Now run your analyses and write the results/images to /home/output.
diff --git a/docker/fsbrain0.5.3dev/R4.1.0/Dockerfile b/docker/fsbrain0.5.3dev/R4.1.0/Dockerfile
@@ -0,0 +1,62 @@
+# Docker build for distributing an fsbrain container.
+# This file is part of fsbrain, https://github.com/dfsp-spirit/fsbrain
+#
+# See the very bottom of this script for info on how to run it.
+
+FROM rocker/r-ver:4.1.0
+
+# Shell setup:
+WORKDIR /root
+
+##### Install tools and system dependencies #####
+RUN apt-get update && apt-get install -y \
+  build-essential \
+  git \
+  libcurl4-openssl-dev \
+  libfreetype6-dev \
+  libgfortran4 \
+  libgl1-mesa-dev \
+  libglu1-mesa-dev \
+  libmagick++-dev \
+  libssh-dev \
+  libx11-dev \
+  libxml2-dev \
+  mesa-common-dev \
+  xvfb \
+  && rm -rf /var/lib/apt/lists/*
+
+##### Install required R packages #####
+
+## Get fsbrain dependencies.
+RUN R -e "install.packages('devtools', repos = 'http://cran.rstudio.com/')"
+
+## We want freesurferformats with all optional dependencies for full file format support.
+RUN R -e "devtools::install_version('freesurferformats', version = '0.1.17', dependencies=TRUE, repos = 'http://cran.rstudio.com')"
+
+RUN R -e "install.packages('rgl', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('viridis', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('RColorBrewer', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('misc3d', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('igraph', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('magick', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('Rvcg', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('pracma', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('reshape', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('squash', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('data.table', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('methods', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('fields', repos = 'http://cran.rstudio.com/')"
+RUN R -e "install.packages('pkgfilecache', repos = 'http://cran.rstudio.com/')"
+
+## Now get fsbrain
+RUN R -e "devtools::install_github('dfsp-spirit/fsbrain', ref='c8213a5eb4ba59c48754736644a3035117a6478a')"
+
+## Create folders for mapping. You should write output to /home/output in the R session.
+RUN mkdir /home/input
+RUN mkdir /home/output
+
+## Run R in xvfb with 2k resolution.
+CMD cd /home/input \
+  && xvfb-run --server-args="-screen 0, 2560x1440x24" R
+
+## Now run your analyses and write the results/images to /home/output.