0.1.1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ClassiPyR
 Title: A Shiny App for Manual Image Classification and Validation of IFCB Data
-Version: 0.1.0
+Version: 0.1.1
 Authors@R: c(
     person("Anders", "Torstensson", email = "anders.torstensson@smhi.se", role = c("aut", "cre"),
            comment = c("Swedish Meteorological and Hydrological Institute", ORCID = "0000-0002-8283-656X")),

NEWS.md

@@ -1,3 +1,10 @@
+# ClassiPyR 0.1.1
+
+## New features
+
+- Added **"Export validation statistics"** checkbox in Settings (below the output folder path). When unchecked, per-sample CSV files are not written to the `validation_statistics/` subfolder. Useful when annotating from scratch where validation statistics are not relevant (#9).
+- Added a **confirmation dialog** before bulk export of SQLite annotations to `.mat` files. The dialog explains that existing `.mat` files in the output folder will be overwritten, preventing accidental data loss (#10).
+
 # ClassiPyR 0.1.0
 
 Initial release of ClassiPyR, a Shiny application for manual classification and validation of Imaging FlowCytobot (IFCB) plankton images.

R/sample_saving.R

@@ -30,6 +30,10 @@ NULL
 #' @param db_folder Path to the database folder for SQLite storage. Defaults to
 #'   \code{\link{get_default_db_dir}()}. Should be a local filesystem path,
 #'   not a network drive.
+#' @param export_statistics Logical. When \code{TRUE} (default), validation
+#'   statistics CSV files are written to a \code{validation_statistics/}
+#'   subfolder inside \code{output_folder}. Set to \code{FALSE} to skip this
+#'   export, e.g. when annotating from scratch.
 #' @return TRUE on success, FALSE on failure
 #' @export
 #' @examples
@@ -61,7 +65,8 @@ save_sample_annotations <- function(sample_name,
                                      annotator = "Unknown",
                                      adc_folder = NULL,
                                      save_format = "sqlite",
-                                     db_folder = get_default_db_dir()) {
+                                     db_folder = get_default_db_dir(),
+                                     export_statistics = TRUE) {
 
   if (is.null(sample_name) || is.null(classifications) || is.null(class2use_path)) {
     return(FALSE)
@@ -74,14 +79,9 @@ save_sample_annotations <- function(sample_name,
 
   tryCatch({
     # Create output folders if needed
-    stats_folder <- file.path(output_folder, "validation_statistics")
-
     if (!dir.exists(output_folder)) {
       dir.create(output_folder, recursive = TRUE)
     }
-    if (!dir.exists(stats_folder)) {
-      dir.create(stats_folder, recursive = TRUE)
-    }
     if (!dir.exists(png_output_folder)) {
       dir.create(png_output_folder, recursive = TRUE)
     }
@@ -126,14 +126,20 @@ save_sample_annotations <- function(sample_name,
       )
     }
 
-    # Save statistics
-    save_validation_statistics(
-      sample_name = sample_name,
-      classifications = classifications,
-      original_classifications = original_classifications,
-      stats_folder = stats_folder,
-      annotator = annotator
-    )
+    # Save statistics (optional)
+    if (isTRUE(export_statistics)) {
+      stats_folder <- file.path(output_folder, "validation_statistics")
+      if (!dir.exists(stats_folder)) {
+        dir.create(stats_folder, recursive = TRUE)
+      }
+      save_validation_statistics(
+        sample_name = sample_name,
+        classifications = classifications,
+        original_classifications = original_classifications,
+        stats_folder = stats_folder,
+        annotator = annotator
+      )
+    }
 
     # Clean up temp folder
     unlink(temp_annotate_folder, recursive = TRUE)

inst/CITATION

@@ -9,12 +9,12 @@ bibentry(
            comment = c(ORCID = "0000-0002-8283-656X"))
   ),
   year     = "2026",
-  note     = "R package version 0.1.0",
+  note     = "R package version 0.1.1",
   url      = "https://doi.org/10.5281/zenodo.18414999",
   textVersion = paste(
     "Torstensson, A. (2026).",
     "ClassiPyR: A Shiny Application for Manual Image Classification and Validation of IFCB Data.",
-    "R package version 0.1.0.",
+    "R package version 0.1.1.",
     "https://doi.org/10.5281/zenodo.18414999"
   )
 )

inst/app/server.R

@@ -103,7 +103,8 @@ server <- function(input, output, session) {
       auto_sync = TRUE,  # Automatically sync folders on startup
       class2use_path = NULL,  # Path to class2use file for auto-loading
       python_venv_path = NULL,  # NULL = use ./venv in working directory
-      save_format = "sqlite"  # "sqlite" (default), "mat", or "both"
+      save_format = "sqlite",  # "sqlite" (default), "mat", or "both"
+      export_statistics = TRUE  # Write validation statistics CSV files
     )
 
     if (file.exists(settings_file)) {
@@ -158,7 +159,8 @@ server <- function(input, output, session) {
     pixels_per_micron = saved_settings$pixels_per_micron,
     auto_sync = saved_settings$auto_sync,
     python_venv_path = saved_settings$python_venv_path,
-    save_format = saved_settings$save_format
+    save_format = saved_settings$save_format,
+    export_statistics = saved_settings$export_statistics
   )
 
   # Initialize class dropdown with default class list on startup
@@ -241,14 +243,19 @@ server <- function(input, output, session) {
       ),
 
       div(
-        style = "display: flex; gap: 5px; align-items: flex-end; margin-bottom: 15px;",
+        style = "display: flex; gap: 5px; align-items: flex-end; margin-bottom: 5px;",
         div(style = "flex: 1;",
             textInput("cfg_output_folder", "Output Folder (MAT/statistics)",
                       value = config$output_folder, width = "100%")),
         shinyDirButton("browse_output_folder", "Browse", "Select Output Folder",
                        class = "btn-outline-secondary", style = "margin-bottom: 15px;")
       ),
 
+      checkboxInput("cfg_export_statistics", "Export validation statistics",
+                    value = config$export_statistics),
+      tags$small(class = "text-muted", style = "display: block; margin-bottom: 15px;",
+                 "Write per-sample CSV files with classification accuracy to the output folder."),
+
       div(
         style = "display: flex; gap: 5px; align-items: flex-end; margin-bottom: 15px;",
         div(style = "flex: 1;",
@@ -688,6 +695,7 @@ server <- function(input, output, session) {
     config$pixels_per_micron <- input$cfg_pixels_per_micron
     config$auto_sync <- input$cfg_auto_sync
     config$save_format <- input$cfg_save_format
+    config$export_statistics <- input$cfg_export_statistics
 
     # Persist settings to file for next session
     # python_venv_path is kept from config (set via run_app() or previous save)
@@ -701,6 +709,7 @@ server <- function(input, output, session) {
       pixels_per_micron = input$cfg_pixels_per_micron,
       auto_sync = input$cfg_auto_sync,
       save_format = input$cfg_save_format,
+      export_statistics = input$cfg_export_statistics,
       class2use_path = rv$class2use_path,
       python_venv_path = config$python_venv_path
     ))
@@ -749,7 +758,7 @@ server <- function(input, output, session) {
     }
   })
 
-  # Export SQLite -> .mat bulk handler
+  # Export SQLite -> .mat bulk handler: show confirmation dialog first
   observeEvent(input$export_db_to_mat_btn, {
     if (is.null(config$output_folder) || config$output_folder == "") {
       showNotification("Output folder is not configured. Set it in Settings first.",
@@ -762,6 +771,27 @@ server <- function(input, output, session) {
       return()
     }
 
+    showModal(modalDialog(
+      title = "Confirm .mat export",
+      p("This will export all annotated samples from the SQLite database as",
+        tags$strong(".mat files"), "into:"),
+      tags$code(config$output_folder),
+      tags$br(), tags$br(),
+      p(tags$strong("Existing .mat files in this folder will be overwritten"),
+        "and cannot be recovered. Make sure you have a backup if needed."),
+      p("Do you want to continue?"),
+      footer = tagList(
+        modalButton("Cancel"),
+        actionButton("confirm_export_mat_btn", "Export", class = "btn-danger")
+      ),
+      easyClose = TRUE
+    ))
+  })
+
+  # Confirmed: run the actual export
+  observeEvent(input$confirm_export_mat_btn, {
+    removeModal()
+
     db_path <- get_db_path(config$db_folder)
 
     withProgress(message = "Exporting SQLite to .mat files...", {
@@ -1561,7 +1591,8 @@ server <- function(input, output, session) {
           annotator = input$annotator_name,
           adc_folder = adc_folder_for_save,
           save_format = config$save_format,
-          db_folder = config$db_folder
+          db_folder = config$db_folder,
+          export_statistics = config$export_statistics
         )
         # Only update annotated samples list if changes were actually saved
         if (isTRUE(saved)) {
@@ -2269,7 +2300,8 @@ server <- function(input, output, session) {
           annotator = annotator,
           adc_folder = adc_folder,
           save_format = save_fmt,
-          db_folder = config$db_folder
+          db_folder = config$db_folder,
+          export_statistics = config$export_statistics
         )
       })
 
@@ -2578,7 +2610,8 @@ server <- function(input, output, session) {
               class2use_path = class2use_path,
               annotator = annotator,
               save_format = isolate(config$save_format),
-              db_folder = isolate(config$db_folder)
+              db_folder = isolate(config$db_folder),
+              export_statistics = isolate(config$export_statistics)
             )
           }, error = function(e) {
             message("Failed to auto-save ", sample_name, " on session end: ", e$message)