Added option to rescale image intensity.

image_data_explorer.R

@@ -61,7 +61,7 @@ ui <- function(request) {
       
       ## Custom CSS to:
       ## - Reduce white space around boxes
-      ## - Chenge font size
+      ## - Change font size
       ## - Change postion and size of notification box
       tags$head(tags$style(HTML(
         '[class*="col-lg-"],[class*="col-md-"],
@@ -145,7 +145,9 @@ ui <- function(request) {
                        ),
                        ## Select column containing image file names
                        uiOutput("fileColumn1"),
-                       uiOutput("fileColumn2")
+                       checkboxInput("normalize.img1", "Rescale intensity for image 1", TRUE),
+                       uiOutput("fileColumn2"),
+                       checkboxInput("normalize.img2", "Rescale intensity for image 2", TRUE)
                   ),
                   box( width = 3,
                        title = "ROIs", solidHeader = TRUE, status = "primary",
@@ -416,7 +418,8 @@ server <- function(input, output, session) {
       settings <- list("selectedVar" = input$selectedVar, "colsOnHover" = input$colsOnHover,
                        "colsToHide" = input$colsToHide, "groupLabels" = input$groupLabels, "roiX" = input$roiX, 
                        "roiY" = input$roiY, "roiFrame" = input$roiFrame, "imgRoot" = rv$inputChoices[["imgRoot"]], 
-                       "fileCol1" = input$fileCol1, "fileCol2" = input$fileCol2)
+                       "fileCol1" = input$fileCol1, "fileCol2" = input$fileCol2, 
+                       "normalize.img1" = input$normalize.img1, "normalize.img2" = input$normalize.img2)
       saveRDS(settings, file)
     }
   )
@@ -440,13 +443,14 @@ server <- function(input, output, session) {
     updateSelectizeInput(session = session, inputId = "roiFrame", selected = rv$inputChoices[["roiFrame"]])
     updateSelectizeInput(session = session, inputId = "fileCol1", selected = rv$inputChoices[["fileCol1"]])
     updateSelectizeInput(session = session, inputId = "fileCol2", selected = rv$inputChoices[["fileCol2"]])
-    
+    updateCheckboxInput(session = session, inputId = "normalize.img1", value = rv$inputChoices[["normalize.img1"]])
+    updateCheckboxInput(session = session, inputId = "normalize.img2", value = rv$inputChoices[["normalize.img2"]])
   })
   
   # Vector of user input names (i.e. inputId) that we may want to restore from file
   # Values are stored in rv$inputChoices
   inputChoices.params <- c("selectedVar", "colsOnHover", "colsToHide", "groupLabels", "roiX", "roiY",
-                           "roiFrame", "imgRoot", "fileCol1", "fileCol2")
+                           "roiFrame", "imgRoot", "fileCol1", "fileCol2", "normalize.img1", "normalize.img2")
   rv <- reactiveValues(inputChoices = setNames(vector("list", length(inputChoices.params)),inputChoices.params),
                        data = NULL, currentRows = NULL, selectedRows = NULL, clusters = NULL, imgRoot = NULL,
                        imgPath1 = NULL, imgPath2 = NULL, pixelPosition = NULL, selectedFrame = NULL,
@@ -864,6 +868,7 @@ server <- function(input, output, session) {
         colorMode(image1) = Color
         image1 <- drawCircle(image1, rv$pixelPosition[1], rv$pixelPosition[2], r, "red", fill=TRUE, z=1)
       }
+      if(input$normalize.img1) { image1 <- normalize(image1)}
       display(image1, method = 'browser')
     }
   })
@@ -877,6 +882,7 @@ server <- function(input, output, session) {
         colorMode(image2) = Color
         image2 <- drawCircle(image2, rv$pixelPosition[1], rv$pixelPosition[2], r, "red", fill=TRUE, z=1)
       }
+      if(input$normalize.img2) { image2 <- normalize(image2)}
       display(image2, method = 'browser')
     }
   })