Update raster slides

instructors/3-raster-slides.qmd

@@ -25,8 +25,24 @@ knitr::opts_chunk$set(
   warning = FALSE,
   error = FALSE
   )
+
+library(tidyverse)
+library(terra)
 ```
 
+```{r echo = FALSE}
+DSM_TUD <- rast("../episodes/data/tud-dsm-5m.tif")
+DSM_TUD_df <- as.data.frame(DSM_TUD, xy = TRUE)
+
+DTM_TUD <- rast("../episodes/data/tud-dtm-5m.tif")
+DTM_TUD_df <- as.data.frame(DTM_TUD, xy = TRUE)
+
+CHM_TUD <- DSM_TUD - DTM_TUD
+CHM_TUD_df <- as.data.frame(CHM_TUD, xy = TRUE)
+
+DTM_hill_TUD <- rast("../episodes/data/tud-dtm-5m-hill-WGS84.tif")
+DTM_hill_TUD_df <- as.data.frame(DTM_hill_TUD, xy = TRUE)
+```
 
 ## Outline
 
@@ -46,7 +62,7 @@ knitr::opts_chunk$set(
 
 ## Challenge 1: **2 mins**
 
-Use `describe()` to determine the following about the `tud-dsm-hill.tif` file:
+Use `describe()` to determine the following about the `tud-dsm-5m-hill.tif` file:
 
 1. Does this file have the same CRS as `DSM_TUD`?
 2. What is resolution of the raster data?
@@ -59,6 +75,34 @@ Use `describe()` to determine the following about the `tud-dsm-hill.tif` file:
 countdown::countdown(minutes = 2)
 ``` 
 
+## Challenge 1 - Solution {.smaller}
+
+:::: {.columns}
+
+::: {.column}
+
+::: {.nonincremental}
+
+1. Does this file have the same CRS as `DSM_TUD`?
+2. What is resolution of the raster data?
+3. How large would a 5x5 pixel area be on the Earth’s surface?
+4. Is the file a multi- or single-band raster?
+
+:::
+
+:::
+
+::: {.column}
+
+```{r}
+# Replace with your own path
+describe("../episodes/data/tud-dsm-5m-hill.tif")
+```
+
+:::
+
+::::
+
 # Plotting raster data
 
 ## Challenge 2: **5 mins**
@@ -74,6 +118,22 @@ Create a plot of the TU Delft Digital Surface Model (`DSM_TUD`) that has:
 countdown::countdown(minutes = 5)
 ``` 
 
+## Challenge 2 - Solution
+
+```{r}
+DSM_TUD_df <- DSM_TUD_df %>%
+  mutate(fct_elevation_6 = cut(`tud-dsm-5m`, breaks = 6))
+
+my_col <- terrain.colors(6)
+
+ggplot() +
+  geom_raster(data = DSM_TUD_df, aes(x = x, y = y,
+                                       fill = fct_elevation_6)) +
+  scale_fill_manual(values = my_col, name = "Elevation") +
+  coord_equal() +
+  labs(title = "Elevation Classes of the Digital Surface Model (DSM)")
+```
+
 # Reprojecting raster data
 
 ## Challenge 3: **2 mins**
@@ -86,6 +146,18 @@ View the CRS for each of these two datasets. What projection does each use?
 countdown::countdown(minutes = 2)
 ``` 
 
+## Challenge 3 - Solution
+
+```{r dtm-crs}
+crs(DTM_TUD, parse = TRUE) %>% head()
+```
+
+```{r hill-crs}
+crs(DTM_hill_TUD, parse = TRUE) %>% head()
+```
+
+`DTM_TUD` is in the Amersfoort / RD New projection, whereas `DTM_hill_TUD` is in WGS 84.
+
 # Raster calculations
 
 ## Challenge 4: **10 mins**
@@ -94,12 +166,67 @@ It’s often a good idea to explore the range of values in a raster dataset just
 
 1. What is the min and max value for the Canopy Height Model `CHM_TUD` that we just created?
 3. What is the distribution of all the pixel values in the CHM?
-5. Plot the `CHM_TUD` raster using breaks that make sense for the data. Include an appropriate color palette for the data, plot title and no axes ticks / labels.
+5. Plot the `CHM_TUD` raster using breaks that make sense for the data.
 
 ``` {r}
 #| echo: false
 #| cache: false
 countdown::countdown(minutes = 10)
 ``` 
 
+## Challenge 4 - Solution part 1
+
+```{r chm-challenge-1}
+min(CHM_TUD_df$`tud-dsm-5m`, na.rm = TRUE)
+max(CHM_TUD_df$`tud-dsm-5m`, na.rm = TRUE)
+```
+
+## Challenge 4 - Solution part 2
+
+```{r chm-challenge-2}
+ggplot(CHM_TUD_df) +
+    geom_histogram(aes(`tud-dsm-5m`))
+```
+
+## Challenge 4 - Solution part 3
+
+```{r chm-challenge-3}
+custom_bins <- c(-5, 0, 10, 20, 30, 100)
+CHM_TUD_df <- CHM_TUD_df |> 
+  mutate(canopy_discrete = cut(`tud-dsm-5m`, breaks = custom_bins))
+
+ggplot() +
+  geom_raster(data = CHM_TUD_df , aes(x = x, y = y,
+                                       fill = canopy_discrete)) + 
+     scale_fill_manual(values = terrain.colors(5)) + 
+     coord_quickmap()
+```
+
+
 # Working with multi-band rasters
+
+## Challenge 5: **5 mins**
+
+We can use the `rast()` function to import specific bands in our raster object by specifying which band we want with `lyrs = N` (N represents the band number we want to work with). To import the green band, we would use `lyrs = 2`. We can convert this data to a data frame and plot the same way we plotted the red band.
+
+Import and plot the green band.
+
+``` {r}
+#| echo: false
+#| cache: false
+countdown::countdown(minutes = 5)
+``` 
+
+## Challenge 5 - Solution
+
+```{r}
+# replace path with your data folder
+RGB_band2_TUD <- rast("../episodes/data/tudlib-rgb.tif", lyrs = 2)
+
+RGB_band2_TUD_df <- as.data.frame(RGB_band2_TUD, xy = TRUE)
+
+ggplot() +
+  geom_raster(data = RGB_band2_TUD_df,
+              aes(x = x, y = y, alpha = `tudlib-rgb_2`)) + 
+  coord_equal() 
+```

instructors/3-raster-slides_files/libs/revealjs/plugin/pdf-export/pdfexport.js

@@ -101,6 +101,9 @@ var PdfExport = ( function( _Reveal ){
 			Reveal = _Reveal;
 			install();
 		};
+		Plugin.togglePdfExport = function () {
+      togglePdfExport();
+    };
 	}
 
 	return Plugin;

instructors/3-raster-slides_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.js

@@ -38,7 +38,7 @@ window.QuartoLineHighlight = function () {
     divSourceCode.forEach((el) => {
       if (el.hasAttribute(kCodeLineNumbersAttr)) {
         const codeLineAttr = el.getAttribute(kCodeLineNumbersAttr);
-        el.removeAttribute("data-code-line-numbers");
+        el.removeAttribute(kCodeLineNumbersAttr);
         if (handleLinesSelector(deck, codeLineAttr)) {
           // Only process if attr is a string to select lines to highlights
           // e.g "1|3,6|8-11"
@@ -165,17 +165,17 @@ window.QuartoLineHighlight = function () {
         if (typeof highlight.last === "number") {
           spanToHighlight = [].slice.call(
             codeBlock.querySelectorAll(
-              ":scope > span:nth-child(n+" +
+              ":scope > span:nth-of-type(n+" +
                 highlight.first +
-                "):nth-child(-n+" +
+                "):nth-of-type(-n+" +
                 highlight.last +
                 ")"
             )
           );
         } else if (typeof highlight.first === "number") {
           spanToHighlight = [].slice.call(
             codeBlock.querySelectorAll(
-              ":scope > span:nth-child(" + highlight.first + ")"
+              ":scope > span:nth-of-type(" + highlight.first + ")"
             )
           );
         }

instructors/3-raster-slides_files/libs/revealjs/plugin/quarto-support/footer.css

@@ -6,6 +6,7 @@
   max-height: 2.2rem;
   height: 100%;
   width: auto;
+  z-index: 2;
 }
 
 .reveal .footer {

instructors/3-raster-slides_files/libs/revealjs/plugin/quarto-support/support.js

@@ -4,6 +4,20 @@ window.QuartoSupport = function () {
     return /print-pdf/gi.test(window.location.search);
   }
 
+  // helper for theme toggling
+  function toggleBackgroundTheme(el, onDarkBackground, onLightBackground) {
+    if (onDarkBackground) {
+      el.classList.add('has-dark-background')
+    } else {
+      el.classList.remove('has-dark-background')
+    }
+    if (onLightBackground) {
+      el.classList.add('has-light-background')
+    } else {
+      el.classList.remove('has-light-background')
+    }
+  }
+
   // implement controlsAudo
   function controlsAuto(deck) {
     const config = deck.getConfig();
@@ -111,8 +125,19 @@ window.QuartoSupport = function () {
     }
   }
 
-  // add footer text
-  function addFooter(deck) {
+  // tweak slide-number element
+  function tweakSlideNumber(deck) {
+    deck.on("slidechanged", function (ev) {
+      const revealParent = deck.getRevealElement();
+      const slideNumberEl = revealParent.querySelector(".slide-number");
+      const onDarkBackground = Reveal.getSlideBackground(ev.indexh, ev.indexv).classList.contains('has-dark-background');
+      const onLightBackground = Reveal.getSlideBackground(ev.indexh, ev.indexv).classList.contains('has-light-background');
+      toggleBackgroundTheme(slideNumberEl, onDarkBackground, onLightBackground);
+    })
+  }
+
+   // add footer text
+   function addFooter(deck) {
     const revealParent = deck.getRevealElement();
     const defaultFooterDiv = document.querySelector(".footer-default");
     if (defaultFooterDiv) {
@@ -127,13 +152,17 @@ window.QuartoSupport = function () {
             prevSlideFooter.remove();
           }
           const currentSlideFooter = ev.currentSlide.querySelector(".footer");
+          const onDarkBackground = Reveal.getSlideBackground(ev.indexh, ev.indexv).classList.contains('has-dark-background')
+          const onLightBackground = Reveal.getSlideBackground(ev.indexh, ev.indexv).classList.contains('has-light-background')
           if (currentSlideFooter) {
             defaultFooterDiv.style.display = "none";
             const slideFooter = currentSlideFooter.cloneNode(true);
             handleLinkClickEvents(deck, slideFooter);
             deck.getRevealElement().appendChild(slideFooter);
+            toggleBackgroundTheme(slideFooter, onDarkBackground, onLightBackground)
           } else {
             defaultFooterDiv.style.display = "block";
+            toggleBackgroundTheme(defaultFooterDiv, onDarkBackground, onLightBackground)
           }
         });
       }
@@ -272,6 +301,23 @@ window.QuartoSupport = function () {
     }
   }
 
+  function handleWhiteSpaceInColumns(deck) {
+    for (const outerDiv of window.document.querySelectorAll("div.columns")) {
+      // remove all whitespace text nodes
+      // whitespace nodes cause the columns to be misaligned
+      // since they have inline-block layout
+      // 
+      // Quarto emits no whitespace nodes, but third-party tooling
+      // has bugs that can cause whitespace nodes to be emitted.
+      // See https://github.com/quarto-dev/quarto-cli/issues/8382
+      for (const node of outerDiv.childNodes) {
+        if (node.nodeType === 3 && node.nodeValue.trim() === "") {
+          outerDiv.removeChild(node);
+        }
+      }
+    }
+  }
+
   return {
     id: "quarto-support",
     init: function (deck) {
@@ -280,11 +326,13 @@ window.QuartoSupport = function () {
       fixupForPrint(deck);
       applyGlobalStyles(deck);
       addLogoImage(deck);
+      tweakSlideNumber(deck);
       addFooter(deck);
       addChalkboardButtons(deck);
       handleTabbyClicks();
       handleSlideChanges(deck);
       workaroundMermaidDistance(deck);
+      handleWhiteSpaceInColumns(deck);
     },
   };
 };

instructors/3-raster-slides_files/libs/revealjs/plugin/reveal-chalkboard/plugin.js

@@ -671,6 +671,15 @@ console.warn( "toggleNotesButton is deprecated, use customcontrols plugin instea
 			} );
 			a.href = window.URL.createObjectURL( blob );
 		} catch ( error ) {
+			// https://stackoverflow.com/a/6234804
+			// escape data for proper handling of quotes and line breaks
+			// in case malicious gets a chance to craft the exception message
+			error = String(error).replace(/&/g, "&")
+					.replace(/</g, "&lt;")
+					.replace(/>/g, "&gt;")
+					.replace(/"/g, "&quot;")
+					.replace(/'/g, "&#039;");
+
 			a.innerHTML += ' (' + error + ')';
 		}
 		a.click();

instructors/3-raster-slides_files/libs/revealjs/plugin/reveal-menu/quarto-menu.js

@@ -37,4 +37,7 @@ window.RevealMenuToolHandlers = {
   downloadDrawings: revealMenuToolHandler(function () {
     RevealChalkboard.download();
   }),
+  togglePdfExport: revealMenuToolHandler(function () {
+    PdfExport.togglePdfExport();
+  }),
 };