m2 dev branch update (#26)

* Refs (#4) * harmonize references theme1 * harmonize references theme3 * harmonize references theme4 * harmonize references theme5 * harmonize references theme6_rockglacier * harmonize references theme6_sandybeach --------- Co-authored-by: uw255 <uw255@stud.uni-heidelberg.de> * Quiz rev (#6) * Added option for multiple choice questions using checkboxes * added description of multiple choice questions --------- Co-authored-by: jdvorak <jakub.dvorak@natur.cuni.cz> * added install notebook to deploy (#7) Co-authored-by: jdvorak <jakub.dvorak@natur.cuni.cz> * Fixed version of notebook in deploy to 6.5.5. Newer versions of notebook don't contain the .base module (#8) * added install notebook to deploy * Fixed version of notebook in deploy to 6.5.5. Newer versions of notebook don't contain the .base module --------- Co-authored-by: jdvorak <jakub.dvorak@natur.cuni.cz> * Update CITATION.cff (#9) * M4 dev (#10) * Create gitkeep * upload images * upload images_cs_floodplain * add content 07_flood_plain_forest.md * add content 07_flood_plain_forest.md * add content 07_flood_plain_forest.md * Create gitkeep * upload images * add content 06_Krkonose_tundra_grasslands.md * add content 07_flood_plain_forest.md * add content 07_flood_plain_forest.md * add content 07_flood_plain_forest.md * added spectra comparision exercise to theme_3:module_4 * added and fixed links * spectra contact probe and integrating sphere exercise - solution added * fixed image link * mkdocs.yml added module_04:theme_03 exercise link * fixed linking + "prerequisites" * higher quality imgs uploaded * language + visuals edit part 1 * language + visuals edit part 2 * upload images * language + visuals edit part 3 * image size edit * language + visuals edit part 1 * language + visuals edit part 2 * higher quality imagery uploaded * higher quality imagery uploaded * higher quality imagery uploaded * higher quality imagery uploaded * image compression * image compression * images not being replaced - solution * images not being replaced - solution * Added R script for case study * added content * references * Moved r script from .ipynb to .R, added multitemporal compositing and MNF transform. * added script link * Changed default wd path to be more descriptive --------- Co-authored-by: sedovaad <142995175+sedovaad@users.noreply.github.com> Co-authored-by: srollera <a.sroller@seznam.cz> Co-authored-by: jdvorak <jakub.dvorak@natur.cuni.cz> * M1 rev (#11) * revision of theme 1 raster time series processing tutorial (xarray) * revision of theme 2sentinel2 stac tutorial * revise theme 2 gee python api tutorial * revise point cloud exploration tutorial: metadata and package management recommendations * revise theme 3 landcover classification tutorial * edit environment setup instructions for theme 2 tutorials (simplified, less specific, refer to software page for easier course maintenance) * revise module1.md practical parts overview * simplify environment setup instructions in theme 1 xarray tutorial * revise theme 3 snow cover time series tutorial * revise theme 3 snow cover time series tutorial with excercise * revise theme 4 tutorial on forest disturbance assessment * theme 3 landcover classification tutorial: add import of folium.plugins * revise theme 6 accuracy assessment tutorial * repair link to t6 excercise section in m1 overview * revise classification accuracy metrics * add links to module 2 * add links to #algorithms in m2t5 * add section about feature selection and links to m2t4 * add ml references * add mlxtend package to list of ml tools * add short explanation of CV and bootstrapping with links to literature and to M2T4 * repair internal links * add links to m2 and m3 * add links to m2 and m3 * repair internal links * correct typos * add link to Module 2 Excercise 2 (tools for reference data acquisition) * snow cover maps: add discrete ticks and colormap to colorscale * minor corrections in comments * Added self-eval quizzes * Adapting question 1 * fix typos * add T5 tutorial: Sentinel-1/-2 fusion for surface water monitoring * add link to theme 5 tutorial (S1/S2 fusion) * add link to theme 5 tutorial (S1/S2 fusion) * update theme 5 theory (spatio-temporal data fusion * add lineplot with s1 s2 water extent * Added exercise video and adapted the instructions. --------- Co-authored-by: unknown <andreas.mayr@uibk.ac.at> Co-authored-by: jdvorak <jakub.dvorak@natur.cuni.cz> * Update CITATION.cff (#13) * module 2 developments update (#14) * M1 rev oct (#17) * revision of theme 1 raster time series processing tutorial (xarray) * revision of theme 2sentinel2 stac tutorial * revise theme 2 gee python api tutorial * revise point cloud exploration tutorial: metadata and package management recommendations * revise theme 3 landcover classification tutorial * edit environment setup instructions for theme 2 tutorials (simplified, less specific, refer to software page for easier course maintenance) * revise module1.md practical parts overview * simplify environment setup instructions in theme 1 xarray tutorial * revise theme 3 snow cover time series tutorial * revise theme 3 snow cover time series tutorial with excercise * revise theme 4 tutorial on forest disturbance assessment * theme 3 landcover classification tutorial: add import of folium.plugins * revise theme 6 accuracy assessment tutorial * repair link to t6 excercise section in m1 overview * revise classification accuracy metrics * add links to module 2 * add links to #algorithms in m2t5 * add section about feature selection and links to m2t4 * add ml references * add mlxtend package to list of ml tools * add short explanation of CV and bootstrapping with links to literature and to M2T4 * repair internal links * add links to m2 and m3 * add links to m2 and m3 * repair internal links * correct typos * add link to Module 2 Excercise 2 (tools for reference data acquisition) * snow cover maps: add discrete ticks and colormap to colorscale * minor corrections in comments * Added self-eval quizzes * Adapting question 1 * fix typos * add T5 tutorial: Sentinel-1/-2 fusion for surface water monitoring * add link to theme 5 tutorial (S1/S2 fusion) * add link to theme 5 tutorial (S1/S2 fusion) * update theme 5 theory (spatio-temporal data fusion * add lineplot with s1 s2 water extent * Added exercise video and adapted the instructions. * update t5 water surface tutorial * add figures * revision of t5, add figures, references, excercise * remove comments * update m1 python env yaml file --------- Co-authored-by: unknown <andreas.mayr@uibk.ac.at> Co-authored-by: jdvorak <jakub.dvorak@natur.cuni.cz> * M1 t5 tutorial (#18) * revision of theme 1 raster time series processing tutorial (xarray) * revision of theme 2sentinel2 stac tutorial * revise theme 2 gee python api tutorial * revise point cloud exploration tutorial: metadata and package management recommendations * revise theme 3 landcover classification tutorial * edit environment setup instructions for theme 2 tutorials (simplified, less specific, refer to software page for easier course maintenance) * revise module1.md practical parts overview * simplify environment setup instructions in theme 1 xarray tutorial * revise theme 3 snow cover time series tutorial * revise theme 3 snow cover time series tutorial with excercise * revise theme 4 tutorial on forest disturbance assessment * theme 3 landcover classification tutorial: add import of folium.plugins * revise theme 6 accuracy assessment tutorial * repair link to t6 excercise section in m1 overview * revise classification accuracy metrics * add links to module 2 * add links to #algorithms in m2t5 * add section about feature selection and links to m2t4 * add ml references * add mlxtend package to list of ml tools * add short explanation of CV and bootstrapping with links to literature and to M2T4 * repair internal links * add links to m2 and m3 * add links to m2 and m3 * repair internal links * correct typos * add link to Module 2 Excercise 2 (tools for reference data acquisition) * snow cover maps: add discrete ticks and colormap to colorscale * minor corrections in comments * Added self-eval quizzes * Adapting question 1 * fix typos * add T5 tutorial: Sentinel-1/-2 fusion for surface water monitoring * add link to theme 5 tutorial (S1/S2 fusion) * add link to theme 5 tutorial (S1/S2 fusion) * update theme 5 theory (spatio-temporal data fusion * add lineplot with s1 s2 water extent * Added exercise video and adapted the instructions. * update t5 water surface tutorial * add figures * revision of t5, add figures, references, excercise * remove comments * update m1 python env yaml file * replace non-recognized t5 notebook with earlier, quasi-identical version --------- Co-authored-by: unknown <andreas.mayr@uibk.ac.at> Co-authored-by: jdvorak <jakub.dvorak@natur.cuni.cz> * Zenodo integration (#20) * Added ORCIDs * Fixing unparseable metadata tags * Added script for creating Zenodo-compatible metadata files * Small cahnge to the license file to trigger the automated workflow for creating zenodo-compatible file * Automated update of Zenodo metadata --------- Co-authored-by: jdvorak <jakub.dvorak@natur.cuni.cz> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> * Added DOI badge to readme (#21) * Added Zenodo DOI badge. * Added _about the project_ to website navbar (#22) Co-authored-by: jdvorak <jakub.dvorak@natur.cuni.cz> * M4 dev (#23) * image change * image sizing + zoom * renamed data folder links * update case study titles + links, - ore mts. cs; + spectral separability cs * module 4 case studies title updates * image size change * case study Krkonoše grasslands added exercise parts + script * added usecase Tundra vegetation monitoring in Krkonoše Mountains * added links to usecase grasses Krkonose * added Tundra vegetation monitoring in Krkonoše Mountains use case * fixed use case in the course list * fixed use case in the course list * mkdocs merge fix * Revert "mkdocs merge fix" This reverts commit 51cb6e8. * Revert "Merge branch 'fixingautomerge' into m4_dev" This reverts commit 7013487, reversing changes made to cdf314f. * zenodo integration * Automated update of Zenodo metadata * zenodo integration * cases study spectral separability grass - part 1 upload * cases study spectral separability grass - part 2 upload missing results + images * cases study spectral separability grass - final upload * minor updates --------- Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> * Python environments temporary quick fix (#24) * temporary change: working env yml files + code * Update software_python.md * module 2 content development (#25) --------- Co-authored-by: SinaZumst <120559481+SinaZumst@users.noreply.github.com> Co-authored-by: uw255 <uw255@stud.uni-heidelberg.de> Co-authored-by: Jakub Dvorak <jacobdvorakcz@gmail.com> Co-authored-by: jdvorak <jakub.dvorak@natur.cuni.cz> Co-authored-by: srollera <134652988+srollera@users.noreply.github.com> Co-authored-by: sedovaad <142995175+sedovaad@users.noreply.github.com> Co-authored-by: srollera <a.sroller@seznam.cz> Co-authored-by: unknown <andreas.mayr@uibk.ac.at> Co-authored-by: Andreas Mayr <135836569+a-mayr@users.noreply.github.com> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: AdrianaM-O <117462776+AdrianaM-O@users.noreply.github.com>
3dgeo-heidelberg · Oct 13, 2023 · 60dabfc · 60dabfc
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diff --git a/.github/workflows/cffconvert.yml b/.github/workflows/cffconvert.yml
@@ -0,0 +1,36 @@
+name: cffconvert
+
+on:
+  push:
+    branches-ignore:
+      - main
+    paths:
+      - CITATION.cff
+
+permissions:
+  contents: write
+
+jobs:
+  convert:
+    name: "convert citations"
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out a copy of the repository
+        uses: actions/checkout@v3
+
+      - name: Convert CITATION.cff to Zenodo metadata format
+        uses: citation-file-format/cffconvert-github-action@2.0.0
+        with:
+          args: "--infile ./CITATION.cff --format zenodo --outfile .zenodo.json"
+
+      - name: Commit and push Zenodo metadata
+        run: |
+          if [[ `git status --porcelain` ]]; then
+            git config user.name 'github-actions[bot]'
+            git config user.email 'github-actions[bot]@users.noreply.github.com'
+            git add .zenodo.json
+            git commit -m "Automated update of Zenodo metadata"
+            git push
+           else
+            echo "No changes to the .zotero.json file."
+           fi
diff --git a/.github/workflows/mkdocs-deploy.yml b/.github/workflows/mkdocs-deploy.yml
@@ -19,7 +19,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: 3.x
+          python-version: 3.11
       - run: pip install --upgrade pip && pip install -U urlextract bs4 requests 
       - run: python scripts/link_checker.py
   deploy:
@@ -28,7 +28,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: 3.x
-      - run: pip install --upgrade pip && pip install -U mkdocs mkdocs-jupyter jupyter_contrib_nbextensions
+          python-version: 3.11
+      - run: pip install --upgrade pip && pip install -U mkdocs mkdocs-jupyter jupyter_contrib_nbextensions notebook==6.5.5
       - run: git config user.name 'github-actions[bot]' && git config user.email 'github-actions[bot]@users.noreply.github.com'
       - run: mkdocs gh-deploy --config-file mkdocs/mkdocs.yml --force --clean
diff --git a/.zenodo.json b/.zenodo.json
@@ -0,0 +1,12 @@
+{
+  "creators": [
+    {
+      "name": "E-TRAINEE Development Team"
+    }
+  ],
+  "description": "E-learning course on Time Series Analysis in Remote Sensing for Understanding Human-Environment Interactions (E-TRAINEE) was developed by research groups from four partner universities – Charles University, Heidelberg University, University of Innsbruck, and University of Warsaw.",
+  "license": {
+    "id": "CC-BY-SA-4.0"
+  },
+  "title": "E-TRAINEE - E-learning course on Time Series Analysis in Remote Sensing for Understanding Human-Environment Interactions"
+}
diff --git a/CITATION.cff b/CITATION.cff
@@ -1,54 +1,77 @@
 cff-version: 1.2.0
-message: "If you use the course material, please cite it as below."
+
+title: >-
+  E-TRAINEE - E-learning course on Time Series Analysis in
+  Remote Sensing for Understanding Human-Environment
+  Interactions
+
+message: 'If you use this course material, please cite it as below.'
+
 authors:
-  - family-names: E-TRAINEE Development Team
-title: "E-TRAINEE - E-learning course on Time Series Analysis in Remote Sensing for Understanding Human-Environment Interactions"
-version: 0.1
-date-released: 2023-06-30
-license: ["MIT License","CC-BY-SA-4.0"]
-repository-code: "https://github.com/3dgeo-heidelberg/etrainee"
-url: "https://web.natur.cuni.cz/gis/etrainee"
-identifiers:
-  - type: doi
-    value: NA
-	description: The versioned DOI for the version 1.0 of the Citation File Format.
+  - name: E-TRAINEE Development Team
+
+repository-code: 'https://github.com/3dgeo-heidelberg/etrainee'
+
+url: 'https://3dgeo-heidelberg.github.io/etrainee'
+
+abstract: >-
+  E-learning course on Time Series Analysis in Remote Sensing
+  for Understanding Human-Environment Interactions (E-TRAINEE)
+  was developed by research groups from four partner
+  universities – Charles University, Heidelberg University,
+  University of Innsbruck, and University of Warsaw.
+
+license: CC-BY-SA-4.0
+
 references:
   - authors:
       - family-names: Potůčková
         given-names: M.
+        orcid: "https://orcid.org/0000-0002-8760-790X"
       - family-names: Albrechtová
         given-names: J.
+        orcid: "https://orcid.org/0000-0001-6912-1992"
       - family-names: Anders
         given-names: K.
+        orcid: "https://orcid.org/0000-0001-5698-7041"
       - family-names: Červená
         given-names: L.
+        orcid: "https://orcid.org/0000-0001-5246-1106"
       - family-names: Dvořák
         given-names: J.
+        orcid: "https://orcid.org/0000-0001-7845-7738"
       - family-names: Gryguc
         given-names: K.
+        orcid: "https://orcid.org/0000-0002-8107-6837"
       - family-names: Höfle
         given-names: B.
+        orcid: "https://orcid.org/0000-0001-5849-1461"
       - family-names: Lhotáková
-        given-names: Z.	
+        given-names: Z.
+        orcid: "https://orcid.org/0000-0003-3060-641X"
       - family-names: Marcinkowska-Ochtyra
-        given-names: A.	
+        given-names: A.
+        orcid: "https://orcid.org/0000-0002-9080-3899"
       - family-names: Mayr
-        given-names: A.	
+        given-names: A.
+        orcid: "https://orcid.org/0000-0001-8305-4765"
       - family-names: Neuwirthová
-        given-names: E.	
+        given-names: E.
+        orcid: "https://orcid.org/0000-0001-5613-847X"
       - family-names: Ochtyra
-        given-names: A.	
+        given-names: A.
+        orcid: "https://orcid.org/0000-0003-4799-8093"
       - family-names: Rutzinger
-        given-names: M.	
+        given-names: M.
+        orcid: "https://orcid.org/0000-0001-6628-4681"
       - family-names: Šedová
         given-names: A.	
       - family-names: Šrollerů
         given-names: A.	
       - family-names: Kupková
-        given-names: L.		
+        given-names: L.
+        orcid: "https://orcid.org/0000-0002-0270-0516"
     journal: "ISPRS Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences"
     title: "E-TRAINEE: Open e-learning course on time series analysis in remote sensing"
     type: article
-    volume: NA
     year: 2023
-	doi: NA
diff --git a/README.md b/README.md
@@ -1,5 +1,7 @@
 # Welcome to the E-TRAINEE course repository!
 
+[![DOI](https://zenodo.org/badge/643862021.svg)](https://zenodo.org/badge/latestdoi/643862021)
+
 This repository hosts the **E-TRAINEE course on Time Series Analysis in Remote Sensing for Understanding Human-Environment Interactions**, which is an open e-learning course containing four main modules. The first one provides a general overview of methods for remote sensing (RS) time series analysis, and the other three focus on specific processing steps connected to different types of data:
 
 * Module 1: Methods of Time Series Analysis in RS

diff --git a/course/assets/javascripts/quiz_evaluation.js b/course/assets/javascripts/quiz_evaluation.js
@@ -49,6 +49,16 @@ function log_answers() {
 			case "range":
 				ans_dict[element.name] = element.value
 				break;
+			case "checkbox":
+				var element_name = element.name
+				var node_list = document.querySelectorAll("input[name="+element_name+"]:checked");
+				// gather all selected values into a string
+				var out_str = ""
+				for (var node of node_list) {
+					out_str = out_str + "&" + node.nextSibling.data
+				}
+				ans_dict[element.name] = out_str
+				break;
 			case "submit":
 				break;
 			case "output":
@@ -101,10 +111,63 @@ function check_answer(user, correct) {
 	return  user_norm == correct_norm
 }
 
+function check_answer_multiple_choice(user, correct) {
+	// checks if answers are correct
+	var correct_temp = structuredClone(correct)
+	var num_correct = 0
+	for (var user_ans of user) {
+		if (correct_temp.includes(user_ans)) {
+			var drop_idx = correct_temp.indexOf(user_ans)
+			correct_temp.splice(drop_idx, 1)
+			num_correct = num_correct + 1
+		}
+	}
+	// is answer correct?
+	if (num_correct == correct.length && num_correct == user.length-1) {
+		return "correct"
+	// is answer wrong?
+	} else if (num_correct == 0) {
+		return "wrong"
+	// otherwise it is partially correct
+	} else {
+		return "partially"
+	}
+}
+
+function format_correct_list(in_list) {
+	if (in_list.length > 1) {
+		var out_str = ' the correct answers are "' + in_list.join('" and "') + '"'
+	} else {
+		var out_str = ' the correct answer is "' + in_list + '"'
+	}
+	return out_str
+}
+
+function eval_multiple_choice(ans, out_element, ans_count, correct_list) {
+	var correct_str =  format_correct_list(correct_list)
+	switch(ans) {
+		case "correct":
+			ans_count["correct"] = ans_count["correct"] + 1
+			out_element.value = "Correct"
+			out_element["style"] = "background-color: #7DCEA0; padding: 3pt 15pt;"
+			break;
+		case "partially":
+			ans_count["partially"] = ans_count["partially"] + 1
+			out_element.value = "Your answer was partially correct," + correct_str
+			out_element["style"] = "background-color: #F7DC6F; padding: 3pt 15pt;"
+			break;
+		case "wrong":
+			ans_count["wrong"] = ans_count["wrong"] + 1
+			out_element.value = "Sorry," + correct_str
+			out_element["style"] = "background-color: #F1948A; padding: 3pt 15pt;"
+			break;
+	}
+}
+
 function display_messages(answers, answers_correct, answer_elements, q_types) {
 	// displays messages
 	// go through individual answers
-	var ans_count = {correct:0, wrong:0}
+	var ans_count = {correct:0, wrong:0, partially:0}
 
 	for (var [key, value] of Object.entries(answers)) {
 		// get correct answer
@@ -122,6 +185,15 @@ function display_messages(answers, answers_correct, answer_elements, q_types) {
 		} else if (q_types[key] == 'text' || q_types[key] == 'textarea') {
 			out_element.value = 'Consider if your answer aligns with our: ' + value_correct
 			out_element["style"] = "background-color: #D7DBDD; padding: 3pt 15pt;"
+		// Was this a multiple choice question? - evaluate how corect it was
+		} else if (q_types[key] == 'checkbox') {
+			// convert answer strings to arrays
+			var value_parts = value.split("&");
+			var value_correct_parts = value_correct.split("&");
+			// Check how correct was the answer
+			var checked_multiple_choice = check_answer_multiple_choice(value_parts, value_correct_parts)
+			// display message based on correctness
+			eval_multiple_choice(checked_multiple_choice, out_element, ans_count, value_correct_parts)
 		// is the answer correct?
 		} else if (check_answer(value, value_correct)) {
 			ans_count["correct"] = ans_count["correct"] + 1
@@ -144,10 +216,10 @@ function display_overall(ans_dict) {
 	var overall_element = document.getElementById("output_overall")
 	overall_element["style"] = "background-color: #D7DBDD; padding: 3pt 15pt;"
 	// compute the number of answered questions
-	var answered_questions = ans_dict["correct"] + ans_dict["wrong"]
+	var answered_questions = ans_dict["correct"] + ans_dict["wrong"] + ans_dict["partially"]
 
 	// Display different messages based on how many questions the user got wrong
-	if (ans_dict["wrong"] < 4) {
+	if (ans_dict["wrong"] + ans_dict["partially"] < 3) {
 		overall_element.value = "Congratulations, you had " + ans_dict["correct"] + " answers correct out of " + answered_questions + " answered questions."
 	} else {
 		overall_element.value = "You had " + ans_dict["correct"] + " answers correct out of " + answered_questions + " answered questions, please consider reviewing the relevant sections again."