+
diff --git a/interpretation/js/graphs.js b/interpretation/js/graphs.js
index fe8d87c..8858405 100644
--- a/interpretation/js/graphs.js
+++ b/interpretation/js/graphs.js
@@ -108,6 +108,7 @@ function plotIntensityDiagram(hover) {
var specimen = getSelectedSpecimen();
var intensities = new Array();
+ var categories = new Array();
var hoverIndex = null;
specimen.steps.forEach(function(step, i) {
@@ -122,11 +123,11 @@ function plotIntensityDiagram(hover) {
hoverIndex = intensities.length;
}
- // Get the treatment step as a number
- var treatmentStep = extractNumbers(step.step);
+ // Use categories to stop mixing AF / TH
+ categories.push(step.step)
intensities.push({
- "x": treatmentStep,
+ "x": i,
"y": new Coordinates(step.x, step.y, step.z).length,
"stepIndex": i
});
@@ -217,7 +218,7 @@ function plotIntensityDiagram(hover) {
"zIndex": 0
});
- createIntensityDiagram(hover, plotSeries);
+ createIntensityDiagram(hover, plotSeries, categories);
}
@@ -447,6 +448,7 @@ function plotZijderveldDiagram(hover) {
"chart": {
"animation": false,
"id": "zijderveld-container",
+ "height": 500,
"zoomType": "xy",
"events": {
"load": resetMarkerSize
@@ -833,7 +835,7 @@ function resetMarkerSize() {
}
-function createIntensityDiagram(hover, series) {
+function createIntensityDiagram(hover, series, categories) {
/*
* Function createIntensityDiagram
@@ -894,6 +896,7 @@ function createIntensityDiagram(hover, series) {
"formatter": intensityTooltip
},
"xAxis": {
+ "categories": categories,
"title": {
"text": "Demagnetization steps"
}
@@ -1099,6 +1102,7 @@ function eqAreaProjection(hover) {
Highcharts.chart(CHART_CONTAINER, {
"chart": {
"polar": true,
+ "height": 500,
"events": {
"load": resetMarkerSize
},
diff --git a/interpretation/js/importing.js b/interpretation/js/importing.js
index d443464..d0593a0 100644
--- a/interpretation/js/importing.js
+++ b/interpretation/js/importing.js
@@ -700,16 +700,8 @@ function importJR6(file) {
var P3 = Number(line.slice(71, 74));
var P4 = Number(line.slice(74, 77));
- // Support for these orientation parameters
- if(P1 !== 12 || P2 !== 0 || P3 !== 12) {
- throw(new Exception("The AGICO orientation format is not supported. Supported: {12, 0, 12, *}."));
- }
-
- // P4 0 means (dip direction / dip) notation is used
- // We use bedding strike so subtract 90
- if(P4 === 0) {
- beddingStrike -= 90;
- }
+ // Convert AGICO orientations
+ orientations = convertAgico(P1, P2, P3, P4, coreAzimuth, coreDip, beddingStrike, beddingDip);
if(!specimenSortObject.hasOwnProperty(sampleName)) {
specimenSortObject[sampleName] = {
@@ -729,10 +721,10 @@ function importJR6(file) {
"sample": sampleName,
"name": sampleName,
"volume": 10.0,
- "beddingStrike": 0,
- "beddingDip": 0,
- "coreAzimuth": coreAzimuth,
- "coreDip": coreDip,
+ "beddingStrike": orientations.beddingStrike,
+ "beddingDip": orientations.beddingDip,
+ "coreAzimuth": orientations.coreAzimuth,
+ "coreDip": orientations.coreDip,
"interpretations": new Array()
}
@@ -750,6 +742,55 @@ function importJR6(file) {
}
+function convertAgico(P1, P2, P3, P4, coreAzimuth, coreDip, beddingStrike, beddingDip) {
+
+ /*
+ * function convertAgico
+ * Converts AGICO orientation parameters to paleomagnetism.org parameters.
+ *
+ * P1 P2 P3 P4
+ * 12 00 12 90
+ * P1 means arrow is measured point to inside core (is fine)
+ * P2 0 Means dip of frontal side is measured (i.e. hade) (90 when horizontal)
+ * P3 Means measured in field (is fine)
+ * P4 90 means strike (RHR) and dip are measured.. same convention
+ */
+
+ if(P1 !== 12) {
+ throw("P1 parameter " + P1 + " not supported. Only the value {12} is supported.");
+ }
+
+ // Is measuring
+ if(P2 === 0) {
+ coreDip = 90 - coreDip
+ } else if(P2 === 90) {
+ coreDip = coreDip;
+ } else {
+ throw("P2 parameter not supported. Only the values {0, 90} are supported.");
+ }
+
+ if(P3 !== 12) {
+ throw("P3 parameter " + P3 + " not supported. Only the value {12} is supported.");
+ }
+
+ // P4 90 means RHR.. otherwise dip direction so take - 90
+ if(P4 === 0) {
+ beddingStrike = beddingStrike - 90;
+ } else if(P4 === 90) {
+ beddingStrike = beddingStrike;
+ } else {
+ throw("P4 parameter not supported. Only the values {0, 90} are supported.");
+ }
+
+ return {
+ "coreAzimuth": coreAzimuth,
+ "coreDip": coreDip,
+ "beddingStrike": beddingStrike,
+ "beddingDip": beddingDip
+ }
+
+}
+
function importRS3(file) {
/*
@@ -779,25 +820,16 @@ function importRS3(file) {
let P3 = Number(header.slice(116, 118));
let P4 = Number(header.slice(119, 121));
- // P1 P2 P3 P4
- // 12 00 12 90
- // P1 means arrow is measured point to inside core (is fine)
- // P2 Means dip of frontal side is measured (i.e. hade) (90 when horizontal)
- // P3 Means measured in field (is fine)
- // P4 90 means strike (RHR) and dip are measured.. same convention
- // Confirm AGICO format is supported
- if(P1 !== 12 || P2 !== 0 || P3 !== 12 || P4 !== 90) {
- throw(new Exception("The AGICO orientation format is not supported. Supported: {12, 0, 12, 90}."));
- }
-
// Core parameters (dip = hade)
var coreAzimuth = Number(header.slice(74, 77).trim())
- var coreDip = 90 - Number(header.slice(79, 82).trim());
+ var coreDip = Number(header.slice(79, 82).trim());
// Bedding parameters
var beddingStrike = Number(header.slice(86, 90).trim());
var beddingDip = Number(header.slice(92, 95).trim());
+ var orientations = convertAgico(P1, P2, P3, P4, coreAzimuth, coreDip, beddingStrike, beddingDip);
+
// Go over each demagnetization step
var steps = lines.slice(2).map(function(line) {
@@ -805,7 +837,7 @@ function importRS3(file) {
// Intensity is in A/m
var intensity = 1E6 * Number(line.slice(15, 27));
- var declination = Number(line.slice(29, 33));
+ var declination = Number(line.slice(28, 33));
var inclination = Number(line.slice(34, 39));
var a95 = Number(line.slice(77, 80))
@@ -832,11 +864,11 @@ function importRS3(file) {
"lithology": null,
"sample": sampleName,
"name": sampleName,
- "volume": 10.0,
- "beddingStrike": beddingStrike,
- "beddingDip": beddingDip,
- "coreAzimuth": coreAzimuth,
- "coreDip": coreDip,
+ "volume": null,
+ "beddingStrike": orientations.beddingStrike,
+ "beddingDip": orientations.beddingDip,
+ "coreAzimuth": orientations.coreAzimuth,
+ "coreDip": orientations.coreDip,
"interpretations": new Array()
});
@@ -1320,7 +1352,7 @@ function importCaltech(file) {
line = lines[i];
var stepType = line.slice(0, 2);
- var step = line.slice(2, 6).trim() || "0";
+ var step = line.slice(0, 6).trim() || "0";
var dec = Number(line.slice(46, 51));
var inc = Number(line.slice(52, 57));
diff --git a/js/table.js b/js/table.js
new file mode 100644
index 0000000..246495d
--- /dev/null
+++ b/js/table.js
@@ -0,0 +1,301 @@
+var Table = function(options) {
+
+ /* Class Table
+ * Returns table with content including
+ * search & pagination functionality
+ */
+
+ // Some configuration
+ this.MINIMUM_ITEMS_PER_PAGE = 5;
+ this.MAXIMUM_NUMBER_PAGES = 10;
+
+ this.header = options.header;
+ this.body = options.body;
+ this.search = options.search && this.body.length !== 0;
+
+ // Generate the HTML for this table
+ var content = new Array();
+
+ // Add search box element
+ if(this.search) {
+ content = content.concat([
+ "
",
+ ])
+ }
+
+ content.push("
")
+
+ document.getElementById(options.id).innerHTML = content.join("\n");
+
+ // Get the search & content elements for this table
+ if(this.search) {
+ this.search = document.getElementById(options.id + "-search");
+ this.search.addEventListener("input", this.draw.bind(this));
+ }
+
+ this.id = document.getElementById(options.id + "-content");
+
+ // Dynamically set the number of items per page
+ this.itemsPerPage = Math.max(
+ this.MINIMUM_ITEMS_PER_PAGE,
+ Math.ceil(this.body.length / this.MAXIMUM_NUMBER_PAGES)
+ );
+
+ // Keep track of the active page through pagination
+ this.activeIndex = 0;
+
+ // Draw the initial table
+ this.draw();
+
+}
+
+Table.prototype.draw = function() {
+
+ /* Function Table.draw
+ * Redraws the table by creating the HTML
+ */
+
+ var filteredRows = this.body;
+
+ if(this.search) {
+
+ var searchTerm = this.search.value;
+ var regex = new RegExp("^.*" + searchTerm + ".*$", "i");
+ var filteredRows = this.body.filter(function(x) {
+ for(var i = 0; i < x.length; i++) {
+ if(String(x[i]).match(regex)) {
+ return true;
+ }
+ }
+ });
+
+ }
+
+ var pagination = this.generatePagination(filteredRows);
+
+ this.id.innerHTML = [
+ "
",
+ this.generateTableHead(this.header),
+ this.generateTableBody(filteredRows),
+ "
",
+ pagination
+ ].join("\n");
+
+ // Add listeners to all the page buttons
+ Array.from(this.id.getElementsByClassName("page-item")).forEach(function(x) {
+ x.addEventListener("click", this.setActiveIndex.bind(this, x));
+ }.bind(this));
+
+ // Enable tooltips
+ $('[data-toggle="tooltip"]').tooltip()
+
+}
+
+Table.prototype.generatePaginationList = function(list) {
+
+ /* Function Table.generatePaginationList
+ * Generates all pagination buttons
+ */
+
+ // No results (1 page)
+ if(list.length === 0) {
+ return this.paginationItem(0)
+ }
+
+ if(this.activeIndex * this.itemsPerPage > list.length) {
+ this.activeIndex = Math.floor(list.length / this.itemsPerPage);
+ }
+
+ // Create the number of pages
+ return list.filter(function(_, i) {
+ return (i % this.itemsPerPage) === 0
+ }.bind(this)).map(function(_, i) {
+ return this.paginationItem(i);
+ }.bind(this)).join("\n");
+
+}
+
+Table.prototype.paginationItem = function(index) {
+
+ /* Function Table.paginationItem
+ * Returns HTML representation of a pagination button
+ */
+
+ return "
" + (index + 1) + " ";
+
+}
+
+Table.prototype.getMaxIndex = function() {
+
+ if(this.body.length === this.itemsPerPage) {
+ return 0;
+ } else {
+ return Math.floor(this.body.length / this.itemsPerPage);
+ }
+
+}
+
+Table.prototype.setActiveIndex = function(context) {
+
+ /* Function Table.setActiveIndex
+ * Updates the table on click
+ */
+
+ var children = context.children[0];
+
+ var maxIndex = this.getMaxIndex();
+
+ switch(children.innerHTML) {
+ case "Next":
+ if(this.activeIndex === maxIndex) return;
+ this.activeIndex++;
+ break;
+ case "Previous":
+ if(this.activeIndex === 0) return;
+ this.activeIndex--;
+ break;
+ default:
+ this.activeIndex = Number(children.innerHTML) - 1;
+ break;
+ }
+
+ // Clamp the active index between 0 and max pages
+ this.activeIndex = Math.max(Math.min(maxIndex, this.activeIndex), 0);
+
+ // Redraw
+ this.draw();
+
+}
+
+Table.prototype.generatePagination = function(list) {
+
+ /* function generatePagination
+ * Generates the pagination for the active table
+ */
+
+ if(list.length < this.MINIMUM_ITEMS_PER_PAGE) {
+ return "";
+ }
+
+ if(this.activeIndex * this.itemsPerPage > list.length) {
+ this.activeIndex = Math.floor(list.length / this.itemsPerPage);
+ }
+
+ var endDisabled = this.getMaxIndex() === this.activeIndex;
+ var startDisabled = this.activeIndex === 0;
+
+ return [
+ "
",
+ "",
+ " "
+ ].join("\n");
+
+}
+
+Table.prototype.generateTableHead = function(header) {
+
+ /* Function generateTableHead
+ * Generates the head row of the table
+ */
+
+ return [
+ "
",
+ " ",
+ this.generateTableHeadContent(header),
+ " ",
+ " "
+ ].join("\n");
+
+}
+
+Table.prototype.generateTableBodyContent = function(body) {
+
+ /* Function generateTableBodyContent
+ * Generates the body of the table
+ */
+
+ const startSlice = this.itemsPerPage * this.activeIndex;
+ const endSlice = startSlice + this.itemsPerPage;
+
+ // Slice the data from memory to what is visible & unfiltered
+ return body.slice(startSlice, endSlice).map(function(x) {
+ return "
" + this.generateTableRowContent(x) + " "
+ }.bind(this)).join("\n");
+
+}
+
+Table.prototype.generateTableHeadContent = function(header) {
+
+ /* Function generateTableHeadContent
+ * Generates the actual content of the table header
+ */
+
+ function addTagTH(x) {
+
+ /* Function addTagTH
+ * Generates a TH HTML element
+ */
+
+ return addTag("th", x);
+
+ }
+
+ return header.map(addTagTH).join("\n");
+
+}
+
+
+Table.prototype.generateTableBody = function(body) {
+
+ /* Function generateTableBody
+ * Generates the actual content of the table body
+ */
+
+ return [
+ "
",
+ this.generateTableBodyContent(body),
+ " "
+ ].join("\n");
+
+}
+
+function addTag(tag, x) {
+
+ /* Function addTag
+ * Generate a HTML element
+ */
+
+ return "<" + tag + ">" + x + "";
+
+}
+
+Table.prototype.generateTableRowContent = function(row) {
+
+ /* function generateTableRowContent
+ * Generates single row content for a table
+ */
+
+ function addTagTD(x) {
+
+ /* Function addTagTD
+ * Generates a TD HTML element
+ */
+
+ return addTag("td", x);
+
+ }
+
+ return row.map(addTagTD).join("\n");
+
+}
\ No newline at end of file
diff --git a/js/utils.js b/js/utils.js
index 7138a63..0a953d5 100644
--- a/js/utils.js
+++ b/js/utils.js
@@ -1,5 +1,5 @@
let __DEBUG__ = false;
-const __VERSION__ = "2.0.0";
+let __VERSION__ = "2.0.1";
const __DOI__ = "10.5281/zenodo.3647864"
const RADIANS = Math.PI / 180;
const PROJECTION_TYPE = "AREA";
@@ -42,6 +42,8 @@ if(document.getElementById("enable-sound")) {
window.addEventListener("online", notify.bind(null, "success", "Your connection to the internet has been recovered."));
window.addEventListener("offline", notify.bind(null, "danger", "Your connection to the internet was dropped."));
+var openedCollection;
+
function padLeft(nr, n){
return Array(n - String(nr).length + 1).join("0") + nr;
}
@@ -221,6 +223,7 @@ function addSiteWindowWrapper() {
"color": null,
"type": "collection",
"name": collectionName,
+ "doi": null,
"components": components,
"created": new Date().toISOString(),
"index": collections.length
@@ -1198,7 +1201,7 @@ function readMultipleFiles(files, callback) {
}
// Next queued file: create a new filereader instance
- file = files.pop();
+ file = files.shift();
reader = new FileReader();
// XML should be readable as text
@@ -1277,9 +1280,17 @@ function addFooter() {
* Adds footer to all HTML pages
*/
+ var isBetaVersion = window.location.href.includes("beta");
+
+ if(isBetaVersion) {
+ document.getElementsByClassName("navbar-brand")[0].innerHTML += "
BETA* ";
+ // Modify the version
+ __VERSION__ += "-beta";
+ }
+
document.getElementById("footer-container").innerHTML = new Array(
"
",
- "
Paleomagnetism.org © " + new Date().getFullYear() + ". All Rights Reserved.",
+ "
Paleomagnetism.org " + (isBetaVersion ? " BETA" : "" ) + " © " + new Date().getFullYear() + ". All Rights Reserved.",
"
Version v" + __VERSION__ + " (" + __DOI__ + " ) ",
"
Source Code ",
"
Licensed under
MIT .",
@@ -1957,5 +1968,46 @@ function doiLookup(doi, callback) {
}
+function generateColorPalette() {
+
+ /*
+ * Function generateColorPalette
+ * Generates the color palette for site color picking
+ */
+
+ function createColorItem(color) {
+
+ /*
+ * Function generateColorPalette::createColorItem
+ * Generates a div for a particular color that can be clicked
+ */
+
+ return "
";
+
+ }
+
+ // Choose from a nice saturated gradient
+ const COLOR_PALETTE = new Array(
+ // First row
+ "#F55", "#FA5", "#FF5",
+ "#AF5", "#5F5", "#5FA",
+ "#5FF", "#5AF", "#55F",
+ "#A5F", "#F5F", "#F5A",
+ // Second row
+ "#A00", "#A50", "#AA0",
+ "#5A0", "#0A0", "#0A5",
+ "#0AA", "#05A", "#00A",
+ "#50A", "#A0A", "#A05",
+ // Third row
+ "#FFF", "#DDD", "#AAA",
+ "#888", "#555", "#222",
+ "#000"
+ );
+
+ // Create color bar
+ return COLOR_PALETTE.map(createColorItem).join("");
+
+}
+
// Add the footer to every page that includes the utils
addFooter();
diff --git a/library/index.html b/library/index.html
index ce77efa..0b5d43e 100644
--- a/library/index.html
+++ b/library/index.html
@@ -94,11 +94,12 @@
Paleomagnetism.org 2 - Data Library
Available Publications in Library
+
+
Map showing the geographical distribution of a total of
+
-
-
Map showing the geographical distribution of publications. Hover over publication marker to shows its geographical coverage.
+
diff --git a/library/js/index.js b/library/js/index.js
index 5ae8ecf..162b8da 100644
--- a/library/js/index.js
+++ b/library/js/index.js
@@ -15,6 +15,12 @@ function loadDigitalObjects() {
return notify("danger", "Could not load the list of publications.");
}
+ var nPublications = publications.length;
+ var nCollections = publications.map(x => x.nCollections).reduce((a, b) => a + b, 0);
+ var nSpecimens = publications.map(x => x.nSpecimens).reduce((a, b) => a + b, 0);
+
+ document.getElementById("counter").innerHTML = "
specimens";
+
// Update the map and table with the returned collections
addCollectionsToMap(publications);
addCollectionsToTable(publications);
@@ -30,36 +36,35 @@ function addCollectionsToTable(publications) {
* Adds the returned publications to a table
*/
- const TABLE_CONTAINER = "publication-table";
+ var TABLE_HEADER = new Array("Name", "Author", "Institution", "Description", "Country", "Age", "Created", "DOI");
var rows = publications.map(function(x) {
- return [
- "
"
- ].join("\n");
+
+ if(x.doiInfo) {
+ var author = x.doiInfo.entryTags.author.split(" and ")[0] + " et al., (" + x.doiInfo.entryTags.journal + ", " + x.doiInfo.entryTags.year + ")";
+ } else {
+ var author = x.author;
+ }
+
+ return new Array(
+ "
",
+ author,
+ x.institution,
+ x.description,
+ x.country || "Unconstrained",
+ x.age,
+ //"
" || "N/A"
+ );
});
- // Update the table container
- document.getElementById(TABLE_CONTAINER).innerHTML = [
- "",
- "
",
- "",
- ].concat(rows).join("\n");
+ new Table({
+ "id": "publication-table",
+ "search": true,
+ "header": TABLE_HEADER,
+ "body": rows
+ });
}
@@ -77,8 +82,6 @@ function addMap() {
// Set map options (bounds)
var mapOptions = {
"minZoom": 1,
- "maxBounds": new L.latLngBounds(new L.latLng(-90, -180), new L.latLng(90, 180)),
- "maxBoundsViscosity": 0.5,
"attributionControl": true
}
diff --git a/miscellaneous/index.html b/miscellaneous/index.html
index da215ca..3cced7d 100644
--- a/miscellaneous/index.html
+++ b/miscellaneous/index.html
@@ -102,7 +102,7 @@