ross/penracourses
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

.

Browse Source
This commit is contained in:
Ross
2021-12-04 16:09:12 +00:00
parent 11cd73ec64
commit 39e93932b7
8 changed files with 427 additions and 8380 deletions
Download Patch File Download Diff File Expand all files Collapse all files
static/css/dicomViewer.css
+1 -1
View File
@@ -44,7 +44,7 @@
color: lightblue;
}
.single-dicom-viewer {
.cornerstone-element {
position: relative;
height: 100%;
}
static/js/anatomy.js
+108 -108
View File
@@ -370,114 +370,114 @@ function setUpDicom(element) {
}
function keyUpHandler(e) {
if (e.key == "Control") {
dicomViewer.registerPrimaryDicomInterface(e);
window.control_pressed = false;
}
}
function keyDownHandler(e) {
// Ignore our custom keybindings if we are currently in a field that
// accepts some kind of input
if ($("*:focus:not(disabled)").is("textarea, input")) {
// unless a modifier key is pressed (not shift)
if (e.altKey ? true : false || e.ctrlKey ? true : false) {} else {
return;
}
}
if (e.key == "Control") {
if (window.control_pressed == false) {
window.control_pressed = true;
dicomViewer.registerAltDicomInterface(e);
}
}
var charCode = typeof e.which == "number" ? e.which : e.keyCode;
console.log(e, charCode);
function numberKeyPressed(e, x) {
if (e.altKey ? true : false) {
dicomViewer.selectThumb(x);
e.preventDefault();
} else {}
}
switch (charCode) {
case 13: // Return
if (e.shiftKey ? true : false) {
//$(".next-button:last").click();
} else {
//$(".check-button:last").click();
}
break;
case 32: // Space
if (e.shiftKey ? true : false) {
//$(".previous-button:last").click();
} else {
//$(".next-button:last").click();
}
e.preventDefault(); // Needed to stop the default action (scroll)
break;
case 46: // .
//toggleFlagged();
break;
// Numbers 1-9 select the corresponding answer (if it exists)
// TODO: fix for multi question questions
case 49: // 1
numberKeyPressed(e, 0);
break;
case 50: // 2
numberKeyPressed(e, 1);
break;
case 51: // 3
numberKeyPressed(e, 2);
break;
case 52: // 4
numberKeyPressed(e, 3);
break;
case 53: // 5
numberKeyPressed(e, 4);
break;
case 54: // 6
numberKeyPressed(e, 5);
break;
case 55: // 7
numberKeyPressed(e, 6);
break;
case 56: // 8
numberKeyPressed(e, 7);
break;
case 57: // 9
numberKeyPressed(e, 8);
break;
case 72: // H
previousQuestion();
break;
case 76: // L
//nextQuestion();
break;
case 102: // f
//$("#filter-toggle").click();
break;
case 103: // g
//$("#options").slideDown("slow");
//$("#goto-question-input").focus();
//e.preventDefault();
break;
// Vim like scrolling (incredibly important)
case 106: // j
//window.scrollBy(0, 25);
break;
case 107: // k
//window.scrollBy(0, -25);
break;
}
}
//function keyUpHandler(e) {
// if (e.key == "Control") {
// dicomViewer.registerPrimaryDicomInterface(e);
// window.control_pressed = false;
// }
//}
//
//function keyDownHandler(e) {
// // Ignore our custom keybindings if we are currently in a field that
// // accepts some kind of input
// if ($("*:focus:not(disabled)").is("textarea, input")) {
// // unless a modifier key is pressed (not shift)
// if (e.altKey ? true : false || e.ctrlKey ? true : false) {} else {
// return;
// }
// }
//
// if (e.key == "Control") {
// if (window.control_pressed == false) {
// window.control_pressed = true;
// dicomViewer.registerAltDicomInterface(e);
// }
// }
//
// var charCode = typeof e.which == "number" ? e.which : e.keyCode;
// console.log(e, charCode);
//
// function numberKeyPressed(e, x) {
// if (e.altKey ? true : false) {
// dicomViewer.selectThumb(x);
// e.preventDefault();
// } else {}
// }
//
// switch (charCode) {
// case 13: // Return
// if (e.shiftKey ? true : false) {
// //$(".next-button:last").click();
// } else {
// //$(".check-button:last").click();
// }
// break;
// case 32: // Space
// if (e.shiftKey ? true : false) {
// //$(".previous-button:last").click();
// } else {
// //$(".next-button:last").click();
// }
// e.preventDefault(); // Needed to stop the default action (scroll)
// break;
// case 46: // .
// //toggleFlagged();
// break;
//
// // Numbers 1-9 select the corresponding answer (if it exists)
// // TODO: fix for multi question questions
// case 49: // 1
// numberKeyPressed(e, 0);
// break;
// case 50: // 2
// numberKeyPressed(e, 1);
// break;
// case 51: // 3
// numberKeyPressed(e, 2);
// break;
// case 52: // 4
// numberKeyPressed(e, 3);
// break;
// case 53: // 5
// numberKeyPressed(e, 4);
// break;
// case 54: // 6
// numberKeyPressed(e, 5);
// break;
// case 55: // 7
// numberKeyPressed(e, 6);
// break;
// case 56: // 8
// numberKeyPressed(e, 7);
// break;
// case 57: // 9
// numberKeyPressed(e, 8);
// break;
// case 72: // H
// previousQuestion();
// break;
// case 76: // L
// //nextQuestion();
// break;
//
// case 102: // f
// //$("#filter-toggle").click();
// break;
// case 103: // g
// //$("#options").slideDown("slow");
// //$("#goto-question-input").focus();
// //e.preventDefault();
// break;
//
// // Vim like scrolling (incredibly important)
// case 106: // j
// //window.scrollBy(0, 25);
// break;
// case 107: // k
// //window.scrollBy(0, -25);
// break;
// }
//}
function create_popup_window(url, title) {
static/js/cornerstone/cornerstone.min.js
Vendored
+3 -3
View File
File diff suppressed because one or more lines are too long
static/js/cornerstone/cornerstoneMath.min.js
Vendored
+3 -3
View File
File diff suppressed because one or more lines are too long
static/js/cornerstone/cornerstoneWADOImageLoader.js
+3 -8077
View File
File diff suppressed because one or more lines are too long
static/js/cornerstone/dicomParser.min.js
Vendored
+3 -17
View File
File diff suppressed because one or more lines are too long
static/js/dicomViewer.js
+198 -63
View File
@@ -9,17 +9,22 @@ cornerstoneBase64ImageLoader.external.cornerstone = cornerstone;
cornerstoneWebImageLoader.external.cornerstone = cornerstone;
cornerstoneWADOImageLoader.external.cornerstone = cornerstone;
cornerstoneTools.init();
cornerstoneTools.init({ keyboardEnabled: true });
let tool_state = {};
export function loadCornerstone(main_element, db, images, annotations_to_load, load_as_stack = false) {
// canvas-panel holds the enabled elements and all tools / menus
main_element.append("<div class='canvas-panel'></div>");
const canvas_panel = $("<div class='canvas-panel'></div>");
main_element.append(canvas_panel);
main_element[0].dataset.collapsed = "none";
$(".canvas-panel").append($("<div class='single-dicom-viewer'></div>"));
$(".canvas-panel").append($(`<div id='dicom-summary-panel'>
const cornerstone_element = $("<div class='cornerstone-element'></div>");
const element = cornerstone_element.get(0);
canvas_panel.append(cornerstone_element);
canvas_panel.append($(`<div id='dicom-summary-panel'>
<span id="dicom-summary-close" class="close-button"><a href="#">close</a></span>
<div class="container-fluid">
<h1>DICOM Summary</h1>
@@ -309,16 +314,14 @@ export function loadCornerstone(main_element, db, images, annotations_to_load, l
</div>
</div>`));
let single_dicom_viewer = main_element.find(".single-dicom-viewer").get(0);
//console.log(single_dicom_viewer);
$(".canvas-panel").append($(`<div id='dicom-log-panel'>
canvas_panel.append($(`<div id='dicom-log-panel'>
<span id="dicom-log-close" class="close-button"><a href="#">close</a></span>
</div>`));
// Add generic settings menus to canvas-panel
$(".canvas-panel").append(
$(`<div id='dicom-settings-panel'>
$(`<div id='dicom-settings-panel'>
<span id="dicom-settings-close" class="close-button"><a href="#">close</a></span>
<span class="view-log-button"><a href="#">view log</a></span>
<h3>Image viewer settings:</h3>
@@ -380,7 +383,7 @@ export function loadCornerstone(main_element, db, images, annotations_to_load, l
</div>
</div>`)
)
)
.append($("<span id='dicom-toggle-mode-button' class='dicom-button' title='toggle stack/thumbnail view'>↻</span>"))
.append($("<span id='dicom-fullscreen-button' class='dicom-button' title='toggle stack/thumbnail view'>⛶</span>"))
.append($("<span id='dicom-settings-button' class='dicom-button' title='open settings'>&#9881;</span>"))
@@ -398,7 +401,7 @@ export function loadCornerstone(main_element, db, images, annotations_to_load, l
</div>`)
);
$(single_dicom_viewer).append(
cornerstone_element.append(
$(
"<div id='dicom-overlay'>Image <span id='current_image_number'></span> of <span id='total_image_number'></span><br />wc: <span id='wc'></span> ww: <span id='ww'></span></div>"
)
@@ -417,15 +420,13 @@ export function loadCornerstone(main_element, db, images, annotations_to_load, l
$("#dicom-window-panel button").each((n, el) => {
$(el).click((e) => {
//console.log(e);
//console.log(e.target);
let button_id = e.target.id;
let [ww, wc] = window_presets[button_id];
let viewport = cornerstone.getViewport(single_dicom_viewer);
let viewport = cornerstone.getViewport(element);
viewport.voi.windowWidth = parseFloat(ww);
viewport.voi.windowCenter = parseFloat(wc);
cornerstone.setViewport(single_dicom_viewer, viewport);
cornerstone.setViewport(element, viewport);
e.preventDefault();
e.stopPropagation();
@@ -454,6 +455,13 @@ export function loadCornerstone(main_element, db, images, annotations_to_load, l
$("#dicom-settings-panel").toggle();
});
$("#dicom-info-button").click(e => {
try {
// todo improve
dumpDataSet(cornerstone.getEnabledElement(element).image.data);
} catch {
console.log("unable to extract dicom data")
}
$("#dicom-summary-panel").toggle();
});
$("#dicom-fullscreen-button").click(e => {
@@ -486,7 +494,7 @@ export function loadCornerstone(main_element, db, images, annotations_to_load, l
$("#dicom-window-panel").show();
$(e.target).removeClass("dicom-button-highlight");
}
resizeHandler();
resizeHandler(element);
//loadCornerstone(main_element, db, images, annotations_to_load, stack)
});
@@ -497,7 +505,6 @@ export function loadCornerstone(main_element, db, images, annotations_to_load, l
images = [images];
}
//console.log("Images", images)
//let annotations = [];
//if (annotations_to_load) {
@@ -510,11 +517,9 @@ export function loadCornerstone(main_element, db, images, annotations_to_load, l
if (!Array.isArray(annotations)) {
annotations = [annotations];
}
//console.log("annon", annotations);
function loadAnnotation(imageId, annotation) {
//console.log("loadAnnotations", imageId, annotation);
const toolStateManager = cornerstoneTools.globalImageIdSpecificToolStateManager;
if (annotation == undefined || annotation.length < 1 || annotation == [undefined]) {
@@ -529,7 +534,6 @@ export function loadCornerstone(main_element, db, images, annotations_to_load, l
}
async function load(images, annotations) {
//console.log("LOAD", images);
let imageIds = [];
for (let i = 0; i < images.length; i++) {
let data_url = images[i];
@@ -593,12 +597,16 @@ export function loadCornerstone(main_element, db, images, annotations_to_load, l
imageIds
};
//cornerstone.loadAndCacheImage(imageIds[0]).then(function(image) {
//console.log("load and cache", imageIds[0])
cornerstone.loadAndCacheImage(imageIds[0]).then(function (image) {
//console.log("LOAD and cache, then", image);
loadCornerstoneMainImage(single_dicom_viewer, image, stack, db, load_as_stack);
})
//console.log("LOAD and cache, then", image);
loadCornerstoneMainImage(element, image, stack, db, load_as_stack);
let load_annotation_image = true;
if (load_annotation_image) {
getNextAnnotationImage(element)
}
})
.catch((err, err2) => {
console.log(err);
$("#dicom-log-panel").append("<br/>").append(err.stack);
@@ -636,13 +644,12 @@ export function loadCornerstone(main_element, db, images, annotations_to_load, l
"</span></div>"
);
$("#image-thumbs").append(thumb);
$("#thumb-" + id).click(selectThumbClick).mousedown(stopEvent);
$("#thumb-" + id).click((evt) => { selectThumbClick(evt, element) }).mousedown(stopEvent);
let image_url = images[id];
let img;
//console.log("load thumb", image_url);
if (image_url.startsWith("data")) {
// based (image) data url, just load the image directly
@@ -670,7 +677,7 @@ export function loadCornerstone(main_element, db, images, annotations_to_load, l
);
cornerstone.loadAndCacheImage(imageId).then(function (image) {
loadCornerstoneThumb(image, id);
});
});
});
}
} else {
@@ -703,12 +710,124 @@ export function loadCornerstone(main_element, db, images, annotations_to_load, l
}
load(images, annotations);
main_element.keydown((evt) => { keyDownHandler(evt, element) });
main_element.keyup((evt) => { keyUpHandler(evt, element) });
}
function keyUpHandler(e, element) {
if (e.key == "Control") {
registerPrimaryDicomInterface(element);
window.control_pressed = false;
}
}
function keyDownHandler(e, element) {
//// Ignore our custom keybindings if we are currently in a field that
//// accepts some kind of input
//if ($("*:focus:not(disabled)").is("textarea, input")) {
// // unless a modifier key is pressed (not shift)
// if (e.altKey ? true : false || e.ctrlKey ? true : false) {} else {
// return;
// }
//}
if (e.key == "Control") {
if (window.control_pressed != true) {
window.control_pressed = true;
registerAltDicomInterface(e, element);
}
}
var charCode = typeof e.which == "number" ? e.which : e.keyCode;
function numberKeyPressed(e, x) {
if (e.altKey ? true : false) {
loadStackIndex(x, element);
e.preventDefault();
} else { }
}
switch (charCode) {
case 13: // Return
getNextAnnotationImage(element);
if (e.shiftKey ? true : false) {
//$(".next-button:last").click();
} else {
//$(".check-button:last").click();
}
break;
case 32: // Space
if (e.shiftKey ? true : false) {
//$(".previous-button:last").click();
} else {
//$(".next-button:last").click();
}
e.preventDefault(); // Needed to stop the default action (scroll)
break;
case 46: // .
//toggleFlagged();
break;
// Numbers 1-9 select the corresponding answer (if it exists)
// TODO: fix for multi question questions
case 49: // 1
numberKeyPressed(e, 0);
break;
case 50: // 2
numberKeyPressed(e, 1);
break;
case 51: // 3
numberKeyPressed(e, 2);
break;
case 52: // 4
numberKeyPressed(e, 3);
break;
case 53: // 5
numberKeyPressed(e, 4);
break;
case 54: // 6
numberKeyPressed(e, 5);
break;
case 55: // 7
numberKeyPressed(e, 6);
break;
case 56: // 8
numberKeyPressed(e, 7);
break;
case 57: // 9
numberKeyPressed(e, 8);
break;
case 72: // H
previousQuestion();
break;
case 76: // L
//nextQuestion();
break;
case 102: // f
//$("#filter-toggle").click();
break;
case 103: // g
//$("#options").slideDown("slow");
//$("#goto-question-input").focus();
//e.preventDefault();
break;
// Vim like scrolling (incredibly important)
case 106: // j
//window.scrollBy(0, 25);
break;
case 107: // k
//window.scrollBy(0, -25);
break;
}
}
function loadCornerstoneMainImage(element, image, stack, db, load_as_stack) {
//dumpDataSet(image.data)
//console.log("loadCornerstoneMainImage")
//console.log("load as stack:", load_as_stack)
// It is probably silly to do this each time we load a question
const PanTool = cornerstoneTools.PanTool;
const ZoomTool = cornerstoneTools.ZoomTool;
@@ -723,11 +842,13 @@ function loadCornerstoneMainImage(element, image, stack, db, load_as_stack) {
const RectangleRoiTool = cornerstoneTools.RectangleRoiTool;
const LengthTool = cornerstoneTools.LengthTool;
//console.log("enable element", element);
cornerstone.enable(element);
element.tabIndex = 0;
cornerstone.displayImage(element, image);
//cornerstoneTools.keyboardInput.enable(element);
cornerstoneTools.addStackStateManager(element, ["stack"]);
cornerstoneTools.addToolState(element, "stack", stack);
@@ -746,8 +867,8 @@ function loadCornerstoneMainImage(element, image, stack, db, load_as_stack) {
cornerstoneTools.addToolForElement(element, ArrowAnnotateTool, {
configuration: {
getTextCallback: () => {},
changeTextCallback: () => {},
getTextCallback: () => { },
changeTextCallback: () => { },
allowEmptyLabel: true,
renderDashed: false,
drawHandles: false,
@@ -765,7 +886,8 @@ function loadCornerstoneMainImage(element, image, stack, db, load_as_stack) {
},
});
cornerstoneTools.setToolEnabledForElement(element, "ArrowAnnotate");
//cornerstoneTools.setToolEnabledForElement(element, "ArrowAnnotate");
//cornerstoneTools.setToolEnabledForElement(element, ArrowAnnotateTool);
let available_tools = [
@@ -789,8 +911,8 @@ function loadCornerstoneMainImage(element, image, stack, db, load_as_stack) {
//$("#middle-mouse-dicom").append(option);
//$("#right-mouse-dicom").append(option);
});
$(".mouse-binding-select").on("change", function (e) {
changeMouseBinding(e, db);
$(".mouse-binding-select").on("change", function (evt) {
changeMouseBinding(evt, db, element);
});
// Set default tools
@@ -799,7 +921,6 @@ function loadCornerstoneMainImage(element, image, stack, db, load_as_stack) {
$("#primary-mouse-binding .mouse-binding-select[data-button=4]").val("Zoom");
//cornerstoneTools.setToolActive("Pan", { mouseButtonMask: 1 });
//console.log(load_as_stack);
if (load_as_stack) {
cornerstoneTools.setToolActiveForElement(element, "StackScrollMouseWheel", {
mouseButtonMask: 3
@@ -821,10 +942,11 @@ function loadCornerstoneMainImage(element, image, stack, db, load_as_stack) {
"WwwcRegion"
);
loadPrimaryDicomInterface(db);
loadPrimaryDicomInterface(db, element);
loadAltDicomInterface(db);
element.addEventListener("cornerstoneimagerendered", onImageRendered);
//element.addEventListener("cornerstonetoolskeydown", keyDownHandler);
//setDicomCanvasNonFullscreen(element);
cornerstone.reset(element);
@@ -846,9 +968,9 @@ function loadCornerstoneMainImage(element, image, stack, db, load_as_stack) {
// .get(0)
// .addEventListener("change", changeControlSelection);
resizeHandler();
resizeHandler(element);
window.addEventListener("resize", resizeHandler);
window.addEventListener("resize", () => { resizeHandler(element) });
element.addEventListener(
"contextmenu",
function (e) {
@@ -864,14 +986,13 @@ function loadCornerstoneMainImage(element, image, stack, db, load_as_stack) {
});
}
function resizeHandler() {
let element = document.getElementsByClassName("single-dicom-viewer")[0];
function resizeHandler(element) {
let h = window.innerHeight - $("#header").height() - 16;
$(element).height(h);
cornerstone.resize(element, true);
}
async function loadPrimaryDicomInterface(db) {
async function loadPrimaryDicomInterface(db, element) {
const bindings = await dicom_settings_db.mouse_bindings.where({
mode: "0"
}).toArray().catch((err) => {
@@ -884,7 +1005,7 @@ async function loadPrimaryDicomInterface(db) {
sel.value = b.tool;
//sel.dispatchEvent(new Event("change"));
});
registerPrimaryDicomInterface();
registerPrimaryDicomInterface(element);
}
async function loadAltDicomInterface(db) {
@@ -904,14 +1025,6 @@ async function loadAltDicomInterface(db) {
// Called when the dicom image is loaded / rendered
function onImageRendered(e) {
const eventData = e.detail;
//console.log(e);
try {
// todo improve
dumpDataSet(eventData.image.data);
} catch {
console.log("unable to extract dicom data")
}
// Update ww/wl
$("#wc").text(Math.round(eventData.viewport.voi.windowCenter));
@@ -945,16 +1058,16 @@ function stopEvent(evt) {
evt.stopPropagation();
}
function selectThumbClick(evt) {
function selectThumbClick(evt, element) {
let new_index = evt.currentTarget.dataset.id;
selectThumb(new_index);
loadStackIndex(new_index, element);
evt.preventDefault();
}
export function registerPrimaryDicomInterface() {
export function registerPrimaryDicomInterface(element) {
console.log("reg primary")
// Set mousetools based upon the selected options
let element = document.getElementsByClassName("single-dicom-viewer")[0];
let selections = $("#primary-mouse-binding select");
selections.each((i, option) => {
cornerstoneTools.setToolActiveForElement(element, option.value, {
@@ -963,11 +1076,12 @@ export function registerPrimaryDicomInterface() {
});
}
export function registerAltDicomInterface(e) {
export function registerAltDicomInterface(e, element) {
// Called when control is pressed
// Set mousetools based upon the selected options
let element = document.getElementsByClassName("single-dicom-viewer")[0];
//let element = document.getElementsByClassName("cornerstone-element")[0];
console.log("reg alt", element)
let selections = $("#secondary-mouse-binding select");
selections.each((i, option) => {
cornerstoneTools.setToolActiveForElement(element, option.value, {
@@ -976,8 +1090,8 @@ export function registerAltDicomInterface(e) {
});
}
function changeMouseBinding(e, db) {
let select = e.currentTarget;
function changeMouseBinding(evt, db, element) {
let select = evt.currentTarget;
let button = select.dataset.button;
let mode = select.dataset.mode;
let tool = select.value;
@@ -985,7 +1099,6 @@ function changeMouseBinding(e, db) {
// Directly activate primary tools (secondary will be activated when modifier
// key is pressed
if (mode == "0") {
let element = document.getElementsByClassName("single-dicom-viewer")[0];
cornerstoneTools.setToolActiveForElement(element, tool, {
mouseButtonMask: parseInt(button)
});
@@ -999,10 +1112,9 @@ function changeMouseBinding(e, db) {
//db.mouse_bindings.put({button: button, mode: mode, tool: tool}).then(loadPrimaryDicomInterface());
}
export function selectThumb(new_index) {
//console.log("select thumb new index", new_index);
export function loadStackIndex(new_index, dicom_element) {
console.log("select new stack index", new_index);
// There must be a better way to do this...
let dicom_element = document.getElementsByClassName("single-dicom-viewer")[0];
if (dicom_element == null) {
return;
}
@@ -1061,4 +1173,27 @@ function dumpDataSet(dataSet) {
$(value).text(text);
});
}
export function getNextAnnotationImage(element) {
const enabled_element = cornerstone.getEnabledElement(element)
const image_ids = enabled_element.toolStateManager.toolState.stack.data[0].imageIds;
const current_image = enabled_element.toolStateManager.toolState.stack.data[0].currentImageIdIndex;
const annotated_images = Object.getOwnPropertyNames(cornerstoneTools.globalImageIdSpecificToolStateManager.toolState);
console.log("getNextAnnotationImage", image_ids, current_image, annotated_images);
if (annotated_images.length > 0) {
let offset = current_image;
for( let i=0; i < image_ids.length; i++) {
console.log("i", i)
let pointer = (i + offset) % image_ids.length;
console.log("pointer", pointer, image_ids[pointer]);
console.log(annotated_images);
if (annotated_images.includes(image_ids[pointer])) {
console.log("load")
loadStackIndex(pointer, element);
}
}
}
}