improve uploading
This commit is contained in:
Ross
@@ -108,7 +108,7 @@
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uploading_el = $(`img[data-input-id='${input.id}'], div[data-input-id='${input.id}']`)
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uploading_el.removeClass("image-ident-loading");
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console.log("found text", l);
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if (l.includes("accesion") || l.includes("number") || l.search(
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if (l.includes("accession") || l.includes("number") || l.search(
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/(ref|rk9|rh8|ra9|rbz)\d+/g) > -1) {
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console.log("Match found ", input);
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$(input).addClass("image-ident-warning");
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@@ -54,7 +54,6 @@ class CaseSchema(ModelSchema):
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model_fields = ["id", "title"]
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@logger.catch()
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@router.post("/upload_dicom", auth=django_auth)
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def upload_dicom(request, files: List[UploadedFile] = File(...)):
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uploaded = []
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@@ -69,7 +68,6 @@ def upload_dicom(request, files: List[UploadedFile] = File(...)):
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uploaded.append((file.name, ud.image_blake3_hash))
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except DuplicateDicom:
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print(ud.check_for_duplicates(ud.image_blake3_hash))
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duplicate.append((file.name, ud.image_blake3_hash))
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pass
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except InvalidDicomError:
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@@ -1110,7 +1110,6 @@ class UncategorisedDicom(models.Model):
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return duplicate
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@logger.catch()
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def save(self, *args, **kwargs):
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"""Override save method to add image hash"""
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if self.image:
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@@ -30,5 +30,7 @@
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Available <a href="https://www.penracourses.org.uk/uploader/insight_rad_up.xml">here</a>
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<h4>Step 3: Integrate the uploader with PACs</h4>
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Whilst in PACs open the settings menu with the keyboard shortcut 'Ctrl+Shift+C'. In the 'General' tab, select 'External Tools' and click 'Add'. Press the Import button and select the xml file you downloaded in Step 2. Modify the file to run path to point the uploader exe downloaded in step 1 (clicking on the 3 dots will allow you to browse and select this file). The remaining fields should have been set via the xml file and should not require modification.
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<h3>Uploading without the uploader tool</h3>
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If you have <b>annonymised</b> dicom files already exported you can uploading them directly using this <a href='{% url "atlas:new_uploads" %}'>form</a>.
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{% endblock %}
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@@ -10,26 +10,156 @@
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Please note this form will not annonymise files. Please ensure that you have done so prior to using it.
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</div>
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<div>This form allows you to quickly upload dicom files to the server. Select the folder containing the dicom files below.</div>
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<div>
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<p>This form allows you to quickly upload dicom files to the server. Select the folder containing the dicom files below. If you wish to upload files directly from Insight you may rather use the <a href='{% url "atlas:help" %}'>Uploader tool.</a></p>
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<details>
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<summary>Help</summary>
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<p>Only valid dicom files will be uploaded. </p>
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<p>It is possible to upload multiple files by selecting the parent (containing) folder. Folders within will then be searched recursively for any valid dicom files.</p>
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<p>Files to be uploaded will be displayed below. </p>
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</details>
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</div>
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<form method="post" enctype="multipart/form-data">
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{% csrf_token %}
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<input type="file" name="dicom_files" id="filepicker" webkitdirectory multiple>
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<input type="submit" value="Upload">
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<button type="button" id="uploadButton">Upload</button>
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</form>
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<div>Selected files:</div>
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<div id="single-dicom-viewer" class="dicom-viewer" data-images="" data-annotations=''></div>
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<ul id="listing"></ul>
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<details id="upload-results"><summary>Upload results</summary>
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<div id="upload-results-list">
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<h5>Uploaded</h5>
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<ul id="uploaded-files"></ul>
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<h5>Duplicates</h5>
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<ul id="duplicate-files"></ul>
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<h5>Failed</h5>
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<ul id="failed-files"></ul>
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</div>
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</details>
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<h4>Selected files:</h4>
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<div id="single-dicom-viewer" class="dicom-viewer" data-images="" data-annotations=''></div>
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<ol id="listing"></ol>
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<div id="loading" class="fullscreen-overlay">
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<div class="progress-block">
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<div id="progress"></div>
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<div class="sk-cube-grid full">
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<div class="sk-cube sk-cube1"></div>
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<div class="sk-cube sk-cube2"></div>
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<div class="sk-cube sk-cube3"></div>
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<div class="sk-cube sk-cube4"></div>
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<div class="sk-cube sk-cube5"></div>
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<div class="sk-cube sk-cube6"></div>
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<div class="sk-cube sk-cube7"></div>
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<div class="sk-cube sk-cube8"></div>
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<div class="sk-cube sk-cube9"></div>
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</div>
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<div id="progress-text">Uploading...</div>
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</div>
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</div>
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{% endblock %}
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{% block js %}
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<script src="{% static 'js/upload_form_helpers.js' %}"></script>
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<script>
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window.to_upload = [];
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window.upload_count = 1;
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function* chunks(arr, n) {
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for (let i = 0; i < arr.length; i += n) {
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yield arr.slice(i, i + n);
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}
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}
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function onUploadButtonClicked(event) {
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event.preventDefault();
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const fileInput = document.getElementById("filepicker");
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const selectedFiles = fileInput.files;
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// Check if any files are selected
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if (selectedFiles.length === 0) {
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alert("Please select at least one file to upload.");
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return;
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}
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//alert(`${window.to_upload.length} files selected. Uploading...`);
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window.upload_results = {
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"uploaded": [],
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"duplicates": [],
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"failed": []
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};
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chunked_files = [...chunks(window.to_upload, 10)];
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$("#loading").show();
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$("#progress-text").text(`Uploading..`);
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for (let i = 0; i < chunked_files.length; i++) {
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uploadFiles(chunked_files[i], i, chunked_files.length);
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}
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}
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function uploadFiles(files_to_upload, current_chunk, total_chunks){
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console.log("uploading", files_to_upload)
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// Create a FormData object to store the form data
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const formData = new FormData();
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// Append each selected file to the FormData object
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for (let i = 0; i < files_to_upload.length; i++) {
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formData.append("files", files_to_upload[i]);
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}
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console.log("formdata", formData)
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const xhr = new XMLHttpRequest();
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xhr.open("POST", "{% url 'api-1:upload_dicom' %}", true);
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xhr.setRequestHeader("X-CSRFToken", "{{ csrf_token }}");
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xhr.onreadystatechange = function () {
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$("#progress-text").text(`Uploading ${window.upload_count} of ${total_chunks} chunks`);
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if (xhr.readyState === XMLHttpRequest.DONE) {
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window.upload_count += 1;
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if (xhr.status === 200) {
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// Handle successful response from the server
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console.log('Files uploaded successfully!');
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console.log(xhr.response);
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window.upload_results["uploaded"].push(...JSON.parse(xhr.response)["uploaded"]);
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window.upload_results["duplicates"].push(...JSON.parse(xhr.response)["duplicates"]);
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window.upload_results["failed"].push(...JSON.parse(xhr.response)["failed"]);
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for (let i = 0; i < JSON.parse(xhr.response)["uploaded"].length; i++) {
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let item = document.createElement("li");
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item.textContent = JSON.parse(xhr.response)["uploaded"][i];
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$("#uploaded-files").append(item);
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}
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for (let i = 0; i < JSON.parse(xhr.response)["duplicates"].length; i++) {
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let item = document.createElement("li");
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item.textContent = JSON.parse(xhr.response)["duplicates"][i];
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$("#duplicate-files").append(item);
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}
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for (let i = 0; i < JSON.parse(xhr.response)["failed"].length; i++) {
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let item = document.createElement("li");
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item.textContent = JSON.parse(xhr.response)["failed"][i];
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$("#failed-files").append(item);
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}
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} else {
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// Handle error response from the server
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console.error('Failed to upload files.');
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alert("Error occurred during file upload. Please try again.");
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}
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if (current_chunk + 1 == total_chunks) {
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$("#loading").hide();
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alert("Uploading complete")
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}
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}
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};
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xhr.send(formData);
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}
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function checkAnnonymisation(byteArray) {
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// We need to setup a try/catch block because parseDicom will throw an exception
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@@ -63,11 +193,11 @@
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for (let i = 0; i < site_codes.length; i++) {
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if (
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accession_number.startsWith(site_codes[i]) ||
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patient_id.startsWith(site_codes[i]) ||
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patient_id.startsWith("pat"))
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{
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not_anon = true;
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}
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patient_id.startsWith(site_codes[i])
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)
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{
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not_anon = true;
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}
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}
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if (not_anon) {
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@@ -88,6 +218,7 @@
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"showMethod": "fadeIn",
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"hideMethod": "fadeOut",
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});
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$("uploadButton").prop("disabled", true);
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}
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// TODO: fix
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@@ -176,12 +307,19 @@
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let output = document.getElementById("listing");
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images = [];
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window.to_upload = [];
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$("#loading").show();
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$("#progress-text").text(`Processing..`);
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n = 0;
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for (const file of file_set) {
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n += 1;
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$("#progress-text").text(`Processing ${file.name} (${n} of ${file_set.length})`);
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//await readFile(file);
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dicom = await readDicomFile(file);
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if (dicom) {
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let item = document.createElement("li");
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item.className = "dicom-file";
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item.textContent = file.webkitRelativePath;
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output.appendChild(item);
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//await readFile(file, item);
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@@ -191,21 +329,23 @@
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console.log(url)
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imageId = `wadouri:${url}`;
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images.push(imageId);
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window.to_upload.push(file);
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const element = $(`<div class='temp-thumb' src=${imageId}></div>`).get(0)
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item.appendChild(element);
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cornerstone.enable(element);
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cornerstone.loadAndCacheImage(imageId).then(function (image) {
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cornerstone.displayImage(element, image);
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$(element).addClass("temp-thumb-large");
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cornerstone.resize(element)
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setTimeout(function () {
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ocr($(element).find("canvas").get(0).toDataURL(), element);
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$(element).removeClass("temp-thumb-large");
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cornerstone.resize(element)
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}, 500);
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let bytesView = image.getPixelData()
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let str = new TextDecoder("utf-8").decode(bytesView, );
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//extractDicomDetails(image.data.byteArray)
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});
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}
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}
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@@ -217,11 +357,58 @@
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"detail": {"images": images, "annontations": undefined}
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});
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$("#loading").hide()
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window.dispatchEvent(event);
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}
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function ocr(url, input) {
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console.log("OCR", input)
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Tesseract.recognize(
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url,
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'eng',
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//{ logger: m => console.log(m) }
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).then(({
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data: {
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text
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}
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}) => {
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l = text.toLowerCase();
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uploading_el = $(`img[data-input-id='${input.id}'], div[data-input-id='${input.id}']`)
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uploading_el.removeClass("image-ident-loading");
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console.log("found text", l);
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if (l.includes("accession") || l.includes("number") || l.search(
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/(ref|rk9|rh8|ra9|rbz)\d+/g) > -1) {
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console.log("Match found ", input);
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$(input).addClass("image-ident-warning");
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uploading_el.addClass("image-ident-warning");
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$("uploadButton").prop("disabled", true);
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toastr.warning(`File does not appear to be annonymised<br/>Image data burned in<br/>${element}`, 'Anonymisation warning', {
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"closeButton": false,
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"debug": false,
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"newestOnTop": false,
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"progressBar": false,
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"positionClass": "toast-top-full-width",
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"preventDuplicates": false,
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"onclick": null,
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"showDuration": "0",
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"hideDuration": "0",
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"timeOut": 0,
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"extendedTimeOut": 0,
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"showEasing": "swing",
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"hideEasing": "linear",
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"showMethod": "fadeIn",
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"hideMethod": "fadeOut",
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});
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} else {
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$(input).addClass("image-ident-ok");
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}
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})
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}
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$(document).ready(function () {
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document.getElementById("filepicker").addEventListener(
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"change",
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@@ -237,6 +424,11 @@
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},
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false,
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);
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// Add event listener to the button element
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const uploadButton = document.getElementById("uploadButton");
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uploadButton.addEventListener("click", onUploadButtonClicked);
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});
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</script>
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@@ -3,6 +3,7 @@
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{% block content %}
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<h2>Uploaded dicoms</h2>
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User: {{user}}<br/>
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<a href="{% url 'atlas:new_uploads' %}">Upload more dicoms</a><br/>
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{% if not case %}
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<div class="alert alert-info" role="alert">
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Series imported from here will be orphaned (not associated with a case). It is usually better to create a case first and then import directly into the case.
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+144
-1
@@ -130,6 +130,12 @@ button:hover {
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background-color: #52057b;
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}
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button:disabled {
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color: gray;
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background-color: #110119;
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border-color: #110119;
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}
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button a {
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text-decoration: none;
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@@ -1122,4 +1128,141 @@ tr:has(> td > a) {
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.no-list-style {
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list-style-type: none;
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padding-left: 1rem;
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}
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}
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#listing .dicom-file {
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clear: both;
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}
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/* Some fancy loading CSS */
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.sk-cube-grid {
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width: 60px;
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height: 60px;
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}
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.sk-cube-grid .sk-cube {
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width: 33%;
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height: 33%;
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background-color: #4527A0;
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float: left;
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-webkit-animation: sk-cubeGridScaleDelay 1.3s infinite ease-in-out;
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animation: sk-cubeGridScaleDelay 1.3s infinite ease-in-out;
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}
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.sk-cube-grid .sk-cube1 {
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-webkit-animation-delay: 0.2s;
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animation-delay: 0.2s;
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}
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.sk-cube-grid .sk-cube2 {
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-webkit-animation-delay: 0.3s;
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animation-delay: 0.3s;
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}
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.sk-cube-grid .sk-cube3 {
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-webkit-animation-delay: 0.4s;
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animation-delay: 0.4s;
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}
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.sk-cube-grid .sk-cube4 {
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-webkit-animation-delay: 0.1s;
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animation-delay: 0.1s;
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}
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.sk-cube-grid .sk-cube5 {
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-webkit-animation-delay: 0.2s;
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animation-delay: 0.2s;
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}
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.sk-cube-grid .sk-cube6 {
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-webkit-animation-delay: 0.3s;
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animation-delay: 0.3s;
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}
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.sk-cube-grid .sk-cube7 {
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-webkit-animation-delay: 0s;
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animation-delay: 0s;
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}
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.sk-cube-grid .sk-cube8 {
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-webkit-animation-delay: 0.1s;
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animation-delay: 0.1s;
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}
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.sk-cube-grid .sk-cube9 {
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-webkit-animation-delay: 0.2s;
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animation-delay: 0.2s;
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}
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@-webkit-keyframes sk-cubeGridScaleDelay {
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||||
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0%,
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70%,
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||||
100% {
|
||||
-webkit-transform: scale3D(1, 1, 1);
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transform: scale3D(1, 1, 1);
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}
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||||
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35% {
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||||
-webkit-transform: scale3D(0, 0, 1);
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transform: scale3D(0, 0, 1);
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||||
}
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||||
}
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||||
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||||
@keyframes sk-cubeGridScaleDelay {
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||||
|
||||
0%,
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||||
70%,
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||||
100% {
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||||
-webkit-transform: scale3D(1, 1, 1);
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||||
transform: scale3D(1, 1, 1);
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||||
}
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||||
|
||||
35% {
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||||
-webkit-transform: scale3D(0, 0, 1);
|
||||
transform: scale3D(0, 0, 1);
|
||||
}
|
||||
}
|
||||
|
||||
.progress-block {
|
||||
position: fixed;
|
||||
top: 50%;
|
||||
left: 50%;
|
||||
transform: translate(-50%, -50%);
|
||||
font-size: smaller;
|
||||
}
|
||||
|
||||
#progress-text {
|
||||
position: absolute;
|
||||
}
|
||||
|
||||
.fullscreen-overlay {
|
||||
position: fixed;
|
||||
display: none;
|
||||
width: 100%;
|
||||
height: 100%;
|
||||
top: 0;
|
||||
left: 0;
|
||||
right: 0;
|
||||
bottom: 0;
|
||||
background-color: rgba(0, 0, 0, 0.9);
|
||||
z-index: 2;
|
||||
cursor: pointer;
|
||||
color: lightgray;
|
||||
overflow: auto;
|
||||
}
|
||||
|
||||
.fullscreen-overlay-transparent {
|
||||
position: fixed;
|
||||
display: none;
|
||||
width: 100%;
|
||||
height: 100%;
|
||||
top: 0;
|
||||
left: 0;
|
||||
right: 0;
|
||||
bottom: 0;
|
||||
z-index: 2;
|
||||
cursor: pointer;
|
||||
color: lightgray;
|
||||
overflow: auto;
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user