Add patient grouping and selection functionality to user uploads
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Ross
@@ -2802,6 +2802,7 @@ class UncategorisedDicom(models.Model):
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"SliceThickness",
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"SeriesNumber",
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"StudyDate",
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"PatientID",
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)
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tags = {}
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@@ -17,7 +17,97 @@
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{% if series_list %}
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<div id="series-list">
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{% if grouped_series %}
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{% if grouped_patients %}
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{% for patient in grouped_patients %}
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<div class="patient-block mb-4 p-3 border rounded" style="background: rgba(255,255,255,0.015); border-color: rgba(255,255,255,0.08) !important;">
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<div class="patient-header d-flex flex-wrap align-items-center justify-content-between pb-2 mb-3 border-bottom border-secondary">
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<span>
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<i class="bi bi-person-badge me-2 text-info"></i>
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<strong>Patient ID:</strong> <span class="badge bg-secondary font-monospace">{{ patient.patient_id }}</span>
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</span>
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<div class="btn-group">
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<button type="button" class="btn btn-sm btn-outline-primary select-all-patient-btn" title="Select all series for this patient">Select Patient Series</button>
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<button type="button" class="btn btn-sm btn-outline-secondary deselect-all-patient-btn" title="Deselect all series for this patient">Deselect all</button>
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</div>
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</div>
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{% for study_uid, study in patient.studies %}
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<details class="study-block {% if study.partial_imported_uids %}study-block--partial-import{% endif %}" open>
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<summary>
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<strong>{{ study.description|default:"(no description)" }}</strong>
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<small class="text-muted"> ({{ study_uid }}) — {{ study.series|length }} series</small>
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<span class="ms-2">
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<button type="button" class="btn btn-sm btn-outline-secondary select-all-btn" title="Select all in study">Select all</button>
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<button type="button" class="btn btn-sm btn-outline-secondary deselect-all-btn" title="Deselect all in study">Deselect all</button>
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</span>
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</summary>
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{% if study.partial_imported_uids %}
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<div class="alert alert-warning py-2 mt-2 mb-2 d-flex flex-wrap align-items-center justify-content-between gap-2">
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<div>
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<strong>Partial import detected:</strong>
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{{ study.partial_imported_count }} series in this study already exist.
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The highlighted rows can finish importing the remaining images.
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{% if study.matched_existing_series %}
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<div class="small mt-1">
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Existing series in Atlas:
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{% for existing_series in study.matched_existing_series %}
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<a href="{% url 'atlas:series_detail' existing_series.pk %}">{{ existing_series }}</a>{% if not forloop.last %}, {% endif %}
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{% endfor %}
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</div>
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{% endif %}
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</div>
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<button
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type="button"
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class="btn btn-sm btn-warning import-partial-series-btn"
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data-series-uids="{{ study.partial_imported_uids|join:',' }}"
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{% if study.preferred_case_id %}data-case-id="{{ study.preferred_case_id }}"{% endif %}
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>Finish these imports</button>
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</div>
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{% endif %}
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{% if study.import_suggestions %}
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<div class="alert alert-info py-2 mt-2 mb-2">
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<strong>Study already imported:</strong>
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{% for suggestion in study.import_suggestions %}
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<div class="d-flex flex-wrap align-items-center gap-2 mt-1">
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<span>
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Case:
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<a href="{% url 'atlas:case_detail' suggestion.case.pk %}">{{ suggestion.case }}</a>
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({{ suggestion.already_imported_count }} series already imported)
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</span>
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<button
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type="button"
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class="btn btn-sm btn-outline-primary import-missing-series-btn"
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data-case-id="{{ suggestion.case.pk }}"
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data-series-uids="{{ suggestion.missing_uids|join:',' }}"
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>
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Import remaining {{ suggestion.missing_uids|length }} series
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</button>
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</div>
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{% endfor %}
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</div>
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{% endif %}
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<ul class="study-series-list">
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{% for series, n, tags, date in study.series %}
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{% if series in study.partial_imported_uids %}
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{% if case %}
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{% include 'atlas/partials/_series_item.html' with show_tags_link=True series_is_partial=True series_item_classes='series-item--partial-import' import_case_id=case.pk %}
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{% else %}
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{% include 'atlas/partials/_series_item.html' with show_tags_link=True series_is_partial=True series_item_classes='series-item--partial-import' import_case_id=study.preferred_case_id %}
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{% endif %}
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{% else %}
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{% if case %}
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{% include 'atlas/partials/_series_item.html' with show_tags_link=True series_is_partial=False series_item_classes='' import_case_id=case.pk %}
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{% else %}
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{% include 'atlas/partials/_series_item.html' with show_tags_link=True series_is_partial=False series_item_classes='' %}
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{% endif %}
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{% endif %}
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{% endfor %}
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</ul>
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</details>
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{% endfor %}
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</div>
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{% endfor %}
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{% elif grouped_series %}
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{% for study_uid, study in grouped_series %}
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<details class="study-block {% if study.partial_imported_uids %}study-block--partial-import{% endif %}" open>
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<summary>
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@@ -233,7 +323,7 @@
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</div>
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</div>
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<div class="modal fade" id="caseSeriesModal" tabindex="-1" aria-hidden="true">
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<div class="modal fade" id="caseSeriesModal" aria-hidden="true">
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<div class="modal-dialog modal-xl modal-dialog-centered modal-dialog-scrollable">
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<div class="modal-content">
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<div class="modal-header">
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@@ -531,7 +621,7 @@
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});
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}
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// Select / Deselect all series within a study block
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// Select / Deselect all series within a study block or patient block
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document.addEventListener('click', function (e) {
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const target = e.target;
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if (target.matches('.select-all-btn')) {
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@@ -562,6 +652,34 @@
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});
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if (typeof updateSelectionCount === 'function') updateSelectionCount();
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}
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if (target.matches('.select-all-patient-btn')) {
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const patientBlock = target.closest('.patient-block');
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if (!patientBlock) return;
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const inputs = patientBlock.querySelectorAll('input[name="selection"]');
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inputs.forEach(cb => {
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if (!cb.disabled) {
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cb.checked = true;
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const li = cb.closest('.series-item');
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if (li) li.classList.add('selected');
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cb.dispatchEvent(new Event('change', { bubbles: true }));
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}
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});
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if (typeof updateSelectionCount === 'function') updateSelectionCount();
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}
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if (target.matches('.deselect-all-patient-btn')) {
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const patientBlock = target.closest('.patient-block');
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if (!patientBlock) return;
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const inputs = patientBlock.querySelectorAll('input[name="selection"]');
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inputs.forEach(cb => {
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if (!cb.disabled) {
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cb.checked = false;
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const li = cb.closest('.series-item');
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if (li) li.classList.remove('selected');
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cb.dispatchEvent(new Event('change', { bubbles: true }));
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}
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});
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if (typeof updateSelectionCount === 'function') updateSelectionCount();
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}
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});
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// Listen for `case:selected` events dispatched by the case-search widget and perform the import
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@@ -884,6 +1002,10 @@
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color: #ffffff;
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}
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.select2-container {
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width: 100% !important;
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}
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#series-list li {
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}
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#series-list .selected {
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@@ -55,4 +55,44 @@ def test_user_uploads_partial_import_button_prefers_case_for_hash_matched_series
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assert response.status_code == 200
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content = response.content.decode("utf-8")
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assert 'class="btn btn-sm btn-warning import-partial-series-btn"' in content
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assert f'data-case-id="{primary_case.pk}"' in content
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assert f'data-case-id="{primary_case.pk}"' in content
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@pytest.mark.django_db
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def test_user_uploads_patient_grouping_and_select2(client, admin_user):
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client.force_login(admin_user)
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# Create UncategorisedDicom with PatientID tag using bulk_create to avoid reading non-existent file
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UncategorisedDicom.objects.bulk_create(
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[
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UncategorisedDicom(
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image="pending-upload-patient.dcm",
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user=admin_user,
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series_instance_uid="uploaded-series-patient-1",
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basic_dicom_tags={
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"SeriesInstanceUID": "uploaded-series-patient-1",
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"StudyInstanceUID": "study-patient-1",
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"StudyDescription": "Patient Study 1",
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"SeriesDescription": "Uploaded series",
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"Modality": "CT",
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"PatientID": "PAT-999-XYZ",
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},
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)
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]
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)
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response = client.get(reverse("atlas:user_uploads"))
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assert response.status_code == 200
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content = response.content.decode("utf-8")
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# Verify patient grouping is rendered
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assert "PAT-999-XYZ" in content
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assert "Patient ID:" in content
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assert "select-all-patient-btn" in content
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# Verify form autocomplete widgets are in context
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form = response.context["case_series_form"]
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from dal import autocomplete
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assert isinstance(form.fields["condition"].widget, autocomplete.ModelSelect2Multiple)
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assert isinstance(form.fields["presentation"].widget, autocomplete.ModelSelect2Multiple)
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assert isinstance(form.fields["procedures"].widget, autocomplete.ModelSelect2Multiple)
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+39
-13
@@ -3343,9 +3343,15 @@ def user_uploads(
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for d in dicoms:
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tags = d.basic_dicom_tags
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if tags is None or "PatientID" not in tags:
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try:
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d.save()
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tags = d.basic_dicom_tags
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except Exception:
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pass
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if tags is None:
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d.save()
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tags = d.basic_dicom_tags
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continue
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series_uid = tags.get("SeriesInstanceUID")
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if not series_uid:
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@@ -3569,6 +3575,36 @@ def user_uploads(
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)
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study_data["preferred_case_id"] = sorted_suggestions[0]["case"].pk
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# Now group the processed studies by PatientID
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patient_groups = defaultdict(lambda: {
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"studies": [],
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"min_date": "99999999",
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})
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for study_uid, study_data in grouped_series:
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patient_id = "Unknown Patient"
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if study_data["series"]:
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first_series_tags = study_data["series"][0][2]
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patient_id = first_series_tags.get("PatientID") or "Unknown Patient"
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pg = patient_groups[patient_id]
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pg["studies"].append((study_uid, study_data))
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study_date = study_data.get("date") or ""
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if study_date and study_date < pg["min_date"]:
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pg["min_date"] = study_date
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grouped_patients = sorted(
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[
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{
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"patient_id": patient_id,
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"studies": pg["studies"],
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"min_date": pg["min_date"],
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}
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for patient_id, pg in patient_groups.items()
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],
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key=lambda x: x["min_date"] or ""
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)
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case = False
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if case_id is not None:
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case = get_object_or_404(Case, pk=case_id)
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@@ -3576,17 +3612,6 @@ def user_uploads(
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case_series_form = CaseForm(user=request.user)
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case_series_form.fields["previous_case"].required = False
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case_series_form.fields["previous_case"].widget = HiddenInput()
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for field_name in ("condition", "presentation", "procedures"):
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field = case_series_form.fields.get(field_name)
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if field is None:
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continue
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field.widget = forms.SelectMultiple(
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attrs={
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"class": "form-select",
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"size": 8,
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}
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)
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field.widget.choices = field.choices
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return render(
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request,
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@@ -3594,6 +3619,7 @@ def user_uploads(
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{
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"series_list": series_list,
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"grouped_series": grouped_series,
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"grouped_patients": grouped_patients,
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"uploaded_series_uids": uploaded_series_uids,
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"case": case,
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"user": user,
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