feat(optimization): Implement series optimization features including downsampling, empty DICOM removal, and reconstruction options

atlas/templates/atlas/case_display_block.html

@@ -5,7 +5,7 @@
         <span class="series-block series-block-interactive" id="series-block-{{ series.pk }}" data-series-id="{{series.pk}}">
             <span>
                 <span class="series-block-series-number">Series {{ forloop.counter }}:</span><br>
-                <a href="{% url 'atlas:series_detail' pk=series.pk }}" class="series-block-title-link">
+                <a href="{% url 'atlas:series_detail' pk=series.pk %}" class="series-block-title-link">
                     {{series.get_block}}
                 </a>
                 <br>

atlas/templates/atlas/partials/_series_split_by_tag.html

@@ -5,9 +5,11 @@
                 class="btn btn-outline-warning btn-sm"
                 hx-get="{% url 'atlas:series_split_by_tag' pk=series.pk %}?analyze=1"
                 hx-target="#series-split-by-tag-panel"
-                hx-swap="outerHTML">
+                hx-swap="outerHTML"
+                hx-indicator="#series-split-analysis-indicator">
             Analyze split options
         </button>
+        <span id="series-split-analysis-indicator" class="spinner-border spinner-border-sm text-warning htmx-indicator" role="status" aria-hidden="true"></span>
     </div>
 
     {% if analyze_requested %}
@@ -16,7 +18,8 @@
                   action="{% url 'atlas:series_split_by_tag' pk=series.pk %}"
                   hx-post="{% url 'atlas:series_split_by_tag' pk=series.pk %}"
                   hx-target="#split-by-tag-result"
-                  hx-swap="innerHTML">
+                hx-swap="innerHTML"
+                hx-indicator="#series-split-submit-indicator">
                 {% csrf_token %}
                 <div class="input-group input-group-sm">
                     <select name="dicom_tag" class="form-select form-select-sm">
@@ -27,6 +30,7 @@
                     <button type="submit" class="btn btn-outline-warning btn-sm">Split</button>
                 </div>
             </form>
+            <span id="series-split-submit-indicator" class="spinner-border spinner-border-sm text-warning htmx-indicator" role="status" aria-hidden="true"></span>
             <p class="small text-muted mb-0">Only tags that can produce more than one output series are shown.</p>
         {% else %}
             <div class="alert alert-secondary mb-0 small">

atlas/templates/atlas/partials/_series_tag_consistency.html

@@ -11,9 +11,11 @@
                     class="btn btn-outline-info btn-sm"
                     hx-get="{% url 'atlas:series_tag_consistency' pk=series.pk %}?analyze=1"
                     hx-target="#series-tag-consistency-panel"
-                    hx-swap="outerHTML">
+                    hx-swap="outerHTML"
+                    hx-indicator="#series-tag-consistency-indicator">
                 Re-run analysis
             </button>
+            <span id="series-tag-consistency-indicator" class="spinner-border spinner-border-sm text-info htmx-indicator" role="status" aria-hidden="true"></span>
             {% if analyze_requested %}
                 <span class="small text-muted">Scanned {{ image_count }} image{{ image_count|pluralize }}</span>
             {% endif %}
@@ -57,7 +59,8 @@
                                                   action="{% url 'atlas:series_split_by_tag' pk=series.pk %}"
                                                   hx-post="{% url 'atlas:series_split_by_tag' pk=series.pk %}"
                                                   hx-target="#tag-consistency-split-result"
-                                                  hx-swap="innerHTML">
+                                                  hx-swap="innerHTML"
+                                                  hx-indicator="#tag-consistency-split-indicator">
                                                 {% csrf_token %}
                                                 <input type="hidden" name="dicom_tag" value="{{ row.tag_name }}">
                                                 <button type="submit" class="btn btn-outline-warning btn-sm">Split</button>
@@ -99,7 +102,8 @@
                                                   action="{% url 'atlas:series_split_by_tag' pk=series.pk %}"
                                                   hx-post="{% url 'atlas:series_split_by_tag' pk=series.pk %}"
                                                   hx-target="#tag-consistency-split-result"
-                                                  hx-swap="innerHTML">
+                                                  hx-swap="innerHTML"
+                                                  hx-indicator="#tag-consistency-split-indicator">
                                                 {% csrf_token %}
                                                 <input type="hidden" name="dicom_tag" value="{{ row.tag_name }}">
                                                 <button type="submit" class="btn btn-outline-warning btn-sm">Split</button>
@@ -143,7 +147,8 @@
                                                   action="{% url 'atlas:series_split_by_tag' pk=series.pk %}"
                                                   hx-post="{% url 'atlas:series_split_by_tag' pk=series.pk %}"
                                                   hx-target="#tag-consistency-split-result"
-                                                  hx-swap="innerHTML">
+                                                  hx-swap="innerHTML"
+                                                  hx-indicator="#tag-consistency-split-indicator">
                                                 {% csrf_token %}
                                                 <input type="hidden" name="dicom_tag" value="{{ row.tag_name }}">
                                                 <button type="submit" class="btn btn-outline-warning btn-sm">Split</button>
@@ -168,6 +173,7 @@
     </div>
 
     <div class="modal-footer">
+        <span id="tag-consistency-split-indicator" class="spinner-border spinner-border-sm text-warning htmx-indicator me-auto" role="status" aria-hidden="true"></span>
         <button type="button" class="btn btn-secondary btn-sm" data-bs-dismiss="modal">Close</button>
     </div>
 </div>

atlas/templates/atlas/series_viewer.html

@@ -32,7 +32,7 @@
                         {% with image_url_array_and_count=series.get_image_url_array_and_count %}
                             <div id="root" 
                                  class="dicom-viewer-root w-100 viewer-frame-standard series-viewer-resizable" 
-                                 style="min-height: clamp(600px, 75vh, 1200px); resize: vertical; overflow: auto;"
+                                   style="height: clamp(640px, 78vh, 1200px); min-height: 640px; resize: vertical; overflow: auto;"
                                  data-images="{{ image_url_array_and_count.0 }}" 
                                  data-auto-cache-stack=false>
                             </div>
@@ -202,10 +202,12 @@
                                 hx-get="{% url 'atlas:series_tag_consistency' pk=series.pk %}?analyze=1"
                                 hx-target="#series-tag-consistency-modal .modal-content"
                                 hx-swap="innerHTML"
+                                hx-indicator="#series-tag-consistency-load-indicator"
                                 data-bs-toggle="modal"
                                 data-bs-target="#series-tag-consistency-modal">
                             Analyze tag consistency
                         </button>
+                        <span id="series-tag-consistency-load-indicator" class="spinner-border spinner-border-sm text-info htmx-indicator" role="status" aria-hidden="true"></span>
                         {% if can_edit %}
                             <button class="btn btn-outline-warning btn-sm"
                                     data-bs-toggle="modal"
@@ -232,89 +234,140 @@
         </div>
     </div>
 
-    <!-- Truncate Series Modal -->
+    <!-- Series Optimization Modal -->
     {% if can_edit %}
         <div id="truncate-series-modal" class="modal modal-blur fade" tabindex="-1">
             <div class="modal-dialog modal-dialog-centered modal-xl">
                 <div class="modal-content">
                     <div class="modal-header">
-                        <h5 class="modal-title">Truncate Series & Optimize Disk Space</h5>
+                        <h5 class="modal-title">Series Optimization</h5>
                         <button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
                     </div>
                     <div class="modal-body">
                         <div class="row g-3">
-                            <!-- Viewer side -->
                             <div class="col-md-6">
                                 <div class="card h-100">
-                                    <div class="card-header fw-semibold">Viewer Preview</div>
+                                    <div class="card-header fw-semibold">Viewer / Compare Preview</div>
-                                    <div class="card-body p-2" style="max-height: 500px; overflow-y: auto;">
+                                    <div class="card-body p-2 d-flex flex-column gap-2">
                                         <div id="truncate-modal-viewer" class="dicom-viewer-root w-100"
-                                             style="height: 400px; background: #222;"
+                                             style="height: 320px; background: #222;"
                                              data-images="{{ image_url_array_and_count.0 }}" 
                                              data-auto-cache-stack="false">
                                         </div>
+                                        <div id="downsample-compare-wrap" class="d-none">
+                                            <div class="small text-muted mb-1">Downsample preview comparison</div>
+                                            <div id="downsample-compare-viewer" class="dicom-viewer-root w-100"
+                                                 style="height: 240px; background: #222;"
+                                                 data-auto-cache-stack="false"></div>
+                                        </div>
                                     </div>
                                 </div>
                             </div>
 
-                            <!-- Controls side -->
                             <div class="col-md-6">
                                 <div class="card">
-                                    <div class="card-header fw-semibold">Truncate Range</div>
+                                    <div class="card-header fw-semibold">Operations</div>
                                     <div class="card-body">
                                         <div class="alert alert-warning" role="alert">
-                                            <strong>⚠️ Warning:</strong> Truncation is irreversible. If you have reordered the series, this may remove the wrong images.
+                                            <strong>Warning:</strong> Destructive actions cannot be undone.
                                         </div>
 
+                                        <form id="series-optimize-form"
+                                              hx-post="{% url 'atlas:series_optimize' series_id=series.pk %}"
+                                              hx-target="#series-optimize-feedback"
+                                              hx-swap="innerHTML"
+                                              hx-indicator="#series-optimize-indicator">
+                                            {% csrf_token %}
+                                            <input type="hidden" name="start" id="opt-start-hidden" value="1">
+                                            <input type="hidden" name="end" id="opt-end-hidden" value="{{ image_url_array_and_count.1 }}">
+
                                             <div class="mb-3">
-                                            <label class="form-label">Start Image</label>
+                                                <label class="form-label">Start image</label>
                                                 <div class="input-group">
                                                     <input id="truncate-lower-input" type="number" class="form-control form-control-sm" value="1" min="1" max="{{image_url_array_and_count.1}}">
-                                                <button id="truncate-set-lower-btn" class="btn btn-outline-secondary btn-sm" type="button">Set</button>
+                                                    <button id="truncate-set-lower-btn" class="btn btn-outline-secondary btn-sm" type="button">Set from viewer</button>
                                                 </div>
                                             </div>
 
                                             <div class="mb-3">
-                                            <label class="form-label">End Image</label>
+                                                <label class="form-label">End image</label>
                                                 <div class="input-group">
                                                     <input id="truncate-upper-input" type="number" class="form-control form-control-sm" value="{{image_url_array_and_count.1}}" min="1" max="{{image_url_array_and_count.1}}">
-                                                <button id="truncate-set-upper-btn" class="btn btn-outline-secondary btn-sm" type="button">Set</button>
+                                                    <button id="truncate-set-upper-btn" class="btn btn-outline-secondary btn-sm" type="button">Set from viewer</button>
                                                 </div>
                                             </div>
 
-                                        <div class="d-flex gap-2 mb-3">
+                                            <div class="d-flex flex-wrap gap-2 mb-3">
-                                            <button id="truncate-test-modal-btn" class="btn btn-sm btn-outline-primary">Test Preview</button>
+                                                <button id="truncate-test-modal-btn" class="btn btn-sm btn-outline-primary" type="button">Test preview</button>
+                                                <button class="btn btn-sm btn-danger" type="submit" name="operation" value="truncate">Apply truncate</button>
+                                                <button class="btn btn-sm btn-outline-warning" type="submit" name="operation" value="remove_empty">Remove empty DICOMs</button>
                                             </div>
 
                                             <hr>
 
                                             <div class="mb-3">
-                                            <h6>Disk Space Optimization</h6>
+                                                <label for="downsample-pct" class="form-label">Downsample percentage</label>
+                                                <select id="downsample-pct" name="downsample_pct" class="form-select form-select-sm">
+                                                    <option value="25">25% reduction</option>
+                                                    <option value="40">40% reduction</option>
+                                                    <option value="50" selected>50% reduction</option>
+                                                    <option value="60">60% reduction</option>
+                                                    <option value="75">75% reduction</option>
+                                                </select>
+                                                <small class="text-muted">Original hash is preserved after downsampling.</small>
+                                            </div>
+
+                                            <div class="d-flex flex-wrap gap-2 mb-3">
+                                                <button class="btn btn-sm btn-outline-info" type="submit" name="operation" value="downsample_preview">Preview downsample compare</button>
+                                                <button class="btn btn-sm btn-outline-success" type="submit" name="operation" value="downsample">Apply downsample</button>
+                                            </div>
+
+                                            <hr>
+
+                                            <div class="mb-2">
+                                                <div class="fw-semibold small mb-2">Generate reconstructions</div>
+                                                <div class="d-flex flex-wrap gap-3 mb-2">
                                                     <div class="form-check">
-                                                <input class="form-check-input" type="checkbox" id="remove-empty-dicoms-check">
+                                                        <input class="form-check-input" type="checkbox" id="recon-axial" name="recon_planes" value="axial" checked>
-                                                <label class="form-check-label" for="remove-empty-dicoms-check">
+                                                        <label class="form-check-label" for="recon-axial">Axial</label>
-                                                    Remove empty DICOMs (no content)
-                                                </label>
-                                                <small class="d-block text-muted mt-1">Removes DICOM files that do not contain usable image data.</small>
                                                     </div>
                                                     <div class="form-check">
-                                                <input class="form-check-input" type="checkbox" id="downsample-pixels-check">
+                                                        <input class="form-check-input" type="checkbox" id="recon-coronal" name="recon_planes" value="coronal" checked>
-                                                <label class="form-check-label" for="downsample-pixels-check">
+                                                        <label class="form-check-label" for="recon-coronal">Coronal</label>
-                                                    Downsample pixel data (by 50%)
+                                                    </div>
-                                                </label>
+                                                    <div class="form-check">
-                                                <small class="d-block text-muted mt-1">Reduces resolution while preserving original hash for duplicate detection.</small>
+                                                        <input class="form-check-input" type="checkbox" id="recon-sagittal" name="recon_planes" value="sagittal" checked>
+                                                        <label class="form-check-label" for="recon-sagittal">Sagittal</label>
                                                     </div>
                                                 </div>
 
-                                        <div id="truncate-modal-output" class="alert alert-info d-none" role="alert"></div>
+                                                <div class="row g-2">
+                                                    <div class="col-6">
+                                                        <label class="form-label small mb-1" for="recon-slice-thickness">Slice thickness (mm)</label>
+                                                        <input type="number" step="0.1" min="0.1" id="recon-slice-thickness" name="recon_slice_thickness" class="form-control form-control-sm" placeholder="e.g. 1.0">
+                                                    </div>
+                                                    <div class="col-6">
+                                                        <label class="form-label small mb-1" for="recon-slice-spacing">Slice spacing (mm)</label>
+                                                        <input type="number" step="0.1" min="0.1" id="recon-slice-spacing" name="recon_slice_spacing" class="form-control form-control-sm" placeholder="e.g. 1.0">
+                                                    </div>
                                                 </div>
 
-                                    <div class="card-footer">
+                                                <div class="mt-2">
-                                        <div class="d-flex gap-2">
+                                                    <button class="btn btn-sm btn-outline-primary" type="submit" name="operation" value="reconstruct">Generate recon series</button>
-                                            <button id="truncate-execute-modal-btn" class="btn btn-danger btn-sm">Execute Truncation</button>
-                                            <button type="button" class="btn btn-secondary btn-sm" data-bs-dismiss="modal">Cancel</button>
                                                 </div>
                                             </div>
+                                        </form>
+                                    </div>
+
+                                    <div class="card-footer d-flex align-items-center gap-2">
+                                        <span id="series-optimize-indicator" class="spinner-border spinner-border-sm text-primary htmx-indicator" role="status" aria-hidden="true"></span>
+                                        <small class="text-muted">Processing operations may take time for large stacks.</small>
+                                        <button type="button" class="btn btn-secondary btn-sm ms-auto" data-bs-dismiss="modal">Close</button>
+                                    </div>
+                                    <div class="px-3 pb-3">
+                                        <div id="series-optimize-feedback" class="small"></div>
+                                        <div id="truncate-modal-output" class="alert alert-info d-none mt-2 mb-0" role="alert"></div>
+                                    </div>
                                 </div>
                             </div>
                         </div>
@@ -338,7 +391,7 @@
                 if (saved) {
                     const viewer = document.getElementById('root');
                     if (viewer) {
-                        viewer.style.minHeight = saved;
+                        viewer.style.height = saved;
                     }
                 }
             }
@@ -360,38 +413,69 @@
                 });
                 resizeObserver.observe(viewer);
                 restoreViewerHeight();
+                requestAnimationFrame(() => {
+                    try {
+                        if (window.resizeDicomViewers) {
+                            window.resizeDicomViewers();
+                        }
+                        window.dispatchEvent(new Event('resize'));
+                    } catch (e) {
+                        console.warn('Viewer resize dispatch failed', e);
+                    }
+                });
             }
 
-            // Modal truncate handlers
+            function syncOptimizeBounds() {
+                const startInput = document.getElementById('truncate-lower-input');
+                const endInput = document.getElementById('truncate-upper-input');
+                const startHidden = document.getElementById('opt-start-hidden');
+                const endHidden = document.getElementById('opt-end-hidden');
+                if (!startInput || !endInput || !startHidden || !endHidden) {
+                    return;
+                }
+                startHidden.value = startInput.value;
+                endHidden.value = endInput.value;
+            }
+
+            // Modal optimization handlers
             const truncateModal = document.getElementById('truncate-series-modal');
             if (truncateModal) {
-                truncateModal.addEventListener('show.bs.modal', function() {
+                truncateModal.addEventListener('show.bs.modal', function () {
-                    // Initialize the modal viewer
                     setTimeout(() => {
                         try {
                             if (window.mountDicomViewers) {
                                 window.mountDicomViewers();
                             }
+                            if (window.resizeDicomViewers) {
+                                window.resizeDicomViewers();
+                            }
                         } catch (e) {
                             console.warn('Modal viewer init failed', e);
                         }
                     }, 200);
                 });
 
+                const getStackPosition = window[`getCurrentStackPosition_${apiKey}`] || window.getCurrentStackPosition_root;
+
                 document.getElementById('truncate-set-lower-btn')?.addEventListener('click', () => {
-                    if (window.getCurrentStackPosition_root) {
+                    if (getStackPosition) {
-                        const pos = window.getCurrentStackPosition_root(0) + 1;
+                        const pos = getStackPosition(0) + 1;
                         document.getElementById('truncate-lower-input').value = pos;
+                        syncOptimizeBounds();
                     }
                 });
 
                 document.getElementById('truncate-set-upper-btn')?.addEventListener('click', () => {
-                    if (window.getCurrentStackPosition_root) {
+                    if (getStackPosition) {
-                        const pos = window.getCurrentStackPosition_root(0) + 1;
+                        const pos = getStackPosition(0) + 1;
                         document.getElementById('truncate-upper-input').value = pos;
+                        syncOptimizeBounds();
                     }
                 });
 
+                document.getElementById('truncate-lower-input')?.addEventListener('input', syncOptimizeBounds);
+                document.getElementById('truncate-upper-input')?.addEventListener('input', syncOptimizeBounds);
+
                 document.getElementById('truncate-test-modal-btn')?.addEventListener('click', () => {
                     const lower = parseInt(document.getElementById('truncate-lower-input').value) - 1;
                     const upper = parseInt(document.getElementById('truncate-upper-input').value) - 1;
@@ -401,76 +485,61 @@
                         return;
                     }
 
-                    if (window.truncateStack_root) {
+                    const truncateFn = window[`truncateStack_${apiKey}`] || window.truncateStack_root;
-                        const ok = window.truncateStack_root(lower, upper);
+                    if (truncateFn) {
+                        const ok = truncateFn(lower, upper);
                         if (ok) {
                             document.getElementById('truncate-modal-output').innerHTML = `Preview shows images ${lower + 1} to ${upper + 1} (${upper - lower + 1} total).`;
                             document.getElementById('truncate-modal-output').classList.remove('d-none');
                         }
                     }
                 });
+            }
 
-                document.getElementById('truncate-execute-modal-btn')?.addEventListener('click', () => {
+            document.body.addEventListener('htmx:configRequest', function (event) {
-                    const lower = parseInt(document.getElementById('truncate-lower-input').value) - 1;
+                const form = document.getElementById('series-optimize-form');
-                    const upper = parseInt(document.getElementById('truncate-upper-input').value) - 1;
+                if (!form || event.target !== form) {
-                    const removeEmpty = document.getElementById('remove-empty-dicoms-check').checked;
+                    return;
-                    const downsample = document.getElementById('downsample-pixels-check').checked;
+                }
+                syncOptimizeBounds();
+            });
 
-                    if (lower >= upper) {
+            document.body.addEventListener('htmx:afterSwap', function (event) {
-                        alert('The lower bound must be less than the upper bound.');
+                if (event.target && event.target.id === 'series-optimize-feedback') {
+                    const payload = document.getElementById('downsample-compare-payload');
+                    if (!payload) {
                         return;
                     }
 
-                    const totalToKeep = upper - lower + 1;
+                    const namedStacks = payload.dataset.namedStacks;
-                    const confirmMsg = `Truncate series to ${totalToKeep} images?${removeEmpty ? '\n- Remove empty DICOMs' : ''}${downsample ? '\n- Downsample pixel data' : ''}`;
+                    if (!namedStacks) {
-                    
-                    if (confirm(confirmMsg)) {
-                        // Build URL with optional parameters
-                        let truncateUrl = `{% url 'atlas:series_truncate' series.pk 0 0 %}`.replace('/0/0/', `/${lower}/${upper}/`);
-                        if (removeEmpty) truncateUrl += '?remove_empty=1';
-                        if (downsample) truncateUrl += (removeEmpty ? '&' : '?') + 'downsample=1';
-
-                        htmx.ajax('GET', truncateUrl, '#truncate-modal-output');
-                        
-                        // Close modal after a delay
-                        setTimeout(() => {
-                            const modal = bootstrap.Modal.getInstance(truncateModal);
-                            if (modal) modal.hide();
-                        }, 1500);
-                    }
-                });
-            }
-
-            // Keep old inline handlers for compatibility
-            $("#set-lower-truncation-bound-button").click(() => {
-                $("#lower-truncation-bound-input").val(getCurrentStackPosition_root(0) + 1);
-            });
-            $("#set-upper-truncation-bound-button").click(() => {
-                $("#upper-truncation-bound-input").val(getCurrentStackPosition_root(0) + 1);
-            });
-            $("#truncate-test-button").click(() => {
-                const lower = parseInt($("#lower-truncation-bound-input").val()) - 1;
-                const upper = parseInt($("#upper-truncation-bound-input").val()) - 1;
-                const ok = window[`truncateStack_${apiKey}`](lower, upper);
-                if (ok) {
-                    $("#truncate-output").text("The truncated images are shown above.");
-                }
-            });
-            $("#truncate-button").click(() => {
-                lower_bound = parseInt($("#lower-truncation-bound-input").val()) - 1;
-                upper_bound = parseInt($("#upper-truncation-bound-input").val()) - 1;
-
-                if (lower_bound >= upper_bound) {
-                    alert("The lower bound must be less than the upper bound.");
                         return;
                     }
 
-                if(confirm(`Truncated series. This will leave ${upper_bound - lower_bound + 1} images.`) == true) {
+                    const compareWrap = document.getElementById('downsample-compare-wrap');
-                    const truncateTemplate = `{% url 'atlas:series_truncate' series.id 0 0 %}`; // e.g. /atlas/series/920/truncate/0/0/
+                    const compareViewer = document.getElementById('downsample-compare-viewer');
-                    const truncateUrl = truncateTemplate.replace('/0/0/', `/${lower_bound}/${upper_bound}/`);
+                    if (!compareWrap || !compareViewer) {
-                    htmx.ajax("GET", truncateUrl, "#truncate-output")
+                        return;
                     }
-            })
+
+                    compareWrap.classList.remove('d-none');
+                    compareViewer.dataset.namedStacks = namedStacks;
+                    compareViewer.dataset.autoCacheStack = 'false';
+
+                    try {
+                        if (window.mountDicomViewers) {
+                            window.mountDicomViewers();
+                        }
+                        if (window.resizeDicomViewers) {
+                            window.resizeDicomViewers();
+                        }
+                    } catch (err) {
+                        console.warn('Failed to mount downsample compare viewer', err);
+                    }
+                }
+            });
+
+            syncOptimizeBounds();
 
             $("#add-finding-button").click(() => {
                 $("#hidden-form").show()

atlas/urls.py

@@ -565,6 +565,11 @@ urlpatterns = [
             views.series_image_size_htmx,
             name="series_image_size",
         ),
+        path(
+            "series/<int:series_id>/optimize/",
+            views.series_optimize_htmx,
+            name="series_optimize",
+        ),
     path("series/<int:pk>/images/", views.series_images_partial, name="series_images"),
     path("series/<int:pk>/authors", views.SeriesAuthorUpdate.as_view(), name="series_authors"),
     path("series/<int:series_id>/finding/related", views.series_finding_related, name="series_finding_related"),

atlas/views.py

@@ -2,6 +2,8 @@ import json
 import pprint
 import csv
 import random
+import copy
+import io
 from typing import Any
 from dal import autocomplete
 from django.db.models.base import Model as Model
@@ -217,9 +219,7 @@ def series_truncate_htmx(request, series_id, start, end):
     """HTMX endpoint to truncate a series' images to the given inclusive
     start/end bounds (zero-based). Returns an HTML fragment with the result.
     
-    Query parameters:
+    This endpoint only performs truncation for backward compatibility.
-    - remove_empty: Remove DICOMs with no content (all pixels zero)
-    - downsample: Downsample pixel data by 50% while preserving original hash
     """
     series = get_object_or_404(Series, pk=series_id)
 
@@ -227,61 +227,18 @@ def series_truncate_htmx(request, series_id, start, end):
         return HttpResponse("<div class=\"alert alert-danger\">Permission denied</div>")
 
     images_removed = []
-    images_downsampled = []
-    remove_empty_dicoms = request.GET.get('remove_empty') in ('1', 'true', 'True')
-    downsample_pixels = request.GET.get('downsample') in ('1', 'true', 'True')
 
     for n, image in enumerate(series.get_images()):
         if n >= int(start) and n <= int(end):
-            # Keep images within bounds
+            continue
-            if remove_empty_dicoms and image.image:
+
-                try:
-                    # Check if DICOM is effectively empty (all zeros)
-                    import pydicom
-                    from io import BytesIO
-                    dcm = pydicom.dcmread(BytesIO(image.image.read()))
-                    if hasattr(dcm, 'pixel_array'):
-                        px_array = dcm.pixel_array
-                        # If all pixels are zero, mark for removal
-                        if (px_array == 0).all():
         image.removed = True
         image.image = None
         image.save()
         images_removed.append(image.pk)
-                            continue
-                except Exception as e:
-                    logger.warning(f"Could not analyze DICOM {image.pk}: {e}")
 
-            if downsample_pixels and image.image:
+    series.modified = Series.SeriesModifiedChocies.TR
-                try:
+    series.save(update_fields=["modified"])
-                    # Downsample pixel data (reduce resolution by 50%)
-                    import pydicom
-                    import numpy as np
-                    from io import BytesIO
-                    
-                    dcm = pydicom.dcmread(BytesIO(image.image.read()))
-                    if hasattr(dcm, 'pixel_array'):
-                        original_array = dcm.pixel_array
-                        # Downsample: take every other pixel in each dimension
-                        downsampled = original_array[::2, ::2] if original_array.ndim == 2 else original_array[:, ::2, ::2]
-                        dcm.pixel_array[:] = downsampled
-                        
-                        # Save back to image field
-                        output = BytesIO()
-                        dcm.save_as(output, write_like_original=False)
-                        output.seek(0)
-                        image.image.save(f'dicom_{image.pk}.dcm', output, save=True)
-                        images_downsampled.append(image.pk)
-                except Exception as e:
-                    logger.warning(f"Could not downsample DICOM {image.pk}: {e}")
-            
-            continue
-        else:
-            # Remove images outside bounds
-            image.removed = True
-            image.image = None
-            image.save()
-            images_removed.append(image.pk)
 
     # Recalculate stored series size
     try:
@@ -295,16 +252,340 @@ def series_truncate_htmx(request, series_id, start, end):
         "atlas/partials/truncate_result.html",
         {
             "images_removed": images_removed,
-            "images_downsampled": images_downsampled,
+            "images_downsampled": [],
             "series": series,
-            "remove_empty_dicoms": remove_empty_dicoms,
+            "remove_empty_dicoms": False,
-            "downsample_pixels": downsample_pixels,
+            "downsample_pixels": False,
         },
         request=request,
     )
     return HttpResponse(html)
 
 
+def _read_series_image_dataset(series_image):
+    if not series_image.image:
+        return None
+
+    try:
+        series_image.image.open("rb")
+        series_image.image.seek(0)
+        return pydicom.dcmread(series_image.image, force=True)
+    except Exception as exc:
+        logger.warning("Failed to read DICOM for image {}: {}", series_image.pk, exc)
+        return None
+
+
+def _is_empty_dicom(ds):
+    try:
+        px = ds.pixel_array
+        return bool((px == 0).all())
+    except Exception:
+        return False
+
+
+def _resize_array_nearest(arr, target_rows, target_cols):
+    import numpy as np
+
+    rows, cols = arr.shape[0], arr.shape[1]
+    row_idx = np.clip(np.round(np.linspace(0, rows - 1, target_rows)).astype(int), 0, rows - 1)
+    col_idx = np.clip(np.round(np.linspace(0, cols - 1, target_cols)).astype(int), 0, cols - 1)
+    return arr[np.ix_(row_idx, col_idx)]
+
+
+def _downsample_dicom_dataset(ds, reduction_pct):
+    if reduction_pct <= 0 or reduction_pct >= 100:
+        raise ValueError("Downsample percentage must be between 1 and 99")
+
+    factor = (100 - reduction_pct) / 100.0
+    px = ds.pixel_array
+
+    if px.ndim != 2:
+        raise ValueError("Only 2D DICOM slices are supported for this downsample operation")
+
+    target_rows = max(1, int(round(px.shape[0] * factor)))
+    target_cols = max(1, int(round(px.shape[1] * factor)))
+    resized = _resize_array_nearest(px, target_rows, target_cols)
+
+    ds.Rows = int(target_rows)
+    ds.Columns = int(target_cols)
+    ds.PixelData = resized.tobytes()
+    ds.pop("SmallestImagePixelValue", None)
+    ds.pop("LargestImagePixelValue", None)
+    return ds
+
+
+def _create_series_derivative(source_series, description_suffix):
+    derived = Series.objects.get(pk=source_series.pk)
+    derived.pk = None
+    derived.id = None
+    derived.series_instance_uid = generate_uid()
+    derived.description = f"{source_series.description or 'Series'} [{description_suffix}]"
+    derived.modified = Series.SeriesModifiedChocies.RE
+    derived.save()
+    derived.case.set(source_series.case.all())
+    derived.author.set(source_series.author.all())
+    return derived
+
+
+def _series_image_urls_json(series):
+    image_url_array_and_count = series.get_image_url_array_and_count()
+    try:
+        urls = json.loads(image_url_array_and_count[0])
+    except Exception:
+        urls = []
+    return urls
+
+
+@login_required
+@require_http_methods(["POST"])
+def series_optimize_htmx(request, series_id):
+    """Run disk optimization operations for a series.
+
+    Scope: Series editors only.
+
+    Supported operations:
+    - remove_empty
+    - downsample
+    - downsample_preview
+    - reconstruct
+    - truncate
+    """
+    series = get_object_or_404(Series, pk=series_id)
+
+    if not series.check_user_can_edit(request.user):
+        return HttpResponse('<div class="alert alert-danger mb-0">Permission denied</div>')
+
+    operation = request.POST.get("operation", "").strip()
+    start = int(request.POST.get("start", "1") or 1) - 1
+    end = int(request.POST.get("end", str(series.get_image_count())) or series.get_image_count()) - 1
+
+    if end < start:
+        return HttpResponse('<div class="alert alert-danger mb-0">Start must be less than or equal to end.</div>')
+
+    images = list(series.get_images())
+    bounded_images = [img for idx, img in enumerate(images) if idx >= start and idx <= end]
+
+    if operation == "truncate":
+        removed = []
+        for idx, image in enumerate(images):
+            if idx < start or idx > end:
+                image.removed = True
+                image.image = None
+                image.save()
+                removed.append(image.pk)
+
+        series.modified = Series.SeriesModifiedChocies.TR
+        series.save(update_fields=["modified"])
+        return HttpResponse(
+            f'<div class="alert alert-success mb-0">Truncate complete. Removed <strong>{len(removed)}</strong> images.</div>'
+        )
+
+    if operation == "remove_empty":
+        removed = []
+        for image in bounded_images:
+            ds = _read_series_image_dataset(image)
+            if ds is None:
+                continue
+            if _is_empty_dicom(ds):
+                image.removed = True
+                image.image = None
+                image.save()
+                removed.append(image.pk)
+
+        if removed:
+            series.modified = Series.SeriesModifiedChocies.TR
+            series.save(update_fields=["modified"])
+
+        return HttpResponse(
+            f'<div class="alert alert-success mb-0">Empty DICOM removal complete. Removed <strong>{len(removed)}</strong> empty images.</div>'
+        )
+
+    if operation in ("downsample", "downsample_preview"):
+        downsample_pct = int(request.POST.get("downsample_pct", "50") or 50)
+
+        if operation == "downsample_preview":
+            preview_series = _create_series_derivative(series, f"Downsample preview {downsample_pct}%")
+            created = 0
+
+            for image in bounded_images:
+                ds = _read_series_image_dataset(image)
+                if ds is None:
+                    continue
+
+                try:
+                    ds_out = _downsample_dicom_dataset(ds, downsample_pct)
+                except Exception as exc:
+                    logger.warning("Downsample preview failed for image {}: {}", image.pk, exc)
+                    continue
+
+                out_io = io.BytesIO()
+                ds_out.save_as(out_io, write_like_original=False)
+                out_io.seek(0)
+
+                new_image = SeriesImage(series=preview_series, position=image.position, upload_filename=image.upload_filename)
+                new_image.image.save(
+                    f"preview_ds_{downsample_pct}_{image.pk}.dcm",
+                    ContentFile(out_io.getvalue()),
+                    save=False,
+                )
+                new_image.save()
+                created += 1
+
+            original_urls = _series_image_urls_json(series)
+            preview_urls = _series_image_urls_json(preview_series)
+            named_stacks = json.dumps(
+                {
+                    "Original": original_urls,
+                    f"Preview {downsample_pct}%": preview_urls,
+                }
+            )
+            escaped_named_stacks = escape(named_stacks)
+
+            return HttpResponse(
+                (
+                    '<div class="alert alert-info mb-2">'
+                    f'Downsample preview series created with <strong>{created}</strong> images. '
+                    f'<a class="alert-link" target="_blank" href="{preview_series.get_absolute_url()}">Open preview series</a>.'
+                    '</div>'
+                    f'<div id="downsample-compare-payload" data-named-stacks="{escaped_named_stacks}"></div>'
+                )
+            )
+
+        downsampled = []
+        for image in bounded_images:
+            ds = _read_series_image_dataset(image)
+            if ds is None:
+                continue
+
+            try:
+                original_hash = image.image_blake3_hash
+                ds_out = _downsample_dicom_dataset(ds, downsample_pct)
+                out_io = io.BytesIO()
+                ds_out.save_as(out_io, write_like_original=False)
+                out_io.seek(0)
+
+                image.image.save(
+                    f"downsample_{downsample_pct}_{image.pk}.dcm",
+                    ContentFile(out_io.getvalue()),
+                    save=False,
+                )
+                # Preserve original hash for duplicate detection continuity.
+                image.image_blake3_hash = original_hash
+                image.save(update_fields=["image", "image_blake3_hash"])
+                downsampled.append(image.pk)
+            except Exception as exc:
+                logger.warning("Downsample failed for image {}: {}", image.pk, exc)
+
+        if downsampled:
+            series.modified = Series.SeriesModifiedChocies.RE
+            series.save(update_fields=["modified"])
+
+        return HttpResponse(
+            f'<div class="alert alert-success mb-0">Downsample complete ({downsample_pct}%). Updated <strong>{len(downsampled)}</strong> images while preserving original hashes.</div>'
+        )
+
+    if operation == "reconstruct":
+        recon_planes = request.POST.getlist("recon_planes")
+        if not recon_planes:
+            return HttpResponse('<div class="alert alert-danger mb-0">Select at least one reconstruction plane.</div>')
+
+        slice_thickness = request.POST.get("recon_slice_thickness", "")
+        slice_spacing = request.POST.get("recon_slice_spacing", "")
+
+        try:
+            slice_thickness_val = float(slice_thickness) if slice_thickness else None
+            slice_spacing_val = float(slice_spacing) if slice_spacing else None
+        except ValueError:
+            return HttpResponse('<div class="alert alert-danger mb-0">Slice thickness and spacing must be numeric values.</div>')
+
+        dicom_items = []
+        for image in bounded_images:
+            ds = _read_series_image_dataset(image)
+            if ds is None:
+                continue
+            try:
+                arr = ds.pixel_array
+                if arr.ndim != 2:
+                    continue
+                dicom_items.append((image, ds, arr))
+            except Exception:
+                continue
+
+        if len(dicom_items) < 2:
+            return HttpResponse('<div class="alert alert-warning mb-0">Need at least 2 valid DICOM images in range for reconstruction.</div>')
+
+        import numpy as np
+
+        base_shape = dicom_items[0][2].shape
+        dicom_items = [item for item in dicom_items if item[2].shape == base_shape]
+        if len(dicom_items) < 2:
+            return HttpResponse('<div class="alert alert-warning mb-0">Not enough consistently-sized slices for reconstruction.</div>')
+
+        volume = np.stack([item[2] for item in dicom_items], axis=0)
+        template_ds = dicom_items[0][1]
+        created_series = []
+
+        for plane in recon_planes:
+            plane_norm = plane.lower()
+            if plane_norm == "axial":
+                recon_slices = [volume[i, :, :] for i in range(volume.shape[0])]
+            elif plane_norm == "coronal":
+                recon_slices = [volume[:, i, :] for i in range(volume.shape[1])]
+            elif plane_norm == "sagittal":
+                recon_slices = [volume[:, :, i] for i in range(volume.shape[2])]
+            else:
+                continue
+
+            recon_series = _create_series_derivative(series, f"Recon {plane_norm.title()}")
+            recon_series.series_instance_uid = generate_uid()
+            recon_series.save(update_fields=["series_instance_uid"])
+
+            for idx, arr2d in enumerate(recon_slices):
+                ds_new = copy.deepcopy(template_ds)
+                arr2d = np.asarray(arr2d, dtype=dicom_items[0][2].dtype)
+
+                ds_new.Rows = int(arr2d.shape[0])
+                ds_new.Columns = int(arr2d.shape[1])
+                ds_new.InstanceNumber = idx + 1
+                ds_new.SOPInstanceUID = generate_uid()
+                ds_new.SeriesInstanceUID = recon_series.series_instance_uid
+                ds_new.PixelData = arr2d.tobytes()
+
+                if slice_thickness_val is not None:
+                    ds_new.SliceThickness = slice_thickness_val
+                if slice_spacing_val is not None:
+                    ds_new.SpacingBetweenSlices = slice_spacing_val
+
+                out_io = io.BytesIO()
+                ds_new.save_as(out_io, write_like_original=False)
+                out_io.seek(0)
+
+                recon_image = SeriesImage(series=recon_series, position=idx + 1, upload_filename=f"recon_{plane_norm}_{idx+1}.dcm")
+                recon_image.image.save(
+                    f"recon_{plane_norm}_{recon_series.pk}_{idx+1}.dcm",
+                    ContentFile(out_io.getvalue()),
+                    save=False,
+                )
+                recon_image.save()
+
+            created_series.append(recon_series)
+
+        if not created_series:
+            return HttpResponse('<div class="alert alert-warning mb-0">No reconstruction plane could be generated.</div>')
+
+        links = " ".join(
+            [
+                f'<a class="alert-link me-2" target="_blank" href="{s.get_absolute_url()}">{escape(s.description or str(s.pk))}</a>'
+                for s in created_series
+            ]
+        )
+        return HttpResponse(
+            f'<div class="alert alert-success mb-0">Created <strong>{len(created_series)}</strong> reconstruction series: {links}</div>'
+        )
+
+    return HttpResponse('<div class="alert alert-danger mb-0">Unknown optimize operation.</div>')
+
+
 @login_required
 def series_image_size_htmx(request, series_id):
     """HTMX endpoint returning the total size of images in a series.