feat(tasks): Add seriesId to stacks in Case model and enhance series viewer with navigation buttons

atlas/models.py

@@ -821,7 +821,7 @@ class Case(models.Model, AuthorMixin, QuestionMixin):
             for series in case_obj.get_ordered_series():
                 images = [f"{REMOTE_URL}{img.image.url}" for img in series.get_images()]
                 name = f"{prefix}: {series}" if prefix else str(series)
-                stacks.append({"name": name, "imageIds": images})
+                stacks.append({"name": name, "imageIds": images, "seriesId": series.pk})
             return stacks
 
         results = []
@@ -1912,7 +1912,7 @@ class CaseDetail(models.Model):
             for series in case_obj.get_ordered_series():
                 images = [f"{REMOTE_URL}{img.image.url}" for img in series.images.all()]
                 name = f"{prefix}: {series}" if prefix else str(series)
-                stacks.append({"name": name, "imageIds": images})
+                stacks.append({"name": name, "imageIds": images, "seriesId": series.pk})
             return stacks
 
         results = []

atlas/tasks.py

@@ -86,7 +86,6 @@ from generic.models import CimarCase
 from rad.settings import REMOTE_URL, CIMAR_USERNAME, CIMAR_PASSWORD
 from helpers.cimar import CimarAPI, NotFoundError
 from pydicom.uid import generate_uid
-from datetime import datetime
 from django.contrib.auth.models import User
 from django.core.files.base import ContentFile
 from django.core.cache import cache
@@ -392,9 +391,6 @@ def series_reconstruct_task(
         recon_series = atlas_views._create_series_derivative(series, f"Recon {plane_norm.title()} ({source_plane.title()} src)")
         recon_series.series_instance_uid = generate_uid()
         recon_series.save(update_fields=["series_instance_uid"])
-        now = datetime.utcnow()
-        date_str = now.strftime("%Y%m%d")
-        time_str = now.strftime("%H%M%S.%f")[:13]
 
         for idx in range(int(cfg["count"])):
             arr2d = cfg["slice_fn"](idx)
@@ -404,18 +400,16 @@ def series_reconstruct_task(
             ds_new.Rows = int(arr2d.shape[0])
             ds_new.Columns = int(arr2d.shape[1])
             ds_new.InstanceNumber = idx + 1
-            ds_new.SOPInstanceUID = generate_uid()
+            atlas_views._stamp_derived_dataset(
-            ds_new.SeriesInstanceUID = recon_series.series_instance_uid
+                ds_new,
-            ds_new.SeriesDescription = recon_series.description or f"Recon {plane_norm.title()}"
+                series_instance_uid=recon_series.series_instance_uid,
-            ds_new.ImageType = ["DERIVED", "SECONDARY", "MPR"]
+                series_description=recon_series.description or f"Recon {plane_norm.title()}",
-            ds_new.DerivationDescription = (
+                derivation_description=(
                 f"{plane_norm.title()} reconstruction; mode={recon_thickness_mode}; "
                 f"thickness={float(cfg['slice_thickness_out']):.3f}mm; spacing={float(cfg['spacing_between_slices_out']):.3f}mm"
+                ),
+                image_type=["DERIVED", "SECONDARY", "MPR"],
             )
-            ds_new.ContentDate = date_str
-            ds_new.ContentTime = time_str
-            ds_new.InstanceCreationDate = date_str
-            ds_new.InstanceCreationTime = time_str
             ds_new.PixelData = arr2d.tobytes()
             ds_new.PixelSpacing = [float(cfg["pixel_spacing_out"][0]), float(cfg["pixel_spacing_out"][1])]
             ds_new.ImageOrientationPatient = cfg["image_orientation_out"]

atlas/templates/atlas/case_display_block.html

@@ -18,10 +18,18 @@
                     </button>
                     <input type="checkbox" class="hide" name="series-ids" value="{{series.pk}}">
                     <button type="button"
-                            class="btn btn-outline-info btn-xs btn-sm series-open-viewer-btn"
+                            class="btn btn-outline-info btn-xs btn-sm series-open-primary-btn"
-                            title="Open series in viewer"
+                            title="Open series in primary viewport"
-                            data-series-id="{{series.pk}}">
+                            data-series-id="{{series.pk}}"
-                        <i class="bi bi-eye"></i> View
+                            data-series-name="{{ series|escape }}">
+                        <i class="bi bi-eye"></i> Open
+                    </button>
+                    <button type="button"
+                            class="btn btn-outline-info btn-xs btn-sm series-open-new-viewport-btn"
+                            title="Add a viewport and open series"
+                            data-series-id="{{series.pk}}"
+                            data-series-name="{{ series|escape }}">
+                        <i class="bi bi-layout-split"></i> Open + viewport
                     </button>
                     <a href="{% url 'atlas:series_detail' pk=series.pk %}" 
                        class="btn btn-outline-secondary btn-xs btn-sm"
@@ -1339,32 +1347,202 @@
             }
         })();
 
-        // Series viewer button handler: open series in viewer or navigate to series page
+        // Series viewer button handlers: open series in primary viewport or new viewport.
         (function initSeriesViewerButtons() {
             if (window.__seriesViewerButtonsBound) return;
             window.__seriesViewerButtonsBound = true;
 
-            document.querySelectorAll('.series-open-viewer-btn').forEach(btn => {
+            function getViewerApi(baseName, fallbackName) {
-                btn.addEventListener('click', function(e) {
+                const fn = window[`${baseName}_main_viewer`] || (fallbackName ? window[fallbackName] : null);
+                return typeof fn === 'function' ? fn : null;
+            }
+
+            function ensureViewerOpen() {
+                const viewerDetails = document.getElementById('dicom-viewer-details');
+                if (viewerDetails && !viewerDetails.hasAttribute('open')) {
+                    viewerDetails.setAttribute('open', 'open');
+                    viewerDetails.dispatchEvent(new Event('toggle', { bubbles: true }));
+                }
+            }
+
+            function flattenNamedStacks(raw) {
+                const out = [];
+                if (!Array.isArray(raw)) {
+                    return out;
+                }
+
+                raw.forEach((item) => {
+                    if (item && typeof item === 'object' && Array.isArray(item.stacks)) {
+                        const caseId = item.caseId;
+                        const studyId = item.studyId;
+                        item.stacks.forEach((stack) => {
+                            if (stack && Array.isArray(stack.imageIds)) {
+                                out.push({
+                                    imageIds: stack.imageIds,
+                                    name: stack.name || '',
+                                    caseId: stack.caseId || caseId,
+                                    studyId: stack.studyId || studyId,
+                                    seriesId: stack.seriesId || null,
+                                });
+                            }
+                        });
+                    } else if (item && typeof item === 'object' && Array.isArray(item.imageIds)) {
+                        out.push({
+                            imageIds: item.imageIds,
+                            name: item.name || '',
+                            caseId: item.caseId || null,
+                            studyId: item.studyId || null,
+                            seriesId: item.seriesId || null,
+                        });
+                    }
+                });
+
+                return out;
+            }
+
+            function getNamedStacksFromMainViewer() {
+                const mainViewer = document.getElementById('main_viewer');
+                if (!mainViewer) {
+                    return [];
+                }
+
+                const raw = mainViewer.getAttribute('data-named-stacks') || '[]';
+                try {
+                    return flattenNamedStacks(JSON.parse(raw));
+                } catch (e) {
+                    console.warn('Failed to parse data-named-stacks', e);
+                    return [];
+                }
+            }
+
+            function findStackBySeries(stacks, seriesId, seriesName) {
+                const idNum = Number(seriesId);
+                let match = stacks.find((stack) => Number(stack.seriesId) === idNum);
+                if (!match && seriesName) {
+                    match = stacks.find((stack) => String(stack.name || '').trim() === String(seriesName).trim());
+                }
+                return match || null;
+            }
+
+            async function openSeriesInPrimary(seriesId, seriesName) {
+                ensureViewerOpen();
+                const mainViewer = document.getElementById('main_viewer');
+                if (!mainViewer) {
+                    return;
+                }
+
+                const stacks = getNamedStacksFromMainViewer();
+                const target = findStackBySeries(stacks, seriesId, seriesName);
+                if (!target) {
+                    alert('Series stack not found in this case viewer.');
+                    return;
+                }
+
+                const reordered = [target, ...stacks.filter((s) => s !== target)];
+                mainViewer.setAttribute('data-named-stacks', JSON.stringify(reordered));
+                try {
+                    await mountDicomViewersSafely();
+                } catch (e) {
+                    console.warn('Failed to remount viewer', e);
+                }
+            }
+
+            async function openSeriesInNewViewport(seriesId, seriesName) {
+                ensureViewerOpen();
+                const stacks = getNamedStacksFromMainViewer();
+                const target = findStackBySeries(stacks, seriesId, seriesName);
+                if (!target) {
+                    alert('Series stack not found in this case viewer.');
+                    return;
+                }
+
+                const exportStateFn = getViewerApi('exportViewerState');
+                const importStateFn = getViewerApi('importViewerState');
+
+                if (!exportStateFn || !importStateFn) {
+                    // Fallback: at least add stack to viewer list and auto-fill an empty viewport if available.
+                    const loadAdditionalStackFn = getViewerApi('loadAdditionalStack');
+                    if (loadAdditionalStackFn) {
+                        await loadAdditionalStackFn(target.imageIds, target.studyId);
+                    }
+                    return;
+                }
+
+                let state = {};
+                try {
+                    state = JSON.parse(exportStateFn() || '{}');
+                } catch (e) {
+                    state = {};
+                }
+
+                const currentStacks = Array.isArray(state.stacks) ? [...state.stacks] : [];
+                const toNorm = (ids) => (Array.isArray(ids) ? ids.map((id) => String(id).replace(/^wadouri:/, '')) : []);
+                const targetNorm = toNorm(target.imageIds);
+
+                let targetIdx = currentStacks.findIndex((stack) => {
+                    const ids = Array.isArray(stack?.i) ? stack.i : [];
+                    const norm = toNorm(ids);
+                    return norm.length === targetNorm.length && norm.every((id, i) => id === targetNorm[i]);
+                });
+
+                if (targetIdx < 0) {
+                    currentStacks.push({ i: target.imageIds, u: target.studyId || undefined });
+                    targetIdx = currentStacks.length - 1;
+                }
+
+                const grid = state.grid && Number.isFinite(state.grid.rows) && Number.isFinite(state.grid.cols)
+                    ? { rows: Math.max(1, Number(state.grid.rows)), cols: Math.max(1, Number(state.grid.cols)) }
+                    : { rows: 1, cols: 1 };
+
+                if ((grid.rows * grid.cols) < 2) {
+                    grid.cols = 2;
+                }
+
+                const numActive = Math.max(2, grid.rows * grid.cols);
+                const stackIdx = Array.isArray(state.stackIdx) ? [...state.stackIdx] : [];
+                const modes = Array.isArray(state.modes) ? [...state.modes] : [];
+                while (stackIdx.length < numActive) {
+                    stackIdx.push(0);
+                }
+                while (modes.length < numActive) {
+                    modes.push('stack');
+                }
+                stackIdx[1] = targetIdx;
+                modes[0] = 'stack';
+                modes[1] = 'stack';
+
+                const nextState = {
+                    ...state,
+                    grid,
+                    stacks: currentStacks,
+                    stackIdx,
+                    modes,
+                };
+
+                importStateFn(JSON.stringify(nextState));
+            }
+
+            document.querySelectorAll('.series-open-primary-btn').forEach((btn) => {
+                btn.addEventListener('click', async function (e) {
                     e.preventDefault();
                     const seriesId = this.getAttribute('data-series-id');
+                    const seriesName = this.getAttribute('data-series-name') || '';
                     if (!seriesId) {
-                        alert('Series ID not found');
                         return;
                     }
+                    await openSeriesInPrimary(seriesId, seriesName);
+                });
+            });
 
-                    // Focus the viewer details element to open it
+            document.querySelectorAll('.series-open-new-viewport-btn').forEach((btn) => {
-                    const viewerDetails = document.getElementById('dicom-viewer-details');
+                btn.addEventListener('click', async function (e) {
-                    if (viewerDetails && !viewerDetails.hasAttribute('open')) {
+                    e.preventDefault();
-                        viewerDetails.setAttribute('open', 'open');
+                    const seriesId = this.getAttribute('data-series-id');
-                        // Trigger the toggle event to ensure viewer initializes
+                    const seriesName = this.getAttribute('data-series-name') || '';
-                        viewerDetails.dispatchEvent(new Event('toggle', { bubbles: true }));
+                    if (!seriesId) {
+                        return;
                     }
-                    
+                    await openSeriesInNewViewport(seriesId, seriesName);
-                    // Note: Direct series loading will be implemented via API in the future.
-                    // For now, this just opens and focuses the viewer.
-                    // When the series page viewer API is available, we can load the specific series here:
-                    // window.loadSeriesInViewer(seriesId);
                 });
             });
         })();

atlas/templates/atlas/series_viewer.html

@@ -5,6 +5,16 @@
         <div class="row">
             <div class="col-12 mb-3">
                 <div class="card shadow-sm">
+                    <div class="card-header d-flex flex-wrap align-items-center justify-content-between gap-2">
+                        <div class="small text-uppercase text-muted fw-semibold">Series Navigation</div>
+                        <div class="d-flex flex-wrap gap-2">
+                            <a class="btn btn-outline-secondary btn-sm" href="{% url 'atlas:series_detail' pk=series.pk %}">Series details</a>
+                            {% if can_edit %}
+                                <a class="btn btn-outline-secondary btn-sm" href="{% url 'atlas:task_overview' %}">Tasks</a>
+                            {% endif %}
+                            <button id="reset-viewport-button" class="btn btn-outline-secondary btn-sm">Reset viewport</button>
+                        </div>
+                    </div>
                     <div class="card-body d-flex flex-column flex-md-row justify-content-between align-items-start gap-3">
                         <div>
                             <h4 class="card-title mb-1">Series: {{ series.modality }} - {{ series.examination }}</h4>
@@ -12,14 +22,6 @@
                             <div class="mt-2">Description: <span class="text-break">{{ series.description }}</span></div>
                             <div class="mt-2 text-muted">Author: {{ series.get_author_display }}</div>
                         </div>
-                        <div class="ms-auto d-flex gap-2">
-                            <a class="btn btn-outline-secondary btn-sm" href="{% url 'atlas:series_detail' pk=series.pk %}">View series</a>
-                            {% if can_edit %}
-                                <button id="reset-viewport-button" class="btn btn-secondary btn-sm">Reset viewport</button>
-                            {% else %}
-                                <button id="reset-viewport-button" class="btn btn-secondary btn-sm">Reset viewport</button>
-                            {% endif %}
-                        </div>
                     </div>
                 </div>
             </div>
@@ -212,7 +214,7 @@
                             <button class="btn btn-outline-warning btn-sm"
                                     data-bs-toggle="modal"
                                     data-bs-target="#truncate-series-modal">
-                                <i class="bi bi-scissors"></i> Truncate series
+                                <i class="bi bi-sliders"></i> Series tools
                             </button>
 
                             <div class="card mt-2">
@@ -255,7 +257,7 @@
             <div class="modal-dialog modal-dialog-centered modal-xl">
                 <div class="modal-content">
                     <div class="modal-header">
-                        <h5 class="modal-title">Series Optimization</h5>
+                        <h5 class="modal-title">Series Tools</h5>
                         <button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
                     </div>
                     <div class="modal-body">

atlas/templates/atlas/task_overview.html

@@ -82,6 +82,7 @@ Atlas Task Overview
                 <option value="reset_selected">Reset selected to READY (skip RUNNING)</option>
                 <option value="delete_completed">Delete selected COMPLETED</option>
                 <option value="delete_failed">Delete selected FAILED</option>
+                <option value="delete_selected_all">Delete ALL selected (including RUNNING)</option>
             </select>
             <button type="submit" class="btn btn-sm btn-primary">Apply to selected</button>
             <div class="form-check ms-2">

atlas/views.py

@@ -307,7 +307,45 @@ def _resize_array_nearest(arr, target_rows, target_cols):
     return arr[np.ix_(row_idx, col_idx)]
 
 
-def _downsample_dicom_dataset(ds, reduction_pct):
+def _stamp_derived_dataset(
+    ds,
+    *,
+    series_instance_uid=None,
+    series_description=None,
+    derivation_description=None,
+    image_type=None,
+    regenerate_sop_instance_uid=True,
+    stamp_series_datetime=True,
+):
+    now = timezone.now()
+    date_str = now.strftime("%Y%m%d")
+    time_str = now.strftime("%H%M%S.%f")[:13]
+
+    if regenerate_sop_instance_uid:
+        ds.SOPInstanceUID = generate_uid()
+    if series_instance_uid:
+        ds.SeriesInstanceUID = series_instance_uid
+    if series_description:
+        ds.SeriesDescription = series_description
+
+    ds.ImageType = image_type or ["DERIVED", "SECONDARY"]
+
+    if derivation_description:
+        ds.DerivationDescription = derivation_description
+
+    ds.ContentDate = date_str
+    ds.ContentTime = time_str
+    ds.InstanceCreationDate = date_str
+    ds.InstanceCreationTime = time_str
+
+    if stamp_series_datetime:
+        ds.SeriesDate = date_str
+        ds.SeriesTime = time_str
+
+    return ds
+
+
+def _downsample_dicom_dataset(ds, reduction_pct, *, series_instance_uid=None, series_description=None):
     if reduction_pct <= 0 or reduction_pct >= 100:
         raise ValueError("Downsample percentage must be between 1 and 99")
 
@@ -321,11 +359,36 @@ def _downsample_dicom_dataset(ds, reduction_pct):
     target_cols = max(1, int(round(px.shape[1] * factor)))
     resized = _resize_array_nearest(px, target_rows, target_cols)
 
+    derivation_description = f"Downsampled by {reduction_pct}% using nearest-neighbour resize"
+    _stamp_derived_dataset(
+        ds,
+        series_instance_uid=series_instance_uid,
+        series_description=series_description,
+        derivation_description=derivation_description,
+        image_type=["DERIVED", "SECONDARY"],
+    )
+
+    if hasattr(ds, "PixelSpacing") and ds.PixelSpacing and len(ds.PixelSpacing) >= 2:
+        row_spacing = _safe_float(ds.PixelSpacing[0], 1.0)
+        col_spacing = _safe_float(ds.PixelSpacing[1], 1.0)
+        ds.PixelSpacing = [float(row_spacing / factor), float(col_spacing / factor)]
+
+    if hasattr(ds, "ImagerPixelSpacing") and ds.ImagerPixelSpacing and len(ds.ImagerPixelSpacing) >= 2:
+        row_spacing = _safe_float(ds.ImagerPixelSpacing[0], 1.0)
+        col_spacing = _safe_float(ds.ImagerPixelSpacing[1], 1.0)
+        ds.ImagerPixelSpacing = [float(row_spacing / factor), float(col_spacing / factor)]
+
+    if hasattr(ds, "NominalScannedPixelSpacing") and ds.NominalScannedPixelSpacing and len(ds.NominalScannedPixelSpacing) >= 2:
+        row_spacing = _safe_float(ds.NominalScannedPixelSpacing[0], 1.0)
+        col_spacing = _safe_float(ds.NominalScannedPixelSpacing[1], 1.0)
+        ds.NominalScannedPixelSpacing = [float(row_spacing / factor), float(col_spacing / factor)]
+
     ds.Rows = int(target_rows)
     ds.Columns = int(target_cols)
     ds.PixelData = resized.tobytes()
     ds.pop("SmallestImagePixelValue", None)
     ds.pop("LargestImagePixelValue", None)
+    ds.pop("PixelAspectRatio", None)
     return ds
 
 
@@ -606,7 +669,12 @@ def series_optimize_htmx(request, series_id):
                     continue
 
                 try:
-                    ds_out = _downsample_dicom_dataset(ds, downsample_pct)
+                    ds_out = _downsample_dicom_dataset(
+                        ds,
+                        downsample_pct,
+                        series_instance_uid=preview_series.series_instance_uid,
+                        series_description=preview_series.description,
+                    )
                 except Exception as exc:
                     logger.warning("Downsample preview failed for image {}: {}", image.pk, exc)
                     continue
@@ -645,6 +713,7 @@ def series_optimize_htmx(request, series_id):
             )
 
         downsampled = []
+        replacement_series_uid = generate_uid()
         for image in full_series_images:
             ds = _read_series_image_dataset(image)
             if ds is None:
@@ -652,7 +721,12 @@ def series_optimize_htmx(request, series_id):
 
             try:
                 original_hash = image.image_blake3_hash
-                ds_out = _downsample_dicom_dataset(ds, downsample_pct)
+                ds_out = _downsample_dicom_dataset(
+                    ds,
+                    downsample_pct,
+                    series_instance_uid=replacement_series_uid,
+                    series_description=series.description,
+                )
                 out_io = io.BytesIO()
                 ds_out.save_as(out_io, write_like_original=False)
                 out_io.seek(0)
@@ -671,7 +745,8 @@ def series_optimize_htmx(request, series_id):
 
         if downsampled:
             series.modified = Series.SeriesModifiedChocies.RE
-            series.save(update_fields=["modified"])
+            series.series_instance_uid = replacement_series_uid
+            series.save(update_fields=["modified", "series_instance_uid"])
 
         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>'
@@ -861,6 +936,9 @@ def task_overview(request):
         elif action == "delete_failed":
             deleted, _ = selected_qs.filter(status="FAILED").delete()
             messages.success(request, f"Deleted {deleted} failed task record(s).")
+        elif action == "delete_selected_all":
+            deleted, _ = selected_qs.delete()
+            messages.success(request, f"Deleted {deleted} selected task record(s).")
         else:
             messages.error(request, "Invalid task action requested.")