Add downsample series functionality and related UI updates

- Implemented asynchronous downsample task for series with progress tracking. - Added new URL endpoint for downsample status. - Updated Series model to include source_series_instance_uid. - Enhanced case display template with new buttons for series actions. - Added password reset functionality in user profile with appropriate alerts. - Created migration for new source_series_instance_uid field in Series model.
2026-05-18 16:20:38 +01:00
parent c55797636a
commit 63ea4cdf23
12 changed files with 606 additions and 294 deletions
@@ -0,0 +1,16 @@
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("atlas", "0103_casecollection_auto_apply_question_template_and_more"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="series",
+            name="source_series_instance_uid",
+            field=models.CharField(blank=True, db_index=True, max_length=255, null=True),
+        ),
+    ]
@@ -1132,6 +1132,7 @@ class Series(SeriesBase):
    )

    series_instance_uid = models.CharField(max_length=255, blank=True, null=True)
+    source_series_instance_uid = models.CharField(max_length=255, blank=True, null=True, db_index=True)
    study_instance_uid = models.CharField(max_length=255, blank=True, null=True, db_index=True)

    # findings = models.TextField(null=True, blank=True, help_text="Findings on the series / stack")
@@ -92,6 +92,106 @@ from django.core.cache import cache
 import copy
 import io

+
+@task(takes_context=True)
+def series_downsample_task(context, series_id, user_id, downsample_pct):
+    """Downsample a series asynchronously while preserving hash continuity."""
+    from loguru import logger
+    from atlas import views as atlas_views
+
+    progress_key = f"series_downsample_progress:{context.task_result.id}"
+    cache.set(
+        progress_key,
+        {"current": 0, "total": 0, "message": "Preparing downsample..."},
+        timeout=60 * 60,
+    )
+
+    series = get_object_or_404(Series, pk=series_id)
+    user = get_object_or_404(User, pk=user_id)
+
+    if not series.check_user_can_edit(user):
+        raise PermissionError("Permission denied")
+
+    images = list(series.get_images())
+    total_images = len(images)
+    replacement_series_uid = generate_uid()
+    source_series_uid = series.series_instance_uid
+    updated_images = []
+
+    cache.set(
+        progress_key,
+        {"current": 0, "total": total_images, "message": "Downsample started"},
+        timeout=60 * 60,
+    )
+
+    for idx, image in enumerate(images, start=1):
+        ds = atlas_views._read_series_image_dataset(image)
+        if ds is None:
+            cache.set(
+                progress_key,
+                {"current": idx, "total": total_images, "message": f"Skipping unreadable image ({idx}/{total_images})"},
+                timeout=60 * 60,
+            )
+            continue
+
+        try:
+            original_hash = image.image_blake3_hash
+            ds_out = atlas_views._downsample_dicom_dataset(
+                ds,
+                int(downsample_pct),
+                series_instance_uid=replacement_series_uid,
+                source_series_instance_uid=source_series_uid,
+                series_description=series.description,
+            )
+            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,
+            )
+            image.image_blake3_hash = original_hash
+            image.save(update_fields=["image", "image_blake3_hash"])
+            updated_images.append(image.pk)
+        except Exception as exc:
+            logger.warning("Downsample failed for image {}: {}", image.pk, exc)
+
+        cache.set(
+            progress_key,
+            {
+                "current": idx,
+                "total": total_images,
+                "message": f"Downsampling image {idx}/{total_images}",
+            },
+            timeout=60 * 60,
+        )
+
+    if updated_images:
+        series.modified = Series.SeriesModifiedChocies.RE
+        series.source_series_instance_uid = source_series_uid
+        series.series_instance_uid = replacement_series_uid
+        series.save(update_fields=["modified", "source_series_instance_uid", "series_instance_uid"])
+
+    cache.set(
+        progress_key,
+        {
+            "current": total_images,
+            "total": total_images,
+            "message": "Downsample complete",
+        },
+        timeout=10 * 60,
+    )
+
+    return {
+        "series_id": series.pk,
+        "downsample_pct": int(downsample_pct),
+        "updated_images": len(updated_images),
+        "series_instance_uid": replacement_series_uid,
+        "source_series_instance_uid": source_series_uid,
+    }
+
@task
 def push_case_to_cimar_task(case_id):
    """Sends an email when the feedback form has been submitted."""
@@ -389,8 +489,6 @@ def series_reconstruct_task(

    for plane_norm, cfg in plane_builders.items():
        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"])

        for idx in range(int(cfg["count"])):
            arr2d = cfg["slice_fn"](idx)
@@ -403,6 +501,7 @@ def series_reconstruct_task(
            atlas_views._stamp_derived_dataset(
                ds_new,
                series_instance_uid=recon_series.series_instance_uid,
+                source_series_instance_uid=series.series_instance_uid,
                series_description=recon_series.description or f"Recon {plane_norm.title()}",
                derivation_description=(
                f"{plane_norm.title()} reconstruction; mode={recon_thickness_mode}; "
@@ -13,7 +13,7 @@
                 draggable="true">
            <input type="checkbox" class="hide" name="series-ids" value="{{series.pk}}">
            <div class="series-card-shell">
-                <button type="button"
+                <div type="button"
                        class="series-card-main"
                        data-series-action="details"
                        data-series-id="{{series.pk}}"
@@ -37,32 +37,31 @@
                            <span class="series-card-image-count">{{ series.visible_image_count }} image{{ series.visible_image_count|pluralize }}</span>
                        </div>
                        <div class="series-card-description">{{ series.description|default:"No description" }}</div>
+                        <button type="button"
+                                class="btn btn-outline-info btn-sm series-open-primary-btn"
+                                title="View series in viewer"
+                                data-series-id="{{series.pk}}"
+                                data-series-name="{{ series|escape }}">
+                            <i class="bi bi-eye"></i> View1
+                        </button>
+                        <div class="series-card-inline-actions">
+                            <button type="button"
+                                    class="btn btn-outline-primary btn-sm select-series-btn"
+                                    style="display: none;"
+                                    data-series-id="{{series.pk}}">
+                                Select
+                            </button>
+                            <button type="button"
+                                    class="btn btn-outline-info btn-sm series-open-new-viewport-btn d-none"
+                                    title="View series in a new pane"
+                                    data-series-id="{{series.pk}}"
+                                    data-series-name="{{ series|escape }}"
+                                    tabindex="-1"
+                                    aria-hidden="true">
+                                <i class="bi bi-layout-split"></i> View in new pane
+                            </button>
+                        </div>
                    </div>
-                </button>
-
-                <div class="series-card-controls">
-                    <button type="button"
-                            class="btn btn-outline-primary btn-sm select-series-btn"
-                            style="display: none;"
-                            data-series-id="{{series.pk}}">
-                        Select
-                    </button>
-                    <button type="button"
-                            class="btn btn-outline-info btn-sm series-open-primary-btn"
-                            title="View series in viewer"
-                            data-series-id="{{series.pk}}"
-                            data-series-name="{{ series|escape }}">
-                        <i class="bi bi-eye"></i> View
-                    </button>
-                    <button type="button"
-                            class="btn btn-outline-info btn-sm series-open-new-viewport-btn d-none"
-                            title="View series in a new pane"
-                            data-series-id="{{series.pk}}"
-                            data-series-name="{{ series|escape }}"
-                            tabindex="-1"
-                            aria-hidden="true">
-                        <i class="bi bi-layout-split"></i> View in new pane
-                    </button>
                </div>
            </div>
        </article>
@@ -2122,7 +2121,7 @@
            min-width: 0;
            display: flex;
            flex-direction: column;
-            gap: 0.15rem;
+            gap: 0.3rem;
        }
        .series-card-heading {
            font-size: 0.85rem;
@@ -2145,14 +2144,14 @@
            -webkit-box-orient: vertical;
            overflow: hidden;
        }
-        .series-card-controls {
+        .series-card-inline-actions {
            display: flex;
+            flex-wrap: wrap;
            gap: 0.4rem;
-            margin-top: auto;
+            margin-top: 0.2rem;
        }
-        .series-card-controls .btn {
-            flex: 1;
-            min-width: 0;
+        .series-card-inline-actions .btn {
+            flex: 0 0 auto;
            padding: 0.3rem 0.4rem;
            font-size: 0.75rem;
        }
@@ -576,6 +576,11 @@ urlpatterns = [
            views.series_reconstruct_status_htmx,
            name="series_reconstruct_status",
        ),
+        path(
+            "series/<int:series_id>/downsample/status/<str:task_id>/",
+            views.series_downsample_status_htmx,
+            name="series_downsample_status",
+        ),
    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"),
@@ -165,7 +165,7 @@ from .filters import (
    NormalCaseFilter,
 )

-from .tasks import push_case_to_cimar_task, series_reconstruct_task
+from .tasks import push_case_to_cimar_task, series_downsample_task, series_reconstruct_task
 try:
    from django_tasks import TaskResultStatus
 except ImportError:
@@ -313,6 +313,7 @@ def _stamp_derived_dataset(
    ds,
    *,
    series_instance_uid=None,
+    source_series_instance_uid=None,
    series_description=None,
    derivation_description=None,
    image_type=None,
@@ -322,6 +323,8 @@ def _stamp_derived_dataset(
    now = timezone.now()
    date_str = now.strftime("%Y%m%d")
    time_str = now.strftime("%H%M%S.%f")[:13]
+    source_sop_instance_uid = getattr(ds, "SOPInstanceUID", None)
+    source_sop_class_uid = getattr(ds, "SOPClassUID", None)

    if regenerate_sop_instance_uid:
        ds.SOPInstanceUID = generate_uid()
@@ -335,6 +338,18 @@ def _stamp_derived_dataset(
    if derivation_description:
        ds.DerivationDescription = derivation_description

+    if source_series_instance_uid:
+        series_ref = pydicom.dataset.Dataset()
+        series_ref.SeriesInstanceUID = str(source_series_instance_uid)
+        ds.ReferencedSeriesSequence = pydicom.sequence.Sequence([series_ref])
+
+    if source_sop_instance_uid:
+        source_ref = pydicom.dataset.Dataset()
+        if source_sop_class_uid:
+            source_ref.ReferencedSOPClassUID = str(source_sop_class_uid)
+        source_ref.ReferencedSOPInstanceUID = str(source_sop_instance_uid)
+        ds.SourceImageSequence = pydicom.sequence.Sequence([source_ref])
+
    ds.ContentDate = date_str
    ds.ContentTime = time_str
    ds.InstanceCreationDate = date_str
@@ -347,7 +362,14 @@ def _stamp_derived_dataset(
    return ds


-def _downsample_dicom_dataset(ds, reduction_pct, *, series_instance_uid=None, series_description=None):
+def _downsample_dicom_dataset(
+    ds,
+    reduction_pct,
+    *,
+    series_instance_uid=None,
+    source_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")

@@ -365,6 +387,7 @@ def _downsample_dicom_dataset(ds, reduction_pct, *, series_instance_uid=None, se
    _stamp_derived_dataset(
        ds,
        series_instance_uid=series_instance_uid,
+        source_series_instance_uid=source_series_instance_uid,
        series_description=series_description,
        derivation_description=derivation_description,
        image_type=["DERIVED", "SECONDARY"],
@@ -399,6 +422,7 @@ def _create_series_derivative(source_series, description_suffix):
    derived.pk = None
    derived.id = None
    derived.series_instance_uid = generate_uid()
+    derived.source_series_instance_uid = source_series.series_instance_uid
    derived.description = f"{source_series.description or 'Series'} [{description_suffix}]"
    derived.modified = Series.SeriesModifiedChocies.RE
    derived.save()
@@ -675,6 +699,7 @@ def series_optimize_htmx(request, series_id):
                        ds,
                        downsample_pct,
                        series_instance_uid=preview_series.series_instance_uid,
+                        source_series_instance_uid=series.series_instance_uid,
                        series_description=preview_series.description,
                    )
                except Exception as exc:
@@ -714,44 +739,22 @@ 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:
-                continue
-
-            try:
-                original_hash = image.image_blake3_hash
-                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)
-
-                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.series_instance_uid = replacement_series_uid
-            series.save(update_fields=["modified", "series_instance_uid"])
+        task_result = series_downsample_task.enqueue(
+            series_id=series.pk,
+            user_id=request.user.pk,
+            downsample_pct=downsample_pct,
+        )

        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>'
+            (
+                '<div class="alert alert-info mb-2">'
+                'Downsample queued. This runs in the background to avoid request timeout.'
+                '</div>'
+                f'<div id="downsample-task-status" hx-get="{reverse("atlas:series_downsample_status", kwargs={"series_id": series.pk, "task_id": task_result.id})}" '
+                'hx-trigger="load, every 2s" hx-swap="outerHTML">'
+                '<div class="d-flex align-items-center gap-2"><span class="spinner-border spinner-border-sm text-primary" role="status"></span>'
+                '<span class="small text-muted">Starting downsample task...</span></div></div>'
+            )
        )

    if operation == "reconstruct":
@@ -881,6 +884,70 @@ def series_reconstruct_status_htmx(request, series_id, task_id):
    )


+@login_required
+def series_downsample_status_htmx(request, series_id, task_id):
+    """HTMX endpoint returning progress for a queued series downsample task."""
+    series = get_object_or_404(Series, pk=series_id)
+    target_id = (request.GET.get("target_id") or "downsample-task-status").strip() or "downsample-task-status"
+    target_id = escape(target_id)
+
+    if not series.check_user_can_edit(request.user):
+        return HttpResponse(f'<div id="{target_id}" class="alert alert-danger mb-0">Permission denied</div>')
+
+    try:
+        task_result = series_downsample_task.get_result(task_id)
+    except NotImplementedError:
+        return HttpResponse(
+            f'<div id="{target_id}" class="alert alert-warning mb-0">Task backend does not support result polling. Configure a backend with result retrieval support.</div>'
+        )
+    except Exception:
+        return HttpResponse(f'<div id="{target_id}" class="alert alert-danger mb-0">Task result not found.</div>')
+
+    task_result.refresh()
+    state = task_result.status
+
+    poll_url = reverse("atlas:series_downsample_status", kwargs={"series_id": series.pk, "task_id": task_id})
+    progress = cache.get(f"series_downsample_progress:{task_id}") or {}
+    current = int(progress.get("current", 0) or 0)
+    total = int(progress.get("total", 0) or 0)
+    message = escape(str(progress.get("message", "Downsample is running...")))
+    pct = int((current / total) * 100) if total > 0 else 0
+
+    if state in (TaskResultStatus.READY, TaskResultStatus.RUNNING):
+        return HttpResponse(
+            (
+                f'<div id="{target_id}" hx-get="{poll_url}?target_id={target_id}" hx-trigger="every 2s" hx-swap="outerHTML">'
+                f'<div class="small text-muted mb-1">{message}</div>'
+                '<div class="progress" style="height: 10px;">'
+                f'<div class="progress-bar progress-bar-striped progress-bar-animated" role="progressbar" style="width: {pct}%" '
+                f'aria-valuenow="{pct}" aria-valuemin="0" aria-valuemax="100"></div>'
+                '</div>'
+                f'<div class="small text-muted mt-1">{current}/{total} images processed</div>'
+                '</div>'
+            )
+        )
+
+    if state == TaskResultStatus.SUCCESSFUL:
+        payload = task_result.return_value or {}
+        updated = int(payload.get("updated_images", 0) or 0)
+        downsample_pct = escape(str(payload.get("downsample_pct", "")))
+        return HttpResponse(
+            f'<div id="{target_id}" class="alert alert-success mb-0">Downsample complete ({downsample_pct}%). Updated <strong>{updated}</strong> images while preserving original hashes.</div>'
+        )
+
+    if state == TaskResultStatus.FAILED:
+        err = "Unknown failure"
+        if task_result.errors:
+            err = escape(task_result.errors[-1].traceback.splitlines()[-1])
+        return HttpResponse(
+            f'<div id="{target_id}" class="alert alert-danger mb-0">Downsample failed: {err}</div>'
+        )
+
+    return HttpResponse(
+        f'<div id="{target_id}" class="alert alert-secondary mb-0">Task state: {escape(str(state))}</div>'
+    )
+
+
@login_required
@user_is_atlas_editor
 def task_overview(request):