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.
This commit is contained in:
Ross
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),
),
]
+1
View File
@@ -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")
+101 -2
View File
@@ -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}; "
+31 -32
View File
@@ -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;
}
+5
View File
@@ -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"),
+105 -38
View File
@@ -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):
+26 -10
View File
@@ -5855,15 +5855,31 @@ def create_user(request, context=None, trainee: bool = False):
if form.is_valid():
try:
username = form.cleaned_data["username"].strip().lower()
existing_user = User.objects.filter(
Q(username__iexact=username) | Q(email__iexact=username)
).first()
user_dict = {
"username": request.POST["username"],
"first_name": request.POST["first_name"],
"last_name": request.POST["last_name"],
"email": request.POST["username"],
"username": username,
"first_name": form.cleaned_data["first_name"],
"last_name": form.cleaned_data["last_name"],
"email": username,
"password": secrets.token_hex(nbytes=16),
}
new_user = User.objects.create_user(**user_dict)
with transaction.atomic():
if existing_user is not None:
existing_user.username = user_dict["username"]
existing_user.email = user_dict["email"]
existing_user.first_name = user_dict["first_name"]
existing_user.last_name = user_dict["last_name"]
existing_user.save(
update_fields=["username", "email", "first_name", "last_name"]
)
new_user = existing_user
else:
new_user = User.objects.create_user(**user_dict)
except Exception as error:
errors = f"Unable to create account: {error}"
return render(
@@ -5873,15 +5889,15 @@ def create_user(request, context=None, trainee: bool = False):
)
try:
user_profile = UserProfile.objects.get(user=new_user)
user_profile, _ = UserProfile.objects.get_or_create(user=new_user)
user_profile.peninsula_trainee = trainee
if request.POST["grade"]:
grade = UserGrades.objects.get(pk=request.POST["grade"])
if form.cleaned_data.get("grade"):
grade = form.cleaned_data["grade"]
user_profile.grade = grade
if "supervisor" in request.POST and request.POST["supervisor"]:
supervisor = Supervisor.objects.get(pk=request.POST["supervisor"])
if trainee and form.cleaned_data.get("supervisor"):
supervisor = form.cleaned_data["supervisor"]
user_profile.supervisor = supervisor
user_profile.save()
+210 -210
View File
File diff suppressed because one or more lines are too long
+51
View File
@@ -1,5 +1,6 @@
from django.urls import reverse
from django.core import mail
from rich.pretty import pprint
@@ -89,3 +90,53 @@ def test_profile_access_and_management(db, client, create_users, create_cid_mana
assert BeautifulSoup(update_profile_response.content, "html.parser").find(id="id_registration_number")["value"]
@pytest.mark.django_db
def test_create_user_reuses_existing_account(client, create_cid_manager, django_user_model):
existing_user = django_user_model.objects.create_user(
username="existing@example.com",
email="existing@example.com",
password="password123",
first_name="Old",
last_name="Name",
)
client.force_login(create_cid_manager)
response = client.post(
reverse("create_user"),
{
"username": "existing@example.com",
"first_name": "Updated",
"last_name": "User",
"grade": "",
},
)
assert response.status_code == 302
assert response.url == reverse("accounts_list")
existing_user.refresh_from_db()
assert existing_user.first_name == "Updated"
assert existing_user.last_name == "User"
@pytest.mark.django_db
def test_cid_manager_can_send_password_reset_from_account_profile(client, create_cid_manager, django_user_model):
managed_user = django_user_model.objects.create_user(
username="managed-user",
email="managed@example.com",
password="password123",
)
client.force_login(create_cid_manager)
response = client.post(
reverse("account_send_password_reset", kwargs={"slug": managed_user.username}),
{"next": reverse("account_profile", kwargs={"slug": managed_user.username})},
)
assert response.status_code == 302
assert "password_reset_action=sent" in response.url
assert len(mail.outbox) == 1
assert mail.outbox[0].to == ["managed@example.com"]
+5
View File
@@ -107,6 +107,11 @@ urlpatterns = [
views.account_set_supervisor,
name="account_set_supervisor",
),
path(
"accounts/profile/<str:slug>/send-password-reset/",
views.account_send_password_reset,
name="account_send_password_reset",
),
#path("", TemplateView.as_view(template_name="index.html"), name="home"),
path("", views.index, name="home"),
path("cid/results/<int:cid>/", views.cid_results, name="cid_results"),
+35
View File
@@ -30,6 +30,7 @@ from django.utils.safestring import mark_safe
# from django.contrib.auth.models import User
from django.contrib.auth.decorators import login_required, user_passes_test
from django.contrib.auth.forms import PasswordResetForm
from django.contrib.auth.models import User
from django.contrib.contenttypes.models import ContentType
@@ -167,6 +168,7 @@ def profile(request):
"is_cid_user_manager": is_cid_user_manager,
"supervisor_account": supervisor_account,
"supervisor_action": request.GET.get("supervisor_action", ""),
"password_reset_action": request.GET.get("password_reset_action", ""),
},
)
@@ -216,6 +218,7 @@ def account_profile(request, slug):
"is_cid_user_manager": is_cid_user_manager,
"supervisor_account": supervisor_account,
"supervisor_action": request.GET.get("supervisor_action", ""),
"password_reset_action": request.GET.get("password_reset_action", ""),
},
)
@@ -257,6 +260,38 @@ def account_set_supervisor(request, slug):
return redirect(f"{next_url}?supervisor_action=created")
@require_POST
@user_is_cid_user_manager
def account_send_password_reset(request, slug):
"""Send a password reset email for an existing user from their profile page."""
user = get_object_or_404(User, username=slug)
next_url = request.POST.get("next") or reverse("account_profile", kwargs={"slug": user.username})
email = (user.email or user.username or "").strip()
if not email:
return redirect(f"{next_url}?password_reset_action=no_email")
if not user.is_active:
return redirect(f"{next_url}?password_reset_action=inactive")
form = PasswordResetForm({"email": email})
if not form.is_valid():
return redirect(f"{next_url}?password_reset_action=invalid")
try:
form.save(
request=request,
use_https=request.is_secure(),
from_email=getattr(settings, "DEFAULT_FROM_EMAIL", None),
)
except Exception:
logger.exception("Failed to send password reset email for user {}", user.pk)
return redirect(f"{next_url}?password_reset_action=error")
return redirect(f"{next_url}?password_reset_action=sent")
@user_passes_test(lambda u: u.is_superuser)
def logs_view(request):
"""Display production logs from log.txt with search filtering.
+20 -2
View File
@@ -104,13 +104,31 @@
<div class="alert alert-danger py-2" role="alert">Cannot link supervisor account: email is already linked to another user.</div>
{% endif %}
<a class="btn btn-outline-primary d-block mb-2" href="{% url 'password_change' %}">Change password</a>
{% if password_reset_action == 'sent' %}
<div class="alert alert-success py-2" role="alert">Password reset email sent.</div>
{% elif password_reset_action == 'no_email' %}
<div class="alert alert-warning py-2" role="alert">Cannot send password reset: user has no email address.</div>
{% elif password_reset_action == 'inactive' %}
<div class="alert alert-warning py-2" role="alert">Cannot send password reset: user account is inactive.</div>
{% elif password_reset_action == 'invalid' %}
<div class="alert alert-danger py-2" role="alert">Cannot send password reset: email address is invalid.</div>
{% elif password_reset_action == 'error' %}
<div class="alert alert-danger py-2" role="alert">Password reset email could not be sent.</div>
{% endif %}
<a class="btn btn-outline-primary d-block mb-2" href="{% url 'password_change' %}" id="password-change">Change password</a>
{% if request.user|has_group:"cid_user_manager" %}
<a class="btn btn-outline-secondary d-block mb-2" href="{% url 'account_update' user.username %}">Update user details</a>
{% endif %}
<a class="btn btn-primary d-block mb-2" href="{% url 'account_profile_update' user.username %}">Edit profile</a>
<a class="btn btn-primary d-block mb-2" href="{% url 'account_profile_update' user.username %}" id="update-profile-link">Edit profile</a>
{% if request.user.is_superuser or is_cid_user_manager %}
<form method="post" action="{% url 'account_send_password_reset' user.username %}" class="mb-2">
{% csrf_token %}
<input type="hidden" name="next" value="{{ request.get_full_path }}">
<button type="submit" class="btn btn-outline-warning d-block w-100">Send password reset link</button>
</form>
{% if not supervisor_account %}
<form method="post" action="{% url 'account_set_supervisor' user.username %}" class="mb-2">
{% csrf_token %}