improve dicom uploading

atlas/api.py

@@ -66,11 +66,17 @@ def upload_dicom(request, files: List[UploadedFile] = File(...)):
     return {"uploaded": uploaded, "duplicates": duplicate}
 
 
-@router.get("/clear_dicoms", auth=django_auth)
+@router.post("/clear_dicoms", auth=django_auth)
 def clear_dicoms(request):
+
+    if "selection" in request.POST:
+        dicoms = UncategorisedDicom.objects.filter(series_instance_uid__in=request.POST.getlist("selection"))
+
+    else:
         dicoms = UncategorisedDicom.objects.filter(user=request.user)
 
     dicoms.delete()
+    print(dicoms)
 
     return True
 
@@ -90,6 +96,11 @@ def uncategorised_dicoms(request):
 
 
 def import_dicoms_helper(request, case_id: int | None = None):
+    #dicoms = UncategorisedDicom.objects.filter(user=request.user)
+    if "selection" in request.POST:
+        dicoms = UncategorisedDicom.objects.filter(series_instance_uid__in=request.POST.getlist("selection"))
+
+    else:
         dicoms = UncategorisedDicom.objects.filter(user=request.user)
 
     data = defaultdict(list)
@@ -136,12 +147,12 @@ def import_dicoms_helper(request, case_id: int | None = None):
     return series_list
 
 
-@router.get("/import_dicoms", auth=django_auth, response=List[SeriesSchema])
+@router.post("/import_dicoms", auth=django_auth, response=List[SeriesSchema])
 def import_dicoms(request):
     return import_dicoms_helper(request)
 
 
-@router.get("/import_dicoms/{case_id}", auth=django_auth, response=List[SeriesSchema])
+@router.post("/import_dicoms/{case_id}", auth=django_auth, response=List[SeriesSchema])
 def import_dicoms_case(request, case_id: int):
     return import_dicoms_helper(request, case_id=case_id)
 

atlas/forms.py

@@ -223,7 +223,7 @@ class SeriesForm(ModelForm):
 
     class Meta:
         model = Series
-        exclude = ["author"]
+        exclude = ["author", "series_instance_uid"]
 
         widgets = {
             "examination": autocomplete.ModelSelect2(

atlas/migrations/0017_series_created_at_series_updated_at.py

@@ -0,0 +1,25 @@
+# Generated by Django 4.1.4 on 2023-10-23 08:53
+
+from django.db import migrations, models
+import django.utils.timezone
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0016_remove_uncategoriseddicom_is_dicom'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='series',
+            name='created_at',
+            field=models.DateTimeField(auto_now_add=True, default=django.utils.timezone.now),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name='series',
+            name='updated_at',
+            field=models.DateTimeField(auto_now=True),
+        ),
+    ]

atlas/migrations/0018_rename_created_at_series_created_date_and_more.py

@@ -0,0 +1,23 @@
+# Generated by Django 4.1.4 on 2023-10-23 09:00
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0017_series_created_at_series_updated_at'),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name='series',
+            old_name='created_at',
+            new_name='created_date',
+        ),
+        migrations.RenameField(
+            model_name='series',
+            old_name='updated_at',
+            new_name='modified_date',
+        ),
+    ]

atlas/migrations/0019_uncategoriseddicom_series_instance_uid.py

@@ -0,0 +1,19 @@
+# Generated by Django 4.1.4 on 2023-10-23 10:45
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0018_rename_created_at_series_created_date_and_more'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='uncategoriseddicom',
+            name='series_instance_uid',
+            field=models.CharField(default='test', max_length=255),
+            preserve_default=False,
+        ),
+    ]

atlas/migrations/0020_alter_uncategoriseddicom_series_instance_uid.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.1.4 on 2023-10-23 10:46
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0019_uncategoriseddicom_series_instance_uid'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='uncategoriseddicom',
+            name='series_instance_uid',
+            field=models.CharField(default='', max_length=255),
+        ),
+    ]

atlas/migrations/0021_alter_uncategoriseddicom_series_instance_uid.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.1.4 on 2023-10-23 10:51
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0020_alter_uncategoriseddicom_series_instance_uid'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='uncategoriseddicom',
+            name='series_instance_uid',
+            field=models.CharField(default='', max_length=255, null=True),
+        ),
+    ]

atlas/migrations/0022_alter_uncategoriseddicom_series_and_more.py

@@ -0,0 +1,24 @@
+# Generated by Django 4.1.4 on 2023-10-23 11:07
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0021_alter_uncategoriseddicom_series_instance_uid'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='uncategoriseddicom',
+            name='series',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='imported_dicoms', to='atlas.series'),
+        ),
+        migrations.AlterField(
+            model_name='uncategoriseddicom',
+            name='series_instance_uid',
+            field=models.CharField(blank=True, max_length=255, null=True),
+        ),
+    ]

atlas/models.py

@@ -811,9 +811,11 @@ class UncategorisedDicom(models.Model):
     )
 
     series = models.ForeignKey(
-        "Series", related_name="imported_dicoms", on_delete=models.SET_NULL, null=True
+        "Series", related_name="imported_dicoms", on_delete=models.SET_NULL, null=True, blank=True
     )
 
+    series_instance_uid = models.CharField(max_length=255, blank=True, null=True)
+
     image_md5_hash = models.CharField(max_length=32, null=True, blank=True)
 
     def check_for_duplicates(self, image_hash):
@@ -833,10 +835,14 @@ class UncategorisedDicom(models.Model):
     def save(self, *args, **kwargs):
         """Override save method to add image hash"""
         if self.image:
+
+            ds = self.get_dicom_info()
+
+            self.series_instance_uid = ds["SeriesInstanceUID"].value
+
             # if self.check_for_duplicates():
             #    return DuplicateDicom
-            image_hash = get_image_dicom_hash(self.image)
+            image_hash = get_image_dicom_hash(None, dataset=ds)
-
 
             self.image_md5_hash = image_hash
 

atlas/tables.py

@@ -110,6 +110,8 @@ class SeriesTable(tables.Table):
             "plane",
             "contrast",
             "author",
+            "created_date",
+            "modified_date",
         )
         sequence = ("view", "popup", "images", "case")
 

atlas/templates/atlas/case_display_block.html

@@ -1,5 +1,5 @@
 <div class="atlas {% if case.scrapped %}atlas-scrapped{% endif %}">
-    <div><a href="https://viewer.penracourses.org.uk/viewer/dicomjson?url=https://www.penracourses.org.uk{% url 'atlas:case_dicom_json' case.pk %}"">View case in OHIF</a></div>
+    <div><a href="https://viewer.penracourses.org.uk/viewer/dicomjson?url=https://www.penracourses.org.uk{% url 'atlas:case_dicom_json' case.pk %}">View case in OHIF</a></div>
 
     <div class="date">
         {{ case.created_date|date:"d/m/Y" }}
@@ -42,7 +42,10 @@
                 </span>
             </span>
         {% endfor %}
+        <span>
             <a href="{% url 'atlas:series_id_create' pk=case.pk %}">Add new series</a><br />
+            <a href="{% url 'atlas:user_uploads_case' case_id=case.pk %}">Import new uploads</a><br />
+        </span>
     </div>
     {% comment %} <p><b>Scrapped:</b> {{ case.scrapped }} <a
             href="{% url 'atlas:case_scrap' pk=case.pk %}">(toggle)</a> {% endcomment %}

atlas/templates/atlas/series_form.html

@@ -411,7 +411,7 @@
     {{ form.media }}
 {% endblock %}
 {% block content %}
-    <h2>Add Series</h2>
+    <h2>Series Form</h2>
     This form will create a image set that can be associated with a atlas question. If the question has already been created
     it can be linked below.
     <form action="" method="post" enctype="multipart/form-data" id="atlas-form">

atlas/templates/atlas/user_uploads.html

@@ -2,14 +2,19 @@
 
 {% block content %}
     <h2>Uploaded dicoms</h2>
+    Click to select cases to import. If no cases are selected all will be seleced/imported.
 
 
     {% if series_list %}
-        <ul>
+            <ul id="series-list">
                 {% for series, n, tags in series_list %}
-                <li>
+                    <li _="
+                    on click toggle .selected on me 
+                    then set i to the first <input/> in me
+                    then set i.checked to not i.checked" >
                         {{series}} [{{n}} images] <br/>
                         {{tags}}
+                        <input class="hidden" type="checkbox" name="selection" value="{{ series }}">
                     </li>
                 {% endfor %}
             </ul>
@@ -18,20 +23,24 @@
                 <p>Importing into case {{case}}</p>
             {% endif %}
 
-        <button
+            <button id="delete-uploads-button"
-            hx-get="{% url 'api-1:clear_dicoms' %}"
+                    hx-post="{% url 'api-1:clear_dicoms' %}"
-            hx-confirm="This will clear all uploads that have not been imported into series, Continue?"
+                    hx-include="[name='selection']"
+                    hx-confirm="This will clear selected uploads, Continue?"
+                    title="Deleted selected uploads"
             >Delete Uploads</button>
             {% if case %}
-        <button
+                <button id="import-dicoms-case-button"
-            hx-get="{% url 'api-1:import_dicoms_case' case.id %}"
+                        hx-post="{% url 'api-1:import_dicoms_case' case.id %}"
                         hx-target=".imported"
-        >Import</button>
+                        hx-include=".selected"
+                >Import into case</button>
 
             {% else %}
-        <button
+                <button id="import-dicoms-button"
-            hx-get="{% url 'api-1:import_dicoms' %}"
+                        hx-post="{% url 'api-1:import_dicoms' %}"
                         hx-target=".imported"
+                        hx-include=".selected"
                 >Import</button>
             {% endif %}
 
@@ -42,6 +51,6 @@
         No uploads awaiting importing have been found.
     {% endif %}
 
-    <p><a href="{% url 'atlas:series_view' %}?case=null">View orphan series</a></p>
+    <p><a href="{% url 'atlas:series_view' %}?case=null&sort=-modified_date">View orphan series</a></p>
 
 {% endblock %}

atlas/urls.py

@@ -35,7 +35,7 @@ urlpatterns = [
     path("collection/", views.CollectionView.as_view(), name="collection_view"),
     path("collection/user", views.user_collections, name="user_collections"),
     path("uploads", views.user_uploads, name="user_uploads"),
-    path("uploads/case/<int:case_id>", views.user_uploads, name="user_uploads"),
+    path("uploads/case/<int:case_id>", views.user_uploads, name="user_uploads_case"),
     path(
         "collection/create",
         views.CaseCollectionCreate.as_view(),

generic/filters.py

@@ -36,6 +36,7 @@ class CidUserFilter(django_filters.FilterSet):
 class UserUserFilter(django_filters.FilterSet):
     userprofile__grade = django_filters.ModelChoiceFilter(queryset=UserGrades.objects.all(),label="Grade")
     userprofile__supervisor = django_filters.ModelChoiceFilter(queryset=Supervisor.objects.all(), label="Supervisor")
+    userprofile__peninsula_trainee = django_filters.BooleanFilter(label="Peninsula Trainee")
     #has_supervisor = django_filters.BooleanFilter(field_name='supervisor', lookup_expr='isnull', exclude=True, label="Has Supervisor")
 
     class Meta:
@@ -50,7 +51,8 @@ class UserUserFilter(django_filters.FilterSet):
             #"userprofile__grade": ["exact"],
             #"userprofile__supervisor": ["exact"],
             "email": ["contains"],
-            "is_active": ["exact"]
+            "is_active": ["exact"],
+            "groups": ["exact"],
         }
 
     @property

generic/models.py

@@ -230,6 +230,9 @@ class SeriesBase(models.Model):
         help_text="If a series should be freely available to browse", default=True
     )
 
+    created_date = models.DateTimeField(auto_now_add=True)
+    modified_date = models.DateTimeField(auto_now=True)
+
     class Meta:
         abstract = True
 
@@ -1271,6 +1274,7 @@ class UserProfile(models.Model):
         on_delete=models.CASCADE,
     )
     peninsula_trainee = models.BooleanField(default=False)
+    #affiliation = models.ForeignKey("Site", on_delete=models.SET_NULL, blank=True, null=True)
 
     def getusername(self):
         return self.user.username

generic/tables.py

@@ -252,8 +252,12 @@ class UserUserTable(tables.Table):
         return "Edit"
 
     def render_user(self, value, record):
+        span_class = ""
+        if record.userprofile.peninsula_trainee:
+            span_class = "peninsula-trainee"
         return format_html(
-            "{} {}<br/>{}<br/>{}",
+            "<div style='flex-flow: row wrap; display: flex;'><div class='{}'></div><div>{} {}<br/>{}<br/>{}</div></div>",
+            span_class,
             record.first_name,
             record.last_name,
             record.username,

helpers/images.py

@@ -155,8 +155,10 @@ def print_dicom(dataset, indent=0):
                                                    repr_value))
     return "\n<br/>".join(l)
 
-def get_image_dicom_hash(img) -> (str, bool):
+def get_image_dicom_hash(img, dataset=None) -> (str, bool):
+    if dataset is None:
         dataset = pydicom.dcmread(img)
+
     md5 = hashlib.md5()
     first = True
     for i in dataset.pixel_array.astype(str).flatten():

longs/migrations/0009_longseries_created_at_longseries_updated_at.py

@@ -0,0 +1,25 @@
+# Generated by Django 4.1.4 on 2023-10-23 08:53
+
+from django.db import migrations, models
+import django.utils.timezone
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('longs', '0008_alter_longseriesimage_series'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='longseries',
+            name='created_at',
+            field=models.DateTimeField(auto_now_add=True, default=django.utils.timezone.now),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name='longseries',
+            name='updated_at',
+            field=models.DateTimeField(auto_now=True),
+        ),
+    ]

longs/migrations/0010_rename_created_at_longseries_created_date_and_more.py

@@ -0,0 +1,23 @@
+# Generated by Django 4.1.4 on 2023-10-23 09:00
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('longs', '0009_longseries_created_at_longseries_updated_at'),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name='longseries',
+            old_name='created_at',
+            new_name='created_date',
+        ),
+        migrations.RenameField(
+            model_name='longseries',
+            old_name='updated_at',
+            new_name='modified_date',
+        ),
+    ]

longs/templates/longs/longseries_form.html

@@ -317,7 +317,7 @@
 {{ form.media }}
 {% endblock %}
 {% block content %}
-<h2>Add Series</h2>
+<h2>Series Form</h2>
 <!-- <a href="{% url 'longs:long_create_defaults' %}">Edit defaults</a> -->
 This form will create a image set that can be associated with a long question. If the question has already been created it can be linked below.
 <form action="" method="post" enctype="multipart/form-data" id="long-form">

rad/filters.py

@@ -20,6 +20,8 @@ class UserListFilter(django_filters.FilterSet):
             "username": ["contains"],
             "email": ["contains"],
             "userprofile__grade": ["exact"],
+            "userprofile__peninsula_trainee": ["exact"],
+
         }
 
     # def __init__(self, data=None, queryset=None, *, request=None, prefix=None):

rad/static/css/anatomy.css

@@ -73,7 +73,7 @@ a:link {
   font-size: 20;
 }
 
-.hide {
+.hide, .hidden {
   display: none;
 }
 
@@ -712,7 +712,8 @@ input {
   text-decoration: underline;
 }
 
-.date,.small-gray {
+.date,
+.small-gray {
   font-size: smaller;
   opacity: 50%;
 }
@@ -1040,3 +1041,18 @@ h6 {
   width: 100%;
 
 }
+
+table .peninsula-trainee::before {
+  content: "Trainee";
+  transform: rotate(-90deg) translate(-45px, -10px);
+  color: darkblue;
+  display: inline-block;
+  float: left;
+  width: 20px;
+}
+
+#series-list .selected {
+  color: white;
+  background-color: #52057b;
+  user-select: none;
+}

rad/views.py

@@ -600,7 +600,7 @@ class UpdateUserView(CidManagerRequiredMixin, UpdateView):
         return reverse(view_name, kwargs={"slug": self.object.username})
 
 
-class UpdateUserProfileView(CidManagerRequiredMixin, UpdateView):
+class UpdateUserProfileAdminView(CidManagerRequiredMixin, UpdateView):
     model = UserProfile
     fields = [
         "supervisor",
@@ -617,6 +617,34 @@ class UpdateUserProfileView(CidManagerRequiredMixin, UpdateView):
         # No need for reverse_lazy here, because it's called inside the method
         return reverse(view_name, kwargs={"slug": self.object.username})
 
+class UpdateUserProfileView(UpdateView):
+    model = UserProfile
+    fields = [
+        "supervisor",
+        "grade",
+        "registration_number",
+        #"peninsula_trainee",
+    ]  # Keep listing whatever fields
+    template_name = "user_update_profile.html"
+    slug_field = "user__username"
+    slug_url_kwarg = "slug"
+
+    def dispatch(self, request, *args, **kwargs):
+        if request.user.is_superuser or request.user.groups.filter(name="cid_user_manager").exists():
+            self.fields = ["supervisor", "grade", "registration_number", "peninsula_trainee"]
+        # Check permissions for the request.user here
+        elif request.user.userprofile.peninsula_trainee:
+            self.fields = ["supervisor", "grade", "registration_number"]
+
+        else:
+            self.fields = ["grade", "registration_number"]
+        return super().dispatch(request, *args, **kwargs)
+
+
+    def get_success_url(self):
+        view_name = "account_profile"
+        # No need for reverse_lazy here, because it's called inside the method
+        return reverse(view_name, kwargs={"slug": self.object.username})
 
 # class UpdateUser(TemplateView):
 #

sbas/migrations/0003_alter_useranswer_answer.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.1.4 on 2023-10-23 08:53
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('sbas', '0002_exam_candidates_only_alter_exam_active_and_more'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='useranswer',
+            name='answer',
+            field=models.CharField(choices=[('a', 'a_answer'), ('b', 'b_answer'), ('c', 'c_answer'), ('d', 'd_answer'), ('e', 'e_answer')], help_text='The user selected answer', max_length=20),
+        ),
+    ]

templates/profile.html

@@ -1,4 +1,5 @@
 {% extends 'base.html' %}
+{% load auth_extras %}
 
 {% block content %}
     <div class="anatomy">
@@ -54,7 +55,10 @@
 
 
         <a href="{% url 'password_change'%}">Change password</a>
+
+        {% if request.user|has_group:"cid_user_manager" %}
             <a href="{% url 'account_update' user.username %}">Update user details</a>
+        {% endif %}
         <a href="{% url 'account_profile_update' user.username %}">Update user profile</a>
     </div>
 {% endblock %}

templates/user_update_profile.html

@@ -1,9 +1,15 @@
 {% extends 'generic/base.html' %}
 {% load crispy_forms_tags %}
+{% load auth_extras %}
 
 {% block content %}
     <h2>Editing user: {{object.username}}</h2>
-This form allows you to edit additional user details. Name and emails can be edited <a href="{% url 'account_update' object.username %}">here</a> 
+    This form allows you to edit additional user details.
+
+    {% if request.user|has_group:"cid_user_manager" %}
+        Name and emails can be edited <a href="{% url 'account_update' object.username %}">here</a>
+    {% endif %}
+
     <form method="post">{% csrf_token %}
         {{ form|crispy }}
         <input type="submit" value="Update">