add the ablitiy to truncate series on the site

atlas/api.py

@@ -180,6 +180,26 @@ def series_remove_duplicate_images(request, series_id: int):
 
     return len(dupes)
 
+@router.get("/series_truncate/{series_id}/{start}/{end}/", auth=django_auth)
+def series_truncate(request, series_id: int, start: int, end:int):
+    print(start, end)
+    series = get_object_or_404(Series, pk=series_id)
+
+    if not series.check_user_can_edit(request.user):
+        return {"status": "permission denied"}
+
+    images_removed = []
+    for n, image in enumerate(series.get_images()):
+        if n >= start and n <=end:
+            continue
+        else:
+            print(n, image)
+            image.removed=True
+            image.image = None
+            image.save()
+            images_removed.append(image.pk)
+    return {"status": "success", "images_removed": images_removed}
+
 
 @router.get("/get_cases_user", auth=django_auth, response=List[CaseSchema])
 def get_cases_user(request):

atlas/migrations/0032_series_modified_seriesimage_removed.py

@@ -0,0 +1,23 @@
+# Generated by Django 4.1.4 on 2023-12-18 10:22
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0031_seriesimage_replaced'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='series',
+            name='modified',
+            field=models.CharField(choices=[('NO', 'Not modified'), ('TR', 'Truncated'), ('RE', 'Resliced/resampled')], default='NO', max_length=2),
+        ),
+        migrations.AddField(
+            model_name='seriesimage',
+            name='removed',
+            field=models.BooleanField(default=False, help_text='Set to true if the file this object refers to has been removed (either from series truncation or merging)'),
+        ),
+    ]

atlas/migrations/0033_alter_seriesimage_image.py

@@ -0,0 +1,19 @@
+# Generated by Django 4.1.4 on 2023-12-18 11:47
+
+import atlas.models
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0032_series_modified_seriesimage_removed'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='seriesimage',
+            name='image',
+            field=models.FileField(blank=True, null=True, upload_to=atlas.models.image_directory_path),
+        ),
+    ]

atlas/models.py

@@ -466,7 +466,7 @@ def extract_image_dicom_json_from_ds(ds, url, image_index):
 
 
 class SeriesImage(SeriesImageBase):
-    image = models.FileField(upload_to=image_directory_path)
+    image = models.FileField(upload_to=image_directory_path, null=True)
     series = models.ForeignKey(
         "Series", related_name="images", on_delete=models.CASCADE, null=True
     )
@@ -479,11 +479,6 @@ class SeriesImage(SeriesImageBase):
         help_text="Reference to the object that has replaced this one.",
     )
 
-    removed = models.BooleanField(
-        default=False,
-        help_text="Set to true if the file this object refers to has been removed (either from series truncation or merging)",
-    )
-
     def get_dicom_data(self):
         try:
             with pydicom.dcmread(self.image) as d:
@@ -563,15 +558,6 @@ class Series(SeriesBase):
         related_name="series",
     )
 
-
-    class SeriesModifiedChocies(models.TextChoices):
-        NO = "NO", "Not modified",
-        TR = "TR", "Truncated",
-        RE = "RE", "Resliced/resampled",
-
-
-    modified = models.CharField(max_length=2, default=SeriesModifiedChocies.NO, choices=SeriesModifiedChocies.choices)
-
     series_instance_uid = models.CharField(max_length=255, blank=True, null=True)
 
     # findings = models.TextField(null=True, blank=True, help_text="Findings on the series / stack")
@@ -603,7 +589,7 @@ class Series(SeriesBase):
 
         # TODO: clean up (this is rather convoluted....)
         image: SeriesImage
-        for series_n, image in enumerate(self.images.all()):
+        for series_n, image in enumerate(self.images.filter(removed=False)):
             ds = image.get_dicom_data()
             if series_n == 0:
                 for tag in to_keep:

atlas/templates/atlas/series_viewer.html

@@ -10,47 +10,64 @@
     This series is not associated with any cases.
 {% endif %}
 
-<div id="single-dicom-viewer" class="dicom-viewer" data-images="{{ series.get_image_url_array }}" data-annotations=''>
+{% with image_url_array_and_count=series.get_image_url_array_and_count %}
-</div>
+    <div id="single-dicom-viewer" class="dicom-viewer" data-images="{{ image_url_array_and_count.0 }}" data-annotations=''>
-
-{% if editing_finding < 1 %}
-    <button id="add-finding-button">Add finding</button>
-{% endif %}
-<button id="reset-viewport-button">Reset viewport</button>
-<div id="finding-form">
-    <div class="hide" id="hidden-form">
-        <form method="post" id="series_finding_form">
-            {% csrf_token %}
-            {{series_finding_form.management_form}}
-            <div>
-                <div>Description: {{ series_finding_form.description }}</div>
-                <div>Findings: {{ series_finding_form.findings }}</div>
-                <div>Structures: {{ series_finding_form.structures }}</div>
-            </div>
-            <input type="submit" value="Submit">
-            <button id="cancel-add-finding-button">Cancel</button>
-        </form>
     </div>
-</div>
 
-<details open>
+    {% if editing_finding < 1 %}
-    <summary>Findings</summary>
+        <button id="add-finding-button">Add finding</button>
-
+    {% endif %}
-    {% for finding in series.findings.all %}
+    <button id="reset-viewport-button">Reset viewport</button>
-        <div class="finding-box">
+    <div id="finding-form">
-            <button class="view-finding-button" data-annotationjson={{finding.annotation_json}}
+        <div class="hide" id="hidden-form">
-                    data-viewportjson={{finding.viewport_json}} data-findingid={{finding.id}}>Click to view</button>
+            <form method="post" id="series_finding_form">
-            <span class="view-finding-details">
+                {% csrf_token %}
-                Finding(s): {% for f in finding.findings.all %}{{f.get_link}}{% endfor %}<br />
+                {{series_finding_form.management_form}}
-                Structure(s): {% for s in finding.structures.all %}{{s.get_link}}{% endfor %}<br />
+                <div>
-                Description: {{finding.description}}<br />
+                    <div>Description: {{ series_finding_form.description }}</div>
-            </span>
+                    <div>Findings: {{ series_finding_form.findings }}</div>
-            <a href="{% url 'atlas:series_edit_finding' pk=series.pk finding_pk=finding.pk %}" class="edit-finding-link">Edit</a>
+                    <div>Structures: {{ series_finding_form.structures }}</div>
-            <a href="{% url 'atlas:delete_finding' pk=finding.pk %}" class="delete-finding-link">Delete</a>
+                </div>
+                <input type="submit" value="Submit">
+                <button id="cancel-add-finding-button">Cancel</button>
+            </form>
         </div>
+    </div>
 
-    {% endfor %}
+    <details open>
-</details>
+        <summary>Findings</summary>
+
+
+
+
+
+        {% for finding in series.findings.all %}
+            <div class="finding-box">
+                <button class="view-finding-button" data-annotationjson={{finding.annotation_json}}
+                        data-viewportjson={{finding.viewport_json}} data-findingid={{finding.id}}>Click to view</button>
+                <span class="view-finding-details">
+                    Finding(s): {% for f in finding.findings.all %}{{f.get_link}}{% endfor %}<br />
+                    Structure(s): {% for s in finding.structures.all %}{{s.get_link}}{% endfor %}<br />
+                    Description: {{finding.description}}<br />
+                </span>
+                <a href="{% url 'atlas:series_edit_finding' pk=series.pk finding_pk=finding.pk %}" class="edit-finding-link">Edit</a>
+                <a href="{% url 'atlas:delete_finding' pk=finding.pk %}" class="delete-finding-link">Delete</a>
+            </div>
+
+        {% endfor %}
+    </details>
+    <details>
+        <summary>Truncate series</summary>
+        <p>
+            This will limit the series to the selected bounds (the rest of the images will be deleted). This is useful when you have a large volume of which only a small area is relevant to the case. NOTE: once deleted the images cannot be recovered on the site (they would have to be reuploaded if required).
+        </p>
+        Start <input id="lower-truncation-bound-input" type="number" value="1"> <button id="set-lower-truncation-bound-button">Set</button><br/>
+        End <input  id="upper-truncation-bound-input"type="number" value="{{image_url_array_and_count.1}}"> <button id="set-upper-truncation-bound-button">Set</button><br/>
+        <button id="truncate-button">Trucate series</button>
+        <div id="trucate-output"></div>
+
+    </details>
+{% endwith %}
 
 
 <div>Author: {{ series.get_author_display }}</div>
@@ -72,20 +89,20 @@
         <summary>
             Image details
         </summary>
-            {% for image in series.images.all %}
+        {% for image in series.get_images %}
-                [{{  image.id  }}] <a href='{% url "atlas:series_image_dicom" image.pk %}'>{{image.image.url}}</a>, pos: {{image.position}}, {{image.upload_filename}}
+            [{{  image.id  }}] <a href='{% url "atlas:series_image_dicom" image.pk %}'>{{image.image.url}}</a>, pos: {{image.position}}, {{image.upload_filename}}
 
 
-                {% if image.image %}
+            {% if image.image %}
-                    [{{image.image.size|filesizeformat}}]
+                [{{image.image.size|filesizeformat}}]
-                {% endif %}
+            {% endif %}
 
-                {{image.image_md5_hash}} ({{image.is_dicom}})
+            {{image.image_md5_hash}} ({{image.is_dicom}})
 
-                <br />
+            <br />
         {% comment %} {{image.get_dicom_info|safe}}<br /> {% endcomment %}
 
-            {% endfor %}
+        {% endfor %}
     </details>
 
     <p>Total image size: {{series.get_total_image_size|filesizeformat}}</p>
@@ -95,6 +112,35 @@
 
 <script>
     $(document).ready(function () {
+        $("#set-lower-truncation-bound-button").click(() => {
+            dicom_element = $(".cornerstone-element").get(0);
+            index = cornerstone.getEnabledElement(dicom_element).toolStateManager.toolState.stack.data[0].currentImageIdIndex
+            $("#lower-truncation-bound-input").val(index+1);
+        });
+        $("#set-upper-truncation-bound-button").click(() => {
+            dicom_element = $(".cornerstone-element").get(0);
+            index = cornerstone.getEnabledElement(dicom_element).toolStateManager.toolState.stack.data[0].currentImageIdIndex
+            $("#upper-truncation-bound-input").val(index+1);
+        });
+        $("#truncate-button").click(() => {
+            console.log("click")
+
+            lower_bound = parseInt($("#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(`Trucated series. This will leave ${upper_bound - lower_bound + 1} images.`) == true) {
+                htmx.ajax("GET", `{% url 'api-1:series_truncate' series.id '****' '++++' %}`.replace("****", lower_bound).replace("++++", upper_bound), "#trucate-output")
+
+            }
+
+
+        })
+
         $("#add-finding-button").click(() => {
             dicom_element = $(".cornerstone-element").get(0);
             cornerstoneTools.globalImageIdSpecificToolStateManager.clear(dicom_element);

generic/models.py

@@ -188,16 +188,27 @@ class SeriesImageBase(models.Model):
     (larger) original file will be deleted but the model object will be persisted so that
     the duplicate check continues to function.
     """
+
     position = models.IntegerField(default=0)
     upload_filename = models.CharField(max_length=255, blank=True)
     series = models.ForeignKey(
         "Series", related_name="images", on_delete=models.SET_NULL, null=True
     )
-    dicom_tags_ohif = models.JSONField(help_text="Holds the dicom tags required for the OHIF viewer", blank=True, null=True)
+    dicom_tags_ohif = models.JSONField(
+        help_text="Holds the dicom tags required for the OHIF viewer",
+        blank=True,
+        null=True,
+    )
 
     image_md5_hash = models.CharField(max_length=32, null=True, blank=True)
     is_dicom = models.BooleanField(default=False)
 
+    removed = models.BooleanField(
+        default=False,
+        help_text="Set to true if the file this object refers to has been removed (either from series truncation or merging)",
+    )
+
+
     class Meta:
         ordering = ["position"]
         abstract = True
@@ -219,7 +230,6 @@ class SeriesImageBase(models.Model):
     def save(self, *args, **kwargs):
         """Override save method to add image hash"""
         if self.image:
-
             if not self.image_md5_hash:
                 image_hash, is_dicom = get_image_hash(self.image)
 
@@ -232,13 +242,19 @@ class SeriesImageBase(models.Model):
 
         super().save(*args, **kwargs)  # Call the "real" save() method.
 
+
 class SeriesBase(models.Model):
     info = models.TextField(
         blank=True,
         help_text="Description of stack, for admin organisation, will not be visible when taking",
     )
 
-    description = models.CharField(null=True, blank=True, max_length=255, help_text="Description of the series. This is usually visable to the user (as the name of the stack)")
+    description = models.CharField(
+        null=True,
+        blank=True,
+        max_length=255,
+        help_text="Description of the series. This is usually visable to the user (as the name of the stack)",
+    )
 
     open_access = models.BooleanField(
         help_text="If a series should be freely available to browse", default=True
@@ -247,12 +263,29 @@ class SeriesBase(models.Model):
     created_date = models.DateTimeField(auto_now_add=True)
     modified_date = models.DateTimeField(auto_now=True)
 
+    class SeriesModifiedChocies(models.TextChoices):
+        NO = "NO", "Not modified",
+        TR = "TR", "Truncated",
+        RE = "RE", "Resliced/resampled",
+
+
+    modified = models.CharField(max_length=2, default=SeriesModifiedChocies.NO, choices=SeriesModifiedChocies.choices)
+
     class Meta:
         abstract = True
 
     def __str__(self):
         return f"{self.pk}:{self.description}"
 
+    def check_user_can_edit(self, user: User):
+        if user.is_superuser:
+            return True
+        
+        if user in self.get_author_objects():
+            return True
+
+        return False
+
     def get_author_objects(self):
         """Returns a comma seperated text list of authors"""
         if self.author:
@@ -280,25 +313,47 @@ class SeriesBase(models.Model):
             contrast = " {}".format(self.contrast)
         return "{}{}{}".format(examination, plane, contrast)
 
+    def get_images(self, include_removed=False):
+        if include_removed:
+            return self.images.all()
+        else:
+            return self.images.filter(removed=False)
+
+    def get_image_count(self):
+        return self.images.filter(removed=False).count()
+
     def get_image_urls(self):
-        images = [f"{REMOTE_URL}{i.image.url}" for i in self.images.all()]
+        images = [
+            f"{REMOTE_URL}{i.image.url}" for i in self.images.filter(removed=False)
+        ]
 
         return ",".join(images)
 
     def get_image_url_array_not_json(self):
         return self.get_image_url_array(json_output=False)
 
-    def get_image_url_array(self, json_output=True):
+    def get_image_url_array_and_count(self, json_output=True):
-        images = [f"{REMOTE_URL}{i.image.url}" for i in self.images.all()]
+        return self.get_image_url_array(json_output=json_output, count=True)
+
+    def get_image_url_array(self, json_output=True, count=False):
+        images = [
+            f"{REMOTE_URL}{i.image.url}" for i in self.images.filter(removed=False)
+        ]
 
         if json_output:
-            return json.dumps(images)
+            if count:
+                return (json.dumps(images), len(images))
+            else:
+                return json.dumps(images)
         else:
             # This is a mess...
-            return format_html('", "'.join(images))
+            if count:
+                return (format_html('", "'.join(images)), len(images))
+            else:
+                return format_html('", "'.join(images))
 
     def get_thumbnail(self):
-        images = self.images.all()
+        images = self.images.filter(removed=False)
 
         if len(images) < 1:
             return "No images", 0
@@ -343,7 +398,7 @@ class SeriesBase(models.Model):
         )
 
     def order_by_upload_filename(self):
-        images = self.images.all()
+        images = self.images.filter(removed=False)
 
         filenames = []
         map = {}
@@ -362,7 +417,7 @@ class SeriesBase(models.Model):
             n = n + 1
 
     def order_by_dicom(self, field="SliceLocation"):
-        images = self.images.all()
+        images = self.images.filter(removed=False)
 
         files = []
 
@@ -400,7 +455,7 @@ class SeriesBase(models.Model):
             n = n + 1
 
     def get_total_image_size(self):
-        images = self.images.all()
+        images = self.images.filter(removed=False)
 
         size = 0
 
@@ -415,7 +470,7 @@ class SeriesBase(models.Model):
         # even with the same dicom...
         anonymizer = dicognito.anonymizer.Anonymizer()
 
-        for series_image in self.images.all():
+        for series_image in self.images.filter(removed=False):
             file_path = os.path.join(settings.MEDIA_ROOT, series_image.image.name)
 
             try:
@@ -1288,6 +1343,7 @@ USER_EXAM_TYPES = (
     # ("CaseCollection", "user_casecollection_exams"),
 )
 
+
 class UserProfile(models.Model):
     user = models.OneToOneField(settings.AUTH_USER_MODEL, on_delete=models.CASCADE)
     supervisor = models.ForeignKey(
@@ -1306,7 +1362,13 @@ class UserProfile(models.Model):
         on_delete=models.CASCADE,
     )
     peninsula_trainee = models.BooleanField(default=False)
-    site = models.ForeignKey("Site", on_delete=models.SET_NULL, blank=True, null=True, help_text="Primary site / rotation location")
+    site = models.ForeignKey(
+        "Site",
+        on_delete=models.SET_NULL,
+        blank=True,
+        null=True,
+        help_text="Primary site / rotation location",
+    )
 
     def getusername(self):
         return self.user.username
@@ -1374,4 +1436,3 @@ def create_user_profile(sender, instance, created, **kwargs):
 @receiver(post_save, sender=User)
 def save_user_profile(sender, instance, **kwargs):
     instance.userprofile.save()
-

longs/migrations/0011_longseries_modified_longseriesimage_removed.py

@@ -0,0 +1,23 @@
+# Generated by Django 4.1.4 on 2023-12-18 11:40
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('longs', '0010_rename_created_at_longseries_created_date_and_more'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='longseries',
+            name='modified',
+            field=models.CharField(choices=[('NO', 'Not modified'), ('TR', 'Truncated'), ('RE', 'Resliced/resampled')], default='NO', max_length=2),
+        ),
+        migrations.AddField(
+            model_name='longseriesimage',
+            name='removed',
+            field=models.BooleanField(default=False, help_text='Set to true if the file this object refers to has been removed (either from series truncation or merging)'),
+        ),
+    ]