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add the ablitiy to truncate series on the site

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Ross
2023-12-18 11:54:00 +00:00
parent e1c81e04b1
commit 7b21b1ad6f
7 changed files with 255 additions and 77 deletions
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atlas/api.py
+20
View File
@@ -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
+23
View File
@@ -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
+19
View File
@@ -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
+2 -16
View File
@@ -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
+91 -45
View File
@@ -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=''>
</div>
{% 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>
{% with image_url_array_and_count=series.get_image_url_array_and_count %}
<div id="single-dicom-viewer" class="dicom-viewer" data-images="{{ image_url_array_and_count.0 }}" data-annotations=''>
</div>
</div>
<details open>
<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>
{% 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>
{% endfor %}
</details>
<details open>
<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 %}
[{{ image.id }}] <a href='{% url "atlas:series_image_dicom" image.pk %}'>{{image.image.url}}</a>, pos: {{image.position}}, {{image.upload_filename}}
{% 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}}
{% if image.image %}
[{{image.image.size|filesizeformat}}]
{% endif %}
{% if image.image %}
[{{image.image.size|filesizeformat}}]
{% 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);