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image findings will now save and reload stack index

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This commit is contained in:
Ross
2024-09-23 14:05:09 +01:00
parent edc9b29233
commit 5a9868a56d
8 changed files with 169 additions and 49 deletions
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atlas/api.py
+67 -33
View File
@@ -29,7 +29,6 @@ from loguru import logger
router = Router()
class SeriesSchema(ModelSchema):
case_id: List[int] = []
@@ -59,6 +58,7 @@ def upload_dicom(request, files: List[UploadedFile] = File(...)):
uploaded = []
duplicate = []
failed = []
duplicate_series = set()
for file in files:
# data = file.read()
try:
@@ -67,26 +67,41 @@ def upload_dicom(request, files: List[UploadedFile] = File(...)):
ud.save()
uploaded.append((file.name, ud.image_blake3_hash))
except DuplicateDicom:
except DuplicateDicom as e:
duplicate.append((file.name, ud.image_blake3_hash))
duplicate_series.add(e.duplicate.get_series().get_absolute_url())
print(duplicate_series)
pass
except InvalidDicomError:
failed.append(file.name)
return {"uploaded": uploaded, "duplicates": duplicate, "failed": failed}
return {
"uploaded": uploaded,
"duplicates": duplicate,
"failed": failed,
"duplicate_series": list(duplicate_series),
}
@router.post("/generate_image_hash", auth=django_auth)
def generate_image_hash(request, id:int):
def generate_image_hash(request, id: int):
s = SeriesImage.objects.get(pk=id)
s.generate_hashes()
return {"md5": s.image_md5_hash, "blake3": s.image_blake3_hash, "is_dicom": s.is_dicom}
return {
"md5": s.image_md5_hash,
"blake3": s.image_blake3_hash,
"is_dicom": s.is_dicom,
}
@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"))
dicoms = UncategorisedDicom.objects.filter(
series_instance_uid__in=request.POST.getlist("selection")
)
else:
dicoms = UncategorisedDicom.objects.filter(user=request.user)
@@ -110,15 +125,17 @@ def uncategorised_dicoms(request):
return data
def import_dicoms_helper(request, case_id: int | None = None):
#dicoms = UncategorisedDicom.objects.filter(user=request.user)
# dicoms = UncategorisedDicom.objects.filter(user=request.user)
if "selection" in request.POST:
dicoms = UncategorisedDicom.objects.filter(series_instance_uid__in=request.POST.getlist("selection"))
dicoms = UncategorisedDicom.objects.filter(
series_instance_uid__in=request.POST.getlist("selection")
)
else:
dicoms = UncategorisedDicom.objects.filter(user=request.user)
if "order-series" in request.POST:
order = request.POST["order-series"]
else:
@@ -136,7 +153,9 @@ def import_dicoms_helper(request, case_id: int | None = None):
tags = data[series_uid][0][1]
# Check if series with the id already exists (in which case we just add to htat)
if Series.objects.filter(series_instance_uid=tags["SeriesInstanceUID"]).exists():
if Series.objects.filter(
series_instance_uid=tags["SeriesInstanceUID"]
).exists():
series = Series.objects.get(series_instance_uid=tags["SeriesInstanceUID"])
else:
series = Series(
@@ -146,16 +165,16 @@ def import_dicoms_helper(request, case_id: int | None = None):
)
if tags["StudyDescription"]:
examination, created = Examination.objects.get_or_create(examination=tags["StudyDescription"])
examination, created = Examination.objects.get_or_create(
examination=tags["StudyDescription"]
)
if created:
examination.modality = modality
examination.save()
series.examination = examination
series.save()
match order:
case "order-series-instance-number":
series.order_by_dicom("InstanceNumber")
@@ -188,12 +207,18 @@ def import_dicoms_helper(request, case_id: int | None = None):
return series_list
@router.post("/import_dicoms", auth=django_auth, response=List[Tuple[ SeriesSchema, str ]])
@router.post(
"/import_dicoms", auth=django_auth, response=List[Tuple[SeriesSchema, str]]
)
def import_dicoms(request):
return import_dicoms_helper(request)
@router.post("/import_dicoms/{case_id}", auth=django_auth, response=List[Tuple[ SeriesSchema, str ]])
@router.post(
"/import_dicoms/{case_id}",
auth=django_auth,
response=List[Tuple[SeriesSchema, str]],
)
def import_dicoms_case(request, case_id: int):
return import_dicoms_helper(request, case_id=case_id)
@@ -220,8 +245,9 @@ 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):
def series_truncate(request, series_id: int, start: int, end: int):
print(start, end)
series = get_object_or_404(Series, pk=series_id)
@@ -230,11 +256,11 @@ def series_truncate(request, series_id: int, start: int, end:int):
images_removed = []
for n, image in enumerate(series.get_images()):
if n >= start and n <=end:
if n >= start and n <= end:
continue
else:
print(n, image)
image.removed=True
image.removed = True
image.image = None
image.save()
images_removed.append(image.pk)
@@ -261,10 +287,11 @@ def check_image_hash(request, hash: str):
data = {"status": "success", "id": False}
return data
@router.post("/check_image_hashes/", auth=django_auth)
def check_images_hashes(request, hashes: List[str]):
"""Checks a list of image hashes and returns the series id / url if found
Return format
{ "hash_id": {"id": "series_id|false", "url": "series_url|false"}, ...}
"""
@@ -278,21 +305,28 @@ def check_images_hashes(request, hashes: List[str]):
data = {
"id": series_image.pk,
"url": series_image.series.get_absolute_url(),
"type": "series"
"type": "series",
}
except SeriesImage.DoesNotExist:
try:
uncategorised_dicom = UncategorisedDicom.objects.get(image_blake3_hash=hash)
data = { "id":uncategorised_dicom.pk, "url": reverse("atlas:user_uploads"), "type": "uncategorised"}
uncategorised_dicom = UncategorisedDicom.objects.get(
image_blake3_hash=hash
)
data = {
"id": uncategorised_dicom.pk,
"url": reverse("atlas:user_uploads"),
"type": "uncategorised",
}
except UncategorisedDicom.DoesNotExist:
data = { "id": False, "url": False}
data = {"id": False, "url": False}
hash_status[hash] = data
return hash_status
#@router.get("/generate_image_hash/{id}", auth=django_auth)
#def generate_image_hash(request, id: int):
# @router.get("/generate_image_hash/{id}", auth=django_auth)
# def generate_image_hash(request, id: int):
# series_image = SeriesImage.objects.get(pk=id)
#
# series_image.image_blake3_hash = ""
@@ -301,21 +335,22 @@ def check_images_hashes(request, hashes: List[str]):
#
# print(series_image)
@router.get("/view_dicom_tags/{hash}", auth=django_auth)
def view_dicom_tags(request, hash: str):
item = SeriesImage.objects.get(image_blake3_hash=hash)
return item.get_dicom_json()
@router.get("/series_split_by_dicom_tag/{series_id}/{dicom_tag}", auth=django_auth)
def series_split_by_tag(request, series_id: int, dicom_tag:str):
def series_split_by_tag(request, series_id: int, dicom_tag: str):
series = get_object_or_404(Series, pk=series_id)
if not series.check_user_can_edit(request.user):
return {"status": "permission denied"}
if dicom_tag.startswith("(") and dicom_tag.endswith(")"):
dicom_tag = tuple([hex(int(i.strip(),16)) for i in dicom_tag[1:-1].split(",")])
dicom_tag = tuple([hex(int(i.strip(), 16)) for i in dicom_tag[1:-1].split(",")])
image_map = defaultdict(list)
@@ -324,7 +359,7 @@ def series_split_by_tag(request, series_id: int, dicom_tag:str):
print(image)
ds = image.get_dicom_data()
#print("2a", ds[dicom_tag])
# print("2a", ds[dicom_tag])
if dicom_tag in ds:
val = ds[dicom_tag].value
@@ -339,7 +374,7 @@ def series_split_by_tag(request, series_id: int, dicom_tag:str):
new_series = []
case = series.case.all()
authors = series.author.all()
for n, option in enumerate(image_map):
if n == 0:
series.images.set(image_map[option])
@@ -353,12 +388,11 @@ def series_split_by_tag(request, series_id: int, dicom_tag:str):
new_series.append(series.pk)
return new_series
@router.get("/split_order_by_dicom_tag/{series_id}/{dicom_tag}", auth=django_auth)
def series_order_by_tag(request, series_id: int, dicom_tag:str):
def series_order_by_tag(request, series_id: int, dicom_tag: str):
series = get_object_or_404(Series, pk=series_id)
series.order_by_dicom(dicom_tag)
atlas/forms.py
+1 -1
View File
@@ -143,7 +143,7 @@ class StructureForm(ModelForm):
class SeriesFindingForm(ModelForm):
class Meta:
model = SeriesFinding
exclude = ["series", "annotation_json", "viewport_json"]
exclude = ["series", "annotation_json", "viewport_json", "current_image_id_index"]
widgets = {
"findings": autocomplete.ModelSelect2Multiple(
atlas/migrations/0060_seriesfinding_current_image_id_index.py
+18
View File
@@ -0,0 +1,18 @@
# Generated by Django 5.0.2 on 2024-09-23 12:45
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('atlas', '0059_alter_casecollection_markers'),
]
operations = [
migrations.AddField(
model_name='seriesfinding',
name='current_image_id_index',
field=models.IntegerField(blank=True, null=True),
),
]
atlas/models.py
+15 -3
View File
@@ -570,6 +570,9 @@ class SeriesImage(SeriesImageBase):
except InvalidDicomError:
return {}
def get_series(self):
return self.series
# def get_image_dicom_json(self, image_index):
# try:
# with pydicom.dcmread(self.image) as ds:
@@ -594,6 +597,7 @@ class SeriesFinding(models.Model):
conditions = models.ManyToManyField(Condition, blank=True)
annotation_json = models.TextField(null=True, blank=True)
viewport_json = models.TextField(null=True, blank=True)
current_image_id_index = models.IntegerField(null=True, blank=True)
def __str__(self) -> str:
findings = self.findings.all().values_list("name")
@@ -1273,9 +1277,12 @@ class UncategorisedDicom(models.Model):
basic_dicom_tags = models.JSONField(null=True, blank=True)
def check_for_duplicates(self, image_hash):
def check_for_duplicates(self, image_hash=None|str):
duplicate = None
if image_hash is None:
image_hash = self.image_blake3_hash
if obj := UncategorisedDicom.objects.filter(
image_blake3_hash=image_hash
).first():
@@ -1310,7 +1317,8 @@ class UncategorisedDicom(models.Model):
if duplicate is not None:
if duplicate != self:
raise DuplicateDicom
raise DuplicateDicom(duplicate)
# Hack for tests
if image_blake3_hash != "1234":
@@ -1349,9 +1357,13 @@ class UncategorisedDicom(models.Model):
except pydicom.errors.InvalidDicomError:
return None
def get_series(self):
return self.series
class DuplicateDicom(Exception):
pass
def __init__(self, duplicate):
self.duplicate = duplicate
class Resource(models.Model, AuthorMixin):
atlas/templates/atlas/new_uploads.html
+11
View File
@@ -41,6 +41,7 @@
<ul id="uploaded-files"></ul>
<h5>Duplicates</h5>
<ul id="duplicate-files"></ul>
<ul id="duplicate-series"></ul>
<h5>Failed</h5>
<ul id="failed-files"></ul>
</div>
@@ -78,6 +79,7 @@
<script>
window.to_upload = [];
window.upload_count = 1;
window.duplicate_series = new Set()
function* chunks(arr, n) {
for (let i = 0; i < arr.length; i += n) {
@@ -149,6 +151,7 @@
item.textContent = JSON.parse(xhr.response)["duplicates"][i];
$("#duplicate-files").append(item);
}
window.duplicate_series.add(...JSON.parse(xhr.response)["duplicate_series"]);
for (let i = 0; i < JSON.parse(xhr.response)["failed"].length; i++) {
let item = document.createElement("li");
@@ -162,6 +165,14 @@
}
if (current_chunk + 1 == total_chunks) {
$("#loading").hide();
window.duplicate_series.forEach((element) => {
let item = document.createElement("a");
item.href = element;
item.textContent = element;
$("#duplicate-series").append(item, "<br/>");
});
//$("#duplicate-series").append([...window.duplicate_series].join("<br/>"));
alert("Uploading complete")
}
}
atlas/templates/atlas/series_viewer.html
+34 -12
View File
@@ -1,3 +1,5 @@
{% load crispy_forms_tags %}
<div>{{ series.modality}}, {{ series.examination }}, {{ series.plane }}, {{ series.contrast }}</div>
<div>Description: {{series.description}}</div>
@@ -22,13 +24,7 @@
<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>Conditions: {{ series_finding_form.conditions }}</div>
</div>
{{series_finding_form|crispy}}
<input type="submit" value="Submit">
<button id="cancel-add-finding-button">Cancel</button>
</form>
@@ -45,14 +41,28 @@
{% 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>
data-viewportjson={{finding.viewport_json}} data-findingid={{finding.id}} data-currentimageid={{finding.current_image_id_index}}>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 />
Condition(s): {% for s in finding.conditions.all %}{{s.get_link}}{% endfor %}<br />
Description: {{finding.description}}<br />
{% if request.user.is_superuser %}
<span _="on click toggle .hidden on next .extra-details">+</span>
<div class="hidden extra-details">
<h4>Annotation JSON</h4>
<pre>{{finding.annotation_json}}</pre>
<h4>Viewport JSON</h4>
<pre>{{finding.viewport_json}}</pre>
<h4>Image ID</h4>
<pre>{{finding.current_image_id_index}}</pre>
</div>
{% endif %}
</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>
@@ -195,6 +205,7 @@
})
$("#add-finding-button").click(() => {
$("#hidden-form").show()
dicom_element = $(".cornerstone-element").get(0);
cornerstoneTools.globalImageIdSpecificToolStateManager.clear(dicom_element);
cornerstone.reset(dicom_element);
@@ -202,7 +213,6 @@
//$("#finding-form").empty().append(
// $("#hidden-form form").clone()
//);
$("#hidden-form").show()
});
$("#cancel-add-finding-button").click((e) => {
@@ -225,7 +235,9 @@
dicom_element = $(".cornerstone-element").get(0);
annotationjson = JSON.parse(e.currentTarget.dataset.annotationjson);
viewport = JSON.parse(e.currentTarget.dataset.viewportjson);
loadAnnotationAndViewportOnElement(annotationjson, viewport, dicom_element);
current_image_id_index = e.currentTarget.dataset.currentimageid;
console.log(e.currentTarget, current_image_id_index)
loadAnnotationAndViewportOnElement(annotationjson, viewport, dicom_element, current_image_id_index);
});
@@ -249,17 +261,26 @@
{% endif %}
});
function loadAnnotationAndViewportOnElement(annotation, viewport, dicom_element) {
function loadAnnotationAndViewportOnElement(annotation, viewport, dicom_element, current_image_id_index) {
cornerstoneTools.globalImageIdSpecificToolStateManager.clear(dicom_element);
cornerstone.getEnabledElement(dicom_element).viewport = viewport
cornerstoneTools.globalImageIdSpecificToolStateManager.restoreToolState(
annotation);
console.log("annotation", annotation)
console.log("viewport", viewport)
//cornerstone.getEnabledElement(dicom_element).toolStateManager.restoreToolState(annotationjson)
cornerstone.resize(dicom_element);
current_image_id_index = parseInt(current_image_id_index);
dicomViewer.getNextAnnotationImage(dicom_element);
console.log(current_image_id_index, Number.isInteger(current_image_id_index))
if (Number.isInteger(current_image_id_index)) {
console.log("loading stack index")
dicomViewer.loadStackIndex(current_image_id_index, dicom_element);
} else {
console.log("loading next annotation image")
dicomViewer.getNextAnnotationImage(dicom_element);
}
}
@@ -276,6 +297,7 @@
description: $('#id_description').val(),
series: {{ series.pk }},
//annotation_json: JSON.stringify(c.toolStateManager.saveToolState()),
current_image_id_index: c.toolStateManager.toolState.stack.data[0].currentImageIdIndex,
annotation_json: JSON.stringify(cornerstoneTools.globalImageIdSpecificToolStateManager
.saveToolState()),
viewport_json: JSON.stringify(c.viewport),
atlas/views.py
+2
View File
@@ -1385,6 +1385,7 @@ def create_series_findings(request):
description = request.POST.get("description")
annotation_json = request.POST.get("annotation_json")
viewport_json = request.POST.get("viewport_json")
current_image_id_index = int(request.POST.get("current_image_id_index"))
series = Series.objects.get(pk=series_id)
findings = Finding.objects.filter(pk__in=findings_ids)
@@ -1408,6 +1409,7 @@ def create_series_findings(request):
sf.findings.set(findings)
sf.structures.set(structures)
sf.conditions.set(conditions)
sf.current_image_id_index = current_image_id_index
sf.save()
return JsonResponse({"success": True})
generic/migrations/0018_alter_supervisor_user.py
+21
View File
@@ -0,0 +1,21 @@
# Generated by Django 5.0.2 on 2024-09-23 12:45
import django.db.models.deletion
from django.conf import settings
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('generic', '0017_cidusergroup_open_access_userusergroup_open_access_and_more'),
migrations.swappable_dependency(settings.AUTH_USER_MODEL),
]
operations = [
migrations.AlterField(
model_name='supervisor',
name='user',
field=models.OneToOneField(blank=True, help_text='If the supervisor has an account on the test system it can be associated here', null=True, on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL),
),
]