class ScanSerializer(serializers.HyperlinkedModelSerializer):
url = serializers.HyperlinkedIdentityField(view_name="mri:scan-detail")
dicom = serializers.HyperlinkedRelatedField(
view_name="dicom:series-detail", queryset=Series.objects.all()
)
subject = serializers.HyperlinkedRelatedField(
view_name="research:subject-detail",
queryset=get_subject_model().objects.all(),
required=False,
)
nifti = serializers.HyperlinkedRelatedField(
view_name="mri:nifti-detail",
queryset=NIfTI.objects.all(),
required=False,
allow_null=True,
)
study_groups = serializers.HyperlinkedRelatedField(
view_name="research:group-detail",
queryset=get_group_model().objects.all(),
many=True,
required=False,
)
sequence_type = serializers.HyperlinkedRelatedField(
view_name="mri:sequencetype-detail",
queryset=SequenceType.objects.all(),
required=False,
allow_null=True,
)
class Meta:
model = Scan
fields = (
"id",
"url",
"dicom",
"subject",
"nifti",
"study_groups",
"sequence_type",
"institution_name",
"time",
"description",
"number",
"echo_time",
"repetition_time",
"inversion_time",
"spatial_resolution",
"comments",
)
def create(self, validated_data):
scan, created = Scan.objects.get_or_create(**validated_data)
if created and scan.dicom and len(validated_data) == 1:
scan.update_fields_from_dicom()
scan.save()
return scan
def scan_subject_to_session(apps, schema_editor):
Subject = get_subject_model()
Scan = apps.get_model("django_mri", "Scan")
Session = apps.get_model("django_mri", "Session")
for scan in Scan.objects.all():
subject = Subject.objects.filter(
id_number=scan.dicom.patient.uid
).first()
first_image = scan.dicom.image_set.first().dcm.path
header = DicomHeader(first_image)
date = header.get("StudyDate") or header.get("SeriesDate")
try:
time = header.get("StudyTime")
except ValueError:
time = datetime.time()
else:
if not time:
time = datetime.time()
session_time = datetime.datetime.combine(date, time)
if not subject:
session = Session.objects.create(time=session_time)
scan.session_id = session.id
else:
session = subject.mri_session_set.filter(
time=session_time
).first()
if not session:
session = Session.objects.create(
subject_id=subject.id, time=session_time
)
else:
existing_scan_number = Scan.objects.filter(
session_id=session.id, number=scan.number
)
if existing_scan_number:
session = Session.objects.create(
subject_id=subject.id, time=session_time
)
scan.session_id = session.id
scan.save()
from django_mri.utils.utils import (
get_group_model,
get_measurement_model,
get_study_model,
get_subject_model,
)
from rest_framework import serializers
Group = get_group_model()
Measurement = get_measurement_model()
Subject = get_subject_model()
Study = get_study_model()
class MiniStudySerializer(serializers.ModelSerializer):
"""
Minified serializer class for the :class:`Study` model.
"""
class Meta:
model = Study
fields = "id", "title", "description"
class MiniGroupSerializer(serializers.ModelSerializer):
"""
Minified serializer class for the :class:`Group` model.
"""
study = MiniStudySerializer()
def test_get_subject_model(self):
result = utils.get_subject_model()
self.assertEqual(result, Subject)