fix a number of things

atlas/models.py

@@ -13,6 +13,7 @@ from django.utils import timezone
 
 
 import pydicom
+import pydicom.multival
 
 from django.core.files.storage import FileSystemStorage
 from django.conf import settings
@@ -272,8 +273,9 @@ class Case(models.Model):
         related_name="atlas_edited_cases",
     )
 
-    scrapped = models.BooleanField(
-        default=False, help_text="Question has been scrapped and will not be shown"
+    archive = models.BooleanField(
+        default=False,
+        help_text="Case has been archived, this will remain on the system but will not be shown",
     )
 
     open_access = models.BooleanField(
@@ -325,6 +327,30 @@ class Case(models.Model):
         examinations = [series.get_examination() for series in self.series.all()]
         return f"{self.pk}:{self.title} {'/'.join([str(c) for c in self.condition.all()])} [{', '.join(examinations)}]"
 
+    def get_case_dicom_json(self):
+        series_json = []
+        for series in self.series.all():
+            series_json.append(series.get_series_dicom_json())
+
+            print(series_json)
+
+        return {
+            "studies": [
+                {
+                    "StudyInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178",
+                    "StudyDate": "20000101",
+                    "StudyTime": "",
+                    "PatientName": "",
+                    "PatientID": "LIDC-IDRI-0001",
+                    "AccessionNumber": "",
+                    "PatientAge": "",
+                    "PatientSex": "",
+                    "series": series_json,
+                }
+            ]
+        }
+        pass
+
 
 class SeriesImage(SeriesImageBase):
     image = models.FileField(upload_to=image_directory_path)
@@ -332,6 +358,50 @@ class SeriesImage(SeriesImageBase):
         "Series", related_name="images", on_delete=models.SET_NULL, null=True
     )
 
+    def get_image_dicom_json(self):
+        try:
+            with pydicom.dcmread(self.image) as ds:
+                to_keep = [
+                    "Columns",
+                    "Rows",
+                    "InstanceNumber",
+                    "SOPClassUID",
+                    "PhotometricInterpretation",
+                    "BitsAllocated",
+                    "BitsStored",
+                    "PixelRepresentation",
+                    "SamplesPerPixel",
+                    "PixelSpacing",
+                    "HighBit",
+                    "ImageOrientationPatient",
+                    "ImagePositionPatient",
+                    "FrameOfReferenceUID",
+                    "ImageType",
+                    "Modality",
+                    "SOPInstanceUID",
+                    "SeriesInstanceUID",
+                    "StudyInstanceUID",
+                    "WindowCenter",
+                    "WindowWidth",
+                    "SeriesDate",
+                ]
+
+                d = {}
+
+                for key in to_keep:
+                    val = ds[key].value
+
+                    if type(val) == pydicom.multival.MultiValue:
+                        d[key] = list(val)
+                    else:
+                        d[key] = val
+
+
+
+                return {"metadata": d, "url": self.image.url}
+        except FileNotFoundError:
+            return []
+
 
 class SeriesFinding(models.Model):
     series = models.ForeignKey(
@@ -411,6 +481,23 @@ class Series(SeriesBase):
             "<a href='{}'>{}</a>", self.get_absolute_url(), self.get_full_str()
         )
 
+    def get_series_dicom_json(self):
+        instances = []
+
+        image: SeriesImage
+        for image in self.images.all():
+            instances.append(image.get_image_dicom_json())
+
+        series_json = {
+            "SeriesInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192",
+            "SeriesNumber": 3000566,
+            "Modality": "CT",
+            "SliceThickness": 2.5,
+            "instances": instances,
+        }
+
+        return series_json
+
 
 class CaseCollection(ExamCollectionGenericBase):
     app_name = "atlas"
@@ -522,10 +609,14 @@ class CaseCollection(ExamCollectionGenericBase):
 
         return False
 
-    def get_case_by_index(self, case_index:int, case_count=False) -> Case | Tuple[Case, int]:
+    def get_case_by_index(
+        self, case_index: int, case_count=False
+    ) -> Case | Tuple[Case, int]:
         # Seems to be a bug when case_number is 0 or 1 the same (first) object gets returned
         # forces a list fixes (but is likely inefficient)
-        cases = list(self.cases.all().order_by("casedetail__sort_order").prefetch_related())
+        cases = list(
+            self.cases.all().order_by("casedetail__sort_order").prefetch_related()
+        )
 
         try:
             case = cases[case_index]
@@ -534,10 +625,20 @@ class CaseCollection(ExamCollectionGenericBase):
             raise Http404(s)
 
         if case_count:
-            return case, len(cases) 
+            return case, len(cases)
         else:
             return case
 
+    def get_case_take_url(self, case):
+        cases = list(
+            self.cases.all().order_by("casedetail__sort_order").prefetch_related()
+        )
+
+        return reverse(
+            "atlas:collection_case_view_take_user",
+            kwargs={"pk": self.pk, "case_number": cases.index(case)},
+        )
+
 
 class CaseDetail(models.Model):
     case = models.ForeignKey(Case, on_delete=models.CASCADE)
@@ -617,9 +718,7 @@ class SelfReview(models.Model):
     review_update_date = models.DateTimeField(auto_now=True)
 
     def get_absolute_url(self):
-        return reverse(
-            "atlas:collection_take_overview_user", kwargs={"pk": self.user_exam.exam.pk}
-        )
+        return self.user_exam.exam.get_case_take_url(self.case)
 
     def get_display_block(self):
         html = """<div class='self-feedback-block'>
@@ -628,15 +727,27 @@ class SelfReview(models.Model):
         Findings: <span class="findings">{findings}</span><br/>
 
         Interpretation: <span class="interpretation">{interpretation}</span><br/>
-        <span class="date">Date: {date}</span><br/>
+        <span class="date">Date: {date}</span><br/><a href="{edit_url}">Edit</a>
         </div>
         
         """
 
+        edit_url = reverse(
+            "atlas:self_review_update",
+            kwargs={
+                "user_exam_id": self.user_exam.pk,
+                "case_id": self.case.pk,
+                "pk": self.pk,
+            },
+        )
+        # edit_url = "TEST"
+
         return format_html(
             html,
             comments=self.comments,
             findings=self.findings,
             interpretation=self.interpretation,
             date=self.review_date,
+            id=self.pk,
+            edit_url=edit_url,
         )