From 522fa6bcb0b362401923daf1d32626fea9e8f59e Mon Sep 17 00:00:00 2001
From: Ross <xkjq@ymail.com>
Date: Mon, 7 Aug 2023 21:46:34 +0100
Subject: [PATCH] improve dicom json support

---
 atlas/models.py | 91 +++++++++++++++++++++++++++----------------------
 1 file changed, 50 insertions(+), 41 deletions(-)

diff --git a/atlas/models.py b/atlas/models.py
index 52ba88dd..74fa1d47 100644
--- a/atlas/models.py
+++ b/atlas/models.py
@@ -352,13 +352,52 @@ class Case(models.Model):
         pass
 
 
+def extract_image_dicom_json_from_ds(ds, url):
+    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": f"dicomweb:{url}"}
+
+
 class SeriesImage(SeriesImageBase):
     image = models.FileField(upload_to=image_directory_path)
     series = models.ForeignKey(
         "Series", related_name="images", on_delete=models.SET_NULL, null=True
     )
 
-    def get_series_dicom_data(self):
+    def get_extra_dicom_data(self):
         print(self.image)
         with pydicom.dcmread(self.image) as d:
             return d
@@ -366,42 +405,7 @@ class SeriesImage(SeriesImageBase):
     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": f"dicomweb:{REMOTE_URL}{self.image.url}"}
+                return extract_image_dicom_json_from_ds(ds, url=f"{REMOTE_URL}{self.image.url}")
         except FileNotFoundError:
             return []
 
@@ -489,12 +493,13 @@ class Series(SeriesBase):
 
         series_json = {}
 
-        to_keep = ["SeriesInstanceUID", "SeriesNumber", "Modality", "SliceThickness"]
+        to_keep = ["SeriesInstanceUID", "SeriesNumber", "Modality", "SliceThickness", "SeriesDescription"]
 
+        # TODO: clean up (this is rather convoluted....)
         image: SeriesImage
         for series_n, image in enumerate(self.images.all()):
             if series_n == 0:
-                ds = image.get_series_dicom_data()
+                ds = image.get_extra_dicom_data()
 
                 for tag in to_keep:
                     if tag in ds:
@@ -505,9 +510,13 @@ class Series(SeriesBase):
                         else:
                             series_json[tag] = val
 
-            instances.append(image.get_image_dicom_json())
+                instances.append(
+                    extract_image_dicom_json_from_ds(ds, url=f"{REMOTE_URL}{image.image.url}")
+                )
+            else:
+                instances.append(image.get_image_dicom_json())
 
-        series_json["instances"]= instances
+        series_json["instances"] = instances
 
         return series_json