Remove retina thumbnail endpoints (#2151)

Co-authored-by: James Meakin <12661555+jmsmkn@users.noreply.github.com>

CODEOWNERS

@@ -17,6 +17,5 @@
 /app/grandchallenge/evaluation/       @jmsmkn
 /app/grandchallenge/reader_studies/   @MikeOverkamp-diag
 /app/grandchallenge/retina_api/       @HarmvZ
-/app/grandchallenge/retina_core/      @HarmvZ
 /app/grandchallenge/products/         @MikeOverkamp-diag
 /app/grandchallenge/workstations/     @jmsmkn

app/config/settings.py

@@ -482,7 +482,6 @@ def strtobool(val) -> bool:
     "grandchallenge.studies",
     "grandchallenge.registrations",
     "grandchallenge.annotations",
-    "grandchallenge.retina_core",
     "grandchallenge.retina_api",
     "grandchallenge.workstations",
     "grandchallenge.workspaces",
@@ -1152,9 +1151,6 @@ def strtobool(val) -> bool:
     os.environ.get("DATA_UPLOAD_MAX_NUMBER_FIELDS", "2048")
 )
 
-# Default maximum width or height for thumbnails in retina workstation
-RETINA_DEFAULT_THUMBNAIL_SIZE = 128
-
 # Retina specific settings
 RETINA_GRADERS_GROUP_NAME = "retina_graders"
 RETINA_ADMINS_GROUP_NAME = "retina_admins"

app/config/urls/root.py

@@ -115,10 +115,6 @@ def handler500(request):
         ),
     ),
     path("summernote/", include("django_summernote.urls")),
-    path(
-        "retina/",
-        include("grandchallenge.retina_core.urls", namespace="retina"),
-    ),
     path(
         "aiforradiology/",
         include("grandchallenge.products.urls", namespace="products"),

app/grandchallenge/cases/models.py

@@ -1,8 +1,7 @@
 import logging
 import os
 from pathlib import Path
-from tempfile import TemporaryDirectory
-from typing import List, Mapping, Union
+from typing import List
 
 from actstream.actions import follow
 from actstream.models import Follow
@@ -17,10 +16,6 @@
 from django.dispatch import receiver
 from django.utils.text import get_valid_filename
 from guardian.shortcuts import assign_perm, get_groups_with_perms, remove_perm
-from panimg.image_builders.metaio_utils import (
-    load_sitk_image,
-    parse_mh_header,
-)
 from panimg.models import ColorSpace, ImageType, PatientSex
 
 from grandchallenge.core.models import UUIDModel
@@ -387,36 +382,6 @@ def shape(self) -> List[int]:
             result.append(color_components)
         return result
 
-    @property
-    def spacing(self) -> List[float]:
-        """
-        Return the voxel spacing (or size if spacing is nonexistent) of the image.
-
-        Returns
-        -------
-            The voxel spacing in mm in NumPy ordering [(z), y, x]
-            Defaults to [(1), 1, 1]
-        """
-        spacing = [
-            self.voxel_depth_mm,
-            self.voxel_height_mm,
-            self.voxel_width_mm,
-        ]
-        if spacing[0] is None:
-            spacing = spacing[-2:]
-        if None in spacing:
-            mh_header = self.get_mh_header()
-            spacing_str = mh_header.get(
-                "ElementSpacing", mh_header.get("ElementSize")
-            )
-            if spacing_str is not None:
-                spacing = list(
-                    reversed([float(x) for x in spacing_str.split(" ")])
-                )
-            else:
-                spacing = [1] * int(mh_header["NDims"])
-        return spacing
-
     def get_metaimage_files(self):
         """
         Return ImageFile object for the related MHA file or MHD and RAW files.
@@ -455,82 +420,6 @@ def get_metaimage_files(self):
 
         return header_file, image_data_file
 
-    def get_mh_header(self) -> Mapping[str, Union[str, None]]:
-        """
-        Return header from mhd/mha file as key value pairs
-
-        Returns
-        -------
-            MetaIO headers as key value pairs.
-
-        Raises
-        ------
-        FileNotFoundError
-            Raised when Image has no related mhd/mha ImageFile or actual file
-            cannot be found on storage
-        """
-
-        mh_file, _ = self.get_metaimage_files()
-        return parse_mh_header(mh_file.file)
-
-    def get_sitk_image(self):
-        """
-        Return the image that belongs to this model as an SimpleITK image.
-
-        Requires that exactly one MHD/RAW file pair is associated with the model.
-        Otherwise it wil raise a MultipleObjectsReturned or ObjectDoesNotExist
-        exception.
-
-        Returns
-        -------
-            A SimpleITK image
-        """
-        files = [i for i in self.get_metaimage_files() if i is not None]
-
-        file_size = 0
-        for file in files:
-            if not file.file.storage.exists(name=file.file.name):
-                raise FileNotFoundError(f"No file found for {file.file}")
-
-            # Add up file sizes of mhd and raw file to get total file size
-            file_size += file.file.size
-
-        # Check file size to guard for out of memory error
-        if file_size > settings.MAX_SITK_FILE_SIZE:
-            raise OSError(
-                f"File exceeds maximum file size. (Size: {file_size}, Max: {settings.MAX_SITK_FILE_SIZE})"
-            )
-
-        with TemporaryDirectory() as tempdirname:
-            for file in files:
-                with file.file.open("rb") as infile, open(
-                    Path(tempdirname) / Path(file.file.name).name, "wb"
-                ) as outfile:
-                    buffer = True
-                    while buffer:
-                        buffer = infile.read(1024)
-                        outfile.write(buffer)
-
-            try:
-                hdr_path = Path(tempdirname) / Path(files[0].file.name).name
-                sitk_image = load_sitk_image(mhd_file=hdr_path)
-            except RuntimeError as e:
-                logging.error(
-                    f"Failed to load SimpleITK image with error: {e}"
-                )
-                raise
-
-        return sitk_image
-
-    def permit_viewing_by_retina_users(self):
-        """Set object level view permissions for retina_graders and retina_admins."""
-        for group_name in (
-            settings.RETINA_GRADERS_GROUP_NAME,
-            settings.RETINA_ADMINS_GROUP_NAME,
-        ):
-            group = Group.objects.get(name=group_name)
-            assign_perm("view_image", group, self)
-
     def update_viewer_groups_permissions(self, *, exclude_jobs=None):
         """
         Update the permissions for the algorithm jobs viewers groups to

app/grandchallenge/retina_api/__init__.py

@@ -0,0 +1 @@
+default_app_config = "grandchallenge.retina_api.apps.RetinaAPIConfig"

app/grandchallenge/retina_core/apps.py → app/grandchallenge/retina_api/apps.py

@@ -10,8 +10,8 @@ def init_retina_groups(*_, **__):
     Group.objects.get_or_create(name=settings.RETINA_GRADERS_GROUP_NAME)
 
 
-class RetinaCoreConfig(AppConfig):
-    name = "grandchallenge.retina_core"
+class RetinaAPIConfig(AppConfig):
+    name = "grandchallenge.retina_api"
 
     def ready(self):
         post_migrate.connect(init_retina_groups)

app/grandchallenge/retina_api/serializers.py

@@ -1,63 +1,9 @@
-import base64
-from io import BytesIO
-
-import SimpleITK
-from PIL import Image as PILImage
-from django.http import Http404
 from rest_framework import serializers
 
 from grandchallenge.cases.models import Image
 from grandchallenge.cases.serializers import HyperlinkedImageSerializer
 
 
-class B64ImageSerializer(serializers.Serializer):
-    """
-    Serializer that returns a b64 encoded image from an Image instance.
-
-    If "width" and "height" are passed as extra serializer content, the
-    PIL image will be resized to those dimensions.
-
-    Subclasses PILImageSerializer, so the image may be resized and only the central
-    slice of a 3d image will be returned
-    """
-
-    content = serializers.SerializerMethodField(read_only=True)
-
-    def get_content(self, obj):
-        try:
-            image_itk = obj.get_sitk_image()
-        except Exception:
-            raise Http404
-
-        pil_image = self.convert_itk_to_pil(image_itk)
-
-        if "width" in self.context and "height" in self.context:
-            new_dims = (self.context["width"], self.context["height"])
-            try:
-                pil_image.thumbnail(
-                    new_dims, PILImage.ANTIALIAS,
-                )
-            except ValueError:
-                pil_image = pil_image.resize(new_dims)
-
-        return self.create_thumbnail_as_b64(pil_image)
-
-    @staticmethod
-    def convert_itk_to_pil(image_itk):
-        depth = image_itk.GetDepth()
-        image_nparray = SimpleITK.GetArrayFromImage(image_itk)
-        if depth > 0:
-            # Get center slice of image if 3D
-            image_nparray = image_nparray[depth // 2]
-        return PILImage.fromarray(image_nparray)
-
-    @staticmethod
-    def create_thumbnail_as_b64(image_pil):
-        buffer = BytesIO()
-        image_pil.save(buffer, format="png")
-        return base64.b64encode(buffer.getvalue())
-
-
 class ImageLevelAnnotationsForImageSerializer(serializers.Serializer):
     quality = serializers.UUIDField(allow_null=True, read_only=True)
     pathology = serializers.UUIDField(allow_null=True, read_only=True)

app/grandchallenge/retina_api/views.py

@@ -1,12 +1,8 @@
-from django.conf import settings
 from django.core.exceptions import ValidationError
 from django.shortcuts import get_object_or_404
 from django_filters import rest_framework as drf_filters
 from rest_framework import mixins, viewsets
 from rest_framework.exceptions import NotFound
-from rest_framework.generics import RetrieveAPIView
-from rest_framework.permissions import DjangoObjectPermissions
-from rest_framework.response import Response
 from rest_framework_guardian import filters
 
 from grandchallenge.annotations.models import (
@@ -41,7 +37,6 @@
 )
 from grandchallenge.retina_api.mixins import RetinaAPIPermission
 from grandchallenge.retina_api.serializers import (
-    B64ImageSerializer,
     ImageLevelAnnotationsForImageSerializer,
     RetinaImageSerializer,
 )
@@ -60,21 +55,6 @@ class ETDRSGridAnnotationViewSet(viewsets.ModelViewSet):
     queryset = ETDRSGridAnnotation.objects.all()
 
 
-class B64ThumbnailAPIView(RetrieveAPIView):
-    permission_classes = (DjangoObjectPermissions, RetinaAPIPermission)
-    filters = (filters.ObjectPermissionsFilter,)
-    queryset = Image.objects.all()
-    serializer_class = B64ImageSerializer
-
-    def retrieve(self, request, *args, **kwargs):
-        instance = self.get_object()
-        width = kwargs.get("width", settings.RETINA_DEFAULT_THUMBNAIL_SIZE)
-        height = kwargs.get("height", settings.RETINA_DEFAULT_THUMBNAIL_SIZE)
-        serializer_context = {"width": width, "height": height}
-        serializer = B64ImageSerializer(instance, context=serializer_context)
-        return Response(serializer.data)
-
-
 class LandmarkAnnotationSetViewSet(viewsets.ModelViewSet):
     permission_classes = (RetinaAPIPermission,)
     serializer_class = LandmarkAnnotationSetSerializer