Merge pull request #10 from LCOGT/feature/line-analysis-backend

Analysis Actions and Line Profile

datalab/datalab_session/analysis/line_profile.py

@@ -0,0 +1,14 @@
+from skimage.measure import profile_line
+
+from datalab.datalab_session.util import scale_points
+
+# For creating an array of brightness along a user drawn line
+def line_profile(input: dict, sci_hdu: object):
+  """
+    Creates an array of luminosity values and the length of the line in arcseconds
+  """
+  points = scale_points(input['width'], input['height'], sci_hdu.data, [(input["x1"], input["y1"]), (input["x2"], input["y2"])])
+  line_profile = profile_line(sci_hdu.data, points[0], points[1], mode="constant", cval=-1)
+  arcsec = len(line_profile) * sci_hdu.header["PIXSCALE"]
+
+  return {"line_profile": line_profile, "arcsec": arcsec}

datalab/datalab_session/util.py

@@ -6,6 +6,7 @@
 import numpy as np
 
 from django.conf import settings
+from django.core.cache import cache
 
 log = logging.getLogger()
 log.setLevel(logging.INFO)
@@ -97,6 +98,29 @@ def get_archive_from_basename(basename: str) -> dict:
 
   return results
 
+def get_hdu(basename: str, extension: str = 'SCI') -> list[fits.HDUList]:
+  """
+  Returns a list of Sci HDUs for the given basenames
+  Warning: this function returns an opened file that must be closed after use
+  """
+
+  # use the basename to fetch and create a list of hdu objects
+  basename = basename.replace('-large', '').replace('-small', '')
+
+  if cache.get(f'{basename}-{extension}') is not None:
+    return cache.get(f'{basename}-{extension}')
+
+  archive_record = get_archive_from_basename(basename)
+
+  try:
+    fits_url = archive_record[0].get('url', 'No URL found')
+  except IndexError:
+    RuntimeWarning(f"No image found with specified basename: {basename}")
+
+  hdu = fits.open(fits_url, use_fsspec=True)
+  cache.set(f'{basename}-{extension}', hdu[extension])
+  return hdu[extension]
+
 def create_fits(key: str, image_arr: np.ndarray) -> fits.HDUList:
 
   header = fits.Header([('KEY', key)])
@@ -118,3 +142,23 @@ def stack_arrays(array_list: list):
   stacked = np.stack(cropped_data_list, axis=2)
 
   return stacked
+
+def scale_points(small_img_width: int, small_img_height: int, img_array: list, points: list[tuple[int, int]]):
+  """
+    Scale the coordinates from a smaller image to the full sized fits so we know the positions of the coords on the 2dnumpy array
+    Returns the list of tuple points with coords scaled for the numpy array
+  """
+
+  large_height, large_width = np.shape(img_array)
+
+  # If the aspect ratios don't match we can't be certain where the point was
+  if small_img_width / small_img_height != large_width / large_height:
+    raise ValueError("Aspect ratios of the two images must match")
+
+  width_scale = large_width / small_img_width
+  height_scale = large_height / small_img_height
+
+  points_array = np.array(points)
+  scaled_points = np.int_(points_array * [width_scale, height_scale])
+
+  return scaled_points

datalab/datalab_session/views.py

@@ -1,8 +1,11 @@
 from rest_framework.generics import RetrieveAPIView
+from rest_framework.views import APIView
 from rest_framework.renderers import JSONRenderer
 from rest_framework.response import Response
 
 from datalab.datalab_session.data_operations.utils import available_operations
+from datalab.datalab_session.analysis.line_profile import line_profile
+from datalab.datalab_session.util import get_hdu
 
 
 class OperationOptionsApiView(RetrieveAPIView):
@@ -15,3 +18,21 @@ def get(self, request):
         for operation_clazz in operations.values():
             operation_details[operation_clazz.name()] = operation_clazz.wizard_description()
         return Response(operation_details)
+
+class AnalysisView(APIView):
+    """ 
+        View to handle analysis actions and return the results
+        To add a new analysis action, add a case to the switch statement and create a new file in the analysis directory
+    """
+    def post(self, request, action):
+        input = request.data
+
+        sci_hdu = get_hdu(input['basename'])
+
+        match action:
+            case 'line-profile':
+                output = line_profile(input, sci_hdu)
+            case _:
+                raise Exception(f'Analysis action {action} not found')
+
+        return Response(output)

datalab/urls.py

@@ -20,7 +20,7 @@
 import ocs_authentication.auth_profile.urls as authprofile_urls
 
 from datalab.datalab_session.viewsets import DataSessionViewSet, DataOperationViewSet
-from datalab.datalab_session.views import OperationOptionsApiView
+from datalab.datalab_session.views import OperationOptionsApiView, AnalysisView
 
 router = routers.SimpleRouter()
 router.register(r'datasessions', DataSessionViewSet, 'datasessions')
@@ -35,6 +35,7 @@
 urlpatterns = [
     path('admin/', admin.site.urls),
     re_path(r'^api/', include(api_urlpatterns)),
+    path(r'api/analysis/<slug:action>/', AnalysisView.as_view(), name='analysis'),
     path('api/available_operations/', OperationOptionsApiView.as_view(), name='available_operations'),
     re_path(r'^authprofile/', include(authprofile_urls)),
 ]