Fix last of the tests, update analysis_utils.

src/kbmod/analysis_utils.py

@@ -123,7 +123,14 @@ def get_all_stamps(self, result_list, search, stamp_radius):
         stamp_edge = stamp_radius * 2 + 1
         for row in result_list.results:
             stamps = kb.StampCreator.get_stamps(search.get_imagestack(), row.trajectory, stamp_radius)
-            row.all_stamps = np.array([np.array(stamp).reshape(stamp_edge, stamp_edge) for stamp in stamps])
+            # TODO: a way to avoid a copy here would be to do
+            # np.array([s.image for s in stamps], dtype=np.single, copy=False)
+            # but that could cause a problem with reference counting at the m
+            # moment. The real fix is to make the stamps return Image not
+            # RawImage, return the Image and avoid a reference to a private
+            # attribute. This risks collecting RawImage but leaving a dangling
+            # ref to its private field. That's a fix for another time.
+            row.all_stamps = np.array([stamp.image for stamp in stamps])
 
     def apply_clipped_sigmaG(self, result_list):
         """This function applies a clipped median filter to the results of a KBMOD
@@ -324,9 +331,16 @@ def apply_stamp_filter(
                 params,
                 kb.HAS_GPU and len(trj_slice) > 100,
             )
+            # TODO: a way to avoid a copy here would be to do
+            # np.array([s.image for s in stamps], dtype=np.single, copy=False)
+            # but that could cause a problem with reference counting at the m
+            # moment. The real fix is to make the stamps return Image not
+            # RawImage and avoid reference to an private attribute and risking
+            # collecting RawImage but leaving a dangling ref to the attribute.
+            # That's a fix for another time so I'm leaving it as a copy here
             for ind, stamp in enumerate(stamps_slice):
                 if stamp.width > 1:
-                    result_list.results[ind + start_idx].stamp = np.array(stamp)
+                    result_list.results[ind + start_idx].stamp = np.array(stamp.image)
                     all_valid_inds.append(ind + start_idx)
 
             # Move to the next chunk.

src/kbmod/search/kernels.cu

@@ -103,8 +103,10 @@ namespace search {
     }
 
     // Get origin pixel for the trajectories in pixel space.
-    const int x = x_i + params.x_start_min;
-    const int y = y_i + params.y_start_min;
+    // TODO: this is an ugly hack to get things to work,
+    // beautify before merge, see also later
+    const int y = x_i + params.x_start_min;
+    const int x = y_i + params.y_start_min;
     const unsigned int n_pixels = width * height;
 
     // Data structures used for filtering.
@@ -149,8 +151,10 @@ namespace search {
       for (int i = 0; i < num_images; ++i) {
         // Predict the trajectory's position.
         float curr_time = image_data.image_times[i];
-        int current_x = x + int(curr_trj.vx * curr_time + 0.5);
-        int current_y = y + int(curr_trj.vy * curr_time + 0.5);
+        // TODO: the hack again, make sure to properly contextualize
+        // before merging
+        int current_y = x + int(curr_trj.vx * curr_time + 0.5);
+        int current_x = y + int(curr_trj.vy * curr_time + 0.5);
 
         // Test if trajectory goes out of the image, in which case we do not
         // look up a pixel value for this time step (allowing trajectories to

src/kbmod/search/raw_image.cpp

@@ -655,6 +655,14 @@ RawImage& RawImage::operator=(RawImage&& source) {
       .def_property("obstime", &rie::get_obstime, &rie::set_obstime)
       .def_property("image", py::overload_cast<>(&rie::get_image, py::const_), &rie::set_image)
       .def_property("imref", py::overload_cast<>(&rie::get_image), &rie::set_image)
+      .def("data", [](rie& cls){
+        for (int j=0; j<cls.get_height(); j++){
+          for (int i=0; i<cls.get_width(); i++){
+            std::cout << cls.get_image()(j, i) << "    ";
+          }
+          std::cout << std::endl;
+        }
+      })
       // pixel accessors and setters
       .def("get_pixel", &rie::get_pixel)
       .def("pixel_has_data", &rie::pixel_has_data)

src/kbmod/search/stack_search.cpp

@@ -276,6 +276,23 @@ namespace search {
   }
 
 
+  Point StackSearch::get_trajectory_position(const Trajectory& t, int i) const {
+    float time = stack.get_zeroed_time(i);
+    return {t.y + time * t.vy, t.x + time * t.vx};
+  }
+
+
+  std::vector<Point> StackSearch::get_trajectory_positions(Trajectory& t) const {
+    std::vector<Point> results;
+    int num_times = stack.img_count();
+    for (int i = 0; i < num_times; ++i) {
+      Point pos = get_trajectory_position(t, i);
+      results.push_back(pos);
+    }
+    return results;
+  }
+
+
   std::vector<float> StackSearch::create_curves(Trajectory t, const std::vector<RawImage>& imgs) {
     /*Create a lightcurve from an image along a trajectory
      *