refactor: bbox coordinates are mapped to embryo number

Author: cdpaiva

snazzy_processing/notebooks/snazzy-processing-pipeline.ipynb

@@ -92,10 +92,10 @@
     "# If necessary, manually change the bboxes size by changing w and h:\n",
     "boundaries = slice_img.increase_bbox(coords, w=190, h=40, shape=img.shape)\n",
     "\n",
-    "rect_coords = [slice_img.boundary_to_rect_coords(b) for b in boundaries]\n",
+    "rect_coords = [slice_img.boundary_to_rect_coords(b) for b in boundaries.values()]\n",
     "recs = [Rectangle((y, x), w, h) for (x, y, w, h) in rect_coords]\n",
     "\n",
-    "centroids = [((x0 + x1) // 2, (y0 + y1) // 2) for (x0, x1, y0, y1) in coords]\n",
+    "centroids = [((x0 + x1) // 2, (y0 + y1) // 2) for (x0, x1, y0, y1) in coords.values()]\n",
     "h = img.shape[0]\n",
     "w = img.shape[1]\n",
     "\n",
@@ -105,8 +105,10 @@
     "ax.set_axis_off()\n",
     "ax.imshow(img)\n",
     "\n",
-    "for i, (y, x) in enumerate(centroids):\n",
-    "    ax.text(x, y, str(i + 1))\n",
+    "for i, (x0, x1, y0, y1) in boundaries.items():\n",
+    "    centroid_x = (x0 + x1) // 2\n",
+    "    centroid_y = (y0 + y1) // 2\n",
+    "    ax.text(centroid_y, centroid_x, str(i))\n",
     "\n",
     "pc = PatchCollection(recs, color=\"red\", alpha=0.7, linewidth=1, facecolor=\"none\")\n",
     "ax.add_collection(pc)\n",
@@ -138,7 +140,7 @@
     "# Delete the individual movies created after the end of the analysis\n",
     "clean_up_data = False\n",
     "# List of the ids of the embryos that should be processed\n",
-    "embryos = list(range(1, 15))\n",
+    "embryos = list(range(1, 4))\n",
     "# Interval used to calculate VNC length\n",
     "vnc_length_interval = 10\n",
     "# Window to calculate VNC ROI (which is then used to calculate activity)\n",
@@ -154,7 +156,7 @@
     "\n",
     "# tif to individual movies\n",
     "print(\"Cropping individual movies\")\n",
-    "slice_img.cut_movies(coords, img_path, embs_dest, embryos=embryos, overwrite=False)\n",
+    "slice_img.cut_movies(boundaries, img_path, embs_dest, embryos=embryos, overwrite=False)\n",
     "\n",
     "# movies to length\n",
     "print(\"Calculating VNC lengths\")\n",

snazzy_processing/snazzy_processing/slice_img.py

@@ -118,15 +118,15 @@ def increase_bbox(coords, w, h, shape):
         w: int Number of pixels to increment in the bbox width (half each side)
         h: int Number of pixels to increment in the bbox height (half each side)
     """
-    new_coords = []
-    for coord in coords:
+    new_coords = {}
+    for emb_id, coord in coords.items():
         x0, x1, y0, y1 = coord
         r, c = shape
         new_x0 = max(x0 - h // 2, 0)
         new_x1 = min(x1 + h // 2, r)
         new_y0 = max(y0 - w // 2, 0)
         new_y1 = min(y1 + w // 2, c)
-        new_coords.append([new_x0, new_x1, new_y0, new_y1])
+        new_coords[emb_id] = [new_x0, new_x1, new_y0, new_y1]
     return new_coords
 
 
@@ -139,7 +139,7 @@ def sort_by_grid_pos(extremes, n_cols):
         for i, (r0, r1, c0, c1) in enumerate(extremes)
     ]
     # determine bin_size from the maximum column value
-    bin_size = (max((c for (r, c, i) in centroids)) // n_cols) + 1
+    bin_size = (max((c[1] for c in centroids)) // n_cols) + 1
 
     bins = [[] for _ in range(n_cols)]
     # add centroids to their respective bins
@@ -150,12 +150,14 @@ def sort_by_grid_pos(extremes, n_cols):
 
     # filter out possibly empty bins
     bins = [b for b in bins if len(b) > 0]
+
     # sort bins by row value
     for b in bins:
         b.sort(key=lambda b: b[0])
+
     # extracts each index
     indices = [b[2] for bin in bins for b in bin]
-    return [extremes[i] for i in indices]
+    return {k + 1: extremes[i] for k, i in enumerate(indices)}
 
 
 def filter_by_embryos(extremes, selected_embryos):
@@ -171,7 +173,6 @@ def read_mmap(mmap_path, num_frames=None):
 
 
 def create_tasks(extremes, channels, active_ch, dest, overwrite):
-    """"""
     tasks = []
     for id, extreme in extremes.items():
         x0, x1, y0, y1 = extreme

snazzy_processing/tests/test_slice_img.py

@@ -22,7 +22,7 @@ def test_can_mark_neighbors():
 
 
 def test_increase_bbox_does_not_mutate_coords():
-    coords = [[30, 80, 30, 80], [100, 300, 50, 250]]
+    coords = {1: [30, 80, 30, 80], 2: [100, 300, 50, 250]}
     orig_coords = coords.copy()
     shape = (300, 300)
 
@@ -34,18 +34,18 @@ def test_increase_bbox_does_not_mutate_coords():
 
 def test_increase_bbox_clips_to_shape():
     """Adding padding should not result in negative or OutOfBounds indices."""
-    coords = [[2, 200, 5, 490]]
-    expected_coords = [[0, 210, 0, 500]]
+    coords = {1: [2, 200, 5, 490]}
+    expected_coords = {1: [0, 210, 0, 500]}
     shape = (300, 500)
 
     actual = slice_img.increase_bbox(coords, w=20, h=20, shape=shape)
-    assert actual[0] == expected_coords[0]
+    assert actual == expected_coords
 
 
 def test_increase_bbox_when_resulting_bbox_inside():
-    coords = [[10, 200, 50, 490]]
-    expected_coords = [[0, 210, 40, 500]]
+    coords = {1: [10, 200, 50, 490]}
+    expected_coords = {1: [0, 210, 40, 500]}
     shape = (600, 600)
 
     actual = slice_img.increase_bbox(coords, w=20, h=20, shape=shape)
-    assert actual[0] == expected_coords[0]
+    assert actual == expected_coords

snazzy_processing/tests/test_sort_by_grid_pos.py

@@ -28,7 +28,7 @@ def shuffle_arr(arr):
 
 
 def test_sorts_a_full_grid(grid_3x3_bboxes):
-    expected = grid_3x3_bboxes.copy()
+    expected = {i + 1: coord for i, coord in enumerate(grid_3x3_bboxes)}
 
     shuffle_arr(grid_3x3_bboxes)
 
@@ -40,7 +40,7 @@ def test_sorts_a_full_grid(grid_3x3_bboxes):
 def test_sorts_a_grid_with_one_missing_embryo(grid_3x3_bboxes):
     """Removed embryo that would take pos 9."""
     bboxes = grid_3x3_bboxes[:-1]
-    expected = bboxes.copy()
+    expected = {i + 1: coord for i, coord in enumerate(bboxes)}
 
     shuffle_arr(bboxes)
 
@@ -50,10 +50,10 @@ def test_sorts_a_grid_with_one_missing_embryo(grid_3x3_bboxes):
 
 def test_sorts_a_grid_with_several_missing_embryos(grid_3x3_bboxes):
     """Removed embryos at index 0, 5, 6, and 7."""
-    keeping_idxs = [1, 2, 3, 4, 7]
+    keeping_idxs = [1, 2, 3, 4, 8]
     bboxes = [grid_3x3_bboxes[i] for i in keeping_idxs]
 
-    expected = bboxes.copy()
+    expected = {i + 1: coord for i, coord in enumerate(bboxes)}
 
     shuffle_arr(bboxes)
 
@@ -67,7 +67,7 @@ def test_sorts_a_grid_with_empty_column(grid_3x3_bboxes):
     pos = [0, 1, 2, 6, 7, 8]
     bboxes = [grid_3x3_bboxes[p] for p in pos]
 
-    expected = bboxes.copy()
+    expected = {i + 1: coord for i, coord in enumerate(bboxes)}
 
     shuffle_arr(bboxes)