Merge pull request #92 from SainsburyWellcomeCentre/smg/timecodes-mat…

…ching Small additions to timecodes matching
SainsburyWellcomeCentre · Nov 23, 2023 · 89844d0 · 89844d0
2 parents 8b61fbc + ff31726
commit 89844d0
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Showing 5 changed files with 14 additions and 10 deletions.
diff --git a/crabs/stereo_calibration/__init__.py b/crabs/stereo_calibration/__init__.py
@@ -1,5 +1,6 @@
 msg = """
-The stereo calibration pipeline code is not ready for use yet so we've temporarily blocked it's use!
-See https://github.com/SainsburyWellcomeCentre/crabs-exploration/issues/90 for more details. Create a branch and remove the NotImplementedError to develop!
+The stereo calibration pipeline code is not ready for use yet so we've temporarily blocked its use!
+See https://github.com/SainsburyWellcomeCentre/crabs-exploration/issues/90 for more details.
+Create a branch and remove the NotImplementedError to develop!
 """
 raise NotImplementedError(msg)
diff --git a/crabs/stereo_calibration/extract_pairs_of_frames.py b/crabs/stereo_calibration/extract_pairs_of_frames.py
@@ -320,6 +320,7 @@ def extract_chessboard_frames_from_video(
             # TODO: append 2d coords of corners?
             frame_gray = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY)
 
+            # TODO: the following is very slow when no chessboard is present
             ret, corners = cv2.findChessboardCorners(
                 frame_gray,
                 (chessboard_config["rows"], chessboard_config["cols"]),

diff --git a/notebooks/notebook_detect_chessboard_in_sampled_frames.py b/notebooks/notebook_detect_chessboard_in_sampled_frames.py
@@ -13,14 +13,12 @@
 
 # %%
 video_path_str = (
-    "/Users/sofia/Documents_local/project_Zoo_crabs/crabs-exploration/"
-    "stereo calibration/check_chessboard_prelim_230809/"
+    "/Users/sofia/Documents_local/project_Zoo_crabs/data/check_chessboard_prelim_230809/"
     "NINJAV__cam1_S001_S001_T001_1.mp4"
 )
 video_path = Path(video_path_str)
 video_output_dir = Path(
-    "/Users/sofia/Documents_local/project_Zoo_crabs/crabs-exploration"
-    "/stereo calibration/check_chessboard_prelim_230809"
+    "/Users/sofia/Documents_local/project_Zoo_crabs/data/check_chessboard_prelim_230809"
 )
 
 
@@ -169,6 +167,7 @@
     img_gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
 
     # try to detect chessboard corners
+    # TODO: the following is very slow when no chessboard is present
     ret, corners = cv2.findChessboardCorners(
         img_gray,
         (chessboard_config["rows"], chessboard_config["cols"]),

diff --git a/notebooks/notebook_detect_chessboard_in_video.py b/notebooks/notebook_detect_chessboard_in_video.py
@@ -11,8 +11,7 @@
 
 # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 video_path_str = (
-    "/Users/sofia/Documents_local/project_Zoo_crabs/crabs-exploration/"
-    "stereo calibration/check_chessboard_prelim_230809/"
+    "/Users/sofia/Documents_local/project_Zoo_crabs/data/check_chessboard_prelim_230809/"
     "NINJAV__cam1_S001_S001_T001_1.mp4"
 )
 video_path = Path(video_path_str)
@@ -70,7 +69,7 @@
 
 
 # %%%%%%%%%%%%%%%%%%%%
-# prepare video writer -------
+# prepare video writer
 output_frame_rate = 1
 
 # initialise capture and videowriter
@@ -115,6 +114,7 @@
         img_gray = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY)
 
         # try to detect chessboard corners
+        # TODO: this function is very slow when a chessboard is not present
         ret, corners = cv2.findChessboardCorners(
             img_gray,
             (chessboard_config["rows"], chessboard_config["cols"]),

diff --git a/notebooks/notebook_timecodes.py b/notebooks/notebook_timecodes.py
@@ -8,7 +8,9 @@
 
 # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 # Input data
-input_videos_parent_dir = "/Users/sofia/Documents_local/project_Zoo_crabs/crabs-exploration/data/crab_courtyard/"
+input_videos_parent_dir = (
+    "/Users/sofia/Documents_local/project_Zoo_crabs/data/crab_courtyard/"
+)
 video_extensions = ["MOV"]
 output_calibration_dir = "./calibration_pairs"
 
@@ -145,6 +147,7 @@
         # find chessboard
         # to check flags:
         # https://docs.opencv.org/4.x/d9/d0c/group__calib3d.html#ga93efa9b0aa890de240ca32b11253dd4a
+        # TODO: the following is very slow when no chessboard is present
         ret, corners = cv2.findChessboardCorners(
             frame_gray,
             chessboard_tuple,