Frame extraction with reencoding (#78)

* edit bash script for Aug23 day3

* draft bash script that copies logs to destination and reencodes videos

* add reencoding step

* add reencoding step and log ffmpeg params (WIP)

* frame extraction with logs but without reencoding

* reencoding and frame extraction for day2

* add loops to logs. change filename of reencoded logs.

* remove parent directory name from extracted image filename

* script for day3 job

* fix for loop

* repeat reencoded failed jobs

* Sep2023 day4 job

* repeat day 1-04 and 05 on reencoded with less frames

* add clarification for array job syntax

* remove logs comment

* remove parent directory from name of extracted frame

* clarify TODO about all files in directory

* clarify sbatch syntax for array job

* add option to reencode or not the videos

* print to log if frame extraction fails

* fix path for new structure

* clarify reencoding is optional

* move check earlier

* check just below input list

* fix number of array jobs

* actually fix number of array jobs...

* fix path and if statements

* derive extension from input video

* bash script for day4 01-Right rep

* delete frame extraction only script and frame extraction local

* clarify array jobs syntax

* rename reencoding only script

* add couple of zeros to frame number when saving file

* use parameter expansion for move command

bash_scripts/run_reencode_and_frame_extraction_array.sh

@@ -0,0 +1,162 @@
+#!/bin/bash
+
+#SBATCH -p gpu # partition
+#SBATCH -N 1   # number of nodes
+#SBATCH --mem 64G # memory pool for all cores
+#SBATCH -n 2 # number of cores
+#SBATCH -t 3-00:00 # time (D-HH:MM)
+#SBATCH --gres gpu:1 # request 1 GPU (of any kind)
+#SBATCH -o slurm_array.%N.%A-%a.out
+#SBATCH -e slurm_array.%N.%A-%a.err
+#SBATCH --mail-type=ALL
+#SBATCH [email protected]
+#SBATCH --array=0-0%5
+
+
+# NOTE on SBATCH command for array jobs
+# with "SBATCH --array=0-n%m" ---> runs n separate jobs, but not more than m at a time.
+# the number of array jobs should match the number of input files
+
+# ---------------------
+# Load required modules
+# ----------------------
+module load SLEAP
+
+# ----------------------
+# Input data
+# ----------------------
+# TODO: change to all files in a directory?
+# INPUT_DIR=/ceph/zoo/raw/CrabField/ramalhete_2023
+# INPUT_DATA_LIST=($(<input.list))
+INPUT_DATA_LIST=(
+    "/ceph/zoo/users/sminano/crabs_reencoded_videos/Sep2023_day4_reencoded/07.09.2023-01-Right_RE.mp4"
+)
+
+# Check len(list of input data) matches max SLURM_ARRAY_TASK_COUNT
+# if not, exit
+if [[ $SLURM_ARRAY_TASK_COUNT -ne ${#INPUT_DATA_LIST[@]} ]]; then
+    echo "The number of array tasks does not match the number of inputs"
+    exit 1
+fi
+
+# ----------------------
+# Video reencoding
+# ----------------------
+# set whether to reencode input videos or not
+flag_reencode_input_videos=false
+
+# ----------------------
+# Output data location
+# ----------------------
+# location of extracted frames
+# TODO: derive subdir name from parent dir
+OUTPUT_DIR=/ceph/zoo/users/sminano/crabs_bboxes_labels
+OUTPUT_SUBDIR="Sep2023_day4_reencoded"
+
+# location of SLURM logs
+LOG_DIR=$OUTPUT_DIR/$OUTPUT_SUBDIR/logs
+mkdir -p $LOG_DIR  # create if it doesnt exist
+
+# set location of reencoded videos if required
+if [ "$flag_reencode_input_videos" = true ] ; then
+    REENCODED_VIDEOS_DIR=/ceph/zoo/users/sminano/crabs_reencoded_videos
+    REENCODED_VIDEOS_SUBDIR=$REENCODED_VIDEOS_DIR/$OUTPUT_SUBDIR
+    mkdir -p $REENCODED_VIDEOS_SUBDIR # create if it doesnt exist
+fi
+
+# ---------------------------------
+# Frame extraction parameters
+# -----------------------------------
+PARAM_INI_SAMPLES=500
+PARAM_SCALE=0.5
+PARAM_N_COMPONENTS=5
+PARAM_N_CLUSTERS=5
+PARAM_PER_CLUSTER=4
+
+
+# ----------------------
+# Script location
+# ----------------------
+# assumes repo located at '/ceph/scratch/sminano'
+SCRATCH_PERSONAL_DIR=/ceph/scratch/sminano
+SCRIPT_DIR=$SCRATCH_PERSONAL_DIR/crabs-exploration/crabs/bboxes_labelling
+
+# -------------------
+# Run python script
+# -------------------
+for i in {1..${SLURM_ARRAY_TASK_COUNT}}
+do
+    # Input video
+    SAMPLE=${INPUT_DATA_LIST[${SLURM_ARRAY_TASK_ID}]}
+    echo "Input video: $SAMPLE"
+    echo "--------"
+
+    # Reencode video if required
+    # following SLEAP's recommendations
+    # https://sleap.ai/help.html#does-my-data-need-to-be-in-a-particular-format
+    if [ "$flag_reencode_input_videos" = true ] ; then
+        echo "Rencoding ...."
+
+        # path to reencoded video
+        filename_no_ext="$(basename "$SAMPLE" | sed 's/\(.*\)\..*/\1/')" # filename without extension
+        REENCODED_VIDEO_PATH="$REENCODED_VIDEOS_SUBDIR/$filename_no_ext"_RE.$reencoded_extension
+
+        ffmpeg -version  # print version to logs
+        ffmpeg -y -i "$SAMPLE" \
+        -c:v libx264 \
+        -pix_fmt yuv420p \
+        -preset superfast \
+        -crf 15 \
+        $REENCODED_VIDEO_PATH
+
+
+        echo "Reencoded video: $REENCODED_VIDEO_PATH"
+        echo "--------"
+        FRAME_EXTRACTION_INPUT_VIDEO=$REENCODED_VIDEO_PATH
+    else
+        echo "Skipping video reencoding..."
+        echo "--------"
+        FRAME_EXTRACTION_INPUT_VIDEO=$SAMPLE
+    fi
+
+    # Get extension of input video
+    video_filename=$(basename -- "$FRAME_EXTRACTION_INPUT_VIDEO")
+    VIDEO_EXT="${video_filename##*.}"
+
+    # Run frame extraction algorithm on video
+    python $SCRIPT_DIR/extract_frames_to_label_w_sleap.py \
+    $FRAME_EXTRACTION_INPUT_VIDEO \
+    --output_path $OUTPUT_DIR \
+    --output_subdir $OUTPUT_SUBDIR \
+    --video_extensions $VIDEO_EXT \
+    --initial_samples $PARAM_INI_SAMPLES \
+    --scale $PARAM_SCALE \
+    --n_components $PARAM_N_COMPONENTS \
+    --n_clusters $PARAM_N_CLUSTERS \
+    --per_cluster $PARAM_PER_CLUSTER \
+    --compute_features_per_video
+
+    if [ "$?" -ne 0 ]; then
+        echo "Frame extraction failed! Please check .err log"
+    else
+        echo "Frames extracted from video: $FRAME_EXTRACTION_INPUT_VIDEO"
+    fi
+    echo "--------"
+
+    # Reencoded videos log
+    # copy .err file to go with reencoded video too if required
+    # filename: {reencoded video name}.{slurm_array}.{slurm_job_id}
+    # TODO: make a nicer log
+    if [ "$flag_reencode_input_videos" = true ] ; then
+        for ext in err out
+        do
+            cp slurm_array.$SLURMD_NODENAME.$SLURM_ARRAY_JOB_ID-$SLURM_ARRAY_TASK_ID.$ext \
+            /$REENCODED_VIDEOS_SUBDIR/"$filename_no_ext"_RE.slurm_array.$SLURM_ARRAY_JOB_ID-$SLURM_ARRAY_TASK_ID.$ext
+        done
+    fi
+
+    # Frame extraction logs
+    # Move logs for this job to subdir with extracted frames
+    mv slurm_array.$SLURMD_NODENAME.$SLURM_ARRAY_JOB_ID-$SLURM_ARRAY_TASK_ID.{err,out} /$LOG_DIR
+
+done

crabs/bboxes_labelling/extract_frames_to_label_w_sleap.py

@@ -325,12 +325,10 @@ def extract_frames_to_label_from_video(
                 raise KeyError(msg)
 
             # If read successfully: save to file
-            # file naming format: parentdir_videoname_frame_XXX.png
+            # file naming format: videoname_frame_XXX.png
             else:
                 file_path = video_output_dir / Path(
-                    f"{Path(vid_str).parent.stem}_"
-                    f"{Path(vid_str).stem}_"
-                    f"frame_{frame_idx:06d}.png",
+                    f"{Path(vid_str).stem}_" f"frame_{frame_idx:08d}.png",
                 )
                 img_saved = cv2.imwrite(str(file_path), frame)
                 if img_saved: