Yoda 205 compression inspection

nextflow/configs/profiles/development.config

@@ -110,6 +110,7 @@ singularity {
 
 process {
     executor = 'local'
+    maxForks = 1
 
     // Since we can't assume local has multiple GPUs, we limit all tasks
     // Note that maxForks attached to GPU label will only limit processes of the same name

nextflow/modules/compression.nf

@@ -0,0 +1,81 @@
+/**
+ * Video compression using quality control
+ *
+ * @param tuple
+ *  - video_file The input video file to compress
+ *  - crf The constant rate factor for the compression
+ *  - keyframe_interval The keyframe interval for the compression
+ *
+ * @return file Path to compressed video
+ */
+process COMPRESS_VIDEO_CRF {
+    label "compression"
+
+    input:
+    tuple path(video_file), val(crf), val(keyframe_interval)
+
+    output:
+    path("${video_file.baseName}_g${keyframe_interval}_crf${crf}.mp4"), emit: file
+
+    script:
+    """
+    ffmpeg -i ${video_file} -c:v libx264 -pix_fmt yuv420p -preset slow -crf ${crf} -g ${keyframe_interval} -f mp4 ${video_file.baseName}_g${keyframe_interval}_crf${crf}.mp4
+    """
+}
+
+/**
+ * Video compression using bitrate control
+ *
+ * Runs a 2-pass encoding of the video with a target bitrate.
+ *
+ * @param tuple
+ *  - video_file The input video file to compress
+ *  - bitrate The target bitrate for the compression
+ *  - keyframe_interval The keyframe interval for the compression
+ *
+ * @return file Path to compressed video
+ *
+ * @note COMPRESS_VIDEO_CRF will typically produce better videos with a low signal-to-noise ratio.
+ */
+process COMPRESS_VIDEO_BR {
+    label "compression"
+
+    input:
+    tuple path(video_file), val(bitrate), val(keyframe_interval)
+
+    output:
+    path("${video_file.baseName}_r${bitrate}_g${keyframe_interval}.mp4"), emit: file
+
+    script:
+    """
+    ffmpeg -i ${video_file} -c:v libx264 -b:v ${bitrate}k -maxrate ${bitrate}k -bufsize \$((${bitrate}*2))k -g ${keyframe_interval} -pass 1 -f mp4 ${video_file.baseName}_r${bitrate}_g${keyframe_interval}_PASS1.mp4 && \
+    ffmpeg -i ${video_file.baseName}_r${bitrate}_g${keyframe_interval}_PASS1.mp4 -c:v libx264 -b:v ${bitrate}k -maxrate ${bitrate}k -bufsize \$((${bitrate}*2))k -g ${keyframe_interval} -pass 2 ${video_file.baseName}_r${bitrate}_g${keyframe_interval}.mp4 && \
+    rm ${video_file.baseName}_r${bitrate}_g${keyframe_interval}_PASS1.mp4 ffmpeg2pass-0.log ffmpeg2pass-0.log.mbtree
+
+    """
+}
+
+/**
+ * Computes a difference between two videos
+ *
+ * @param in_video1 The first input video file
+ * @param in_video2 The second input video file
+ *
+ * @return The output video file with the computed difference
+ *
+ * @note Difference videos are useful in comparing changes due to compression.
+ */
+process COMPUTE_VIDEO_DIFFERENCE {
+    label "tracking"
+
+    input:
+    tuple path(in_video1), path(in_video2)
+
+    output:
+    path "${in_video2.baseName}_diff.mp4"
+
+    script:
+    """
+    ffmpeg -i ${in_video1} -i ${in_video2} -filter_complex '[0:v]setsar=1:1[v1];[v1][1:v]blend=all_mode=difference128' -c:v mpeg4 -q 0 ${in_video2.baseName}_diff.mp4
+    """
+}

nextflow/modules/pose_qc.nf

@@ -0,0 +1,23 @@
+/**
+ * Render pose on video
+ *
+ * @param in_video The input video file
+ * @param in_pose The input pose file
+ *
+ * @return Rendered video
+ */
+process RENDER_POSE {
+    label "tracking"
+    publishDir "compressed/pose/", mode:'copy'
+
+    input:
+    tuple path(in_video), path(in_pose)
+
+    output:
+    path "${in_video.baseName}_pose.mp4"
+
+    script:
+    """
+    python3 /kumar_lab_models/mouse-tracking-runtime/render_pose.py --in-vid ${in_video} --in-pose ${in_pose} --out-vid ${in_video.baseName}_pose.mp4
+    """
+}

nextflow/workflows/multi_mouse_pipeline.nf

@@ -10,6 +10,7 @@ include { PREDICT_ARENA_CORNERS;
 include { VIDEO_TO_POSE;
           PUBLISH_RESULT_FILE as PUBLISH_MM_POSE_V6;
  } from "${projectDir}/nextflow/modules/utils"
+ include { COMPRESS_VIDEO_CRF } from "${projectDir}/nextflow/modules/compression"
 
 workflow MULTI_MOUSE_TRACKING {
     take:
@@ -33,6 +34,12 @@ workflow MULTI_MOUSE_TRACKING {
     }
     PUBLISH_MM_POSE_V6(v_6_poses_renamed)
 
+    // Compress the original video
+    compressed_videos = COMPRESS_VIDEO_CRF(input_video.combine([23]).combine([3000]))
+    compressed_renamed = compressed_videos.map { video -> 
+        tuple(video, "results/${video.baseName.replace("_g3000_crf23", "")}_compressed.mp4")
+    }
+
     emit:
     pose_v6
 }