First release of M3ED build system

.gitignore

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+utils/
+__pycache__
+Log/

build_system/README.md

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+![alt text](https://github.com/daniilidis-group/m3ed/blob/master/M3ED_banner.webp)
+
+# M3ED Processing Scripts
+
+This repo contains the scripts used to process the M3ED data. These scripts are
+run automatically in Jenkins.
+
+## Dockerfile
+
+We provide a `Dockerfile` to run the data conversions. We used this docker
+environment to process the bags automatically and generate the bag reports.
+
+### Jenkins build architecture
+
+Jenkins was used as our deployment platform. There are three Jenkins pipelines:
+
+ - Dispatcher: this pipeline gathers all the input files, and orchestrates the
+ execution of the work among the different nodes. The `Jenkinsfile_dispatcher` is used for this
+ pipeline.
+
+ - Docker-build: this pipeline builds the docker image **in each node**. This
+   ensures that the processing pipelines have the most up-to-date docker image.
+   The `Jenkinsfile_docker_build` is used for this pipeline.
+
+ - Processing: Runs the processing scripts. The `Jenkinsfile_processing` is used
+   for this pipeline.
+
+### Jenkins Master Setup
+
+1. Install Jenkins
+2. Create three jobs: `M3ED-dispatcher`, `M3ED-docker-build`, `M3ED-processing`
+3. Ensure that `M3ED-docker-build` and `M3ED-dispatcher` are executed for all
+   branches (Branch Specifier).
+4. Choose the Branch Specifier that you want for `M3ED-dispatcher`.
+
+## Scripts
+
+- `preliminary.sh`: this script is executed in each build node and it verifies that
+the docker image is properly built, we have access to the processing folder and
+files.
+
+- `bag_processing/rosbag2verify.py`: verifies bag timestamps and integrity.
+
+- `bag_processing/rosbag2hdf5.py`: converts the bag data into HDF5.
+
+- `bag_processing/hdf52media.py`: generates media output from the HDF5 (videos, plots, images).
+
+## License
+M3ED is released under the (Creative Commons Attribution-ShareAlike 4.0 International License)[https://creativecommons.org/licenses/by-sa/4.0/].

build_system/bag_processing/hdf52imu_plot.py

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+import os
+import pdb
+import argparse
+
+import numpy as np
+import h5py
+import matplotlib.pyplot as plt
+
+from scipy.interpolate import splev, splrep, barycentric_interpolate
+from scipy.spatial.transform import Rotation
+from scipy import signal
+
+def resample_imu(imu, imu_ts, sample_times):
+    spl = splrep(imu_ts, imu)
+    return splev( sample_times, spl)
+
+def filter_imu_sample(imu, numtaps=7, f=0.10):
+    coeffs = signal.firwin(numtaps, f)
+    filtered = np.zeros(imu.shape)
+    filtered[:,0] = signal.lfilter(coeffs, 1.0, imu[:,0])
+    filtered[:,1] = signal.lfilter(coeffs, 1.0, imu[:,1])
+    filtered[:,2] = signal.lfilter(coeffs, 1.0, imu[:,2])
+    return filtered
+
+def align_imus(ovc_omega, ovc_accel, ouster_omega, ouster_accel):
+    """
+    Solving ouster_R_ovc * ovc_omega = ouster_omega
+    """
+    ovc_measurements = np.concatenate( [ovc_omega] ).T
+    ouster_measurements = np.concatenate( [ouster_omega] ).T
+
+    ouster_R_ovc = (ouster_measurements @ np.linalg.pinv(ovc_measurements))
+    U,S,Vh = np.linalg.svd(ouster_R_ovc)
+    ouster_R_ovc = U@Vh
+    ouster_R_ovc[:,0] = -ouster_R_ovc[:,0]
+    ouster_R_ovc[:,2] = np.cross(ouster_R_ovc[:,0],ouster_R_ovc[:,1])
+
+    assert np.all(np.isclose( np.linalg.det(ouster_R_ovc), 1.0 ))
+
+    return ouster_R_ovc
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Creates vids and imgs from h5.")
+    # input h5 file
+    parser.add_argument("--h5fn", help="The h5 file to convert.",
+                        required=True)
+    args = parser.parse_args()
+
+    if not os.path.isfile(args.h5fn):
+        sys.exit("The input h5 file %s does not exist." % args.h5fn)
+
+    h5f = h5py.File(args.h5fn, 'r')
+
+    ovc_mask = np.isfinite(h5f['/ovc/imu/accel'][:,0])
+    ovc_ts = h5f['/ovc/imu/ts'][...][ovc_mask]
+    ovc_accel = h5f['/ovc/imu/accel'][...][ovc_mask,:]
+    ovc_omega = h5f['/ovc/imu/omega'][...][ovc_mask,:]
+
+    ouster_mask = np.isfinite(h5f['/ouster/imu/accel'][1000:-1000,0])
+    ouster_ts = h5f['/ouster/imu/ts'][1000:-1000][ouster_mask]
+    ouster_accel = h5f['/ouster/imu/accel'][1000:-1000][ouster_mask,:]
+    ouster_omega = h5f['/ouster/imu/omega'][1000:-1000][ouster_mask,:]
+
+    ovc_resampled_omega = np.stack( [resample_imu(ovc_omega[:,i], ovc_ts, ouster_ts) for i in range(3)], axis=-1 )
+    ovc_resampled_accel = np.stack( [resample_imu(ovc_accel[:,i], ovc_ts, ouster_ts) for i in range(3)], axis=-1 )
+
+    ouster_accel = filter_imu_sample(ouster_accel)
+    ouster_omega = filter_imu_sample(ouster_omega)
+
+    ovc_omega = filter_imu_sample(ovc_resampled_omega)
+    ovc_accel = filter_imu_sample(ovc_resampled_accel)
+    ovc_ts = ouster_ts
+
+    ouster_R_ovc = align_imus(ovc_omega, ovc_accel, ouster_omega, ouster_accel)
+
+    print(ouster_R_ovc)
+    print(np.rad2deg(Rotation.from_matrix(ouster_R_ovc).as_euler('xyz')))
+    print(np.linalg.det(ouster_R_ovc))
+
+    transformed_ovc_omega = (ouster_R_ovc @ ovc_omega.T).T
+    transformed_ovc_accel = (ouster_R_ovc @ ovc_accel.T).T
+
+    fig, axes = plt.subplots(3,2,sharex=True,sharey=True)
+
+    axes[0,0].set_title('OVC gyro')
+    axes[0,0].plot( ovc_ts, transformed_ovc_omega[:,0] )
+    axes[1,0].plot( ovc_ts, transformed_ovc_omega[:,1] )
+    axes[2,0].plot( ovc_ts, transformed_ovc_omega[:,2] )
+
+    axes[0,1].set_title('Ouster gyro')
+    axes[0,1].plot( ouster_ts[:-1], ouster_omega[:-1,0] )
+    axes[1,1].plot( ouster_ts[:-1], ouster_omega[:-1,1] )
+    axes[2,1].plot( ouster_ts[:-1], ouster_omega[:-1,2] )
+
+    fig, axes = plt.subplots(3,2,sharex=True,sharey=True)
+
+    axes[0,0].set_title('OVC accel')
+    axes[0,0].plot( ovc_ts, transformed_ovc_accel[:,0] )
+    axes[1,0].plot( ovc_ts, transformed_ovc_accel[:,1] )
+    axes[2,0].plot( ovc_ts, transformed_ovc_accel[:,2] )
+
+    axes[0,1].set_title('Ouster accel')
+    axes[0,1].plot( ouster_ts[:-1], ouster_accel[:-1,0] )
+    axes[1,1].plot( ouster_ts[:-1], ouster_accel[:-1,1] )
+    axes[2,1].plot( ouster_ts[:-1], ouster_accel[:-1,2] )
+
+    plt.figure()
+    plt.plot(ovc_ts, transformed_ovc_omega[:,0] )
+    plt.plot( ouster_ts, ouster_omega[:,0])
+
+    plt.figure()
+    plt.plot(ovc_ts, transformed_ovc_omega[:,1] )
+    plt.plot( ouster_ts, ouster_omega[:,1])
+
+    plt.figure()
+    plt.plot(ovc_ts, transformed_ovc_omega[:,2] )
+    plt.plot( ouster_ts, ouster_omega[:,2])
+
+    plt.show()

build_system/bag_processing/hdf52media.bash

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+#!/bin/bash
+
+source ./build_system/preamble.bash
+
+output_files=("$EVENTS_VIDEO_RAW" "$RGB_VIDEO_RAW")
+check_files output_files
+check_free_space fixed
+
+# create tmp variables for videos
+EVENTS_VIDEO_RAW_TMP="${EVENTS_VIDEO_RAW%.*}_tmp.${EVENTS_VIDEO_RAW##*.}"
+RGB_VIDEO_RAW_TMP="${RGB_VIDEO_RAW%.*}_tmp.${RGB_VIDEO_RAW##*.}"
+
+# Run bag processing
+echo -e "${BLUE}Generating raw videos${NC}"
+python3 build_system/bag_processing/hdf52media.py \
+  --h5fn "$H5_PATH" \
+  --out_events_gray "$EVENTS_VIDEO_RAW_TMP" \
+  --out_rgb "$RGB_VIDEO_RAW_TMP"
+if [ $? -ne 0 ]; then
+  echo -e "${RED}Error creating media files for $H5_PATH${NC}"
+  rm "$EVENTS_VIDEO_RAW_TMP" "$RGB_VIDEO_RAW_TMP"
+  exit 1
+fi
+echo -e "${GREEN}Raw videos finished${NC}"
+mv "$EVENTS_VIDEO_RAW_TMP" "$EVENTS_VIDEO_RAW"
+mv "$RGB_VIDEO_RAW_TMP" "$RGB_VIDEO_RAW"
+
+# Compress videos
+echo -e "${BLUE}Generating compressed videos${NC}"
+compress_with_ffmpeg "$EVENTS_VIDEO_RAW"
+compress_with_ffmpeg "$RGB_VIDEO_RAW"
+echo -e "${GREEN}Compressed videos finished${NC}"