Colmap docker image

As we want the possibility to choose the Python version we use, for example 3.8, and the provided docker image are based on Ubuntu 18.04 that ship Python 3.6 & 3.7, we need to create our own Dockerfile.

This has been done in docker/colmap/Dockerfile with:

• Python 3.8
• Colmap 3.7

Build the docker image

To build the docker image, use the Dockerfile in docker/colmap/:

image_name="roboticsmicrofarms/colmap"
image_version="3.7"
docker build -t="$image_name:$image_version" docker/colmap/.
docker tag "$image_name:$image_version" "$image_name:latest"

Test the container

Let's test the image we just created!

Start a container

You can start by creating a running container with:

docker run -it --gpus all \
  -v /tmp/integration_tests/2019-02-01_10-56-33/:/tmp/ \
  roboticsmicrofarms/colmap:3.7

Try to call the colmap executable to get the version number with:

colmap -v

As we also installed Python, try to call it after activating the venv with:

. /venv/bin/activate
python -V

Get a test dataset

To further test the built image, let's try to use colmap on a typical set of data. If you do not have your own dataset, we provide a test dataset that you can download (to the temporary folder) as follows:

cd /tmp
wget https://db.romi-project.eu/models/test_db.tar.gz
tar -xf test_db.tar.gz

Extract images poses

We use the "poses" (camera locations) provided in the images' metadata (JSON file associated to each images) by the plant-imager to create a poses.txt file containing each image coordinates:

import os
import json

posefile = open(f"/tmp/poses.txt", mode='w')
# - Try to get the pose from each file metadata:
for i, file in enumerate(sorted(os.listdir("/tmp/metadata/images"))):
    with open(f"/tmp/metadata/images/{file}", mode='r') as f:
        jdict = json.load(f)
    # print(jdict)
    try:
        p = jdict['approximate_pose']
    except KeyError:
        p = jdict['pose']  # backward compatibility, should work for provided test dataset
    s = '%s %d %d %d\n' % (file.split('.')[0] + ".jpg", p[0], p[1], p[2])
    posefile.write(s)

posefile.close()

Test colmap tools

You can test that the colmap tools are working properly by calling them as follows:

DATASET_PATH=/tmp

colmap feature_extractor \
    --database_path $DATASET_PATH/database.db \
    --image_path $DATASET_PATH/images

colmap exhaustive_matcher \
    --database_path $DATASET_PATH/database.db

mkdir $DATASET_PATH/sparse

colmap mapper \
    --database_path $DATASET_PATH/database.db \
    --image_path $DATASET_PATH/images \
    --output_path $DATASET_PATH/sparse

colmap model_aligner \
    --ref_images_path $DATASET_PATH/poses.txt \
    --input_path $DATASET_PATH/sparse/0 \
    --output_path $DATASET_PATH/sparse/0 \
    --ref_is_gps 0 \
    --robust_alignment_max_error 10

colmap model_converter \
    --input_path $DATASET_PATH/sparse/0 \
    --output_path $DATASET_PATH/sparse/0/sparse.ply \
    --output_type PLY

mkdir $DATASET_PATH/dense

colmap image_undistorter \
    --image_path $DATASET_PATH/images \
    --input_path $DATASET_PATH/sparse/0 \
    --output_path $DATASET_PATH/dense \
    --output_type COLMAP \
    --max_image_size 2000

colmap patch_match_stereo \
    --workspace_path $DATASET_PATH/dense \
    --workspace_format COLMAP \
    --PatchMatchStereo.geom_consistency true

colmap stereo_fusion \
    --workspace_path $DATASET_PATH/dense \
    --workspace_format COLMAP \
    --input_type geometric \
    --output_path $DATASET_PATH/dense/fused.ply

Test geometric pipeline

If you have plant-3d-vision installed on your machine, you can further test the colmap image with the reconstruction pipelines using our test scripts and datasets.

Test it on real data

export COLMAP_EXE="roboticsmicrofarms/colmap"
./tests/check_geom_pipe.sh --tmp

Test it on virtual data

export COLMAP_EXE="roboticsmicrofarms/colmap"
./tests/check_geom_pipe.sh --tmp --virtual

Test it on your (real) data

export COLMAP_EXE="roboticsmicrofarms/colmap"
./tests/check_geom_pipe.sh --tmp --database /path/to/my/dataset

Upload the built image

Once you have checked the obtained image leads to functional containers, you can upload the image to docker hub!

Start by login in to docker hub with:

docker login

Then you can upload with:

docker push "$image_name"