This is a Clowder extractor used to stitch drone images into one orthomosaic image and pointcloud using OpenDroneMap.
In the extractors-opendronemap folder containing the file named Dockerfile run the following command.
docker build -t clowder/extractors-opendronemap .
Suggested allocation is 10GB memory for docker to run the extractor.
- Start the docker container.
docker run --name=opendronemap-py2 -d --restart=always -e 'RABBITMQ_URI=amqp://user1:pass1@rabbitmq.ncsa.illinois.edu:5672/clowder-dev' -e 'RABBITMQ_EXCHANGE=clowder' -e 'TZ=/usr/share/zoneinfo/US/Central' -e 'REGISTRATION_ENDPOINTS=http://clowderhostname:9000/api/extractors?key=key1' clowder/extractors-opendronemap
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Create an empty file named extractors-opendronemap.txt.
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Login to Clowder and create a dataset. Next upload drone images into that dataset. Finally, upload the extractors-opendronemap.txt file to trigger opendronemap extractor to process the images.
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Upon completion, .tif, .laz, .shp, and all associated shape files will be shown in the dataset. If the docker container has been configured to not upload one or more of these files, they won't be available.
NOTE: ODM processes within the container are not thread-safe. To run an additional thread, another extractor container can be started.
Suggested allocation is 10GB memory for docker to run the extractor.
Each numbered section below corresponds to the numbered list in the Quick Start above.
There is an environment variable named DENYFILETYPES that can be set when starting the docker container which affect what data is allowed to be uploaded to Clowder.
An additional three environment variables can be specified to override the names of the files uploaded to the dataset; ORTHOPHOTONAME, POINTCLOUDNAME, and SHAPEFILENAME.
The extractors-opendronemap.txt file used to start processing may contain overrides of the DENYFILETYPES environment variable.
With DENYFILETYPES, the overrides only prevent additional, presumeably unwanted, files from being uploaded.
More information on this variable is below.
Refer to the extractors-opendronemap.txt.sample file for more information on the overrides.
To specify these variables on container startup, use the -e command line option to define them.
An example of this is -e 'DENYFILETYPES=shp' which prevents the odm_georeferenced_model.bounds.shp and its associated files from uploading.
The orthomosaic odm_orthophoto.tif and odm_georeferencing.laz files will still be uploaded.
The command to start the docker container could then be modified to look like the following.
docker run --name=opendronemap-py2 -d --restart=always -e 'DENYFILETYPES=shp' -e 'RABBITMQ_URI=amqp://user1:pass1@rabbitmq.ncsa.illinois.edu:5672/clowder-dev' -e 'RABBITMQ_EXCHANGE=clowder' -e 'TZ=/usr/share/zoneinfo/US/Central' -e 'REGISTRATION_ENDPOINTS=http://clowderhostname:9000/api/extractors?key=key1' clowder/extractors-opendronemap
By default all ODM generated orthomosaic and pointcloud files are uploaded into Clowder. The purpose of this variable is to prevent files of certain types from being uploaded for as long as the container is running (including auto restart). The variable, when defined, contains a comma-separated list of file extensions. The valid extensions that will prevent files from being uploaded are:
- tif - orthomosaic image
- laz - point cloud
- shp - outer boundary of merged image footprints
Use this environment variable to change the file name of the uploaded ortho photo.
This is helpful when running this extractor in an environment where particular file names are used for further processing.
The extension of the file remains unchanged from the original.
For example, if the original file has the .tif extension, the renamed file will as well.
If the orthophoto image is not uploaded to the dataset, this variable has no effect.
This environment variable changes the file name of any point cloud files uploaded to the datasets. As with the orthophoto file name override, this override is helpful when a particular file name is used for further processing. For any files uploaded to the datasets, the file's extension remains unchanged. For example. if the original file has the '.las' extension, the renamed file will as well.
If a point cloud file is not uploaded to the dataset, this variable has no effect.
This environment variable changes the file name of any shapefile files uploaded to the datasets. As with the orthophoto file name override, this override is helpful when a particular file name is used for further processing. For any files uploaded to the datasets, the file's extension remains unchanged. For example. if the original file has the '.shp' or '.dbf' extension, the renamed file will as well.
If a shapefile is not uploaded to the dataset, this variable has no effect.
Note: when using overrides it's possible to create a configuration that will cause the extractor to stop working properly. Monitor the extractor when using this feature for multiple uploads of the same file, signifying a recovered crash, or no file uploads, signifying an un-recovered crash.
Creating an empty extractors-opendronemap.txt file will produce the default results from the OpenDroneMap docker extractor instance.
To override, or fine tune, the default behavior, copy the extractors-opendronemap.txt.sample file to extractors-opendronemap.txt and modify the contents. The extractors-opendronemap.txt.sample file is a modified version of the extractors-opendronemap configuration file and has fewer options. The removed options are ones that could negatively impact the running of the docker container and are ignored even if they are added back to the extractors-opendronemap.txt file.
This step is the same as the one in the Quick Start section above.
Depending upon how the extractor-opendronemap container was started, and which options may have been set in the extractors-opendronemap.txt file, the results will show up in the dataset once the OpenDroneMap extraction job is completed