CLI
dacapo
dacapo [OPTIONS] COMMAND [ARGS]...
Options
- --log-level <log_level>
- Options:
DEBUG | INFO | WARNING | ERROR | CRITICAL
apply
dacapo apply [OPTIONS]
Options
- -r, --run-name <run_name>
Required The name of the run to apply.
- -ic, --input_container <input_container>
Required
- -id, --input_dataset <input_dataset>
Required
- -op, --output_path <output_path>
Required
- -vd, --validation_dataset <validation_dataset>
- -c, --criterion <criterion>
- -i, --iteration <iteration>
- -p, --parameters <parameters>
- -roi, --roi <roi>
The roi to predict on. Passed in as [lower:upper, lower:upper, … ]
- -w, --num_workers <num_workers>
- -dt, --output_dtype <output_dtype>
- -ow, --overwrite
predict
dacapo predict [OPTIONS]
Options
- -r, --run-name <run_name>
Required The name of the run to apply.
- -i, --iteration <iteration>
Required The training iteration of the model to use for prediction.
- -ic, --input_container <input_container>
Required
- -id, --input_dataset <input_dataset>
Required
- -op, --output_path <output_path>
Required
- -roi, --output_roi <output_roi>
The roi to predict on. Passed in as [lower:upper, lower:upper, … ]
- -w, --num_workers <num_workers>
- -dt, --output_dtype <output_dtype>
- -ow, --overwrite
run-blockwise
dacapo run-blockwise [OPTIONS]
Options
- -ic, --input_container <input_container>
Required
- -id, --input_dataset <input_dataset>
Required
- -oc, --output_container <output_container>
Required
- -od, --output_dataset <output_dataset>
Required
- -w, --worker_file <worker_file>
Required The path to the worker file.
- -tr, --total_roi <total_roi>
Required The total roi to be processed. Format is [start:end, start:end, … ] in voxels. Defaults to the roi of the input dataset. Do not use spaces in CLI argument.
- -rr, --read_roi_size <read_roi_size>
Required The size of the roi to be read for each block, in the format of [z,y,x] in voxels.
- -wr, --write_roi_size <write_roi_size>
Required The size of the roi to be written for each block, in the format of [z,y,x] in voxels.
- -nw, --num_workers <num_workers>
- -mr, --max_retries <max_retries>
- -t, --timeout <timeout>
- -ow, --overwrite
- -co, -channels_out <co>
- -dt, --output_dtype <output_dtype>
segment-blockwise
dacapo segment-blockwise [OPTIONS]
Options
- -ic, --input_container <input_container>
Required
- -id, --input_dataset <input_dataset>
Required
- -oc, --output_container <output_container>
Required
- -od, --output_dataset <output_dataset>
Required
- -sf, --segment_function_file <segment_function_file>
Required
- -tr, --total_roi <total_roi>
The total roi to be processed. Format is [start:end,start:end,…] in voxels. Defaults to the roi of the input dataset. Do not use spaces in CLI argument.
- -rr, --read_roi_size <read_roi_size>
Required The size of the roi to be read for each block, in the format of [z,y,x] in voxels.
- -wr, --write_roi_size <write_roi_size>
Required The size of the roi to be written for each block, in the format of [z,y,x] in voxels.
- -c, --context <context>
The context to be used, in the format of [z,y,x] in voxels. Defaults to the difference between the read and write rois.
- -nw, --num_workers <num_workers>
- -mr, --max_retries <max_retries>
- -t, --timeout <timeout>
- -ow, --overwrite
- -co, --channels_out <channels_out>
train
dacapo train [OPTIONS]
Options
- -r, --run-name <run_name>
Required The NAME of the run to train.
validate
dacapo validate [OPTIONS]
Options
- -r, --run-name <run_name>
Required The name of the run to validate.
- -i, --iteration <iteration>
Required The iteration at which to validate the run.
- -w, --num_workers <num_workers>
- -dt, --output_dtype <output_dtype>
- -ow, --overwrite