Analyse data command

Description

Analyse a dataset.

Overview diagram

Command arguments

Argument	Type	Description	Required?
--subvolume_dir	directory	Directory of the subvolume that was labelled.	yes
--label_dirs	list of directories	Space separated list of directories, each of which represents a label and contains the slices in subvolume_dir with the regions that are not part of the label being blacked out.	yes
--config_fullfname	full file name	Full path to configuration file specifying how to extract the dataset (*.json).	yes
--highlight_radius	whole number	The radius of the squares that mark the sampled voxels in the slices.	yes
--results_dir	directory	Directory to the folder that will contain the results.	yes
--data_sample_seed	whole number	Seed for the random number generator which samples voxels. If left out then the random number generator will be non-deterministic.	no
--checkpoint_fullfname	full file name	Full path to file that is used to let the process save its progress and continue from where it left off in case of interruption (*.json). If left out then the process will run from beginning to end without saving any checkpoints.	no
--checkpoint_namespace	string	Unique name for the group of checkpoints used by this command.	no
--reset_checkpoint	yes/no	Whether to clear the checkpoints about this command from the checkpoint file and start afresh or not (default is no).	no
--log_file_fullfname	full file name	Full path to file that is used to store a log of what is displayed on screen (*.txt).	no
--print_output	yes/no	Whether to output to the screen (default is yes).	no
--debug_mode	yes/no	Whether to give full error messages (default is no).	no

Command line example

python ASEMI-segmenter/Python/asemi_segmenter/bin/analyse_data.py \
    --subvolume_dir "training_set/subvolume" \
    --label_dirs \
        "training_set/labels/air" \
        "training_set/labels/tissues" \
        "training_set/labels/bones" \
    --config "configs/analyse_data_config.json" \
    --highlight_radius 3 \
    --results_dir "output/analyse_data" \
    --data_sample_seed 0 \
    --checkpoint_fullfname "output/checkpoint.json" \
    --log_file_fullfname "output/log.txt"

Stages

#	Log message	Description
1	Loading data	Load input data, validate it, and initialise the checkpoint.
2	Analysing	Performing the analysis process.

Checkpoints

#	Checkpoint name	In stage	Description
1	overlap_matrices	2	Overlap matrices have been created.
2	visualising_dataset	2	Dataset visuals have been created.

Further information

• Data analysis result format
• Data analysis configuration