Command line interface¶

Besides the main zea API documentation, zea also provides a command line interface (CLI).

File reading and visualization¶

zea¶

Load and process ultrasound data based on a configuration file.

usage: zea [-h] [-c CONFIG] [-t {view}] [--skip_validate_file]

-h, --help¶: show this help message and exit

-c <config>, --config <config>¶: path to the config file.

-t {view}, --task {view}¶: Which task to run. Currently only ‘view’ is supported.

--skip_validate_file¶: Skip zea file integrity checks. Use with caution.

Convert datasets¶

python -m zea.data.convert¶

Convert raw data to a zea dataset.

usage: python -m zea.data.convert [-h]
                                  {echonet,echonetlvh,camus,cetus,picmus,verasonics}
                                  ...

-h, --help¶: show this help message and exit

python -m zea.data.convert camus¶

usage: python -m zea.data.convert camus [-h] [--download]
                                        [--no_hyperthreading]
                                        src dst

src¶: Source folder path, should contain either manually downloaded dataset or will be target location for automated download with the –download flag

dst¶: Destination folder path

-h, --help¶: show this help message and exit

--download¶: Download the CAMUS dataset from the server, will be saved to the –src path

--no_hyperthreading¶: Disable hyperthreading for multiprocessing

python -m zea.data.convert cetus¶

usage: python -m zea.data.convert cetus [-h] [--download]
                                        [--no_hyperthreading] [--upload]
                                        src dst

src¶: Source folder path, should contain either manually downloaded dataset or will be target location for automated download with the –download flag

dst¶: Destination folder path

-h, --help¶: show this help message and exit

--download¶: Download the CETUS dataset from the server, will be saved to the –src path

--no_hyperthreading¶: Disable hyperthreading for multiprocessing

--upload¶: Upload the converted dataset to HuggingFace Hub (zeahub/cetus-miccai-2014)

python -m zea.data.convert echonet¶

usage: python -m zea.data.convert echonet [-h] [--split_path SPLIT_PATH]
                                          [--no_hyperthreading]
                                          src dst

src¶: Source folder path

dst¶: Destination folder path

-h, --help¶: show this help message and exit

--split_path <split_path>¶: Path to the split.yaml file containing the dataset split if a split should be copied

--no_hyperthreading¶: Disable hyperthreading for multiprocessing

python -m zea.data.convert echonetlvh¶

usage: python -m zea.data.convert echonetlvh [-h] [--no_rejection]
                                             [--rejection_path REJECTION_PATH]
                                             [--batch BATCH]
                                             [--convert_measurements]
                                             [--convert_images]
                                             [--max_files MAX_FILES] [--force]
                                             src dst

src¶: Source folder path

dst¶: Destination folder path

-h, --help¶: show this help message and exit

--no_rejection¶: Do not reject sequences in manual_rejections.txt

--rejection_path <rejection_path>¶: Path to custom rejection txt file (defaults to manual_rejections.txt)

--batch <batch>¶: Specify which BatchX directory to process, e.g. –batch=Batch2

--convert_measurements¶: Only convert measurements CSV file

--convert_images¶: Only convert image files

--max_files <max_files>¶: Maximum number of files to process (for testing)

--force¶: Force recomputation even if parameters already exist

python -m zea.data.convert picmus¶

usage: python -m zea.data.convert picmus [-h] src dst

src¶: Source folder path

dst¶: Destination folder path

-h, --help¶: show this help message and exit

python -m zea.data.convert verasonics¶

usage: python -m zea.data.convert verasonics [-h]
                                             [--frames FRAMES [FRAMES ...]]
                                             [--allow_accumulate]
                                             [--device DEVICE]
                                             [--no_compression]
                                             src dst

src¶: Source folder path

dst¶: Destination folder path

-h, --help¶: show this help message and exit

--frames <frames>¶: The frames to add to the file. This can be a list of integers, a range of integers (e.g. 4-8), or ‘all’. Defaults to ‘all’, unless specified in a convert.yaml file.

--allow_accumulate¶: Sometimes, some transmits are already accumulated on the Verasonics system (e.g. harmonic imaging through pulse inversion). In this case, the mode in the Receive structure is set to 1 (accumulate). If this flag is set, such files will be processed. Otherwise, an error is raised when such a mode is detected.

--device <device>¶: Device to use for conversion (e.g., ‘cpu’ or ‘gpu:0’).

--no_compression¶: Disable compression when saving the zea dataset. By default, compression is enabled, which reduces disk space at the cost of increased conversion time.

Data copying¶

python -m zea.data¶

Copy a zea.Folder to a new location.

usage: python -m zea.data [-h] [--mode {a,w,r+,x}] src dst key

src¶: Source folder path

dst¶: Destination folder path

key¶: Key to access in the hdf5 files

-h, --help¶: show this help message and exit

--mode {a,w,r+,x}¶: Mode in which to open the destination files (default: ‘a’)

Data file manipulation¶

python -m zea.data.file_operations¶

Manipulate zea data files.

usage: python -m zea.data.file_operations [-h]
                                          {sum,compound_frames,compound_transmits,resave,extract}
                                          ...

-h, --help¶: show this help message and exit

python -m zea.data.file_operations compound_frames¶

usage: python -m zea.data.file_operations compound_frames [-h] [--overwrite]
                                                          input_path
                                                          output_path

input_path¶: Input HDF5 file.

output_path¶: Output HDF5 file.

-h, --help¶: show this help message and exit

--overwrite¶: Overwrite existing output file.

python -m zea.data.file_operations compound_transmits¶

usage: python -m zea.data.file_operations compound_transmits
       [-h] [--overwrite] input_path output_path

input_path¶: Input HDF5 file.

output_path¶: Output HDF5 file.

-h, --help¶: show this help message and exit

--overwrite¶: Overwrite existing output file.

python -m zea.data.file_operations extract¶

usage: python -m zea.data.file_operations extract [-h]
                                                  [--transmits TRANSMITS [TRANSMITS ...]]
                                                  [--frames FRAMES [FRAMES ...]]
                                                  [--overwrite]
                                                  input_path output_path

input_path¶: Input HDF5 file.

output_path¶: Output HDF5 file.

-h, --help¶: show this help message and exit

--transmits <transmits>¶: Target transmits. Can be a list of integers or ranges (e.g. 0-3 7).

--frames <frames>¶: Target frames. Can be a list of integers or ranges (e.g. 0-3 7).

--overwrite¶: Overwrite existing output file.

python -m zea.data.file_operations resave¶

usage: python -m zea.data.file_operations resave [-h] [--overwrite]
                                                 input_path output_path

input_path¶: Input HDF5 file.

output_path¶: Output HDF5 file.

-h, --help¶: show this help message and exit

--overwrite¶: Overwrite existing output file.

python -m zea.data.file_operations sum¶

usage: python -m zea.data.file_operations sum [-h] [--overwrite]
                                              input_paths [input_paths ...]
                                              output_path

input_paths¶: Paths to the input files.

output_path¶: Output HDF5 file.

-h, --help¶: show this help message and exit

--overwrite¶: Overwrite existing output file.