volume_segmantics.utilities
def
get_2d_training_parser() -> argparse.ArgumentParser:
40def get_2d_training_parser() -> argparse.ArgumentParser: 41 """Argument parser for scripts that train a 2d network on a 3d volume. 42 43 Returns: 44 argparse.ArgumentParser: An argument parser with the appropriate 45 command line args contained within. 46 """ 47 parser = argparse.ArgumentParser( 48 usage="%(prog)s --data <path(s)/to/data/file(s)> --labels <path(s)/to/segmentation/file(s)> --data_dir path/to/data_directory", 49 description="Train a 2d model on the 3d data and corresponding" 50 " segmentation provided in the files.", 51 ) 52 parser.add_argument( 53 "-v", "--version", action="version", version=f"{parser.prog} version 1.0.0" 54 ) 55 parser.add_argument( 56 "--" + cfg.TRAIN_DATA_ARG, 57 metavar="Path(s) to training image data volume(s)", 58 type=str, 59 action=CheckExt(cfg.TRAIN_DATA_EXT), 60 nargs="+", 61 required=True, 62 help="the path(s) to file(s) containing the imaging data volume for training", 63 ) 64 parser.add_argument( 65 "--" + cfg.LABEL_DATA_ARG, 66 metavar="Path(s) to label volume(s)", 67 type=str, 68 action=CheckExt(cfg.LABEL_DATA_EXT), 69 nargs="+", 70 required=True, 71 help="the path(s) to file(s) containing a segmented volume for training", 72 ) 73 parser.add_argument( 74 "--" + cfg.DATA_DIR_ARG, 75 metavar="Path to settings and output directory (optional)", 76 type=str, 77 nargs="?", 78 default=Path.cwd(), 79 help='path to a directory containing the "volseg-settings", data will be also be output to this location', 80 ) 81 return parser
Argument parser for scripts that train a 2d network on a 3d volume.
Returns
argparse.ArgumentParser: An argument parser with the appropriate command line args contained within.
def
get_2d_prediction_parser() -> argparse.ArgumentParser:
84def get_2d_prediction_parser() -> argparse.ArgumentParser: 85 """Argument parser for scripts that use a 2d network to predict segmenation for a 3d volume. 86 87 Returns: 88 argparse.ArgumentParser: An argument parser with the appropriate 89 command line args contained within. 90 """ 91 parser = argparse.ArgumentParser( 92 usage="%(prog)s path/to/model/file.zip path/to/data/file [path/to/data_directory]", 93 description="Predict segmentation of a 3d data volume using the 2d" 94 " model provided.", 95 ) 96 parser.add_argument( 97 "-v", "--version", action="version", version=f"{parser.prog} version 1.0.0" 98 ) 99 parser.add_argument( 100 cfg.MODEL_PTH_ARG, 101 metavar="Model file path", 102 type=str, 103 action=CheckExt(cfg.MODEL_DATA_EXT), 104 help="the path to a zip file containing the model weights.", 105 ) 106 parser.add_argument( 107 cfg.PREDICT_DATA_ARG, 108 metavar="Path to prediction data volume", 109 type=str, 110 action=CheckExt(cfg.PREDICT_DATA_EXT), 111 help="the path to an HDF5 file containing the imaging data to segment", 112 ) 113 parser.add_argument( 114 "--" + cfg.DATA_DIR_ARG, 115 metavar="Path to settings and output directory (optional)", 116 type=str, 117 nargs="?", 118 default=Path.cwd(), 119 help='path to a directory containing the "volseg-settings", data will be also be output to this location', 120 ) 121 return parser
Argument parser for scripts that use a 2d network to predict segmenation for a 3d volume.
Returns
argparse.ArgumentParser: An argument parser with the appropriate command line args contained within.
class
Quality(enum.Enum):
An enumeration.
LOW = <Quality.LOW: 1>
MEDIUM = <Quality.MEDIUM: 3>
HIGH = <Quality.HIGH: 12>
Inherited Members
- enum.Enum
- name
- value