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run_infer.py
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run_infer.py
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"""run_infer.py
Usage:
run_infer.py [options] [--help] <command> [<args>...]
run_infer.py --version
run_infer.py (-h | --help)
Options:
-h --help Show this string.
--version Show version.
--gpu=<id> GPU list. [default: 0]
--nr_types=<n> Number of nuclei types to predict. [default: 0]
--type_info_path=<path> Path to a json define mapping between type id, type name,
and expected overlaid color. [default: '']
--model_path=<path> Path to saved checkpoint.
--model_mode=<mode> Original HoVer-Net or the reduced version used PanNuke and MoNuSAC,
'original' or 'fast'. [default: fast]
--nr_inference_workers=<n> Number of workers during inference. [default: 8]
--nr_post_proc_workers=<n> Number of workers during post-processing. [default: 16]
--batch_size=<n> Batch size per 1 GPU. [default: 32]
Two command mode are `tile` and `wsi` to enter corresponding inference mode
tile run the inference on tile
wsi run the inference on wsi
Use `run_infer.py <command> --help` to show their options and usage.
"""
tile_cli = """
Arguments for processing tiles.
usage:
tile (--input_dir=<path>) (--output_dir=<path>) \
[--draw_dot] [--save_qupath] [--save_raw_map] [--mem_usage=<n>]
options:
--input_dir=<path> Path to input data directory. Assumes the files are not nested within directory.
--output_dir=<path> Path to output directory..
--mem_usage=<n> Declare how much memory (physical + swap) should be used for caching.
By default it will load as many tiles as possible till reaching the
declared limit. [default: 0.2]
--draw_dot To draw nuclei centroid on overlay. [default: False]
--save_qupath To optionally output QuPath v0.2.3 compatible format. [default: False]
--save_raw_map To save raw prediction or not. [default: False]
"""
wsi_cli = """
Arguments for processing wsi
usage:
wsi (--input_dir=<path>) (--output_dir=<path>) [--proc_mag=<n>]\
[--cache_path=<path>] [--input_mask_dir=<path>] \
[--ambiguous_size=<n>] [--chunk_shape=<n>] [--tile_shape=<n>] \
[--save_thumb] [--save_mask]
options:
--input_dir=<path> Path to input data directory. Assumes the files are not nested within directory.
--output_dir=<path> Path to output directory.
--cache_path=<path> Path for cache. Should be placed on SSD with at least 100GB. [default: cache]
--mask_dir=<path> Path to directory containing tissue masks.
Should have the same name as corresponding WSIs. [default: '']
--proc_mag=<n> Magnification level (objective power) used for WSI processing. [default: 40]
--ambiguous_size=<int> Define ambiguous region along tiling grid to perform re-post processing. [default: 128]
--chunk_shape=<n> Shape of chunk for processing. [default: 10000]
--tile_shape=<n> Shape of tiles for processing. [default: 2048]
--save_thumb To save thumb. [default: False]
--save_mask To save mask. [default: False]
"""
import torch
import logging
import os
import copy
from misc.utils import log_info
from docopt import docopt
#-------------------------------------------------------------------------------------------------------
if __name__ == '__main__':
sub_cli_dict = {'tile' : tile_cli, 'wsi' : wsi_cli}
args = docopt(__doc__, help=False, options_first=True,
version='HoVer-Net Pytorch Inference v1.0')
sub_cmd = args.pop('<command>')
sub_cmd_args = args.pop('<args>')
# ! TODO: where to save logging
logging.basicConfig(
level=logging.INFO,
format='|%(asctime)s.%(msecs)03d| [%(levelname)s] %(message)s',datefmt='%Y-%m-%d|%H:%M:%S',
handlers=[
logging.FileHandler("debug.log"),
logging.StreamHandler()
]
)
if args['--help'] and sub_cmd is not None:
if sub_cmd in sub_cli_dict:
print(sub_cli_dict[sub_cmd])
else:
print(__doc__)
exit()
if args['--help'] or sub_cmd is None:
print(__doc__)
exit()
sub_args = docopt(sub_cli_dict[sub_cmd], argv=sub_cmd_args, help=True)
args.pop('--version')
gpu_list = args.pop('--gpu')
os.environ['CUDA_VISIBLE_DEVICES'] = gpu_list
nr_gpus = torch.cuda.device_count()
log_info('Detect #GPUS: %d' % nr_gpus)
args = {k.replace('--', '') : v for k, v in args.items()}
sub_args = {k.replace('--', '') : v for k, v in sub_args.items()}
if args['model_path'] == None:
raise Exception('A model path must be supplied as an argument with --model_path.')
nr_types = int(args['nr_types']) if int(args['nr_types']) > 0 else None
method_args = {
'method' : {
'model_args' : {
'nr_types' : nr_types,
'mode' : args['model_mode'],
},
'model_path' : args['model_path'],
},
'type_info_path' : None if args['type_info_path'] == '' \
else args['type_info_path'],
}
# ***
run_args = {
'batch_size' : int(args['batch_size']) * nr_gpus,
'nr_inference_workers' : int(args['nr_inference_workers']),
'nr_post_proc_workers' : int(args['nr_post_proc_workers']),
}
if args['model_mode'] == 'fast':
run_args['patch_input_shape'] = 256
run_args['patch_output_shape'] = 164
else:
run_args['patch_input_shape'] = 270
run_args['patch_output_shape'] = 80
if sub_cmd == 'tile':
run_args.update({
'input_dir' : sub_args['input_dir'],
'output_dir' : sub_args['output_dir'],
'mem_usage' : float(sub_args['mem_usage']),
'draw_dot' : sub_args['draw_dot'],
'save_qupath' : sub_args['save_qupath'],
'save_raw_map': sub_args['save_raw_map'],
})
if sub_cmd == 'wsi':
run_args.update({
'input_dir' : sub_args['input_dir'],
'output_dir' : sub_args['output_dir'],
'input_mask_dir' : sub_args['input_mask_dir'],
'cache_path' : sub_args['cache_path'],
'proc_mag' : int(sub_args['proc_mag']),
'ambiguous_size' : int(sub_args['ambiguous_size']),
'chunk_shape' : int(sub_args['chunk_shape']),
'tile_shape' : int(sub_args['tile_shape']),
'save_thumb' : sub_args['save_thumb'],
'save_mask' : sub_args['save_mask'],
})
# ***
if sub_cmd == 'tile':
from infer.tile import InferManager
infer = InferManager(**method_args)
infer.process_file_list(run_args)
else:
from infer.wsi import InferManager
infer = InferManager(**method_args)
infer.process_wsi_list(run_args)