21946156830

Committed 12 Feb 2026 12:13PM UTC coverage: 86.453%. Remained the same

Build # 21946156830

Build Type

push

github

Committed by

GGoetzelmann

Commit Message

Configure pyright to ignore test and codegen folder and

Type safety is not important for tests
codegen folder may not be directly fixable

add exception for false positive type error on custom exception exit

Run Details

0 of 3 new or added lines in 1 file covered. (0.0%)

2425 of 2805 relevant lines covered (86.45%)

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45.45

/mapping_cli.py

import argparse
import json
import logging
import os
from sys import exit

from src.IO.MappingAbortionError import MappingAbortionError
from src.IO.sem.InputReader import InputReader as InputReader_SEM
from src.IO.tomo.InputReader import InputReader as InputReader_TOMO
from src.IO.tomo.OutputWriter import OutputWriter
from src.resources.maps.parsing import map_from_flag

# make log level configurable from ENV, defaults to info level
logging.basicConfig(
    level=os.environ.get('LOGLEVEL', 'INFO').upper()
)

def add_tomo_parser(subparsers):
    parser_t = subparsers.add_parser(
        "tomo",
        help="Tomography mapping functionality",
        description='Extracting of SEM FIB Tomography metadata to unified json format'
    )
    # Add arguments for input, output, and map
    parser_t.add_argument('-i', '--input', help='Input zip file or folder as path', required=True)
    parser_t.add_argument('-o', '--output', help='Path to output json file', required=True)

    # Create a group for the mutually exclusive map options
    map_group = parser_t.add_mutually_exclusive_group(required=True)

    # Add the map file option to the group
    map_group.add_argument('-m', '--map', help='Map file as path or remote URI')

    # Add the default map option to the group with the allowed values
    map_group.add_argument('-dm', '--default-map', help='Use a default map for a vendor', choices=map_from_flag.keys(), type=str.lower)

    parser_t.set_defaults(func=run_tomo_mapper)


def add_sem_parser(subparsers):
    parser_s = subparsers.add_parser(
        "sem",
        help="SEM mapping functionality",
        description='Extracting of SEM metadata to unified json format'
    )
    parser_s.add_argument('-i','--input', help='Input file as file path', required=True)
    parser_s.add_argument('-m', '--map', help='Map file as path or remote URI', required=True)
    parser_s.add_argument('-o', '--output', help='Path to output json file', required=True)
    parser_s.set_defaults(func=run_sem_mapper)

def run_cli():
    main_parser = argparse.ArgumentParser(prog="SEM-FIB-TOMO Mapper")
    subparsers = main_parser.add_subparsers(dest='command', help="Choose one of the subcommands to use mapper")
    add_tomo_parser(subparsers)
    add_sem_parser(subparsers)

    args = main_parser.parse_args()
    if args.command:
        args.func(args)
    else:
        main_parser.print_help()

def run_tomo_mapper(args):
    argdict = vars(args)
    INPUT_SOURCE = argdict.get('input')
    MAP_SOURCE = argdict.get('map') or str(map_from_flag.get(argdict.get('default_map')))
    OUTPUT_PATH = argdict.get('output')

    reader = None
    try:
        reader = InputReader_TOMO(MAP_SOURCE, INPUT_SOURCE)
        tmpdir = reader.temp_dir_path
    except MappingAbortionError as e:
        if reader:
            reader.clean_up()
        exit(e)  # pyright: ignore[reportArgumentType]

    output = None
    try:
        setup_infos = reader.retrieve_setup_info()

        run_infos = reader.retrieve_run_info()

        imgs = reader.retrieve_image_info()

        # Now all cases are taken into account
        #si = setup_infos if len(setup_infos) >= 1 else None
        #ri = run_infos if len(run_infos) >= 1 else None

        output = OutputWriter.stitch_together(setup_infos, run_infos, imgs)
        OutputWriter.writeOutput(output, OUTPUT_PATH)
    except MappingAbortionError as e:
        reader.clean_up()
        exit(e) # pyright: ignore[reportArgumentType]

    logging.info("Tomography mapping completed.")
    reader.clean_up()
    return output

def run_sem_mapper(args):
    argdict = vars(args)
    INPUT_SOURCE = argdict.get('input')
    MAP_SOURCE = argdict.get('map')
    OUTPUT_PATH = argdict.get('output')

    try:
        reader = InputReader_SEM(MAP_SOURCE, INPUT_SOURCE)

        img_info = reader.retrieve_image_info(INPUT_SOURCE)
        if not img_info:
            logging.error('Could not retrieve image information due to unknown error. Aborting.')
            exit(1)
        with open(OUTPUT_PATH, 'w', encoding="utf-8") as f:
            json.dump(img_info, f, indent=4, ensure_ascii=False)
    except MappingAbortionError as e:
        exit(e) # pyright: ignore[reportArgumentType]


if __name__ == '__main__':
    run_cli()

1	import argparse	1✔
2	import json	1✔
3	import logging	1✔
4	import os	1✔
5	from sys import exit	1✔
6
7	from src.IO.MappingAbortionError import MappingAbortionError	1✔
8	from src.IO.sem.InputReader import InputReader as InputReader_SEM	1✔
9	from src.IO.tomo.InputReader import InputReader as InputReader_TOMO	1✔
10	from src.IO.tomo.OutputWriter import OutputWriter	1✔
11	from src.resources.maps.parsing import map_from_flag	1✔
12
13	# make log level configurable from ENV, defaults to info level
14	logging.basicConfig(	1✔
15	level=os.environ.get('LOGLEVEL', 'INFO').upper()
16	)
17
18	def add_tomo_parser(subparsers):	1✔
19	parser_t = subparsers.add_parser(	×
20	"tomo",
21	help="Tomography mapping functionality",
22	description='Extracting of SEM FIB Tomography metadata to unified json format'
23	)
24	# Add arguments for input, output, and map
25	parser_t.add_argument('-i', '--input', help='Input zip file or folder as path', required=True)	×
26	parser_t.add_argument('-o', '--output', help='Path to output json file', required=True)	×
27
28	# Create a group for the mutually exclusive map options
29	map_group = parser_t.add_mutually_exclusive_group(required=True)	×
30
31	# Add the map file option to the group
32	map_group.add_argument('-m', '--map', help='Map file as path or remote URI')	×
33
34	# Add the default map option to the group with the allowed values
35	map_group.add_argument('-dm', '--default-map', help='Use a default map for a vendor', choices=map_from_flag.keys(), type=str.lower)	×
36
37	parser_t.set_defaults(func=run_tomo_mapper)	×
38
39
40	def add_sem_parser(subparsers):	1✔
41	parser_s = subparsers.add_parser(	×
42	"sem",
43	help="SEM mapping functionality",
44	description='Extracting of SEM metadata to unified json format'
45	)
46	parser_s.add_argument('-i','--input', help='Input file as file path', required=True)	×
47	parser_s.add_argument('-m', '--map', help='Map file as path or remote URI', required=True)	×
48	parser_s.add_argument('-o', '--output', help='Path to output json file', required=True)	×
49	parser_s.set_defaults(func=run_sem_mapper)	×
50
51	def run_cli():	1✔
52	main_parser = argparse.ArgumentParser(prog="SEM-FIB-TOMO Mapper")	×
53	subparsers = main_parser.add_subparsers(dest='command', help="Choose one of the subcommands to use mapper")	×
54	add_tomo_parser(subparsers)	×
55	add_sem_parser(subparsers)	×
56
57	args = main_parser.parse_args()	×
58	if args.command:	×
59	args.func(args)	×
60	else:
61	main_parser.print_help()	×
62
63	def run_tomo_mapper(args):	1✔
64	argdict = vars(args)	1✔
65	INPUT_SOURCE = argdict.get('input')	1✔
66	MAP_SOURCE = argdict.get('map') or str(map_from_flag.get(argdict.get('default_map')))	1✔
67	OUTPUT_PATH = argdict.get('output')	1✔
68
69	reader = None	1✔
70	try:	1✔
71	reader = InputReader_TOMO(MAP_SOURCE, INPUT_SOURCE)	1✔
72	tmpdir = reader.temp_dir_path	1✔
73	except MappingAbortionError as e:	×
74	if reader:	×
75	reader.clean_up()	×
NEW 76	exit(e) # pyright: ignore[reportArgumentType]	×
77
78	output = None	1✔
79	try:	1✔
80	setup_infos = reader.retrieve_setup_info()	1✔
81
82	run_infos = reader.retrieve_run_info()	1✔
83
84	imgs = reader.retrieve_image_info()	1✔
85
86	# Now all cases are taken into account
87	#si = setup_infos if len(setup_infos) >= 1 else None
88	#ri = run_infos if len(run_infos) >= 1 else None
89
90	output = OutputWriter.stitch_together(setup_infos, run_infos, imgs)	1✔
91	OutputWriter.writeOutput(output, OUTPUT_PATH)	1✔
92	except MappingAbortionError as e:	×
93	reader.clean_up()	×
NEW 94	exit(e) # pyright: ignore[reportArgumentType]	×
95
96	logging.info("Tomography mapping completed.")	1✔
97	reader.clean_up()	1✔
98	return output	1✔
99
100	def run_sem_mapper(args):	1✔
101	argdict = vars(args)	×
102	INPUT_SOURCE = argdict.get('input')	×
103	MAP_SOURCE = argdict.get('map')	×
104	OUTPUT_PATH = argdict.get('output')	×
105
106	try:	×
107	reader = InputReader_SEM(MAP_SOURCE, INPUT_SOURCE)	×
108
109	img_info = reader.retrieve_image_info(INPUT_SOURCE)	×
110	if not img_info:	×
111	logging.error('Could not retrieve image information due to unknown error. Aborting.')	×
112	exit(1)	×
113	with open(OUTPUT_PATH, 'w', encoding="utf-8") as f:	×
114	json.dump(img_info, f, indent=4, ensure_ascii=False)	×
115	except MappingAbortionError as e:	×
NEW 116	exit(e) # pyright: ignore[reportArgumentType]	×
117
118
119	if __name__ == '__main__':	1✔
120	run_cli()	×

kit-data-manager / tomo_mapper / 21946156830

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