raise error when run demo

[ghost]

I run the demo net_segment for inference ,that's OK,but raise error when train :
net_segment train -c ./extensions/dense_vnet_abdominal_ct/config.ini

`Traceback (most recent call last):
File "/usr/local/bin/net_segment", line 11, in
sys.exit(main())
File "/usr/local/lib/python3.5/dist-packages/niftynet/init.py", line 54, in main
app_driver.initialise_application(system_param, input_data_param)
File "/usr/local/lib/python3.5/dist-packages/niftynet/engine/application_driver.py", line 131, in initialise_application
self.app.initialise_dataset_loader(data_param, app_param)
File "/usr/local/lib/python3.5/dist-packages/niftynet/application/segmentation_application.py", line 63, in initialise_dataset_loader
self.reader.initialise_reader(data_param, task_param)
File "/usr/local/lib/python3.5/dist-packages/niftynet/io/image_reader.py", line 98, in initialise_reader
self._file_list = util_csv.load_and_merge_csv_files(data_to_load)
File "/usr/local/lib/python3.5/dist-packages/niftynet/utilities/util_csv.py", line 254, in load_and_merge_csv_files
match_and_write_filenames_to_csv([matcher], csv_file)
File "/usr/local/lib/python3.5/dist-packages/niftynet/utilities/util_csv.py", line 209, in match_and_write_filenames_to_csv
KeywordsMatching.matching_subjects_and_filenames(c)
File "/usr/local/lib/python3.5/dist-packages/niftynet/utilities/filename_matching.py", line 73, in matching_subjects_and_filenames
self.dict))
OSError: no file matched based on this matcher: {'filename_not_contains': (), 'filename_contains': ('Label',), 'path_to_search': ('/home/yyydido/niftynet/data/dense_vnet_abdominal_ct',)}'

[wyli]

Hi @yyydido the ground truth labels are not included in the model zoo at the moment, please have a look at the promise12 demo for more information on training a network (https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyNet/tree/dev/demos/PROMISE12)

[ghost]

Thanks, I got it. But I try this https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyNet/tree/dev/demos/BRATS17 that contains label，I placed brats_segmentation.py and anisotropic_nets
on the $PYTHONPATH of the system environment,however,raise error ：

net_run train -c ./extensions/anisotropic_nets_brats_challenge/whole_tumor_sagittal.ini -a brats_seg_app.BRATSApp --name anisotropic_nets.wt_net.WTNet

`NiftyNet version 0.2.1
CRITICAL:niftynet: ImportError("No module named 'brats_seg_app'",)
CRITICAL:niftynet: application: Could not import object"BRATSApp" from "brats_seg_app"
Traceback (most recent call last):
File "/usr/local/lib/python3.5/dist-packages/niftynet/engine/application_factory.py", line 153, in select_module
the_module = importlib.import_module(module_str)
File "/usr/lib/python3.5/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 986, in _gcd_import
File "", line 969, in _find_and_load
File "", line 956, in _find_and_load_unlocked
ImportError: No module named 'brats_seg_app'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/usr/local/bin/net_run", line 11, in
sys.exit(main())
File "/usr/local/lib/python3.5/dist-packages/niftynet/init.py", line 52, in main
system_param, input_data_param = user_parameters_parser.run()
File "/usr/local/lib/python3.5/dist-packages/niftynet/utilities/user_parameters_parser.py", line 108, in run
app_module = ApplicationFactory.create(module_name)
File "/usr/local/lib/python3.5/dist-packages/niftynet/engine/application_factory.py", line 197, in create
return select_module(name, cls.type_str, cls.SUPPORTED)
File "/usr/local/lib/python3.5/dist-packages/niftynet/engine/application_factory.py", line 182, in select_module
raise ValueError(err)
ValueError: application: Could not import object"BRATSApp" from "brats_seg_app"
`

[wyli]

Hi @yyydido no problem, and for the BRATS demo it's also available in the model zoo (https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyNetExampleServer/blob/master/anisotropic_nets_brats_challenge_model_zoo.md) net_download command would download the modules to ~/niftynet/extensions/anisotropic_nets_brats_challenge by default. Perhaps this is easier to use.

Sorry for suggesting links in demo and model zoo back and forth, we've been migrating demos to the model zoo, documentation will be improved soon.

[ghost]

Thanks for your reply,I am new in DL and thanks for your guide again.

[ghost]

Hi @wyli I'll bother you again.
Now,I try https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyNet/tree/dev/demos/BRATS17 for train not inference.
First, this is my structure:
/home/yyydido/niftynet/

Second,I added the directory /home/yyydido/niftynet/ on the PYTHONPATH of system environment:
export PYTHONPATH=/home/yyydido/niftynet:$PYTHONPATH

Thirdly,net_run at /home/yyydido/niftynet/ like this:
net_run train -c ./extensions/anisotropic_nets_brats_challenge/whole_tumor_sagittal.ini -a brats_seg_app.BRATSApp --name anisotropic_nets.wt_net.WTNet

The last,raise error:
`NiftyNet version 0.2.1
CRITICAL:niftynet: ImportError("No module named 'brats_seg_app'",)
CRITICAL:niftynet: application: Could not import object"BRATSApp" from "brats_seg_app"
Traceback (most recent call last):
File "/usr/local/lib/python3.5/dist-packages/niftynet/engine/application_factory.py", line 153, in select_module
the_module = importlib.import_module(module_str)
File "/usr/lib/python3.5/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 986, in _gcd_import
File "", line 969, in _find_and_load
File "", line 956, in _find_and_load_unlocked
ImportError: No module named 'brats_seg_app'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/usr/local/bin/net_run", line 11, in
sys.exit(main())
File "/usr/local/lib/python3.5/dist-packages/niftynet/init.py", line 52, in main
system_param, input_data_param = user_parameters_parser.run()
File "/usr/local/lib/python3.5/dist-packages/niftynet/utilities/user_parameters_parser.py", line 108, in run
app_module = ApplicationFactory.create(module_name)
File "/usr/local/lib/python3.5/dist-packages/niftynet/engine/application_factory.py", line 197, in create
return select_module(name, cls.type_str, cls.SUPPORTED)
File "/usr/local/lib/python3.5/dist-packages/niftynet/engine/application_factory.py", line 182, in select_module
raise ValueError(err)
ValueError: application: Could not import object"BRATSApp" from "brats_seg_app"
`
Could you help me find the cause of the error? Tanks a lot
Is it need specify the path for "-a extensions.anisotropic_nets_brats_challenge.brats_seg_app.BRATSApp" and for "--name extensions.anisotropic_nets.wt_net.WTNet" ?

[ghost]

I have solved above problem.