Open Madeypo opened 2 months ago
Dear Madeypo,
Thank you for your kind words and interest in hooknet-tls!
I understand that the code could be a bit confusing, i will try to explain a bit: The hooknet-tls pipeline is defined via this config file:
By looking at the error trace it seems something goes wrong when loading the mask file. However, could please also provide me the actual error? I hope it will allow me to give you more information what actual goes wrong.
Best wishes, Mart
Dear Mart,
Hooknettls is a very good article, and I really appreciate your contribution. I encountered some issues when trying to reproduce it using Docker.
1.Is there any hidden code inside the Docker container after creation? For example, I noticed that the 'IOPaths' defined in hooknettls/io.py is not being used. I also couldn't find the file containing the complete code for the dataloader, and some parameters seem to be undefined as well.
2.When I'm testing with my own data, I encounter the following error. How should I resolve it.
Traceback (most recent call last): File "/usr/lib/python3.8/runpy.py", line 194, in _run_module_as_main return _run_code(code, main_globals, None, File "/usr/lib/python3.8/runpy.py", line 87, in _run_code exec(code, run_globals) File "/home/user/pathology-hooknet-tls/hooknettls/main.py", line 8, in
objects = build_config(config_reader.read()["default"])
File "/usr/local/lib/python3.8/dist-packages/dicfg/factory.py", line 124, in build_config
return _ObjectFactory(deepcopy(config)).build_config()
File "/usr/local/lib/python3.8/dist-packages/dicfg/factory.py", line 26, in build_config
return self._build(self._configuration)
File "/usr/lib/python3.8/functools.py", line 912, in _method
return method.get(obj, cls)(*args, *kwargs)
File "/usr/local/lib/python3.8/dist-packages/dicfg/factory.py", line 38, in _build_dict
config[key] = self._build_object(value)
File "/usr/local/lib/python3.8/dist-packages/dicfg/factory.py", line 67, in _build_object
return attribute(args, *kwargs)
File "/usr/local/lib/python3.8/dist-packages/wholeslidedata/iterators/patchiterator.py", line 46, in create_patch_iterator
commander = commander_class(
File "/usr/local/lib/python3.8/dist-packages/wholeslidedata/buffer/patchcommander.py", line 50, in init
self.reset()
File "/usr/local/lib/python3.8/dist-packages/wholeslidedata/buffer/patchcommander.py", line 68, in reset
messages = self.get_patch_messages()
File "/usr/local/lib/python3.8/dist-packages/wholeslidedata/buffer/patchcommander.py", line 91, in get_patch_messages
self._mask = WholeSlideImage(self._mask_path, backend=self._backend, auto_resample=True)
File "/usr/local/lib/python3.8/dist-packages/wholeslidedata/image/wholeslideimage.py", line 39, in init
self._spacings = self._backend._init_spacings(self._downsamplings)
File "/usr/local/lib/python3.8/dist-packages/wholeslidedata/interoperability/asap/backend.py", line 43, in _init_spacings
return [
File "/usr/local/lib/python3.8/dist-packages/wholeslidedata/interoperability/asap/backend.py", line 44, in
self.getSpacing()[0] downsampling for downsampling in downsamplings