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pytorch implementation of paper https://www.frontiersin.org/articles/10.3389/fcomp.2020.00035/full

License: MIT License

Python 46.59% Jupyter Notebook 53.41%
centralized-image-processing computer-vision convolutional-neural-networks cross-validation custom-data-loader-pytorch custom-dataloader fundus-image graph-algorithms image-procesing machine-learning multiple-gpu pytorch pytorch-implementation pytorch-vizualization retinal-vessel-segmentation u-net unet universal-pytorch-framework vessel-segmentation

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deepdyn's Issues

Mask not applied & PicklingError

Hi again,

I tried to run the main.py but the logs do not look good...

**Click to open run log** 

Total Params: 1864322
Total Params: 31042434
### SPLIT FOUND:  data\STARE\splits\STARE_0.json Loaded
### Mask not applied.  im0077.ppm
### Mask not applied.  im0081.ppm
### Mask not applied.  im0236.ppm
### Mask not applied.  im0255.ppm
### Mask not applied.  im0005.ppm
### Mask not applied.  im0003.ppm
### Mask not applied.  im0235.ppm
### Mask not applied.  im0139.ppm
### Mask not applied.  im0319.ppm
### Mask not applied.  im0001.ppm
### Mask not applied.  im0163.ppm
### Mask not applied.  im0044.ppm
Patches: 144
### Mask not applied.  im0002.ppm
Patches: 12
### Mask not applied.  im0162.ppm
Patches: 12
### Mask not applied.  im0291.ppm
Patches: 12
### Mask not applied.  im0082.ppm
Patches: 12
Training...
### SPLIT FOUND:  data\STARE\splits\STARE_1.json Loaded
Traceback (most recent call last):
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\unet\__init__.py", line 52, in run
	epoch_run=trainer.epoch_ce_loss)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\torchtrainer\torchtrainer.py", line 84, in train
	epoch_run(epoch=epoch, data_loader=data_loader, logger=self.train_logger)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\torchtrainer\torchtrainer.py", line 221, in epoch_ce_loss
	for i, data in enumerate(kw['data_loader'], 1):
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\site-packages\torch\utils\data\dataloader.py", line 279, in __iter__
	return _MultiProcessingDataLoaderIter(self)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\site-packages\torch\utils\data\dataloader.py", line 719, in __init__
	w.start()
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\process.py", line 112, in start
	self._popen = self._Popen(self)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\context.py", line 223, in _Popen
	return _default_context.get_context().Process._Popen(process_obj)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\context.py", line 322, in _Popen
	return Popen(process_obj)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\popen_spawn_win32.py", line 89, in __init__
	reduction.dump(process_obj, to_child)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\reduction.py", line 60, in dump
	ForkingPickler(file, protocol).dump(obj)
_pickle.PicklingError: Can't pickle <function <lambda> at 0x000002DA8D01B318>: attribute lookup <lambda> on testarch.unet.runs failed
### Mask not applied.  im0324.ppm
### Mask not applied.  im0239.ppm
### Mask not applied.  im0240.ppm
### Mask not applied.  im0004.ppm
### Mask not applied.  im0005.ppm
### Mask not applied.  im0003.ppm
### Mask not applied.  im0235.ppm
### Mask not applied.  im0139.ppm
### Mask not applied.  im0319.ppm
### Mask not applied.  im0001.ppm
### Mask not applied.  im0163.ppm
### Mask not applied.  im0044.ppm
Patches: 144
### Mask not applied.  im0077.ppm
Patches: 12
### Mask not applied.  im0081.ppm
Patches: 12
### Mask not applied.  im0236.ppm
Patches: 12
### Mask not applied.  im0255.ppm
Patches: 12
Training...
Traceback (most recent call last):
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\unet\__init__.py", line 52, in run
	epoch_run=trainer.epoch_ce_loss)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\torchtrainer\torchtrainer.py", line 84, in train
	epoch_run(epoch=epoch, data_loader=data_loader, logger=self.train_logger)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\torchtrainer\torchtrainer.py", line 221, in epoch_ce_loss
	for i, data in enumerate(kw['data_loader'], 1):
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\site-packages\torch\utils\data\dataloader.py", line 279, in __iter__
	return _MultiProcessingDataLoaderIter(self)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\site-packages\torch\utils\data\dataloader.py", line 719, in __init__
	w.start()
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\process.py", line 112, in start
	self._popen = self._Popen(self)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\context.py", line 223, in _Popen
	return _default_context.get_context().Process._Popen(process_obj)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\context.py", line 322, in _Popen
	return Popen(process_obj)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\popen_spawn_win32.py", line 89, in __init__
	reduction.dump(process_obj, to_child)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\reduction.py", line 60, in dump
	ForkingPickler(file, protocol).dump(obj)
_pickle.PicklingError: Can't pickle <function <lambda> at 0x000002DA8D01B318>: attribute lookup <lambda> on testarch.unet.runs failed
### SPLIT FOUND:  data\STARE\splits\STARE_2.json Loaded
### Mask not applied.  im0324.ppm
### Mask not applied.  im0239.ppm
### Mask not applied.  im0240.ppm
### Mask not applied.  im0004.ppm
### Mask not applied.  im0002.ppm
### Mask not applied.  im0162.ppm
### Mask not applied.  im0291.ppm
### Mask not applied.  im0082.ppm
### Mask not applied.  im0319.ppm
### Mask not applied.  im0001.ppm
### Mask not applied.  im0163.ppm
### Mask not applied.  im0044.ppm
Patches: 144
### Mask not applied.  im0005.ppm
Patches: 12
### Mask not applied.  im0003.ppm
Patches: 12
### Mask not applied.  im0235.ppm
Patches: 12
### Mask not applied.  im0139.ppm
Patches: 12
Training...
Traceback (most recent call last):
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\unet\__init__.py", line 52, in run
	epoch_run=trainer.epoch_ce_loss)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\torchtrainer\torchtrainer.py", line 84, in train
	epoch_run(epoch=epoch, data_loader=data_loader, logger=self.train_logger)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\torchtrainer\torchtrainer.py", line 221, in epoch_ce_loss
	for i, data in enumerate(kw['data_loader'], 1):
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\site-packages\torch\utils\data\dataloader.py", line 279, in __iter__
	return _MultiProcessingDataLoaderIter(self)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\site-packages\torch\utils\data\dataloader.py", line 719, in __init__
	w.start()
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\process.py", line 112, in start
	self._popen = self._Popen(self)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\context.py", line 223, in _Popen
	return _default_context.get_context().Process._Popen(process_obj)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\context.py", line 322, in _Popen
	return Popen(process_obj)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\popen_spawn_win32.py", line 89, in __init__
	reduction.dump(process_obj, to_child)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\reduction.py", line 60, in dump
	ForkingPickler(file, protocol).dump(obj)
_pickle.PicklingError: Can't pickle <function <lambda> at 0x000002DA8D01B318>: attribute lookup <lambda> on testarch.unet.runs failed
### SPLIT FOUND:  data\STARE\splits\STARE_3.json Loaded
### Mask not applied.  im0324.ppm
### Mask not applied.  im0239.ppm
### Mask not applied.  im0240.ppm
### Mask not applied.  im0004.ppm
### Mask not applied.  im0002.ppm
### Mask not applied.  im0162.ppm
### Mask not applied.  im0291.ppm
### Mask not applied.  im0082.ppm
### Mask not applied.  im0077.ppm
### Mask not applied.  im0081.ppm
### Mask not applied.  im0236.ppm
### Mask not applied.  im0255.ppm
Patches: 144
### Mask not applied.  im0319.ppm
Patches: 12
### Mask not applied.  im0001.ppm
Patches: 12
### Mask not applied.  im0163.ppm
Patches: 12
### Mask not applied.  im0044.ppm
Patches: 12
Training...
Traceback (most recent call last):
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\unet\__init__.py", line 52, in run
	epoch_run=trainer.epoch_ce_loss)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\torchtrainer\torchtrainer.py", line 84, in train
	epoch_run(epoch=epoch, data_loader=data_loader, logger=self.train_logger)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\torchtrainer\torchtrainer.py", line 221, in epoch_ce_loss
	for i, data in enumerate(kw['data_loader'], 1):
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\site-packages\torch\utils\data\dataloader.py", line 279, in __iter__
	return _MultiProcessingDataLoaderIter(self)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\site-packages\torch\utils\data\dataloader.py", line 719, in __init__
	w.start()
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\process.py", line 112, in start
	self._popen = self._Popen(self)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\context.py", line 223, in _Popen
	return _default_context.get_context().Process._Popen(process_obj)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\context.py", line 322, in _Popen
	return Popen(process_obj)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\popen_spawn_win32.py", line 89, in __init__
	reduction.dump(process_obj, to_child)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\reduction.py", line 60, in dump
	ForkingPickler(file, protocol).dump(obj)
_pickle.PicklingError: Can't pickle <function <lambda> at 0x000002DA8D01B318>: attribute lookup <lambda> on testarch.unet.runs failed
### SPLIT FOUND:  data\STARE\splits\STARE_4.json Loaded
Total Params: 1864322
Total Params: 31042434
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\spawn.py", line 105, in spawn_main
	exitcode = _main(fd)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\spawn.py", line 115, in _main
	self = reduction.pickle.load(from_parent)
EOFError: Ran out of input
### Mask not applied.  im0002.ppm
### Mask not applied.  im0162.ppm
### Mask not applied.  im0291.ppm
### Mask not applied.  im0082.ppm
### Mask not applied.  im0077.ppm
### Mask not applied.  im0081.ppm
### Mask not applied.  im0236.ppm
### Mask not applied.  im0255.ppm
### Mask not applied.  im0005.ppm
### Mask not applied.  im0003.ppm
### Mask not applied.  im0235.ppm
### Mask not applied.  im0139.ppm
Patches: 144
### Mask not applied.  im0324.ppm
Patches: 12
### Mask not applied.  im0239.ppm
Patches: 12
### Mask not applied.  im0240.ppm
Patches: 12
### Mask not applied.  im0004.ppm
Patches: 12
Training...
[0, 0, 0, 0]
Traceback (most recent call last):
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\unet\__init__.py", line 52, in run
	epoch_run=trainer.epoch_ce_loss)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\torchtrainer\torchtrainer.py", line 84, in train
	epoch_run(epoch=epoch, data_loader=data_loader, logger=self.train_logger)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\torchtrainer\torchtrainer.py", line 221, in epoch_ce_loss
	for i, data in enumerate(kw['data_loader'], 1):
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\site-packages\torch\utils\data\dataloader.py", line 279, in __iter__
	return _MultiProcessingDataLoaderIter(self)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\site-packages\torch\utils\data\dataloader.py", line 719, in __init__
	w.start()
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\process.py", line 112, in start
	self._popen = self._Popen(self)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\context.py", line 223, in _Popen
	return _default_context.get_context().Process._Popen(process_obj)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\context.py", line 322, in _Popen
	return Popen(process_obj)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\popen_spawn_win32.py", line 89, in __init__
	reduction.dump(process_obj, to_child)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\reduction.py", line 60, in dump
	ForkingPickler(file, protocol).dump(obj)
_pickle.PicklingError: Can't pickle <function <lambda> at 0x000002DA8D01B318>: attribute lookup <lambda> on testarch.unet.runs failed
### SPLIT FOUND:  data\STARE\splits\STARE_0.json Loaded
### Mask not applied.  im0077.ppm
Total Params: 1864322
### SPLIT FOUND:  data\STARE\splits\STARE_1.json Loaded
Traceback (most recent call last):
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\__init__.py", line 42, in run
	mode='train')
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\torchtrainer\datagen.py", line 88, in get_loader
	gen = cls(conf=conf, images=images, transforms=transforms, shuffle_indices=True, mode=mode)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\miniunet_dataloader.py", line 29, in __init__
	self._load_indices()
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\miniunet_dataloader.py", line 35, in _load_indices
	img_obj = self._get_image_obj(img_file)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\miniunet_dataloader.py", line 60, in _get_image_obj
	self.unet_dir + sep + img_obj.file_name.split('.')[0] + self.input_image_ext, 1)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\utils\img_utils.py", line 186, in get_image_as_array
	img = IMG.open(image_file)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\site-packages\PIL\Image.py", line 2809, in open
	fp = builtins.open(filename, "rb")
FileNotFoundError: [Errno 2] No such file or directory: 'logs\\STARE\\UNET_1_100_1\\im0077.png'
### Mask not applied.  im0324.ppm
### SPLIT FOUND:  data\STARE\splits\STARE_2.json Loaded
Traceback (most recent call last):
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\__init__.py", line 42, in run
	mode='train')
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\torchtrainer\datagen.py", line 88, in get_loader
	gen = cls(conf=conf, images=images, transforms=transforms, shuffle_indices=True, mode=mode)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\miniunet_dataloader.py", line 29, in __init__
	self._load_indices()
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\miniunet_dataloader.py", line 35, in _load_indices
	img_obj = self._get_image_obj(img_file)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\miniunet_dataloader.py", line 60, in _get_image_obj
	self.unet_dir + sep + img_obj.file_name.split('.')[0] + self.input_image_ext, 1)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\utils\img_utils.py", line 186, in get_image_as_array
	img = IMG.open(image_file)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\site-packages\PIL\Image.py", line 2809, in open
	fp = builtins.open(filename, "rb")
FileNotFoundError: [Errno 2] No such file or directory: 'logs\\STARE\\UNET_1_100_1\\im0324.png'
Traceback (most recent call last):
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\__init__.py", line 42, in run
	mode='train')
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\torchtrainer\datagen.py", line 88, in get_loader
	gen = cls(conf=conf, images=images, transforms=transforms, shuffle_indices=True, mode=mode)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\miniunet_dataloader.py", line 29, in __init__
	self._load_indices()
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\miniunet_dataloader.py", line 35, in _load_indices
	img_obj = self._get_image_obj(img_file)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\miniunet_dataloader.py", line 60, in _get_image_obj
	self.unet_dir + sep + img_obj.file_name.split('.')[0] + self.input_image_ext, 1)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\utils\img_utils.py", line 186, in get_image_as_array
	img = IMG.open(image_file)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\site-packages\PIL\Image.py", line 2809, in open
	fp = builtins.open(filename, "rb")
FileNotFoundError: [Errno 2] No such file or directory: 'logs\\STARE\\UNET_1_100_1\\im0324.png'
### Mask not applied.  im0324.ppm
### SPLIT FOUND:  data\STARE\splits\STARE_3.json Loaded
### Mask not applied.  im0324.ppm
### SPLIT FOUND:  data\STARE\splits\STARE_4.json Loaded
Traceback (most recent call last):
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\__init__.py", line 42, in run
	mode='train')
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\torchtrainer\datagen.py", line 88, in get_loader
	gen = cls(conf=conf, images=images, transforms=transforms, shuffle_indices=True, mode=mode)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\miniunet_dataloader.py", line 29, in __init__
	self._load_indices()
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\miniunet_dataloader.py", line 35, in _load_indices
	img_obj = self._get_image_obj(img_file)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\miniunet_dataloader.py", line 60, in _get_image_obj
	self.unet_dir + sep + img_obj.file_name.split('.')[0] + self.input_image_ext, 1)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\utils\img_utils.py", line 186, in get_image_as_array
	img = IMG.open(image_file)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\site-packages\PIL\Image.py", line 2809, in open
	fp = builtins.open(filename, "rb")
FileNotFoundError: [Errno 2] No such file or directory: 'logs\\STARE\\UNET_1_100_1\\im0324.png'
### Mask not applied.  im0002.ppm
[0, 0, 0, 0]
### SPLIT FOUND:  data\STARE\splits\STARE_0.json Loaded
Traceback (most recent call last):
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\__init__.py", line 42, in run
	mode='train')
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\torchtrainer\datagen.py", line 88, in get_loader
	gen = cls(conf=conf, images=images, transforms=transforms, shuffle_indices=True, mode=mode)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\miniunet_dataloader.py", line 29, in __init__
	self._load_indices()
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\miniunet_dataloader.py", line 35, in _load_indices
	img_obj = self._get_image_obj(img_file)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\miniunet\miniunet_dataloader.py", line 60, in _get_image_obj
	self.unet_dir + sep + img_obj.file_name.split('.')[0] + self.input_image_ext, 1)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\utils\img_utils.py", line 186, in get_image_as_array
	img = IMG.open(image_file)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\site-packages\PIL\Image.py", line 2809, in open
	fp = builtins.open(filename, "rb")
FileNotFoundError: [Errno 2] No such file or directory: 'logs\\STARE\\UNET_1_100_1\\im0002.png'
Total Params: 31042434
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\spawn.py", line 105, in spawn_main
	exitcode = _main(fd)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\spawn.py", line 115, in _main
	self = reduction.pickle.load(from_parent)
EOFError: Ran out of input
Total Params: 1864322
### Mask not applied.  im0077.ppm
### Mask not applied.  im0081.ppm
### Mask not applied.  im0236.ppm
### Mask not applied.  im0255.ppm
### Mask not applied.  im0005.ppm
### Mask not applied.  im0003.ppm
### Mask not applied.  im0235.ppm
### Mask not applied.  im0139.ppm
### Mask not applied.  im0319.ppm
### Mask not applied.  im0001.ppm
### Mask not applied.  im0163.ppm
### Mask not applied.  im0044.ppm
Patches: 144
### Mask not applied.  im0002.ppm
Patches: 12
### Mask not applied.  im0162.ppm
Patches: 12
### Mask not applied.  im0291.ppm
Patches: 12
### Mask not applied.  im0082.ppm
Patches: 12
Training...
Traceback (most recent call last):
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\testarch\unet\__init__.py", line 52, in run
	epoch_run=trainer.epoch_ce_loss)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\torchtrainer\torchtrainer.py", line 84, in train
	epoch_run(epoch=epoch, data_loader=data_loader, logger=self.train_logger)
  File "C:\Users\Cookie\Documents\GitKraken\deepdyn\torchtrainer\torchtrainer.py", line 221, in epoch_ce_loss
	for i, data in enumerate(kw['data_loader'], 1):
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\site-packages\torch\utils\data\dataloader.py", line 279, in __iter__
	return _MultiProcessingDataLoaderIter(self)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\site-packages\torch\utils\data\dataloader.py", line 719, in __init__
	w.start()
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\process.py", line 112, in start
	self._popen = self._Popen(self)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\context.py", line 223, in _Popen
	return _default_context.get_context().Process._Popen(process_obj)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\context.py", line 322, in _Popen
	return Popen(process_obj)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\popen_spawn_win32.py", line 89, in __init__
	reduction.dump(process_obj, to_child)
  File "C:\Users\Cookie\Anaconda3\envs\deepdyn\lib\multiprocessing\reduction.py", line 60, in dump
	ForkingPickler(file, protocol).dump(obj)
_pickle.PicklingError: Can't pickle <function <lambda> at 0x000002DA8D01B318>: attribute lookup <lambda> on testarch.unet.runs failed
### SPLIT FOUND:  data\STARE\splits\STARE_1.json Loaded

Process finished with exit code -1

I get a lot of warnings regarding:

Mask not applied

That's probably not very good.
Furthermore I get a lot of pickle errors:

_pickle.PicklingError: Can't pickle <function at 0x000002DA8D01B318>: attribute lookup on testarch.unet.runs failed

Do you know why this could be happening?

Best,
Karol

Execution problem

image
Can you help me in executing this code? I am having a problem because epochs do not start

unet_trainer evaluate() accuracy log

unet_trainer evaluate() accuracy has to be adjusted based on new tensore shape as we have now an image as output and label as opposed to one output and one label in previously used simple network.

Getting error when installing dependencies

@sraashis

After making a new environment with conda and insatalling pythion 3.7 on that, I try to install required dependencies but getting the following error.

Screenshot from 2020-06-05 18-07-20

Am I supposed to install any other packages before running the following command?
pip install -r deepdyn/assets/requirements.txt

strange output

when I run this code the following output is given
C:\Users\HI\Desktop\ature-master>python main.py
Total Params: 31042434
[0, 0, 0, 0]
what is it, how I get the correct output
I am using windows

ModuleNotFoundError

Traceback (most recent call last):
File "main.py", line 1, in
import testarch.unet as net
File "C:\Users\HI\Desktop\ature-master\testarch\unet_init_.py", line 14, in
from utils.measurements import ScoreAccumulator
File "C:\Users\HI\Desktop\ature-master\utils\measurements.py", line 14, in
import imgcommons.utils as imgutils
ModuleNotFoundError: No module named 'imgcommons'

Execution error

err
Hi,
Could you help me in executing this code. It stops on 150 epoc.

Thanks

Pls provide weights

Hi,

could you provide your best pretrained weigths, so we can evaluate out of the box?
That would be really nice! :)

Best,
Karol

Where to see segmentation result images?

I finished running train/test but I am unsure where I can find the segmentation results for training and testing (similar to the ones in the readme). Could you point me to where the result images are? Thanks!

unclear

  • Architecture
  1. Combination of unet and pixelwise
  • Merging final patches
  • Last patch issue
  • Last layer which 0 or 1 to take
  • Rotation of image and ground truth for more data but need same size image.

Training

  • Smart initialization
  • Less data

weight file

thank you for the great code
how can I get weight file?

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