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mousegrooming's Issues

Error in training network

When I run Train_3DConv_Binary.py on the annotated dataset I get the following errors:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\Windows\anaconda3\envs\grooming\lib\multiprocessing\spawn.py", line 105, in spawn_main
    exitcode = _main(fd)
  File "C:\Users\Windows\anaconda3\envs\grooming\lib\multiprocessing\spawn.py", line 115, in _main
    self = reduction.pickle.load(from_parent)
AttributeError: 'Groom_Dataset' object has no attribute '__get_train_example_queue'
Exception in thread Thread-2:
Traceback (most recent call last):
  File "C:\Users\Windows\anaconda3\envs\grooming\lib\threading.py", line 916, in _bootstrap_inner
    self.run()
  File "C:\Users\Windows\anaconda3\envs\grooming\lib\threading.py", line 864, in run
    self._target(*self._args, **self._kwargs)
  File "C:\Users\Windows\anaconda3\envs\grooming\lib\site-packages\keras\utils\data_utils.py", line 560, in data_generator_task
    generator_output = next(self._generator)
  File "C:\Users\Windows\Desktop\Grooming_2\MouseGrooming\Training\ReadHDF5.py", line 274, in get_train_generator_parallel
    pool_index.start()
  File "C:\Users\Windows\anaconda3\envs\grooming\lib\multiprocessing\process.py", line 105, in start
    self._popen = self._Popen(self)
  File "C:\Users\Windows\anaconda3\envs\grooming\lib\multiprocessing\context.py", line 223, in _Popen
    return _default_context.get_context().Process._Popen(process_obj)
  File "C:\Users\Windows\anaconda3\envs\grooming\lib\multiprocessing\context.py", line 322, in _Popen
    return Popen(process_obj)
  File "C:\Users\Windows\anaconda3\envs\grooming\lib\multiprocessing\popen_spawn_win32.py", line 65, in __init__
    reduction.dump(process_obj, to_child)
  File "C:\Users\Windows\anaconda3\envs\grooming\lib\multiprocessing\reduction.py", line 60, in dump
    ForkingPickler(file, protocol).dump(obj)
BrokenPipeError: [Errno 32] Broken pipe

Traceback (most recent call last):
  File "Train_3DConv_Binary.py", line 136, in <module>
    main(sys.argv[1:])
  File "Train_3DConv_Binary.py", line 131, in main
    multigpunet.fit_generator(dataset.get_train_generator_parallel(n_threads), train_steps_per_epoch, epochs=200, verbose=2, validation_data=dataset.get_valid_generator_parallel(n_threads), validation_steps=valid_steps_per_epoch, initial_epoch=0, workers=1, callbacks=[ckpt_saver, tensorboard_out, early_stopper, reduce_lr])
  File "C:\Users\Windows\anaconda3\envs\grooming\lib\site-packages\keras\legacy\interfaces.py", line 87, in wrapper
    return func(*args, **kwargs)
  File "C:\Users\Windows\anaconda3\envs\grooming\lib\site-packages\keras\engine\training.py", line 1809, in fit_generator
    generator_output = next(output_generator)
StopIteration

I'm running the code on Windows 10 and using the same versions of software listed in the documentation: Python 3.6.2, Tensorflow 1.2.1, Keras 2.0.6, OpenCV 3.3.0, R 3.3.0

Activation video colors are not green-purple and are instead red-blue

The activation video produced creates a red-blue color scaling. In the paper, we show purple-green scaling.

How I transformed the data (using ffmpeg):

ffmpeg -i VIDEO_out_Activations.avi -vf "geq=r='0.51r(X,Y)+0.49g(X,Y)':g='0.43g(X,Y)+0.57b(X,Y)':b='0.59r(X,Y)+0.19g(X,Y)+0.22*b(X,Y)'" -q 0 -t 10 TRANSFORMED_VIDEO.avi

While I haven't tested it, one could also modify the code to use purple-green colormaps. This won't be an exact match, but these are the following lines to change:
cm.bwr to cm.BrBG on this line
[200,0,0] to [64,0,75] and [0,0,200] to [0,72,29] on lines 83 and 85 respectively.

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