Config File Refactors

As a result of the June 19 Hackathon, a number of potential changes to the config file have been identified and should be considered for implementation:

• Move preprocessing fields from 'NETWORK' to each 'Input' section

Move Preprocessing Fields from 'NETWORK' to each 'Input' section

There is an assumption at present that the pre-processing fields are applied consistently across inputs, or at least that there is, in the application, conventions that some of the fields are applied to images and some to labels.

This approach is fine for network types that have a single set of inputs and a single set of labels, for example, but doesn't cover the possibility that a user's overall dataset is composed of a number of discreet sub-datasets, which are not necessarily consistent in the processing that needs to be performed. As such, it makes sense that the input preprocessing flags currently defined in NETWORK would be better associated with each input.

Before

[T1]
path_to_search = ./path/to/some/t1s
filename_contains = T1
filename_not_contains =
spatial_window_size = (96, 96, 96)
pixdim = (1.0, 1.0, 1.0)
axcodes=(A, R, S)
interp_order = 3

[NETWORK]
name = unet
activation_function = prelu
batch_size = 1
decay = 0
reg_type = L2
volume_padding_size = 44
<b>histogram_ref_file = ./path/to/histograms.txt</b>
<b>norm_type = percentile</b>
<b>cutoff = (0.01, 0.99)</b>
<b>normalisation = True</b>
<b>whitening = True</b>
<b>normalise_foreground_only=True</b>
<b>foreground_type = otsu_plus</b>
<b>multimod_foreground_type = and</b>
queue_length = 128
window_sampling = uniform

After

[T1]
path_to_search = ./path/to/some/t1s
filename_contains = T1
filename_not_contains =
spatial_window_size = (96, 96, 96)
pixdim = (1.0, 1.0, 1.0)
axcodes=(A, R, S)
interp_order = 3
histogram_ref_file = ./path/to/histograms.txt
norm_type = percentile
cutoff = (0.01, 0.99)
normalisation = True
whitening = True
normalise_foreground_only=True
foreground_type = otsu_plus
multimod_foreground_type = and

[NETWORK]
name = unet
activation_function = prelu
batch_size = 1
decay = 0
reg_type = L2
volume_padding_size = 44
queue_length = 128
window_sampling = uniform