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Helper Module for Deep Learning with pytorch.

This work is made available by a community of people, amoung which the CEA Neurospin BAOBAB laboratory.

Important links

Where to start

You can list all available Deep Learning tools by executing in a Python shell:

from pprint import pprint
import pynet
pprint(pynet.get_tools())

The 'get_tools' function returns a dictionary with all available 'networks', 'losses', 'regularizers', and 'metrics'.

Then each network has been embeded in a Deep Learning training interface providing a 'training' and a 'testing' method. Network parameters are set using the NetParameters object. You can list all these interfaces by executing in a Python shell:

from pprint import pprint
import pynet
pprint(pynet.get_interfaces(family=None))
params = pynet.NetParameters(param1=1, param2=2)
params.param3 = 3

The 'get_interfaces' function returns a dictionary with interfaces sorted by family names. You can filter the result by providing the family name or a list of family names of interest.

You can list also all available data fetchers by executing in a Python shell:

from pprint import pprint
import pynet.datasets import get_fetchers
pprint(get_fetchers())

The 'get_fetchers' function returns a dictionary with all the declared fetchers. Finally you may want to look at the data manger class that provides convenient tools to split/stratify your dataset:

from pynet.datasets import DataManager

Install

Make sure you have installed all the package dependencies. Further instructions are available here.

pynet's People

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pynet's Issues

Weird behavior of affine transformations

Hi, and sorry for opening many issues in a short period of time :)

I'm facing a strange issue w/ affine transformations (rotation).
I'm working with a segmentation dataset, therefore, I need to apply the exact same transformation to my MRI and its manual labels.
Thus, I wrapped affine() into a RandomAffine class, appling map_coordinate(...) to both objects... And it's changing the unique values of my ground truth from [0,1,2] to [-1,0,1,2,3] even if using rotations only.

Shouldn't an affine transformation just move points in space w/o changing their values?

Here is a little code snippet to replicate the issue: https://colab.research.google.com/drive/1alUMLINz9n9mpmCwMQZPkr7-phbUlYSv?usp=sharing

Thanks!

[Data Augmentation] `random_zooms` incorrectly defined

I'm currently modifying some data augmentations implemented in PyNet, and something seems strange in pynet/pynet/augmentation/spatial.py, for affine transformations:

random_zooms = random_generator(
    translation, arr.ndim, dist=dist, seed=seed)
np.random.seed(seed)
random_zooms = np.random.uniform(
    low=(1 - zoom), high=(1 + zoom), size=arr.ndim)

The variable random_zooms is first defined from the translation argument then overwritten. LMK if I should do a PR :)

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