Helper Module for Deep Learning.

pynet network helpers overview¶

Credit: A Grigis

pynet is a Python package related to deep learning and its application in MRI mediacal data analysis. It is accessible to everybody, and is reusable in various contexts. The project is hosted on github: https://github.com/neurospin/pynet.

First checks¶

In order to test if the ‘pynet’ package is installed on your machine, you can check the package version.

import pynet
print(pynet.__version__)

Now you can run the the configuration info function to see if all the dependencies are installed properly.

import pynet.configure
print(pynet.configure.info())

Load a network¶

From the available netwoks load the UNet.

import os
import torch
from pynet.models import UNet
from pynet.plotting.network import plot_net, plot_net_rescue

model = UNet(
    num_classes=2,
    in_channels=1,
    depth=3,
    start_filts=8,
    up_mode="upsample",
    merge_mode="concat",
    batchnorm=True)
if "CI_MODE" not in os.environ:
    plot_net_rescue(model, shape=(1, 1, 64, 64, 64), outfileroot=None)

Inspect a network¶

The module propose utilities to inspect easyly some layers of the network.

from pynet.utils import test_model
from pprint import pprint
import numpy as np
from pynet.utils import get_named_layers
from pynet.utils import layer_at
from pynet.plotting import plot_data

out = test_model(model, shape=(1, 1, 64, 64, 64))
layers = get_named_layers(model)
pprint(layers)
hook_x, weight = layer_at(
    model=model,
    layer_name="down.1.doubleconv.conv1-8.16",
    x=torch.FloatTensor(np.random.random((1, 1, 64, 64, 64))))
print(hook_x.shape)
print(weight.shape)
plot_data(hook_x[:, :1])

if "CI_MODE" not in os.environ:
    import matplotlib.pyplot as plt
    plt.show()

Total running time of the script: ( 0 minutes 0.000 seconds)

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Helper Module for Deep Learning.

pynet network helpers overview¶

First checks¶

Load a network¶

Inspect a network¶

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