.. image:: https://badge.fury.io/py/pyronn.svg :target: https://badge.fury.io/py/pyronn :alt: PyPI version
The python framework for the PYRO-NN layers implemented in (https://github.com/csyben/PYRO-NN-Layers)
PYRO-NN brings state-of-the-art reconstruction algorithm to neural networks integrated into Tensorflow. Open access paper available under: https://aapm.onlinelibrary.wiley.com/doi/full/10.1002/mp.13753
pyronn depends on the pyronn_layers. They are now installed via pip. The source code of the pyronn_layers can be found under: https://github.com/csyben/PYRO-NN-Layers
If you find this helpful, we would kindly ask you to reference our article published in medical physics:
.. code-block::
@article{PYRONN2019, author = {Syben, Christopher and Michen, Markus and Stimpel, Bernhard and Seitz, Stephan and Ploner, Stefan and Maier, Andreas K.}, title = {Technical Note: PYRO-NN: Python reconstruction operators in neural networks}, year = {2019}, journal = {Medical Physics}, }
With the new pyronn 0.1.0 Tensorflow 2.x will be supported. The default mode for pyronn is eager execution like Tensorflow itself. Major features in the update are:
Install via pip :
.. code-block:: bash
pip install pyronn
or if you downloaded this repository (https://github.com/csyben/PYRO-NN) using:
.. code-block:: bash
pip install -e .
If you encounter a problem during the installation have a look at our wiki: https://github.com/csyben/PYRO-NN/wiki
Can be found CHANGELOG.md <https://github.com/csyben/PYRO-NN/blob/master/CHANGELOG.md>_.
PYRO-NN comes with all relevant helper classes to easily run the projection and back-projection operators within the Tensorflow context.
To use the Layers a geometry object is needed:
.. code-block:: python
from pyronn.ct_reconstruction.geometry.geometry_parallel_2d import GeometryParallel2D
volume_size = 256
volume_shape = [volume_size, volume_size]
volume_spacing = [1, 1]
# Detector Parameters:
detector_shape = 512
detector_spacing = 1
# Trajectory Parameters:
number_of_par_projections = 360
angular_range = 2 * np.pi
# create Geometry class
par_geometry = GeometryParallel(volume_shape, volume_spacing, detector_shape, detector_spacing, number_of_fan_projections, angular_range)After defining the basic geometry parameters, a trajectory need to be set. The circular_trajectory class computes an idealiyed circular trajectory for a given geometry. For 2D parallel- and fan-beam geometry a trajectory is described using the central ray vectors. For 3D cone-beam geometry the trajectory is described with projection matrices.
The trajectory can be calculated and set as follows:
.. code-block:: python
from pyronn.ct_reconstruction.helpers.trajectories import circular_trajectory
par_geometry.set_trajectory(circular_trajectory.circular_trajectory_2d(par_geometry))At this point the geometry is fully setup and can be used to create projections and reconstructions. The Layers just takes the respective input tensor and the geometry object to conduct the projection, reconstruction respectively. PYRO-NN also provides convinient general way to create sinograms and reconstructions. The generate methods are generalized and take the input data, the layer to be used and the geometry. The only restriction is that the generation methods are within the Tensorflow session scope:
.. code-block:: python
from pyronn.ct_reconstruction.layers.projection_2d import parallel_projection2d
from pyronn.ct_reconstruction.layers.backprojection_2d import parallel_backprojection2d
from pyronn.ct_reconstruction.helpers.misc import generate_sinogram as sino_helper
from pyronn.ct_reconstruction.helpers.misc import generate_reco as reco_helper
from pyronn.ct_reconstruction.helpers.phantoms import shepp_logan
phantom = shepp_logan.shepp_logan_enhanced(par_geometry.volume_shape)
sinogram = sino_helper.generate_sinogram(phantom, parallel_projection2d, par_geometry)
reconstruction = reco_helper.generate_reco(sinogram, parallel_backprojection2d, par_geometry)In the following the example using the Layers directly is shown (Note that the Layers are within the Tensorflow graph context and therefore need to be evaluated before the result can be accessed):
.. code-block:: python
from pyronn.ct_reconstruction.layers.projection_2d import parallel_projection2d
from pyronn.ct_reconstruction.helpers.phantoms import shepp_logan
phantom = shepp_logan.shepp_logan_enhanced(par_geometry.volume_shape)
sinogram = parallel_projection2d(phantom, par_geometry)Using the PYRO-NN Layers directly registers the respective gradient, thus they can be used as normal Tensorflow Layers within the graph. For more details checkout the examples which are covering the different geometry and application cases.
Memory consumption on the graphics card can be a problem with CT datasets. For the reconstruction operators the input data is passed via a Tensorflow tensor, which is already allocated on the graphicscard by Tensorflow itself. In fact without any manual configuration Tensorflow will allocate most of the graphics card memory and handle the memory management internally. This leads to the problem that CUDA malloc calls in the operators itself will allocate memory outside of the Tensorflow context, which can easily lead to out of memory errors, although the memory is not full.
There exist two ways of dealing with this problem:
.. code-block:: python
gpus = tf.config.experimental.list_physical_devices('GPU')
if gpus:
try:
for gpu in gpus:
tf.config.experimental.set_memory_growth(gpu, True)
except RunetimeError as e:
print(e)Note that the hardware interpolation is the default setup for all operators.