Merge pull request odlgroup#1403 from olivierverdier/rm_stir

Remove STIR bindings
kohr-h · Jun 29, 2018 · f65adfd · f65adfd
2 parents a64b190 + 423e693
commit f65adfd
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diff --git a/doc/source/getting_started/about_odl.rst b/doc/source/getting_started/about_odl.rst
@@ -166,7 +166,7 @@ If we now exchange ``matrix_op`` and ``data`` with a tomographic projector and l
 Further features
 ================
 * A unified structure `Geometry` for representing tomographic acquisition geometries
-* Interfaces to fast external libraries, e.g. `ASTRA`_ for X-ray tomography, `STIR`_ for emission tomography (preliminary), `pyFFTW`_ for fast Fourier transforms, ...
+* Interfaces to fast external libraries, e.g. `ASTRA`_ for X-ray tomography, `pyFFTW`_ for fast Fourier transforms, ...
 * A growing number of "must-have" operators like `Gradient`, `FourierTransform`, `WaveletTransform`
 * Several solvers for variational inverse problems, ranging from simple `gradient methods <steepest_descent>` to state-of-the-art non-smooth primal-dual splitting methods like `Douglas-Rachford <douglas_rachford_pd>`
 * Standardized tests for the correctness of implementations of operators and spaces, e.g. does the adjoint operator fulfill its defining relation?
@@ -193,6 +193,5 @@ Further reading
 .. _real numbers: https://en.wikipedia.org/wiki/Real_number
 .. _rectangular boxes: https://en.wikipedia.org/wiki/Hypercube
 .. _set: https://en.wikipedia.org/wiki/Set_%28mathematics%29
-.. _STIR: http://stir.sourceforge.net/
 .. _vector space: https://en.wikipedia.org/wiki/Vector_space
 .. _vectorized: https://en.wikipedia.org/wiki/Array_programming
diff --git a/doc/source/getting_started/installing_extensions.rst b/doc/source/getting_started/installing_extensions.rst
@@ -30,11 +30,6 @@ Astra is most easily installed using conda:
 For further instructions, check `the ASTRA GitHub page <https://github.com/astra-toolbox/astra-toolbox>`_.
 
 
-STIR for emission tomography
-============================
-For applications in emission tomography, i.e. PET or SPECT, install `STIR`_ with Python bindings.
-Support for STIR is currently very limited.
-
 
 CUDA backend for linear arrays
 ==============================
@@ -121,4 +116,3 @@ If the above command instead raises a ``MemoryError`` or similar, your graphics
 .. _odlcuda: https://github.com/odlgroup/odlcuda
 .. _CUDA toolkit: https://developer.nvidia.com/cuda-toolkit
 .. _ASTRA: https://github.com/astra-toolbox/astra-toolbox
-.. _STIR: https://github.com/UCL/STIR
diff --git a/examples/tomo/README.md b/examples/tomo/README.md
@@ -52,12 +52,3 @@ Example | Purpose | Complexity
 [`filtered_backprojection_cone_3d_short_scan.py`](filtered_backprojection_cone_3d_short_scan.py) | (Inexact) FBP reconstruction in 3D circular cone beam geometry **with short scan (less than 360 degrees)** | middle
 [`filtered_backprojection_helical_3d.py`](filtered_backprojection_helical_3d.py) | (Inexact) FBP reconstruction in 3D helical cone beam geometry | middle
 
-
-# Other
-
-[comment]: <> (This stuff will be removed from core ODL, just putting it to "Other" for now)
-
-Example | Purpose | Complexity
-------- | ------- | ----------
-[`stir_project.py`](stir_project.py) | Projection and back-projection in 3D PET geometry using the `stir` back-end | middle
-[`stir_reconstruct.py`](stir_reconstruct.py) | Iterative reconstruction in 3D PET geometry using the `stir` back-end | middle
diff --git a/examples/tomo/data/stir/initial.hv b/examples/tomo/data/stir/initial.hv
diff --git a/examples/tomo/data/stir/initial.v b/examples/tomo/data/stir/initial.v
diff --git a/examples/tomo/data/stir/small.hs b/examples/tomo/data/stir/small.hs
diff --git a/examples/tomo/data/stir/small.s b/examples/tomo/data/stir/small.s
diff --git a/examples/tomo/stir_project.py b/examples/tomo/stir_project.py
diff --git a/examples/tomo/stir_reconstruct.py b/examples/tomo/stir_reconstruct.py
diff --git a/odl/test/largescale/tomo/data/stir/initial.hv b/odl/test/largescale/tomo/data/stir/initial.hv
diff --git a/odl/test/largescale/tomo/data/stir/initial.v b/odl/test/largescale/tomo/data/stir/initial.v
diff --git a/odl/test/largescale/tomo/data/stir/small.hs b/odl/test/largescale/tomo/data/stir/small.hs
diff --git a/odl/test/largescale/tomo/data/stir/small.s b/odl/test/largescale/tomo/data/stir/small.s
diff --git a/odl/test/largescale/tomo/stir_slow_test.py b/odl/test/largescale/tomo/stir_slow_test.py
diff --git a/odl/test/test_examples.py b/odl/test/test_examples.py
@@ -31,7 +31,7 @@
 except ImportError:
     pass
 
-ignore_prefix = ['stir', 'proximal_lang']
+ignore_prefix = ['proximal_lang']
 
 # Make a fixture for all examples
 here = os.path.dirname(os.path.abspath(__file__))

diff --git a/odl/tomo/backends/__init__.py b/odl/tomo/backends/__init__.py
@@ -12,8 +12,6 @@
 
 __all__ = ()
 
-from . import stir_bindings
-
 from .astra_setup import *
 __all__ += astra_setup.__all__