Merge pull request #1149 from mantidproject/1023-algotom

Switch from sarepy to algotom

conda/meta.yaml

@@ -39,6 +39,7 @@ requirements:
     - cil-astra=21.2.*
     - ccpi-regulariser=20.9
     - tomophantom=1.4.*
+    - algotom=1.0.*
 
 build:
   number: 1

docs/overview.rst

@@ -3,7 +3,7 @@ Overview
 
 Mantid Imaging contains tools for loading data from neutron imaging experiments, preprocessing to enhance images and tomographic reconstruction into 3 dimensional data that can be output for further analysis.
 
-Mantid Imaging makes use of a range of algorithms, some from external tools including `Astra <http://www.astra-toolbox.com/>`_ and `Tomopy <https://tomopy.readthedocs.io/en/latest/>`_. Many of these are optimised for multithreading and GPU computing.
+Mantid Imaging makes use of a range of algorithms, some from external tools including `Astra <http://www.astra-toolbox.com/>`_, `Tomopy <https://tomopy.readthedocs.io/en/latest/>`_, `Algotom <https://github.com/algotom/algotom>`_ and the `Core Imaging Library <https://github.com/TomographicImaging/CIL>`_. Many of these are optimised for multithreading and GPU computing.
 
 Mantid Imaging is written in Python and requires a CUDA capable GPU for full functionality. It runs on Linux. See :ref:`Installation` for more details.
 

docs/release_notes/next.rst

@@ -7,6 +7,7 @@ New Features
 ------------
 
 - #1044 : Command line argument to load a dataset
+- #1023 : Switch from Sarepy to Algotom
 
 Fixes
 -----

environment-dev.yml

@@ -5,6 +5,7 @@ channels:
   - astra-toolbox/label/dev
   - conda-forge
   - ccpi
+  - algotom
 dependencies:
   - mantidimaging
   - pip

environment.yml

@@ -5,6 +5,7 @@ channels:
   - astra-toolbox/label/dev
   - conda-forge
   - ccpi
+  - algotom
 # Dependencies that can be installed with conda should be in conda/meta.yaml
 dependencies:
   - mantidimaging

mantidimaging/core/operations/remove_all_stripe/remove_all_stripe.py

@@ -5,7 +5,7 @@
 from mantidimaging.core.data.images import Images
 
 from PyQt5.QtWidgets import QSpinBox, QDoubleSpinBox
-from sarepy.prep.stripe_removal_original import remove_all_stripe
+from algotom.prep.removal import remove_all_stripe
 
 from mantidimaging.core.operations.base_filter import BaseFilter, FilterGroup
 from mantidimaging.core.parallel import shared as ps
@@ -16,7 +16,7 @@ class RemoveAllStripesFilter(BaseFilter):
     """Stripe and ring artifact removal. Remove all types of stripe artifacts by
     combining algorithm 6, 5, and 3  in Vo et al., Optics Express 28396 (2018).
 
-    Source: https://github.com/nghia-vo/sarepy
+    Source: https://github.com/algotom/algotom
 
     Intended to be used on: Sinograms
 

mantidimaging/core/operations/remove_dead_stripe/remove_dead_stripe.py

@@ -5,7 +5,7 @@
 from mantidimaging.core.data.images import Images
 
 from PyQt5.QtWidgets import QDoubleSpinBox, QSpinBox
-from sarepy.prep.stripe_removal_original import remove_unresponsive_and_fluctuating_stripe
+from algotom.prep.removal import remove_dead_stripe
 
 from mantidimaging.core.operations.base_filter import BaseFilter, FilterGroup
 from mantidimaging.core.parallel import shared as ps
@@ -16,7 +16,7 @@ class RemoveDeadStripesFilter(BaseFilter):
     """Stripe and ring artifact removal. Algorithm 6 in Vo et al., Optics Express 28396 (2018).
     Remove unresponsive or fluctuating stripes by: locating stripes, correction by interpolation.
 
-    Source: https://github.com/nghia-vo/sarepy
+    Source: https://github.com/algotom/algotom
 
     Intended to be used on: Sinograms
 
@@ -31,12 +31,7 @@ class RemoveDeadStripesFilter(BaseFilter):
 
     @staticmethod
     def filter_func(images: Images, snr=3, size=61, cores=None, chunksize=None, progress=None):
-        f = ps.create_partial(
-            remove_unresponsive_and_fluctuating_stripe,
-            ps.return_to_self,
-            snr=snr,
-            size=size,
-        )
+        f = ps.create_partial(remove_dead_stripe, ps.return_to_self, snr=snr, size=size, residual=False)
         ps.shared_list = [images.data]
         ps.execute(f, images.num_projections, progress, cores=cores)
         return images

mantidimaging/core/operations/remove_large_stripe/remove_large_stripe.py

@@ -4,7 +4,7 @@
 from functools import partial
 
 from PyQt5.QtWidgets import QSpinBox, QDoubleSpinBox
-from sarepy.prep.stripe_removal_original import remove_large_stripe
+from algotom.prep.removal import remove_large_stripe
 
 from mantidimaging.core.operations.base_filter import BaseFilter, FilterGroup
 from mantidimaging.core.parallel import shared as ps
@@ -16,7 +16,7 @@ class RemoveLargeStripesFilter(BaseFilter):
     Remove large stripes by: locating stripes, normalizing them to remove full stripes, using
     the sorting technique to remove partial stripes.
 
-    Source: https://github.com/nghia-vo/sarepy
+    Source: https://github.com/algotom/algotom
 
     Intended to be used on: Sinograms
     When: If stripes artifacts are present that have not been

mantidimaging/core/operations/remove_stripe_filtering/remove_stripe_filtering.py

@@ -5,8 +5,7 @@
 from mantidimaging.core.data.images import Images
 
 from PyQt5.QtWidgets import QSpinBox
-from sarepy.prep.stripe_removal_improved import remove_stripe_based_filtering_sorting, \
-    remove_stripe_based_2d_filtering_sorting
+from algotom.prep.removal import remove_stripe_based_filtering, remove_stripe_based_2d_filtering_sorting
 
 from mantidimaging.core.operations.base_filter import BaseFilter, FilterGroup
 from mantidimaging.core.parallel import shared as ps
@@ -17,7 +16,7 @@ class RemoveStripeFilteringFilter(BaseFilter):
     """Stripe and ring artifact removal. Combination of algorithm 2 and algorithm 3 in Vo et al.,
     Optics Express 28396 (2018). Removing stripes using the filtering and sorting technique.
 
-    Source: https://github.com/nghia-vo/sarepy
+    Source: https://github.com/algotom/algotom
 
     Intended to be used on: Sinograms
 
@@ -40,11 +39,12 @@ def filter_func(images: Images,
                     chunksize=None,
                     progress=None):
         if filtering_dim == 1:
-            f = ps.create_partial(remove_stripe_based_filtering_sorting,
+            f = ps.create_partial(remove_stripe_based_filtering,
                                   ps.return_to_self,
                                   sigma=sigma,
                                   size=size,
-                                  dim=window_dim)
+                                  dim=window_dim,
+                                  sort=True)
         else:
             f = ps.create_partial(remove_stripe_based_2d_filtering_sorting,
                                   ps.return_to_self,

mantidimaging/core/operations/remove_stripe_sorting_fitting/remove_stripe_sorting_fitting.py

@@ -5,7 +5,7 @@
 from mantidimaging.core.data.images import Images
 
 from PyQt5.QtWidgets import QSpinBox
-from sarepy.prep.stripe_removal_improved import remove_stripe_based_sorting_fitting
+from algotom.prep.removal import remove_stripe_based_fitting
 
 from mantidimaging.core.operations.base_filter import BaseFilter, FilterGroup
 from mantidimaging.core.parallel import shared as ps
@@ -16,7 +16,7 @@ class RemoveStripeSortingFittingFilter(BaseFilter):
     """Stripe and ring artifact removal. Combination of algorithm 3 and 1 in Vo et al.,
     Optics Express 28396 (2018). Remove stripes using the sorting and fitting technique.
 
-    Source: https://github.com/nghia-vo/sarepy
+    Source: https://github.com/algotom/algotom
 
     Intended to be used on: Sinograms
 
@@ -30,12 +30,8 @@ class RemoveStripeSortingFittingFilter(BaseFilter):
     link_histograms = True
 
     @staticmethod
-    def filter_func(images: Images, order=1, sigmax=3, sigmay=3, cores=None, chunksize=None, progress=None):
-        f = ps.create_partial(remove_stripe_based_sorting_fitting,
-                              ps.return_to_self,
-                              order=order,
-                              sigmax=sigmax,
-                              sigmay=sigmay)
+    def filter_func(images: Images, order=1, sigma=3, cores=None, chunksize=None, progress=None):
+        f = ps.create_partial(remove_stripe_based_fitting, ps.return_to_self, order=order, sigma=sigma, sort=True)
 
         ps.shared_list = [images.data]
         ps.execute(f, images.num_projections, progress, cores=cores)
@@ -54,28 +50,19 @@ def register_gui(form, on_change, view):
                                         default_value=1,
                                         form=form,
                                         on_change=on_change,
-                                        tooltip="Polynomial fit order. Check sarepy for more information")
-        _, sigmax = add_property_to_form('Sigma X',
-                                         Type.INT,
-                                         default_value=3,
-                                         form=form,
-                                         on_change=on_change,
-                                         tooltip="Sigma of the Gaussian window in the x-direction")
-        _, sigmay = add_property_to_form('Sigma Y',
-                                         Type.INT,
-                                         default_value=3,
-                                         form=form,
-                                         on_change=on_change,
-                                         tooltip="Sigma of the Gaussian window in the y-direction")
-
-        return {'order': order, 'sigmax': sigmax, 'sigmay': sigmay}
+                                        tooltip="Polynomial fit order. Check algotom docs for more information")
+        _, sigma = add_property_to_form('Sigma',
+                                        Type.INT,
+                                        default_value=3,
+                                        form=form,
+                                        on_change=on_change,
+                                        tooltip="Sigma of the Gaussian window in the x-direction")
+
+        return {'order': order, 'sigma': sigma}
 
     @staticmethod
-    def execute_wrapper(order: QSpinBox, sigmax: QSpinBox, sigmay: QSpinBox):  # type: ignore
-        return partial(RemoveStripeSortingFittingFilter.filter_func,
-                       order=order.value(),
-                       sigmax=sigmax.value(),
-                       sigmay=sigmay.value())
+    def execute_wrapper(order: QSpinBox, sigma: QSpinBox):  # type: ignore
+        return partial(RemoveStripeSortingFittingFilter.filter_func, order=order.value(), sigma=sigma.value())
 
     @staticmethod
     def group_name() -> FilterGroup:

mantidimaging/core/operations/remove_stripe_sorting_fitting/test/remove_stripe_sorting_fitting_test.py

@@ -31,19 +31,16 @@ def test_execute_wrapper_return_is_runnable(self):
         """
         order = mock.Mock()
         order.value = mock.Mock(return_value=1)
-        sigmax = mock.Mock()
-        sigmax.value = mock.Mock(return_value=2)
-        sigmay = mock.Mock()
-        sigmay.value = mock.Mock(return_value=2)
+        sigma = mock.Mock()
+        sigma.value = mock.Mock(return_value=2)
 
-        execute_func = RemoveStripeSortingFittingFilter.execute_wrapper(order, sigmax, sigmay)
+        execute_func = RemoveStripeSortingFittingFilter.execute_wrapper(order, sigma)
 
         images = th.generate_images()
         execute_func(images)
 
         self.assertEqual(order.value.call_count, 1)
-        self.assertEqual(sigmax.value.call_count, 1)
-        self.assertEqual(sigmay.value.call_count, 1)
+        self.assertEqual(sigma.value.call_count, 1)
 
 
 if __name__ == '__main__':