CIL

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TotalVariation proximal in place

1

TotalVariation proximal is not calculated in place correctly. This was spotted when trying to run SIRT with a TV constraint in https://github.com/TomographicImaging/CIL/issues/1514. ```python data = dataexample.SIMPLE_PHANTOM_2D.get(size=(128,128)) plt.figure() plt.imshow(data.as_array()) plt.show() out=data.geometry.allocate('random')...

MargaretDuff

TotalGeneralisedVariation Function class

3

## Describe your changes Implements `TotalGeneralisedVariation` `Function` where the `proximal` method configures and runs the PDHG algorithm,i.e.  Using the definition of TGV, we have  And PDHG solves the...

epapoutsellis

Readers could be standalone plugins `conda install -cil_reader_nikon -c ccpi -c conda-forge` This would mean that specific dependencies aren't required for the core CIL installation.

gfardell

In the KL function the mask is not used by the numpy implementation but this is not mentioned in the documentation

MargaretDuff

ZeissDataReader Shifts and Metadata

5

For about one month, I have been trying to reconstruct a dataset (cone-beam geometry) using the [ZeissDataReader](https://github.com/TomographicImaging/CIL/blob/master/Wrappers/Python/cil/io/ZEISSDataReader.py), and I found some bugs in terms of reading the actual `data` and...

epapoutsellis

Looking at this documentation I noticed that we use 'center' rather than 'centre' in the Function methods: https://github.com/TomographicImaging/CIL/blob/ff4741092b7f10bde5e0572c0ac103288a163ffc/Wrappers/Python/cil/optimisation/functions/Function.py#L151 This is inconsistent with our: https://github.com/TomographicImaging/CIL/blob/ff4741092b7f10bde5e0572c0ac103288a163ffc/Wrappers/Python/cil/processors/CentreOfRotationCorrector.py#L25 And we should be consistent across...

lauramurgatroyd

This was suggested from @mehrhardt and code is available [here](https://github.com/mehrhardt/spdhg).

epapoutsellis

## Describe your changes Add a random seed to the power method and relevant unit tests ## Describe any testing you have performed *Please add any demo scripts to [CIL-Demos/misc/](https://github.com/TomographicImaging/CIL-Demos/tree/main/misc)*...

MargaretDuff

show1D does not work if the VectorData does not have a dimension_label

2

`show1D` does not work if the `VectorData` does not have a `dimension_label` The `dimension_labels` property is not mandatory for the data container nor does it show in any way when...

tommheik

Spdhg unit tests - speed up

1

## Describe your changes Reduced image dimension, max iterations and update objective interval in order to speed up the Spdhg unit tests. Changing to GPU didn't seem to have any...

MargaretDuff