samdporter

https://github.com/SyneRBI/SIRF/blob/1bb1b111a80f48df5e491a8ee9201715d4e9db42/src/xSTIR/pSTIR/STIR.py#L757C6-L759C27 Documentation for ImageDataProcessor a little light on detail. It would also be useful to have a more informative error message when the error occurs from code such as ```...

"set_keep_views_in_cache(True)" for SPECTUBMatrix results in zero image on reconstruction

5

https://github.com/SyneRBI/SIRF/blob/9ef5044e8d939e27290f0876205f041cbdc60460/src/xSTIR/pSTIR/STIR.py#L830 Keep_all_views_in_cache = True results in zero image after reconstruction. SPECTUBMatrix.set_up() is not exposed in SIRF. Could this be the issue? See https://github.com/samdporter/SPECTissues/blob/main/minimal.py for demonstration. Change "keep_views_in_cache" variable to True

`OSMAPOSLReconstructor(\path\to\file.par)` ignores `number of subiterations:= n` in parameter file. Needs to be reset with `reconstructor.set_num_subiterations(n)` otherwise will only run for 1 subiteration. I'll add some more information soon. Leaving this...

SPECT reconstruction causes error with CIL GradientOperator if OPENMP=ON

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`Segmentation error (core dumped)` After running `minimalCIL.py` @ [https://github.com/samdporter/SPECTissues.git](url) CIL's admm causes failure. OSEM reconstruction works OK. Ran valgrind & will post in next comment

BlockDataContainers with (1,1) shape

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I'm currently doing some reconstructions where I end up with `BlockDataContainers` with `shape=(1,1)`. A 1xn `BlockOperator` needs to take a nx1 `BlockDataContainer` and output a 1x1 DataContainer so that this...

## Changes in this pull request Added method for `ImageData` to zoom image using geometrical information from a template image ## Testing performed - Compared `ImageData` zoomed using `zoom_image_from_template()` and...

removal of intel conda channel resulting in error when building docker image

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See: [https://community.intel.com/t5/oneAPI-Registration-Download/Disappearance-of-intel-conda-channel/m-p/1614250#M2163](https://community.intel.com/t5/oneAPI-Registration-Download/Disappearance-of-intel-conda-channel/m-p/1614250#M2163) Dockerfile: ``` FROM synerbi/sirf:latest-gpu USER root RUN conda install pytorch && fix-permissions "${CONDA_DIR}" /home/${NB_USER} USER ${NB_UID} ``` Error: ``` => ERROR [2/2] RUN conda install pytorch && fix-permissions...

https://github.com/SyneRBI/SIRF/blob/b2053845e25f87149d1a7406846110e4bf66817e/src/xSTIR/cSTIR/cstir.cpp#L1212 ObjectiveFunction gradient incorrect when passed the same object for input argument and out Fails when used with CIL: `obj_fun.gradient(x, out=x)` suggestion for fix: ``` extern "C" void* cSTIR_computeObjectiveFunctionGradient(void* ptr_f,...

data_processor only applied in forward pass for ParallelProj Projector

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Observed behaviour: - ParallelProj: data_processor applied in forward projection only. - RayTracing: data_processor applied in both forward and backprojection. - Matrix (e.g. SPECTUB): data_processor applied in both forward and backprojection....

## Description: Currently, when using a slopes file (e.g., [ct_slopes.json](https://github.com/UCL/STIR/blob/master/src/config/ct_slopes.json)), the conversion from CT attenuation coefficients (ctac) to μ values relies on a hard-coded keV/kvP value. ## Feature Request: Implement...