Merge pull request #113 from DiamondLightSource/library

fixes to go with the gpuloop PR in httomo
DiamondLightSource · Apr 24, 2024 · 063e026 · 063e026
2 parents 0b6ab7d + e9b0861
commit 063e026
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Showing 26 changed files with 1,125 additions and 1,656 deletions.
diff --git a/conda/environment.yml b/conda/environment.yml
@@ -4,9 +4,10 @@ channels:
   - anaconda
   - astra-toolbox
   - httomo
+  - rapidsai
 dependencies:
-  - conda-forge::cupy
-  - conda-forge::numpy<=1.23
+  - conda-forge::cupy=12.3.0
+  - conda-forge::numpy<=1.24
   - conda-forge::nvtx
   - conda-forge::scipy
   - conda-forge::python
@@ -22,4 +23,4 @@ dependencies:
   - anaconda::h5py
   - astra-toolbox::astra-toolbox
   - httomo::tomobar
-
+  - rapidsai::cucim
diff --git a/conda/recipe/meta.yaml b/conda/recipe/meta.yaml
@@ -23,6 +23,7 @@ requirements:
     - python
     - numpy
     - cupy
+    - cucim
     - astra-toolbox
     - nvtx
     - tomobar

diff --git a/httomolibgpu/__init__.py b/httomolibgpu/__init__.py
@@ -1,4 +1,3 @@
-from .decorator import *
 from httomolibgpu.misc.corr import *
 from httomolibgpu.misc.morph import *
 from httomolibgpu.prep.alignment import *

diff --git a/httomolibgpu/cuda_kernels/median_kernel.cu b/httomolibgpu/cuda_kernels/median_kernel.cu
@@ -1,5 +1,5 @@
 template <typename Type, int diameter>
-__global__ void median_general_kernel(const Type *in, Type *out, float dif,
+__global__ void median_general_kernel3d(const Type *in, Type *out, float dif,
                                       int Z, int M, int N) {
   constexpr int radius = diameter / 2;
   constexpr int d3 = diameter * diameter * diameter;
@@ -53,4 +53,4 @@ __global__ void median_general_kernel(const Type *in, Type *out, float dif,
     out[index] =
         fabsf(in_value - ValVec[midpoint]) >= dif ? ValVec[midpoint] : in_value;
   }
-}
+}
diff --git a/httomolibgpu/decorator.py b/httomolibgpu/decorator.py