use skimage 0.19: .github/workflows/CI.yml; dgsres/singlextal/workflo…

…w.py
mcvine · Aug 20, 2023 · 1987818 · 1987818
1 parent 2950cef
commit 1987818
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -55,7 +55,7 @@ jobs:
         shell: pwsh
         run: |
           conda install mamba
-          mamba install mcvine mantid-framework=6 pytest click=7 tqdm pylatex lmfit cloudpickle scikit-image=0.15
+          mamba install mcvine mantid-framework=6 pytest click=7 tqdm pylatex lmfit cloudpickle scikit-image=0.19
           mcvine
         env:
           PYTHON_VERSION: ${{ matrix.python-version }}

diff --git a/dgsres/singlextal/workflow.py b/dgsres/singlextal/workflow.py
@@ -634,7 +634,7 @@ def _find_outliers_1(img, max_deviation):
     # change image value range to 0-240. scikit image median does not work for random floats
     scale = 240; amax = np.nanmax(img); amin = np.nanmin(img)
     img1 = img-amin; img1 *= scale/(amax-amin) 
-    from skimage.filters import median
+    from skimage.filters.rank import median
     alpha_median = median(img1.astype('uint8'), mask=(img==img))
     return np.abs(img1-alpha_median) > max_deviation*scale/(amax-amin), alpha_median*(amax-amin)/scale+amin