Merge pull request #71 from SamirMoustafa/patch-1

Fix device mismatch errors in torchstain color space conversion functions

Author: carloalbertobarbano

.github/workflows/build.yaml

@@ -6,7 +6,7 @@ on:
 jobs:
   build_wheels:
     name: Build release
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4
@@ -26,7 +26,7 @@ jobs:
 
   upload_pypi:
     needs: build_wheels
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
 

.github/workflows/tests_full.yml

@@ -1,26 +1,26 @@
 name: Full Tests
 
 on:
-  push:
-    branches:
-      - main
-  pull_request:
-    branches:
-      - main
+  # push:
+  #   branches:
+  #     - main
+  # pull_request:
+  #   branches-ignore:
+  #     - main
   workflow_dispatch:
 
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     if: startsWith(github.ref, 'refs/tags/v') != true
 
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.6
+      - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
-          python-version: 3.6
+          python-version: 3.8
 
       - name: Install dependencies
         run: pip install wheel setuptools
@@ -40,8 +40,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ windows-2019, ubuntu-20.04, macos-13 ]
-        python-version: [ 3.7, 3.8, 3.9 ]
+        os: [ windows-latest, ubuntu-latest, macos-latest ]
+        python-version: [ 3.8, 3.9]
         tf-version: [2.7.0, 2.8.0, 2.9.0]
 
     steps:
@@ -71,8 +71,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ windows-2019, ubuntu-20.04, macos-13 ]
-        python-version: [ 3.7, 3.8, 3.9 ]
+        os: [ windows-latest, ubuntu-latest, macos-latest ]
+        python-version: [ 3.8, 3.9 ]
         pytorch-version: [1.8.0, 1.9.0, 1.10.0, 1.11.0, 1.12.0, 1.13.0]
 
     steps:

.github/workflows/tests_quick.yml

@@ -1,23 +1,23 @@
 name: Quick Tests
 
-on:
-  push:
-    branches-ignore:
-      - main
-  pull_request:
-    branches-ignore:
-      - main
-  workflow_dispatch:
+on: [push, pull_request, workflow_dispatch]
+  # push:
+    #branches-ignore:
+    #  - main
+  # pull_request:
+    #branches-ignore:
+    #  - main
+  # workflow_dispatch:
 
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.6
+      - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
-          python-version: 3.6
+          python-version: 3.8
 
       - name: Install dependencies
         run: pip install wheel setuptools
@@ -34,7 +34,7 @@ jobs:
 
   test-tf:
     needs: build
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4
@@ -60,7 +60,7 @@ jobs:
 
   test-torch:
     needs: build
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4

setup.py

@@ -6,7 +6,7 @@
 
 setup(
     name='torchstain',
-    version='1.4.0',
+    version='1.4.1',
     description='Stain normalization tools for histological analysis and computational pathology',
     long_description=README,
     long_description_content_type='text/markdown',

torchstain/torch/utils/lab2rgb.py

@@ -6,6 +6,11 @@
 def lab2rgb(lab):
     lab = lab.type(torch.float32)
 
+    # Move constant tensors to the same device as input
+    device = lab.device
+    _white_device = _white.to(device)
+    _xyz2rgb_device = _xyz2rgb.to(device)
+    
     # rescale back from OpenCV format and extract LAB channel
     L, a, b = lab[0] / 2.55, lab[1] - 128, lab[2] - 128
 
@@ -24,10 +29,10 @@ def lab2rgb(lab):
     out.masked_scatter_(not_mask, (torch.masked_select(out, not_mask) - 16 / 116) / 7.787)
 
     # rescale to the reference white (illuminant)
-    out = torch.mul(out, _white.type(out.dtype).unsqueeze(dim=-1).unsqueeze(dim=-1))
+    out = torch.mul(out, _white_device.type(out.dtype).unsqueeze(dim=-1).unsqueeze(dim=-1))
 
     # convert XYZ -> RGB color domain
-    arr = torch.tensordot(out, torch.t(_xyz2rgb).type(out.dtype), dims=([0], [0]))
+    arr = torch.tensordot(out, torch.t(_xyz2rgb_device).type(out.dtype), dims=([0], [0]))
     mask = arr > 0.0031308
     not_mask = torch.logical_not(mask)
     arr.masked_scatter_(mask, 1.055 * torch.pow(torch.masked_select(arr, mask), 1 / 2.4) - 0.055)

torchstain/torch/utils/rgb2lab.py

@@ -9,17 +9,21 @@
 
 def rgb2lab(rgb):
     arr = rgb.type(torch.float32)
-
+    # Move constant tensors to the same device as input
+    device = arr.device
+    _rgb2xyz_device = _rgb2xyz.to(device)
+    _white_device = _white.to(device)
+  
     # convert rgb -> xyz color domain
     mask = arr > 0.04045
     not_mask = torch.logical_not(mask)
     arr.masked_scatter_(mask, torch.pow((torch.masked_select(arr, mask) + 0.055) / 1.055, 2.4))
     arr.masked_scatter_(not_mask, torch.masked_select(arr, not_mask) / 12.92)
 
-    xyz = torch.tensordot(torch.t(_rgb2xyz), arr, dims=([0], [0]))
+    xyz = torch.tensordot(torch.t(_rgb2xyz_device), arr, dims=([0], [0]))
 
     # scale by CIE XYZ tristimulus values of the reference white point
-    arr = torch.mul(xyz, 1 / _white.type(xyz.dtype).unsqueeze(dim=-1).unsqueeze(dim=-1))
+    arr = torch.mul(xyz, 1 / _white_device.type(xyz.dtype).unsqueeze(dim=-1).unsqueeze(dim=-1))
 
     # nonlinear distortion and linear transformation
     mask = arr > 0.008856