Merge pull request #8 from andreped/workflow

Workflows to produce binaries

Author: taigw

.github/workflows/CI-build.yaml

@@ -0,0 +1,57 @@
+name: Build and upload wheels
+
+on:
+  push:
+    branches: 
+      - '*'
+  pull_request:
+    branches: 
+      - '*'
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [windows-2019, ubuntu-18.04, macos-10.15]
+        python-version: [3.6, 3.7, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        pip install wheel setuptools
+        pip install -r requirements.txt
+
+    - name: Build wheel
+      run: python setup.py bdist_wheel
+
+    - name: Install software
+      run: pip install --find-links=${{github.workspace}}/dist/ SimpleCRF
+
+    - name: Test import
+      run: python -c "import denseCRF, maxflow"
+
+    - name: Install deps for demos
+      run: pip install SimpleITK pillow matplotlib
+
+    - name: Test maxflow demo
+      run: cd ${{github.workspace}}/examples && python demo_maxflow.py 0
+
+    - name: Test denseCRF demo
+      run: cd ${{github.workspace}}/examples && python demo_densecrf.py 1
+
+    - name: Test denseCRF 3D demo
+      run: cd ${{github.workspace}}/examples && python demo_densecrf.py 1
+
+    - name: Upload Python wheel
+      uses: actions/upload-artifact@v2
+      with:
+        name: Python wheel
+        path: ${{github.workspace}}/dist/SimpleCRF-*.whl
+        if-no-files-found: error

examples/demo_densecrf.py

@@ -2,6 +2,7 @@
 import numpy as np
 from PIL import Image
 import matplotlib.pyplot as plt
+import sys
 
 def densecrf(I, P, param):
     """
@@ -72,10 +73,11 @@ def demo_densecrf1():
     param = (w1, alpha, beta, w2, gamma, it)
     lab = densecrf(Iq, prob, param)
     lab = Image.fromarray(lab*255)
+    fig = plt.figure()
     plt.subplot(1,3,1); plt.axis('off'); plt.imshow(I); plt.title('input image')
     plt.subplot(1,3,2); plt.axis('off'); plt.imshow(L); plt.title('initial label')
     plt.subplot(1,3,3); plt.axis('off'); plt.imshow(lab); plt.title('after dense CRF')
-    plt.show()
+    fig.savefig('./demo_result.png')
 
 def demo_densecrf2():
     I  = Image.open('../dependency/densecrf/examples/im3.ppm')
@@ -99,21 +101,22 @@ def demo_densecrf2():
     lab = densecrf(Iq, prob, param)
     lab = colorize_label_map(lab, color_list)
     lab = Image.fromarray(lab)
+    fig = plt.figure()
     plt.subplot(1,3,1); plt.axis('off'); plt.imshow(I); plt.title('input image')
     plt.subplot(1,3,2); plt.axis('off'); plt.imshow(L); plt.title('initial label')
     plt.subplot(1,3,3); plt.axis('off'); plt.imshow(lab); plt.title('after dense CRF')
-    plt.show()
+    fig.savefig('./demo_result.png')
 
 if __name__ == "__main__":
     print("example list")
     print(" 0 -- Dense CRF example for a binary segmentation")
     print(" 1 -- Dense CRF example for a multi-class segmentation")
-    print("please enter the index of an example:")
-    method = input()
-    method = "{0:}".format(method)
+    if len(sys.argv) == 1:
+        raise ValueError("Please, provide an argument.")
+    method = sys.argv[1]
     if(method == '0'):
         demo_densecrf1()
     elif(method == '1'):
         demo_densecrf2()
     else:
-        print("invalid number : {0:}".format(method))
+        raise ValueError("Invalid number: " + method)

examples/demo_densecrf3d.py

@@ -3,6 +3,7 @@
 import numpy as np
 from PIL import Image
 import matplotlib.pyplot as plt
+import sys
 
 def densecrf3d(I, P, param):
     """
@@ -91,14 +92,12 @@ def demo_densecrf3d_2():
     print("example list")
     print(" 0 -- 3D Dense CRF example for single-modal segmentation")
     print(" 1 -- 3D Dense CRF example for multi-modal segmentation")
-    print("please enter the index of an example:")
-    method = input()
-    method = "{0:}".format(method)
+    if len(sys.argv) == 1:
+        raise ValueError("Please, provide an argument.")
+    method = sys.argv[1]
     if(method == '0'):
         demo_densecrf3d_1()
     elif(method == '1'):
         demo_densecrf3d_2()
     else:
-        print("invalid number : {0:}".format(method))
-
-
+        raise ValueError("Invalid number: " + method)

examples/demo_maxflow.py

@@ -1,9 +1,9 @@
-
 import numpy as np
 import SimpleITK as sitk
 import maxflow
 from PIL import Image
 import matplotlib.pyplot as plt
+import sys
 
 def maxflow2d(I, P, param):
     """
@@ -96,10 +96,11 @@ def demo_maxflow():
     param = (lamda, sigma)
     lab = maxflow2d(Iq, Prob, param)
 
+    fig = plt.figure()
     plt.subplot(1,3,1); plt.axis('off'); plt.imshow(I);  plt.title('input image')
     plt.subplot(1,3,2); plt.axis('off'); plt.imshow(fP);   plt.title('initial \n segmentation')
     plt.subplot(1,3,3); plt.axis('off'); plt.imshow(lab); plt.title('CRF result')
-    plt.show()
+    fig.savefig('./demo_result.png')
 
 def demo_interactive_maxflow():
     I = Image.open('../data/brain.png')
@@ -121,10 +122,11 @@ def demo_interactive_maxflow():
     param = (lamda, sigma)
     lab = interactive_maxflow2d(Iq, Prob, Seed, param)
 
+    fig = plt.figure()
     plt.subplot(1,3,1); plt.axis('off'); plt.imshow(I);  plt.title('input image')
     plt.subplot(1,3,2); plt.axis('off'); plt.imshow(fP);   plt.title('initial \n segmentation')
     plt.subplot(1,3,3); plt.axis('off'); plt.imshow(lab); plt.title('CRF result')
-    plt.show()
+    fig.savefig('./demo_result.png')
 
 def demo_maxflow3d():
     img_name   = "../data/2013_12_1_img.nii.gz"
@@ -188,9 +190,9 @@ def test_interactive_max_flow3d():
     print(" 1 -- 2D max flow with interactions")
     print(" 2 -- 3D max flow without interactions")
     print(" 3 -- 3D max flow with interactions")
-    print("please enter the index of an example:")
-    method = input()
-    method = "{0:}".format(method)
+    if len(sys.argv) == 1:
+        raise ValueError("Please, provide an argument.")
+    method = sys.argv[1]
     if(method == '0'):
         demo_maxflow()
     elif(method == '1'):
@@ -200,4 +202,4 @@ def test_interactive_max_flow3d():
     elif(method == '3'):
         test_interactive_max_flow3d()
     else:
-        print("invalid number : {0:}".format(method))
+        raise ValueError("Invalid number: " + method)

setup.py

@@ -25,7 +25,8 @@ def finalize_options(self):
                                'maxflow_python/util.cpp',
                                'dependency/maxflow-v3.0/graph.cpp', 
                                'dependency/maxflow-v3.0/maxflow.cpp',
-                                maxflow_source])
+                                maxflow_source],
+                    py_limited_api=False)
 
 module_name2    = 'denseCRF'
 densecrf_source = "densecrf_python/wrap2D_py{0:}.cpp".format(py_version)
@@ -45,7 +46,8 @@ def finalize_options(self):
                             './dependency/densecrf/src/util.cpp',
                             './dependency/densecrf/external/liblbfgs/lib/lbfgs.c', 
                             densecrf_source,
-                            ])
+                            ],
+                    py_limited_api=False)
 
 module_name3    = 'denseCRF3D'
 densecrf_source = "densecrf_python/wrap3D_py{0:}.cpp".format(py_version)
@@ -65,13 +67,14 @@ def finalize_options(self):
                             './dependency/densecrf3d/src/util.cpp',
                             './dependency/densecrf/external/liblbfgs/lib/lbfgs.c', 
                             densecrf_source,
-                            ])
+                            ],
+                    py_limited_api=False)
 
 # Get the summary
 description = 'An open-source toolkit for conditional random field (CRF) and dense CRF'
 
 # Get the long description
-if(sys.version[0] == '2'):
+if (sys.version[0] == '2'):
     import io
     with io.open('README.md', 'r', encoding='utf-8') as f:
         long_description = f.read()
@@ -92,13 +95,16 @@ def finalize_options(self):
       ext_modules = [module1, module2, module3],
       classifiers=[
             'License :: OSI Approved :: BSD License',
-            'Programming Language :: Python',
-            'Programming Language :: Python :: 2',
-            'Programming Language :: Python :: 3',
+            'Programming Language :: Python :: 3 :: Only',
+            'Programming Language :: Python :: 3.6',
+            'Programming Language :: Python :: 3.7',
+            'Programming Language :: Python :: 3.8',
+            'Programming Language :: Python :: 3.9',
+            'Programming Language :: Python :: 3.10',
       ],
       python_requires = '>=3.6',
       cmdclass={'build_ext': build_ext},)
 
 
-# to build, run python stup.py build or python setup.py build_ext --inplace
+# to build, run python setup.py build or python setup.py build_ext --inplace
 # to install, run python setup.py install