Merge pull request #191 from JesseMckinzie/featurize_pytests_v2

Add pytests for featurize_directory and featurize_files

.github/workflows/build_and_test_mac.yml

@@ -69,7 +69,7 @@ jobs:
     - name: Install Conda Dependencies
       run: |
         conda install mamba
-        mamba install compilers pytest --file ${{github.workspace}}/ci-utils/envs/conda_cpp.txt --file ${{github.workspace}}/ci-utils/envs/conda_py.txt 
+        mamba install compilers pytest bfio --file ${{github.workspace}}/ci-utils/envs/conda_cpp.txt --file ${{github.workspace}}/ci-utils/envs/conda_py.txt 
 
     - name: Install Nyxus
       working-directory: ${{github.workspace}}

.github/workflows/build_and_test_ubuntu.yml

@@ -68,7 +68,7 @@ jobs:
     - name: Install Conda Dependencies
       run: |
         conda install mamba
-        mamba install compilers=1.1.1 pytest --file ${{github.workspace}}/ci-utils/envs/conda_cpp.txt --file ${{github.workspace}}/ci-utils/envs/conda_py.txt
+        mamba install compilers=1.1.1 pytest bfio --file ${{github.workspace}}/ci-utils/envs/conda_cpp.txt --file ${{github.workspace}}/ci-utils/envs/conda_py.txt
 
     - name: Install Nyxus
       working-directory: ${{github.workspace}}

.github/workflows/build_and_test_windows.yml

@@ -72,7 +72,7 @@ jobs:
       working-directory: ${{github.workspace}}
       run: |
         conda install mamba
-        mamba install pytest --file ./ci-utils/envs/conda_cpp.txt --file ./ci-utils/envs/conda_py.txt
+        mamba install pytest bfio --file ./ci-utils/envs/conda_cpp.txt --file ./ci-utils/envs/conda_py.txt
 
     - name: Install Nyxus
       working-directory: ${{github.workspace}}

.github/workflows/build_wheels.yml

@@ -60,7 +60,7 @@ jobs:
           CIBW_REPAIR_WHEEL_COMMAND_MACOS: DYLD_LIBRARY_PATH=$REPAIR_LIBRARY_PATH delocate-listdeps {wheel} && DYLD_LIBRARY_PATH=$REPAIR_LIBRARY_PATH delocate-wheel --require-archs {delocate_archs} -w {dest_dir} {wheel}
           CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: "delvewheel repair -w {dest_dir} {wheel}"
           CIBW_ARCHS: ${{ matrix.cibw_archs }}
-          CIBW_TEST_REQUIRES: numpy pandas pytest pyarrow
+          CIBW_TEST_REQUIRES: numpy pandas pyarrow pytest bfio
           CIBW_TEST_COMMAND: pytest {project}/tests/python
 
       - name: Upload Artifact

.github/workflows/publish_pypi.yml

@@ -61,7 +61,7 @@ jobs:
           CIBW_REPAIR_WHEEL_COMMAND_MACOS: DYLD_LIBRARY_PATH=$REPAIR_LIBRARY_PATH delocate-listdeps {wheel} && DYLD_LIBRARY_PATH=$REPAIR_LIBRARY_PATH delocate-wheel --require-archs {delocate_archs} -w {dest_dir} {wheel}
           CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: "delvewheel repair -w {dest_dir} {wheel}"
           CIBW_ARCHS: ${{ matrix.cibw_archs }}
-          CIBW_TEST_REQUIRES: numpy pandas pytest pyarrow
+          CIBW_TEST_REQUIRES: numpy pandas pyarrow pytest bfio
           CIBW_TEST_COMMAND: pytest {project}/tests/python
 
       - name: Install Dependencies

setup.py

@@ -109,5 +109,5 @@ def build_extension(self, ext):
     zip_safe=False,
     python_requires=">=3.8",
     install_requires=["numpy", "pandas"],
-    tests_require = ["pyarrow"]
+    tests_require = ["pyarrow", "bfio"]
 )

tests/python/test_nyxus.py

@@ -6,11 +6,14 @@
 import pandas as pd
 import math
 from pathlib import Path
+import pathlib
 from test_data import intens, seg
 import os
 import shutil
 import time
 
+from test_tissuenet_data import tissuenet_int, tissuenet_seg
+
 class TestImport():
     def test_import(self):
         assert nyxus.__name__ == "nyxus"  
@@ -34,8 +37,77 @@ def teardown_class(cls):
                 os.remove('NyxusFeatures.parquet')
             except:
                 print('No .parquet file to delete')
+
+        def test_featurize_all(self):
+            path = str(pathlib.Path(__file__).parent.resolve())
+
+            data_path = path + '/data/'
+
+            nyx = nyxus.Nyxus (["*ALL*"])
+            assert nyx is not None
+
+            directory_features = nyx.featurize_directory(data_path + 'int/', data_path + 'seg/')
+            directory_features.replace([np.inf, -np.inf, np.nan], 0, inplace=True)
+
+            files_features = nyx.featurize_files(
+                [data_path + 'int/p0_y1_r1_c0.ome.tif', data_path + 'int/p0_y1_r1_c1.ome.tif'],
+                [data_path + 'seg/p0_y1_r1_c0.ome.tif', data_path + 'seg/p0_y1_r1_c1.ome.tif'],
+                single_roi=False,
+            )
+
+            files_features.replace([np.inf, -np.inf, np.nan], 0, inplace=True)
+
+            directory_columns = directory_features.columns
+            files_columns = files_features.columns
+
+            assert len(directory_columns) == len(files_columns)
+
+            files_not_equal = []
+
+            for col in directory_columns:
+                directory_list = directory_features[col].tolist()
+                files_list = files_features[col].tolist()
+
+                for directory_val, files_val in zip(directory_list, files_list):
+                    if not directory_val == pytest.approx(files_val, rel=1e-5, abs=1e-5):
+                        files_not_equal.append(col)
+                        break
+
+            assert len(files_not_equal) == 0
+
+        def test_featurize_montage(self):
+
+            path = str(pathlib.Path(__file__).parent.resolve())
+
+            data_path = path + '/data/'
+
+            nyx = nyxus.Nyxus (["*ALL_INTENSITY*"])
+            assert nyx is not None
+
+            montage_features = nyx.featurize(tissuenet_int, tissuenet_seg, intensity_names=['p0_y1_r1_c0.ome.tif', 'p0_y1_r1_c1.ome.tif'], label_names=['p0_y1_r1_c0.ome.tif', 'p0_y1_r1_c1.ome.tif'])
+            directory_features = nyx.featurize_directory(data_path + 'int/', data_path + 'seg/')
+
+            montage_features.replace([np.inf, -np.inf, np.nan], 0, inplace=True)
+            directory_features.replace([np.inf, -np.inf, np.nan], 0, inplace=True)
+
+            directory_columns = directory_features.columns
+            montage_columns = montage_features.columns
+
+            assert len(directory_columns) == len(montage_columns)
+
+            montage_not_equal = []
+
+            for col in directory_columns:
+                directory_list = directory_features[col].tolist()
+                montage_list = montage_features[col].tolist()
+
+                for directory_val, montage_val in zip(directory_list, montage_list):
+                    if not directory_val == pytest.approx(montage_val, rel=1e-4, abs=1e-4): # higher error tolerance for COVERED_IMAGE_INTENSITY_RANGE
+                        montage_not_equal.append(col)
+                        break
+
+            assert len(montage_not_equal) == 0
 
-
         def test_gabor_gpu(self):
             # cpu gabor
             cpu_nyx = nyxus.Nyxus(["GABOR"])
@@ -562,3 +634,4 @@ def test_arrow_ipc_path(self):
             arrow_path = nyx.featurize(intens, seg, output_type="arrowipc")
 
             assert arrow_path == 'NyxusFeatures.arrow'           
+

tests/python/test_tissuenet_data.py

@@ -0,0 +1,20 @@
+import numpy as np
+from bfio import BioReader
+from pathlib import Path
+
+path = str(Path(__file__).parent.resolve())
+
+with BioReader(path + '/data/int/p0_y1_r1_c0.ome.tif') as br:
+    int_p0_y1_r1_c0 = br.read()
+
+with BioReader(path + '/data/int/p0_y1_r1_c1.ome.tif') as br:
+    int_p0_y1_r1_c1 = br.read()
+
+with BioReader(path + '/data/seg/p0_y1_r1_c0.ome.tif') as br:
+    seg_p0_y1_r1_c0 = br.read()
+
+with BioReader(path + '/data/seg/p0_y1_r1_c1.ome.tif') as br:
+    seg_p0_y1_r1_c1 = br.read()
+
+tissuenet_int = np.array([int_p0_y1_r1_c0, int_p0_y1_r1_c1])
+tissuenet_seg = np.array([seg_p0_y1_r1_c0, seg_p0_y1_r1_c1])