Test action

.github/workflows/github-actions-demo.yml

@@ -0,0 +1,25 @@
+name: GitHub Actions Demo
+run-name: ${{ github.actor }} is testing out GitHub Actions 🚀
+on:
+  pull_request:
+    types: [opened, reopened]
+jobs:
+  Explore-GitHub-Actions:
+    runs-on: [self-hosted, macOS, ARM64]
+    defaults:
+     run:
+       shell: zsh {0}
+    steps:
+      #- uses: actions/checkout@v2
+      - name: Activate Conda
+        run: |
+          /Users/spichardo/miniconda3/etc/profile.d/conda.sh
+          conda activate BabelBrain
+      - name: Copy config files
+        run: |
+         cp /Users/spichardo/Public/TempForSim/config.ini Tests/
+      - name: run pytest
+        run: |
+          /Users/spichardo/miniconda3/etc/profile.d/conda.sh
+          conda activate BabelBrain
+          coverage run -m pytest Tests -k 'test_step1_normal[SDR_0p55-CT-H317-Deep_Target-brainsight]' 

Tests/Integration/test_integration_step1.py

@@ -8,7 +8,27 @@
 
 class TestStep1:
 
-    def test_step1_valid_case(self,qtbot,trajectory,transducer,scan_type,dataset,babelbrain_widget,load_files,compare_data,mock_NotifyError,mock_UpdateMask,tmp_path):
+    def test_step1_normal(self,qtbot,babelbrain_widget):
+
+          # Run Step 1
+        babelbrain_widget.testing_error = False
+        babelbrain_widget.Widget.CalculatePlanningMask.click()
+
+        # Wait for step 1 completion before continuing. Test timeouts after 15 min have past
+        qtbot.waitUntil(babelbrain_widget.Widget.tabWidget.isEnabled,timeout=900000)
+
+        # Check if step 1 failed
+        if babelbrain_widget.testing_error == True:
+            pytest.fail(f"Test failed due to error in execution")
+
+
+    def test_step1_valid_case(self,qtbot,trajectory,
+                              transducer,
+                              scan_type,
+                              dataset,
+                              babelbrain_widget,
+                              load_files,
+                              compare_data,mock_NotifyError,mock_UpdateMask,tmp_path):
 
         # Truth folder path
         if scan_type == "NONE":

Tests/Unit/GPU_Functions/test_GPUMedianFilter.py

@@ -1,6 +1,7 @@
 import os
 import sys
-sys.path.append('BabelBrain/GPUMedianFilter')
+sys.path.append('BabelBrain/GPUFunctions/GPUMedianFilter')
+sys.path.append('BabelBrain/GPUFunctions')
 import logging
 
 import pytest
@@ -16,12 +17,8 @@ def test_median_filter(computing_backend,dataset,check_os,get_gpu_device,load_fi
 
      # Initialize GPU Backend
      gpu_device = get_gpu_device()
-     if computing_backend['type'] == 'OpenCL':
-          MedianFilter.InitOpenCL(gpu_device)
-     elif computing_backend['type'] == 'CUDA':
-          MedianFilter.InitCUDA(gpu_device)
-     elif computing_backend['type'] == 'Metal':
-          MedianFilter.InitMetal(gpu_device)
+     MedianFilter.InitResample(DeviceName=gpu_device,GPUBackend=computing_backend['type'])
+
 
      # Load inputs
      input_files = {

Tests/Unit/GPU_Functions/test_GPUResample.py

@@ -1,6 +1,7 @@
 import os
 import sys
-sys.path.append('BabelBrain/GPUResample')
+sys.path.append('BabelBrain/GPUFunctions/GPUResample')
+sys.path.append('BabelBrain/GPUFunctions')
 import logging
 
 import pytest

Tests/Unit/GPU_Functions/test_GPUVoxelize.py

@@ -1,6 +1,7 @@
 import os
 import sys
-sys.path.append('BabelBrain/GPUVoxelize')
+sys.path.append('BabelBrain/GPUFunctions/GPUVoxelize')
+sys.path.append('BabelBrain/GPUFunctions')
 import logging
 
 import pytest
@@ -17,12 +18,7 @@ def test_voxelize(computing_backend,dataset,spatial_step,check_os,get_gpu_device
 
      # Initialize GPU Backend
      gpu_device = get_gpu_device()
-     if computing_backend['type'] == 'OpenCL':
-          Voxelize.InitOpenCL(gpu_device)
-     elif computing_backend['type'] == 'CUDA':
-          Voxelize.InitCUDA(gpu_device)
-     elif computing_backend['type'] == 'Metal':
-          Voxelize.InitMetal(gpu_device)
+     Voxelize.InitVoxelize(DeviceName=gpu_device,GPUBackend=computing_backend['type'])
 
      # Load inputs
      input_files = {

Tests/conftest.py

@@ -29,9 +29,10 @@
 config.read('Tests' + os.sep + 'config.ini')
 test_data_folder = config['Paths']['data_folder_path']
 gpu_device = config['GPU']['device_name']
+print('gpu_device',gpu_device)
 
 # PARAMETERS
-trajectory_type = {
+test_trajectory_type = {
     'brainsight': 0,
     'slicer': 1
 }
@@ -65,9 +66,9 @@
     'yes': 1
 }
 thermal_profiles = {
-    'thermal_profile_1': test_data_folder + 'Thermal_Profiles' + os.sep + 'Profile_1.yaml',
-    'thermal_profile_2': test_data_folder + 'Thermal_Profiles' + os.sep + 'Profile_1.yaml',
-    'thermal_profile_3': test_data_folder + 'Thermal_Profiles' + os.sep + 'Profile_1.yaml'
+    'thermal_profile_1': test_data_folder + 'Profiles' + os.sep + 'Thermal_Profile_1.yaml',
+    'thermal_profile_2': test_data_folder + 'Profiles' + os.sep + 'Thermal_Profile_2.yaml',
+    'thermal_profile_3': test_data_folder + 'Profiles' + os.sep + 'Thermal_Profile_3.yaml'
 }
 transducers = [
     {'name': 'Single', 'dropdown_index': 0, 'diameter': 0}, # EDIT DIAMETER
@@ -352,7 +353,7 @@ def get_freq():
 
     def _get_freq(tx):
         if tx == 'H317':
-            freq = '700'
+            freq = '250'
         elif tx == 'BSonix':
             freq = '650'
         else:
@@ -362,7 +363,10 @@ def _get_freq(tx):
     return _get_freq
 
 @pytest.fixture()
-def babelbrain_widget(qtbot,trajectory,transducer,scan_type,dataset,selfiles_widget,get_freq,tmp_path):
+def babelbrain_widget(qtbot,trajectory,
+                      trajectory_type,
+                      transducer,
+                      scan_type,dataset,selfiles_widget,get_freq,tmp_path):
 
     # Folder paths
     input_folder = dataset['folder_path']
@@ -377,7 +381,7 @@ def babelbrain_widget(qtbot,trajectory,transducer,scan_type,dataset,selfiles_wid
     trajectory_file = trajectory_folder + f"{trajectory}.txt"
 
     # Set SelFiles Parameters
-    selfiles_widget.ui.TrajectoryTypecomboBox.setCurrentIndex(trajectory_type['slicer'])
+    selfiles_widget.ui.TrajectoryTypecomboBox.setCurrentIndex(test_trajectory_type[trajectory_type])
     selfiles_widget.ui.TrajectorylineEdit.setText(trajectory_file)
     selfiles_widget.ui.SimbNIBSTypecomboBox.setCurrentIndex(SimNIBS_type['charm'])
     selfiles_widget.ui.SimbNIBSlineEdit.setText(simNIBS_folder)
@@ -420,9 +424,10 @@ def babelbrain_widget(qtbot,trajectory,transducer,scan_type,dataset,selfiles_wid
         bb_widget.Config['CT_or_ZTE_input'] = os.path.join(tmp_path,os.path.basename(bb_widget.Config['CT_or_ZTE_input']))
 
     # Set Sim Parameters
-    freq = get_freq(transducer)
+    freq = get_freq(transducer['name'])
 
     freq_index = bb_widget.Widget.USMaskkHzDropDown.findText(freq)
+
     bb_widget.Widget.USMaskkHzDropDown.setCurrentIndex(freq_index)
     bb_widget.Widget.USPPWSpinBox.setProperty('UserData',6) # 6 PPW
     if scan_type != 'NONE':
@@ -474,8 +479,13 @@ def pytest_generate_tests(metafunc):
 
     if 'trajectory' in metafunc.fixturenames and 'invalid' in metafunc.function.__name__:
         metafunc.parametrize('trajectory', tuple(invalid_trajectories))
-    elif 'trajectory' in metafunc.fixturenames and 'valid' in metafunc.function.__name__:
+    elif 'trajectory' in metafunc.fixturenames and ('valid' in metafunc.function.__name__ or
+                                                    'normal' in metafunc.function.__name__):
         metafunc.parametrize('trajectory', tuple(valid_trajectories)) 
+
+
+    if 'trajectory_type' in metafunc.fixturenames:
+        metafunc.parametrize('trajectory_type', tuple(test_trajectory_type)) 
 
     if 'computing_backend' in metafunc.fixturenames:
         metafunc.parametrize('computing_backend',tuple(computing_backends),ids=tuple(cb['type'] for cb in computing_backends))