Advanced Testing

This guide is for developers who want to run detailed tests on MuscleX using the source repository.

Testing Methodology

Tests reside in musclex/tests/. The module testing framework has two modes:

testrecord: generates expected output and serializes it to Pickle files
testverify: runs the same input again, serializes the output, and compares it to testrecord

Running testrecord

cd musclex/tests/
python test_utils.py testrecord

Pickle files are saved under <module_name>/test_pickles.

Running testverify

python test_utils.py testverify

Temporary results are stored in tmp_verify_<settings> and deleted after testing. Set keeppickles=True to retain them.

Testing Data

Located in musclex/tests/test_images/. Outputs are compared to Pickle files to confirm correctness.

Global Testing Module

Scripts used:

musclex/musclex_tester.sh
musclex/musclex_headless_generator.sh
musclex/musclex_headless_compare.sh

These verify reproducibility and GUI/headless consistency.

Unit Test Suite

Located in musclex/tests/module_test.py.

Run all tests:

python test_utils.py testverify

Test Examples

These tests are run using Python’s unittest module. The configuration dictionaries shown in Python blocks are defined inside the test scripts and do not need to be passed manually. You can execute each test using the accompanying bash command.

Some tests (like testHDFRead, testGPUIntegratePyFAI, and testOpenCLDevice) do not require configuration settings.

Equator Image:

Python test settings:

settingsA = {
  "left_sigmac": 1.0,
  "right_sigmac": 1.0,
  "orientation_model": 0,
  "nPeaks": 2,
  "model": "Gaussian",
  "isSkeletal": True,
  "mask_thres": -1.0,
  "90rotation": False,
  "blank_mask": False
}

Run with:

python musclex_test/tests/test_suite.py MuscleXTest.testEquatorImage

Quadrant Folder:

Python test settings:

settingsQF = {
  'bgsub': 'None',
  'sigmoid': 0.0,
  'no_cache': True,
  'orientation_model': 0
}

Run with:

python musclex_test/tests/test_suite.py MuscleXTest.testQuadrantFolder

Diffraction Centroids:

Python test settings:

settingsDC = {
  'orientation_model': 0,
  '90rotation': False,
  'no_cache': True
}

Run with:

python musclex_test/tests/test_suite.py MuscleXTest.testDiffractionCentroids

Projection Traces:

Python test settings:

settingsPT = {
  'boxes': {'box1': ((200, 800), (500, 600))},
  'bgsubs': {'box1': 0},
  'types': {'box1': 'h'},
  'peaks': {'box1': [100]},
  'bgsub': 'None',
  'sigmoid': 0.0,
  'no_cache': True,
  'orientation_model': 0
}

Run with:

python musclex_test/tests/test_suite.py MuscleXTest.testProjectionTraces

Scanning Diffraction:

Python test settings:

settings = {}

Run with:

python musclex_test/tests/test_suite.py MuscleXTest.testScanningDiffraction

HDF Read:

No settings required.

python musclex_test/tests/test_suite.py MuscleXTest.testHDFRead

pyFAI Integration:

No settings required.

python musclex_test/tests/test_suite.py MuscleXTest.testGPUIntegratePyFAI

GPU Device:

No settings required.

python musclex_test/tests/test_suite.py MuscleXTest.testOpenCLDevice