tests: ensure new array processing results in identical values

docs/README.md

@@ -6,6 +6,7 @@ To install the requirements for building the documentation, run
 
 To compile the documentation, run
 
+    cd docs
     sphinx-build . _build
 
 

docs/requirements.txt

@@ -1,4 +1,3 @@
-sphinx==4.3.0
-sphinxcontrib.bibtex>=2.0
-sphinx_rtd_theme==1.0
-
+sphinx
+sphinxcontrib.bibtex
+sphinx_rtd_theme

examples/requirements.txt

@@ -0,0 +1 @@
+matplotlib

tests/conftest.py

@@ -2,9 +2,11 @@
 import shutil
 import tempfile
 import time
+import numpy as np
 
-import qpretrieve
+import pytest
 
+import qpretrieve
 
 TMPDIR = tempfile.mkdtemp(prefix=time.strftime(
     "qpretrieve_test_%H.%M_"))
@@ -22,3 +24,22 @@ def pytest_configure(config):
     # creating FFTW wisdom. Also, it makes the tests more reproducible
     # by sticking to simple numpy FFTs.
     qpretrieve.fourier.PREFERRED_INTERFACE = "FFTFilterNumpy"
+
+
+@pytest.fixture
+def hologram(size=64):
+    x = np.arange(size).reshape(-1, 1) - size / 2
+    y = np.arange(size).reshape(1, -1) - size / 2
+
+    amp = np.linspace(.9, 1.1, size * size).reshape(size, size)
+    pha = np.linspace(0, 2, size * size).reshape(size, size)
+
+    rad = x ** 2 + y ** 2 > (size / 3) ** 2
+    pha[rad] = 0
+    amp[rad] = 1
+
+    # frequencies must match pixel in Fourier space
+    kx = 2 * np.pi * -.3
+    ky = 2 * np.pi * -.3
+    image = (amp ** 2 + np.sin(kx * x + ky * y + pha) + 1) * 255
+    return image

tests/test_data_input.py

@@ -0,0 +1,46 @@
+import numpy as np
+import pytest
+
+from qpretrieve.data_input import check_data_input_format
+
+
+def test_check_data_input_2d():
+    data = np.zeros(shape=(256, 256))
+
+    data_new, data_format = check_data_input_format(data)
+
+    assert data_new.shape == (1, 256, 256)
+    assert np.array_equal(data_new[0], data)
+    assert data_format == "2d"
+
+
+def test_check_data_input_3d_image_stack():
+    data = np.zeros(shape=(50, 256, 256))
+
+    data_new, data_format = check_data_input_format(data)
+
+    assert data_new.shape == (50, 256, 256)
+    assert np.array_equal(data_new, data)
+    assert data_format == "3d"
+
+
+def test_check_data_input_3d_rgb():
+    data = np.zeros(shape=(256, 256, 3))
+
+    with pytest.warns(UserWarning):
+        data_new, data_format = check_data_input_format(data)
+
+    assert data_new.shape == (1, 256, 256)
+    assert np.array_equal(data_new[0], data[:, :, 0])
+    assert data_format == "rgb"
+
+
+def test_check_data_input_3d_rgba():
+    data = np.zeros(shape=(256, 256, 4))
+
+    with pytest.warns(UserWarning):
+        data_new, data_format = check_data_input_format(data)
+
+    assert data_new.shape == (1, 256, 256)
+    assert np.array_equal(data_new[0], data[:, :, 0])
+    assert data_format == "rgba"

tests/test_fourier_base.py

@@ -136,12 +136,23 @@ def test_scale_to_filter_qlsi():
     }
 
     ifh = interfere.QLSInterferogram(image, **pipeline_kws)
-    ifh.run_pipeline()
+    raw_wavefront = ifh.run_pipeline()
+    assert raw_wavefront.shape == (1, 720, 720)
+    assert ifh.phase.shape == (1, 720, 720)
+    assert ifh.amplitude.shape == (1, 720, 720)
+    assert ifh.field.shape == (1, 720, 720)
 
     ifr = interfere.QLSInterferogram(refer, **pipeline_kws)
     ifr.run_pipeline()
+    assert ifr.phase.shape == (1, 720, 720)
+    assert ifr.amplitude.shape == (1, 720, 720)
+    assert ifr.field.shape == (1, 720, 720)
+
+    ifh_phase = ifh.phase[0]
+    ifr_phase = ifr.phase[0]
+
+    phase = unwrap_phase(ifh_phase - ifr_phase)
 
-    phase = unwrap_phase(ifh.phase - ifr.phase)
     assert phase.shape == (720, 720)
     assert np.allclose(phase.mean(), 0.12434563269684816, atol=1e-6)
 
@@ -152,6 +163,6 @@ def test_scale_to_filter_qlsi():
     ifr.run_pipeline(**pipeline_kws_scale)
     phase_scaled = unwrap_phase(ifh.phase - ifr.phase)
 
-    assert phase_scaled.shape == (126, 126)
+    assert phase_scaled.shape == (1, 126, 126)
 
     assert np.allclose(phase_scaled.mean(), 0.1257080793074251, atol=1e-6)

tests/test_interfere_base.py

@@ -0,0 +1,40 @@
+import pathlib
+import numpy as np
+import pytest
+
+import qpretrieve
+
+data_path = pathlib.Path(__file__).parent / "data"
+
+
+def test_interfere_base_best_interface():
+    edata = np.load(data_path / "hologram_cell.npz")
+
+    holo = qpretrieve.OffAxisHologram(data=edata["data"])
+    assert holo.ff_iface.is_available
+    assert issubclass(holo.ff_iface,
+                      qpretrieve.fourier.base.FFTFilter)
+    assert issubclass(holo.ff_iface,
+                      qpretrieve.fourier.ff_numpy.FFTFilterNumpy)
+
+
+def test_interfere_base_choose_interface():
+    edata = np.load(data_path / "hologram_cell.npz")
+
+    holo = qpretrieve.OffAxisHologram(
+        data=edata["data"],
+        fft_interface=qpretrieve.fourier.FFTFilterNumpy)
+    assert holo.ff_iface.is_available
+    assert issubclass(holo.ff_iface,
+                      qpretrieve.fourier.base.FFTFilter)
+    assert issubclass(holo.ff_iface,
+                      qpretrieve.fourier.ff_numpy.FFTFilterNumpy)
+
+
+def test_interfere_base_bad_interface():
+    edata = np.load(data_path / "hologram_cell.npz")
+
+    with pytest.raises(ValueError):
+        _ = qpretrieve.OffAxisHologram(
+            data=edata["data"],
+            fft_interface="MyReallyCoolFFTInterface")