def test_make_otf(tmp_path):
"""Test that it can make an otf file from a psf."""
dest = str(tmp_path / "otf_test.tif")
result = make_otf(PSF_PATH, dest)
assert Path(result).exists()
# make sure it matches the known OTF
assert np.allclose(imread(result), imread(OTF_PATH), atol=0.05)
def setUp(self):
self.raw = os.path.join(os.path.dirname(__file__), 'test_data',
'im_raw.tif')
self.deskewed = os.path.join(os.path.dirname(__file__), 'test_data',
'im_deskewed.tif')
self.raw = imread(self.raw)
self.deskewed = imread(self.deskewed)
def test_make_otf(self):
"""
Test that it can make an otf file from a psf
"""
result = make_otf(self.psf, self.dest)
self.assertTrue(os.path.isfile(result))
known = imread(self.otf)
# make sure it matches the known OTF
self.assertTrue(np.allclose(imread(result), known))
os.remove(self.dest)
def test_decon_wrapper_with_psf_array(self):
"""
test that we can deconvolve an image
"""
psf = imread(self.psf)
decon_result = decon(self.deskewed, psf, **self.config)
self.assertTrue(np.allclose(decon_result, self.stored_decon))
def test_rotate(self):
"""
test that rotateGPU rotates the image on the Y axis by some angle
"""
rotated = rotateGPU(self.deskewed, 0.3, dxdata=0.1, angle=31.5)
stored_rot = os.path.join(os.path.dirname(__file__), 'test_data',
'im_rotated.tif')
stored_rot = imread(stored_rot)
self.assertTrue(np.allclose(rotated, stored_rot))
def setUp(self):
self.raw = os.path.join(os.path.dirname(__file__), 'test_data',
'im_raw.tif')
self.deskewed = os.path.join(os.path.dirname(__file__), 'test_data',
'im_deskewed.tif')
self.stored_decon = os.path.join(os.path.dirname(__file__),
'test_data', 'im_decon.tif')
self.otf = os.path.join(os.path.dirname(__file__), 'test_data',
'otf.tif')
self.psf = os.path.join(os.path.dirname(__file__), 'test_data',
'psf.tif')
self.raw = imread(self.raw)
self.deskewed = imread(self.deskewed)
self.stored_decon = imread(self.stored_decon)
self.config = {
'dzdata': 0.3,
'deskew': 0,
'n_iters': 10,
'background': 98,
}
def rotated_image():
return imread(str(DATA / "im_rotated.tif"))
def decon_image():
return imread(str(DATA / "im_decon.tif"))
def deskewed_image():
return imread(str(DATA / "im_deskewed.tif"))
def raw_image():
return imread(str(DATA / "im_raw.tif"))
def test_decon_wrapper_with_psf_array(deskewed_image, decon_image, config):
"""test that we can deconvolve an image with psf as array"""
decon_result = decon(deskewed_image, imread(PSF_PATH), **config)
npt.assert_allclose(decon_result, decon_image, atol=ATOL)