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remove old tests
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@rpauszek
rpauszek committed Nov 10, 2023
1 parent d98b169 commit e48f385
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229 changes: 0 additions & 229 deletions lumicks/pylake/tests/test_imaging_confocal_old/test_scan.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,126 +10,6 @@
from ..data.mock_confocal import generate_scan


def test_scan_attrs(test_scans):
scan = test_scans["fast Y slow X"]
assert repr(scan) == "Scan(pixels=(4, 5))"

# fmt: off
reference_timestamps = np.array(
[
[20062500000, 20812500000, 22187500000, 23562500000, 24937500000],
[20250000000, 21625000000, 22375000000, 23750000000, 25125000000],
[20437500000, 21812500000, 23187500000, 23937500000, 25312500000],
[20625000000, 22000000000, 23375000000, 24750000000, 25500000000],
]
).T

np.testing.assert_allclose(scan.timestamps, np.transpose(reference_timestamps))
assert scan.num_frames == 1
assert scan.pixels_per_line == 4
assert scan.lines_per_frame == 5
assert len(scan.infowave) == 90
assert scan.get_image("rgb").shape == (4, 5, 3)
assert scan.get_image("red").shape == (4, 5)
assert scan.get_image("blue").shape == (4, 5)
assert scan.get_image("green").shape == (4, 5)

assert scan.fast_axis == "Y"
np.testing.assert_allclose(scan.pixelsize_um, [197 / 1000, 191 / 1000])
np.testing.assert_allclose(scan.center_point_um["x"], 58.075877109272604)
np.testing.assert_allclose(scan.center_point_um["y"], 31.978375270573267)
np.testing.assert_allclose(scan.center_point_um["z"], 0)
np.testing.assert_allclose(scan.size_um, [0.197 * 5, 0.191 * 4])

scan = test_scans["fast Y slow X multiframe"]
reference_timestamps2 = np.zeros((2, 4, 3))
reference_timestamps2[0, :, :] = reference_timestamps.T[:, :3]
reference_timestamps2[1, :, :2] = reference_timestamps.T[:, 3:]

np.testing.assert_allclose(scan.timestamps, reference_timestamps2)
assert scan.num_frames == 2
assert scan.pixels_per_line == 4
assert scan.lines_per_frame == 3
assert len(scan.infowave) == 90
assert scan.get_image("rgb").shape == (2, 4, 3, 3)
assert scan.get_image("red").shape == (2, 4, 3)
assert scan.get_image("blue").shape == (2, 4, 3)
assert scan.get_image("green").shape == (2, 4, 3)
assert scan.fast_axis == "Y"
np.testing.assert_allclose(scan.pixelsize_um, [197 / 1000, 191 / 1000])
np.testing.assert_allclose(scan.center_point_um["x"], 58.075877109272604)
np.testing.assert_allclose(scan.center_point_um["y"], 31.978375270573267)
np.testing.assert_allclose(scan.center_point_um["z"], 0)
np.testing.assert_allclose(scan.size_um, [0.197 * 3, 0.191 * 4])

scan = test_scans["fast X slow Z multiframe"]
reference_timestamps2 = np.zeros((2, 4, 3))
reference_timestamps2[0, :, :] = reference_timestamps.T[:, :3]
reference_timestamps2[1, :, :2] = reference_timestamps.T[:, 3:]
reference_timestamps2 = reference_timestamps2.transpose([0, 2, 1])

np.testing.assert_allclose(scan.timestamps, reference_timestamps2)
assert scan.num_frames == 2
assert scan.pixels_per_line == 4
assert scan.lines_per_frame == 3
assert len(scan.infowave) == 90
assert scan.get_image("rgb").shape == (2, 3, 4, 3)
assert scan.get_image("red").shape == (2, 3, 4)
assert scan.get_image("blue").shape == (2, 3, 4)
assert scan.get_image("green").shape == (2, 3, 4)
assert scan.fast_axis == "X"
np.testing.assert_allclose(scan.pixelsize_um, [191 / 1000, 197 / 1000])
np.testing.assert_allclose(scan.center_point_um["x"], 58.075877109272604)
np.testing.assert_allclose(scan.center_point_um["y"], 31.978375270573267)
np.testing.assert_allclose(scan.center_point_um["z"], 0)
np.testing.assert_allclose(scan.size_um, [0.191 * 4, 0.197 * 3])

scan = test_scans["fast Y slow Z multiframe"]
reference_timestamps2 = np.zeros((2, 4, 3))
reference_timestamps2[0, :, :] = reference_timestamps.T[:, :3]
reference_timestamps2[1, :, :2] = reference_timestamps.T[:, 3:]
reference_timestamps2 = reference_timestamps2.transpose([0, 2, 1])

np.testing.assert_allclose(scan.timestamps, reference_timestamps2)
assert scan.num_frames == 2
assert scan.pixels_per_line == 4
assert scan.lines_per_frame == 3
assert len(scan.infowave) == 90
assert scan.get_image("rgb").shape == (2, 3, 4, 3)
assert scan.get_image("red").shape == (2, 3, 4)
assert scan.get_image("blue").shape == (2, 3, 4)
assert scan.get_image("green").shape == (2, 3, 4)
assert scan.fast_axis == "Y"
np.testing.assert_allclose(scan.pixelsize_um, [191 / 1000, 197 / 1000])
np.testing.assert_allclose(scan.center_point_um["x"], 58.075877109272604)
np.testing.assert_allclose(scan.center_point_um["y"], 31.978375270573267)
np.testing.assert_allclose(scan.center_point_um["z"], 0)
np.testing.assert_allclose(scan.size_um, [0.191 * 4, 0.197 * 3])

scan = test_scans["red channel missing"]
rgb = scan.get_image("rgb")
assert rgb.shape == (4, 5, 3)
assert not np.any(rgb[:, :, 0])
np.testing.assert_equal(scan.get_image("red"), np.zeros((4, 5)))

assert scan.get_image("blue").shape == (4, 5)
assert scan.get_image("green").shape == (4, 5)

scan = test_scans["rb channels missing"]
rgb = scan.get_image("rgb")
assert rgb.shape == (4, 5, 3)
assert not np.any(rgb[:, :, 0])
assert not np.any(rgb[:, :, 2])
np.testing.assert_equal(scan.get_image("red"), np.zeros((4, 5)))
np.testing.assert_equal(scan.get_image("blue"), np.zeros((4, 5)))
assert scan.get_image("green").shape == (4, 5)

scan = test_scans["all channels missing"]
np.testing.assert_equal(scan.get_image("red"), np.zeros((4, 5)))
np.testing.assert_equal(scan.get_image("green"), np.zeros((4, 5)))
np.testing.assert_equal(scan.get_image("blue"), np.zeros((4, 5)))


def test_slicing(test_scans):
scan0 = test_scans["multiframe_poisson"]
assert scan0.num_frames == 10
Expand Down Expand Up @@ -176,22 +56,6 @@ def compare_frames(original_frames, new_scan):
assert scan0.num_frames == 10


def test_damaged_scan(test_scans):
# Assume the user incorrectly exported only a partial scan (62500000 is the time step)
scan = test_scans["truncated_scan"]
with pytest.raises(RuntimeError):
scan.get_image("red").shape

# Test for workaround for a bug in the STED delay mechanism which could result in scan start times ending up
# within the sample time.
scan = test_scans["sted bug"]
middle = test_scans["fast Y slow X"].red_photon_count.timestamps[5]
scan.get_image(
"red"
).shape # should not raise, but change the start appropriately to work around sted bug
np.testing.assert_allclose(scan.start, middle)


def test_plotting(test_scans):
scan = test_scans["fast Y slow X multiframe"]
scan.plot(channel="blue")
Expand Down Expand Up @@ -304,85 +168,6 @@ def test_movie_export(tmpdir_factory, test_scans):
scan.export_video("gray", "dummy.gif") # Gray is not a color!


@pytest.mark.parametrize(
"dim_x, dim_y, line_padding, start, dt, samples_per_pixel",
[
(5, 6, 3, 14, 4, 4),
(3, 4, 60, 1592916040906356300, 12800, 30),
(3, 2, 60, 1592916040906356300, 12800, 3000),
],
)
def test_single_frame_times(dim_x, dim_y, line_padding, start, dt, samples_per_pixel):
img = np.ones((dim_x, dim_y))
scan = generate_scan(
"test",
img,
[1, 1],
start=start,
dt=dt,
samples_per_pixel=samples_per_pixel,
line_padding=line_padding,
)
frame_times = scan.frame_timestamp_ranges()
assert len(frame_times) == 1
assert frame_times[0][0] == start + line_padding * dt
line_time = dt * (img.shape[1] * samples_per_pixel + 2 * line_padding) * img.shape[0]
assert frame_times[0][1] == start + line_time - line_padding * dt

# For the single frame case, there is no dead time, so these are identical
frame_times_inclusive = scan.frame_timestamp_ranges(include_dead_time=True)
assert len(frame_times_inclusive) == 1
assert frame_times_inclusive[0][0] == frame_times[0][0]
assert frame_times_inclusive[0][1] == frame_times[0][1]


@pytest.mark.parametrize(
"dim_x, dim_y, frames, line_padding, start, dt, samples_per_pixel",
[
(5, 6, 3, 3, 14, 4, 4),
(3, 4, 4, 60, 1592916040906356300, 12800, 30),
(3, 2, 3, 60, 1592916040906356300, 12800, 3000),
],
)
def test_multiple_frame_times(dim_x, dim_y, frames, line_padding, start, dt, samples_per_pixel):
img = np.ones((frames, dim_x, dim_y))
scan = generate_scan(
"test",
img,
[1, 1],
start=start,
dt=dt,
samples_per_pixel=samples_per_pixel,
line_padding=line_padding,
)
frame_times = scan.frame_timestamp_ranges()

line_time = dt * (img.shape[2] * samples_per_pixel + 2 * line_padding) * img.shape[1]
assert scan.num_frames == frames
assert len(frame_times) == scan.num_frames
assert frame_times[0][0] == start + line_padding * dt
assert frame_times[0][1] == start + line_time - line_padding * dt
assert frame_times[1][0] == start + line_padding * dt + line_time
assert frame_times[1][1] == start + 2 * line_time - line_padding * dt
assert frame_times[-1][0] == start + line_padding * dt + (len(frame_times) - 1) * line_time
assert frame_times[-1][1] == start + len(frame_times) * line_time - line_padding * dt

def compare_inclusive(frame_times_inclusive):
# Start times should be the same
assert len(frame_times_inclusive) == scan.num_frames
assert frame_times_inclusive[0][0] == frame_times[0][0]
assert frame_times_inclusive[1][0] == frame_times[1][0]
assert frame_times_inclusive[-1][0] == frame_times[-1][0]

assert frame_times_inclusive[0][1] == frame_times[1][0]
assert frame_times_inclusive[1][1] == frame_times[2][0]
assert frame_times_inclusive[-1][1] == frame_times[-1][0] + (
frame_times[1][0] - frame_times[0][0]
)

compare_inclusive(scan.frame_timestamp_ranges(include_dead_time=True))


def test_scan_plot_rgb_absolute_color_adjustment(test_scans):
"""Tests whether we can set an absolute color range for an RGB plot."""
scan = test_scans["fast Y slow X"]
Expand Down Expand Up @@ -465,20 +250,6 @@ def test_plot_single_channel_percentile_color_adjustment(test_scans):
plt.close(fig)


@pytest.mark.parametrize(
"scan, pixel_time",
[
("fast Y slow X", 0.1875),
("fast X slow Z multiframe", 0.1875),
("fast Y slow X multiframe", 0.1875),
("fast Y slow Z multiframe", 0.1875),
("fast Y slow X", 0.1875),
],
)
def test_scan_pixel_time(test_scans, scan, pixel_time):
np.testing.assert_allclose(test_scans[scan].pixel_time_seconds, pixel_time)


@pytest.mark.parametrize(
"x_min, x_max, y_min, y_max",
[
Expand Down

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