def test_no_search_missing_file_slices():
radius = 30
pxsize = 1e-6
_qpi, path, dout = setup_test_data(radius=radius, pxsize=pxsize)
try:
drymass.extract_roi(path,
dir_out=dout,
size_m=2 * radius * pxsize,
search_enabled=False)
except ValueError:
pass
else:
assert False, "should not be possible to disable search without ROIs"
def test_ret_changed():
radius = 30
pxsize = 1e-6
_qpi, path, dout = setup_test_data(radius=radius, pxsize=pxsize)
_p1, ch1 = drymass.extract_roi(path,
dir_out=dout,
size_m=2 * radius * pxsize,
ret_changed=True)
_p2, ch2 = drymass.extract_roi(path,
dir_out=dout,
size_m=2 * radius * pxsize,
ret_changed=True)
assert ch1, "First call should create data on disk"
assert not ch2, "Second call should reuse data on disk"
def test_bg_corr_mask():
radius = 30
pxsize = 1e-6
size = 200
bg = np.zeros((size, size)) + .1
bg += np.linspace(-.3, .5, size).reshape(-1, 1)
_, path, dout = setup_test_data(radius=radius,
size=size,
pxsize=pxsize,
bg=bg)
qpiref, p2, d2 = setup_test_data(radius=radius,
size=size,
pxsize=pxsize,
bg=None)
bg_pha_kw = {
"fit_offset": "mean",
"fit_profile": "tilt",
"border_perc": 0,
"border_px": 0
}
path_out = drymass.extract_roi(path,
dir_out=dout,
size_m=2 * radius * pxsize,
bg_pha_kw=bg_pha_kw,
bg_pha_mask_radial_clearance=1.1)
with qpimage.QPSeries(h5file=path_out, h5mode="r") as qpso:
assert np.allclose(np.min(qpso[0].pha), 0, atol=4e-9, rtol=0)
assert np.allclose(np.max(qpso[0].pha),
np.max(qpiref.pha),
atol=1.1e-7,
rtol=0)
def test_basic():
radius = 30
pxsize = 1e-6
qpi, path, dout = setup_test_data(radius=radius, pxsize=pxsize)
path_out = drymass.extract_roi(path,
dir_out=dout,
size_m=2 * radius * pxsize)
with qpimage.QPSeries(h5file=path_out, h5mode="r") as qpso:
assert len(qpso) == 1
qpi2 = qpso.get_qpimage(0)
assert qpi != qpi2
assert qpi.shape != qpi2.shape
def test_no_search():
radius = 30
pxsize = 1e-6
identifier = "asdkn179"
_qpi, path, dout = setup_test_data(radius=radius,
pxsize=pxsize,
identifier=identifier)
_p1, rm1 = drymass.extract_roi(path,
dir_out=dout,
size_m=2 * radius * pxsize,
ret_roimgr=True)
_p2, rm2 = drymass.extract_roi(
path,
dir_out=dout,
size_m=2 * radius * pxsize,
search_enabled=False,
ret_roimgr=True,
)
assert rm1.rois == rm2.rois
assert rm1.identifier == identifier
assert rm2.identifier == identifier
def test_recompute_reuse():
cx = 14
cy = 16
radius = 7
size = 30
pxsize = 1e-6
_qpi, path, dout = setup_test_data_roi(num=2,
radius=radius,
pxsize=pxsize,
size=size,
cx=cx,
cy=cy)
# extract ROIs
roikw = {"size_m": 2 * radius * pxsize, "dist_border": 0, "pad_border": 3}
path_rois = drymass.extract_roi(path, dir_out=dout, **roikw)
# perform sphere analysis
ta0 = time.perf_counter()
drymass.analyze_sphere(path_rois,
dir_out=dout,
method="image",
model="projection")
ta1 = time.perf_counter()
# extract ROIs, ignoring first image
drymass.extract_roi(path, dir_out=dout, ignore_data=["1"], **roikw)
# this time it should be very fast
tb0 = time.perf_counter()
_out, changed = drymass.analyze_sphere(path_rois,
dir_out=dout,
method="image",
model="projection",
ret_changed=True)
tb1 = time.perf_counter()
assert changed, "One ROI was removed, thus change"
# there should still be a marging of .6s
assert 10 * (tb1 - tb0) < ta1 - ta0
def test_bg_corr_thresh():
radius = 30
pxsize = 1e-6
bg = .3
qpi, path, dout = setup_test_data(radius=radius, pxsize=pxsize, bg=bg)
bg_pha_kw = {
"fit_offset": "mean",
"fit_profile": "tilt",
"border_perc": 0,
"border_px": 0
}
path_out = drymass.extract_roi(path,
dir_out=dout,
size_m=2 * radius * pxsize,
bg_pha_kw=bg_pha_kw,
bg_pha_bin=bg * 1.1)
with qpimage.QPSeries(h5file=path_out, h5mode="r") as qpso:
assert np.min(qpso[0].pha) == 0
assert np.allclose(np.max(qpso[0].pha), np.max(qpi.pha) - bg)