def test_no_roi_found():
_, path_in, path_out = setup_test_data(radius_px=0)
with pytest.raises(SystemExit) as pytest_wrapped_e:
# catches sys.exit() calls
cli_extract_roi(path=path_in, ret_data=True)
assert pytest_wrapped_e.type == SystemExit
assert pytest_wrapped_e.value.code == 1
def test_exclude_roi_bad():
_, path_in, path_out = setup_test_data(num=2)
cli_extract_roi(path=path_in)
cfg = config.ConfigFile(path_out)
h5data = cli_extract_roi(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data) as qps:
assert len(qps) == 2
# bad image
cfg.set_value(section="roi", key="ignore data", value="3")
try:
cli_extract_roi(path=path_in, ret_data=True)
except ValueError:
pass
else:
assert False
# bad roi
cfg.set_value(section="roi", key="ignore data", value="1.2")
try:
cli_extract_roi(path=path_in, ret_data=True)
except ValueError:
pass
else:
assert False
# bad image and roi
cfg.set_value(section="roi", key="ignore data", value="4.2")
try:
cli_extract_roi(path=path_in, ret_data=True)
except ValueError:
pass
else:
assert False
def test_reuse():
_, path_in, path_out = setup_test_data(num=2)
cfg = config.ConfigFile(path_out)
cfg.set_value(section="meta", key="pixel size um", value=1)
h5data = cli_extract_roi(path=path_in, ret_data=True)
time = h5data.stat().st_mtime
# Do the same thing
cli_extract_roi(path=path_in, ret_data=True)
assert time == h5data.stat().st_mtime
# Change something
cfg.set_value(section="meta", key="pixel size um", value=1.01)
cli_extract_roi(path=path_in, ret_data=True)
assert time != h5data.stat().st_mtime
def test_force_roi():
qpi, path_in, path_out = setup_test_data(num=2)
cfg = config.ConfigFile(path_out)
cfg.set_value(section="meta", key="pixel size um", value=1)
cfg.set_value(section="roi", key="force", value=((10, 160), (24, 178)))
h5data = cli_extract_roi(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data) as qps:
assert qps[0].shape == (150, 154)
assert np.allclose(qpi.pha[10:160, 24:178], qps[0].pha)
assert np.all(qps[0].pha == qps[1].pha)
def test_exclude_roi():
_, path_in, path_out = setup_test_data(num=2)
cli_extract_roi(path=path_in)
cfg = config.ConfigFile(path_out)
h5data = cli_extract_roi(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data) as qps:
assert len(qps) == 2
# remove first image
cfg.set_value(section="roi", key="ignore data", value="1.1")
h5data = cli_extract_roi(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data) as qps:
assert len(qps) == 1
# remove second image
cfg.set_value(section="roi", key="ignore data", value="2")
h5data = cli_extract_roi(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data) as qps:
assert len(qps) == 1
# remove all
cfg.set_value(section="roi", key="ignore data", value=["1", "2"])
h5data = cli_extract_roi(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data) as qps:
assert len(qps) == 0
def test_base():
_, path_in, path_out = setup_test_data(num=2)
h5data = cli_extract_roi(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data, h5mode="r") as qps:
assert len(qps) == 2
# This might fail when the algorithms or default parameters for
# finding ROIs change:
assert qps[0].shape == (139, 139)
# check existence of files
pathtif = path_out / FILE_ROI_DATA_TIF
assert pathtif.exists()
assert pathtif.stat().st_size > 1500
pathsl = path_out / FILE_SLICES
assert pathsl.exists()
assert len(pathsl.read_bytes()) > 100
# setup output directory
path_in, path_out = cli.dialog.main(path)
cfg = path_out / "drymass.cfg"
if cfg.exists():
# cleanup first
cfg.unlink()
# set metadata
cfg = cli.config.ConfigFile(path_out)
cfg.set_value("meta", "medium index", 1.335)
cfg.set_value("meta", "pixel size um", 0.107)
cfg.set_value("meta", "wavelength nm", 633)
# extract ROIs
cli.cli_extract_roi(path=path_in)
# get image 27
# Note: Remove the DHM_HL60_cells.zip_dm folder to reproduce the figure
senpath = path_out / cli.extracting.FILE_SENSOR_WITH_ROI_IMAGE
sentif = imageio.mimread(senpath)[26]
imageio.imsave("_t02_roi_search1.jpg", sentif[..., :3])
# rerun with updated configuration
cfg.set_value("specimen", "size um", 13)
cfg.set_value("roi", "pad border px", 80)
cfg.set_value("roi", "size variation", .2)
cfg.set_value("roi", "exclude overlap px", 100)
cli.cli_extract_roi(path=path_in)
# remove ROI slices
from drymass import cli
import matplotlib.pylab as plt
import qpimage
path = "data/QLSR_PAA_beads_modified.h5"
# setup output directory
path_in, path_out = cli.dialog.main(path)
shutil.rmtree(path_out)
# Select 2nd order polynomial background correction
# -------------------------------------------------
# initial run with standard parameters
h5roi = cli.cli_extract_roi(path=path_in, ret_data=True)
h5sim = cli.cli_analyze_sphere(path=path_in, ret_data=True)
# get qpimage data of phase images with quadratic background
with qpimage.QPSeries(h5file=h5roi, h5mode="r") as qproi, \
qpimage.QPSeries(h5file=h5sim, h5mode="r") as qpsim:
qe1 = [qproi[3].pha - qpsim[3].pha, qproi[4].pha - qpsim[4].pha]
# get configuration handle
cfg = cli.config.ConfigFile(path_out)
kwerr = {
"px_um": cfg["meta"]["pixel size um"],
"imtype": "phase error",
"vmin": -0.5,
"vmax": +0.5,