def test_fiducials_3():
"""
Basic fiducials test.
"""
peaks = {
"x": numpy.array([1.0, 2.0, 3.0]),
"y": numpy.array([1.0, 1.0, 1.0])
}
filename = "test_fiducials.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
for i in range(3):
temp = {}
for elt in peaks:
temp[elt] = peaks[elt][i:]
h5.addLocalizations(temp, i)
h5.addMovieInformation(FakeReader(n_frames=4))
# Track fiducials..
fiducials.trackFiducials(h5_name, radius=0.1, reference_frame=2)
# Check.
with saH5Py.SAH5Py(h5_name) as h5:
expected = numpy.array([-1, -1, 0])
for fnum, locs in h5.localizationsIterator(fields=["fiducial_id"]):
assert numpy.allclose(locs["fiducial_id"], expected[fnum:])
def test_fiducials_10():
"""
Test fiducial averaging (preload_all = False).
"""
peaks = {
"x": numpy.array([1.0, 2.0, 3.0]),
"y": numpy.array([1.0, 1.0, 1.0])
}
filename = "test_fiducials.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
for i in range(3):
h5.addLocalizations(peaks, i)
h5.addMovieInformation(FakeReader(n_frames=3))
# Track fiducials..
fiducials.trackFiducials(h5_name, radius=0.1)
# Check
with fiducials.SAH5Fiducials(h5_name) as h5:
[ave, n] = h5.averageFiducials(fields=["y"], preload_all=False)
assert (numpy.allclose(ave["y"], numpy.ones(3)))
def test_fiducials_1():
"""
Basic fiducials test.
"""
peaks = {
"x": numpy.array([1.0, 2.0, 3.0]),
"y": numpy.array([1.0, 1.0, 1.0])
}
filename = "test_fiducials.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
for i in range(3):
h5.addLocalizations(peaks, i)
h5.addMovieInformation(FakeReader(n_frames=3))
# Track fiducials..
fiducials.trackFiducials(h5_name, radius=0.1)
# Check.
with saH5Py.SAH5Py(h5_name) as h5:
for fnum, locs in h5.localizationsIterator(fields=["fiducial_id"]):
assert (numpy.allclose(locs["fiducial_id"], numpy.arange(3)))
def test_fiducials_7():
"""
Iterator test.
"""
peaks = {
"x": numpy.array([1.0, 2.0, 3.0]),
"y": numpy.array([1.0, 1.0, 1.0])
}
filename = "test_fiducials.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
for i in range(3):
temp = {}
for elt in peaks:
temp[elt] = peaks[elt][i:]
h5.addLocalizations(temp, i)
h5.addMovieInformation(FakeReader(n_frames=4))
# Track fiducials..
fiducials.trackFiducials(h5_name, radius=0.1, reference_frame=2)
# Check.
with fiducials.SAH5Fiducials(h5_name) as h5:
for fdcl in h5.fiducialsIterator():
assert (numpy.allclose(fdcl["frame"], numpy.arange(3)))
def test_fiducials_8():
"""
Gap test.
"""
peaks = {
"x": numpy.array([1.0, 2.0, 3.0]),
"y": numpy.array([1.0, 1.0, 1.0])
}
filename = "test_fiducials.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
for i in [0, 1, 3]:
h5.addLocalizations(peaks, i)
h5.addMovieInformation(FakeReader(n_frames=4))
# Track fiducials..
fiducials.trackFiducials(h5_name, radius=0.1, max_gap=1)
# Check.
with fiducials.SAH5Fiducials(h5_name) as h5:
expected = numpy.array([0, 1, 3])
for fdcl in h5.fiducialsIterator():
assert (numpy.allclose(fdcl["frame"], expected))
def test_fiducials_3():
"""
Basic fiducials test.
"""
peaks = {"x" : numpy.array([1.0, 2.0, 3.0]),
"y" : numpy.array([1.0, 1.0, 1.0])}
filename = "test_fiducials.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
for i in range(3):
temp = {}
for elt in peaks:
temp[elt] = peaks[elt][i:]
h5.addLocalizations(temp, i)
h5.addMovieInformation(FakeReader(n_frames = 4))
# Track fiducials..
fiducials.trackFiducials(h5_name, radius = 0.1, reference_frame = 2)
# Check.
with saH5Py.SAH5Py(h5_name) as h5:
expected = numpy.array([-1,-1,0])
for fnum, locs in h5.localizationsIterator(fields = ["fiducial_id"]):
assert numpy.allclose(locs["fiducial_id"], expected[fnum:])
def test_fiducials_4():
"""
Test no localizations in reference frame.
"""
peaks = {
"x": numpy.array([1.0, 2.0, 3.0]),
"y": numpy.array([1.0, 1.0, 1.0])
}
filename = "test_fiducials.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
for i in range(3):
h5.addLocalizations(peaks, i)
h5.addMovieInformation(FakeReader(n_frames=5))
# Track fiducials..
okay = False
try:
fiducials.trackFiducials(h5_name, radius=0.1, reference_frame=3)
except fiducials.FiducialException:
okay = True
assert okay
def test_fiducials_1():
"""
Basic fiducials test.
"""
peaks = {"x" : numpy.array([1.0, 2.0, 3.0]),
"y" : numpy.array([1.0, 1.0, 1.0])}
filename = "test_fiducials.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
for i in range(3):
h5.addLocalizations(peaks, i)
h5.addMovieInformation(FakeReader(n_frames = 3))
# Track fiducials..
fiducials.trackFiducials(h5_name, radius = 0.1)
# Check.
with saH5Py.SAH5Py(h5_name) as h5:
for fnum, locs in h5.localizationsIterator(fields = ["fiducial_id"]):
assert(numpy.allclose(locs["fiducial_id"], numpy.arange(3)))
def test_fiducials_9():
"""
Test fiducial averaging.
"""
peaks = {"x" : numpy.array([1.0, 2.0, 3.0]),
"y" : numpy.array([1.0, 1.0, 1.0])}
filename = "test_fiducials.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
for i in range(3):
h5.addLocalizations(peaks, i)
h5.addMovieInformation(FakeReader(n_frames = 3))
# Track fiducials..
fiducials.trackFiducials(h5_name, radius = 0.1)
# Check
with fiducials.SAH5Fiducials(h5_name) as h5:
[ave, n] = h5.averageFiducials(fields = ["y"])
assert(numpy.allclose(ave["y"], numpy.ones(3)))
def test_fiducials_8():
"""
Gap test.
"""
peaks = {"x" : numpy.array([1.0, 2.0, 3.0]),
"y" : numpy.array([1.0, 1.0, 1.0])}
filename = "test_fiducials.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
for i in [0,1,3]:
h5.addLocalizations(peaks, i)
h5.addMovieInformation(FakeReader(n_frames = 4))
# Track fiducials..
fiducials.trackFiducials(h5_name, radius = 0.1, max_gap = 1)
# Check.
with fiducials.SAH5Fiducials(h5_name) as h5:
expected = numpy.array([0,1,3])
for fdcl in h5.fiducialsIterator():
assert(numpy.allclose(fdcl["frame"], expected))
def test_fiducials_7():
"""
Iterator test.
"""
peaks = {"x" : numpy.array([1.0, 2.0, 3.0]),
"y" : numpy.array([1.0, 1.0, 1.0])}
filename = "test_fiducials.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
for i in range(3):
temp = {}
for elt in peaks:
temp[elt] = peaks[elt][i:]
h5.addLocalizations(temp, i)
h5.addMovieInformation(FakeReader(n_frames = 4))
# Track fiducials..
fiducials.trackFiducials(h5_name, radius = 0.1, reference_frame = 2)
# Check.
with fiducials.SAH5Fiducials(h5_name) as h5:
for fdcl in h5.fiducialsIterator():
assert(numpy.allclose(fdcl["frame"], numpy.arange(3)))
def test_fiducials_4():
"""
Test no localizations in reference frame.
"""
peaks = {"x" : numpy.array([1.0, 2.0, 3.0]),
"y" : numpy.array([1.0, 1.0, 1.0])}
filename = "test_fiducials.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
for i in range(3):
h5.addLocalizations(peaks, i)
h5.addMovieInformation(FakeReader(n_frames = 5))
# Track fiducials..
okay = False
try:
fiducials.trackFiducials(h5_name, radius = 0.1, reference_frame = 3)
except fiducials.FiducialException:
okay = True
assert okay