def test_sa_h5py_17():
"""
Test that localizations iterator does not skip empty frames (when requested not to).
"""
peaks = {"x" : numpy.zeros(10),
"y" : numpy.ones(10)}
empty = {"x" : numpy.array([]),
"y" : numpy.array([])}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing = False, overwrite = True) as h5:
h5.setMovieInformation(100, 100, 5, "")
h5.addLocalizations(peaks, 0)
h5.addLocalizations(empty, 1)
h5.addLocalizations(peaks, 2)
# Read data.
with saH5Py.SAH5Py(h5_name) as h5:
for i, [fnum, locs] in enumerate(h5.localizationsIterator(skip_empty = False)):
assert(i == fnum)
def test_merge_2():
"""
Test file merging, skipping files with no tracks.
"""
metadata = "<xml><field1><data1>data</data1></field></xml>"
ref_tracks = {"x" : numpy.random.randint(0,10,10),
"y" : numpy.random.randint(0,10,10)}
# Create HDF5 files to merge.
h5_names = []
for i in range(3):
h5_name = storm_analysis.getPathOutputTest("test_merge_f" + str(i) + ".hdf5")
h5_names.append(h5_name)
with saH5Py.SAH5Py(h5_name, is_existing = False, overwrite = True) as h5:
h5.addMetadata(metadata)
h5.setMovieInformation(20,20,1,"")
h5.setPixelSize(100.0)
if(i != 1):
h5.addTracks(ref_tracks)
# Merge.
merge_name = storm_analysis.getPathOutputTest("test_merge.hdf5")
storm_analysis.removeFile(merge_name)
mergeHDF5.mergeHDF5(h5_names, merge_name)
# Check merge.
with saH5Py.SAH5Py(merge_name) as h5:
assert(metadata == h5.getMetadata())
for tracks in h5.tracksIterator():
assert(numpy.allclose(ref_tracks["x"], tracks["x"]))
def test_sa_h5py_9():
"""
Test setting the track id field.
"""
peaks = {"x": numpy.zeros(10), "y": numpy.ones(10)}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Add localizations and track id.
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
h5.addLocalizations(peaks, 1)
h5.addTrackID(numpy.ones(10), 1)
# Check track id.
with saH5Py.SAH5Py(h5_name) as h5:
locs = h5.getLocalizationsInFrame(1)
assert (numpy.allclose(locs["track_id"], numpy.ones(10)))
# Change track id.
with saH5Py.SAH5Py(h5_name) as h5:
h5.addTrackID(numpy.zeros(10), 1)
# Check track id.
with saH5Py.SAH5Py(h5_name) as h5:
locs = h5.getLocalizationsInFrame(1)
assert (numpy.allclose(locs["track_id"], numpy.zeros(10)))
def test_sa_h5py_6():
"""
Test adding tracks.
"""
tracks = {"x": numpy.zeros(10), "y": numpy.ones(10)}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write tracks.
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
h5.addTracks(tracks)
# Read tracks.
with saH5Py.SAH5Py(h5_name) as h5:
assert (h5.getNTracks() == tracks["x"].size)
# Write tracks again, this should overwrite above.
with saH5Py.SAH5Py(h5_name) as h5:
h5.addTracks(tracks)
h5.addTracks(tracks)
# Read tracks.
with saH5Py.SAH5Py(h5_name) as h5:
assert (h5.getNTracks() == 2 * tracks["x"].size)
def test_sa_h5py_7():
"""
Test tracks iterator.
"""
tracks = {"x": numpy.zeros(10), "y": numpy.ones(10)}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# No tracks.
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
pass
with saH5Py.SAH5Py(h5_name) as h5:
for t in h5.tracksIterator():
assert (False) # We should not get here.
# Tracks.
storm_analysis.removeFile(h5_name)
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
h5.addTracks(tracks)
with saH5Py.SAH5Py(h5_name) as h5:
for t in h5.tracksIterator():
assert (numpy.allclose(t["x"], tracks["x"]))
# Only get one field.
for t in h5.tracksIterator(["x"]):
assert (not "y" in t)
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_sa_h5py_4():
"""
Test handling of drift correction.
"""
peaks = {"x": numpy.zeros(10), "y": numpy.ones(10)}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
h5.addLocalizations(peaks, 1)
h5.setDriftCorrection(1, dx=1.0, dy=-1.0)
# Read data.
with saH5Py.SAH5Py(h5_name) as h5:
# not corrected.
locs = h5.getLocalizationsInFrame(1)
assert (numpy.allclose(peaks["x"], locs["x"]))
assert (numpy.allclose(peaks["y"], locs["y"]))
# corrected.
locs = h5.getLocalizationsInFrame(1, drift_corrected=True)
assert (numpy.allclose(peaks["x"] + 1.0, locs["x"]))
assert (numpy.allclose(peaks["y"] - 1.0, locs["y"]))
def test_sa_h5py_2():
"""
Test data round trip.
"""
peaks = {"x": numpy.zeros(10), "y": numpy.ones(10)}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
h5.setMovieInformation(1, 1, 2, "")
h5.addLocalizations(peaks, 1)
h5.addLocalizations(peaks, 1, channel=1)
# Read data.
with saH5Py.SAH5Py(h5_name) as h5:
# Check that frame 0 is empty.
locs = h5.getLocalizationsInFrame(0)
assert (not bool(locs))
# Check frame1.
locs = h5.getLocalizationsInFrame(1)
assert (numpy.allclose(peaks["x"], locs["x"]))
assert (numpy.allclose(peaks["y"], locs["y"]))
assert (numpy.allclose(peaks["x"], locs["c1_x"]))
assert (numpy.allclose(peaks["y"], locs["c1_y"]))
# Check getting a specific field.
locs = h5.getLocalizationsInFrame(1, fields=["x"])
assert ("x" in locs)
assert (not "y" in locs)
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_cl_sa_h5py_2():
"""
Test basic cluster file mechanics (using tracks).
"""
tracks = {
"x": numpy.arange(11, dtype=numpy.float),
"y": numpy.arange(11, dtype=numpy.float)
}
filename = "test_clusters_sa_h5py.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write track data.
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
h5.setMovieInformation(1, 1, 2, "")
h5.addTracks(tracks)
# Write clustering data for tracks.
cluster_id = numpy.remainder(numpy.arange(11), 3)
cluster_data = {
"track_id": numpy.zeros(11, dtype=numpy.int),
"loc_id": numpy.arange(11)
}
cl_size = [0, 4, 4, 3]
with clSAH5Py.SAH5Clusters(h5_name) as cl_h5:
cl_h5.addClusters(cluster_id, cluster_data)
assert (cl_h5.getNClusters() == (len(cl_size) - 1))
for index, cluster in cl_h5.clustersIterator(skip_unclustered=False):
for field in cluster:
assert (cluster[field].size == cl_size[index])
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_cl_sa_h5py_6():
"""
Test getting all of the tracks for clustering.
"""
tracks = {
"category": numpy.arange(4, dtype=numpy.int32),
"x": numpy.arange(4, dtype=numpy.float),
"y": numpy.arange(4, dtype=numpy.float),
"z": numpy.arange(4, dtype=numpy.float)
}
filename = "test_clusters_sa_h5py.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write tracks data.
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
h5.setMovieInformation(1, 1, 2, "")
h5.setPixelSize(100.0)
h5.addTracks(tracks)
h5.addTracks(tracks)
# Test getting all the tracking data.
with clSAH5Py.SAH5Clusters(h5_name) as cl_h5:
[x, y, z, c, cl_dict] = cl_h5.getDataForClustering()
assert (numpy.allclose(x, cl_dict['loc_id']))
assert (numpy.allclose(y, cl_dict['loc_id']))
assert (numpy.allclose(z, cl_dict['loc_id']))
assert (numpy.allclose(c, cl_dict['loc_id']))
assert (numpy.allclose(cl_dict['track_id'],
numpy.array([0, 0, 0, 0, 1, 1, 1, 1])))
def test_cl_sa_h5py_5():
"""
Test getting all of the localizations for clustering.
"""
locs = {
"category": numpy.arange(4, dtype=numpy.int32),
"x": numpy.arange(4, dtype=numpy.float),
"y": numpy.arange(4, dtype=numpy.float)
}
filename = "test_clusters_sa_h5py.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write localization data.
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
h5.setMovieInformation(1, 1, 5, "")
h5.setPixelSize(100.0)
h5.addLocalizations(locs, 1)
h5.addLocalizations(locs, 3)
# Test getting all the localization data.
with clSAH5Py.SAH5Clusters(h5_name) as cl_h5:
[x, y, z, c, cl_dict] = cl_h5.getDataForClustering()
assert (numpy.allclose(x, cl_dict['loc_id']))
assert (numpy.allclose(y, cl_dict['loc_id']))
assert (numpy.allclose(z, numpy.zeros(x.size)))
assert (numpy.allclose(c, cl_dict['loc_id']))
assert (numpy.allclose(cl_dict['frame'],
numpy.array([1, 1, 1, 1, 3, 3, 3, 3])))
def test_cl_sa_h5py_4():
"""
Test cluster info string round trip.
"""
locs = {
"x": numpy.arange(10, dtype=numpy.float),
"y": numpy.arange(10, dtype=numpy.float)
}
filename = "test_clusters_sa_h5py.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write localization data.
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
h5.setMovieInformation(1, 1, 2, "")
h5.addLocalizations(locs, 1)
# Write clustering data for localizations.
cluster_id = numpy.remainder(numpy.arange(10), 3)
cluster_data = {
"frame": numpy.ones(10, dtype=numpy.int),
"loc_id": numpy.arange(10)
}
info_string = "dbscan,eps,10.0,mc,5"
with clSAH5Py.SAH5Clusters(h5_name) as cl_h5:
cl_h5.addClusters(cluster_id, cluster_data)
cl_h5.setClusteringInfo(info_string)
assert (cl_h5.getClusteringInfo() == info_string)
def test_sa_h5py_10():
"""
Test 'is_existing' and 'overwrite' parameters.
"""
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Test failure on trying to open a file that does not exist.
try:
with saH5Py.SAH5Py(h5_name) as h5:
pass
except saH5Py.SAH5PyException:
pass
else:
assert (False)
# Test failure on trying to overwrite a file that does exist.
# Create the file.
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
pass
# Test that we cannot overwrite it.
try:
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
pass
except saH5Py.SAH5PyException:
pass
else:
assert (False)
# Test that we can overwrite it.
with saH5Py.SAH5Py(h5_name, is_existing=False, overwrite=True) as h5:
pass
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_sa_h5py_12():
"""
Test handling of multiple channels.
"""
peaks = {"x": numpy.zeros(3), "y": numpy.ones(3)}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
h5.setMovieInformation(1, 1, 2, "")
h5.addLocalizations(peaks, 1)
peaks["x"] += 1
peaks["y"] += 1
h5.addLocalizations(peaks, 1, channel=1)
peaks["x"] += 1
peaks["y"] += 1
h5.addLocalizations(peaks, 1, channel=2)
# Read data.
with saH5Py.SAH5Py(h5_name) as h5:
# Check getting number of channels.
assert (h5.getNChannels() == 3)
for [fnum, locs] in h5.localizationsIterator():
for i, elt in enumerate(h5.splitByChannel(locs)):
assert (numpy.allclose(elt["x"], i * numpy.ones(3)))
assert (numpy.allclose(elt["y"], i * numpy.ones(3) + 1.0))
def test_sa_h5py_2():
"""
Test data round trip.
"""
peaks = {"x" : numpy.zeros(10),
"y" : numpy.ones(10)}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
h5.setMovieInformation(1,1,2,"")
h5.addLocalizations(peaks, 1)
h5.addLocalizations(peaks, 1, channel = 1)
# Read data.
with saH5Py.SAH5Py(h5_name) as h5:
# Check that frame 0 is empty.
locs = h5.getLocalizationsInFrame(0)
assert(not bool(locs))
# Check frame1.
locs = h5.getLocalizationsInFrame(1)
assert(numpy.allclose(peaks["x"], locs["x"]))
assert(numpy.allclose(peaks["y"], locs["y"]))
assert(numpy.allclose(peaks["x"], locs["c1_x"]))
assert(numpy.allclose(peaks["y"], locs["c1_y"]))
# Check getting a specific field.
locs = h5.getLocalizationsInFrame(1, fields = ["x"])
assert("x" in locs)
assert(not "y" in locs)
def test_sa_h5py_3():
"""
Test getting data from multiple frames.
"""
peaks = {"x": numpy.zeros(10), "y": numpy.ones(10)}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
fr = FakeReader()
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
h5.addMovieInformation(fr)
for i in range(fr.getMovieL()):
h5.addLocalizations(peaks, i)
# Read data.
with saH5Py.SAH5Py(h5_name) as h5:
# Check localizations in first 5 frames.
locs = h5.getLocalizationsInFrameRange(0, 5)
assert (locs["x"].size == 50)
# Get all the localizations.
locs = h5.getLocalizations()
assert (locs["x"].size == (10.0 * fr.getMovieL()))
def test_sa_h5py_12():
"""
Test handling of multiple channels.
"""
peaks = {"x" : numpy.zeros(3),
"y" : numpy.ones(3)}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
h5.setMovieInformation(1,1,2,"")
h5.addLocalizations(peaks, 1)
peaks["x"] += 1
peaks["y"] += 1
h5.addLocalizations(peaks, 1, channel = 1)
peaks["x"] += 1
peaks["y"] += 1
h5.addLocalizations(peaks, 1, channel = 2)
# Read data.
with saH5Py.SAH5Py(h5_name) as h5:
# Check getting number of channels.
assert(h5.getNChannels() == 3)
for [fnum, locs] in h5.localizationsIterator():
for i, elt in enumerate(h5.splitByChannel(locs)):
assert(numpy.allclose(elt["x"], i * numpy.ones(3)))
assert(numpy.allclose(elt["y"], i * numpy.ones(3) + 1.0))
def test_sa_h5py_16():
"""
Test that localizations iterator skips empty frames.
"""
peaks = {"x" : numpy.zeros(10),
"y" : numpy.ones(10)}
empty = {"x" : numpy.array([]),
"y" : numpy.array([])}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing = False, overwrite = True) as h5:
h5.setMovieInformation(100, 100, 5, "")
h5.addLocalizations(peaks, 0)
h5.addLocalizations(empty, 1)
h5.addLocalizations(peaks, 2)
# Read data.
with saH5Py.SAH5Py(h5_name) as h5:
for fnum, locs in h5.localizationsIterator():
assert(fnum != 1)
def test_sa_h5py_10():
"""
Test 'is_existing' and 'overwrite' parameters.
"""
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Test failure on trying to open a file that does not exist.
try:
with saH5Py.SAH5Py(h5_name) as h5:
pass
except saH5Py.SAH5PyException:
pass
else:
assert(False)
# Test failure on trying to overwrite a file that does exist.
# Create the file.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
pass
# Test that we cannot overwrite it.
try:
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
pass
except saH5Py.SAH5PyException:
pass
else:
assert(False)
# Test that we can overwrite it.
with saH5Py.SAH5Py(h5_name, is_existing = False, overwrite = True) as h5:
pass
def test_sa_h5py_11():
"""
Test hasLocalizationField() and hasTracksField()
"""
peaks = {"x" : numpy.zeros(10),
"y" : numpy.ones(10)}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
h5.setMovieInformation(256, 256, 10, "XYZZY")
h5.addLocalizations(peaks, 1)
h5.addTracks(peaks)
# Check.
with saH5Py.SAH5Py(h5_name) as h5:
assert(h5.hasLocalizationsField("x"))
assert(not h5.hasLocalizationsField("x1"))
assert(h5.hasTracksField("x"))
assert(not h5.hasTracksField("x1"))
def test_sa_h5py_9():
"""
Test setting the track id field.
"""
peaks = {"x" : numpy.zeros(10),
"y" : numpy.ones(10)}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Add localizations and track id.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
h5.addLocalizations(peaks, 1)
h5.addTrackID(numpy.ones(10), 1)
# Check track id.
with saH5Py.SAH5Py(h5_name) as h5:
locs = h5.getLocalizationsInFrame(1)
assert(numpy.allclose(locs["track_id"], numpy.ones(10)))
# Change track id.
with saH5Py.SAH5Py(h5_name) as h5:
h5.addTrackID(numpy.zeros(10), 1)
# Check track id.
with saH5Py.SAH5Py(h5_name) as h5:
locs = h5.getLocalizationsInFrame(1)
assert(numpy.allclose(locs["track_id"], numpy.zeros(10)))
def test_sa_h5py_7():
"""
Test tracks iterator.
"""
tracks = {"x" : numpy.zeros(10),
"y" : numpy.ones(10)}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# No tracks.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
pass
with saH5Py.SAH5Py(h5_name) as h5:
for t in h5.tracksIterator():
assert(False) # We should not get here.
# Tracks.
storm_analysis.removeFile(h5_name)
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
h5.addTracks(tracks)
with saH5Py.SAH5Py(h5_name) as h5:
for t in h5.tracksIterator():
assert(numpy.allclose(t["x"], tracks["x"]))
# Only get one field.
for t in h5.tracksIterator(["x"]):
assert(not "y" in t)
def test_sa_h5py_6():
"""
Test adding tracks.
"""
tracks = {"x" : numpy.zeros(10),
"y" : numpy.ones(10)}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write tracks.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
h5.addTracks(tracks)
# Read tracks.
with saH5Py.SAH5Py(h5_name) as h5:
assert(h5.getNTracks() == tracks["x"].size)
# Write tracks again, this should overwrite above.
with saH5Py.SAH5Py(h5_name) as h5:
h5.addTracks(tracks)
h5.addTracks(tracks)
# Read tracks.
with saH5Py.SAH5Py(h5_name) as h5:
assert(h5.getNTracks() == 2*tracks["x"].size)
def test_cl_sa_h5py_2():
"""
Test basic cluster file mechanics (using tracks).
"""
tracks = {"x" : numpy.arange(11, dtype = numpy.float),
"y" : numpy.arange(11, dtype = numpy.float)}
filename = "test_clusters_sa_h5py.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write track data.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
h5.setMovieInformation(1,1,2,"")
h5.addTracks(tracks)
# Write clustering data for tracks.
cluster_id = numpy.remainder(numpy.arange(11), 3)
cluster_data = {"track_id" : numpy.zeros(11, dtype = numpy.int),
"loc_id" : numpy.arange(11)}
cl_size = [0, 4, 4, 3]
with clSAH5Py.SAH5Clusters(h5_name) as cl_h5:
cl_h5.addClusters(cluster_id, cluster_data)
assert(cl_h5.getNClusters() == (len(cl_size) - 1))
for index, cluster in cl_h5.clustersIterator(skip_unclustered = False):
for field in cluster:
assert(cluster[field].size == cl_size[index])
def test_sa_h5py_3():
"""
Test getting data from multiple frames.
"""
peaks = {"x" : numpy.zeros(10),
"y" : numpy.ones(10)}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
fr = FakeReader()
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
h5.addMovieInformation(fr)
for i in range(fr.getMovieL()):
h5.addLocalizations(peaks, i)
# Read data.
with saH5Py.SAH5Py(h5_name) as h5:
# Check localizations in first 5 frames.
locs = h5.getLocalizationsInFrameRange(0,5)
assert(locs["x"].size == 50)
# Get all the localizations.
locs = h5.getLocalizations()
assert(locs["x"].size == (10.0 * fr.getMovieL()))
def test_cl_sa_h5py_5():
"""
Test getting all of the localizations for clustering.
"""
locs = {"category" : numpy.arange(4, dtype = numpy.int32),
"x" : numpy.arange(4, dtype = numpy.float),
"y" : numpy.arange(4, dtype = numpy.float)}
filename = "test_clusters_sa_h5py.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write localization data.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
h5.setMovieInformation(1,1,5,"")
h5.setPixelSize(100.0)
h5.addLocalizations(locs, 1)
h5.addLocalizations(locs, 3)
# Test getting all the localization data.
with clSAH5Py.SAH5Clusters(h5_name) as cl_h5:
[x, y, z, c, cl_dict] = cl_h5.getDataForClustering()
assert(numpy.allclose(x, cl_dict['loc_id']))
assert(numpy.allclose(y, cl_dict['loc_id']))
assert(numpy.allclose(z, numpy.zeros(x.size)))
assert(numpy.allclose(c, cl_dict['loc_id']))
assert(numpy.allclose(cl_dict['frame'], numpy.array([1,1,1,1,3,3,3,3])))
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_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_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_sa_h5py_4():
"""
Test handling of drift correction.
"""
peaks = {"x" : numpy.zeros(10),
"y" : numpy.ones(10)}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
h5.addLocalizations(peaks, 1)
h5.setDriftCorrection(1, dx = 1.0, dy = -1.0)
# Read data.
with saH5Py.SAH5Py(h5_name) as h5:
# not corrected.
locs = h5.getLocalizationsInFrame(1)
assert(numpy.allclose(peaks["x"], locs["x"]))
assert(numpy.allclose(peaks["y"], locs["y"]))
# corrected.
locs = h5.getLocalizationsInFrame(1, drift_corrected = True)
assert(numpy.allclose(peaks["x"] + 1.0, locs["x"]))
assert(numpy.allclose(peaks["y"] - 1.0, locs["y"]))
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_hdf5_to_bin_2():
"""
Test tracks conversion.
"""
peaks = {"x" : numpy.zeros(10),
"y" : numpy.ones(10)}
h5_name = storm_analysis.getPathOutputTest("test_sa_hdf5.hdf5")
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
h5.addMetadata("<settings/>")
h5.setMovieInformation(256, 256, 10, "XYZZY")
h5.setPixelSize(100.0)
h5.addTracks(peaks)
# Convert.
i3_name = storm_analysis.getPathOutputTest("test_mlist.bin")
storm_analysis.removeFile(i3_name)
hdf5ToBin.hdf5ToBin(h5_name, i3_name)
# Load Insight3 file and check values.
i3_data = readinsight3.loadI3File(i3_name, verbose = False)
assert(numpy.allclose(peaks["x"], i3_data['x'] - 1.0))
assert(numpy.allclose(peaks["y"], i3_data['y'] - 1.0))
assert(numpy.allclose(i3_data['fr'], numpy.ones(10)))
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_tracker_5():
"""
Test that nearest track is assigned to the nearest object.
"""
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
peaks = {"x" : numpy.array([1.0, 2.0, 3.0]),
"y" : numpy.array([1.0, 1.0, 1.0]),
"sum" : numpy.array([4.0, 4.0, 4.0])}
h5.addLocalizations(peaks, 0)
peaks = {"x" : numpy.array([2.0]),
"y" : numpy.array([1.0]),
"sum" : numpy.array([4.0])}
h5.addLocalizations(peaks, 1)
h5.addMovieInformation(FakeReader(n_frames = 2))
# Track.
tracker.tracker(h5_name, radius = 1.1)
# Tracking.
with saH5Py.SAH5Py(h5_name) as h5:
assert(h5.getNTracks() == 3)
for t in h5.tracksIterator():
assert(numpy.allclose(numpy.array([1,3,2]), t["x"]))
assert(numpy.allclose(numpy.array([0,2,1]), t["track_id"]))
assert(numpy.allclose(numpy.array([1,1,2]), t["track_length"]))
def test_cl_sa_h5py_6():
"""
Test getting all of the tracks for clustering.
"""
tracks = {"category" : numpy.arange(4, dtype = numpy.int32),
"x" : numpy.arange(4, dtype = numpy.float),
"y" : numpy.arange(4, dtype = numpy.float),
"z" : numpy.arange(4, dtype = numpy.float)}
filename = "test_clusters_sa_h5py.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write tracks data.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
h5.setMovieInformation(1,1,2,"")
h5.setPixelSize(100.0)
h5.addTracks(tracks)
h5.addTracks(tracks)
# Test getting all the tracking data.
with clSAH5Py.SAH5Clusters(h5_name) as cl_h5:
[x, y, z, c, cl_dict] = cl_h5.getDataForClustering()
assert(numpy.allclose(x, cl_dict['loc_id']))
assert(numpy.allclose(y, cl_dict['loc_id']))
assert(numpy.allclose(z, cl_dict['loc_id']))
assert(numpy.allclose(c, cl_dict['loc_id']))
assert(numpy.allclose(cl_dict['track_id'], numpy.array([0,0,0,0,1,1,1,1])))
def test_tracker_6():
"""
Test max_gap parameter.
"""
peaks = {"x" : numpy.array([1.0, 2.0, 3.0]),
"y" : numpy.array([1.0, 1.0, 1.0]),
"sum" : numpy.array([4.0, 4.0, 4.0])}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
h5.addLocalizations(peaks, 0)
h5.addLocalizations(peaks, 2)
h5.addMovieInformation(FakeReader(n_frames = 3))
# Track.
tracker.tracker(h5_name, radius = 0.1)
# Tracking.
with saH5Py.SAH5Py(h5_name) as h5:
assert(h5.getNTracks() == 6)
for t in h5.tracksIterator():
assert(numpy.allclose(t["track_length"], numpy.ones(6)))
# Redo the tracking allowing single frame gaps.
tracker.tracker(h5_name, max_gap = 1, radius = 0.1)
with saH5Py.SAH5Py(h5_name) as h5:
assert(h5.getNTracks() == 3)
for t in h5.tracksIterator():
assert(numpy.allclose(t["track_length"], 2.0*numpy.ones(3)))
def test_tracker_8():
"""
Test tracking over an empty frame.
"""
peaks = {"x" : numpy.array([1.0, 2.0, 3.0]),
"y" : numpy.array([1.0, 1.0, 1.0]),
"sum" : numpy.array([4.0, 4.0, 4.0])}
empty = {"x" : numpy.array([]),
"y" : numpy.array([]),
"sum" : numpy.array([])}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
h5.addLocalizations(peaks, 0)
h5.addLocalizations(empty, 1)
h5.addLocalizations(peaks, 2)
h5.addMovieInformation(FakeReader(n_frames = 3))
# Track.
tracker.tracker(h5_name, descriptor = "111", radius = 0.1)
# Tracking.
with saH5Py.SAH5Py(h5_name) as h5:
assert(h5.getNTracks() == 6)
for t in h5.tracksIterator():
assert(numpy.allclose(numpy.ones(6), t["track_length"]))
def test_cl_sa_h5py_4():
"""
Test cluster info string round trip.
"""
locs = {"x" : numpy.arange(10, dtype = numpy.float),
"y" : numpy.arange(10, dtype = numpy.float)}
filename = "test_clusters_sa_h5py.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write localization data.
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
h5.setMovieInformation(1,1,2,"")
h5.addLocalizations(locs, 1)
# Write clustering data for localizations.
cluster_id = numpy.remainder(numpy.arange(10), 3)
cluster_data = {"frame" : numpy.ones(10, dtype = numpy.int),
"loc_id" : numpy.arange(10)}
info_string = "dbscan,eps,10.0,mc,5"
with clSAH5Py.SAH5Clusters(h5_name) as cl_h5:
cl_h5.addClusters(cluster_id, cluster_data)
cl_h5.setClusteringInfo(info_string)
assert (cl_h5.getClusteringInfo() == info_string)
def test_sa_h5py_19():
"""
Test getting specific fields.
"""
peaks = {"bar" : numpy.zeros(10),
"x" : numpy.zeros(10),
"y" : numpy.zeros(10)}
filename = "test_sa_hdf5.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write data.
with saH5Py.SAH5Py(h5_name, is_existing = False, overwrite = True) as h5:
h5.setMovieInformation(100, 100, 1, "")
h5.addLocalizations(peaks, 0)
# Get data.
with saH5Py.SAH5Py(h5_name) as h5:
locs = h5.getLocalizationsInFrame(0)
for elt in ["bar", "x", "y"]:
assert elt in locs
locs = h5.getLocalizationsInFrame(0, fields = ["x"])
assert "x" in locs
for elt in ["bar", "y"]:
assert not elt in locs
def _test_psf_to_spline_2D():
psf = storm_analysis.getPathOutputTest("test_spliner_psf_2d.psf")
spline = storm_analysis.getPathOutputTest("test_spliner_psf_2d.spline")
storm_analysis.removeFile(spline)
from storm_analysis.spliner.psf_to_spline import psfToSpline
psfToSpline(psf, spline, 7)
def test_setup_A_matrix():
# Test setupAMatrix.
a_matrix_file = storm_analysis.getPathOutputTest("test_l1h")
storm_analysis.removeFile(a_matrix_file)
from storm_analysis.L1H.setup_A_matrix import setupAMatrix
setupAMatrix("theoritical", a_matrix_file, 1.0, False)
def test_setup_A_matrix():
# Test setupAMatrix.
a_matrix_file = storm_analysis.getPathOutputTest("test_l1h")
storm_analysis.removeFile(a_matrix_file)
from storm_analysis.L1H.setup_A_matrix import setupAMatrix
setupAMatrix("theoritical", a_matrix_file, 1.0, False)
def test_measure_psf():
movie = storm_analysis.getData("test/data/test_spliner.dax")
mlist = storm_analysis.getData("test/data/test_spliner_ref.hdf5")
psf = storm_analysis.getPathOutputTest("test_spliner_psf.psf")
storm_analysis.removeFile(psf)
from storm_analysis.spliner.measure_psf import measurePSF
measurePSF(movie, "", mlist, psf)
def test_3ddao_2d_fixed_non_square():
movie_name = storm_analysis.getData("test/data/test_300x200.dax")
settings = storm_analysis.getData("test/data/test_3d_2d_fixed.xml")
mlist = storm_analysis.getPathOutputTest("test_3d_2d_300x200.bin")
storm_analysis.removeFile(mlist)
from storm_analysis.daostorm_3d.mufit_analysis import analyze
analyze(movie_name, mlist, settings)
def test_homotopy_psf():
movie = storm_analysis.getData("test/data/test.dax")
mlist = storm_analysis.getData("test/data/test_olist.bin")
psf = storm_analysis.getPathOutputTest("l1h_psf.psf")
storm_analysis.removeFile(psf)
from storm_analysis.L1H.homotopy_psf import homotopyPSF
homotopyPSF(movie, mlist, psf)
def test_3ddao_Z():
movie_name = storm_analysis.getData("test/data/test.dax")
settings = storm_analysis.getData("test/data/test_3d_Z.xml")
mlist = storm_analysis.getPathOutputTest("test_3d_Z.bin")
storm_analysis.removeFile(mlist)
from storm_analysis.daostorm_3d.mufit_analysis import analyze
analyze(movie_name, mlist, settings)
def test_measure_psf_2D():
movie = storm_analysis.getData("test/data/test.dax")
mlist = storm_analysis.getData("test/data/test_ref.hdf5")
psf = storm_analysis.getPathOutputTest("test_spliner_psf_2d.psf")
storm_analysis.removeFile(psf)
from storm_analysis.spliner.measure_psf import measurePSF
measurePSF(movie, "", mlist, psf, want2d=True, aoi_size=5)
def test_homotopy_psf():
movie = storm_analysis.getData("test/data/test.dax")
mlist = storm_analysis.getData("test/data/test_olist.bin")
psf = storm_analysis.getPathOutputTest("l1h_psf.psf")
storm_analysis.removeFile(psf)
from storm_analysis.L1H.homotopy_psf import homotopyPSF
homotopyPSF(movie, mlist, psf)
def create2DSpline():
movie = storm_analysis.getData("test/data/test.dax")
mlist = storm_analysis.getData("test/data/test_ref.hdf5")
psf = storm_analysis.getPathOutputTest("test_spliner_psf_2d.psf")
spline = storm_analysis.getPathOutputTest("test_spliner_psf_2d.spline")
storm_analysis.removeFile(psf)
storm_analysis.removeFile(spline)
measurePSF.measurePSF(movie, "", mlist, psf, want2d=True, aoi_size=5)
psfToSpline.psfToSpline(psf, spline, 4)
def test_voronoi_clustering_1():
numpy.random.seed(1)
filename = "test_clustering_sa_h5py.hdf5"
h5_name = storm_analysis.getPathOutputTest(filename)
storm_analysis.removeFile(h5_name)
# Write tracks data.
category = numpy.zeros(10, dtype=numpy.int32)
x = 10.0 * numpy.arange(10)
y = 10.0 * numpy.arange(10)
z = numpy.zeros(10)
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
h5.setMovieInformation(1, 1, 2, "")
h5.setPixelSize(1.0)
for i in range(100):
tracks = {
"category": category,
"x": x + numpy.random.normal(scale=0.1, size=10),
"y": y + numpy.random.normal(scale=0.1, size=10),
"z": z + numpy.random.normal(scale=0.1, size=10)
}
h5.addTracks(tracks)
# Cluster data with voronoi.
voronoiAnalysis.findClusters(h5_name, 0.1, 10, verbose=False)
# Check clustering results.
with clSAH5Py.SAH5Clusters(h5_name) as cl_h5:
assert (cl_h5.getNClusters() == 10)
for index, cluster in cl_h5.clustersIterator(skip_unclustered=True,
fields=["x", "y", "z"]):
for elt in ['x', 'y', 'z']:
dev = numpy.std(cluster[elt])
assert (dev > 0.07)
assert (dev < 0.12)
# Calculate common cluster statistics.
stats_name = dbscanAnalysis.clusterStats(h5_name, 50, verbose=False)
# Check statistics.
stats = numpy.loadtxt(stats_name, skiprows=1)
index = numpy.argsort(stats[:, 3])
assert (stats.shape[0] == 10)
assert (numpy.allclose(stats[:, 0], numpy.arange(10) + 1))
assert (numpy.allclose(stats[:, 1], numpy.zeros(10)))
assert (numpy.count_nonzero(
numpy.greater(stats[:, 2], 80.0 * numpy.ones(10))) == 10)
assert (numpy.allclose(stats[index, 3], x, rtol=0.2, atol=2.0))
assert (numpy.allclose(stats[index, 4], y, rtol=0.2, atol=2.0))
assert (numpy.allclose(stats[index, 5], z, rtol=0.2, atol=20.0))
def create3DSpline():
movie = storm_analysis.getData("test/data/test_spliner.dax")
mlist = storm_analysis.getData("test/data/test_spliner_ref.hdf5")
psf = storm_analysis.getPathOutputTest("test_spliner_psf.psf")
spline = storm_analysis.getPathOutputTest("test_spliner_psf.spline")
storm_analysis.removeFile(psf)
storm_analysis.removeFile(spline)
measurePSF.measurePSF(movie, "", mlist, psf, aoi_size=6)
psfToSpline.psfToSpline(psf, spline, 5)
def test_align_merge_2():
"""
Test aligning and merging two HDF5 files with offset.
"""
n_locs = 500
tracks = {"x" : numpy.random.normal(loc = 10.0, scale = 0.2, size = n_locs),
"y" : numpy.random.normal(loc = 10.0, scale = 0.2, size = n_locs),
"z" : numpy.random.normal(scale = 0.05, size = n_locs)}
h5_in1 = storm_analysis.getPathOutputTest("test_align_merge_1.hdf5")
h5_in2 = storm_analysis.getPathOutputTest("test_align_merge_2.hdf5")
h5_alm = storm_analysis.getPathOutputTest("test_align_merge_3.hdf5")
# Create input files.
t_dx = 2.0
t_dz = 0.3
with saH5Py.SAH5Py(h5_in1, is_existing = False, overwrite = True) as h5:
h5.addMetadata("<xml><field1><data1>1</data1></field></xml>")
h5.setMovieInformation(20, 20, 2, "")
h5.setPixelSize(100.0)
h5.addTracks(tracks)
with saH5Py.SAH5Py(h5_in2, is_existing = False, overwrite = True) as h5:
h5.addMetadata("<xml><field1><data1>2</data1></field></xml>")
h5.setMovieInformation(20, 20, 2, "")
h5.setPixelSize(100.0)
tracks["x"] += t_dx
tracks["z"] += t_dz
h5.addTracks(tracks)
# Align and merge with offset.
storm_analysis.removeFile(h5_alm)
[dx, dy, dz] = alignAndMerge.alignAndMerge(h5_in1, h5_in2, h5_alm, dx = -t_dx)
# Check that we got the right offsets.
assert(numpy.allclose(numpy.array([dx, dy, dz]),
numpy.array([-t_dx, 0.0, -t_dz]),
atol = 0.001,
rtol = 0.1))
# Check that the output file is correctly aligned.
with saH5Py.SAH5Py(h5_alm) as h5:
tracks = h5.getTracks(fields = ["x", "y", "z"])
assert(numpy.allclose(numpy.array([numpy.std(tracks["x"]),
numpy.std(tracks["y"]),
numpy.std(tracks["z"])]),
numpy.array([0.2, 0.2, 0.05]),
atol = 0.001,
rtol = 0.1))
def test_scmos_Z():
movie_name = storm_analysis.getData("test/data/test.dax")
settings = storm_analysis.getData("test/data/test_sc_Z.xml")
mlist = storm_analysis.getPathOutputTest("test_sc_Z.bin")
storm_analysis.removeFile(mlist)
from storm_analysis.sCMOS.scmos_analysis import analyze
analyze(movie_name, mlist, settings)
# Verify number of localizations found.
num_locs = veri.verifyNumberLocalizations(mlist)
if not veri.verifyIsCloseEnough(num_locs, 1958):
raise Exception(
"sCMOS Z did not find the expected number of localizations.")
def test_3ddao_Z():
movie_name = storm_analysis.getData("test/data/test.dax")
settings = storm_analysis.getData("test/data/test_3d_Z.xml")
mlist = storm_analysis.getPathOutputTest("test_3d_Z.hdf5")
storm_analysis.removeFile(mlist)
from storm_analysis.daostorm_3d.mufit_analysis import analyze
analyze(movie_name, mlist, settings)
# Verify number of localizations found.
num_locs = veri.verifyNumberLocalizations(mlist)
if not veri.verifyIsCloseEnough(num_locs, 1955):
raise Exception(
"3D-DAOSTORM Z did not find the expected number of localizations.")
def test_3ddao_2d_fixed_non_square():
movie_name = storm_analysis.getData("test/data/test_300x200.dax")
settings = storm_analysis.getData("test/data/test_3d_2d_fixed.xml")
mlist = storm_analysis.getPathOutputTest("test_3d_2d_300x200.bin")
storm_analysis.removeFile(mlist)
from storm_analysis.daostorm_3d.mufit_analysis import analyze
analyze(movie_name, mlist, settings)
# Verify number of localizations found.
num_locs = veri.verifyNumberLocalizations(mlist)
if not veri.verifyIsCloseEnough(num_locs, 991):
raise Exception(
"3D-DAOSTORM 2D fixed non square did not find the expected number of localizations."
)