def test_simulate_3():
"""
No photo-physics, spline PSF, sCMOS camera.
"""
# Only test for Python3 due to pickle incompatibility issues.
if (sys.version_info < (3, 0)):
return
dax_name = storm_analysis.getPathOutputTest("test_sim3.dax")
bin_name = storm_analysis.getData("test/data/test_sim.hdf5")
cal_name = storm_analysis.getData("test/data/calib.npy")
spline_name = storm_analysis.getData("test/data/test_spliner_psf.spline")
sim = simulate.Simulate(
background_factory=lambda settings, xs, ys, i3data: background.
UniformBackground(settings, xs, ys, i3data, photons=20),
camera_factory=lambda settings, xs, ys, i3data: camera.SCMOS(
settings, xs, ys, i3data, cal_name),
photophysics_factory=lambda settings, xs, ys, i3data: photophysics.
AlwaysOn(settings, xs, ys, i3data, 2000.0),
psf_factory=lambda settings, xs, ys, i3data: psf.Spline(
settings, xs, ys, i3data, 160.0, spline_name))
sim.simulate(dax_name, bin_name, 5)
def test_drift_correction():
# Calculate drift correction.
param_name = storm_analysis.getData("test/data/test_drift.xml")
parameters = params.ParametersAnalysis().initFromFile(param_name)
mlist_name = storm_analysis.getData("test/data/test_drift_mlist.bin")
drift_output = storm_analysis.getPathOutputTest("test_drift_drift.txt")
xyzDriftCorrection.xyzDriftCorrection(mlist_name,
drift_output,
parameters.getAttr("frame_step"),
parameters.getAttr("d_scale"),
correct_z=True)
# Verify results.
diffs = veri.verifyDriftCorrection(
storm_analysis.getData("test/data/test_drift.txt"), drift_output)
if (diffs[0] > 0.1):
raise Exception("Frame numbers do not match.")
# These thresholds are somewhat arbitrary.
if (diffs[1] > 0.1) or (diffs[2] > 0.1):
raise Exception("XY drift correction error.")
if (diffs[3] > 30.0):
raise Exception("Z drift correction error.")
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_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_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_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_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_scmos_2d_fixed():
movie_name = storm_analysis.getData("test/data/test.dax")
settings = storm_analysis.getData("test/data/test_sc_2d_fixed.xml")
mlist = storm_analysis.getPathOutputTest("test_sc_2d_fixed.bin")
storm_analysis.removeFile(mlist)
from storm_analysis.sCMOS.scmos_analysis import analyze
analyze(movie_name, mlist, settings)
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 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 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 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_l1h():
# Test L1H.
movie_name = storm_analysis.getData("test/data/test_l1h.dax")
settings = storm_analysis.getData("test/data/test_l1h.xml")
hres = storm_analysis.getPathOutputTest("test_l1h_list.hres")
mlist = storm_analysis.getPathOutputTest("test_l1h_list.bin")
storm_analysis.removeFile(hres)
storm_analysis.removeFile(mlist)
from storm_analysis.L1H.cs_analysis import analyze
analyze(movie_name, settings, hres, mlist)
def test_3ddao_2d():
movie_name = storm_analysis.getData("test/data/test.dax")
settings = storm_analysis.getData("test/data/test_3d_2d.xml")
mlist = storm_analysis.getPathOutputTest("test_3d_2d.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, 1970):
raise Exception("3D-DAOSTORM 2D did not find the expected number of localizations.")
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.hdf5")
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, 1942):
raise Exception("sCMOS Z did not find the expected number of localizations.")
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_tracker():
# Test tracking.
import shutil
settings = storm_analysis.getData("test/data/test_drift.xml")
alist_name = storm_analysis.getPathOutputTest("test_drift_alist.bin")
# Copy mlist so that it is in the same directory as alist.
mlist_data = storm_analysis.getData("test/data/test_drift_mlist.bin")
mlist_output = storm_analysis.getPathOutputTest("test_drift_mlist.bin")
shutil.copyfile(mlist_data, mlist_output)
from storm_analysis.sa_utilities.track_average_correct import trackAverageCorrect
trackAverageCorrect(mlist_output, alist_name, settings)
def test_tracker():
# Test tracking.
import shutil
settings = storm_analysis.getData("test/data/test_drift.xml")
alist_name = storm_analysis.getPathOutputTest("test_drift_alist.bin")
# Copy mlist so that it is in the same directory as alist.
mlist_data = storm_analysis.getData("test/data/test_drift_mlist.bin")
mlist_output = storm_analysis.getPathOutputTest("test_drift_mlist.bin")
shutil.copyfile(mlist_data, mlist_output)
from storm_analysis.sa_utilities.track_average_correct import trackAverageCorrect
trackAverageCorrect(mlist_output, alist_name, settings)
def test_simulate_3():
"""
No photo-physics, spline PSF, sCMOS camera.
"""
dax_name = storm_analysis.getPathOutputTest("test_sim3.dax")
bin_name = storm_analysis.getData("test/data/test_sim_olist.bin")
cal_name = storm_analysis.getData("test/data/calib.npy")
spline_name = storm_analysis.getData("test/data/test_spliner_psf.spline")
sim = simulate.Simulate(lambda settings, xs, ys, i3data : background.UniformBackground(settings, xs, ys, i3data, photons = 20),
lambda settings, xs, ys, i3data : camera.SCMOS(settings, xs, ys, i3data, 100.0, cal_name),
lambda settings, xs, ys, i3data : photophysics.AlwaysOn(settings, xs, ys, i3data, 2000.0),
lambda settings, xs, ys, i3data : psf.Spline(settings, xs, ys, i3data, 160.0, spline_name))
sim.simulate(dax_name, bin_name, 5)
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_wavelet_bgr():
movie_in = storm_analysis.getData("test/data/test_bg_sub.dax")
movie_out = storm_analysis.getPathOutputTest("test_bg_sub_wbgr.dax")
from storm_analysis.wavelet_bgr.wavelet_bgr import waveletBGRSub
waveletBGRSub(movie_in, movie_out, "db4", 2, 2, 10)
def test_scmos_scmos_cal():
"""
Test that scmos calibration data is initialized correctly.
"""
settings = storm_analysis.getData("test/data/test_sc_2d_fixed.xml")
parameters = params.ParametersSCMOS().initFromFile(settings)
# Create analysis object and reach deep into it..
find_fit = findPeaks.initFindAndFit(parameters)
fitter = find_fit.peak_fitter
mfitter = fitter.mfitter
# Get sCMOS calibration value.
scmos_cal_value = mfitter.scmos_cal[0, 0]
# Initialize with an image.
image = numpy.ones(mfitter.scmos_cal.shape)
fitter.newImage(image)
# Verify that the image has the sCMOS term added.
resp = mfitter.getResidual()
assert (numpy.max(resp - (1.0 + scmos_cal_value)) < 1.0e-6)
# Cleanup.
fitter.cleanUp()
def test_rolling_ball():
movie_in = storm_analysis.getData("test/data/test_bg_sub.dax")
movie_out = storm_analysis.getPathOutputTest("test_bg_sub_rb.dax")
from storm_analysis.rolling_ball_bgr.rolling_ball import rollingBallSub
rollingBallSub(movie_in, movie_out, 10, 1)
def test_dbscan_clustering():
# Test dbscan
import shutil
# Copy alist to the output directory so that the DBSCAN results end up in the right place.
alist_data = storm_analysis.getData("test/data/test_clustering_list.bin")
alist_output = storm_analysis.getPathOutputTest(
"test_clustering_alist.bin")
shutil.copyfile(alist_data, alist_output)
from storm_analysis.dbscan.dbscan_analysis import dbscanAnalysis
dbscanAnalysis(alist_output, 0)
# Verify number of clusters found.
stats_file = storm_analysis.getPathOutputTest(
"test_clustering_aclusters_stats.txt")
n_clusters = len(open(stats_file).readlines())
if (n_clusters != 99):
raise Exception(
"DBSCAN did not identify the expected number of clusters.")
# Make pictures.
clist_name = storm_analysis.getPathOutputTest(
"test_clustering_aclusters_size_list.bin")
image_name = storm_analysis.getPathOutputTest("test_clustering_db")
from storm_analysis.dbscan.cluster_images import clusterImages
clusterImages(clist_name, "DBSCAN Clustering", 50, 20, image_name,
[256, 256])
def test_simulate_2():
"""
(Simple) STORM photo-physics, pure astigmatism PSF, EMCCD camera.
"""
dax_name = storm_analysis.getPathOutputTest("test_sim2.dax")
bin_name = storm_analysis.getData("test/data/test_sim.hdf5")
sim = simulate.Simulate(
background_factory=lambda settings, xs, ys, i3data: background.
UniformBackground(settings, xs, ys, i3data, photons=20),
camera_factory=lambda settings, xs, ys, i3data: camera.EMCCD(
settings,
xs,
ys,
i3data,
100.0,
emccd_gain=5.0,
preamp_gain=1.0,
read_noise=5),
photophysics_factory=lambda settings, xs, ys, i3data: photophysics.
SimpleSTORM(settings, xs, ys, i3data, 4000.0, off_time=10.0),
psf_factory=lambda settings, xs, ys, i3data: psf.PupilFunction(
settings, xs, ys, i3data, 160.0, [[1.3, 2, 2]]),
x_size=100,
y_size=75)
sim.simulate(dax_name, bin_name, 5)
def test_fitz_c_5():
"""
Test that fitz_c.wXwYCurveDistance works correctly.
"""
# Load 3D parameters.
settings = storm_analysis.getData("test/data/test_3d_3d.xml")
parameters = params.ParametersDAO().initFromFile(settings)
[wx_params, wy_params] = parameters.getWidthParams()
[min_z, max_z] = parameters.getZRange()
pixel_size = parameters.getAttr("pixel_size")
# Calculate widths.
z_vals = numpy.arange(-250.0, 251.0, 50)
[sx, sy] = fitzC.calcSxSy(wx_params, wy_params, z_vals)
# Distances should be very close to zero.
dist = fitzC.wXwYCurveDistance(wx_params, wy_params, 2.0*sx, 2.0*sy, min_z, max_z, 0.001)
assert numpy.allclose(dist, numpy.zeros(sx.size))
# First distance should be larger.
sx[0] += 10.0
dist = fitzC.wXwYCurveDistance(wx_params, wy_params, 2.0*sx, 2.0*sy, min_z, max_z, 0.001)
expected = numpy.zeros(sx.size)
expected[0] = 0.0345862
assert numpy.allclose(dist, expected)
def test_fitz_c_5():
"""
Test that fitz_c.wXwYCurveDistance works correctly.
"""
# Load 3D parameters.
settings = storm_analysis.getData("test/data/test_3d_3d.xml")
parameters = params.ParametersDAO().initFromFile(settings)
[wx_params, wy_params] = parameters.getWidthParams()
[min_z, max_z] = parameters.getZRange()
pixel_size = parameters.getAttr("pixel_size")
# Calculate widths.
z_vals = numpy.arange(-250.0, 251.0, 50)
[sx, sy] = fitzC.calcSxSy(wx_params, wy_params, z_vals)
# Distances should be very close to zero.
dist = fitzC.wXwYCurveDistance(wx_params, wy_params, 2.0 * sx, 2.0 * sy,
min_z, max_z, 0.001)
assert numpy.allclose(dist, numpy.zeros(sx.size))
# First distance should be larger.
sx[0] += 10.0
dist = fitzC.wXwYCurveDistance(wx_params, wy_params, 2.0 * sx, 2.0 * sy,
min_z, max_z, 0.001)
expected = numpy.zeros(sx.size)
expected[0] = 0.0345862
assert numpy.allclose(dist, expected)
def test_frc():
mlist_name = storm_analysis.getData("test/data/test_drift_mlist.bin")
results_name = storm_analysis.getPathOutputTest("test_drift_frc.txt")
from storm_analysis.frc.frc_calc2d import frcCalc2d
frcCalc2d(mlist_name, results_name, False)
def test_3ddao_2d_fixed_gt_text():
"""
Start fitting from ground truth locations (text file version).
"""
movie_name = storm_analysis.getData("test/data/test.dax")
settings = storm_analysis.getData("test/data/test_3d_2d_fixed_gt_text.xml")
mlist = storm_analysis.getPathOutputTest("test_3d_2d_fixed_gt_text.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, 200):
raise Exception("3D-DAOSTORM 2D fixed ground truth 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."
)
def test_voronoi_clustering():
# Test voronoi
alist_name = storm_analysis.getData("test/data/test_clustering_list.bin")
output_dir = storm_analysis.getPathOutputTest("./")
from storm_analysis.voronoi.voronoi_analysis import voronoiAnalysis
voronoiAnalysis(alist_name, 0.1, output_dir)
# Verify number of clusters found.
stats_file = storm_analysis.getPathOutputTest(
"test_clustering_srt_stats.txt")
n_clusters = len(open(stats_file).readlines())
if (n_clusters != 100):
raise Exception(
"Voronoi did not identify the expected number of clusters.")
# Make pictures.
clist_name = storm_analysis.getPathOutputTest(
"test_clustering_srt_size_list.bin")
image_name = storm_analysis.getPathOutputTest("test_clustering_vr")
from storm_analysis.dbscan.cluster_images import clusterImages
clusterImages(clist_name, "Voronoi Clustering", 50, 20, image_name,
[256, 256])
def test_rcc():
mlist_name = storm_analysis.getData("test/data/test_drift_mlist.bin")
drift_name = storm_analysis.getPathOutputTest("test_drift.txt")
from storm_analysis.rcc.rcc_drift_correction import rccDriftCorrection
rccDriftCorrection(mlist_name, drift_name, 2000, 1, True, False)
def test_scmos_scmos_cal():
"""
Test that scmos calibration data is initialized correctly.
"""
settings = storm_analysis.getData("test/data/test_sc_2d_fixed.xml")
parameters = params.ParametersSCMOS().initFromFile(settings)
# Create analysis object and reach deep into it..
find_fit = findPeaks.initFindAndFit(parameters)
fitter = find_fit.peak_fitter
mfitter = fitter.mfitter
# Get sCMOS calibration value.
scmos_cal_value = mfitter.scmos_cal[0,0]
# Initialize with an image.
image = numpy.ones(mfitter.scmos_cal.shape)
fitter.newImage(image)
# Verify that the image has the sCMOS term added.
resp = mfitter.getResidual()
assert(numpy.max(resp - (1.0 + scmos_cal_value)) < 1.0e-6)
# Cleanup.
fitter.cleanUp()
def test_rolling_ball():
movie_in = storm_analysis.getData("test/data/test_bg_sub.dax")
movie_out = storm_analysis.getPathOutputTest("test_bg_sub_rb.dax")
from storm_analysis.rolling_ball_bgr.rolling_ball import rollingBallSub
rollingBallSub(movie_in, movie_out, 10, 1)
def test_scmos_3d():
movie_name = storm_analysis.getData("test/data/test.dax")
settings = storm_analysis.getData("test/data/test_sc_3d.xml")
mlist = storm_analysis.getPathOutputTest("test_sc_3d.hdf5")
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, 1950):
raise Exception("sCMOS 3D did not find the expected number of localizations.")
# Verify that the Z values actually got calculated.
if not veri.verifyZWasCalculated(mlist):
raise Exception("Z values were not calculated for sCMOS 3D fitting.")
def test_3ddao_2d_fixed_gt_text():
"""
Start fitting from ground truth locations (text file version).
"""
movie_name = storm_analysis.getData("test/data/test.dax")
settings = storm_analysis.getData("test/data/test_3d_2d_fixed_gt_text.xml")
mlist = storm_analysis.getPathOutputTest("test_3d_2d_fixed_gt_text.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, 200):
raise Exception(
"3D-DAOSTORM 2D fixed ground truth did not find the expected number of localizations."
)
def test_spliner_std_2D():
# Only test for Python3 due to pickle incompatibility issues.
if (sys.version_info < (3, 0)):
return
movie_name = storm_analysis.getData("test/data/test.dax")
settings = storm_analysis.getData("test/data/test_spliner_2D.xml")
mlist = storm_analysis.getPathOutputTest("test_spliner_2D.hdf5")
storm_analysis.removeFile(mlist)
from storm_analysis.spliner.spline_analysis import analyze
analyze(movie_name, mlist, settings)
# Verify number of localizations found.
num_locs = veri.verifyNumberLocalizations(mlist)
if not veri.verifyIsCloseEnough(num_locs, 2004):
raise Exception(
"Spliner 2D did not find the expected number of localizations.")
def test_get_help_1():
"""
Test getting help.
"""
# Load some parameters.
original = storm_analysis.getData("test/data/test_3d_2d_fixed.xml")
p1 = params.ParametersDAO().initFromFile(original, warnings=True)
v1 = p1.helpAttr("max_frame")
v1 = p1.helpAttr("convert_to")
def test_scmos_3d():
movie_name = storm_analysis.getData("test/data/test.dax")
settings = storm_analysis.getData("test/data/test_sc_3d.xml")
mlist = storm_analysis.getPathOutputTest("test_sc_3d.hdf5")
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, 1950):
raise Exception(
"sCMOS 3D did not find the expected number of localizations.")
# Verify that the Z values actually got calculated.
if not veri.verifyZWasCalculated(mlist):
raise Exception("Z values were not calculated for sCMOS 3D fitting.")
def test_l1h():
# Test L1H.
movie_name = storm_analysis.getData("test/data/test_l1h.dax")
settings = storm_analysis.getData("test/data/test_l1h.xml")
hres = storm_analysis.getPathOutputTest("test_l1h_list.hres")
mlist = storm_analysis.getPathOutputTest("test_l1h_list.bin")
storm_analysis.removeFile(hres)
storm_analysis.removeFile(mlist)
from storm_analysis.L1H.cs_analysis import analyze
analyze(movie_name, settings, hres, mlist)
# Verify number of localizations found.
num_locs = veri.verifyNumberLocalizations(mlist)
if not veri.verifyIsCloseEnough(num_locs, 1986):
raise Exception(
"L1H did not find the expected number of localizations.")
def test_get_attr_3():
"""
Test getting parameters.
"""
# Load some parameters.
original = storm_analysis.getData("test/data/test_3d_2d_fixed.xml")
p1 = params.ParametersDAO().initFromFile(original, warnings=True)
v1 = p1.getAttr("start_frame")
v1 = p1.getAttr("x_start", 1)
def test_simulate_3():
"""
No photo-physics, spline PSF, sCMOS camera.
"""
# Only test for Python3 due to pickle incompatibility issues.
if (sys.version_info < (3, 0)):
return
dax_name = storm_analysis.getPathOutputTest("test_sim3.dax")
bin_name = storm_analysis.getData("test/data/test_sim.hdf5")
cal_name = storm_analysis.getData("test/data/calib.npy")
spline_name = storm_analysis.getData("test/data/test_spliner_psf.spline")
sim = simulate.Simulate(background_factory = lambda settings, xs, ys, i3data : background.UniformBackground(settings, xs, ys, i3data, photons = 20),
camera_factory = lambda settings, xs, ys, i3data : camera.SCMOS(settings, xs, ys, i3data, cal_name),
photophysics_factory = lambda settings, xs, ys, i3data : photophysics.AlwaysOn(settings, xs, ys, i3data, 2000.0),
psf_factory = lambda settings, xs, ys, i3data : psf.Spline(settings, xs, ys, i3data, 160.0, spline_name))
sim.simulate(dax_name, bin_name, 5)
def test_pretty_print_1():
# This just tests that it doesn't fail. It does not check the
# formatting of the output file.
original = storm_analysis.getData("test/data/test_3d_2d_fixed.xml")
output = storm_analysis.getPathOutputTest("test_pp1.xml")
# Load parameters.
p1 = params.ParametersDAO().initFromFile(original, warnings=True)
# Convert back to XML.
p1.toXMLFile(output, pretty=True)
def _test_l1h():
# Test L1H.
movie_name = storm_analysis.getData("test/data/test_l1h.dax")
settings = storm_analysis.getData("test/data/test_l1h.xml")
hres = storm_analysis.getPathOutputTest("test_l1h_list.hres")
mlist = storm_analysis.getPathOutputTest("test_l1h_list.bin")
storm_analysis.removeFile(hres)
storm_analysis.removeFile(mlist)
from storm_analysis.L1H.cs_analysis import analyze
analyze(movie_name, settings, hres, mlist)
# Verify number of localizations found.
#
# FIXME: Change L1H to use the HDF5 format.
#
num_locs = readinsight3.loadI3File(mlist)["x"].size
if not veri.verifyIsCloseEnough(num_locs, 1986):
raise Exception("L1H did not find the expected number of localizations.")
def _test_rcc_1():
"""
Test RCC drift correction.
"""
# Calculate drift correction.
param_name = storm_analysis.getData("test/data/test_drift.xml")
parameters = params.ParametersCommon().initFromFile(param_name)
data_name = storm_analysis.getData("test/data/test_drift.hdf5")
h5_name = storm_analysis.getPathOutputTest("test_rcc_hdf5.hdf5")
# Make a copy of the original as it will get modified and then
# git will pick this up.
shutil.copyfile(data_name, h5_name)
drift_output = storm_analysis.getPathOutputTest("test_drift_drift.txt")
[min_z, max_z] = parameters.getZRange()
rccDriftCorrection.rccDriftCorrection(h5_name,
drift_output,
parameters.getAttr("frame_step"),
parameters.getAttr("d_scale"),
min_z,
max_z,
True)
# Verify results.
diffs = veri.verifyDriftCorrection(storm_analysis.getData("test/data/test_drift.txt"),
drift_output)
if (diffs[0] > 0.1):
raise Exception("Frame numbers do not match.")
# These thresholds are somewhat arbitrary.
if (diffs[1] > 0.1) or (diffs[2] > 0.1):
raise Exception("XY drift correction error.")
if (diffs[3] > 0.03):
raise Exception("Z drift correction error.")
def _test_l1h():
# Test L1H.
movie_name = storm_analysis.getData("test/data/test_l1h.dax")
settings = storm_analysis.getData("test/data/test_l1h.xml")
hres = storm_analysis.getPathOutputTest("test_l1h_list.hres")
mlist = storm_analysis.getPathOutputTest("test_l1h_list.bin")
storm_analysis.removeFile(hres)
storm_analysis.removeFile(mlist)
from storm_analysis.L1H.cs_analysis import analyze
analyze(movie_name, settings, hres, mlist)
# Verify number of localizations found.
#
# FIXME: Change L1H to use the HDF5 format.
#
num_locs = readinsight3.loadI3File(mlist)["x"].size
if not veri.verifyIsCloseEnough(num_locs, 1986):
raise Exception(
"L1H did not find the expected number of localizations.")
def test_rcc():
# Calculate drift correction.
mlist_name = storm_analysis.getData("test/data/test_drift_mlist.bin")
drift_name = storm_analysis.getPathOutputTest("test_rcc_drift.txt")
from storm_analysis.rcc.rcc_drift_correction import rccDriftCorrection
rccDriftCorrection(mlist_name, drift_name, 1000, 1, True, False)
# Verify results.
diffs = veri.verifyDriftCorrection(
storm_analysis.getData("test/data/test_drift.txt"), drift_name)
if (diffs[0] > 0.1):
raise Exception("Frame numbers do not match.")
# These thresholds are somewhat arbitrary.
if (diffs[1] > 0.1) or (diffs[2] > 0.1):
raise Exception("XY drift correction error.")
if (diffs[3] > 30.0):
raise Exception("Z drift correction error.")
def test_voronoi_clustering():
# Test voronoi
alist_name = storm_analysis.getData("test/data/test_drift_alist.bin")
output_dir = storm_analysis.getPathOutputTest("./")
from storm_analysis.voronoi.voronoi_analysis import voronoiAnalysis
voronoiAnalysis(alist_name, 1.25, output_dir)
clist_name = storm_analysis.getPathOutputTest("test_drift_asrt_size_list.bin")
image_name = storm_analysis.getPathOutputTest("test_drift_vr")
from storm_analysis.dbscan.cluster_images import clusterImages
clusterImages(clist_name, "Voronoi Clustering", 50, 20, image_name, [256, 256])
def test_simulate_1():
"""
No photo-physics, simple PSF, ideal camera.
"""
dax_name = storm_analysis.getPathOutputTest("test_sim1.dax")
bin_name = storm_analysis.getData("test/data/test_sim.hdf5")
sim = simulate.Simulate(background_factory = lambda settings, xs, ys, i3data : background.UniformBackground(settings, xs, ys, i3data),
camera_factory = lambda settings, xs, ys, i3data : camera.Ideal(settings, xs, ys, i3data, 100.0),
photophysics_factory = lambda settings, xs, ys, i3data : photophysics.AlwaysOn(settings, xs, ys, i3data, 1000.0),
psf_factory = lambda settings, xs, ys, i3data : psf.GaussianPSF(settings, xs, ys, i3data, 160.0),
x_size = 100, y_size = 75)
sim.simulate(dax_name, bin_name, 5)
def test_simulate_2():
"""
(Simple) STORM photo-physics, pure astigmatism PSF, EMCCD camera.
"""
dax_name = storm_analysis.getPathOutputTest("test_sim2.dax")
bin_name = storm_analysis.getData("test/data/test_sim.hdf5")
sim = simulate.Simulate(background_factory = lambda settings, xs, ys, i3data : background.UniformBackground(settings, xs, ys, i3data, photons = 20),
camera_factory = lambda settings, xs, ys, i3data : camera.EMCCD(settings, xs, ys, i3data, 100.0, emccd_gain = 5.0, preamp_gain = 1.0, read_noise = 5),
photophysics_factory = lambda settings, xs, ys, i3data : photophysics.SimpleSTORM(settings, xs, ys, i3data, 4000.0, off_time = 10.0),
psf_factory = lambda settings, xs, ys, i3data : psf.PupilFunction(settings, xs, ys, i3data, 160.0, [[1.3, 2, 2]]),
x_size = 100, y_size = 75)
sim.simulate(dax_name, bin_name, 5)
def test_get_help_2():
"""
Test getting help with a parameter that does not exist.
"""
# Load some parameters.
original = storm_analysis.getData("test/data/test_3d_2d_fixed.xml")
p1 = params.ParametersDAO().initFromFile(original, warnings=True)
try:
v1 = p1.helpAttr("foo")
except params.ParametersException:
return
assert False
def test_get_attr_2():
"""
Test no such parameter with default value.
"""
# Load some parameters.
original = storm_analysis.getData("test/data/test_3d_2d_fixed.xml")
p1 = params.ParametersDAO().initFromFile(original, warnings=True)
try:
v1 = p1.getAttr("foo", default="bar")
except params.ParametersException:
return
assert False
def test_psf_spline3D_1():
"""
Test that spline PSF agrees with spliner (for 0.0 offset).
"""
# Only test for Python3 due to pickle incompatibility issues.
if (sys.version_info < (3, 0)):
return
spline_name = storm_analysis.getData("test/data/test_spliner_psf.spline")
psf_sp_3d = psf.Spline3D(spline_name)
sp_3d = splineToPSF.SplineToPSF3D(spline_name)
psf_im = psf_sp_3d.getPSF(0.1, 0.0, 0.0)
sp_im = sp_3d.getPSF(0.1, normalize = False)
assert numpy.allclose(psf_im, sp_im)
def test_dbscan_clustering():
# Test dbscan
import shutil
# Copy alist to the output directory so that the DBSCAN results end up in the right place.
alist_data = storm_analysis.getData("test/data/test_drift_alist.bin")
alist_output = storm_analysis.getPathOutputTest("test_drift_alist.bin")
shutil.copyfile(alist_data, alist_output)
from storm_analysis.dbscan.dbscan_analysis import dbscanAnalysis
dbscanAnalysis(alist_output, 0)
clist_name = storm_analysis.getPathOutputTest("test_drift_aclusters_size_list.bin")
image_name = storm_analysis.getPathOutputTest("test_drift_db")
from storm_analysis.dbscan.cluster_images import clusterImages
clusterImages(clist_name, "DBSCAN Clustering", 50, 20, image_name, [256, 256])
def test_fitz_c_4():
"""
Test that tracks with wx, wy values that are not near the calibration
curve are assigned z values less than z minimum.
Their category remains unchanged as this is done in a separate step.
"""
# Load 3D parameters.
settings = storm_analysis.getData("test/data/test_3d_3d.xml")
parameters = params.ParametersDAO().initFromFile(settings)
[wx_params, wy_params] = parameters.getWidthParams()
[min_z, max_z] = parameters.getZRange()
pixel_size = parameters.getAttr("pixel_size")
# Calculate widths.
z_vals = numpy.arange(-250.0, 251.0, 50)
[sx, sy] = fitzC.calcSxSy(wx_params, wy_params, z_vals)
# Create HDF5 file with these widths.
track_length = numpy.ones(sx.size)
track_length[:2] = 2
tracks = {"category" : numpy.ones(sx.size, dtype = numpy.int32),
"track_length" : track_length,
"x" : numpy.zeros(sx.size),
"xsigma" : track_length*(sx/pixel_size + numpy.ones(sx.size)),
"ysigma" : track_length*(sy/pixel_size + numpy.ones(sx.size))}
h5_name = storm_analysis.getPathOutputTest("test_sa_hdf5.hdf5")
storm_analysis.removeFile(h5_name)
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
h5.setMovieInformation(256, 256, 10, "XYZZY")
h5.setPixelSize(pixel_size)
h5.addTracks(tracks)
# Calculate Z values.
fitzC.fitzTracks(h5_name, 1.5, wx_params, wy_params, min_z, max_z, 1.0e-3)
# Check Z values.
with saH5Py.SAH5Py(h5_name) as h5:
for tracks in h5.tracksIterator():
assert(numpy.allclose(tracks["z"], min_z*numpy.ones(sx.size)-1.0e-3))
assert(numpy.allclose(tracks["category"], numpy.ones(sx.size)))
def test_psf_2D_dy():
# Only test for Python3 due to pickle incompatibility issues.
if (sys.version_info < (3, 0)):
return
spline_filename = storm_analysis.getData("test/data/test_spliner_psf_2d.spline")
with open(spline_filename, "rb") as fp:
spline_data = pickle.load(fp)
py_spline = spline2D.Spline2D(spline_data["spline"], spline_data["coeff"])
c_spline = cubicSplineC.CSpline2D(py_spline)
size = py_spline.getSize() - 1.0e-6
for i in range(reps):
x = random.uniform(1.0e-6, size)
y = random.uniform(1.0e-6, size)
#print("{0:.3f} {1:.3f}".format(py_spline.dyf(x, y), c_spline.dyf(x, y)))
assert (abs(py_spline.dyf(x, y) - c_spline.dyf(x, y)) < 1.0e-6)
def test_std_analysis_1():
"""
Test zCheck.
"""
# Load 3D parameters.
settings = storm_analysis.getData("test/data/test_3d_3d.xml")
parameters = params.ParametersDAO().initFromFile(settings)
[min_z, max_z] = parameters.getZRange()
assert(abs(min_z + 0.5) < 1.0e-6)
assert(abs(max_z - 0.5) < 1.0e-6)
# Create HDF5 file with localizations and tracks.
zvals = numpy.arange(-1.0, 1.05, 0.2)
peaks = {"category" : numpy.ones(zvals.size, dtype = numpy.int32),
"x" : numpy.zeros(zvals.size),
"z" : zvals}
h5_name = storm_analysis.getPathOutputTest("test_sa_hdf5.hdf5")
storm_analysis.removeFile(h5_name)
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
h5.setMovieInformation(256, 256, 10, "XYZZY")
h5.addLocalizations(peaks, 1)
h5.addTracks(peaks)
# Run z check on the file.
stdAnalysis.zCheck(h5_name, parameters)
# Check track and localization categories.
category = numpy.ones(zvals.size, dtype = numpy.int32)
z_mask = (zvals < min_z) | (zvals > max_z)
category[z_mask] = 9
with saH5Py.SAH5Py(h5_name) as h5:
for fnum, locs in h5.localizationsIterator(fields = ["category"]):
assert(numpy.allclose(locs["category"], category))
for tracks in h5.tracksIterator(fields = ["category"]):
assert(numpy.allclose(tracks["category"], category))
