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_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.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."
)
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_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_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_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_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.")
