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.")