def analyzeData():
dirs = sorted(glob.glob("test*"))
total_time = 0.0
for a_dir in dirs:
print()
print("Analyzing:", a_dir)
print()
hdf5 = a_dir + "/test.hdf5"
# Do tracking and drift correction using the ground truth positions.
if True:
shutil.copyfile(a_dir + "/test_ref.hdf5", hdf5)
# Run analysis.
#
# This will just do the drift correction as it will see that the
# movie has been completely analyzed.
#
start_time = time.time()
dao3d.analyze(a_dir + "/test.dax", hdf5, "dao.xml")
stop_time = time.time()
# Save timing results.
total_time += stop_time - start_time
print("Analysis completed in {0:.2f} seconds.".format(stop_time - start_time))
with open(a_dir + "/timing.txt", "w") as fp:
fp.write(str(stop_time - start_time) + "\n")
print()
print("{0:d} directories analyzed in {1:.2f} seconds.".format(len(dirs), total_time))
def analyzeData():
dirs = sorted(glob.glob("test*"))
total_time = 0.0
for a_dir in dirs:
print()
print("Analyzing:", a_dir)
print()
hdf5 = a_dir + "/test.hdf5"
# Do tracking and drift correction using the ground truth positions.
if True:
shutil.copyfile(a_dir + "/test_ref.hdf5", hdf5)
# Run analysis.
#
# This will just do the drift correction as it will see that the
# movie has been completely analyzed.
#
start_time = time.time()
dao3d.analyze(a_dir + "/test.dax", hdf5, "dao.xml")
stop_time = time.time()
# Save timing results.
total_time += stop_time - start_time
print("Analysis completed in {0:.2f} seconds.".format(stop_time -
start_time))
with open(a_dir + "/timing.txt", "w") as fp:
fp.write(str(stop_time - start_time) + "\n")
print()
print("{0:d} directories analyzed in {1:.2f} seconds.".format(
len(dirs), total_time))
def analyzeData():
dirs = sorted(glob.glob("test*"))
total_time = 0.0
for a_dir in dirs:
print()
print("Analyzing:", a_dir)
print()
hdf5 = a_dir + "/test.hdf5"
# Remove stale results, if any.
if os.path.exists(hdf5):
os.remove(hdf5)
# Run analysis.
start_time = time.time()
dao3d.analyze(a_dir + "/test.dax", hdf5, "dao.xml")
stop_time = time.time()
# Save timing results.
total_time += stop_time - start_time
print("Analysis completed in {0:.2f} seconds.".format(stop_time - start_time))
with open(a_dir + "/timing.txt", "w") as fp:
fp.write(str(stop_time - start_time) + "\n")
print()
print("{0:d} directories analyzed in {1:.2f} seconds.".format(len(dirs), total_time))
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_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_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_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."
)
dirs = sorted(glob.glob("test*"))
total_time = 0.0
for a_dir in dirs:
print()
print("Analyzing:", a_dir)
print()
hdf5 = a_dir + "/test.hdf5"
# Do tracking and drift correction using the ground truth positions.
if True:
shutil.copyfile(a_dir + "/test_ref.hdf5", hdf5)
# Run analysis.
start_time = time.time()
dao3d.analyze(a_dir + "/test.dax", hdf5, "dao.xml")
stop_time = time.time()
# Save timing results.
total_time += stop_time - start_time
print("Analysis completed in {0:.2f} seconds.".format(stop_time -
start_time))
with open(a_dir + "/timing.txt", "w") as fp:
fp.write(str(stop_time - start_time) + "\n")
print()
print("{0:d} directories analyzed in {1:.2f} seconds.".format(
len(dirs), total_time))