def addMoleculesWithXYZCat(self, x, y, z, cat):
i3data = i3dtype.createDefaultI3Data(x.size)
i3dtype.posSet(i3data, 'x', x)
i3dtype.posSet(i3data, 'y', y)
i3dtype.posSet(i3data, 'z', z)
i3dtype.setI3Field(i3data, 'c', cat)
self.addMolecules(i3data)
def addDAOSTORMMolecules(self, frame, xc, yc, br, be, msky, niter, sharp, chi, err):
"""
This is for localizations identified by the original DAOSTORM
algorithm, not the 3D-DAOSTORM algorithm.
DAOSTORM -> Insight3 format mapping.
xc - xcenter
yc - ycenter
br - brightness -> peak height
be - brightness error (?) -> peak area
msky - background -> peak background
niter - fit iterations
sharp - sharpness (?) -> peak angle
chi - fit quality -> peak width
err - error flag -> link
"""
i3data = i3dtype.createDefaultI3Data(xc.size)
i3dtype.posSet(i3data, 'x', xc)
i3dtype.posSet(i3data, 'y', yc)
i3dtype.setI3Field(i3data, 'h', br)
i3dtype.setI3Field(i3data, 'a', be)
i3dtype.setI3Field(i3data, 'bg', msky)
i3dtype.setI3Field(i3data, 'fi', niter)
i3dtype.setI3Field(i3data, 'phi', sharp)
i3dtype.setI3Field(i3data, 'w', chi)
i3dtype.setI3Field(i3data, 'lk', err)
self.addMolecules(i3data)
def addDAOSTORMMolecules(self, frame, xc, yc, br, be, msky, niter, sharp, chi, err):
#
# DAOSTORM -> Insight3 format mapping.
#
# xc - xcenter
# yc - ycenter
# br - brightness -> peak height
# be - brightness error (?) -> peak area
# msky - background -> peak background
# niter - fit iterations
# sharp - sharpness (?) -> peak angle
# chi - fit quality -> peak width
# err - error flag -> link
#
i3data = i3dtype.createDefaultI3Data(xc.size)
i3dtype.posSet(i3data, 'x', xc)
i3dtype.posSet(i3data, 'y', yc)
i3dtype.setI3Field(i3data, 'h', br)
i3dtype.setI3Field(i3data, 'a', be)
i3dtype.setI3Field(i3data, 'bg', msky)
i3dtype.setI3Field(i3data, 'fi', niter)
i3dtype.setI3Field(i3data, 'phi', sharp)
i3dtype.setI3Field(i3data, 'w', chi)
i3dtype.setI3Field(i3data, 'lk', err)
self.addMolecules(i3data)
def addMoleculesWithXYAFrame(self, x, y, pa, frame):
i3data = i3dtype.createDefaultI3Data(x.size)
i3dtype.posSet(i3data, 'x', x)
i3dtype.posSet(i3data, 'y', y)
i3dtype.setI3Field(i3data, 'a', pa)
i3dtype.setI3Field(i3data, 'fr', frame)
self.addMolecules(i3data)
def addMoleculesWithXYCatF(self, x, y, cat,f):
i3data = i3dtype.createDefaultI3Data(x.size)
i3dtype.posSet(i3data, 'x', x)
i3dtype.posSet(i3data, 'y', y)
i3dtype.setI3Field(i3data, 'c', cat)
i3dtype.setI3Field(i3data, 'fr', f)
self.addMolecules(i3data)
def addMoleculesWithXYIWFrame(self, x, y, pi, width, frame):
i3data = i3dtype.createDefaultI3Data(x.size)
i3dtype.posSet(i3data, 'x', x)
i3dtype.posSet(i3data, 'y', y)
i3dtype.setI3Field(i3data, 'i', pi)
i3dtype.setI3Field(i3data, 'w', width)
i3dtype.setI3Field(i3data, 'fr', frame)
self.addMolecules(i3data)
def addMoleculesWithXYZIFrame(self, x, y, z, pi, f):
i3data = i3dtype.createDefaultI3Data(x.size)
i3dtype.posSet(i3data, 'x', x)
i3dtype.posSet(i3data, 'y', y)
i3dtype.posSet(i3data, 'z', z)
i3dtype.setI3Field(i3data, 'i', pi)
i3dtype.setI3Field(i3data, 'fr', f)
self.addMolecules(i3data)
def test_i3dtype_2():
"""
Test creation and setting position with an array.
"""
i3_locs = i3dtype.createDefaultI3Data(10)
i3dtype.posSet(i3_locs, 'x', numpy.arange(10))
for i in range(10):
assert(abs(i3_locs["x"][i] - i) < 1.0e-6)
assert(abs(i3_locs["xc"][i] - i) < 1.0e-6)
def test_i3dtype_3():
"""
Test creation and setting with a scalar.
"""
i3_locs = i3dtype.createDefaultI3Data(10)
i3dtype.posSet(i3_locs, 'x', 10.0)
for i in range(10):
assert(abs(i3_locs["x"][i] - 10.0) < 1.0e-6)
assert(abs(i3_locs["xc"][i] - 10.0) < 1.0e-6)
def test_good_i3():
mlist_name = storm_analysis.getPathOutputTest("test_i3_io_mlist.bin")
# Create data.
locs = i3dtype.createDefaultI3Data(100)
# Save the data.
with writeinsight3.I3Writer(mlist_name) as i3w:
i3w.addMolecules(locs)
# Read the data.
locs = readinsight3.loadI3File(mlist_name)
assert(locs.shape[0] == 100)
def test_bad_i3():
mlist_name = storm_analysis.getPathOutputTest("test_i3_io_mlist.bin")
# Create data.
locs = i3dtype.createDefaultI3Data(100)
# Save the data.
i3w = writeinsight3.I3Writer(mlist_name)
i3w.addMolecules(locs)
i3w.fp.close()
# Read the data.
locs = readinsight3.loadI3File(mlist_name)
assert(locs is None)
def test_write_read_1():
"""
Test writing and reading.
"""
bin_name = storm_analysis.getPathOutputTest("test_insight3io.bin")
i3_locs = i3dtype.createDefaultI3Data(10)
i3dtype.posSet(i3_locs, 'x', 10.0)
with writeinsight3.I3Writer(bin_name) as i3:
i3.addMolecules(i3_locs)
i3_in = readinsight3.loadI3File(bin_name, verbose = False)
assert(numpy.allclose(i3_locs['x'], i3_in['x']))
def test_write_read_3():
"""
Test I3Reader on an empty file.
"""
bin_name = storm_analysis.getPathOutputTest("test_insight3io.bin")
i3_locs = i3dtype.createDefaultI3Data(10)
i3dtype.posSet(i3_locs, 'x', 10.0)
with writeinsight3.I3Writer(bin_name) as i3:
pass
i3_reader = readinsight3.I3Reader(bin_name)
# Read localizations.
i3_in = i3_reader.nextBlock()
assert(i3_in is False)
def test_good_i3_metadata():
mlist_name = storm_analysis.getPathOutputTest("test_i3_io_mlist.bin")
# Create data.
locs = i3dtype.createDefaultI3Data(100)
# Save data and metadata.
i3w = writeinsight3.I3Writer(mlist_name)
i3w.addMolecules(locs)
etree = ElementTree.Element("xml")
test = ElementTree.SubElement(etree, "test")
test.text = "test"
i3w.closeWithMetadata(ElementTree.tostring(etree, 'ISO-8859-1'))
# Read the data.
locs = readinsight3.loadI3File(mlist_name)
assert(locs.shape[0] == 100)
# Read the metadata.
metadata = readinsight3.loadI3Metadata(mlist_name)
assert(metadata.find("test").text == "test")
def test_write_read_2():
"""
Test I3Reader.
"""
bin_name = storm_analysis.getPathOutputTest("test_insight3io.bin")
i3_locs = i3dtype.createDefaultI3Data(10)
i3dtype.posSet(i3_locs, 'x', 10.0)
with writeinsight3.I3Writer(bin_name) as i3:
i3.addMolecules(i3_locs)
i3_reader = readinsight3.I3Reader(bin_name)
# Read localizations.
i3_in = i3_reader.nextBlock()
assert(numpy.allclose(i3_locs['x'], i3_in['x']))
assert(i3_in is not False)
# This should return False because there are no more localizations.
i3_in = i3_reader.nextBlock()
assert(i3_in is False)
def test_i3dtype_1():
"""
Test conversion to and from the fitter format.
"""
x_size = 100
y_size = 100
frame = 10
nm_per_pixel = 100.0
data_in = i3dtype.createDefaultI3Data(10)
i3dtype.posSet(data_in, 'x', numpy.arange(10))
i3dtype.posSet(data_in, 'y', numpy.arange(10) + 30.0)
i3dtype.posSet(data_in, 'z', numpy.arange(10) + 60.0)
i3dtype.setI3Field(data_in, 'fr', frame)
peaks = i3dtype.convertToMultiFit(data_in, frame, nm_per_pixel)
data_out = i3dtype.createFromMultiFit(peaks, frame, nm_per_pixel)
fields = ['x', 'ax', 'w']
for i in range(10):
for field in fields:
assert(abs(data_in[field][i] - data_out[field][i]) < 1.0e-6)
random.seed(0)
nx = args.nx
ny = args.ny
spacing = args.spacing
z_range = args.zrange
if (nx * ny > 1):
curz = -z_range
z_inc = 2.0 * z_range / (nx * ny - 1)
else:
curz = 0.0
z_inc = 0.0
i3data = i3dtype.createDefaultI3Data(nx * ny)
curx = spacing
for i in range(nx):
cury = spacing
for j in range(ny):
k = i * ny + j
i3data['x'][k] = curx + random.random() - 0.5
i3data['y'][k] = cury + random.random() - 0.5
i3data['z'][k] = curz
i3data['xc'][k] = i3data['x'][k]
i3data['yc'][k] = i3data['y'][k]
i3data['zc'][k] = i3data['z'][k]
# Record emitter id in the 'i' field.
def addMoleculesWithXY(self, x, y):
i3data = i3dtype.createDefaultI3Data(x.size)
i3dtype.posSet(i3data, 'x', x)
i3dtype.posSet(i3data, 'y', y)
self.addMolecules(i3data)
def addMoleculesWithXYFrame(self, x, y, frame):
i3data = i3dtype.createDefaultI3Data(x.size)
i3dtype.posSet(i3data, 'x', x)
i3dtype.posSet(i3data, 'y', y)
i3dtype.setI3Field(i3data, 'fr', frame)
self.addMolecules(i3data)
def addMoleculesWithXYI(self, x, y, pi):
i3data = i3dtype.createDefaultI3Data(x.size)
i3dtype.posSet(i3data, 'x', x)
i3dtype.posSet(i3data, 'y', y)
i3dtype.setI3Field(i3data, 'i', pi)
self.addMolecules(i3data)
def addMoleculesWithXYZ(self, x, y, z):
i3data = i3dtype.createDefaultI3Data(x.size)
i3dtype.posSet(i3data, 'x', x)
i3dtype.posSet(i3data, 'y', y)
i3dtype.posSet(i3data, 'z', z)
self.addMolecules(i3data)
def addMoleculesWithXYI(self, x, y, pi):
i3data = i3dtype.createDefaultI3Data(x.size)
i3dtype.posSet(i3data, 'x', x)
i3dtype.posSet(i3data, 'y', y)
i3dtype.setI3Field(i3data, 'i', pi)
self.addMolecules(i3data)
random.seed(0)
nx = args.nx
ny = args.ny
spacing = args.spacing
z_range = args.zrange
if (nx*ny > 1):
curz = -z_range
z_inc = 2.0 * z_range/(nx*ny - 1)
else:
curz = 0.0
z_inc = 0.0
i3data = i3dtype.createDefaultI3Data(nx * ny)
curx = spacing
for i in range(nx):
cury = spacing
for j in range(ny):
k = i*ny+j
i3data['x'][k] = curx + random.random() - 0.5
i3data['y'][k] = cury + random.random() - 0.5
i3data['z'][k] = curz
i3data['xc'][k] = i3data['x'][k]
i3data['yc'][k] = i3data['y'][k]
i3data['zc'][k] = i3data['z'][k]
# Record emitter id in the 'i' field.
help="Stopping value for z position, default is 500nm.")
args = parser.parse_args()
# Create line segments.
lines = []
for i in range(args.nlines):
lines.append(
Line(x_pos=random.uniform(0.0, args.sx),
y_pos=random.uniform(0.0, args.sy),
z_pos=random.uniform(args.z_start, args.z_stop),
angle=random.uniform(args.start_a, args.stop_a),
length=random.uniform(args.minl, args.maxl)))
# Generate emitter locations.
i3data = i3dtype.createDefaultI3Data(args.nemitters)
i = 0
printed = False
while (i < args.nemitters):
if ((i % 1000) == 0):
if not printed:
print("Adding point", i)
printed = True
else:
printed = False
# Get a random line.
line = random.choice(lines)
# Get a random point on the line.
# Save the image.
dax_data.addFrame(image)
# Save the molecule locations.
a_vals = PSF.PSFIntegral(z_vals, h_vals)
ax = numpy.ones(num_objects)
ww = 2.0 * 160.0 * numpy.ones(num_objects)
if (PSF.psf_type == "astigmatic"):
sx_vals = objects[:,3]
sy_vals = objects[:,4]
ax = sy_vals/sx_vals
ww = 2.0*160.0*numpy.sqrt(sx_vals*sy_vals)
mols = i3dtype.createDefaultI3Data(num_objects)
i3dtype.posSet(mols, 'x', x_vals + 1.0)
i3dtype.posSet(mols, 'y', y_vals + 1.0)
i3dtype.posSet(mols, 'z', z_vals)
i3dtype.setI3Field(mols, 'a', a_vals)
i3dtype.setI3Field(mols, 'h', h_vals)
i3dtype.setI3Field(mols, 'w', ww)
i3dtype.setI3Field(mols, 'ax', ax)
i3dtype.setI3Field(mols, 'fr', i+1)
i3_data.addMolecules(mols)
dax_data.close()
i3_data.close()
#
import storm_analysis.sa_library.writeinsight3 as writeinsight3
parser = argparse.ArgumentParser(description = 'Generate test data for Micrometry')
parser.add_argument('--total', dest='total', type=int, required=True,
help = "The total number of localizations.")
parser.add_argument('--match', dest='match', type=float, required=True,
help = "The fraction of localizations that match.")
args = parser.parse_args()
im_size = 512
# Create matching points.
total_match = int(args.total * args.match)
m_data = i3dtype.createDefaultI3Data(total_match)
i3dtype.posSet(m_data, "x", numpy.random.uniform(high = im_size, size = total_match))
i3dtype.posSet(m_data, "y", numpy.random.uniform(high = im_size, size = total_match))
# Create noise 1.
total_noise = args.total - total_match
n1_data = i3dtype.createDefaultI3Data(total_noise)
i3dtype.posSet(n1_data, "x", numpy.random.uniform(high = im_size, size = total_noise))
i3dtype.posSet(n1_data, "y", numpy.random.uniform(high = im_size, size = total_noise))
# Create noise 2.
n2_data = i3dtype.createDefaultI3Data(total_noise)
i3dtype.posSet(n2_data, "x", numpy.random.uniform(high = im_size, size = total_noise))
zp = None
for clc in cl_centers:
if xp is None:
xp = numpy.random.normal(scale=args.dev, size=args.nlocs) + clc[0]
yp = numpy.random.normal(scale=args.dev, size=args.nlocs) + clc[1]
# Z is in nm, we'll assume a 100nm pixel size.
zp = numpy.random.normal(scale=args.dev * 100.0,
size=args.nlocs) + clc[2]
else:
xp = numpy.append(
xp,
numpy.random.normal(scale=args.dev, size=args.nlocs) + clc[0])
yp = numpy.append(
yp,
numpy.random.normal(scale=args.dev, size=args.nlocs) + clc[1])
zp = numpy.append(
zp,
numpy.random.normal(scale=args.dev * 100.0, size=args.nlocs) +
clc[2])
# Create a molecule list structure & save it.
i3data = i3dtype.createDefaultI3Data(args.ncl * args.nlocs)
i3dtype.posSet(i3data, "x", xp)
i3dtype.posSet(i3data, "y", yp)
i3dtype.posSet(i3data, "z", zp)
with writeinsight3.I3Writer(args.i3bin) as i3w:
i3w.addMolecules(i3data)
