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 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 addMoleculesWithXYICat(self, x, y, pi, cat):
i3data = i3dtype.createDefaultI3Data(x.size)
i3dtype.posSet(i3data, 'x', x)
i3dtype.posSet(i3data, 'y', y)
i3dtype.setI3Field(i3data, 'i', pi)
i3dtype.setI3Field(i3data, 'c', cat)
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 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):
"""
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 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 addMoleculesWithXYICat(self, x, y, pi, cat):
i3data = i3dtype.createDefaultI3Data(x.size)
i3dtype.posSet(i3data, 'x', x)
i3dtype.posSet(i3data, 'y', y)
i3dtype.setI3Field(i3data, 'i', pi)
i3dtype.setI3Field(i3data, 'c', cat)
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 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 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_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_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 addMoleculesWithXYZI(self, x, y, z, pi):
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)
self.addMolecules(i3data)
def addMoleculesWithXYZI(self, x, y, z, pi):
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)
self.addMolecules(i3data)
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 addMoleculesWithXYZICatFrame(self, x, y, z, pi, cat, 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, 'c', cat)
i3dtype.setI3Field(i3data, 'fr', f)
self.addMolecules(i3data)
def addMoleculesWithXYZICatFrame(self, x, y, z, pi, cat, 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, 'c', cat)
i3dtype.setI3Field(i3data, 'fr', f)
self.addMolecules(i3data)
def drift(self, frame_number, i3_data):
# Check that frame number is in range.
if (frame_number >= self.drift_data.shape[0]):
frame_number = self.drift_data.shape[0] - 1
dx = self.drift_data[frame_number, 0]
dy = self.drift_data[frame_number, 1]
dz = self.drift_data[frame_number, 2]
i3dtype.posSet(i3_data, "x", i3_data["x"] + dx)
i3dtype.posSet(i3_data, "y", i3_data["y"] + dy)
i3dtype.posSet(i3_data, "z", i3_data["z"] + dz)
def addMultiFitMolecules(self,
molecules,
x_size,
y_size,
frame,
nm_per_pixel,
inverted=False):
n_molecules = molecules.shape[0]
h = molecules[:, 0]
if inverted:
xc = y_size - molecules[:, 1]
yc = x_size - molecules[:, 3]
wx = 2.0 * molecules[:, 2] * nm_per_pixel
wy = 2.0 * molecules[:, 4] * nm_per_pixel
else:
xc = molecules[:, 3] + 1
yc = molecules[:, 1] + 1
wx = 2.0 * molecules[:, 4] * nm_per_pixel
wy = 2.0 * molecules[:, 2] * nm_per_pixel
bg = molecules[:, 5]
zc = molecules[:,
6] * 1000.0 # fitting is done in um, insight works in nm
st = numpy.round(molecules[:, 7])
err = molecules[:, 8]
# calculate peak area, which is saved in the "a" field.
parea = 2.0 * 3.14159 * h * molecules[:, 2] * molecules[:, 4]
ax = wy / wx
ww = numpy.sqrt(wx * wy)
i3data = i3dtype.createDefaultI3Data(xc.size)
i3dtype.posSet(i3data, 'x', xc)
i3dtype.posSet(i3data, 'y', yc)
i3dtype.posSet(i3data, 'z', zc)
i3dtype.setI3Field(i3data, 'h', h)
i3dtype.setI3Field(i3data, 'bg', bg)
i3dtype.setI3Field(i3data, 'fi', st)
i3dtype.setI3Field(i3data, 'a', parea)
i3dtype.setI3Field(i3data, 'w', ww)
i3dtype.setI3Field(i3data, 'ax', ax)
i3dtype.setI3Field(i3data, 'fr', frame)
i3dtype.setI3Field(i3data, 'i', err)
self.addMolecules(i3data)
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)
def addMoleculesWithXY(self, x, y):
i3data = i3dtype.createDefaultI3Data(x.size)
i3dtype.posSet(i3data, 'x', x)
i3dtype.posSet(i3data, 'y', y)
self.addMolecules(i3data)
cx = numpy.random.uniform(low = 20.0, high = 236.0, size = clusters)
cy = numpy.random.uniform(low = 20.0, high = 236.0, size = clusters)
cz = numpy.random.uniform(low = -300.0, high = 300.0, size = clusters)
with writeinsight3.I3Writer("../data/test_clustering_list.bin") as i3_fp:
for i in range(length):
if((i % 500) == 0):
print("Creating frame", i)
on = (numpy.random.uniform(size = clusters) < p_on)
number_on = numpy.count_nonzero(on)
x = cx + numpy.random.normal(scale = 0.5, size = clusters)
y = cy + numpy.random.normal(scale = 0.5, size = clusters)
z = cz + numpy.random.normal(scale = 50.0, size = clusters)
# Add background
x = numpy.concatenate((x[on], numpy.random.uniform(high = 256.0, size = background)))
y = numpy.concatenate((y[on], numpy.random.uniform(high = 256.0, size = background)))
z = numpy.concatenate((z[on], numpy.random.uniform(low = -500.0, high = 500.0, size = background)))
i3d = i3dtype.createDefaultI3Data(number_on + background)
i3dtype.posSet(i3d, "x", x)
i3dtype.posSet(i3d, "y", y)
i3dtype.posSet(i3d, "z", z)
i3dtype.setI3Field(i3d, "fr", i+1)
i3_fp.addMolecules(i3d)
cy = numpy.random.uniform(low = 20.0, high = 236.0, size = clusters)
cz = numpy.random.uniform(low = -300.0, high = 300.0, size = clusters)
with open("../data/test_drift.txt", "w") as drift_fp:
with writeinsight3.I3Writer("../data/test_drift_mlist.bin") as i3_fp:
for i in range(length):
if((i % 500) == 0):
print("Creating frame", i)
drift_x = i * dx
drift_y = i * dy
drift_z = i * dz
drift_fp.write("{0:0d}\t{1:.3f}\t{2:.3f}\t{3:.3f}\n".format(i+1, drift_x, drift_y, drift_z))
on = (numpy.random.uniform(size = clusters) < p_on)
number_on = numpy.count_nonzero(on)
x = cx + drift_x + numpy.random.normal(scale = 0.5, size = clusters)
y = cy + drift_y + numpy.random.normal(scale = 0.5, size = clusters)
z = cz + drift_z + numpy.random.normal(scale = 50.0, size = clusters)
i3d = i3dtype.createDefaultI3Data(number_on)
i3dtype.posSet(i3d, "x", x[on])
i3dtype.posSet(i3d, "y", y[on])
i3dtype.posSet(i3d, "z", z[on])
i3dtype.setI3Field(i3d, "fr", i+1)
i3_fp.addMolecules(i3d)
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)
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))
i3dtype.posSet(n2_data, "y", numpy.random.uniform(high = im_size, size = total_noise))
# Load x,y locations.
i3_in = readinsight3.loadI3File(args.i3bin)
xi = i3_in["x"]
yi = i3_in["y"]
# Map to back channel 0 if necessary.
if (args.channel != 0):
xt_name = str(args.channel) + "_0_x"
yt_name = str(args.channel) + "_0_y"
[xi, yi] = mapXYLocations(xi, yi, mappings[xt_name], mappings[yt_name])
for i in range(8):
if (i == 0):
i3dtype.posSet(i3_in, "x", xi)
i3dtype.posSet(i3_in, "y", yi)
else:
xt_name = "0_" + str(i) + "_x"
yt_name = "0_" + str(i) + "_y"
if xt_name in mappings:
[xf, yf] = mapXYLocations(xi, yi, mappings[xt_name],
mappings[yt_name])
i3dtype.posSet(i3_in, "x", xf)
i3dtype.posSet(i3_in, "y", yf)
else:
break
i3_out_name = basename + "_mapb_c" + str(i) + ".bin"
with writeinsight3.I3Writer(i3_out_name) as i3w:
i3w.addMolecules(i3_in)
# 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()
#
# The MIT License
#z_planes = [-250.0, 250.0]
#z_planes = [-750.0, -250.0, 250.0, 750.0]
z_value = -500.0
# Load emitter locations.
i3_locs = readinsight3.loadI3File("emitters.bin")
if False:
i3_locs = i3_locs[0]
# Make a bin file with emitter locations for each frame.
with writeinsight3.I3Writer("test_olist.bin") as i3w:
for i in range(frames):
i3_temp = i3_locs.copy()
i3dtype.setI3Field(i3_temp, "fr", i + 1)
i3dtype.posSet(i3_temp, "z", z_value)
i3w.addMolecules(i3_temp)
# Load channel to channel mapping file.
with open("map.map", 'rb') as fp:
mappings = pickle.load(fp)
# Create bin files for each plane.
for i, z_plane in enumerate(z_planes):
cx = mappings["0_" + str(i) + "_x"]
cy = mappings["0_" + str(i) + "_y"]
i3_temp = i3_locs.copy()
xi = i3_temp["x"]
yi = i3_temp["y"]
xf = cx[0] + cx[1] * xi + cx[2] * yi
yf = cy[0] + cy[1] * xi + cy[2] * yi
def addMoleculesWithXY(self, x, y):
i3data = i3dtype.createDefaultI3Data(x.size)
i3dtype.posSet(i3data, 'x', x)
i3dtype.posSet(i3data, 'y', y)
self.addMolecules(i3data)
# 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()
#
# The MIT License
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)
