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 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 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 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 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 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 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 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 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 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 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 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 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 = np.round(molecules[:,7])
err = molecules[:,8]
# calculate peak area, which is saved in the "a" field.
sum = 2.0*3.14159*h*molecules[:,2]*molecules[:,4]
ax = wy/wx
ww = np.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', sum)
i3dtype.setI3Field(i3data, 'w', ww)
i3dtype.setI3Field(i3data, 'ax', ax)
i3dtype.setI3Field(i3data, 'fr', frame)
i3dtype.setI3Field(i3data, 'i', err)
self.addMolecules(i3data)
c = 1 # default to 1
channelName = field[0]
if (channelName == 'Z Rejected'):
c = 0
else:
for ch, name in enumerate(channelNames):
if channelName == name:
c = ch + 1
break
fi = int(field[15]) #"valid" for iteration
fr = int(field[12])
tl = int(field[13])
lk = int(field[14])
z = float(field[16])
zc = float(field[17])
i3dtype.setI3Field(data, 'x', x)
i3dtype.setI3Field(data, 'y', y)
i3dtype.setI3Field(data, 'xc', xc)
i3dtype.setI3Field(data, 'yc', yc)
i3dtype.setI3Field(data, 'h', h)
i3dtype.setI3Field(data, 'a', a)
i3dtype.setI3Field(data, 'w', w)
i3dtype.setI3Field(data, 'phi', phi)
i3dtype.setI3Field(data, 'ax', ax)
i3dtype.setI3Field(data, 'bg', bg)
i3dtype.setI3Field(data, 'i', i)
i3dtype.setI3Field(data, 'c', c)
i3dtype.setI3Field(data, 'fi', fi)
i3dtype.setI3Field(data, 'fr', fr)
i3dtype.setI3Field(data, 'tl', tl)
i3dtype.setI3Field(data, 'lk', lk)
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)