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 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 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 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):
#
# 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 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 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 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 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 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 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)
def merge_SVC_bin_files(self):
i3multi = readinsight3.I3Reader(self.i3TestIndivSVCBinNames['multi'])
i3single = readinsight3.I3Reader(self.i3TestIndivSVCBinNames['single'])
num_frames = int(np.max([i3multi.getNumberFrames(),i3single.getNumberFrames()]))
i3out = writeinsight3.I3Writer(self.i3TestCombSVCBinName, frames=num_frames)
im1 = i3multi.getMoleculesInFrameRange(0,num_frames+1)
is1 = i3single.getMoleculesInFrameRange(0,num_frames+1)
n_mol0 = im1.shape[0]
n_mol1 = is1.shape[0]
i3new = i3dtype.createDefaultI3Data(n_mol0+n_mol1)
for i in range(n_mol0):
i3new[i] = im1[i]
for j in range(n_mol1):
i3new[n_mol0+j] = is1[j]
i3new = np.sort(i3new,order=['fr','x','y'])
i3out.addMoleculesWithXYZHCatFrame(i3new['x'],i3new['y'],i3new['z'],i3new['h'],i3new['c'],i3new['fr'])
i3multi.close()
i3single.close()
i3out.close()
im1 = None
is1 = None
i3new = None
return True
if (field[0] != 'Z Rejected'):
if (field[0] not in channelNames):
channelNames.append(field[0])
frameNumber = int(field[12])
if (frameNumber > MaxFrameNumber):
MaxFrameNumber = frameNumber
print(channelNames, MaxFrameNumber)
binWriter = writeinsight3new.I3Writer(file_path + ".bin", MaxFrameNumber)
for idx, line in enumerate(lines):
p1["value"] = idx / len(lines) * 100
root.update()
if idx > 0:
data = i3dtype.createDefaultI3Data(1)
field = line.split('\t')
x = float(field[1])
y = float(field[2])
xc = float(field[3])
yc = float(field[4])
h = float(field[5])
a = float(field[6])
w = float(field[7])
phi = float(field[8])
ax = float(field[9])
bg = float(field[10])
i = float(field[11])
c = 1 # default to 1
channelName = field[0]
def addMoleculesWithXY(self, x, y):
i3data = i3dtype.createDefaultI3Data(x.size)
i3dtype.posSet(i3data, 'x', x)
i3dtype.posSet(i3data, 'y', y)
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 addMoleculesWithXY(self, x, y):
i3data = i3dtype.createDefaultI3Data(x.size)
i3dtype.posSet(i3data, 'x', x)
i3dtype.posSet(i3data, 'y', y)
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)