def __init__(self, mainWidget, *args, **kwargs):
super().__init__(*args, **kwargs)
self.main = mainWidget
self.npoints = 200
self.setAntialiasing(True)
# First plot for the number of molecules
self.plot1 = self.plotItem
self.plot1.setLabels(bottom=('Tiempo', 's'),
left=('Number of single molecules'))
self.plot1.showGrid(x=True, y=True)
self.curve1 = self.plot1.plot(pen='y')
self.plot1.vb.setLimits(yMin=-0.5)
# Second plot for the number of overlaps
self.plot2 = pg.ViewBox()
self.ax2 = pg.AxisItem('right')
self.plot1.layout.addItem(self.ax2, 2, 3)
self.plot1.setLimits(yMin=-0.5)
self.plot1.scene().addItem(self.plot2)
self.ax2.linkToView(self.plot2)
self.plot2.setXLink(self.plot1)
self.ax2.setLabel('Number of overlaps')
self.curve2 = pg.PlotCurveItem(pen='r')
self.plot2.addItem(self.curve2)
self.plot2.setLimits(yMin=-0.5)
# Handle view resizing
self.updateViews()
self.plot1.vb.sigResized.connect(self.updateViews)
self.fwhm = tools.get_fwhm(670, 1.42) / 120
self.kernel = tools.kernel(self.fwhm)
def __init__(self,
image,
fit_par=None,
dt=0,
fw=None,
win_size=None,
kernel=None,
xkernel=None,
bkg_image=None):
self.image = image
self.bkg_image = bkg_image
# Noise removal by convolving with a null sum gaussian. Its FWHM
# has to match the one of the objects we want to detect.
try:
self.fwhm = fw
self.win_size = win_size
self.kernel = kernel
self.xkernel = xkernel
self.image_conv = convolve(self.image.astype(float), self.kernel)
except RuntimeError:
# If the kernel is None, I assume all the args must be calculated
self.fwhm = tools.get_fwhm(670, 1.42) / 120
self.win_size = int(np.ceil(self.fwhm))
self.kernel = tools.kernel(self.fwhm)
self.xkernel = tools.xkernel(self.fwhm)
self.image_conv = convolve(self.image.astype(float), self.kernel)
# TODO: FIXME
if self.bkg_image is None:
self.bkg_image = self.image_conv
self.fit_par = fit_par
self.dt = dt
def __init__(self, filename=None, imagename='data'):
if filename is None:
filename = ask_file('Select hdf5 file')
self.file = hdf.File(filename, 'r')
# Loading of measurements (i.e., images) in HDF5 file
self.imageData = self.file[imagename].value
self.nframes = len(self.imageData)
# Attributes loading as attributes of the stack
self.attrs = self.file[imagename].attrs
try:
self.lambda_em = self.attrs['lambda_em']
except:
self.lambda_em = 670
try:
self.NA = self.attrs['NA']
except:
self.NA = 1.42
try:
self.nm_per_px = 1000 * self.attrs['element_size_um'][2]
except:
self.nm_per_px = 120
self.frame = 0
self.fwhm = tools.get_fwhm(self.lambda_em, self.NA) / self.nm_per_px
self.win_size = int(np.ceil(self.fwhm))
self.kernel = tools.kernel(self.fwhm)
self.xkernel = tools.xkernel(self.fwhm)
def __init__(self, mainWidget, *args, **kwargs):
super().__init__(*args, **kwargs)
self.main = mainWidget
self.npoints = 200
self.setAntialiasing(True)
# First plot for the number of molecules
self.plot1 = self.plotItem
self.plot1.setLabels(bottom=('Tiempo', 's'),
left=('Number of single molecules'))
self.plot1.showGrid(x=True, y=True)
self.curve1 = self.plot1.plot(pen='y')
self.plot1.vb.setLimits(yMin=-0.5)
# Second plot for the number of overlaps
self.plot2 = pg.ViewBox()
self.ax2 = pg.AxisItem('right')
self.plot1.layout.addItem(self.ax2, 2, 3)
self.plot1.setLimits(yMin=-0.5)
self.plot1.scene().addItem(self.plot2)
self.ax2.linkToView(self.plot2)
self.plot2.setXLink(self.plot1)
self.ax2.setLabel('Number of overlaps')
self.curve2 = pg.PlotCurveItem(pen='r')
self.plot2.addItem(self.curve2)
self.plot2.setLimits(yMin=-0.5)
# Handle view resizing
self.updateViews()
self.plot1.vb.sigResized.connect(self.updateViews)
self.fwhm = tools.get_fwhm(670, 1.42) / 120
self.kernel = tools.kernel(self.fwhm)
def __init__(self, image, fit_par=None, dt=0, fw=None, win_size=None,
kernel=None, xkernel=None, bkg_image=None):
self.image = image
self.bkg_image = bkg_image
# Noise removal by convolving with a null sum gaussian. Its FWHM
# has to match the one of the objects we want to detect.
try:
self.fwhm = fw
self.win_size = win_size
self.kernel = kernel
self.xkernel = xkernel
self.image_conv = convolve(self.image.astype(float), self.kernel)
except RuntimeError:
# If the kernel is None, I assume all the args must be calculated
self.fwhm = tools.get_fwhm(670, 1.42) / 120
self.win_size = int(np.ceil(self.fwhm))
self.kernel = tools.kernel(self.fwhm)
self.xkernel = tools.xkernel(self.fwhm)
self.image_conv = convolve(self.image.astype(float), self.kernel)
# TODO: FIXME
if self.bkg_image is None:
self.bkg_image = self.image_conv
self.fit_par = fit_par
self.dt = dt