def doGaussianFilter(imp, radius=30):
"""This function takes an input stack, and subtracts a gaussian filtered image
from each individual frame. Thereby, everything that is not moving
in a timeseries is filtered away.
Args:
imp (ImagePlus): An input stack as ImagePlus object.
projectionMethod (str, optional): Choose the projection method. Options are
'Average Intensity', 'Max Intensity', 'Min Intensity', 'Sum Slices', 'Standard Deviation', 'Median'.
Defaults to "Median".
Returns:
ImagePlus: The resulting stack.
"""
#Start by getting the active image window and get the current active channel and other stats
cal = imp.getCalibration()
title = imp.getTitle()
# Make gaussian filtered image.
gaussian = IJ.run(imp, "Gaussian Blur...", "sigma=30 stack")
# Subtract Z-Projection and return output ImagePlus.
impout = ImageCalculator().run("Subtract create 32-bit stack", imp,
gaussian)
impout.setCalibration(cal)
return impout
def subtractzproject(imp, projectionMethod="Median"):
"""This function takes an input stack, and subtracts a projection from the
whole stack from each individual frame. Thereby, everything that is not moving
in a timeseries is filtered away.
Args:
imp (ImagePlus): An input stack as ImagePlus object.
projectionMethod (str, optional): Choose the projection method. Options are
'Average Intensity', 'Max Intensity', 'Min Intensity', 'Sum Slices', 'Standard Deviation', 'Median'.
Defaults to "Median".
Returns:
ImagePlus: The resulting stack.
"""
#Start by getting the active image window and get the current active channel and other stats
cal = imp.getCalibration()
title = imp.getTitle()
# Define a dictionary containg method_name:const_fieled_value pairs for the projection methods.
methods_as_strings = [
'Average Intensity', 'Max Intensity', 'Min Intensity', 'Sum Slices',
'Standard Deviation', 'Median'
]
methods_as_const = [
ZProjector.AVG_METHOD, ZProjector.MAX_METHOD, ZProjector.MIN_METHOD,
ZProjector.SUM_METHOD, ZProjector.SD_METHOD, ZProjector.MEDIAN_METHOD
]
method_dict = dict(zip(methods_as_strings, methods_as_const))
# Run Z-Projection.
zp = ZProjector(imp)
zp.setMethod(method_dict[projectionMethod])
zp.doProjection()
impMedian = zp.getProjection()
# Subtract Z-Projection and return output ImagePlus.
impout = ImageCalculator().run("Subtract create 32-bit stack", imp,
impMedian)
impout.setCalibration(cal)
return impout
