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Remove method objects3d.get_objects_within_intensity #123

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Remove method objects3d.get_objects_within_intensity #123

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34 changes: 0 additions & 34 deletions src/imcflibs/imagej/objects3d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -117,40 +117,6 @@ def segment_3d_image(imp, title=None, min_thresh=1, min_vol=None, max_vol=None):
return seg.getImagePlus()


def get_objects_within_intensity(obj_pop, imp, min_intensity, max_intensity):
"""Filter a population for objects within the given intensity range.

Parameters
----------
obj_pop : mcib3d.geom.Objects3DPopulation
A population of 3D objects.
imp : ij.ImagePlus
An ImagePlus on which the population is based.
min_intensity : float
Minimum mean intensity threshold for filtering objects.
max_intensity : float
Maximum mean intensity threshold for filtering objects.

Returns
-------
Objects3DPopulation
New population with the objects filtered by intensity.
"""
objects_within_intensity = []

# Iterate over all objects in the population
for i in range(0, obj_pop.getNbObjects()):
obj = obj_pop.getObject(i)
# Calculate the mean intensity of the object
mean_intensity = obj.getPixMeanValue(ImageHandler.wrap(imp))
# Check if the object is within the specified intensity range
if mean_intensity >= min_intensity and mean_intensity < max_intensity:
objects_within_intensity.append(obj)

# Return the new population with the filtered objects
return Objects3DPopulation(objects_within_intensity)


def maxima_finder_3d(imp, min_threshold=0, noise=100, rxy=1.5, rz=1.5):
"""Find local maxima in a 3D image.

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