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add documentation to peak_finder

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Hannes F. Kuchelmeister
2021-07-22 10:07:24 +02:00
parent e4bdf315d6
commit 334f908e82
1 changed files with 31 additions and 4 deletions
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35
situr/registration/peak_finder.py
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@@ -17,7 +17,8 @@ class PeakFinder:
self.__class__.__name__ + '.find_peaks') self.__class__.__name__ + '.find_peaks')
def get_channel_peaks(self, img: SituImage, channel: int, focus_level: int = 0) -> np.ndarray: def get_channel_peaks(self, img: SituImage, channel: int, focus_level: int = 0) -> np.ndarray:
"""Returns the coordinates of peaks (local maxima) in the specified channel and focus_level. It uses the self. """Returns the coordinates of peaks (local maxima) in the specified channel and focus_level.
It uses the method find_peaks.
Args: Args:
img (SituImage): The image to find the peaks on. img (SituImage): The image to find the peaks on.
@@ -29,14 +30,20 @@ class PeakFinder:
""" """
return self.find_peaks(img.get_data()[channel, focus_level, :, :]) return self.find_peaks(img.get_data()[channel, focus_level, :, :])
def show_channel_peaks(self, img: SituImage, channel: int, focus_level: int = 0, img_show=True) -> Image: def show_channel_peaks(self,
"""Returns and shows the found peaks drawn onto the image. Uses get_channel_peaks internally. img: SituImage,
channel: int,
focus_level: int = 0,
img_show=True) -> Image:
"""Returns and shows the found peaks drawn onto the image.
Uses get_channel_peaks internally.
Args: Args:
img (SituImage): The image to find the peaks on. img (SituImage): The image to find the peaks on.
channel (int): The channel that should be used when printing channel (int): The channel that should be used when printing
focus_level (int, optional): The focus level that should be used. Defaults to 0. focus_level (int, optional): The focus level that should be used. Defaults to 0.
img_show (bool, optional): Specifies if img.show is to be called or if just the image should be returned. Defaults to True. img_show (bool, optional): Specifies if img.show is to be called or if just the image
should be returned. Defaults to True.
Returns: Returns:
Image: The image of the specified focus level and channel with encircled peaks. Image: The image of the specified focus level and channel with encircled peaks.
@@ -62,12 +69,32 @@ class PeakFinder:
class PeakFinderDifferenceOfGaussian(PeakFinder): class PeakFinderDifferenceOfGaussian(PeakFinder):
"""A class using difference of gaussian to find peaks. It uses skimage blob_dog internally.
...
Attributes
----------
min_sigma (float)
max_sigma (int)
threshold (float)
"""
def __init__(self, min_sigma=0.75, max_sigma=3, threshold=0.1): def __init__(self, min_sigma=0.75, max_sigma=3, threshold=0.1):
""" For more detailed information about the parameters in the constructor
refer to blob_dog from skimage.feature.
Args:
min_sigma (float, optional): Defaults to 0.75.
max_sigma (int, optional): Defaults to 3.
threshold (float, optional): Defaults to 0.1.
"""
self.min_sigma = min_sigma self.min_sigma = min_sigma
self.max_sigma = max_sigma self.max_sigma = max_sigma
self.threshold = threshold self.threshold = threshold
def find_peaks(self, img_array: np.ndarray) -> np.ndarray: def find_peaks(self, img_array: np.ndarray) -> np.ndarray:
"""Finds the peaks in the input image"""
img = img_as_float(img_array) img = img_as_float(img_array)
peaks = blob_dog(img, min_sigma=self.min_sigma, peaks = blob_dog(img, min_sigma=self.min_sigma,
max_sigma=self.max_sigma, threshold=self.threshold) max_sigma=self.max_sigma, threshold=self.threshold)