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Make image2blackwhite functions user-accessible #360

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Make image2blackwhite functions user-accessible #360

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2 changes: 1 addition & 1 deletion pyopia/__init__.py
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
__version__ = "2.12.0"
__version__ = "2.15.0"
20 changes: 16 additions & 4 deletions pyopia/process.py
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Original file line number Diff line number Diff line change
Expand Up @@ -376,13 +376,16 @@ def measure_particles(imbw, max_particles=5000):
return region_properties


def segment(img, threshold=0.98, minimum_area=12, fill_holes=True):
def segment(img, binary_method='fast', threshold=0.98, minimum_area=12, fill_holes=True):
'''Create a binary image from a background-corrected image.

Parameters
----------
img : np.array
background-corrected image
binary_method : str
method used to convert the background-corrected image to a binary image.
Options are 'fast' or 'accurate', by default 'fast'
threshold : float, optional
segmentation threshold, by default 0.98
minimum_area : int, optional
Expand All @@ -397,7 +400,11 @@ def segment(img, threshold=0.98, minimum_area=12, fill_holes=True):
'''
logger.info('segment')

imbw = image2blackwhite_fast(img, threshold)
match binary_method:
case 'accurate':
imbw = image2blackwhite_accurate(img, threshold)
case 'fast':
imbw = image2blackwhite_fast(img, threshold)

logger.info('clean')

Expand Down Expand Up @@ -484,6 +491,9 @@ class Segment():

Parameters
----------
binary_method : str
method used to convert the background-corrected image to a binary image.
Options are 'fast' or 'accurate'. Defaults to 'fast'.
minimum_area : (int, optional)
minimum number of pixels for particle detection. Defaults to 12.
threshold : (float, optional)
Expand All @@ -503,19 +513,21 @@ class Segment():
'''

def __init__(self,
binary_method='fast',
minimum_area=12,
threshold=0.98,
fill_holes=True,
segment_source='im_corrected'):

self.binary_method = binary_method
self.minimum_area = minimum_area
self.threshold = threshold
self.fill_holes = fill_holes
self.segment_source = segment_source

def __call__(self, data):
data['imbw'] = segment(data[self.segment_source], threshold=self.threshold, fill_holes=self.fill_holes,
minimum_area=self.minimum_area)
data['imbw'] = segment(data[self.segment_source], binary_method=self.binary_method, threshold=self.threshold,
fill_holes=self.fill_holes, minimum_area=self.minimum_area)
return data


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