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segmenter: operations, add simple threshold and change kernel size

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(cherry picked from commit f142cfafe74691bcf22a94616adb189755095669)
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Romain Bazile 2021-06-02 18:33:50 +02:00 committed by Romain Bazile
parent 43f01fa893
commit 6675b2ebfc
1 changed files with 13 additions and 21 deletions
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34
scripts/planktoscope/segmenter/operations.py
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@ -19,7 +19,7 @@ def adaptative_threshold(img):
# start = time.monotonic() # start = time.monotonic()
# logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) # logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss)
logger.debug("Threshold calc") logger.debug("Adaptative threshold calc")
# img_hsv = cv2.cvtColor(img, cv2.COLOR_BGR2HSV) # img_hsv = cv2.cvtColor(img, cv2.COLOR_BGR2HSV)
img_gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY) img_gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
# ret, mask = cv2.threshold(img_gray, 127, 200, cv2.THRESH_OTSU) # ret, mask = cv2.threshold(img_gray, 127, 200, cv2.THRESH_OTSU)
@ -36,13 +36,12 @@ def adaptative_threshold(img):
# logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) # logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss)
# logger.debug(time.monotonic() - start) # logger.debug(time.monotonic() - start)
# logger.success(f"Threshold used was {ret}") # logger.success(f"Threshold used was {ret}")
logger.success(f"Threshold is done") logger.success(f"Adaptative threshold is done")
return mask return mask
def simple_threshold(img): def simple_threshold(img):
"""Apply a threshold to a color image to get a mask from it """Apply a threshold to a color image to get a mask from it
Uses an adaptative threshold with a blocksize of 19 and reduction of 4.
Args: Args:
img (cv2 img): Image to extract the mask from img (cv2 img): Image to extract the mask from
@ -53,24 +52,17 @@ def simple_threshold(img):
# start = time.monotonic() # start = time.monotonic()
# logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) # logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss)
logger.debug("Threshold calc") logger.debug("Simple threshold calc")
# img_hsv = cv2.cvtColor(img, cv2.COLOR_BGR2HSV) # img_hsv = cv2.cvtColor(img, cv2.COLOR_BGR2HSV)
img_gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY) img_gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
# ret, mask = cv2.threshold(img_gray, 127, 200, cv2.THRESH_OTSU) ret, mask = cv2.threshold(
mask = cv2.adaptiveThreshold( img_gray, 127, 255, cv2.THRESH_BINARY_INV + cv2.THRESH_TRIANGLE
img_gray,
maxValue=255,
adaptiveMethod=cv2.ADAPTIVE_THRESH_MEAN_C,
thresholdType=cv2.THRESH_BINARY_INV,
blockSize=19, # must be odd
C=4,
) )
# mask = 255 - img_tmaskhres
# logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) # logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss)
# logger.debug(time.monotonic() - start) # logger.debug(time.monotonic() - start)
# logger.success(f"Threshold used was {ret}") logger.info(f"Threshold value used was {ret}")
logger.success(f"Threshold is done") logger.success(f"Simple threshold is done")
return mask return mask
@ -97,7 +89,7 @@ def erode(mask):
def dilate(mask): def dilate(mask):
"""Apply a dilate operation to the given mask, with an elliptic kernel of 4x4 """Apply a dilate operation to the given mask, with an elliptic kernel of 8x8
Args: Args:
mask (cv2 img): mask to apply the operation on mask (cv2 img): mask to apply the operation on
@ -109,7 +101,7 @@ def dilate(mask):
# start = time.monotonic() # start = time.monotonic()
# logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) # logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss)
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (4, 4)) kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (8, 8))
mask_dilate = cv2.dilate(mask, kernel) mask_dilate = cv2.dilate(mask, kernel)
# logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) # logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss)
@ -119,7 +111,7 @@ def dilate(mask):
def close(mask): def close(mask):
"""Apply a close operation to the given mask, with an elliptic kernel of 4x4 """Apply a close operation to the given mask, with an elliptic kernel of 8x8
Args: Args:
mask (cv2 img): mask to apply the operation on mask (cv2 img): mask to apply the operation on
@ -131,7 +123,7 @@ def close(mask):
# start = time.monotonic() # start = time.monotonic()
# logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) # logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss)
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (4, 4)) kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (8, 8))
mask_close = cv2.morphologyEx(mask, cv2.MORPH_CLOSE, kernel) mask_close = cv2.morphologyEx(mask, cv2.MORPH_CLOSE, kernel)
# logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) # logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss)
@ -141,7 +133,7 @@ def close(mask):
def erode2(mask): def erode2(mask):
"""Apply an erode operation to the given mask, with an elliptic kernel of 4x4 """Apply an erode operation to the given mask, with an elliptic kernel of 8x8
Args: Args:
mask (cv2 img): mask to apply the operation on mask (cv2 img): mask to apply the operation on
@ -153,7 +145,7 @@ def erode2(mask):
# start = time.monotonic() # start = time.monotonic()
# logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) # logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss)
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (4, 4)) kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (8, 8))
mask_erode_2 = cv2.erode(mask, kernel) mask_erode_2 = cv2.erode(mask, kernel)
# logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss) # logger.debug(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss)