Update zebrafishAnalysis.py

bugs

Author: ver228

tierpsy/analysis/ske_create/zebrafishAnalysis/zebrafishAnalysis.py

@@ -77,8 +77,7 @@ def getOrientation(frame, config):
     th_val = 1
 
     ret, binary_img = cv2.threshold(frame, th_val, 255, cv2.THRESH_BINARY)
-
-	contours, hierarchy = cv2.findContours(binary_img, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)[-2:]
+    contours, hierarchy = cv2.findContours(binary_img, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)[-2:]
 
 
     # Sort contours by area
@@ -133,9 +132,9 @@ def _get_range(l):
     # Find rotation angle again, this time only using the head half
 
 
-	contours, hierarchy = cv2.findContours(head_half.copy(), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)[-2:]
-	contours.sort(key=lambda ar: ar.size)
-	largest_contour = contours[-1]
+    contours, hierarchy = cv2.findContours(head_half.copy(), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)[-2:]
+    contours.sort(key=lambda ar: ar.size)
+    largest_contour = contours[-1]
 
 
     [vx, vy, x, y] = cv2.fitLine(largest_contour, cv2.DIST_L2, 0, 0.01, 0.01)
@@ -177,9 +176,9 @@ def getHeadMask(frame):
     head_mask = np.zeros((img_thresh.shape[0], img_thresh.shape[1]), np.uint8)
 
 
-	contours, hierarchy = cv2.findContours(img_thresh, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)[-2:]
-	contours.sort(key=lambda ar: ar.size)
-	head_contour = contours[-1]
+    contours, hierarchy = cv2.findContours(img_thresh, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)[-2:]
+    contours.sort(key=lambda ar: ar.size)
+    head_contour = contours[-1]
 
 
     cv2.drawContours(head_mask, [head_contour], 0, 255, cv2.FILLED)
@@ -192,11 +191,11 @@ def getHeadPoint(rotated_img, angle):
     theta = math.radians(- angle)
 
 
-	img_binary = np.zeros(rotated_img.shape, np.uint8)
-	contours, hierarchy = cv2.findContours(rotated_img.copy(), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)[-2:]
-	contours.sort(key=lambda ar: ar.size)
-	largest_contour = contours[-1]
-	cv2.drawContours(img_binary, [largest_contour], 0, 255, cv2.FILLED)
+    img_binary = np.zeros(rotated_img.shape, np.uint8)
+    contours, hierarchy = cv2.findContours(rotated_img.copy(), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)[-2:]
+    contours.sort(key=lambda ar: ar.size)
+    largest_contour = contours[-1]
+    cv2.drawContours(img_binary, [largest_contour], 0, 255, cv2.FILLED)
 
 
     valid_pixels = np.nonzero(img_binary)
@@ -225,8 +224,8 @@ def getTailStartPoint(head_mask, head_point, config):
 	# Calculate the angle from the head point to the contour center
 	# Then, 'walk' down the line from the head point to the contour center point a set length
 
-	contours, hierarchy = cv2.findContours(head_mask.copy(), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)[-2:]
-	contour = contours[-1]
+    contours, hierarchy = cv2.findContours(head_mask.copy(), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)[-2:]
+    contour = contours[-1]
 
 
     # Get contour center
@@ -504,7 +503,7 @@ def getZebrafishMask(frame, config):
 
     worm_mask = cleaned_mask.copy()
 
-	contours, hierarchy = cv2.findContours(cleaned_mask.copy(), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)[-2:]
+    contours, hierarchy = cv2.findContours(cleaned_mask.copy(), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)[-2:]