def run_analysis(contours, filename, message):
filename = filename.replace("images\\", "").replace("images/", "")
if message != "":
results = message
sys.stdout.write(str(results))
sys.stdout.flush()
else:
properties = imgpheno.contour_properties(contours, (
'Area',
'MajorAxisLength',
))
if properties is None:
pass
else:
properties = imgpheno.contour_properties(contours, (
'Area',
'MajorAxisLength',
))
major_axes = [i['MajorAxisLength'] for i in properties]
if yml.detailed_size_classes is True:
b_0_1 = [i for i in major_axes if i < 4]
b_1_4 = [i for i in major_axes if 4 <= i < 15]
b_4_7 = [i for i in major_axes if 15 <= i < 26]
b_7_12 = [i for i in major_axes if 26 <= i < 45]
larger_12 = [i for i in major_axes if i >= 45]
areas = [i['Area'] for i in properties]
average_area = np.mean(areas)
number_of_insects = (len(b_0_1) + len(b_1_4) + len(b_4_7) +
len(b_7_12) + len(larger_12))
results = """%s \t %s \t %f \t %s \t %s \t %s \t %s \t %s
""" % (filename, number_of_insects, (average_area / 4), len(b_0_1),
len(b_1_4), len(b_4_7), len(b_7_12), len(larger_12))
sys.stdout.write(str(results.replace(" ", "")))
sys.stdout.flush()
else:
smaller_than_4 = [i for i in major_axes if 4 <= i < 15]
between_4_and_10 = [i for i in major_axes if 15 <= i < 38]
larger_than_10 = [i for i in major_axes if 38 <= i < 45]
areas = [i['Area'] for i in properties]
average_area = np.mean(areas)
number_of_insects = (len(smaller_than_4) +
len(between_4_and_10) +
len(larger_than_10))
results = """%s \t %s \t %d \t %s \t %s \t %s
""" % (filename, number_of_insects,
(average_area / 4), len(smaller_than_4),
len(between_4_and_10), len(larger_than_10))
sys.stdout.write(str(results.replace(" ", "")))
sys.stdout.flush()
def process_image(args, path):
global img, img_src
img = cv2.imread(path)
if img == None or img.size == 0:
logging.error("Failed to read %s" % path)
exit(1)
logging.info("Processing %s..." % path)
# Scale the image down if its perimeter exceeds the maximum (if set).
img = common.scale_max_perimeter(img, args.max_size)
img_src = img.copy()
# Perform segmentation
logging.info("- Segmenting...")
mask = common.grabcut(img, args.iters, None, args.margin)
bin_mask = np.where((mask==cv2.GC_FGD) + (mask==cv2.GC_PR_FGD), 255, 0).astype('uint8')
contours, hierarchy = cv2.findContours(bin_mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
# Calculate contour properties.
logging.info("- Computing contour properties...")
props = ft.contour_properties(contours, 'all')
# Print properties.
pprint.pprint(props)
# Draw some properties.
draw_props(props)
def process_image(args, path):
global img, img_src, outline, box, bin_mask
img = cv2.imread(path)
if img == None or img.size == 0:
logging.error("Failed to read %s" % path)
exit(1)
logging.info("Processing %s..." % path)
# Scale the image down if its perimeter exceeds the maximum (if set).
img = common.scale_max_perimeter(img, args.max_size)
img_src = img.copy()
# Perform segmentation.
logging.info("- Segmenting...")
mask = common.grabcut(img, args.iters, None, args.margin)
bin_mask = np.where((mask == cv2.GC_FGD) + (mask == cv2.GC_PR_FGD), 255,
0).astype('uint8')
# Obtain contours (all points) from the mask.
contour = ft.get_largest_contour(bin_mask.copy(), cv2.RETR_EXTERNAL,
cv2.CHAIN_APPROX_NONE)
# Get bounding rectange of the largest contour.
props = ft.contour_properties([contour], 'BoundingRect')
box = props[0]['BoundingRect']
# And draw it.
logging.info("- Done")
draw_sections(0, args.bins)
def process_image(args, path):
global img, img_src, outline, box, bin_mask
img = cv2.imread(path)
if img == None or img.size == 0:
logging.error("Failed to read %s" % path)
exit(1)
logging.info("Processing %s..." % path)
# Scale the image down if its perimeter exceeds the maximum (if set).
img = common.scale_max_perimeter(img, args.max_size)
img_src = img.copy()
# Perform segmentation.
logging.info("- Segmenting...")
mask = common.grabcut(img, args.iters, None, args.margin)
bin_mask = np.where((mask==cv2.GC_FGD) + (mask==cv2.GC_PR_FGD),
255, 0).astype('uint8')
# Obtain contours (all points) from the mask.
contour = ft.get_largest_contour(bin_mask.copy(), cv2.RETR_EXTERNAL,
cv2.CHAIN_APPROX_NONE)
# Get bounding rectange of the largest contour.
props = ft.contour_properties([contour], 'BoundingRect')
box = props[0]['BoundingRect']
# And draw it.
logging.info("- Done")
draw_sections(0, args.bins)
def shape_360_v2(contour, rotation=0, step=1, t=8):
"""Returns a shape feature from a contour.
The rotation in degrees of the contour can be set with `rotation`, which
must be a value between 0 and 179 inclusive. A rotation above 90 degrees
is interpreted as a rotation to the left (e.g. a rotation of 120 is
interpreted as 60 degrees to the left). The returned shape is shifted by
the rotation. The step size for the angle can be set with `step`. Argument
`t` is passed to :meth:`weighted_points_nearest`. The returned shape is
rotation invariant provided that the rotation argument is set properly and
the rotation is no more than 90 degrees left or right.
Shape is returned as a tuple ``(intersects, center)``, where ``intersects``
is a dict where the keys are 0 based angles and the values are lists
of intersecting points. If `step` is set to 1, then the dict will contain
the intersections for 360 degrees. ``center`` specifies the center of the
contour and can be used to calculate distances from center to contour.
"""
if len(contour) < 6:
raise ValueError("Contour must have at least 6 points, found %d" % len(contour))
if not 0 <= rotation <= 179:
raise ValueError("The rotation must be between 0 and 179 inclusive, found %d" % rotation)
# Get the center.
props = ft.contour_properties([contour], 'Centroid')
center = props[0]['Centroid']
# If the rotation is more than 90 degrees, assume the object is rotated to
# the left.
if rotation <= 90:
a = 0
b = 180
else:
a = 180
b = 0
# Define the slope for each point and group points by slope.
slopes = {}
for p in contour:
p = tuple(p[0])
x = p[0] - center[0]
y = p[1] - center[1]
if x == 0:
s = float('inf')
else:
s = float(y) / x
s = round(s, 4)
if s in slopes:
slopes[s].append(p)
else:
slopes[s] = [p]
# Get the intersecting points with the contour for every degree from the
# symmetry axis.
intersects = {}
for angle in range(0, 180, step):
# Get the slope for the linear function of this angle and account for
# the rotation of the object.
slope = ft.slope_from_angle(angle + rotation, inverse=True)
# Since pixel points can only be defined with natural numbers,
# resulting in gaps in between two points, means the maximum
# gap is equal to the slope of the linear function.
gap_max = math.ceil(abs(slope))
# Dmax set empirically.
dmax = gap_max * 0.20
# Make a selection of the contour points which somewhat fit the
# slope for this angle.
candidates = []
for s in slopes:
if math.isinf(slope):
if math.isinf(s):
d = 0
else:
continue
else:
d = abs(slope - s)
if d == 0 or d <= dmax:
for p in slopes[s]:
candidates.append(p)
# Find the contour points from the list of candidate points that
# closely fit the angle's linear function.
# Only save points for which the distance to the expected point is
# no more than the maximum gap. Save each point with a weight value,
# which is used for clustering.
weighted_points = []
for p in candidates:
x = p[0] - center[0]
y = p[1] - center[1]
if math.isinf(slope):
if x == 0:
# Save points that are on the vertical axis.
weighted_points.append( (1, tuple(p)) )
else:
y_exp = slope * x
d = abs(y - y_exp)
if d <= gap_max:
w = 1 / (d+1)
weighted_points.append( (w, tuple(p)) )
assert len(weighted_points) > 0, "No intersections found for angle %d" % angle
# Cluster the points.
weighted_points = ft.weighted_points_nearest(weighted_points, t)
_, points = zip(*weighted_points)
# Figure out on which side of the symmetry the points lie.
# Create a line that separates points on the left from points on
# the right.
if (angle + rotation) != 0:
division_line = ft.angled_line(center, angle + rotation + 90, 100)
else:
# Points cannot be separated when the division line is horizontal.
# So make a division line that is rotated 45 degrees to the left
# instead, so that the points are properly separated.
division_line = ft.angled_line(center, angle + rotation - 45, 100)
intersects[angle] = []
intersects[angle+180] = []
for p in points:
side = ft.side_of_line(division_line, p)
if side < 0:
intersects[angle+a].append(p)
elif side > 0:
intersects[angle+b].append(p)
else:
assert side != 0, "A point cannot be on the division line"
return (intersects, center)
def run_analysis(contours, filename, message):
filename = filename.replace("images/sticky-traps\\", "").replace("images/sticky-traps/", "")
if message != "":
results = message
if yml.result_file == "":
pass
else:
resultfile = open(yml.result_file, "a+")
resultfile.write(str(results))
resultfile.close()
else:
properties = imgpheno.contour_properties(contours, ('Area', 'MajorAxisLength',))
if properties is None:
pass
else:
properties = imgpheno.contour_properties(contours, ('Area', 'MajorAxisLength',))
major_axes = [i['MajorAxisLength'] for i in properties]
if yml.detailed_size_classes is True:
b_0_1 = [i for i in major_axes if i < 4]
b_1_4 = [i for i in major_axes if 4 <= i < 15]
b_4_7 = [i for i in major_axes if 15 <= i < 26]
b_7_12 = [i for i in major_axes if 26 <= i < 45]
larger_12 = [i for i in major_axes if i >= 45]
areas = [i['Area'] for i in properties]
average_area = np.mean(areas)
number_of_insects = (len(b_0_1) + len(b_1_4) + len(b_4_7) + len(b_7_12) + len(larger_12))
print """There are %s insects on the trap in %s.
The average area of the insects in %s is %f mm square.
The number of insects between 0 and 1 mm is %s
The number of insects between 1 and 4 mm is %s
The number of insects between 4 and 7 mm is %s
The number of insects between 7 and 12 mm is %s
The number of insects larger than 12 mm is %s
""" % (number_of_insects, filename, filename,
(average_area / 4), len(b_0_1), len(b_1_4), len(b_4_7), len(b_7_12), len(larger_12))
results = """%s \t %s \t %f \t %s \t %s \t %s \t %s \t %s
""" % (filename, number_of_insects, (average_area / 4), len(b_0_1),
len(b_1_4), len(b_4_7), len(b_7_12), len(larger_12))
if yml.result_file == "":
pass
else:
resultfile = open(yml.result_file, "a+")
resultfile.write(str(results.replace(" ", "")))
resultfile.close()
else:
smaller_than_4 = [i for i in major_axes if 4 <= i < 15]
between_4_and_10 = [i for i in major_axes if 15 <= i < 38]
larger_than_10 = [i for i in major_axes if 38 <= i < 45]
areas = [i['Area'] for i in properties]
average_area = np.mean(areas)
number_of_insects = (len(smaller_than_4) + len(between_4_and_10) + len(larger_than_10))
print """There are %s insects on the trap in %s.
The average area of the insects in %s is %d mm square.
The number of insects smaller than 4 mm is %s
The number of insects between 4 and 10 mm is %s
The number of insects larger than 10 mm is %s
""" % (number_of_insects, filename, filename,
(average_area / 4), len(smaller_than_4), len(between_4_and_10), len(larger_than_10))
results = """%s \t %s \t %d \t %s \t %s \t %s
""" % (filename, number_of_insects, (average_area / 4),
len(smaller_than_4),
len(between_4_and_10), len(larger_than_10))
if yml.result_file == "":
pass
else:
resultfile = open(yml.result_file, "a+")
resultfile.write(str(results.replace(" ", "")))
resultfile.close()
def shape_360_v2(contour, rotation=0, step=1, t=8):
"""Returns a shape feature from a contour.
The rotation in degrees of the contour can be set with `rotation`, which
must be a value between 0 and 179 inclusive. A rotation above 90 degrees
is interpreted as a rotation to the left (e.g. a rotation of 120 is
interpreted as 60 degrees to the left). The returned shape is shifted by
the rotation. The step size for the angle can be set with `step`. Argument
`t` is passed to :meth:`weighted_points_nearest`. The returned shape is
rotation invariant provided that the rotation argument is set properly and
the rotation is no more than 90 degrees left or right.
Shape is returned as a tuple ``(intersects, center)``, where ``intersects``
is a dict where the keys are 0 based angles and the values are lists
of intersecting points. If `step` is set to 1, then the dict will contain
the intersections for 360 degrees. ``center`` specifies the center of the
contour and can be used to calculate distances from center to contour.
"""
if len(contour) < 6:
raise ValueError("Contour must have at least 6 points, found %d" %
len(contour))
if not 0 <= rotation <= 179:
raise ValueError(
"The rotation must be between 0 and 179 inclusive, found %d" %
rotation)
# Get the center.
props = ft.contour_properties([contour], 'Centroid')
center = props[0]['Centroid']
# If the rotation is more than 90 degrees, assume the object is rotated to
# the left.
if rotation <= 90:
a = 0
b = 180
else:
a = 180
b = 0
# Define the slope for each point and group points by slope.
slopes = {}
for p in contour:
p = tuple(p[0])
x = p[0] - center[0]
y = p[1] - center[1]
if x == 0:
s = float('inf')
else:
s = float(y) / x
s = round(s, 4)
if s in slopes:
slopes[s].append(p)
else:
slopes[s] = [p]
# Get the intersecting points with the contour for every degree from the
# symmetry axis.
intersects = {}
for angle in range(0, 180, step):
# Get the slope for the linear function of this angle and account for
# the rotation of the object.
slope = ft.slope_from_angle(angle + rotation, inverse=True)
# Since pixel points can only be defined with natural numbers,
# resulting in gaps in between two points, means the maximum
# gap is equal to the slope of the linear function.
gap_max = math.ceil(abs(slope))
# Dmax set empirically.
dmax = gap_max * 0.20
# Make a selection of the contour points which somewhat fit the
# slope for this angle.
candidates = []
for s in slopes:
if math.isinf(slope):
if math.isinf(s):
d = 0
else:
continue
else:
d = abs(slope - s)
if d == 0 or d <= dmax:
for p in slopes[s]:
candidates.append(p)
# Find the contour points from the list of candidate points that
# closely fit the angle's linear function.
# Only save points for which the distance to the expected point is
# no more than the maximum gap. Save each point with a weight value,
# which is used for clustering.
weighted_points = []
for p in candidates:
x = p[0] - center[0]
y = p[1] - center[1]
if math.isinf(slope):
if x == 0:
# Save points that are on the vertical axis.
weighted_points.append((1, tuple(p)))
else:
y_exp = slope * x
d = abs(y - y_exp)
if d <= gap_max:
w = 1 / (d + 1)
weighted_points.append((w, tuple(p)))
assert len(
weighted_points) > 0, "No intersections found for angle %d" % angle
# Cluster the points.
weighted_points = ft.weighted_points_nearest(weighted_points, t)
_, points = zip(*weighted_points)
# Figure out on which side of the symmetry the points lie.
# Create a line that separates points on the left from points on
# the right.
if (angle + rotation) != 0:
division_line = ft.angled_line(center, angle + rotation + 90, 100)
else:
# Points cannot be separated when the division line is horizontal.
# So make a division line that is rotated 45 degrees to the left
# instead, so that the points are properly separated.
division_line = ft.angled_line(center, angle + rotation - 45, 100)
intersects[angle] = []
intersects[angle + 180] = []
for p in points:
side = ft.side_of_line(division_line, p)
if side < 0:
intersects[angle + a].append(p)
elif side > 0:
intersects[angle + b].append(p)
else:
assert side != 0, "A point cannot be on the division line"
return (intersects, center)
