def process_wrapper(self, **kwargs):
"""
Contrast Limited Adaptive Histogram Equalization (CLAHE)
Equalizes image using multiple histograms
Real time : Yes
Keyword Arguments (in parentheses, argument name):
* Color space (color_space): Selected color space, default: RGB
* Median filter size (median_filter_size): if >0 a median filter will be applied before, odd values only
* Clip limit (clip_limit): Local histogram clipping limit
* Tile grid size (tile_grid_size): Image partition size
* Overlay text on top of images (text_overlay): Draw description text on top of images
"""
wrapper = self.init_wrapper(**kwargs)
if wrapper is None:
return False
clip_limit = self.get_value_of("clip_limit")
tile_grid_size = self.get_value_of("tile_grid_size")
color_space = self.get_value_of("color_space")
median_filter_size = self.get_value_of("median_filter_size")
text_overlay = self.get_value_of("text_overlay") == 1
res = False
try:
median_filter_size = (0 if median_filter_size == 1 else
ensure_odd(median_filter_size))
if median_filter_size > 0:
src_img = cv2.medianBlur(wrapper.current_image,
median_filter_size)
else:
src_img = wrapper.current_image
self.result = wrapper.apply_CLAHE(
src_img,
color_space=color_space,
clip_limit=(clip_limit, clip_limit, clip_limit),
tile_grid_size=(tile_grid_size, tile_grid_size),
)
wrapper.store_image(
self.result,
f"CLAHE_{self.input_params_as_str()}",
text_overlay=text_overlay,
)
except Exception as e:
res = False
logger.error(f'Failed to process {self. name}: "{repr(e)}"')
else:
res = True
finally:
return res
def process_wrapper(self, **kwargs):
"""
Gaussian filtering:
'Apply Gaussian filter
Real time: True
Keyword Arguments (in parentheses, argument name):
* Activate tool (enabled): Toggle whether or not tool is active
* Source (source):
* Gaussian filter size (odd values only) (kernel_size):"""
wrapper = self.init_wrapper(**kwargs)
if wrapper is None:
return False
res = False
try:
if self.get_value_of("enabled") == 1:
kernel_size = ensure_odd(self.get_value_of("kernel_size"))
img = wrapper.current_image
if self.output_type == ipc.IO_MASK:
mask = self.get_mask()
if mask is None:
logger.error(
"Failure Match image and mask resolution: mask must be initialized"
)
return
else:
mask = None
self.result = cv2.GaussianBlur(
src=img if self.output_type == ipc.IO_IMAGE else mask,
ksize=(kernel_size, kernel_size),
sigmaX=(kernel_size - 1) / 6,
sigmaY=(kernel_size - 1) / 6,
)
if self.output_type == ipc.IO_MASK:
self.result[self.result != 0] = 255
wrapper.store_image(self.result, "current_image")
res = True
else:
wrapper.store_image(wrapper.current_image, "current_image")
res = True
except Exception as e:
res = False
logger.error(f"Median Fileter FAILED, exception: {repr(e)}")
else:
pass
finally:
return res
def process_wrapper(self, **kwargs):
# Copy here the docstring generated by IPSO Phen
wrapper = self.init_wrapper(**kwargs)
if wrapper is None:
return False
res = False
try:
if self.get_value_of("enabled") == 1:
img = wrapper.current_image
threshold = self.get_value_of("threshold")
max_value = self.get_value_of("max_value")
median_filter_size = self.get_value_of("median_filter_size")
median_filter_size = (0 if median_filter_size == 1 else
ipc.ensure_odd(median_filter_size))
c = wrapper.get_channel(img, self.get_value_of("channel"), "",
[], False, median_filter_size)
self.result = pcv.threshold.binary(
c, threshold, max_value, self.get_value_of("object_type"))
# Write your code here
wrapper.store_image(self.result, "current_image")
res = True
else:
wrapper.store_image(wrapper.current_image, "current_image")
res = True
except Exception as e:
res = False
wrapper.error_holder.add_error(
new_error_text=f'Failed to process {self. name}: "{repr(e)}"',
new_error_level=35,
target_logger=logger,
)
else:
pass
finally:
return res
def process_wrapper(self, **kwargs):
"""
Median Filter:
'Apply median filter
Real time: True
Keyword Arguments (in parentheses, argument name):
* Activate tool (enabled): Toggle whether or not tool is active
* Median filter size (odd values only) (median_filter_size):
"""
wrapper = self.init_wrapper(**kwargs)
if wrapper is None:
return False
res = False
try:
if self.get_value_of("enabled") == 1:
median_filter_size = self.get_value_of("median_filter_size")
self.result = cv2.medianBlur(
wrapper.current_image,
ensure_odd(median_filter_size),
)
wrapper.store_image(self.result, "current_image")
res = True
else:
wrapper.store_image(wrapper.current_image, "current_image")
res = True
except Exception as e:
res = False
logger.error(f"Median Fileter FAILED, exception: {repr(e)}")
else:
pass
finally:
return res
def process_wrapper(self, **kwargs):
"""
Print channels:
Real time : True
Keyword Arguments (in parentheses, argument name):
* Channel (channel):
* Normalize channel (normalize):
* Median filter size (odd values only) (median_filter_size):
* Overlay text on top of images (text_overlay): Draw description text on top of images
"""
wrapper = self.init_wrapper(**kwargs)
if wrapper is None:
return False
res = False
try:
median_filter_size = self.get_value_of("median_filter_size")
channel = self.get_value_of("channel")
text_overlay = self.get_value_of("text_overlay") == 1
normalize = self.get_value_of("normalize") == 1
if self.get_value_of("print_mosaic") == 1:
if wrapper.file_handler.is_msp:
_, c = wrapper.build_msp_mosaic(
normalize=normalize,
median_filter_size=median_filter_size,
)
else:
_, c = wrapper.build_channels_mosaic(
src_img=wrapper.current_image,
normalize=normalize,
median_filter_size=median_filter_size,
)
wrapper.store_image(
c,
"channel_mosaic",
text_overlay=text_overlay,
)
else:
median_filter_size = (
0 if median_filter_size == 1 else ensure_odd(median_filter_size)
)
c = wrapper.get_channel(
channel=channel,
median_filter_size=median_filter_size,
normalize=normalize,
)
wrapper.store_image(
c,
f"channel_{self.input_params_as_str()}",
text_overlay=text_overlay,
)
self.result = c
except Exception as e:
res = False
wrapper.error_holder.add_error(
new_error_text=f'Failed to process {self. name}: "{repr(e)}"',
new_error_level=35,
target_logger=logger,
)
else:
res = True
finally:
return res
def process_wrapper(self, **kwargs):
"""
Keep countours near ROIs:
Keep big contours inside a series of ROIs.
Small contours inside ROIs may be added on conditions.
Contours outsside ROIs may be added to root contours if close enough
Real time: False
Keyword Arguments (in parentheses, argument name):
* Activate tool (enabled): Toggle whether or not tool is active
* Name of ROI to be used (roi_names): Operation will only be applied inside of ROI
* ROI selection mode (roi_selection_mode):
* Maximum distance to ROI (init_max_distance):
Maximum distance to add a contour on initialization phase.
If distance is >0, ROIs will dilated with a kernel of size distance.
* Minimum contour size (init_min_size): Minimum accepted size for a contour on initialization phase
* Delete all contours smaller than (delete_all_bellow):
All contours below this size will be permanently ignored.
The more smaller contours are delete, the faster the algorithm
* Merge distance for root contours (root_merge_distance):
* Aggregate small contours inside ROIs distance (small_contours_distance_tolerance):
Aggregate small contours inside ROIs if closer than x to any root contour.
Any aggregated contour is considered as a root one.
* Aggregate unknown contours distance (unk_contours_distance_tolerance):
Aggregate unknown contours if closer than x to any root contour.
Any aggregated contour is considered as a root one.
"""
wrapper = self.init_wrapper(**kwargs)
if wrapper is None:
return False
res = False
try:
if self.get_value_of("enabled") == 1:
img = wrapper.current_image
mask = self.get_mask()
if mask is None:
logger.error(f"FAIL {self.name}: mask must be initialized")
return
# Get ROIs as mask
rois = self.get_ipt_roi(
wrapper=wrapper,
roi_names=self.get_value_of("roi_names").replace(
" ", "").split(","),
selection_mode=self.get_value_of("roi_selection_mode"),
)
if rois:
rois_mask = np.zeros_like(mask)
for roi in rois:
rois_mask = roi.draw_to(dst_img=rois_mask,
line_width=-1,
color=255)
else:
self.result = mask
logger.error(
f"Warning {self.name}: must have at least one ROI")
res = True
return
wrapper.store_image(rois_mask, "rois_as_mask")
# Get source contours
contours = ipc.get_contours(
mask=mask,
retrieve_mode=cv2.RETR_LIST,
method=cv2.CHAIN_APPROX_SIMPLE,
)
# Dilate ROIs
init_max_distance = self.get_value_of("init_max_distance")
if init_max_distance > 0:
rois_mask = wrapper.dilate(
image=rois_mask,
kernel_size=ipc.ensure_odd(i=init_max_distance,
min_val=3),
)
wrapper.store_image(rois_mask, "dilated_rois")
# Remove smaller contours
delete_all_bellow = self.get_value_of("delete_all_bellow")
if delete_all_bellow > 0:
fnt = (cv2.FONT_HERSHEY_SIMPLEX, 0.6)
small_img = mask.copy()
small_img = np.dstack((small_img, small_img, small_img))
for cnt in contours:
area_ = cv2.contourArea(cnt)
if area_ < delete_all_bellow:
# Delete
cv2.drawContours(mask, [cnt], 0, (0, 0, 0), -1)
# Print debug image
x, y, w, h = cv2.boundingRect(cnt)
x += w // 2 - 10
y += h // 2
cv2.drawContours(small_img, [cnt], -1, ipc.C_RED,
-1)
cv2.putText(
small_img,
f"Area: {area_}",
(x, y),
fnt[0],
fnt[1],
ipc.C_FUCHSIA,
2,
)
else:
cv2.drawContours(small_img, [cnt], -1, ipc.C_GREEN,
-1)
wrapper.store_image(small_img, "small_removed_mask")
# Find root contours
root_cnts = []
small_cnts = []
unk_cnts = []
init_min_size = self.get_value_of("init_min_size")
tmp_img = np.zeros_like(mask)
for i, cnt in enumerate(contours):
cv2.drawContours(
image=tmp_img,
contours=[cnt],
contourIdx=0,
color=255,
thickness=-1,
)
intersection = cv2.bitwise_and(tmp_img, rois_mask)
cv2.drawContours(
image=tmp_img,
contours=[cnt],
contourIdx=0,
color=0,
thickness=-1,
)
if np.sum(intersection[intersection != 0]) > 0:
if cv2.contourArea(cnt) > init_min_size:
root_cnts.append(cnt)
else:
small_cnts.append(cnt)
else:
unk_cnts.append(cnt)
# approx_eps = self.get_value_of("approx_eps") / 10000
cnt_approx = {
"root": [{
"cnt": cnt,
"label": i
} for i, cnt in enumerate(root_cnts)],
"small": [{
"cnt": cnt,
"label": i + len(root_cnts)
} for i, cnt in enumerate(small_cnts)],
"unk": [{
"cnt": cnt,
"label": i + len(root_cnts) + len(small_cnts)
} for i, cnt in enumerate(unk_cnts)],
"discarded": [],
}
cnt_data = [
{
"name": "root",
"start_color": (0, 50, 0),
"stop_color": (0, 255, 0),
"print_label": True,
},
{
"name": "small",
"start_color": (50, 0, 0),
"stop_color": (255, 0, 0),
"print_label": False,
},
{
"name": "unk",
"start_color": (0, 0, 50),
"stop_color": (0, 0, 255),
"print_label": False,
},
]
bck_img = wrapper.current_image
for roi in rois:
bck_img = roi.draw_to(dst_img=bck_img,
line_width=2,
color=ipc.C_WHITE)
self.draw_contours(
canvas=bck_img,
contours=cnt_approx,
image_name="contours_after_init",
contours_data=cnt_data,
)
# Merge root contours by label
root_merge_distance = self.get_value_of("root_merge_distance")
stable = False
step = 1
while not stable and step < 100:
stable = True
for left_index, left in enumerate(cnt_approx["root"]):
for right_index, right in enumerate(
cnt_approx["root"]):
if left_index == right_index:
continue
if (left["label"] != right["label"]
and wrapper.contours_min_distance(
left["cnt"],
right["cnt"]) < root_merge_distance):
right["label"] = left["label"]
stable = False
self.draw_contours(
canvas=wrapper.current_image,
contours=cnt_approx,
image_name=f"merging_root_{step}",
contours_data=cnt_data,
)
step += 1
self.draw_contours(
canvas=wrapper.current_image,
contours=cnt_approx,
image_name="root_labels_merged",
contours_data=cnt_data,
)
# Merge small contours
small_contours_distance_tolerance = self.get_value_of(
"small_contours_distance_tolerance")
stable = False
step = 1
while not stable and step < 100:
stable = True
for root in cnt_approx["root"]:
i = 0
while i < len(cnt_approx["small"]):
small = cnt_approx["small"][i]
if (wrapper.contours_min_distance(
root["cnt"], small["cnt"]) <
small_contours_distance_tolerance):
new_root = cnt_approx["small"].pop(i)
new_root["label"] = root["label"]
cnt_approx["root"].append(new_root)
stable = False
else:
i += 1
if not stable:
self.draw_contours(
canvas=wrapper.current_image,
contours=cnt_approx,
image_name=f"merging_small_{step}",
contours_data=cnt_data,
)
step += 1
self.draw_contours(
canvas=wrapper.current_image,
contours=cnt_approx,
image_name="small_labels_merged",
contours_data=cnt_data,
)
# Merge unknown contours
unk_contours_distance_tolerance = self.get_value_of(
"unk_contours_distance_tolerance")
stable = False
step = 1
while not stable and step < 100:
stable = True
for root in cnt_approx["root"]:
i = 0
while i < len(cnt_approx["unk"]):
unk = cnt_approx["unk"][i]
if (wrapper.contours_min_distance(
root["cnt"], unk["cnt"]) <
unk_contours_distance_tolerance):
new_root = cnt_approx["unk"].pop(i)
new_root["label"] = root["label"]
cnt_approx["root"].append(new_root)
stable = False
else:
i += 1
if not stable:
self.draw_contours(
canvas=wrapper.current_image,
contours=cnt_approx,
image_name=f"merging_unk_{step}",
contours_data=cnt_data,
)
step += 1
self.demo_image = self.draw_contours(
canvas=wrapper.current_image,
contours=cnt_approx,
image_name="unk_labels_merged",
contours_data=cnt_data,
)
# Clean mask
contours = ipc.get_contours(
mask=mask,
retrieve_mode=cv2.RETR_LIST,
method=cv2.CHAIN_APPROX_SIMPLE,
)
src_image = wrapper.current_image
for cnt in contours:
is_good_one = False
for root in cnt_approx["root"]:
if wrapper.contours_min_distance(root["cnt"],
cnt) <= 0:
is_good_one = True
break
if is_good_one:
cv2.drawContours(src_image, [cnt], 0, (0, 255, 0), 2)
else:
cv2.drawContours(src_image, [cnt], 0, (0, 0, 255), 2)
cv2.drawContours(mask, [cnt], 0, 0, -1)
wrapper.store_image(src_image, "kcnr_img_wth_tagged_cnt")
wrapper.store_image(mask, "kcnr_final")
self.result = mask
res = True
else:
wrapper.store_image(wrapper.current_image, "current_image")
res = True
except Exception as e:
res = False
wrapper.error_holder.add_error(
new_error_text=f'Failed to process {self. name}: "{repr(e)}"',
new_error_level=35,
target_logger=logger,
)
else:
pass
finally:
return res
def process_wrapper(self, **kwargs):
"""
Adaptive threshold:
Real time : True
Keyword Arguments (in parentheses, argument name):
* Activate tool (enabled): Toggle whether or not tool is active
* Select source file type (source_file): no clue
* Channel (channel):
* Invert mask (invert_mask): Invert result
* Max value (max_value): Non-zero value assigned to the pixels for which the condition
is satisfied
* Adaptive method (method): Adaptive thresholding algorithm to use,
see cv::AdaptiveThresholdTypes
* Block size (block_size): Size of a pixel neighborhood that is used to calculate a
threshold value for the pixel: 3, 5, 7, and so on.
* C (C): Constant subtracted from the mean or weighted mean (see the details below).
Normally, it is positive but may be zero or negative as well.
* Build mosaic (build_mosaic): If true source and result will be displayed side by side
* Median filter size (odd values only) (median_filter_size):
* Morphology operator (morph_op):
* Kernel size (kernel_size):
* Kernel shape (kernel_shape):
* Iterations (proc_times):
* Overlay text on top of images (text_overlay): Draw description text on top of images
"""
wrapper = self.init_wrapper(**kwargs)
if wrapper is None:
return False
res = False
try:
src_img = self.wrapper.current_image
wrapper.store_image(src_img, "source")
if self.get_value_of("enabled") == 1:
median_filter_size = self.get_value_of("median_filter_size")
median_filter_size = (
0 if median_filter_size == 1 else ensure_odd(median_filter_size)
)
if self.get_value_of("invert_mask") == 1:
invert = cv2.THRESH_BINARY_INV
else:
invert = cv2.THRESH_BINARY
max_value = self.get_value_of("max_value")
method = self.get_value_of("method")
if method == "gauss":
method = cv2.ADAPTIVE_THRESH_GAUSSIAN_C
elif method == "mean":
method = cv2.ADAPTIVE_THRESH_MEAN_C
else:
logger.error(f"Unknown method {method}")
return False
block_size = self.get_value_of("block_size")
if block_size % 2 == 0:
block_size += 1
c_value = self.get_value_of("C")
channel = self.get_value_of("channel")
text_overlay = self.get_value_of("text_overlay") == 1
build_mosaic = self.get_value_of("build_mosaic") == 1
c = wrapper.get_channel(
src_img, channel, median_filter_size=median_filter_size
)
if c is None:
self.do_channel_failure(channel)
return
# Crop if channel is msp
if (c.shape != src_img.shape) and (
self.get_value_of("source_file", "source") == "cropped_source"
):
c = wrapper.crop_to_keep_roi(c)
mask = cv2.adaptiveThreshold(
src=c,
maxValue=max_value,
adaptiveMethod=method,
thresholdType=invert,
blockSize=block_size,
C=c_value,
)
self.result = self.apply_morphology_from_params(mask)
wrapper.store_image(
self.result,
f"adaptive_threshold_{self.input_params_as_str()}",
text_overlay=text_overlay,
)
if build_mosaic:
wrapper.store_image(c, "source_channel")
canvas = wrapper.build_mosaic(
image_names=np.array(
[
"source_channel",
f"adaptive_threshold_{self.input_params_as_str()}",
]
)
)
wrapper.store_image(canvas, "mosaic")
res = True
except Exception as e:
res = False
logger.error(f'Failed to process {self. name}: "{repr(e)}"')
else:
pass
finally:
return res
def process_wrapper(self, **kwargs):
"""
Performs channel subtraction while ensure 8bit range, each channel can have a weight.
If threshold min or max are set a threshold operation will be performed.
Real time : Yes
Keyword Arguments (in parentheses, argument name):
* Channel 1 (channel_1): First channel
* Weight of the first channel (alpha): Weight of the first channel
* Channel 2 (channel_2): Second channel
* Weight of the second channel (beta): Weight of the second channel
* Threshold min value (min): Lower threshold bound, if >0 threshold will be applied
* Threshold max value (max): Upper threshold bound, if <255 threshold will be applied
* Median filter size (median_filter_size): odd values only, if not 1 will be added
* Morphology operator (morphology_op): Can be none
* Morphology kernel size (kernel_size): Kernel is elliptical
"""
wrapper = self.init_wrapper(**kwargs)
if wrapper is None:
return False
channel_1 = self.get_value_of("channel_1")
alpha = self.get_value_of("alpha") / 100
channel_2 = self.get_value_of("channel_2")
beta = self.get_value_of("beta") / 100
post_processing = self.get_value_of("post_processing")
min_ = self.get_value_of("min")
max_ = self.get_value_of("max")
median_filter_size = self.get_value_of("median_filter_size")
median_filter_size = (0 if median_filter_size == 1 else
ensure_odd(median_filter_size))
res = False
try:
img = self.wrapper.current_image
c1 = wrapper.get_channel(img, channel_1)
c2 = wrapper.get_channel(img, channel_2)
if c1 is None:
self.do_channel_failure(channel_1)
return
if c2 is None:
self.do_channel_failure(channel_2)
return
wrapper.store_image(c1, f"Channel 1: {channel_1}")
wrapper.store_image(c2, f"Channel 1: {channel_2}")
tmp = (c1 * alpha) - (c2 * beta)
if post_processing == "normalize":
tmp = ((tmp - tmp.min()) / (tmp.max() - tmp.min()) *
255).astype(np.uint8)
elif post_processing == "cut_negative":
tmp[tmp < 0] = 0
tmp = tmp.astype(np.uint8)
elif post_processing == "cut_negative_and_normalize":
tmp[tmp < 0] = 0
tmp = ((tmp - tmp.min()) / (tmp.max() - tmp.min()) *
255).astype(np.uint8)
elif post_processing == "rescale":
tmp = (tmp - tmp.min()).astype(np.uint8)
else:
logger.error(f"Unknown postprocessing {post_processing}")
res = False
return
wrapper.store_image(
tmp,
f"Subtraction_{self.input_params_as_str(exclude_defaults=True)}",
text_overlay=True,
)
if (min_ > 0) or (max_ < 255):
mask, _ = wrapper.get_mask(
tmp, "", min_, max_, median_filter_size=median_filter_size)
mask = self.apply_morphology_from_params(mask)
wrapper.store_image(
mask,
f"sub_threshold_{self.input_params_as_str(exclude_defaults=True)}",
text_overlay=True,
)
self.result = mask.copy()
else:
self.result = tmp.copy()
except Exception as e:
res = False
logger.error(f'Failed to process {self. name}: "{repr(e)}"')
else:
res = True
finally:
return res
def process_wrapper(self, **kwargs):
"""
Smooth contours:
'Smooth contours
Real time: True
Keyword Arguments (in parentheses, argument name):
* Activate tool (enabled): Toggle whether or not tool is active
* Degree of spline curve (spline_degree): Degree of the spline. Cubic splines are recommended. Even values of k should be avoided especially with a small s-value. 1 <= k <= 5, default is 3.
* Smoothing condition (smoothing): Value will be divide by 10"""
wrapper = self.init_wrapper(**kwargs)
if wrapper is None:
return False
res = False
try:
if self.get_value_of("enabled") == 1:
img = wrapper.current_image
mask = self.get_mask()
if mask is None:
logger.error(
"Failure Smooth contours: mask must be initialized")
return
# Get source contours
contours = [
c for c in ipc.get_contours(
mask=mask,
retrieve_mode=cv2.RETR_LIST,
method=cv2.CHAIN_APPROX_SIMPLE,
) if (cv2.contourArea(c, True) < 0)
]
contours.sort(key=lambda x: cv2.contourArea(x), reverse=True)
output = mask.copy()
for contour in contours:
x, y = contour.T
# Convert from np arrays to normal arrays
tck, u, = splprep(
[x.tolist()[0], y.tolist()[0]],
u=None,
k=ipc.ensure_odd(self.get_value_of("spline_degree")),
s=self.get_value_of("smoothing") / 10,
per=1,
)
u_new = np.linspace(u.min(), u.max(), 1000)
x_new, y_new = splev(u_new, tck, der=0)
cv2.drawContours(
output,
[
np.asarray(
[[[int(i[0]), int(i[1])]]
for i in zip(x_new, y_new)],
dtype=np.int32,
)
],
0,
255,
-1,
)
self.result = output
# Write your code here
wrapper.store_image(output, "current_image")
res = True
else:
wrapper.store_image(wrapper.current_image, "current_image")
res = True
except Exception as e:
res = False
logger.error(f"Smooth contours FAILED, exception: {repr(e)}")
else:
pass
finally:
return res
def process_wrapper(self, **kwargs):
"""
Triangle binarization:
Real time : No
Keyword Arguments (in parentheses, argument name):
* Channel (channel): Selected channel
* Invert mask (invert_mask): Invert result
* Median filter size (odd values only) (median_filter_size): Size of median filter to be applied
* Morphology operator (morphology_op): Morphology operator to be applied afterwards
* Morphology kernel size (kernel_size): -
* Overlay text on top of images (text_overlay): Draw description text on top of images
"""
wrapper = self.init_wrapper(**kwargs)
if wrapper is None:
return False
median_filter_size = self.get_value_of("median_filter_size")
invert_mask = self.get_value_of("invert_mask") == 1
channel = self.get_value_of("channel")
text_overlay = self.get_value_of("text_overlay") == 1
build_mosaic = self.get_value_of("build_mosaic") == 1
res = False
try:
src_img = self.wrapper.current_image
median_filter_size = (0 if median_filter_size == 1 else
ensure_odd(median_filter_size))
c = wrapper.get_channel(src_img,
channel,
median_filter_size=median_filter_size)
if c is None:
self.do_channel_failure(channel)
return
# Crop if channel is msp
if (c.shape != src_img.shape) and (self.get_value_of(
"source_file", "source") == "cropped_source"):
c = wrapper.crop_to_keep_roi(c)
_, mask = cv2.threshold(c, 0, 255, cv2.THRESH_TRIANGLE)
if invert_mask:
mask = 255 - mask
self.result = self.apply_morphology_from_params(mask)
wrapper.store_image(
self.result,
f"triangle_binarization_{self.input_params_as_str(exclude_defaults=True)}",
text_overlay=text_overlay,
)
if build_mosaic:
wrapper.store_image(c, "source_channel")
canvas = wrapper.build_mosaic(image_names=np.array([
"source_channel",
f"triangle_binarization_{self.input_params_as_str(exclude_defaults=True)}",
]))
wrapper.store_image(canvas, "mosaic")
res = True
except Exception as e:
res = False
logger.error(f'Failed to process {self. name}: "{repr(e)}"')
else:
pass
finally:
return res
def process_wrapper(self, **kwargs):
"""
Edge detectors:
Performs edge detection with various common operators.
Mostly used by other tools.
Real time: True
Keyword Arguments (in parentheses, argument name):
* Activate tool (enabled): Toggle whether or not tool is active
* Select source file type (source_file): no clue
* Channel (channel):
* Normalize channel (normalize): Normalize channel before edge detection
* Median filter size (odd values only) (median_filter_size):
* Select edge detection operator (operator):
* Canny's sigma for scikit, aperture for OpenCV (canny_sigma): Sigma.
* Canny's first Threshold (canny_first): First threshold for the hysteresis procedure.
* Canny's second Threshold (canny_second): Second threshold for the hysteresis procedure.
* Kernel size (kernel_size):
* Threshold (threshold): Threshold for kernel based operators
* Apply threshold (apply_threshold):
* Overlay text on top of images (text_overlay): Draw description text on top of images
"""
wrapper = self.init_wrapper(**kwargs)
if wrapper is None:
return False
res = False
try:
operator_ = self.get_value_of("operator")
canny_sigma = self.get_value_of("canny_sigma")
canny_first = self.get_value_of("canny_first")
canny_second = self.get_value_of("canny_second")
channel = self.get_value_of("channel")
kernel_size = self.get_value_of("kernel_size")
threshold = self.get_value_of("threshold")
text_overlay = self.get_value_of("text_overlay") == 1
input_kind = self.get_value_of("source_selector")
if input_kind == "mask":
src_img = self.get_mask()
elif input_kind == "current_image":
src_img = wrapper.current_image
else:
src_img = None
logger.error(f"Unknown source: {input_kind}")
self.result = None
return
if self.get_value_of("enabled") == 1:
c = wrapper.get_channel(
src_img=src_img,
channel=channel,
normalize=self.get_value_of("normalize") == 1,
median_filter_size=self.get_value_of("median_filter_size"),
)
if c is None:
self.do_channel_failure(channel)
return
# Crop if channel is msp
ch, cw, *_ = c.shape
sh, sw, *_ = src_img.shape
if ((ch != sh) or (cw != sh)) and (self.get_value_of(
"source_file", "source") == "cropped_source"):
c = wrapper.crop_to_keep_roi(c)
if operator_ == "canny_scik":
edges = canny(
c,
sigma=canny_sigma,
low_threshold=canny_first,
high_threshold=canny_second,
)
elif operator_ == "canny_opcv":
edges = cv2.Canny(
c,
threshold1=canny_first,
threshold2=canny_second,
apertureSize=ipc.ensure_odd(i=canny_sigma,
min_val=3,
max_val=7),
)
elif operator_ == "laplacian":
if kernel_size == 1:
kernel_size = 0
elif (kernel_size > 0) and (kernel_size % 2 == 0):
kernel_size += 1
if kernel_size >= 3:
gauss = cv2.GaussianBlur(c, (kernel_size, kernel_size),
0)
wrapper.store_image(
gauss,
f"filtered_image_{self.input_params_as_str()}",
text_overlay=True,
)
edges = cv2.Laplacian(gauss, cv2.CV_64F)
else:
edges = cv2.Laplacian(c, cv2.CV_64F)
elif operator_ == "sobel":
edges = sobel(c)
elif operator_ == "sobel_v":
edges = sobel_v(c)
elif operator_ == "sobel_h":
edges = sobel_h(c)
elif operator_ == "roberts":
edges = roberts(c)
elif operator_ == "prewitt":
edges = prewitt(c)
else:
edges = c.copy()
edges = self.to_uint8(edges)
if (operator_ in [
"laplacian",
"sobel",
"sobel_v",
"sobel_h",
"roberts",
"prewitt",
] and self.get_value_of("apply_threshold", default_value=1)):
edges[edges < threshold] = 0
edges[edges >= threshold] = 255
self.result = edges
img_name = f"edges_{self.input_params_as_str()}"
if text_overlay:
wrapper.store_image(
self.result,
img_name,
text_overlay=self.input_params_as_str(
exclude_defaults=False,
excluded_params=("progress_callback", ),
).replace(", ", "\n"),
)
else:
wrapper.store_image(self.result,
img_name,
text_overlay=text_overlay)
else:
wrapper.store_image(src_img, "source")
self.demo_image = self.result
res = True
except Exception as e:
res = False
logger.error(f'Failed to process {self. name}: "{repr(e)}"')
else:
pass
finally:
return res
def process_wrapper(self, **kwargs):
"""
Local binary pattern threshold:
Gray scale and rotation invariant LBP (Local Binary Patterns).
LBP is an invariant descriptor that can be used for texture classification.
Real time: False
Keyword Arguments (in parentheses, argument name):
* Activate tool (enabled): Toggle whether or not tool is active
* Channel (channel):
* Number of circularly symmetric neighbor (P): Number of circularly symmetric neighbor set points (quantization of the angular space)
* Radius of circle (R): Radius of circle (spatial resolution of the operator)
* Method to determine the pattern (method):
* Transformation applied to output (transformation):
* Cut x%% lower values (lower_cut): Increase to smooth low frequency textures regions and add detail to high frequencies
* Cut x%% upper values (upper_cut): Increase to smooth high frequency textures regions and add detail to low frequencies
* Postprocessing option (post_processing):
* Threshold min value (min_t):
* Threshold max value (max_t):
* Median filter size (odd values only) (median_filter_size):
* Morphology operator (morph_op):
* Kernel size (kernel_size):
* Kernel shape (kernel_shape):
* Iterations (proc_times):
* Select pseudo color map (color_map):
"""
wrapper = self.init_wrapper(**kwargs)
if wrapper is None:
return False
res = False
try:
if self.get_value_of("enabled") == 1:
c = ipc.resize_image(
wrapper.get_channel(
wrapper.current_image, self.get_value_of("channel")
),
target_rect=RectangleRegion(width=800, height=600),
keep_aspect_ratio=True,
output_as_bgr=False,
)
c = local_binary_pattern(
image=c,
P=self.get_value_of("P", scale_factor=wrapper.scale_factor),
R=self.get_value_of("R", scale_factor=wrapper.scale_factor),
method=self.get_value_of("method"),
)
# Transform
ct = self.get_value_of(f"transformation")
if ct == "sigmoid":
c = np.interp(c, (c.min(), c.max()), (0, 5))
c = expit(c)
elif ct == "log":
c = np.log(c + 1)
elif ct == "logit":
c = np.interp(c, (c.min(), c.max()), (0.5, 0.99))
c = logit(c)
elif ct == "arcsin":
c = np.interp(c, (c.min(), c.max()), (0, 1))
c = np.arcsin(c)
elif ct == "sqrt":
c = np.interp(c, (c.min(), c.max()), (0, 1))
c = np.sqrt(c)
# Cut
lower_cut = self.get_value_of("lower_cut")
if lower_cut > 0:
c[c < np.max(c) * (lower_cut / 100)] = 0
upper_cut = self.get_value_of("upper_cut")
if upper_cut > 0:
upper_cut = np.max(c) * ((100 - upper_cut) / 100)
c[c > upper_cut] = upper_cut
c = self.to_uint8(c)
# Post processing
pp = self.get_value_of("post_processing")
if pp == "threshold":
median_filter_size = self.get_value_of("median_filter_size")
median_filter_size = (
0
if median_filter_size == 1
else ipc.ensure_odd(median_filter_size)
)
c, _ = wrapper.get_mask(
src_img=c,
channel=None,
min_t=self.get_value_of("min_t"),
max_t=self.get_value_of("max_t"),
median_filter_size=median_filter_size,
)
self.result = self.apply_morphology_from_params(c)
elif pp == "false_color":
color_map = self.get_value_of("color_map")
_, color_map = color_map.split("_")
self.result = cv2.applyColorMap(c, int(color_map))
else:
self.result = c
# Store
wrapper.store_image(self.result, "local_binary_pattern")
res = True
else:
wrapper.store_image(wrapper.current_image, "current_image")
res = True
except Exception as e:
res = False
logger.error(f'Failed to process {self. name}: "{repr(e)}"')
else:
pass
finally:
return res
def process_wrapper(self, **kwargs):
"""
Grab cut:
Implementation of OpenCV grab cut function.
Better if used with a ROI.
Better if ROI is extracted from mask.
Even better if used after keep linked contours builds a ROI & and a mask.
Real time: False
Keyword Arguments (in parentheses, argument name):
* Name of ROI to be used (roi_names): Operation will only be applied inside of ROI
* ROI selection mode (roi_selection_mode):
* Size of dilation's kernel (prob_dilate_size): Size of kernel for the morphology operator applied to grow the source mask to set a probable mask
* Size of errode's kernel (sure_erode_size): Size of kernel for the morphology operator applied to shrink the source mask to set a sure mask
* Select pseudo color map (color_map):
* GraphCut iterations allowed (gc_iter_count):
* Build mosaic (build_mosaic):
* Name of ROI to be used (roi_names): Operation will only be applied inside of ROI
* ROI selection mode (roi_selection_mode):
"""
wrapper = self.init_wrapper(**kwargs)
if wrapper is None:
return False
res = False
try:
# Get Source image
img = wrapper.current_image
# Get starting mask
mask = self.get_mask()
if mask is None:
logger.error(f"FAIL {self.name}: mask must be initialized")
return
# Get ROI
rois = self.get_ipt_roi(
wrapper=wrapper,
roi_names=self.get_value_of("roi_names").replace(
" ", "").split(","),
selection_mode=self.get_value_of("roi_selection_mode"),
)
if len(rois) > 0:
roi = rois[0]
else:
roi = None
# Initialize mask
gc_in_mask = np.full_like(mask, cv2.GC_BGD)
if roi is not None:
gc_in_mask = roi.draw_to(gc_in_mask,
line_width=-1,
color=cv2.GC_PR_BGD)
# Apply dilation
dks = self.get_value_of("prob_dilate_size")
0 if dks == 1 else ensure_odd(dks)
if dks > 0:
d_mask = wrapper.dilate(image=mask, kernel_size=dks)
gc_in_mask[d_mask != 0] = cv2.GC_PR_FGD
# Apply erosion
eks = self.get_value_of("sure_erode_size")
0 if eks == 1 else ensure_odd(eks)
if eks > 0:
e_mask = wrapper.erode(image=mask, kernel_size=eks)
gc_in_mask[e_mask != 0] = cv2.GC_FGD
else:
gc_in_mask[mask != 0] = cv2.GC_FGD
color_map = self.get_value_of("color_map")
_, color_map = color_map.split("_")
dbg_img = cv2.applyColorMap(
self.to_uint8(gc_in_mask, normalize=True), int(color_map))
if roi is not None:
dbg_img = roi.draw_to(dbg_img, line_width=wrapper.width // 200)
wrapper.store_image(dbg_img, "grabcut_initialized_mask")
# Initialize the other ones
bgd_model = np.zeros((1, 65), np.float64)
fgd_model = np.zeros((1, 65), np.float64)
# Grab the cut
cv2.grabCut(
img=img,
mask=gc_in_mask,
rect=None if roi is None else roi.to_opencv(),
bgdModel=bgd_model,
fgdModel=fgd_model,
iterCount=self.get_value_of("gc_iter_count"),
mode=cv2.GC_INIT_WITH_MASK,
)
wrapper.store_image(
cv2.applyColorMap(self.to_uint8(gc_in_mask, normalize=True),
int(color_map)),
"grabcut_false_color_mask",
)
self.result = np.where(gc_in_mask == cv2.GC_FGD, 255,
0).astype("uint8")
wrapper.store_image(self.result, "grabcut_mask")
wrapper.store_image(
image=self.wrapper.draw_image(
src_image=img,
src_mask=self.result,
background="bw",
foreground="source",
),
text="result_on_bw",
)
res = True
if self.get_value_of("build_mosaic") == 1:
canvas = wrapper.build_mosaic(image_names=np.array([
[
"current_image",
"grabcut_initialized_mask",
"grabcut_false_color_mask",
],
["grabcut_mask", "", "result_on_bw"],
]))
wrapper.store_image(canvas, "mosaic")
except Exception as e:
logger.error(f'Failed to process {self. name}: "{repr(e)}"')
res = False
else:
pass
finally:
return res
