def flip(img, direction):
"""Flip image.
Inputs:
img = RGB or grayscale image data
direction = "horizontal" or "vertical"
Returns:
vh_img = flipped image
:param img: numpy.ndarray
:param direction: str
:return vh_img: numpy.ndarray
"""
params.device += 1
if direction.upper() == "VERTICAL":
vh_img = cv2.flip(img, 1)
elif direction.upper() == "HORIZONTAL":
vh_img = cv2.flip(img, 0)
else:
fatal_error(str(direction) + " is not a valid direction, must be horizontal or vertical")
if params.debug == 'print':
print_image(vh_img, os.path.join(params.debug_outdir, str(params.device) + "_flipped.png"))
elif params.debug == 'plot':
if len(np.shape(vh_img)) == 3:
plot_image(vh_img)
else:
plot_image(vh_img, cmap='gray')
return vh_img
def image_add(gray_img1, gray_img2):
"""This is a function used to add images. The numpy addition function '+' is used. This is a modulo operation
rather than the cv2.add fxn which is a saturation operation. ddepth = -1 specifies that the dimensions of output
image will be the same as the input image.
Inputs:
gray_img1 = Grayscale image data to be added to image 2
gray_img2 = Grayscale image data to be added to image 1
Returns:
added_img = summed images
:param gray_img1: numpy.ndarray
:param gray_img2: numpy.ndarray
:return added_img: numpy.ndarray
"""
added_img = gray_img1 + gray_img2
params.device += 1
if params.debug == 'print':
print_image(added_img, os.path.join(params.debug_outdir, str(params.device) + '_added' + '.png'))
elif params.debug == 'plot':
plot_image(added_img, cmap='gray')
return added_img
def median_blur(gray_img, ksize):
"""Applies a median blur filter (applies median value to central pixel within a kernel size).
Inputs:
gray_img = Grayscale image data
ksize = kernel size => integer or tuple, ksize x ksize box if integer, (n, m) size box if tuple
Returns:
img_mblur = blurred image
:param gray_img: numpy.ndarray
:param ksize: int or tuple
:return img_mblur: numpy.ndarray
"""
# Make sure ksize is valid
if type(ksize) is not int and type(ksize) is not tuple:
fatal_error("Invalid ksize, must be integer or tuple")
img_mblur = median_filter(gray_img, size=ksize)
params.device += 1
if params.debug == 'print':
print_image(img_mblur, os.path.join(params.debug_outdir,
str(params.device) + '_median_blur' + str(ksize) + '.png'))
elif params.debug == 'plot':
plot_image(img_mblur, cmap='gray')
return img_mblur
def distance_transform(bin_img, distance_type, mask_size):
"""Creates an image where for each object pixel, a number is assigned that corresponds to the distance to the
nearest background pixel.
Inputs:
img = Binary image data
distance_type = Type of distance. It can be CV_DIST_L1, CV_DIST_L2 , or CV_DIST_C which are 1, 2 and 3,
respectively.
mask_size = Size of the distance transform mask. It can be 3, 5, or CV_DIST_MASK_PRECISE (the latter option
is only supported by the first function). In case of the CV_DIST_L1 or CV_DIST_C distance type,
the parameter is forced to 3 because a 3 by 3 mask gives the same result as 5 by 5 or any larger
aperture.
Returns:
norm_image = grayscale distance-transformed image normalized between [0, 1]
:param bin_img: numpy.ndarray
:param distance_type: int
:param mask_size: int
:return norm_image: numpy.ndarray
"""
params.device += 1
dist = cv2.distanceTransform(src=bin_img, distanceType=distance_type, maskSize=mask_size)
norm_image = cv2.normalize(src=dist, dst=dist, alpha=0, beta=1, norm_type=cv2.NORM_MINMAX, dtype=cv2.CV_32F)
if params.debug == 'print':
print_image(norm_image, os.path.join(params.debug, str(params.device) + '_distance_transform.png'))
elif params.debug == 'plot':
plot_image(norm_image, cmap='gray')
return norm_image
def resize(img, resize_x, resize_y):
"""Resize image.
Inputs:
img = RGB or grayscale image data to resize
resize_x = scaling factor
resize_y = scaling factor
Returns:
reimg = resized image
:param img: numpy.ndarray
:param resize_x: int
:param resize_y: int
:return reimg: numpy.ndarray
"""
params.device += 1
if resize_x <= 0 and resize_y <= 0:
fatal_error("Resize values both cannot be 0 or negative values!")
reimg = cv2.resize(img, (0, 0), fx=resize_x, fy=resize_y)
if params.debug == 'print':
print_image(reimg, os.path.join(params.debug_outdir, str(params.device) + "_resize1.png"))
elif params.debug == 'plot':
plot_image(reimg)
return reimg
def opening(gray_img, kernel=None):
"""Wrapper for scikit-image opening functions. Opening can remove small bright spots (i.e. salt).
Inputs:
gray_img = input image (grayscale or binary)
kernel = optional neighborhood, expressed as an array of 1s and 0s. If None, use cross-shaped structuring element.
:param gray_img: ndarray
:param kernel = ndarray
:return filtered_img: ndarray
"""
params.device += 1
# Make sure the image is binary/grayscale
if len(np.shape(gray_img)) != 2:
fatal_error("Input image must be grayscale or binary")
# If image is binary use the faster method
if len(np.unique(gray_img)) == 2:
bool_img = morphology.binary_opening(gray_img, kernel)
filtered_img = np.copy(bool_img.astype(np.uint8) * 255)
# Otherwise use method appropriate for grayscale images
else:
filtered_img = morphology.opening(gray_img, kernel)
if params.debug == 'print':
print_image(filtered_img, os.path.join(params.debug_outdir, str(params.device) + '_opening' + '.png'))
elif params.debug == 'plot':
plot_image(filtered_img, cmap='gray')
return filtered_img
def laplace_filter(gray_img, ksize, scale):
"""This is a filtering method used to identify and highlight fine edges based on the 2nd derivative. A very
sensetive method to highlight edges but will also amplify background noise. ddepth = -1 specifies that the
dimensions of output image will be the same as the input image.
Inputs:
gray_img = Grayscale image data
ksize = apertures size used to calculate 2nd derivative filter, specifies the size of the kernel
(must be an odd integer: 1,3,5...)
scale = scaling factor applied (multiplied) to computed Laplacian values (scale = 1 is unscaled)
Returns:
lp_filtered = laplacian filtered image
:param gray_img: numpy.ndarray
:param kernel: int
:param scale: int
:return lp_filtered: numpy.ndarray
"""
lp_filtered = cv2.Laplacian(src=gray_img, ddepth=-1, ksize=ksize, scale=scale)
params.device += 1
if params.debug == 'print':
print_image(lp_filtered,
os.path.join(params.debug_outdir,
str(params.device) + '_lp_out_k' + str(ksize) + '_scale' + str(scale) + '.png'))
elif params.debug == 'plot':
plot_image(lp_filtered, cmap='gray')
return lp_filtered
def find_objects(img, mask):
"""Find all objects and color them blue.
Inputs:
img = RGB or grayscale image data for plotting
mask = Binary mask used for contour detection
Returns:
objects = list of contours
hierarchy = contour hierarchy list
:param img: numpy.ndarray
:param mask: numpy.ndarray
:return objects: list
:return hierarchy: numpy.ndarray
"""
params.device += 1
mask1 = np.copy(mask)
ori_img = np.copy(img)
# If the reference image is grayscale convert it to color
if len(np.shape(ori_img)) == 2:
ori_img = cv2.cvtColor(ori_img, cv2.COLOR_GRAY2BGR)
objects, hierarchy = cv2.findContours(mask1, cv2.RETR_TREE, cv2.CHAIN_APPROX_NONE)[-2:]
for i, cnt in enumerate(objects):
cv2.drawContours(ori_img, objects, i, (255, 102, 255), -1, lineType=8, hierarchy=hierarchy)
if params.debug == 'print':
print_image(ori_img, os.path.join(params.debug_outdir, str(params.device) + '_id_objects.png'))
elif params.debug == 'plot':
plot_image(ori_img)
return objects, hierarchy
def skeletonize(mask):
"""Reduces binary objects to 1 pixel wide representations (skeleton)
Inputs:
mask = Binary image data
Returns:
skeleton = skeleton image
:param mask: numpy.ndarray
:return skeleton: numpy.ndarray
"""
# Store debug
debug = params.debug
params.debug = None
# Convert mask to boolean image, rather than 0 and 255 for skimage to use it
skeleton = skmorph.skeletonize(mask.astype(bool))
skeleton = skeleton.astype(np.uint8) * 255
# Reset debug mode
params.debug = debug
# Auto-increment device
params.device += 1
if params.debug == 'print':
print_image(skeleton, os.path.join(params.debug_outdir, str(params.device) + '_skeleton.png'))
elif params.debug == 'plot':
plot_image(skeleton, cmap='gray')
return skeleton
def scharr_filter(img, dx, dy, scale):
"""This is a filtering method used to identify and highlight gradient edges/features using the 1st derivative.
Typically used to identify gradients along the x-axis (dx = 1, dy = 0) and y-axis (dx = 0, dy = 1) independently.
Performance is quite similar to Sobel filter. Used to detect edges / changes in pixel intensity. ddepth = -1
specifies that the dimensions of output image will be the same as the input image.
Inputs:
gray_img = Grayscale image data
dx = derivative of x to analyze (1-3)
dy = derivative of x to analyze (1-3)
scale = scaling factor applied (multiplied) to computed Scharr values (scale = 1 is unscaled)
Returns:
sr_img = Scharr filtered image
:param img: numpy.ndarray
:param dx: int
:param dy: int
:param scale: int
:return sr_img: numpy.ndarray
"""
sr_img = cv2.Scharr(src=img, ddepth=-1, dx=dx, dy=dy, scale=scale)
params.device += 1
if params.debug == 'print':
name = os.path.join(params.debug_outdir, str(params.device))
name += '_sr_img_dx' + str(dx) + '_dy' + str(dy) + '_scale' + str(scale) + '.png'
print_image(sr_img, name)
elif params.debug == 'plot':
plot_image(sr_img, cmap='gray')
return sr_img
def erode(gray_img, ksize, i):
"""Perform morphological 'erosion' filtering. Keeps pixel in center of the kernel if conditions set in kernel are
true, otherwise removes pixel.
Inputs:
gray_img = Grayscale (usually binary) image data
ksize = Kernel size (int). A ksize x ksize kernel will be built. Must be greater than 1 to have an effect.
i = interations, i.e. number of consecutive filtering passes
Returns:
er_img = eroded image
:param gray_img: numpy.ndarray
:param ksize: int
:param i: int
:return er_img: numpy.ndarray
"""
if ksize <= 1:
raise ValueError('ksize needs to be greater than 1 for the function to have an effect')
kernel1 = int(ksize)
kernel2 = np.ones((kernel1, kernel1), np.uint8)
er_img = cv2.erode(src=gray_img, kernel=kernel2, iterations=i)
params.device += 1
if params.debug == 'print':
print_image(er_img, os.path.join(params.debug_outdir,
str(params.device) + '_er_image' + str(ksize) + '_itr_' + str(i) + '.png'))
elif params.debug == 'plot':
plot_image(er_img, cmap='gray')
return er_img
def gaussian_blur(img, ksize, sigma_x=0, sigma_y=None):
"""Applies a Gaussian blur filter.
Inputs:
# img = RGB or grayscale image data
# ksize = Tuple of kernel dimensions, e.g. (5, 5)
# sigmax = standard deviation in X direction; if 0, calculated from kernel size
# sigmay = standard deviation in Y direction; if sigmaY is None, sigmaY is taken to equal sigmaX
Returns:
img_gblur = blurred image
:param img: numpy.ndarray
:param ksize: tuple
:param sigmax: int
:param sigmay: str or int
:return img_gblur: numpy.ndarray
"""
img_gblur = cv2.GaussianBlur(img, ksize, sigma_x, sigma_y)
params.device += 1
if params.debug == 'print':
print_image(img_gblur, os.path.join(params.debug_outdir, str(params.device) + '_gaussian_blur.png'))
elif params.debug == 'plot':
if len(np.shape(img_gblur)) == 3:
plot_image(img_gblur)
else:
plot_image(img_gblur, cmap='gray')
return img_gblur
def sobel_filter(gray_img, dx, dy, ksize):
"""This is a filtering method used to identify and highlight gradient edges/features using the 1st derivative.
Typically used to identify gradients along the x-axis (dx = 1, dy = 0) and y-axis (dx = 0, dy = 1) independently.
Performance is quite similar to Scharr filter. Used to detect edges / changes in pixel intensity. ddepth = -1
specifies that the dimensions of output image will be the same as the input image.
Inputs:
gray_img = Grayscale image data
dx = derivative of x to analyze
dy = derivative of x to analyze
ksize = specifies the size of the kernel (must be an odd integer: 1,3,5, ... , 31)
Returns:
sb_img = Sobel filtered image
:param gray_img: numpy.ndarray
:param dx: int
:param dy: int
:param ksize: int
:param scale: int
:return sb_img: numpy.ndarray
"""
params.device += 1
sb_img = cv2.Sobel(src=gray_img, ddepth=-1, dx=dx, dy=dy, ksize=ksize)
if params.debug == 'print':
name = os.path.join(params.debug_outdir,
str(params.device) + '_sb_img_dx' + str(dx) + '_dy' + str(dy) + '_kernel' + str(ksize) + '.png')
print_image(sb_img, name)
elif params.debug == 'plot':
plot_image(sb_img, cmap='gray')
return sb_img
def image_subtract(gray_img1, gray_img2):
"""This is a function used to subtract values of one gray-scale image array from another gray-scale image array. The
resulting gray-scale image array has a minimum element value of zero. That is all negative values resulting from the
subtraction are forced to zero.
Inputs:
gray_img1 = Grayscale image data from which gray_img2 will be subtracted
gray_img2 = Grayscale image data which will be subtracted from gray_img1
Returns:
new_img = subtracted image
:param gray_img1: numpy.ndarray
:param gray_img2: numpy.ndarray
:return new_img: numpy.ndarray
"""
params.device += 1 # increment device
# check inputs for gray-scale
if len(np.shape(gray_img1)) != 2 or len(np.shape(gray_img2)) != 2:
fatal_error("Input image is not gray-scale")
new_img = gray_img1.astype(np.float64) - gray_img2.astype(np.float64) # subtract values
new_img[np.where(new_img < 0)] = 0 # force negative array values to zero
new_img = new_img.astype(np.uint8) # typecast image to 8-bit image
# print-plot handling
if params.debug == 'print':
print_image(new_img, os.path.join(params.debug_outdir, str(params.device) + "_subtraction.png"))
elif params.debug == 'plot':
plot_image(new_img, cmap='gray')
return new_img # return
def watershed_segmentation(rgb_img, mask, distance=10):
"""Uses the watershed algorithm to detect boundary of objects. Needs a marker file which specifies area which is
object (white), background (grey), unknown area (black).
Inputs:
rgb_img = image to perform watershed on needs to be 3D (i.e. np.shape = x,y,z not np.shape = x,y)
mask = binary image, single channel, object in white and background black
distance = min_distance of local maximum
Returns:
analysis_images = list of output images
:param rgb_img: numpy.ndarray
:param mask: numpy.ndarray
:param distance: int
:return analysis_images: list
"""
params.device += 1
# # Will be depricating opencv version 2
# if cv2.__version__[0] == '2':
# dist_transform = cv2.distanceTransform(mask, cv2.cv.CV_DIST_L2, maskSize=0)
# else:
dist_transform = cv2.distanceTransformWithLabels(mask, cv2.DIST_L2, maskSize=0)[0]
localMax = peak_local_max(dist_transform, indices=False, min_distance=distance, labels=mask)
markers = ndi.label(localMax, structure=np.ones((3, 3)))[0]
dist_transform1 = -dist_transform
labels = watershed(dist_transform1, markers, mask=mask)
img1 = np.copy(rgb_img)
for x in np.unique(labels):
rand_color = color_palette(len(np.unique(labels)))
img1[labels == x] = rand_color[x]
img2 = apply_mask(img1, mask, 'black')
joined = np.concatenate((img2, rgb_img), axis=1)
estimated_object_count = len(np.unique(markers)) - 1
analysis_image = []
analysis_image.append(joined)
if params.debug == 'print':
print_image(dist_transform, os.path.join(params.debug_outdir, str(params.device) + '_watershed_dist_img.png'))
print_image(joined, os.path.join(params.debug_outdir, str(params.device) + '_watershed_img.png'))
elif params.debug == 'plot':
plot_image(dist_transform, cmap='gray')
plot_image(joined)
outputs.add_observation(variable='estimated_object_count', trait='estimated object count',
method='plantcv.plantcv.watershed', scale='none', datatype=int,
value=estimated_object_count, label='none')
# Store images
outputs.images.append(analysis_image)
return analysis_image
def prune(skel_img, size):
"""
The pruning algorithm was inspired by Jean-Patrick Pommier: https://gist.github.com/jeanpat/5712699
Iteratively remove endpoints (tips) from a skeletonized image. "Prunes" barbs off a skeleton.
Inputs:
skel_img = Skeletonized image
size = Size to get pruned off each branch
Returns:
pruned_img = Pruned image
:param skel_img: numpy.ndarray
:param size: int
:return pruned_img: numpy.ndarray
"""
# Store debug
debug = params.debug
params.debug = None
pruned_img = skel_img.copy()
# Check to see if the skeleton has multiple objects
objects, _ = find_objects(pruned_img, pruned_img)
if not len(objects) == 1:
print("Warning: Multiple objects detected! Pruning will further separate the difference pieces.")
# Iteratively remove endpoints (tips) from a skeleton
for i in range(0, size):
endpoints = find_tips(pruned_img)
pruned_img = image_subtract(pruned_img, endpoints)
# Make debugging image
pruned_plot = np.zeros(skel_img.shape[:2], np.uint8)
pruned_plot = cv2.cvtColor(pruned_plot, cv2.COLOR_GRAY2RGB)
skel_obj, skel_hierarchy = find_objects(skel_img, skel_img)
pruned_obj, pruned_hierarchy = find_objects(pruned_img, pruned_img)
cv2.drawContours(pruned_plot, skel_obj, -1, (0, 0, 255), params.line_thickness,
lineType=8, hierarchy=skel_hierarchy)
cv2.drawContours(pruned_plot, pruned_obj, -1, (255, 255, 255), params.line_thickness,
lineType=8, hierarchy=pruned_hierarchy)
# Reset debug mode
params.debug = debug
params.device += 1
if params.debug == 'print':
print_image(pruned_img, os.path.join(params.debug_outdir, str(params.device) + '_pruned.png'))
print_image(pruned_plot, os.path.join(params.debug_outdir, str(params.device) + '_pruned_debug.png'))
elif params.debug == 'plot':
plot_image(pruned_img, cmap='gray')
plot_image(pruned_plot)
return pruned_img
def segment_skeleton(skel_img, mask=None):
""" Segment a skeleton image into pieces
Inputs:
skel_img = Skeletonized image
mask = (Optional) binary mask for debugging. If provided, debug image will be overlaid on the mask.
Returns:
segmented_img = Segmented debugging image
objects = list of contours
hierarchy = contour hierarchy list
:param skel_img: numpy.ndarray
:param mask: numpy.ndarray
:return segmented_img: numpy.ndarray
:return segment_objects: list
"return segment_hierarchies: numpy.ndarray
"""
# Store debug
debug = params.debug
params.debug = None
# Find branch points
bp = find_branch_pts(skel_img)
bp = dilate(bp, 3, 1)
# Subtract from the skeleton so that leaves are no longer connected
segments = image_subtract(skel_img, bp)
# Gather contours of leaves
segment_objects, _ = find_objects(segments, segments)
# Color each segment a different color
rand_color = color_palette(len(segment_objects))
if mask is None:
segmented_img = skel_img.copy()
else:
segmented_img = mask.copy()
segmented_img = cv2.cvtColor(segmented_img, cv2.COLOR_GRAY2RGB)
for i, cnt in enumerate(segment_objects):
cv2.drawContours(segmented_img, segment_objects, i, rand_color[i], params.line_thickness, lineType=8)
# Reset debug mode
params.debug = debug
# Auto-increment device
params.device += 1
if params.debug == 'print':
print_image(segmented_img, os.path.join(params.debug_outdir, str(params.device) + '_segmented.png'))
elif params.debug == 'plot':
plot_image(segmented_img)
return segmented_img, segment_objects
def segment_id(skel_img, objects, mask=None):
""" Plot segment ID's
Inputs:
skel_img = Skeletonized image
objects = List of contours
mask = (Optional) binary mask for debugging. If provided, debug image will be overlaid on the mask.
Returns:
segmented_img = Segmented image
labeled_img = Labeled image
:param skel_img: numpy.ndarray
:param objects: list
:param mask: numpy.ndarray
:return segmented_img: numpy.ndarray
:return labeled_img: numpy.ndarray
"""
label_coord_x = []
label_coord_y = []
if mask is None:
segmented_img = skel_img.copy()
else:
segmented_img = mask.copy()
segmented_img = cv2.cvtColor(segmented_img, cv2.COLOR_GRAY2RGB)
# Color each segment a different color
rand_color = color_palette(len(objects))
# Plot all segment contours
for i, cnt in enumerate(objects):
cv2.drawContours(segmented_img, objects, i, rand_color[i], params.line_thickness, lineType=8)
# Store coordinates for labels
label_coord_x.append(objects[i][0][0][0])
label_coord_y.append(objects[i][0][0][1])
labeled_img = segmented_img.copy()
for i, cnt in enumerate(objects):
# Label slope lines
w = label_coord_x[i]
h = label_coord_y[i]
text = "ID:{}".format(i)
cv2.putText(img=labeled_img, text=text, org=(w, h), fontFace=cv2.FONT_HERSHEY_SIMPLEX,
fontScale=params.text_size, color=rand_color[i], thickness=params.text_thickness)
# Auto-increment device
params.device += 1
if params.debug == 'print':
print_image(labeled_img, os.path.join(params.debug_outdir, str(params.device) + '_segmented_ids.png'))
elif params.debug == 'plot':
plot_image(labeled_img)
return segmented_img, labeled_img
def colorize_masks(masks, colors):
"""Plot masks with different colors
Inputs:
masks = list of masks to colorize
colors = list of colors (either keys from the color_dict or a list of custom tuples)
:param masks: list
:param colors: list
:return colored_img: ndarray
"""
# Users must enter the exact same number of colors as classes they'd like to color
num_classes = len(masks)
num_colors = len(colors)
if not num_classes == num_colors:
fatal_error("The number of colors provided doesn't match the number of class masks provided.")
# Check to make sure user provided at least one mask and color
if len(colors) == 0 or len(masks) == 0:
fatal_error("At least one class mask and color must be provided.")
# Dictionary of colors and the BGR values, based on some of the colors listed here:
# https://en.wikipedia.org/wiki/X11_color_names
color_dict = {'white': (255,255,255), 'black': (0,0,0), 'aqua': (0,255,255), 'blue': (255,0,0), 'blue violet':
(228,44,138), 'brown': (41,41,168), 'chartreuse': (0,255,128), 'dark blue': (140,0,0), 'gray': (169,169,169),
'yellow': (0, 255, 255), 'turquoise': (210,210,64), 'red': (0, 0, 255), 'purple': (241,33,161), 'orange red':
(0,69, 255), 'orange': (0,166,255), 'lime': (0, 255, 0), 'lime green': (52,205,52), 'fuchsia': (255,0,255),
'crimson': (61,20,220), 'beige': (197,220,246), 'chocolate': (31,105,210), 'coral': (79,128,255), 'dark green':
(0,100,0), 'dark orange': (0,140,255), 'green yellow': (46,255,174), 'light blue': (230,218,174), 'tomato':
(72,100,255), 'slate gray': (143,128,113), 'gold': (0,215,255), 'goldenrod': (33,166,218), 'light green':
(143,238,143), 'sea green': (77,141,46), 'dark red': (0,0,141), 'pink': (204,192,255), 'dark yellow': (0,205,255),
'green': (0,255,0)}
ix, iy = np.shape(masks[0])
colored_img = np.zeros((ix,iy,3), dtype=np.uint8)
# Assign pixels to the selected color
for i in range(0, len(masks)):
mask = np.copy(masks[i])
mask = cv2.cvtColor(mask, cv2.COLOR_GRAY2BGR)
if isinstance(colors[i], tuple):
mask[masks[i] > 0] = colors[i]
elif isinstance(colors[i], str):
mask[masks[i] > 0] = color_dict[colors[i]]
else:
fatal_error("All elements of the 'colors' list must be either str or tuple")
colored_img = colored_img + mask
if params.debug == 'print':
print_image(colored_img, os.path.join(params.debug_outdir, str(params.device) + '_classes_plot.png'))
elif params.debug == 'plot':
plot_image(colored_img)
return colored_img
def object_composition(img, contours, hierarchy):
"""Groups objects into a single object, usually done after object filtering.
Inputs:
img = RGB or grayscale image data for plotting
contours = Contour list
hierarchy = Contour hierarchy NumPy array
Returns:
group = grouped contours list
mask = image mask
:param img: numpy.ndarray
:param contours: list
:param hierarchy: numpy.ndarray
:return group: list
:return mask: numpy.ndarray
"""
params.device += 1
ori_img = np.copy(img)
# If the reference image is grayscale convert it to color
if len(np.shape(ori_img)) == 2:
ori_img = cv2.cvtColor(ori_img, cv2.COLOR_GRAY2BGR)
stack = np.zeros((len(contours), 1))
r, g, b = cv2.split(ori_img)
mask = np.zeros(g.shape, dtype=np.uint8)
for c, cnt in enumerate(contours):
# if hierarchy[0][c][3] == -1:
if hierarchy[0][c][2] == -1 and hierarchy[0][c][3] > -1:
stack[c] = 0
else:
stack[c] = 1
ids = np.where(stack == 1)[0]
if len(ids) > 0:
group = np.vstack(contours[i] for i in ids)
cv2.drawContours(mask, contours, -1, 255, -1, hierarchy=hierarchy)
if params.debug is not None:
cv2.drawContours(ori_img, group, -1, (255, 0, 0), params.line_thickness)
for cnt in contours:
cv2.drawContours(ori_img, cnt, -1, (255, 0, 0), params.line_thickness)
if params.debug == 'print':
print_image(ori_img, os.path.join(params.debug_outdir, str(params.device) + '_objcomp.png'))
print_image(ori_img, os.path.join(params.debug_outdir, str(params.device) + '_objcomp_mask.png'))
elif params.debug == 'plot':
plot_image(ori_img)
return group, mask
else:
print("Warning: Invalid contour.")
return None, None
def _call_adaptive_threshold(gray_img, max_value, adaptive_method, threshold_method, method_name):
# Threshold the image
bin_img = cv2.adaptiveThreshold(gray_img, max_value, adaptive_method, threshold_method, 11, 2)
# Print or plot the binary image if debug is on
if params.debug == 'print':
print_image(bin_img, os.path.join(params.debug_outdir,
str(params.device) + method_name + '.png'))
elif params.debug == 'plot':
plot_image(bin_img, cmap='gray')
return bin_img
def rotate(img, rotation_deg, crop):
"""Rotate image, sometimes it is necessary to rotate image, especially when clustering for
multiple plants is needed.
Inputs:
img = RGB or grayscale image data
rotation_deg = rotation angle in degrees, can be a negative number,
positive values move counter clockwise.
crop = either true or false, if true, dimensions of rotated image will be same as original image.
Returns:
rotated_img = rotated image
:param img: numpy.ndarray
:param rotation_deg: double
:param crop: bool
:return rotated_img: numpy.ndarray
"""
params.device += 1
if len(np.shape(img)) == 3:
iy, ix, iz = np.shape(img)
else:
iy, ix = np.shape(img)
m = cv2.getRotationMatrix2D((ix / 2, iy / 2), rotation_deg, 1)
cos = np.abs(m[0, 0])
sin = np.abs(m[0, 1])
if not crop:
# compute the new bounding dimensions of the image
nw = int((iy * sin) + (ix * cos))
nh = int((iy * cos) + (ix * sin))
# adjust the rotation matrix to take into account translation
m[0, 2] += (nw / 2) - (ix / 2)
m[1, 2] += (nh / 2) - (iy / 2)
rotated_img = cv2.warpAffine(img, m, (nw, nh))
else:
rotated_img = cv2.warpAffine(img, m, (ix, iy))
if params.debug == 'print':
print_image(rotated_img, os.path.join(params.debug_outdir, str(params.device) + str(rotation_deg) + '_rotated_img.png'))
elif params.debug == 'plot':
if len(np.shape(img)) == 3:
plot_image(rotated_img)
else:
plot_image(rotated_img, cmap='gray')
return rotated_img
def segment_path_length(segmented_img, objects):
""" Use segments to calculate geodesic distance per segment
Inputs:
segmented_img = Segmented image to plot lengths on
objects = List of contours
Returns:
labeled_img = Segmented debugging image with lengths labeled
:param segmented_img: numpy.ndarray
:param objects: list
:return labeled_img: numpy.ndarray
"""
label_coord_x = []
label_coord_y = []
segment_lengths = []
labeled_img = segmented_img.copy()
for i, cnt in enumerate(objects):
# Calculate geodesic distance, divide by two since cv2 seems to be taking the perimeter of the contour
segment_lengths.append(cv2.arcLength(objects[i], False) / 2)
# Store coordinates for labels
label_coord_x.append(objects[i][0][0][0])
label_coord_y.append(objects[i][0][0][1])
segment_ids = []
# Put labels of length
for c, value in enumerate(segment_lengths):
text = "{:.2f}".format(value)
w = label_coord_x[c]
h = label_coord_y[c]
cv2.putText(img=labeled_img, text=text, org=(w, h), fontFace=cv2.FONT_HERSHEY_SIMPLEX,
fontScale=params.text_size, color=(150, 150, 150), thickness=params.text_thickness)
segment_label = "ID" + str(c)
segment_ids.append(c)
outputs.add_observation(variable='segment_path_length', trait='segment path length',
method='plantcv.plantcv.morphology.segment_path_length', scale='pixels', datatype=list,
value=segment_lengths, label=segment_ids)
# Auto-increment device
params.device += 1
if params.debug == 'print':
print_image(labeled_img, os.path.join(params.debug_outdir, str(params.device) + '_segment_path_lengths.png'))
elif params.debug == 'plot':
plot_image(labeled_img)
return labeled_img
def _draw_roi(img, roi_contour):
"""Draw an ROI
:param img: numpy.ndarray
:param roi_contour: list
"""
# Make a copy of the reference image
ref_img = np.copy(img)
# If the reference image is grayscale convert it to color
if len(np.shape(ref_img)) == 2:
ref_img = cv2.cvtColor(ref_img, cv2.COLOR_GRAY2BGR)
# Draw the contour on the reference image
cv2.drawContours(ref_img, roi_contour, -1, (255, 0, 0), params.line_thickness)
if params.debug == "print":
# If debug is print, save the image to a file
print_image(ref_img, os.path.join(params.debug_outdir, str(params.device) + "_roi.png"))
elif params.debug == "plot":
# If debug is plot, print to the plotting device
plot_image(ref_img)
def readimage(filename, mode="native"):
"""Read image from file.
Inputs:
filename = name of image file
mode = mode of imread ("native", "rgb", "rgba", "gray")
Returns:
img = image object as numpy array
path = path to image file
img_name = name of image file
:param filename: str
:param mode: str
:return img: numpy.ndarray
:return path: str
:return img_name: str
"""
if mode.upper() == "GRAY" or mode.upper() == "GREY":
img = cv2.imread(filename, 0)
elif mode.upper() == "RGB":
img = cv2.imread(filename)
elif mode.upper() == "RGBA":
img = cv2.imread(filename, -1)
else:
img = cv2.imread(filename, -1)
# Default to drop alpha channel if user doesn't specify 'rgba'
if len(np.shape(img))==3 and np.shape(img)[2] == 4 and mode.upper() == "NATIVE":
img = cv2.imread(filename)
if img is None:
fatal_error("Failed to open " + filename)
# Split path from filename
path, img_name = os.path.split(filename)
if params.debug == "print":
print_image(img, os.path.join(params.debug_outdir, "input_image.png"))
elif params.debug == "plot":
plot_image(img)
return img, path, img_name
def rgb2gray(rgb_img):
"""Convert image from RGB colorspace to Gray.
Inputs:
rgb_img = RGB image data
Returns:
gray = grayscale image
:param rgb_img: numpy.ndarray
:return gray: numpy.ndarray
"""
gray = cv2.cvtColor(rgb_img, cv2.COLOR_BGR2GRAY)
params.device += 1
if params.debug == 'print':
print_image(gray, os.path.join(params.debug_outdir, str(params.device) + '_gray.png'))
elif params.debug == 'plot':
plot_image(gray, cmap='gray')
return gray
def logical_or(bin_img1, bin_img2):
"""Join two images using the bitwise OR operator.
Inputs:
bin_img1 = Binary image data to be compared to bin_img2
bin_img2 = Binary image data to be compared to bin_img1
Returns:
merged = joined binary image
:param bin_img1: numpy.ndarray
:param bin_img2: numpy.ndarray
:return merged: numpy.ndarray
"""
params.device += 1
merged = cv2.bitwise_or(bin_img1, bin_img2)
if params.debug == 'print':
print_image(merged, os.path.join(params.debug_outdir, str(params.device) + '_or_joined.png'))
elif params.debug == 'plot':
plot_image(merged, cmap='gray')
return merged
def logical_xor(bin_img1, bin_img2):
"""Join two images using the bitwise XOR operator.
Inputs:
bin_img1 = Binary image data to be compared to bin_img2
bin_img2 = Binary image data to be compared to bin_img1
Returns:
merged = joined binary image
:param bin_img1: numpy.ndarray
:param bin_img2: numpy.ndarray
:return merged: numpy.ndarray
"""
params.device += 1
merged = cv2.bitwise_xor(bin_img1, bin_img2)
if params.debug == 'print':
print_image(merged, os.path.join(params.debug_outdir, str(params.device) + '_xor_joined.png'))
elif params.debug == 'plot':
plot_image(merged, cmap='gray')
return merged
def fill(bin_img, size):
"""Identifies objects and fills objects that are less than size.
Inputs:
bin_img = Binary image data
size = minimum object area size in pixels (integer)
Returns:
filtered_img = image with objects filled
:param bin_img: numpy.ndarray
:param size: int
:return filtered_img: numpy.ndarray
"""
params.device += 1
# Make sure the image is binary
if len(np.shape(bin_img)) != 2 or len(np.unique(bin_img)) != 2:
fatal_error("Image is not binary")
# Cast binary image to boolean
bool_img = bin_img.astype(bool)
# Find and fill contours
bool_img = remove_small_objects(bool_img, size)
# Cast boolean image to binary and make a copy of the binary image for returning
filtered_img = np.copy(bool_img.astype(np.uint8) * 255)
if params.debug == 'print':
print_image(
filtered_img,
os.path.join(params.debug_outdir,
str(params.device) + '_fill' + str(size) + '.png'))
elif params.debug == 'plot':
plot_image(filtered_img, cmap='gray')
return filtered_img
def rgb2gray_lab(rgb_img, channel):
"""Convert image from RGB colorspace to LAB colorspace. Returns the specified subchannel as a gray image.
Inputs:
rgb_img = RGB image data
channel = color subchannel (l = lightness, a = green-magenta, b = blue-yellow)
Returns:
l | a | b = grayscale image from one LAB color channel
:param rgb_img: numpy.ndarray
:param channel: str
:return channel: numpy.ndarray
"""
# Auto-increment the device counter
params.device += 1
# The allowable channel inputs are l, a or b
names = {"l": "lightness", "a": "green-magenta", "b": "blue-yellow"}
if channel not in names:
fatal_error("Channel " + str(channel) + " is not l, a or b!")
# Convert the input BGR image to LAB colorspace
lab = cv2.cvtColor(rgb_img, cv2.COLOR_BGR2LAB)
# Split LAB channels
l, a, b = cv2.split(lab)
# Create a channel dictionaries for lookups by a channel name index
channels = {"l": l, "a": a, "b": b}
if params.debug == "print":
print_image(
channels[channel],
os.path.join(
params.debug_outdir,
str(params.device) + "_lab_" + names[channel] + ".png"))
elif params.debug == "plot":
plot_image(channels[channel], cmap="gray")
return channels[channel]
def scharr_filter(img, dX, dY, scale, device, debug=None):
"""This is a filtering method used to identify and highlight gradient edges/features using the 1st derivative.
Typically used to identify gradients along the x-axis (dx = 1, dy = 0) and y-axis (dx = 0, dy = 1) independently.
Performance is quite similar to Sobel filter. Used to detect edges / changes in pixel intensity. ddepth = -1
specifies that the dimensions of output image will be the same as the input image.
Inputs:
# img = image
# dx = derivative of x to analyze (1-3)
# dy = derivative of x to analyze (1-3)
# scale = scaling factor applied (multiplied) to computed Scharr values (scale = 1 is unscaled)
# device = device number. Used to count steps in the pipeline
# debug = None, print, or plot. Print = save to file, Plot = print to screen.
Returns:
device = device number
sr_img = Scharr filtered image
:param img: numpy array
:param dX: int
:param dY: int
:param scale: int
:param device: int
:param debug: str
:return device: int
:return sr_img: numpy array
"""
sr_img = cv2.Scharr(src=img, ddepth=-1, dx=dX, dy=dY, scale=scale)
device += 1
if debug == 'print':
print_image(
sr_img,
str(device) + '_sr_img_dx' + str(dX) + '_dy' + str(dY) + '_scale' +
str(scale) + '.png')
elif debug == 'plot':
plot_image(sr_img, cmap='gray')
return device, sr_img
def distance_transform(img, distanceType, maskSize, device, debug=None):
"""Creates an image where for each object pixel, a number is assigned that corresponds to the distance to the
nearest background pixel.
Inputs:
img = img object, binary
distanceType = Type of distance. It can be CV_DIST_L1, CV_DIST_L2 , or CV_DIST_C which are 1, 2 and 3,
respectively.
device = device number. Used to count steps in the pipeline
debug = None, print, or plot. Print = save to file, Plot = print to screen.
maskSize = Size of the distance transform mask. It can be 3, 5, or CV_DIST_MASK_PRECISE (the latter option
is only supported by the first function). In case of the CV_DIST_L1 or CV_DIST_C distance type,
the parameter is forced to 3 because a 3 by 3 mask gives the same result as 5 by 5 or any larger
aperture.
Returns:
device = device number
norm_image = grayscale distance-transformed image normalized between [0,1]
:param img: numpy array
:param distanceType: int
:param maskSize: int
:param device: int
:param debug: str
:return device: int
:return norm_image: numpy array
"""
device += 1
dist = cv2.distanceTransform(src=img, distanceType=distanceType, maskSize=maskSize)
norm_image = cv2.normalize(src=dist, dst=dist, alpha=0, beta=1, norm_type=cv2.NORM_MINMAX, dtype=cv2.CV_32F)
if debug == 'print':
print_image(norm_image, (str(device) + '_distance_transform.png'))
elif debug == 'plot':
plot_image(norm_image, cmap='gray')
return device, norm_image
def _draw_roi(img, roi_contour):
"""Draw an ROI
:param img: numpy.ndarray
:param roi_contour: list
"""
# Make a copy of the reference image
ref_img = np.copy(img)
# If the reference image is grayscale convert it to color
if len(np.shape(ref_img)) == 2:
ref_img = cv2.cvtColor(ref_img, cv2.COLOR_GRAY2BGR)
# Draw the contour on the reference image
cv2.drawContours(ref_img, roi_contour, -1, (255, 0, 0),
params.line_thickness)
if params.debug == "print":
# If debug is print, save the image to a file
print_image(
ref_img,
os.path.join(params.debug_outdir,
str(params.device) + "_roi.png"))
elif params.debug == "plot":
# If debug is plot, print to the plotting device
plot_image(ref_img)
def rgb2gray(rgb_img):
"""Convert image from RGB colorspace to Gray.
Inputs:
rgb_img = RGB image data
Returns:
gray = grayscale image
:param rgb_img: numpy.ndarray
:return gray: numpy.ndarray
"""
gray = cv2.cvtColor(rgb_img, cv2.COLOR_BGR2GRAY)
params.device += 1
if params.debug == 'print':
print_image(
gray,
os.path.join(params.debug_outdir,
str(params.device) + '_gray.png'))
elif params.debug == 'plot':
plot_image(gray, cmap='gray')
return gray
def median_blur(gray_img, ksize):
"""Applies a median blur filter (applies median value to central pixel within a kernel size ksize x ksize).
Inputs:
gray_img = Grayscale image data
ksize = kernel size => ksize x ksize box
Returns:
img_mblur = blurred image
:param gray_img: numpy.ndarray
:param ksize: int
:return img_mblur: numpy.ndarray
"""
img_mblur = cv2.medianBlur(gray_img, ksize)
params.device += 1
if params.debug == 'print':
print_image(img_mblur, os.path.join(params.debug_outdir,
str(params.device) + '_median_blur' + str(ksize) + '.png'))
elif params.debug == 'plot':
plot_image(img_mblur, cmap='gray')
return img_mblur
def erode(gray_img, ksize, i):
"""Perform morphological 'erosion' filtering. Keeps pixel in center of the kernel if conditions set in kernel are
true, otherwise removes pixel.
Inputs:
gray_img = Grayscale (usually binary) image data
ksize = Kernel size (int). A ksize x ksize kernel will be built. Must be greater than 1 to have an effect.
i = interations, i.e. number of consecutive filtering passes
Returns:
er_img = eroded image
:param gray_img: numpy.ndarray
:param ksize: int
:param i: int
:return er_img: numpy.ndarray
"""
if ksize <= 1:
raise ValueError(
'ksize needs to be greater than 1 for the function to have an effect'
)
kernel1 = int(ksize)
kernel2 = np.ones((kernel1, kernel1), np.uint8)
er_img = cv2.erode(src=gray_img, kernel=kernel2, iterations=i)
params.device += 1
if params.debug == 'print':
print_image(
er_img,
os.path.join(
params.debug_outdir,
str(params.device) + '_er_image' + str(ksize) + '_itr_' +
str(i) + '.png'))
elif params.debug == 'plot':
plot_image(er_img, cmap='gray')
return er_img
def readimage(filename, mode="native"):
"""Read image from file.
Inputs:
filename = name of image file
mode = mode of imread ("native", "rgb", "gray")
Returns:
img = image object as numpy array
path = path to image file
img_name = name of image file
:param filename: str
:param mode: str
:return img: numpy.ndarray
:return path: str
:return img_name: str
"""
if mode.upper() == "GRAY" or mode.upper() == "GREY":
img = cv2.imread(filename, 0)
elif mode.upper() == "RGB":
img = cv2.imread(filename)
else:
img = cv2.imread(filename, -1)
if img is None:
fatal_error("Failed to open " + filename)
# Split path from filename
path, img_name = os.path.split(filename)
if params.debug == "print":
print_image(img, os.path.join(params.debug_outdir, "input_image.png"))
elif params.debug == "plot":
plot_image(img)
return img, path, img_name
def rgb2gray_hsv(rgb_img, channel):
"""Convert an RGB color image to HSV colorspace and return a gray image (one channel).
Inputs:
rgb_img = RGB image data
channel = color subchannel (h = hue, s = saturation, v = value/intensity/brightness)
Returns:
h | s | v = image from single HSV channel
:param rgb_img: numpy.ndarray
:param channel: str
:return channel: numpy.ndarray
"""
# Auto-increment the device counter
params.device += 1
# The allowable channel inputs are h, s or v
names = {"h": "hue", "s": "saturation", "v": "value"}
channel = channel.lower()
if channel not in names:
fatal_error("Channel " + str(channel) + " is not h, s or v!")
# Convert the input BGR image to HSV colorspace
hsv = cv2.cvtColor(rgb_img, cv2.COLOR_BGR2HSV)
# Split HSV channels
h, s, v = cv2.split(hsv)
# Create a channel dictionaries for lookups by a channel name index
channels = {"h": h, "s": s, "v": v}
if params.debug == "print":
print_image(channels[channel], os.path.join(params.debug_outdir,
str(params.device) + "_hsv_" + names[channel] + ".png"))
elif params.debug == "plot":
plot_image(channels[channel], cmap="gray")
return channels[channel]
def gaussian_blur(device, img, ksize, sigmax=0, sigmay=None, debug=None):
"""Applies a Gaussian blur filter.
Inputs:
# device = device number. Used to count steps in the pipeline
# img = img object
# ksize = kernel size => ksize x ksize box, e.g. (5,5)
# sigmax = standard deviation in X direction; if 0, calculated from kernel size
# sigmay = standard deviation in Y direction; if sigmaY is None, sigmaY is taken to equal sigmaX
# debug = None, print, or plot. Print = save to file, Plot = print to screen.
Returns:
device = device number
img_gblur = blurred image
:param img: numpy array
:param ksize: tuple
:param sigmax: int
:param sigmay: str or int
:param device: int
:param debug: str
:return device: int
:return img_gblur: numpy array
"""
img_gblur = cv2.GaussianBlur(img, ksize, sigmax, sigmay)
device += 1
if debug == 'print':
print_image(img_gblur, (str(device) + '_gaussian_blur.png'))
elif debug == 'plot':
if len(img_gblur) == 3:
plot_image(img_gblur)
else:
plot_image(img_gblur, cmap='gray')
return device, img_gblur
def fill(bin_img, size):
"""Identifies objects and fills objects that are less than size.
Inputs:
bin_img = Binary image data
size = minimum object area size in pixels (integer)
Returns:
filtered_img = image with objects filled
:param bin_img: numpy.ndarray
:param size: int
:return filtered_img: numpy.ndarray
"""
params.device += 1
# Make sure the image is binary
if len(np.shape(bin_img)) != 2 or len(np.unique(bin_img)) != 2:
fatal_error("Image is not binary")
# Cast binary image to boolean
bool_img = bin_img.astype(bool)
# Find and fill contours
bool_img = remove_small_objects(bool_img, size)
# Cast boolean image to binary and make a copy of the binary image for returning
filtered_img = np.copy(bool_img.astype(np.uint8) * 255)
if params.debug == 'print':
print_image(filtered_img, os.path.join(params.debug_outdir, str(params.device) + '_fill' + str(size) + '.png'))
elif params.debug == 'plot':
plot_image(filtered_img, cmap='gray')
return filtered_img
def rescale(gray_img, min_value=0, max_value=255):
"""Rescale image.
Inputs:
gray_img = Grayscale image data
min_value = (optional) new minimum value for range of interest. default = 0
max_value = (optional) new maximum value for range of interest. default = 255
Returns:
rescaled_img = rescaled image
:param gray_img: numpy.ndarray
:param min_value: int
:param max_value: int
:return c: numpy.ndarray
"""
if len(np.shape(gray_img)) != 2:
fatal_error("Image is not grayscale")
rescaled_img = np.interp(gray_img,
(np.nanmin(gray_img), np.nanmax(gray_img)),
(min_value, max_value))
rescaled_img = (rescaled_img).astype('uint8')
# Autoincrement the device counter
params.device += 1
if params.debug == 'print':
print_image(
rescaled_img,
os.path.join(params.debug_outdir,
str(params.device) + "_rescaled.png"))
elif params.debug == 'plot':
plot_image(rescaled_img, cmap='gray')
return rescaled_img
def stdev_filter(img, ksize, borders='nearest'):
"""Creates a binary image from a grayscale image using skimage texture calculation for thresholding.
This function is quite slow.
Inputs:
gray_img = Grayscale image data
ksize = Kernel size for texture measure calculation
borders = How the array borders are handled, either 'reflect',
'constant', 'nearest', 'mirror', or 'wrap'
Returns:
output = Standard deviation values image
:param img: numpy.ndarray
:param ksize: int
:param borders: str
:return output: numpy.ndarray
"""
# Make an array the same size as the original image
output = np.zeros(img.shape, dtype=img.dtype)
# Apply the texture function over the whole image
generic_filter(img, np.std, size=ksize, output=output, mode=borders)
if params.debug == "print":
# If debug is print, save the image to a file
print_image(
output,
os.path.join(params.debug_outdir,
str(params.device) + "_variance.png"))
elif params.debug == "plot":
# If debug is plot, print to the plotting device
plot_image(output)
return output
def image_subtract(gray_img1, gray_img2):
"""This is a function used to subtract values of one gray-scale image array from another gray-scale image array. The
resulting gray-scale image array has a minimum element value of zero. That is all negative values resulting from the
subtraction are forced to zero.
Inputs:
gray_img1 = a gray-scale or binary image from which gray_img2 will be subtracted
gray_img2 = a gray-scale or binary image which will be subtracted from gray_img1
Returns:
new_img = subtracted image
:param gray_img1: numpy array
:param gray_img2: numpy array
:return new_img: numpy array
"""
params.device += 1 # increment device
# check inputs for gray-scale
if len(np.shape(gray_img1)) != 2 or len(np.shape(gray_img2)) != 2:
fatal_error("Input image is not gray-scale")
new_img = gray_img1.astype(np.float64) - gray_img2.astype(
np.float64) # subtract values
new_img[np.where(new_img < 0)] = 0 # force negative array values to zero
new_img = new_img.astype(np.uint8) # typecast image to 8-bit image
# print-plot handling
if params.debug == 'print':
print_image(
new_img,
os.path.join(params.debug_outdir,
str(params.device) + "_subtraction.png"))
elif params.debug == 'plot':
plot_image(new_img, cmap='gray')
return new_img # return
def rgb2gray_lab(rgb_img, channel):
"""Convert image from RGB colorspace to LAB colorspace. Returns the specified subchannel as a gray image.
Inputs:
rgb_img = RGB image data
channel = color subchannel (l = lightness, a = green-magenta, b = blue-yellow)
Returns:
l | a | b = grayscale image from one LAB color channel
:param rgb_img: numpy.ndarray
:param channel: str
:return channel: numpy.ndarray
"""
# Auto-increment the device counter
params.device += 1
# The allowable channel inputs are l, a or b
names = {"l": "lightness", "a": "green-magenta", "b": "blue-yellow"}
channel = channel.lower()
if channel not in names:
fatal_error("Channel " + str(channel) + " is not l, a or b!")
# Convert the input BGR image to LAB colorspace
lab = cv2.cvtColor(rgb_img, cv2.COLOR_BGR2LAB)
# Split LAB channels
l, a, b = cv2.split(lab)
# Create a channel dictionaries for lookups by a channel name index
channels = {"l": l, "a": a, "b": b}
if params.debug == "print":
print_image(channels[channel], os.path.join(params.debug_outdir,
str(params.device) + "_lab_" + names[channel] + ".png"))
elif params.debug == "plot":
plot_image(channels[channel], cmap="gray")
return channels[channel]
def laplace_filter(img, k, scale, device, debug=None):
"""This is a filtering method used to identify and highlight fine edges based on the 2nd derivative. A very
sensetive method to highlight edges but will also amplify background noise. ddepth = -1 specifies that the
dimensions of output image will be the same as the input image.
Inputs:
img = input image
k = apertures size used to calculate 2nd derivative filter, specifies the size of the kernel
(must be an odd integer: 1,3,5...)
scale = scaling factor applied (multiplied) to computed Laplacian values (scale = 1 is unscaled)
device = device number. Used to count steps in the pipeline
debug = None, print, or plot. Print = save to file, Plot = print to screen.
Returns:
device = device number
lp_filtered = laplacian filtered image
:param img: numpy array
:param k: int
:param scale: int
:param device: int
:param debug: str
:return device: int
:return lp_filtered: numpy array
"""
lp_filtered = cv2.Laplacian(src=img, ddepth=-1, ksize=k, scale=scale)
device += 1
if debug == 'print':
print_image(
lp_filtered,
str(device) + '_lp_out_k' + str(k) + '_scale' + str(scale) +
'.png')
elif debug == 'plot':
plot_image(lp_filtered, cmap='gray')
return device, lp_filtered
def flip(img, direction):
"""Flip image.
Inputs:
img = RGB or grayscale image data
direction = "horizontal" or "vertical"
Returns:
vh_img = flipped image
:param img: numpy.ndarray
:param direction: str
:return vh_img: numpy.ndarray
"""
params.device += 1
if direction == "vertical":
vh_img = cv2.flip(img, 1)
elif direction == "horizontal":
vh_img = cv2.flip(img, 0)
else:
fatal_error(
str(direction) +
" is not a valid direction, must be horizontal or vertical")
if params.debug == 'print':
print_image(
vh_img,
os.path.join(params.debug_outdir,
str(params.device) + "_flipped.png"))
elif params.debug == 'plot':
if len(np.shape(vh_img)) == 3:
plot_image(vh_img)
else:
plot_image(vh_img, cmap='gray')
return vh_img
def resize(img, resize_x, resize_y, device, debug=None):
"""Resize image.
Inputs:
img = image to resize
resize_x = scaling factor
resize_y = scaling factor
device = device counter
debug = None, print, or plot. Print = save to file, Plot = print to screen.
Returns:
device = device number
reimg = resized image
:param img: numpy array
:param resize_x: int
:param resize_y: int
:param device: int
:param debug: str
:return device: int
:return reimg: numpy array
"""
device += 1
if resize_x <= 0 and resize_y <= 0:
fatal_error("Resize values both cannot be 0 or negative values!")
reimg = cv2.resize(img, (0, 0), fx=resize_x, fy=resize_y)
if debug == 'print':
print_image(reimg, (str(device) + "_resize1.png"))
elif debug == 'plot':
plot_image(reimg, cmap='gray')
return device, reimg
def fill_holes(bin_img):
"""Flood fills holes in a binary mask
Inputs:
bin_img = Binary image data
Returns:
filtered_img = image with objects filled
:param bin_img: numpy.ndarray
:return filtered_img: numpy.ndarray
"""
params.device += 1
# Make sure the image is binary
if len(np.shape(bin_img)) != 2 or len(np.unique(bin_img)) != 2:
fatal_error("Image is not binary")
# Cast binary image to boolean
bool_img = bin_img.astype(bool)
# Flood fill holes
bool_img = binary_fill_holes(bool_img)
# Cast boolean image to binary and make a copy of the binary image for returning
filtered_img = np.copy(bool_img.astype(np.uint8) * 255)
if params.debug == 'print':
print_image(
filtered_img,
os.path.join(params.debug_outdir,
str(params.device) + '_fill_holes' + '.png'))
elif params.debug == 'plot':
plot_image(filtered_img, cmap='gray')
return filtered_img
def pseudocolor(gray_img,
obj=None,
mask=None,
cmap=None,
background="image",
min_value=0,
max_value=255,
axes=True,
colorbar=True,
obj_padding="auto"):
"""Pseudocolor any grayscale image to custom colormap
Inputs:
gray_img = grayscale image data
obj = (optional) ROI or plant contour object. If provided, the pseudocolored image gets cropped
down to the region of interest. default = None
mask = (optional) binary mask
cmap = (optional) colormap. default is the matplotlib default, viridis
background = (optional) background color/type, options are "image" (gray_img), "white", or "black" (requires a mask). default = 'image'
min_value = (optional) minimum value for range of interest. default = 0
max_value = (optional) maximum value for range of interest. default = 255
axes = (optional) if False then x- and y-axis won't be displayed, nor will the title. default = True
colorbar = (optional) if False then colorbar won't be displayed. default = True
obj_padding = (optional) if "auto" (default) and an obj is supplied, then the image is cropped to an extent 20%
larger in each dimension than the object. An single integer is also accepted to define the padding
in pixels
Returns:
pseudo_image = pseudocolored image
:param gray_img: numpy.ndarray
:param obj: numpy.ndarray
:param mask: numpy.ndarray
:param cmap: str
:param background: str
:param min_value: numeric
:param max_value: numeric
:param dpi: int
:param axes: bool
:param obj_padding: str, int
:return pseudo_image: numpy.ndarray
"""
# Auto-increment the device counter
params.device += 1
# Make copies of the gray image
gray_img1 = np.copy(gray_img)
# Check if the image is grayscale
if len(np.shape(gray_img)) != 2:
fatal_error("Image must be grayscale.")
# Apply the mask if given
if mask is not None:
if obj is not None:
# Copy the image
img_copy = np.copy(gray_img1)
# Extract contour size
x, y, w, h = cv2.boundingRect(obj)
cv2.rectangle(img_copy, (x, y), (x + w, y + h), (0, 255, 0), 5)
# Crop down the image
crop_img = gray_img[y:y + h, x:x + w]
# Setup a buffer around the bounding box of obj
if type(obj_padding) is int:
offsetx = obj_padding
offsety = obj_padding
elif type(obj_padding) is str and obj_padding.upper() == "AUTO":
# Calculate the buffer size based on the contour size
offsetx = int(w / 5)
offsety = int(h / 5)
else:
fatal_error("Padding must either be 'auto' or an integer.")
if background.upper() == "IMAGE":
gray_img1 = gray_img1[y - offsety:y + h + offsety,
x - offsetx:x + w + offsetx]
else:
# Crop img including buffer
gray_img1 = cv2.copyMakeBorder(crop_img,
offsety,
offsety,
offsetx,
offsetx,
cv2.BORDER_CONSTANT,
value=(0, 0, 0))
# Crop the mask to the same size as the image
crop_mask = mask[y:y + h, x:x + w]
mask = cv2.copyMakeBorder(crop_mask,
offsety,
offsety,
offsetx,
offsetx,
cv2.BORDER_CONSTANT,
value=(0, 0, 0))
# Apply the mask
masked_img = np.ma.array(gray_img1, mask=~mask.astype(np.bool))
# Set the background color or type
if background.upper() == "BLACK":
# Background is all zeros
bkg_img = np.zeros(np.shape(gray_img1), dtype=np.uint8)
# Use the gray cmap for the background
bkg_cmap = "gray"
elif background.upper() == "WHITE":
# Background is all 255 (white)
bkg_img = np.zeros(np.shape(gray_img1), dtype=np.uint8)
bkg_img += 255
bkg_cmap = "gray"
elif background.upper() == "IMAGE":
# Set the background to the input gray image
bkg_img = gray_img1
bkg_cmap = "gray"
else:
fatal_error(
"Background type {0} is not supported. Please use 'white', 'black', or 'image'."
.format(background))
# Pseudocolor the image, plot the background first
pseudo_img1 = plt.imshow(bkg_img, cmap=bkg_cmap)
# Overlay the masked grayscale image with the user input colormap
plt.imshow(masked_img, cmap=cmap, vmin=min_value, vmax=max_value)
if colorbar:
plt.colorbar(fraction=0.033, pad=0.04)
if axes:
# Include image title
plt.title('Pseudocolored image')
else:
# Remove axes
plt.xticks([])
plt.yticks([])
# Store the current figure
pseudo_img = plt.gcf()
# Print or plot if debug is turned on
if params.debug == 'print':
plt.savefig(os.path.join(params.debug_outdir,
str(params.device) +
'_pseudocolored.png'),
dpi=params.dpi)
plt.close()
elif params.debug == 'plot':
plot_image(pseudo_img1)
# Use non-blocking mode in case the function is run more than once
plt.show(block=False)
elif params.debug == None:
plt.show(block=False)
else:
# Pseudocolor the image
pseudo_img1 = plt.imshow(gray_img1,
cmap=cmap,
vmin=min_value,
vmax=max_value)
if colorbar:
# Include the colorbar
plt.colorbar(fraction=0.033, pad=0.04)
if axes:
# Include image title
plt.title(
'Pseudocolored image') # + os.path.splitext(filename)[0])
else:
# Remove axes
plt.xticks([])
plt.yticks([])
pseudo_img = plt.gcf()
# Print or plot if debug is turned on
if params.debug == 'print':
plt.savefig(os.path.join(params.debug_outdir,
str(params.device) +
'_pseudocolored.png'),
dpi=params.dpi)
pseudo_img.clear()
plt.close()
elif params.debug == 'plot':
plot_image(pseudo_img1)
# Use non-blocking mode in case the function is run more than once
plt.show(block=False)
elif params.debug == None:
plt.show(block=False)
return pseudo_img
def custom_range(rgb_img, lower_thresh, upper_thresh, channel='gray'):
"""Creates a thresholded image and mask from an RGB image and threshold values.
Inputs:
rgb_img = RGB image data
lower_thresh = List of lower threshold values (0-255)
upper_thresh = List of upper threshold values (0-255)
channel = Color-space channels of interest (RGB, HSV, LAB, or gray)
Returns:
mask = Mask, binary image
masked_img = Masked image, keeping the part of image of interest
:param rgb_img: numpy.ndarray
:param lower_thresh: list
:param upper_thresh: list
:param channel: str
:return mask: numpy.ndarray
:return masked_img: numpy.ndarray
"""
# Auto-increment the device counter
params.device += 1
if channel.upper() == 'HSV':
# Check threshold inputs
if not (len(lower_thresh) == 3 and len(upper_thresh) == 3):
fatal_error("If using the HSV colorspace, 3 thresholds are needed for both lower_thresh and " +
"upper_thresh. If thresholding isn't needed for a channel, set lower_thresh=0 and " +
"upper_thresh=255")
# Convert the RGB image to HSV colorspace
hsv_img = cv2.cvtColor(rgb_img, cv2.COLOR_BGR2HSV)
# Separate channels
hue = hsv_img[:, :, 0]
saturation = hsv_img[:, :, 1]
value = hsv_img[:, :, 2]
# Make a mask for each channel
h_mask = cv2.inRange(hue, lower_thresh[0], upper_thresh[0])
s_mask = cv2.inRange(saturation, lower_thresh[1], upper_thresh[1])
v_mask = cv2.inRange(value, lower_thresh[2], upper_thresh[2])
# Apply the masks to the image
result = cv2.bitwise_and(rgb_img, rgb_img, mask=h_mask)
result = cv2.bitwise_and(result, result, mask=s_mask)
masked_img = cv2.bitwise_and(result, result, mask=v_mask)
# Combine masks
mask = cv2.bitwise_and(s_mask, h_mask)
mask = cv2.bitwise_and(mask, v_mask)
elif channel.upper() == 'RGB':
# Check threshold inputs
if not (len(lower_thresh) == 3 and len(upper_thresh) == 3):
fatal_error("If using the RGB colorspace, 3 thresholds are needed for both lower_thresh and " +
"upper_thresh. If thresholding isn't needed for a channel, set lower_thresh=0 and " +
"upper_thresh=255")
# Separate channels (pcv.readimage reads RGB images in as BGR)
blue = rgb_img[:, :, 0]
green = rgb_img[:, :, 1]
red = rgb_img[:, :, 2]
# Make a mask for each channel
b_mask = cv2.inRange(blue, lower_thresh[0], upper_thresh[0])
g_mask = cv2.inRange(green, lower_thresh[1], upper_thresh[1])
r_mask = cv2.inRange(red, lower_thresh[2], upper_thresh[2])
# Apply the masks to the image
result = cv2.bitwise_and(rgb_img, rgb_img, mask=b_mask)
result = cv2.bitwise_and(result, result, mask=g_mask)
masked_img = cv2.bitwise_and(result, result, mask=r_mask)
# Combine masks
mask = cv2.bitwise_and(b_mask, g_mask)
mask = cv2.bitwise_and(mask, r_mask)
elif channel.upper() == 'LAB':
# Check threshold inputs
if not (len(lower_thresh) == 3 and len(upper_thresh) == 3):
fatal_error("If using the LAB colorspace, 3 thresholds are needed for both lower_thresh and " +
"upper_thresh. If thresholding isn't needed for a channel, set lower_thresh=0 and " +
"upper_thresh=255")
# Convert the RGB image to LAB colorspace
lab_img = cv2.cvtColor(rgb_img, cv2.COLOR_BGR2LAB)
# Separate channels (pcv.readimage reads RGB images in as BGR)
lightness = lab_img[:, :, 0]
green_magenta = lab_img[:, :, 1]
blue_yellow = lab_img[:, :, 2]
# Make a mask for each channel
l_mask = cv2.inRange(lightness, lower_thresh[0], upper_thresh[0])
gm_mask = cv2.inRange(green_magenta, lower_thresh[1], upper_thresh[1])
by_mask = cv2.inRange(blue_yellow, lower_thresh[2], upper_thresh[2])
# Apply the masks to the image
result = cv2.bitwise_and(rgb_img, rgb_img, mask=l_mask)
result = cv2.bitwise_and(result, result, mask=gm_mask)
masked_img = cv2.bitwise_and(result, result, mask=by_mask)
# Combine masks
mask = cv2.bitwise_and(l_mask, gm_mask)
mask = cv2.bitwise_and(mask, by_mask)
elif channel.upper() == 'GRAY' or channel.upper() == 'GREY':
# Check threshold input
if not (len(lower_thresh) == 1 and len(upper_thresh) == 1):
fatal_error("If useing a grayscale colorspace, 1 threshold is needed for both the " +
"lower_thresh and upper_thresh.")
if len(np.shape(rgb_img))==3:
# Convert RGB image to grayscale colorspace
gray_img = cv2.cvtColor(rgb_img, cv2.COLOR_BGR2GRAY)
else:
gray_img = rgb_img
# Make a mask
mask = cv2.inRange(gray_img, lower_thresh[0], upper_thresh[0])
# Apply the masks to the image
masked_img = cv2.bitwise_and(rgb_img, rgb_img, mask=mask)
else:
fatal_error(str(channel) + " is not a valid colorspace. Channel must be either 'RGB', 'HSV', or 'gray'.")
# Print or plot the binary image if debug is on
if params.debug == 'print':
print_image(masked_img, os.path.join(params.debug_outdir,
str(params.device) + channel + 'custom_thresh.png'))
print_image(mask, os.path.join(params.debug_outdir,
str(params.device) + channel + 'custom_thresh_mask.png'))
elif params.debug == 'plot':
plot_image(masked_img)
plot_image(mask)
return mask, masked_img
def _pseudocolored_image(histogram, bins, img, mask, background, channel,
filename, analysis_images):
"""Pseudocolor image.
Inputs:
histogram = a normalized histogram of color values from one color channel
bins = number of color bins the channel is divided into
img = input image
mask = binary mask image
background = what background image?: channel image (img) or white
channel = color channel name
filename = input image filename
analysis_images = list of analysis image filenames
Returns:
analysis_images = list of analysis image filenames
:param histogram: list
:param bins: int
:param img: numpy array
:param mask: numpy array
:param background: str
:param channel: str
:param filename: str
:param analysis_images: list
:return analysis_images: list
"""
mask_inv = cv2.bitwise_not(mask)
cplant = cv2.applyColorMap(histogram, colormap=2)
cplant1 = cv2.bitwise_and(cplant, cplant, mask=mask)
output_imgs = {
"pseudo_on_img": {
"background": "img",
"img": None
},
"pseudo_on_white": {
"background": "white",
"img": None
}
}
if background == 'img' or background == 'both':
# mask the background and color the plant with color scheme 'jet'
img_gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
img_back = cv2.bitwise_and(img_gray, img_gray, mask=mask_inv)
img_back3 = np.dstack((img_back, img_back, img_back))
output_imgs["pseudo_on_img"]["img"] = cv2.add(cplant1, img_back3)
if background == 'white' or background == 'both':
# Get the image size
if np.shape(img)[2] == 3:
ix, iy, iz = np.shape(img)
else:
ix, iy = np.shape(img)
size = ix, iy
back = np.zeros(size, dtype=np.uint8)
w_back = back + 255
w_back3 = np.dstack((w_back, w_back, w_back))
img_back3 = cv2.bitwise_and(w_back3, w_back3, mask=mask_inv)
output_imgs["pseudo_on_white"]["img"] = cv2.add(cplant1, img_back3)
if filename:
for key in output_imgs:
if output_imgs[key]["img"] is not None:
fig_name_pseudo = str(filename[0:-4]) + '_' + str(channel) + '_pseudo_on_' + \
output_imgs[key]["background"] + '.jpg'
path = os.path.dirname(filename)
print_image(output_imgs[key]["img"], fig_name_pseudo)
analysis_images.append(['IMAGE', 'pseudo', fig_name_pseudo])
else:
path = "."
if params.debug is not None:
if params.debug == 'print':
for key in output_imgs:
if output_imgs[key]["img"] is not None:
print_image(
output_imgs[key]["img"],
os.path.join(
params.debug_outdir,
str(params.device) + "_" +
output_imgs[key]["background"] +
'_pseudocolor.jpg'))
fig_name = 'VIS_pseudocolor_colorbar_' + str(
channel) + '_channel.svg'
if not os.path.isfile(os.path.join(params.debug_outdir, fig_name)):
plot_colorbar(path, fig_name, bins)
elif params.debug == 'plot':
for key in output_imgs:
if output_imgs[key]["img"] is not None:
plot_image(output_imgs[key]["img"])
return analysis_images
def naive_bayes_classifier(img, pdf_file, device, debug=None):
"""Use the Naive Bayes classifier to output a plant binary mask.
Inputs:
img = image object (NumPy ndarray), BGR colorspace
pdf_file = filename of file containing PDFs output from the Naive Bayes training method (see plantcv-train.py)
device = device number. Used to count steps in the pipeline
debug = None, print, or plot. Print = save to file, Plot = print to screen.
Returns:
device = device number
mask = binary mask (ndarray)
:param img: ndarray
:param pdf_file: str
:param device: int
:param debug: str
:return device: int
:return masks: dict
"""
device += 1
# Initialize PDF dictionary
pdfs = {}
# Read the PDF file
pf = open(pdf_file, "r")
# Read the first line (header)
pf.readline()
# Read each line of the file and parse the PDFs, store in the PDF dictionary
for row in pf:
# Remove newline character
row = row.rstrip("\n")
# Split the row into columns on tab characters
cols = row.split("\t")
# Make sure there are the correct number of columns (i.e. is this a valid PDF file?)
if len(cols) != 258:
fatal_error(
"Naive Bayes PDF file is not formatted correctly. Error on line:\n"
+ row)
# Store the PDFs. Column 0 is the class, Column 1 is the color channel, the rest are p at
# intensity values 0-255. Cast text p values as float
class_name = cols[0]
channel = cols[1]
if class_name not in pdfs:
pdfs[class_name] = {}
pdfs[class_name][channel] = [float(i) for i in cols[2:]]
# Split the input BGR image into component channels for BGR, HSV, and LAB colorspaces
# b, g, r = cv2.split(img)
h, s, v = cv2.split(cv2.cvtColor(img, cv2.COLOR_BGR2HSV))
# l, gm, by = cv2.split(cv2.cvtColor(img, cv2.COLOR_BGR2LAB))
# Calculate the dimensions of the input image
width, height, depth = np.shape(img)
# Initialize an empty ndarray for plant and background. These will be used to store the joint probabilities
px_p = {}
for class_name in pdfs.keys():
px_p[class_name] = np.zeros([width, height])
# Loop over the image coordinates (each i, j pixel)
for i in range(0, width):
for j in range(0, height):
for class_name in pdfs.keys():
# Calculate the joint probability that this is in the class
px_p[class_name][i][j] = pdfs[class_name]["hue"][h[i][j]] * pdfs[class_name]["saturation"][s[i][j]] * \
pdfs[class_name]["value"][v[i][j]]
# Initialize empty masks
masks = {}
for class_name in pdfs.keys():
masks[class_name] = np.zeros([width, height], dtype=np.uint8)
# Set pixel intensities to 255 (white) for the mask where the class has the highest probability
for class_name in masks:
background_classes = []
for name in masks:
if class_name is not name:
background_classes.append(px_p[name])
background_class = np.maximum.reduce(background_classes)
masks[class_name][np.where(px_p[class_name] > background_class)] = 255
# mask[np.where(plant > bg)] = 255
# Print or plot the mask if debug is not None
if debug == "print":
for class_name, mask in masks.items():
print_image(
mask,
(str(device) + "_naive_bayes_" + class_name + "_mask.jpg"))
elif debug == "plot":
for class_name, mask in masks.items():
plot_image(mask, cmap="gray")
return device, masks
def analyze_index(index_array,
mask,
histplot=False,
bins=100,
min_bin=0,
max_bin=1):
"""This extracts the hyperspectral index statistics and writes the values as observations out to
the Outputs class.
Inputs:
index_array = Instance of the Spectral_data class, usually the output from pcv.hyperspectral.extract_index
mask = Binary mask made from selected contours
histplot = if True plots histogram of intensity values
bins = optional, number of classes to divide spectrum into
min_bin = optional, minimum bin value ("auto" or user input minimum value)
max_bin = optional, maximum bin value ("auto" or user input maximum value)
:param array: __main__.Spectral_data
:param mask: numpy array
:param histplot: bool
:param bins: int
:param max_bin: float, str
:param min_bin: float, str
:return analysis_image: ggplot, None
"""
params.device += 1
debug = params.debug
params.debug = None
analysis_image = None
if len(np.shape(mask)) > 2 or len(np.unique(mask)) > 2:
fatal_error("Mask should be a binary image of 0 and nonzero values.")
if len(np.shape(index_array.array_data)) > 2:
fatal_error("index_array data should be a grayscale image.")
# Mask data and collect statistics about pixels within the masked image
masked_array = index_array.array_data[np.where(mask > 0)]
index_mean = np.average(masked_array)
index_median = np.median(masked_array)
index_std = np.std(masked_array)
# Set starting point and max bin values
maxval = max_bin
b = min_bin
# Calculate observed min and max pixel values of the masked array
observed_max = np.nanmax(masked_array)
observed_min = np.nanmin(masked_array)
# Auto calculate max_bin if set
if type(max_bin) is str and (max_bin.upper() == "AUTO"):
maxval = float(
round(observed_max, 8)
) # Auto bins will detect maxval to use for calculating labels/bins
if type(min_bin) is str and (min_bin.upper() == "AUTO"):
b = float(round(observed_min,
8)) # If bin_min is auto then overwrite starting value
# Print a warning if observed min/max outside user defined range
if observed_max > maxval or observed_min < b:
print(
"WARNING!!! The observed range of pixel values in your masked index provided is ["
+ str(observed_min) + ", " + str(observed_max) +
"] but the user defined range of bins for pixel frequencies is [" +
str(b) + ", " + str(maxval) +
"]. Adjust min_bin and max_bin in order to avoid cutting off data being collected."
)
# Calculate histogram
hist_val = [
float(l[0]) for l in cv2.calcHist([masked_array.astype(np.float32)],
[0], None, [bins], [b, maxval])
]
bin_width = (maxval - b) / float(bins)
bin_labels = [float(b)]
plotting_labels = [float(b)]
for i in range(bins - 1):
b += bin_width
bin_labels.append(b)
plotting_labels.append(round(b, 2))
# Make hist percentage for plotting
pixels = cv2.countNonZero(mask)
hist_percent = [(p / float(pixels)) * 100 for p in hist_val]
params.debug = debug
if histplot is True:
dataset = pd.DataFrame({
'Index Reflectance': bin_labels,
'Proportion of pixels (%)': hist_percent
})
fig_hist = (
ggplot(data=dataset,
mapping=aes(x='Index Reflectance',
y='Proportion of pixels (%)')) +
geom_line(color='red') +
scale_x_continuous(breaks=bin_labels, labels=plotting_labels))
analysis_image = fig_hist
if params.debug == 'print':
fig_hist.save(
os.path.join(
params.debug_outdir,
str(params.device) + index_array.array_type + "hist.png"))
elif params.debug == 'plot':
print(fig_hist)
outputs.add_observation(
variable='mean_' + index_array.array_type,
trait='Average ' + index_array.array_type + ' reflectance',
method='plantcv.plantcv.hyperspectral.analyze_index',
scale='reflectance',
datatype=float,
value=float(index_mean),
label='none')
outputs.add_observation(
variable='med_' + index_array.array_type,
trait='Median ' + index_array.array_type + ' reflectance',
method='plantcv.plantcv.hyperspectral.analyze_index',
scale='reflectance',
datatype=float,
value=float(index_median),
label='none')
outputs.add_observation(
variable='std_' + index_array.array_type,
trait='Standard deviation ' + index_array.array_type + ' reflectance',
method='plantcv.plantcv.hyperspectral.analyze_index',
scale='reflectance',
datatype=float,
value=float(index_std),
label='none')
outputs.add_observation(variable='index_frequencies_' +
index_array.array_type,
trait='index frequencies',
method='plantcv.plantcv.analyze_index',
scale='frequency',
datatype=list,
value=hist_percent,
label=bin_labels)
if params.debug == "plot":
plot_image(masked_array)
elif params.debug == "print":
print_image(img=masked_array,
filename=os.path.join(
params.debug_outdir,
str(params.device) + index_array.array_type + ".png"))
# Store images
outputs.images.append(analysis_image)
return analysis_image
def report_size_marker_area(img,
roi_contour,
roi_hierarchy,
marker='define',
objcolor='dark',
thresh_channel=None,
thresh=None):
"""Detects a size marker in a specified region and reports its size and eccentricity
Inputs:
img = An RGB or grayscale image to plot the marker object on
roi_contour = A region of interest contour (e.g. output from pcv.roi.rectangle or other methods)
roi_hierarchy = A region of interest contour hierarchy (e.g. output from pcv.roi.rectangle or other methods)
marker = 'define' or 'detect'. If define it means you set an area, if detect it means you want to
detect within an area
objcolor = Object color is 'dark' or 'light' (is the marker darker or lighter than the background)
thresh_channel = 'h', 's', or 'v' for hue, saturation or value
thresh = Binary threshold value (integer)
Returns:
analysis_images = List of output images
:param img: numpy.ndarray
:param roi_contour: list
:param roi_hierarchy: numpy.ndarray
:param marker: str
:param objcolor: str
:param thresh_channel: str
:param thresh: int
:return: analysis_images: list
"""
# Store debug
debug = params.debug
params.debug = None
params.device += 1
# Make a copy of the reference image
ref_img = np.copy(img)
# If the reference image is grayscale convert it to color
if len(np.shape(ref_img)) == 2:
ref_img = cv2.cvtColor(ref_img, cv2.COLOR_GRAY2BGR)
# Marker components
# If the marker type is "defined" then the marker_mask and marker_contours are equal to the input ROI
# Initialize a binary image
roi_mask = np.zeros(np.shape(img)[:2], dtype=np.uint8)
# Draw the filled ROI on the mask
cv2.drawContours(roi_mask, roi_contour, -1, (255), -1)
marker_mask = []
marker_contour = []
# If the marker type is "detect" then we will use the ROI to isolate marker contours from the input image
if marker.upper() == 'DETECT':
# We need to convert the input image into an one of the HSV channels and then threshold it
if thresh_channel is not None and thresh is not None:
# Mask the input image
masked = apply_mask(rgb_img=ref_img,
mask=roi_mask,
mask_color="black")
# Convert the masked image to hue, saturation, or value
marker_hsv = rgb2gray_hsv(rgb_img=masked, channel=thresh_channel)
# Threshold the HSV image
marker_bin = binary_threshold(gray_img=marker_hsv,
threshold=thresh,
max_value=255,
object_type=objcolor)
# Identify contours in the masked image
contours, hierarchy = find_objects(img=ref_img, mask=marker_bin)
# Filter marker contours using the input ROI
kept_contours, kept_hierarchy, kept_mask, obj_area = roi_objects(
img=ref_img,
object_contour=contours,
obj_hierarchy=hierarchy,
roi_contour=roi_contour,
roi_hierarchy=roi_hierarchy,
roi_type="partial")
# If there are more than one contour detected, combine them into one
# These become the marker contour and mask
marker_contour, marker_mask = object_composition(
img=ref_img, contours=kept_contours, hierarchy=kept_hierarchy)
else:
fatal_error(
'thresh_channel and thresh must be defined in detect mode')
elif marker.upper() == "DEFINE":
# Identify contours in the masked image
contours, hierarchy = find_objects(img=ref_img, mask=roi_mask)
# If there are more than one contour detected, combine them into one
# These become the marker contour and mask
marker_contour, marker_mask = object_composition(img=ref_img,
contours=contours,
hierarchy=hierarchy)
else:
fatal_error(
"marker must be either 'define' or 'detect' but {0} was provided.".
format(marker))
# Calculate the moments of the defined marker region
m = cv2.moments(marker_mask, binaryImage=True)
# Calculate the marker area
marker_area = m['m00']
# Fit a bounding ellipse to the marker
center, axes, angle = cv2.fitEllipse(marker_contour)
major_axis = np.argmax(axes)
minor_axis = 1 - major_axis
major_axis_length = axes[major_axis]
minor_axis_length = axes[minor_axis]
# Calculate the bounding ellipse eccentricity
eccentricity = np.sqrt(1 - (axes[minor_axis] / axes[major_axis])**2)
cv2.drawContours(ref_img, marker_contour, -1, (255, 0, 0), 5)
analysis_image = ref_img
# Reset debug mode
params.debug = debug
if params.debug is 'print':
print_image(
ref_img,
os.path.join(params.debug_outdir,
str(params.device) + '_marker_shape.png'))
elif params.debug is 'plot':
plot_image(ref_img)
outputs.add_observation(variable='marker_area',
trait='marker area',
method='plantcv.plantcv.report_size_marker_area',
scale='pixels',
datatype=int,
value=marker_area,
label='pixels')
outputs.add_observation(variable='marker_ellipse_major_axis',
trait='marker ellipse major axis length',
method='plantcv.plantcv.report_size_marker_area',
scale='pixels',
datatype=int,
value=major_axis_length,
label='pixels')
outputs.add_observation(variable='marker_ellipse_minor_axis',
trait='marker ellipse minor axis length',
method='plantcv.plantcv.report_size_marker_area',
scale='pixels',
datatype=int,
value=minor_axis_length,
label='pixels')
outputs.add_observation(variable='marker_ellipse_eccentricity',
trait='marker ellipse eccentricity',
method='plantcv.plantcv.report_size_marker_area',
scale='none',
datatype=float,
value=eccentricity,
label='none')
# Store images
outputs.images.append(analysis_image)
return analysis_image
def custom_range(rgb_img, lower_thresh, upper_thresh, channel='gray'):
"""Creates a thresholded image and mask from an RGB image and threshold values.
Inputs:
rgb_img = RGB image data
lower_thresh = List of lower threshold values (0-255)
upper_thresh = List of upper threshold values (0-255)
channel = Color-space channels of interest (RGB, HSV, LAB, or gray)
Returns:
mask = Mask, binary image
masked_img = Masked image, keeping the part of image of interest
:param rgb_img: numpy.ndarray
:param lower_thresh: list
:param upper_thresh: list
:param channel: str
:return mask: numpy.ndarray
:return masked_img: numpy.ndarray
"""
if channel.upper() == 'HSV':
# Check threshold inputs
if not (len(lower_thresh) == 3 and len(upper_thresh) == 3):
fatal_error(
"If using the HSV colorspace, 3 thresholds are needed for both lower_thresh and "
+
"upper_thresh. If thresholding isn't needed for a channel, set lower_thresh=0 and "
+ "upper_thresh=255")
# Convert the RGB image to HSV colorspace
hsv_img = cv2.cvtColor(rgb_img, cv2.COLOR_BGR2HSV)
# Separate channels
hue = hsv_img[:, :, 0]
saturation = hsv_img[:, :, 1]
value = hsv_img[:, :, 2]
# Make a mask for each channel
h_mask = cv2.inRange(hue, lower_thresh[0], upper_thresh[0])
s_mask = cv2.inRange(saturation, lower_thresh[1], upper_thresh[1])
v_mask = cv2.inRange(value, lower_thresh[2], upper_thresh[2])
# Apply the masks to the image
result = cv2.bitwise_and(rgb_img, rgb_img, mask=h_mask)
result = cv2.bitwise_and(result, result, mask=s_mask)
masked_img = cv2.bitwise_and(result, result, mask=v_mask)
# Combine masks
mask = cv2.bitwise_and(s_mask, h_mask)
mask = cv2.bitwise_and(mask, v_mask)
elif channel.upper() == 'RGB':
# Check threshold inputs
if not (len(lower_thresh) == 3 and len(upper_thresh) == 3):
fatal_error(
"If using the RGB colorspace, 3 thresholds are needed for both lower_thresh and "
+
"upper_thresh. If thresholding isn't needed for a channel, set lower_thresh=0 and "
+ "upper_thresh=255")
# Separate channels (pcv.readimage reads RGB images in as BGR)
blue = rgb_img[:, :, 0]
green = rgb_img[:, :, 1]
red = rgb_img[:, :, 2]
# Make a mask for each channel
b_mask = cv2.inRange(blue, lower_thresh[0], upper_thresh[0])
g_mask = cv2.inRange(green, lower_thresh[1], upper_thresh[1])
r_mask = cv2.inRange(red, lower_thresh[2], upper_thresh[2])
# Apply the masks to the image
result = cv2.bitwise_and(rgb_img, rgb_img, mask=b_mask)
result = cv2.bitwise_and(result, result, mask=g_mask)
masked_img = cv2.bitwise_and(result, result, mask=r_mask)
# Combine masks
mask = cv2.bitwise_and(b_mask, g_mask)
mask = cv2.bitwise_and(mask, r_mask)
elif channel.upper() == 'LAB':
# Check threshold inputs
if not (len(lower_thresh) == 3 and len(upper_thresh) == 3):
fatal_error(
"If using the LAB colorspace, 3 thresholds are needed for both lower_thresh and "
+
"upper_thresh. If thresholding isn't needed for a channel, set lower_thresh=0 and "
+ "upper_thresh=255")
# Convert the RGB image to LAB colorspace
lab_img = cv2.cvtColor(rgb_img, cv2.COLOR_BGR2LAB)
# Separate channels (pcv.readimage reads RGB images in as BGR)
lightness = lab_img[:, :, 0]
green_magenta = lab_img[:, :, 1]
blue_yellow = lab_img[:, :, 2]
# Make a mask for each channel
l_mask = cv2.inRange(lightness, lower_thresh[0], upper_thresh[0])
gm_mask = cv2.inRange(green_magenta, lower_thresh[1], upper_thresh[1])
by_mask = cv2.inRange(blue_yellow, lower_thresh[2], upper_thresh[2])
# Apply the masks to the image
result = cv2.bitwise_and(rgb_img, rgb_img, mask=l_mask)
result = cv2.bitwise_and(result, result, mask=gm_mask)
masked_img = cv2.bitwise_and(result, result, mask=by_mask)
# Combine masks
mask = cv2.bitwise_and(l_mask, gm_mask)
mask = cv2.bitwise_and(mask, by_mask)
elif channel.upper() == 'GRAY' or channel.upper() == 'GREY':
# Check threshold input
if not (len(lower_thresh) == 1 and len(upper_thresh) == 1):
fatal_error(
"If useing a grayscale colorspace, 1 threshold is needed for both the "
+ "lower_thresh and upper_thresh.")
if len(np.shape(rgb_img)) == 3:
# Convert RGB image to grayscale colorspace
gray_img = cv2.cvtColor(rgb_img, cv2.COLOR_BGR2GRAY)
else:
gray_img = rgb_img
# Make a mask
mask = cv2.inRange(gray_img, lower_thresh[0], upper_thresh[0])
# Apply the masks to the image
masked_img = cv2.bitwise_and(rgb_img, rgb_img, mask=mask)
else:
fatal_error(
str(channel) +
" is not a valid colorspace. Channel must be either 'RGB', 'HSV', or 'gray'."
)
# Auto-increment the device counter
params.device += 1
# Print or plot the binary image if debug is on
if params.debug == 'print':
print_image(
masked_img,
os.path.join(params.debug_outdir,
str(params.device) + channel + 'custom_thresh.png'))
print_image(
mask,
os.path.join(
params.debug_outdir,
str(params.device) + channel + 'custom_thresh_mask.png'))
elif params.debug == 'plot':
plot_image(masked_img)
plot_image(mask)
return mask, masked_img
def segment_euclidean_length(segmented_img, objects, label="default"):
""" Use segmented skeleton image to gather euclidean length measurements per segment
Inputs:
segmented_img = Segmented image to plot lengths on
objects = List of contours
label = optional label parameter, modifies the variable name of observations recorded
Returns:
labeled_img = Segmented debugging image with lengths labeled
:param segmented_img: numpy.ndarray
:param objects: list
:param label: str
:return labeled_img: numpy.ndarray
"""
x_list = []
y_list = []
segment_lengths = []
# Create a color scale, use a previously stored scale if available
rand_color = color_palette(num=len(objects), saved=True)
labeled_img = segmented_img.copy()
# Store debug
debug = params.debug
params.debug = None
for i, cnt in enumerate(objects):
# Store coordinates for labels
x_list.append(objects[i][0][0][0])
y_list.append(objects[i][0][0][1])
# Draw segments one by one to group segment tips together
finding_tips_img = np.zeros(segmented_img.shape[:2], np.uint8)
cv2.drawContours(finding_tips_img,
objects,
i, (255, 255, 255),
1,
lineType=8)
segment_tips = find_tips(finding_tips_img)
tip_objects, tip_hierarchies = find_objects(segment_tips, segment_tips)
points = []
if not len(tip_objects) == 2:
fatal_error("Too many tips found per segment, try pruning again")
for t in tip_objects:
# Gather pairs of coordinates
x, y = t.ravel()
coord = (x, y)
points.append(coord)
# Draw euclidean distance lines
cv2.line(labeled_img, points[0], points[1], rand_color[i], 1)
# Calculate euclidean distance between tips of each contour
segment_lengths.append(float(euclidean(points[0], points[1])))
segment_ids = []
# Reset debug mode
params.debug = debug
# Put labels of length
for c, value in enumerate(segment_lengths):
text = "{:.2f}".format(value)
w = x_list[c]
h = y_list[c]
cv2.putText(img=labeled_img,
text=text,
org=(w, h),
fontFace=cv2.FONT_HERSHEY_SIMPLEX,
fontScale=params.text_size,
color=(150, 150, 150),
thickness=params.text_thickness)
# segment_label = "ID" + str(c)
segment_ids.append(c)
outputs.add_observation(
sample=label,
variable='segment_eu_length',
trait='segment euclidean length',
method='plantcv.plantcv.morphology.segment_euclidean_length',
scale='pixels',
datatype=list,
value=segment_lengths,
label=segment_ids)
# Auto-increment device
params.device += 1
if params.debug == 'print':
print_image(
labeled_img,
os.path.join(params.debug_outdir,
str(params.device) + '_segment_eu_lengths.png'))
elif params.debug == 'plot':
plot_image(labeled_img)
return labeled_img
def apply_transformation_matrix(source_img, target_img, transformation_matrix):
""" Apply the transformation matrix to the source_image.
Inputs:
source_img = an RGB image to be corrected to the target color space
target_img = an RGB image with the target color space
transformation_matrix = a 9x9 matrix of tranformation coefficients
Outputs:
corrected_img = an RGB image in correct color space
:param source_img: numpy.ndarray
:param target_img: numpy.ndarray
:param transformation_matrix: numpy.ndarray
:return corrected_img: numpy.ndarray
"""
# check transformation_matrix for 9x9
if np.shape(transformation_matrix) != (9, 9):
fatal_error(
"transformation_matrix must be a 9x9 matrix of transformation coefficients."
)
# Check for RGB input
if len(np.shape(source_img)) != 3:
fatal_error("Source_img is not an RGB image.")
# Autoincrement the device counter
params.device += 1
# split transformation_matrix
red, green, blue, red2, green2, blue2, red3, green3, blue3 = np.split(
transformation_matrix, 9, 1)
# find linear, square, and cubic values of source_img color channels
source_b, source_g, source_r = cv2.split(source_img)
source_b2 = np.square(source_b)
source_b3 = np.power(source_b, 3)
source_g2 = np.square(source_g)
source_g3 = np.power(source_g, 3)
source_r2 = np.square(source_r)
source_r3 = np.power(source_r, 3)
# apply linear model to source color channels
b = 0 + source_r * blue[0] + source_g * blue[1] + source_b * blue[
2] + source_r2 * blue[3] + source_g2 * blue[4] + source_b2 * blue[
5] + source_r3 * blue[6] + source_g3 * blue[7] + source_b3 * blue[8]
g = 0 + source_r * green[0] + source_g * green[1] + source_b * green[
2] + source_r2 * green[3] + source_g2 * green[4] + source_b2 * green[
5] + source_r3 * green[6] + source_g3 * green[
7] + source_b3 * green[8]
r = 0 + source_r * red[0] + source_g * red[1] + source_b * red[
2] + source_r2 * red[3] + source_g2 * red[4] + source_b2 * red[
5] + source_r3 * red[6] + source_g3 * red[7] + source_b3 * red[8]
# merge corrected color channels onto source_image
bgr = [b, g, r]
corrected_img = cv2.merge(bgr)
# round corrected_img elements to be within range and of the correct data type
corrected_img = np.rint(corrected_img)
corrected_img[np.where(corrected_img > 255)] = 255
corrected_img = corrected_img.astype(np.uint8)
if params.debug == "print":
# If debug is print, save the image to a file
print_image(
corrected_img,
os.path.join(params.debug_outdir,
str(params.device) + "_corrected.png"))
elif params.debug == "plot":
# If debug is plot, print a horizontal view of source_img, corrected_img, and target_img to the plotting device
# plot horizontal comparison of source_img, corrected_img (with rounded elements) and target_img
plot_image(np.hstack([source_img, corrected_img, target_img]))
# return corrected_img
return corrected_img
def segment_sort(skel_img, objects, mask=None, first_stem=True):
""" Calculate segment curvature as defined by the ratio between geodesic and euclidean distance
Inputs:
skel_img = Skeletonized image
objects = List of contours
mask = (Optional) binary mask for debugging. If provided, debug image will be overlaid on the mask.
first_stem = (Optional) if True, then the first (bottom) segment always gets classified as stem
Returns:
labeled_img = Segmented debugging image with lengths labeled
secondary_objects = List of secondary segments (leaf)
primary_objects = List of primary objects (stem)
:param skel_img: numpy.ndarray
:param objects: list
:param mask: numpy.ndarray
:param first_stem: bool
:return secondary_objects: list
:return other_objects: list
"""
# Store debug
debug = params.debug
params.debug = None
secondary_objects = []
primary_objects = []
if mask is None:
labeled_img = np.zeros(skel_img.shape[:2], np.uint8)
else:
labeled_img = mask.copy()
tips_img = find_tips(skel_img)
tips_img = dilate(tips_img, 3, 1)
# Loop through segment contours
for i, cnt in enumerate(objects):
segment_plot = np.zeros(skel_img.shape[:2], np.uint8)
cv2.drawContours(segment_plot, objects, i, 255, 1, lineType=8)
is_leaf = False
overlap_img = logical_and(segment_plot, tips_img)
# The first contour is the base, and while it contains a tip, it isn't a leaf
if i == 0 and first_stem:
primary_objects.append(cnt)
# Sort segments
else:
if np.sum(overlap_img) > 0:
secondary_objects.append(cnt)
is_leaf = True
else:
primary_objects.append(cnt)
# Plot segments where green segments are leaf objects and fuschia are other objects
labeled_img = cv2.cvtColor(labeled_img, cv2.COLOR_GRAY2RGB)
for i, cnt in enumerate(primary_objects):
cv2.drawContours(labeled_img, primary_objects, i, (255, 0, 255), params.line_thickness, lineType=8)
for i, cnt in enumerate(secondary_objects):
cv2.drawContours(labeled_img, secondary_objects, i, (0, 255, 0), params.line_thickness, lineType=8)
# Reset debug mode
params.debug = debug
# Auto-increment device
params.device += 1
if params.debug == 'print':
print_image(labeled_img, os.path.join(params.debug_outdir, str(params.device) + '_sorted_segments.png'))
elif params.debug == 'plot':
plot_image(labeled_img)
return secondary_objects, primary_objects
def create_color_card_mask(rgb_img,
radius,
start_coord,
spacing,
nrows,
ncols,
exclude=[]):
"""Create a labeled mask for color card chips
Inputs:
rgb_img = Input RGB image data containing a color card.
radius = Radius of color masks.
start_coord = Two-element tuple of the first chip mask starting x and y coordinate.
spacing = Two-element tuple of the horizontal and vertical spacing between chip masks.
nrows = Number of chip rows.
ncols = Number of chip columns.
exclude = Optional list of chips to exclude.
Returns:
mask = Labeled mask of chips
:param rgb_img: numpy.ndarray
:param radius: int
:param start_coord: tuple
:param spacing: tuple
:param nrows: int
:param ncols: int
:param exclude: list
:return mask: numpy.ndarray
"""
# Autoincrement the device counter
params.device += 1
# Initialize chip list
chips = []
# Loop over each color card row
for i in range(0, nrows):
# The upper left corner is the y starting coordinate + the chip offset * the vertical spacing between chips
y = start_coord[1] + i * spacing[1]
# Loop over each column
for j in range(0, ncols):
# The upper left corner is the x starting coordinate + the chip offset * the
# horizontal spacing between chips
x = start_coord[0] + j * spacing[0]
# Create a chip ROI
chips.append(circle(img=rgb_img, x=x, y=y, r=radius))
# Sort excluded chips from largest to smallest
exclude.sort(reverse=True)
# Remove any excluded chips
for chip in exclude:
del chips[chip]
# Create mask
mask = np.zeros(shape=np.shape(rgb_img)[:2], dtype=np.uint8())
# Mask label index
i = 1
# Draw labeled chip boxes on the mask
for chip in chips:
mask = cv2.drawContours(mask, chip[0], -1, (i * 10), -1)
i += 1
if params.debug is not None:
# Create a copy of the input image for plotting
canvas = np.copy(rgb_img)
# Draw chip ROIs on the canvas image
for chip in chips:
cv2.drawContours(canvas, chip[0], -1, (255, 255, 0),
params.line_thickness)
if params.debug == "print":
print_image(img=canvas,
filename=os.path.join(
params.debug_outdir,
str(params.device) + "_color_card_mask_rois.png"))
print_image(img=mask,
filename=os.path.join(
params.debug_outdir,
str(params.device) + "_color_card_mask.png"))
elif params.debug == "plot":
plot_image(canvas)
return mask
def acute_vertex(obj, win, thresh, sep, img):
"""acute_vertex: identify corners/acute angles of an object
For each point in contour, get a point before (pre) and after (post) the point of interest,
calculate the angle between the pre and post point.
Inputs:
obj = a contour of the plant object (this should be output from the object_composition.py fxn)
win = win argument specifies the pre and post point distances (a value of 30 worked well for a sample image)
thresh = an threshold to set for acuteness; keep points with an angle more acute than the threshold (a value of 15
worked well for sample image)
sep = the number of contour points to search within for the most acute value
img = the original image
:param obj: ndarray
:param win: int
:param thresh: int
:param sep: int
:param img: ndarray
:return acute: ndarray
"""
params.device += 1
chain = []
if not np.any(obj):
acute = ('NA', 'NA')
return acute
for i in range(len(obj) - win):
x, y = obj[i].ravel()
pre_x, pre_y = obj[i - win].ravel()
post_x, post_y = obj[i + win].ravel()
# print "The iterator i is currently " + str(i)
# print "Here are the values: " + str(x) + " " + str(y)
# print "Here are the pre values: " + str(pre_x) + " " + str(pre_y)
# print "Here are the post values: " + str(post_x) + " " + str(post_y)
# Angle in radians derived from Law of Cosines, converted to degrees
P12 = np.sqrt((x - pre_x) * (x - pre_x) + (y - pre_y) * (y - pre_y))
P13 = np.sqrt((x - post_x) * (x - post_x) + (y - post_y) *
(y - post_y))
P23 = np.sqrt((pre_x - post_x) * (pre_x - post_x) + (pre_y - post_y) *
(pre_y - post_y))
if (2 * P12 * P13) > 0.001:
dot = (P12 * P12 + P13 * P13 - P23 * P23) / (2 * P12 * P13)
elif (2 * P12 * P13) < 0.001:
dot = (P12 * P12 + P13 * P13 - P23 * P23) / 0.001
if dot > 1: # If float excedes 1 prevent arcos error and force to equal 1
dot = 1
elif dot < -1: # If float excedes -1 prevent arcos error and force to equal -1
dot = -1
ang = math.degrees(math.acos(dot))
# print "Here is the angle: " + str(ang)
chain.append(ang)
# Select points in contour that have an angle more acute than thresh
index = []
for c in range(len(chain)):
if float(chain[c]) <= thresh:
index.append(c)
# There oftentimes several points around tips with acute angles
# Here we try to pick the most acute angle given a set of contiguous point
# Sep is the number of points to evaluate the number of verticies
out = []
tester = []
for i in range(len(index) - 1):
# print str(index[i])
if index[i + 1] - index[i] < sep:
tester.append(index[i])
if index[i + 1] - index[i] >= sep:
tester.append(index[i])
# print(tester)
angles = ([chain[d] for d in tester])
keeper = angles.index(min(angles))
t = tester[keeper]
# print str(t)
out.append(t)
tester = []
# Store the points in the variable acute
flag = 0
acute = obj[[out]]
# If no points found as acute get the largest point
# if len(acute) == 0:
# acute = max(obj, key=cv2.contourArea)
# flag = 1
# img2 = np.copy(img)
# cv2.circle(img2,(int(cmx),int(cmy)),30,(0,215,255),-1)
# cv2.circle(img2,(int(cmx),int(bly)),30,(255,0,0),-1)
# Plot each of these tip points on the image
# for i in acute:
# x,y = i.ravel()
# cv2.circle(img2,(x,y),15,(153,0,153),-1)
# cv2.imwrite('tip_points_centroid_and_base.png', img2)
if params.debug == 'print':
# Lets make a plot of these values on the
img2 = np.copy(img)
# Plot each of these tip points on the image
for i in acute:
x, y = i.ravel()
cv2.circle(img2, (x, y), 15, (255, 204, 255), -1)
print_image(
img2,
os.path.join(params.debug_outdir,
str(params.device) + '_acute_vertices.png'))
elif params.debug == 'plot':
# Lets make a plot of these values on the
img2 = np.copy(img)
# Plot each of these tip points on the image
for i in acute:
x, y = i.ravel()
# cv2.circle(img2,(x,y),15,(255,204,255),-1)
cv2.circle(img2, (x, y), 15, (0, 0, 255), -1)
plot_image(img2)
# If flag was true (no points found as acute) reformat output appropriate type
# if flag == 1:
# acute = np.asarray(acute)
# acute = acute.reshape(1, 1, 2)
# Store into global measurements
if not 'landmark_reference' in outputs.measurements:
outputs.measurements['landmark_reference'] = {}
outputs.measurements['landmark_reference']['tip_points'] = acute
return acute