def main():
# Get options
args = options()
if args.debug:
print("Analyzing your image dude...")
# Read image
device = 0
img = cv2.imread(args.image, flags=0)
path, img_name = os.path.split(args.image)
# Read in image which is average of average of backgrounds
img_bkgrd = cv2.imread("bkgrd_ave_z3500.png", flags=0)
# NIR images for burnin2 are up-side down. This may be fixed in later experiments
img = ndimage.rotate(img, 180)
img_bkgrd = ndimage.rotate(img_bkgrd, 180)
# Subtract the image from the image background to make the plant more prominent
device, bkg_sub_img = pcv.image_subtract(img, img_bkgrd, device, args.debug)
if args.debug:
pcv.plot_hist(bkg_sub_img, 'bkg_sub_img')
device, bkg_sub_thres_img = pcv.binary_threshold(bkg_sub_img, 145, 255, 'dark', device, args.debug)
bkg_sub_thres_img = cv2.inRange(bkg_sub_img, 30, 220)
if args.debug:
cv2.imwrite('bkgrd_sub_thres.png', bkg_sub_thres_img)
#device, bkg_sub_thres_img = pcv.binary_threshold_2_sided(img_bkgrd, 50, 190, device, args.debug)
# if a region of interest is specified read it in
roi = cv2.imread(args.roi)
# Start by examining the distribution of pixel intensity values
if args.debug:
pcv.plot_hist(img, 'hist_img')
# Will intensity transformation enhance your ability to isolate object of interest by thesholding?
device, he_img = pcv.HistEqualization(img, device, args.debug)
if args.debug:
pcv.plot_hist(he_img, 'hist_img_he')
# Laplace filtering (identify edges based on 2nd derivative)
device, lp_img = pcv.laplace_filter(img, 1, 1, device, args.debug)
if args.debug:
pcv.plot_hist(lp_img, 'hist_lp')
# Lapacian image sharpening, this step will enhance the darkness of the edges detected
device, lp_shrp_img = pcv.image_subtract(img, lp_img, device, args.debug)
if args.debug:
pcv.plot_hist(lp_shrp_img, 'hist_lp_shrp')
# Sobel filtering
# 1st derivative sobel filtering along horizontal axis, kernel = 1, unscaled)
device, sbx_img = pcv.sobel_filter(img, 1, 0, 1, 1, device, args.debug)
if args.debug:
pcv.plot_hist(sbx_img, 'hist_sbx')
# 1st derivative sobel filtering along vertical axis, kernel = 1, unscaled)
device, sby_img = pcv.sobel_filter(img, 0, 1, 1, 1, device, args.debug)
if args.debug:
pcv.plot_hist(sby_img, 'hist_sby')
# Combine the effects of both x and y filters through matrix addition
# This will capture edges identified within each plane and emphesize edges found in both images
device, sb_img = pcv.image_add(sbx_img, sby_img, device, args.debug)
if args.debug:
pcv.plot_hist(sb_img, 'hist_sb_comb_img')
# Use a lowpass (blurring) filter to smooth sobel image
device, mblur_img = pcv.median_blur(sb_img, 1, device, args.debug)
device, mblur_invert_img = pcv.invert(mblur_img, device, args.debug)
# combine the smoothed sobel image with the laplacian sharpened image
# combines the best features of both methods as described in "Digital Image Processing" by Gonzalez and Woods pg. 169
device, edge_shrp_img = pcv.image_add(mblur_invert_img, lp_shrp_img, device, args.debug)
if args.debug:
pcv.plot_hist(edge_shrp_img, 'hist_edge_shrp_img')
# Perform thresholding to generate a binary image
device, tr_es_img = pcv.binary_threshold(edge_shrp_img, 145, 255, 'dark', device, args.debug)
# Prepare a few small kernels for morphological filtering
kern = np.zeros((3,3), dtype=np.uint8)
kern1 = np.copy(kern)
kern1[1,1:3]=1
kern2 = np.copy(kern)
kern2[1,0:2]=1
kern3 = np.copy(kern)
kern3[0:2,1]=1
kern4 = np.copy(kern)
kern4[1:3,1]=1
# Prepare a larger kernel for dilation
kern[1,0:3]=1
kern[0:3,1]=1
# Perform erosion with 4 small kernels
device, e1_img = pcv.erode(tr_es_img, kern1, 1, device, args.debug)
device, e2_img = pcv.erode(tr_es_img, kern2, 1, device, args.debug)
device, e3_img = pcv.erode(tr_es_img, kern3, 1, device, args.debug)
device, e4_img = pcv.erode(tr_es_img, kern4, 1, device, args.debug)
# Combine eroded images
device, c12_img = pcv.logical_or(e1_img, e2_img, device, args.debug)
device, c123_img = pcv.logical_or(c12_img, e3_img, device, args.debug)
device, c1234_img = pcv.logical_or(c123_img, e4_img, device, args.debug)
# Perform dilation
# device, dil_img = pcv.dilate(c1234_img, kern, 1, device, args.debug)
device, comb_img = pcv.logical_or(c1234_img, bkg_sub_thres_img, device, args.debug)
# Get masked image
# The dilated image may contain some pixels which are not plant
device, masked_erd = pcv.apply_mask(img, comb_img, 'black', device, args.debug)
# device, masked_erd_dil = pcv.apply_mask(img, dil_img, 'black', device, args.debug)
# Need to remove the edges of the image, we did that by generating a set of rectangles to mask the edges
# img is (254 X 320)
# mask for the bottom of the image
device, box1_img, rect_contour1, hierarchy1 = pcv.rectangle_mask(img, (100,210), (230,252), device, args.debug)
# mask for the left side of the image
device, box2_img, rect_contour2, hierarchy2 = pcv.rectangle_mask(img, (1,1), (85,252), device, args.debug)
# mask for the right side of the image
device, box3_img, rect_contour3, hierarchy3 = pcv.rectangle_mask(img, (240,1), (318,252), device, args.debug)
# mask the edges
device, box4_img, rect_contour4, hierarchy4 = pcv.border_mask(img, (1,1), (318,252), device, args.debug)
# combine boxes to filter the edges and car out of the photo
device, bx12_img = pcv.logical_or(box1_img, box2_img, device, args.debug)
device, bx123_img = pcv.logical_or(bx12_img, box3_img, device, args.debug)
device, bx1234_img = pcv.logical_or(bx123_img, box4_img, device, args.debug)
device, inv_bx1234_img = pcv.invert(bx1234_img, device, args.debug)
# Make a ROI around the plant, include connected objects
# Apply the box mask to the image
# device, masked_img = pcv.apply_mask(masked_erd_dil, inv_bx1234_img, 'black', device, args.debug)
device, edge_masked_img = pcv.apply_mask(masked_erd, inv_bx1234_img, 'black', device, args.debug)
device, roi_img, roi_contour, roi_hierarchy = pcv.rectangle_mask(img, (100,75), (220,208), device, args.debug)
plant_objects, plant_hierarchy = cv2.findContours(edge_masked_img,cv2.RETR_TREE,cv2.CHAIN_APPROX_NONE)
device, roi_objects, hierarchy5, kept_mask, obj_area = pcv.roi_objects(img, 'partial', roi_contour, roi_hierarchy, plant_objects, plant_hierarchy, device, args.debug)
# Apply the box mask to the image
# device, masked_img = pcv.apply_mask(masked_erd_dil, inv_bx1234_img, 'black', device, args.debug)
device, masked_img = pcv.apply_mask(kept_mask, inv_bx1234_img, 'black', device, args.debug)
rgb = cv2.cvtColor(img,cv2.COLOR_GRAY2RGB)
# Generate a binary to send to the analysis function
device, mask = pcv.binary_threshold(masked_img, 1, 255, 'light', device, args.debug)
mask3d = np.copy(mask)
plant_objects_2, plant_hierarchy_2 = cv2.findContours(mask3d,cv2.RETR_TREE,cv2.CHAIN_APPROX_NONE)
device, o, m = pcv.object_composition(rgb, roi_objects, hierarchy5, device, args.debug)
### Analysis ###
device, hist_header, hist_data, h_norm = pcv.analyze_NIR_intensity(img, args.image, mask, 256, device, args.debug, args.outdir + '/' + img_name)
device, shape_header, shape_data, ori_img = pcv.analyze_object(rgb, args.image, o, m, device, args.debug, args.outdir + '/' + img_name)
pcv.print_results(args.image, hist_header, hist_data)
pcv.print_results(args.image, shape_header, shape_data)
def main():
# Get options
args = options()
if args.debug:
print("Analyzing your image dude...")
# Read image
device = 0
img = cv2.imread(args.image, flags=0)
path, img_name = os.path.split(args.image)
# Read in image which is average of average of backgrounds
img_bkgrd = cv2.imread("bkgrd_ave_z2500.png", flags=0)
# NIR images for burnin2 are up-side down. This may be fixed in later experiments
img = ndimage.rotate(img, 180)
img_bkgrd = ndimage.rotate(img_bkgrd, 180)
# Subtract the image from the image background to make the plant more prominent
device, bkg_sub_img = pcv.image_subtract(img, img_bkgrd, device, args.debug)
if args.debug:
pcv.plot_hist(bkg_sub_img, "bkg_sub_img")
device, bkg_sub_thres_img = pcv.binary_threshold(bkg_sub_img, 145, 255, "dark", device, args.debug)
bkg_sub_thres_img = cv2.inRange(bkg_sub_img, 30, 220)
if args.debug:
cv2.imwrite("bkgrd_sub_thres.png", bkg_sub_thres_img)
# device, bkg_sub_thres_img = pcv.binary_threshold_2_sided(img_bkgrd, 50, 190, device, args.debug)
# if a region of interest is specified read it in
roi = cv2.imread(args.roi)
# Start by examining the distribution of pixel intensity values
if args.debug:
pcv.plot_hist(img, "hist_img")
# Will intensity transformation enhance your ability to isolate object of interest by thesholding?
device, he_img = pcv.HistEqualization(img, device, args.debug)
if args.debug:
pcv.plot_hist(he_img, "hist_img_he")
# Laplace filtering (identify edges based on 2nd derivative)
device, lp_img = pcv.laplace_filter(img, 1, 1, device, args.debug)
if args.debug:
pcv.plot_hist(lp_img, "hist_lp")
# Lapacian image sharpening, this step will enhance the darkness of the edges detected
device, lp_shrp_img = pcv.image_subtract(img, lp_img, device, args.debug)
if args.debug:
pcv.plot_hist(lp_shrp_img, "hist_lp_shrp")
# Sobel filtering
# 1st derivative sobel filtering along horizontal axis, kernel = 1, unscaled)
device, sbx_img = pcv.sobel_filter(img, 1, 0, 1, 1, device, args.debug)
if args.debug:
pcv.plot_hist(sbx_img, "hist_sbx")
# 1st derivative sobel filtering along vertical axis, kernel = 1, unscaled)
device, sby_img = pcv.sobel_filter(img, 0, 1, 1, 1, device, args.debug)
if args.debug:
pcv.plot_hist(sby_img, "hist_sby")
# Combine the effects of both x and y filters through matrix addition
# This will capture edges identified within each plane and emphesize edges found in both images
device, sb_img = pcv.image_add(sbx_img, sby_img, device, args.debug)
if args.debug:
pcv.plot_hist(sb_img, "hist_sb_comb_img")
# Use a lowpass (blurring) filter to smooth sobel image
device, mblur_img = pcv.median_blur(sb_img, 1, device, args.debug)
device, mblur_invert_img = pcv.invert(mblur_img, device, args.debug)
# combine the smoothed sobel image with the laplacian sharpened image
# combines the best features of both methods as described in "Digital Image Processing" by Gonzalez and Woods pg. 169
device, edge_shrp_img = pcv.image_add(mblur_invert_img, lp_shrp_img, device, args.debug)
if args.debug:
pcv.plot_hist(edge_shrp_img, "hist_edge_shrp_img")
# Perform thresholding to generate a binary image
device, tr_es_img = pcv.binary_threshold(edge_shrp_img, 145, 255, "dark", device, args.debug)
# Prepare a few small kernels for morphological filtering
kern = np.zeros((3, 3), dtype=np.uint8)
kern1 = np.copy(kern)
kern1[1, 1:3] = 1
kern2 = np.copy(kern)
kern2[1, 0:2] = 1
kern3 = np.copy(kern)
kern3[0:2, 1] = 1
kern4 = np.copy(kern)
kern4[1:3, 1] = 1
# Prepare a larger kernel for dilation
kern[1, 0:3] = 1
kern[0:3, 1] = 1
# Perform erosion with 4 small kernels
device, e1_img = pcv.erode(tr_es_img, kern1, 1, device, args.debug)
device, e2_img = pcv.erode(tr_es_img, kern2, 1, device, args.debug)
device, e3_img = pcv.erode(tr_es_img, kern3, 1, device, args.debug)
device, e4_img = pcv.erode(tr_es_img, kern4, 1, device, args.debug)
# Combine eroded images
device, c12_img = pcv.logical_or(e1_img, e2_img, device, args.debug)
device, c123_img = pcv.logical_or(c12_img, e3_img, device, args.debug)
device, c1234_img = pcv.logical_or(c123_img, e4_img, device, args.debug)
# Perform dilation
# device, dil_img = pcv.dilate(c1234_img, kern, 1, device, args.debug)
device, comb_img = pcv.logical_or(c1234_img, bkg_sub_thres_img, device, args.debug)
# Get masked image
# The dilated image may contain some pixels which are not plant
device, masked_erd = pcv.apply_mask(img, comb_img, "black", device, args.debug)
# device, masked_erd_dil = pcv.apply_mask(img, dil_img, 'black', device, args.debug)
# Need to remove the edges of the image, we did that by generating a set of rectangles to mask the edges
# img is (254 X 320)
# mask for the bottom of the image
device, box1_img, rect_contour1, hierarchy1 = pcv.rectangle_mask(img, (120, 184), (215, 252), device, args.debug)
# mask for the left side of the image
device, box2_img, rect_contour2, hierarchy2 = pcv.rectangle_mask(img, (1, 1), (85, 252), device, args.debug)
# mask for the right side of the image
device, box3_img, rect_contour3, hierarchy3 = pcv.rectangle_mask(img, (240, 1), (318, 252), device, args.debug)
# mask the edges
device, box4_img, rect_contour4, hierarchy4 = pcv.border_mask(img, (1, 1), (318, 252), device, args.debug)
# combine boxes to filter the edges and car out of the photo
device, bx12_img = pcv.logical_or(box1_img, box2_img, device, args.debug)
device, bx123_img = pcv.logical_or(bx12_img, box3_img, device, args.debug)
device, bx1234_img = pcv.logical_or(bx123_img, box4_img, device, args.debug)
device, inv_bx1234_img = pcv.invert(bx1234_img, device, args.debug)
# Make a ROI around the plant, include connected objects
# Apply the box mask to the image
# device, masked_img = pcv.apply_mask(masked_erd_dil, inv_bx1234_img, 'black', device, args.debug)
device, edge_masked_img = pcv.apply_mask(masked_erd, inv_bx1234_img, "black", device, args.debug)
device, roi_img, roi_contour, roi_hierarchy = pcv.rectangle_mask(img, (120, 75), (200, 184), device, args.debug)
plant_objects, plant_hierarchy = cv2.findContours(edge_masked_img, cv2.RETR_TREE, cv2.CHAIN_APPROX_NONE)
device, roi_objects, hierarchy5, kept_mask, obj_area = pcv.roi_objects(
img, "partial", roi_contour, roi_hierarchy, plant_objects, plant_hierarchy, device, args.debug
)
# Apply the box mask to the image
# device, masked_img = pcv.apply_mask(masked_erd_dil, inv_bx1234_img, 'black', device, args.debug)
device, masked_img = pcv.apply_mask(kept_mask, inv_bx1234_img, "black", device, args.debug)
rgb = cv2.cvtColor(img, cv2.COLOR_GRAY2RGB)
# Generate a binary to send to the analysis function
device, mask = pcv.binary_threshold(masked_img, 1, 255, "light", device, args.debug)
mask3d = np.copy(mask)
plant_objects_2, plant_hierarchy_2 = cv2.findContours(mask3d, cv2.RETR_TREE, cv2.CHAIN_APPROX_NONE)
device, o, m = pcv.object_composition(rgb, roi_objects, hierarchy5, device, args.debug)
### Analysis ###
device, hist_header, hist_data, h_norm = pcv.analyze_NIR_intensity(
img, args.image, mask, 256, device, args.debug, args.outdir + "/" + img_name
)
device, shape_header, shape_data, ori_img = pcv.analyze_object(
rgb, args.image, o, m, device, args.debug, args.outdir + "/" + img_name
)
pcv.print_results(args.image, hist_header, hist_data)
pcv.print_results(args.image, shape_header, shape_data)
def main():
# Get options
args = options()
if args.debug:
print("Analyzing your image dude...")
# Read image
img = cv2.imread(args.image, flags=0)
# if a region of interest is specified read it in
roi = cv2.imread(args.roi)
# Pipeline step
device = 0
# Start by examining the distribution of pixel intensity values
if args.debug:
pcv.plot_hist(img, 'hist_img')
# Will intensity transformation enhance your ability to isolate object of interest by thesholding?
device, he_img = pcv.HistEqualization(img, device, args.debug)
if args.debug:
pcv.plot_hist(he_img, 'hist_img_he')
# Laplace filtering (identify edges based on 2nd derivative)
device, lp_img = pcv.laplace_filter(img, 1, 1, device, args.debug)
if args.debug:
pcv.plot_hist(lp_img, 'hist_lp')
# Lapacian image sharpening, this step will enhance the darkness of the edges detected
device, lp_shrp_img = pcv.image_subtract(img, lp_img, device, args.debug)
if args.debug:
pcv.plot_hist(lp_shrp_img, 'hist_lp_shrp')
# Sobel filtering
# 1st derivative sobel filtering along horizontal axis, kernel = 1, unscaled)
device, sbx_img = pcv.sobel_filter(img, 1, 0, 1, 1, device, args.debug)
if args.debug:
pcv.plot_hist(sbx_img, 'hist_sbx')
# 1st derivative sobel filtering along vertical axis, kernel = 1, unscaled)
device, sby_img = pcv.sobel_filter(img, 0, 1, 1, 1, device, args.debug)
if args.debug:
pcv.plot_hist(sby_img, 'hist_sby')
# Combine the effects of both x and y filters through matrix addition
# This will capture edges identified within each plane and emphesize edges found in both images
device, sb_img = pcv.image_add(sbx_img, sby_img, device, args.debug)
if args.debug:
pcv.plot_hist(sb_img, 'hist_sb_comb_img')
# Use a lowpass (blurring) filter to smooth sobel image
device, mblur_img = pcv.median_blur(sb_img, 1, device, args.debug)
device, mblur_invert_img = pcv.invert(mblur_img, device, args.debug)
# combine the smoothed sobel image with the laplacian sharpened image
# combines the best features of both methods as described in "Digital Image Processing" by Gonzalez and Woods pg. 169
device, edge_shrp_img = pcv.image_add(mblur_invert_img, lp_shrp_img, device, args.debug)
if args.debug:
pcv.plot_hist(edge_shrp_img, 'hist_edge_shrp_img')
# Perform thresholding to generate a binary image
device, tr_es_img = pcv.binary_threshold(edge_shrp_img, 145, 255, 'dark', device, args.debug)
# Prepare a few small kernels for morphological filtering
kern = np.zeros((3,3), dtype=np.uint8)
kern1 = np.copy(kern)
kern1[1,1:3]=1
kern2 = np.copy(kern)
kern2[1,0:2]=1
kern3 = np.copy(kern)
kern3[0:2,1]=1
kern4 = np.copy(kern)
kern4[1:3,1]=1
# Prepare a larger kernel for dilation
kern[1,0:3]=1
kern[0:3,1]=1
# Perform erosion with 4 small kernels
device, e1_img = pcv.erode(tr_es_img, kern1, 1, device, args.debug)
device, e2_img = pcv.erode(tr_es_img, kern2, 1, device, args.debug)
device, e3_img = pcv.erode(tr_es_img, kern3, 1, device, args.debug)
device, e4_img = pcv.erode(tr_es_img, kern4, 1, device, args.debug)
# Combine eroded images
device, c12_img = pcv.logical_or(e1_img, e2_img, device, args.debug)
device, c123_img = pcv.logical_or(c12_img, e3_img, device, args.debug)
device, c1234_img = pcv.logical_or(c123_img, e4_img, device, args.debug)
# Perform dilation
device, dil_img = pcv.dilate(c1234_img, kern, 1, device, args.debug)
# Get masked image
# The dilated image may contain some pixels which are not plant
device, masked_erd = pcv.apply_mask(img, c1234_img, 'black', device, args.debug)
device, masked_erd_dil = pcv.apply_mask(img, dil_img, 'black', device, args.debug)
# Need to remove the edges of the image, we did that by generating a set of rectangles to mask the edges
# img is (254 X 320)
device, box1_img, rect_contour1, hierarchy1 = pcv.rectangle_mask(img, (1,1), (64,252), device, args.debug)
device, box2_img, rect_contour2, hierarchy2 = pcv.rectangle_mask(img, (256,1), (318,252), device, args.debug)
device, box3_img, rect_contour3, hierarchy3 = pcv.rectangle_mask(img, (1,184), (318,252), device, args.debug)
device, box4_img, rect_contour4, hierarchy4 = pcv.border_mask(img, (1,1), (318,252), device, args.debug)
# combine boxes to filter the edges and car out of the photo
device, bx12_img = pcv.logical_or(box1_img, box2_img, device, args.debug)
device, bx123_img = pcv.logical_or(bx12_img, box3_img, device, args.debug)
device, bx1234_img = pcv.logical_or(bx123_img, box4_img, device, args.debug)
device, inv_bx1234_img = pcv.invert(bx1234_img, device, args.debug)
# Apply the box mask to the image
device, masked_img = pcv.apply_mask(masked_erd_dil, inv_bx1234_img, 'black', device, args.debug)
# Generate a binary to send to the analysis function
device, mask = pcv.binary_threshold(masked_img, 1, 255, 'light', device, args.debug)
pcv.analyze_NIR_intensity(img, args.image, mask, 256, device, args.debug, 'example')