def main(): # Get options args = options() # Read image img, path, filename = pcv.readimage(args.image) #roi = cv2.imread(args.roi) # Pipeline step device = 0 # Convert RGB to HSV and extract the Saturation channel device, s = pcv.rgb2gray_hsv(img, 's', device, args.debug) # Threshold the Saturation image device, s_thresh = pcv.binary_threshold(s, 36, 255, 'light', device, args.debug) # Median Filter device, s_mblur = pcv.median_blur(s_thresh, 5, device, args.debug) device, s_cnt = pcv.median_blur(s_thresh, 5, device, args.debug) # Fill small objects device, s_fill = pcv.fill(s_mblur, s_cnt, 0, device, args.debug) # Convert RGB to LAB and extract the Blue channel device, b = pcv.rgb2gray_lab(img, 'b', device, args.debug) # Threshold the blue image device, b_thresh = pcv.binary_threshold(b, 138, 255, 'light', device, args.debug) device, b_cnt = pcv.binary_threshold(b, 138, 255, 'light', device, args.debug) # Fill small objects device, b_fill = pcv.fill(b_thresh, b_cnt, 150, device, args.debug) # Join the thresholded saturation and blue-yellow images device, bs = pcv.logical_and(s_fill, b_fill, device, args.debug) # Apply Mask (for vis images, mask_color=white) device, masked = pcv.apply_mask(img, bs, 'white', device, args.debug) # Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels device, masked_a = pcv.rgb2gray_lab(masked, 'a', device, args.debug) device, masked_b = pcv.rgb2gray_lab(masked, 'b', device, args.debug) # Threshold the green-magenta and blue images device, maskeda_thresh = pcv.binary_threshold(masked_a, 122, 255, 'dark', device, args.debug) device, maskedb_thresh = pcv.binary_threshold(masked_b, 133, 255, 'light', device, args.debug) # Join the thresholded saturation and blue-yellow images (OR) device, ab = pcv.logical_or(maskeda_thresh, maskedb_thresh, device, args.debug) device, ab_cnt = pcv.logical_or(maskeda_thresh, maskedb_thresh, device, args.debug) # Fill small objects device, ab_fill = pcv.fill(ab, ab_cnt, 200, device, args.debug) # Apply mask (for vis images, mask_color=white) device, masked2 = pcv.apply_mask(masked, ab_fill, 'white', device, args.debug) # Select area with black bars and find overlapping plant material device, roi1, roi_hierarchy1= pcv.define_roi(masked2,'rectangle', device, None, 'default', args.debug,True, 0, 0,-1900,0) device, id_objects1,obj_hierarchy1 = pcv.find_objects(masked2, ab_fill, device, args.debug) device,roi_objects1, hierarchy1, kept_mask1, obj_area1 = pcv.roi_objects(masked2,'cutto',roi1,roi_hierarchy1,id_objects1,obj_hierarchy1,device, args.debug) device, masked3 = pcv.apply_mask(masked2, kept_mask1, 'white', device, args.debug) device, masked_a1 = pcv.rgb2gray_lab(masked3, 'a', device, args.debug) device, masked_b1 = pcv.rgb2gray_lab(masked3, 'b', device, args.debug) device, maskeda_thresh1 = pcv.binary_threshold(masked_a1, 122, 255, 'dark', device, args.debug) device, maskedb_thresh1 = pcv.binary_threshold(masked_b1, 170, 255, 'light', device, args.debug) device, ab1 = pcv.logical_or(maskeda_thresh1, maskedb_thresh1, device, args.debug) device, ab_cnt1 = pcv.logical_or(maskeda_thresh1, maskedb_thresh1, device, args.debug) device, ab_fill1 = pcv.fill(ab1, ab_cnt1, 300, device, args.debug) device, roi2, roi_hierarchy2= pcv.define_roi(masked2,'rectangle', device, None, 'default', args.debug,True, 1900, 0,0,0) device, id_objects2,obj_hierarchy2 = pcv.find_objects(masked2, ab_fill, device, args.debug) device,roi_objects2, hierarchy2, kept_mask2, obj_area2 = pcv.roi_objects(masked2,'cutto',roi2,roi_hierarchy2,id_objects2,obj_hierarchy2,device, args.debug) device, masked4 = pcv.apply_mask(masked2, kept_mask2, 'white', device, args.debug) device, masked_a2 = pcv.rgb2gray_lab(masked4, 'a', device, args.debug) device, masked_b2 = pcv.rgb2gray_lab(masked4, 'b', device, args.debug) device, maskeda_thresh2 = pcv.binary_threshold(masked_a2, 122, 255, 'dark', device, args.debug) device, maskedb_thresh2 = pcv.binary_threshold(masked_b2, 170, 255, 'light', device, args.debug) device, ab2 = pcv.logical_or(maskeda_thresh2, maskedb_thresh2, device, args.debug) device, ab_cnt2 = pcv.logical_or(maskeda_thresh2, maskedb_thresh2, device, args.debug) device, ab_fill2 = pcv.fill(ab2, ab_cnt2, 200, device, args.debug) device, ab_cnt3 = pcv.logical_or(ab_fill1, ab_fill2, device, args.debug) device, masked3 = pcv.apply_mask(masked2, ab_cnt3, 'white', device, args.debug) # Identify objects device, id_objects3,obj_hierarchy3 = pcv.find_objects(masked2, ab_fill, device, args.debug) # Define ROI device, roi3, roi_hierarchy3= pcv.define_roi(masked2,'rectangle', device, None, 'default', args.debug,True, 500, 0,-450,-530) # Decide which objects to keep and combine with objects overlapping with black bars device,roi_objects3, hierarchy3, kept_mask3, obj_area1 = pcv.roi_objects(img,'cutto',roi3,roi_hierarchy3,id_objects3,obj_hierarchy3,device, args.debug) device, kept_mask4_1 = pcv.logical_or(ab_cnt3, kept_mask3, device, args.debug) device, kept_cnt = pcv.logical_or(ab_cnt3, kept_mask3, device, args.debug) device, kept_mask4 = pcv.fill(kept_mask4_1, kept_cnt, 200, device, args.debug) device, masked5 = pcv.apply_mask(masked2, kept_mask4, 'white', device, args.debug) device, id_objects4,obj_hierarchy4 = pcv.find_objects(masked5, kept_mask4, device, args.debug) device, roi4, roi_hierarchy4= pcv.define_roi(masked2,'rectangle', device, None, 'default', args.debug,False, 0, 0,0,0) device,roi_objects4, hierarchy4, kept_mask4, obj_area = pcv.roi_objects(img,'partial',roi4,roi_hierarchy4,id_objects4,obj_hierarchy4,device, args.debug) # Object combine kept objects device, obj, mask = pcv.object_composition(img, roi_objects4, hierarchy4, device, args.debug) ############## Analysis ################ # Find shape properties, output shape image (optional) device, shape_header,shape_data,shape_img = pcv.analyze_object(img, args.image, obj, mask, device,args.debug,args.outdir+'/'+filename) # Shape properties relative to user boundary line (optional) device, boundary_header,boundary_data, boundary_img1= pcv.analyze_bound(img, args.image,obj, mask, 950, device,args.debug,args.outdir+'/'+filename) # Tiller Tool Test device, tillering_header, tillering_data, tillering_img= pcv.tiller_count(img, args.image,obj, mask, 965, device,args.debug,args.outdir+'/'+filename) # Determine color properties: Histograms, Color Slices and Pseudocolored Images, output color analyzed images (optional) device, color_header,color_data,norm_slice= pcv.analyze_color(img, args.image, kept_mask4, 256, device, args.debug,'all','rgb','v',args.outdir+'/'+filename) # Output shape and color data pcv.print_results(args.image, shape_header, shape_data) pcv.print_results(args.image, color_header, color_data) pcv.print_results(args.image, boundary_header, boundary_data) pcv.print_results(args.image, tillering_header,tillering_data)
def main(): # Get options args = options() # Read image img, path, filename = pcv.readimage(args.image) #roi = cv2.imread(args.roi) # Pipeline step device = 0 # Convert RGB to HSV and extract the Saturation channel device, s = pcv.rgb2gray_hsv(img, 's', device, args.debug) # Threshold the Saturation image device, s_thresh = pcv.binary_threshold(s, 36, 255, 'light', device, args.debug) # Median Filter device, s_mblur = pcv.median_blur(s_thresh, 5, device, args.debug) device, s_cnt = pcv.median_blur(s_thresh, 5, device, args.debug) # Fill small objects device, s_fill = pcv.fill(s_mblur, s_cnt, 0, device, args.debug) # Convert RGB to LAB and extract the Blue channel device, b = pcv.rgb2gray_lab(img, 'b', device, args.debug) # Threshold the blue image device, b_thresh = pcv.binary_threshold(b, 138, 255, 'light', device, args.debug) device, b_cnt = pcv.binary_threshold(b, 138, 255, 'light', device, args.debug) # Fill small objects device, b_fill = pcv.fill(b_thresh, b_cnt, 150, device, args.debug) # Join the thresholded saturation and blue-yellow images device, bs = pcv.logical_and(s_fill, b_fill, device, args.debug) # Apply Mask (for vis images, mask_color=white) device, masked = pcv.apply_mask(img, bs, 'white', device, args.debug) # Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels device, masked_a = pcv.rgb2gray_lab(masked, 'a', device, args.debug) device, masked_b = pcv.rgb2gray_lab(masked, 'b', device, args.debug) # Threshold the green-magenta and blue images device, maskeda_thresh = pcv.binary_threshold(masked_a, 122, 255, 'dark', device, args.debug) device, maskedb_thresh = pcv.binary_threshold(masked_b, 133, 255, 'light', device, args.debug) # Join the thresholded saturation and blue-yellow images (OR) device, ab = pcv.logical_or(maskeda_thresh, maskedb_thresh, device, args.debug) device, ab_cnt = pcv.logical_or(maskeda_thresh, maskedb_thresh, device, args.debug) # Fill small objects device, ab_fill = pcv.fill(ab, ab_cnt, 200, device, args.debug) # Apply mask (for vis images, mask_color=white) device, masked2 = pcv.apply_mask(masked, ab_fill, 'white', device, args.debug) # Identify objects device, id_objects,obj_hierarchy = pcv.find_objects(masked2, ab_fill, device, args.debug) # Define ROI device, roi1, roi_hierarchy= pcv.define_roi(img,'rectangle', device, None, 'default', args.debug,True, 0, 0,0,-900) # Decide which objects to keep device,roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(img,'partial',roi1,roi_hierarchy,id_objects,obj_hierarchy,device, args.debug) # Object combine kept objects device, obj, mask = pcv.object_composition(img, roi_objects, hierarchy3, device, args.debug) ############## Analysis ################ # Find shape properties, output shape image (optional) device, shape_header,shape_data,shape_img = pcv.analyze_object(img, args.image, obj, mask, device,args.debug,args.outdir+'/'+filename) # Shape properties relative to user boundary line (optional) device, boundary_header,boundary_data, boundary_img1= pcv.analyze_bound(img, args.image,obj, mask, 830, device,args.debug,args.outdir+'/'+filename) # Tiller Tool Test device, tillering_header, tillering_data, tillering_img= pcv.tiller_count(img, args.image,obj, mask, 895, device,args.debug,args.outdir+'/'+filename) # Determine color properties: Histograms, Color Slices and Pseudocolored Images, output color analyzed images (optional) device, color_header,color_data,norm_slice= pcv.analyze_color(img, args.image, kept_mask, 256, device, args.debug,'all','rgb','v',args.outdir+'/'+filename) # Output shape and color data pcv.print_results(args.image, shape_header, shape_data) pcv.print_results(args.image, color_header, color_data) pcv.print_results(args.image, boundary_header, boundary_data) pcv.print_results(args.image, tillering_header,tillering_data)
def main():
# Get options
args = options()
# Read image
img, path, filename = pcv.readimage(args.image)
#roi = cv2.imread(args.roi)
# Pipeline step
device = 0
# Convert RGB to HSV and extract the Saturation channel
device, s = pcv.rgb2gray_hsv(img, 's', device, args.debug)
# Threshold the Saturation image
device, s_thresh = pcv.binary_threshold(s, 36, 255, 'light', device,
args.debug)
# Median Filter
device, s_mblur = pcv.median_blur(s_thresh, 5, device, args.debug)
device, s_cnt = pcv.median_blur(s_thresh, 5, device, args.debug)
# Fill small objects
device, s_fill = pcv.fill(s_mblur, s_cnt, 0, device, args.debug)
# Convert RGB to LAB and extract the Blue channel
device, b = pcv.rgb2gray_lab(img, 'b', device, args.debug)
# Threshold the blue image
device, b_thresh = pcv.binary_threshold(b, 138, 255, 'light', device,
args.debug)
device, b_cnt = pcv.binary_threshold(b, 138, 255, 'light', device,
args.debug)
# Fill small objects
device, b_fill = pcv.fill(b_thresh, b_cnt, 0, device, args.debug)
# Join the thresholded saturation and blue-yellow images
device, bs = pcv.logical_and(s_fill, b_fill, device, args.debug)
# Apply Mask (for vis images, mask_color=white)
device, masked = pcv.apply_mask(img, bs, 'white', device, args.debug)
# Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
device, masked_a = pcv.rgb2gray_lab(masked, 'a', device, args.debug)
device, masked_b = pcv.rgb2gray_lab(masked, 'b', device, args.debug)
# Threshold the green-magenta and blue images
device, maskeda_thresh = pcv.binary_threshold(masked_a, 122, 255, 'dark',
device, args.debug)
device, maskedb_thresh = pcv.binary_threshold(masked_b, 133, 255, 'light',
device, args.debug)
# Join the thresholded saturation and blue-yellow images (OR)
device, ab = pcv.logical_or(maskeda_thresh, maskedb_thresh, device,
args.debug)
device, ab_cnt = pcv.logical_or(maskeda_thresh, maskedb_thresh, device,
args.debug)
# Fill small objects
device, ab_fill = pcv.fill(ab, ab_cnt, 200, device, args.debug)
# Apply mask (for vis images, mask_color=white)
device, masked2 = pcv.apply_mask(masked, ab_fill, 'white', device,
args.debug)
# Select area with black bars and find overlapping plant material
device, roi1, roi_hierarchy1 = pcv.define_roi(masked2, 'rectangle', device,
None, 'default', args.debug,
True, 0, 0, -1900, 0)
device, id_objects1, obj_hierarchy1 = pcv.find_objects(
masked2, ab_fill, device, args.debug)
device, roi_objects1, hierarchy1, kept_mask1, obj_area1 = pcv.roi_objects(
masked2, 'cutto', roi1, roi_hierarchy1, id_objects1, obj_hierarchy1,
device, args.debug)
device, masked3 = pcv.apply_mask(masked2, kept_mask1, 'white', device,
args.debug)
device, masked_a1 = pcv.rgb2gray_lab(masked3, 'a', device, args.debug)
device, masked_b1 = pcv.rgb2gray_lab(masked3, 'b', device, args.debug)
device, maskeda_thresh1 = pcv.binary_threshold(masked_a1, 122, 255, 'dark',
device, args.debug)
device, maskedb_thresh1 = pcv.binary_threshold(masked_b1, 170, 255,
'light', device, args.debug)
device, ab1 = pcv.logical_or(maskeda_thresh1, maskedb_thresh1, device,
args.debug)
device, ab_cnt1 = pcv.logical_or(maskeda_thresh1, maskedb_thresh1, device,
args.debug)
device, ab_fill1 = pcv.fill(ab1, ab_cnt1, 200, device, args.debug)
device, roi2, roi_hierarchy2 = pcv.define_roi(masked2, 'rectangle', device,
None, 'default', args.debug,
True, 1900, 0, 0, 0)
device, id_objects2, obj_hierarchy2 = pcv.find_objects(
masked2, ab_fill, device, args.debug)
device, roi_objects2, hierarchy2, kept_mask2, obj_area2 = pcv.roi_objects(
masked2, 'cutto', roi2, roi_hierarchy2, id_objects2, obj_hierarchy2,
device, args.debug)
device, masked4 = pcv.apply_mask(masked2, kept_mask2, 'white', device,
args.debug)
device, masked_a2 = pcv.rgb2gray_lab(masked4, 'a', device, args.debug)
device, masked_b2 = pcv.rgb2gray_lab(masked4, 'b', device, args.debug)
device, maskeda_thresh2 = pcv.binary_threshold(masked_a2, 122, 255, 'dark',
device, args.debug)
device, maskedb_thresh2 = pcv.binary_threshold(masked_b2, 170, 255,
'light', device, args.debug)
device, ab2 = pcv.logical_or(maskeda_thresh2, maskedb_thresh2, device,
args.debug)
device, ab_cnt2 = pcv.logical_or(maskeda_thresh2, maskedb_thresh2, device,
args.debug)
device, ab_fill2 = pcv.fill(ab2, ab_cnt2, 200, device, args.debug)
device, ab_cnt3 = pcv.logical_or(ab_fill1, ab_fill2, device, args.debug)
device, masked3 = pcv.apply_mask(masked2, ab_cnt3, 'white', device,
args.debug)
# Identify objects
device, id_objects3, obj_hierarchy3 = pcv.find_objects(
masked2, ab_fill, device, args.debug)
# Define ROI
device, roi3, roi_hierarchy3 = pcv.define_roi(masked2, 'rectangle', device,
None, 'default', args.debug,
True, 525, 0, -500, -110)
# Decide which objects to keep and combine with objects overlapping with black bars
device, roi_objects3, hierarchy3, kept_mask3, obj_area1 = pcv.roi_objects(
img, 'cutto', roi3, roi_hierarchy3, id_objects3, obj_hierarchy3,
device, args.debug)
device, kept_mask4_1 = pcv.logical_or(ab_cnt3, kept_mask3, device,
args.debug)
device, kept_cnt = pcv.logical_or(ab_cnt3, kept_mask3, device, args.debug)
device, kept_mask4 = pcv.fill(kept_mask4_1, kept_cnt, 200, device,
args.debug)
device, masked5 = pcv.apply_mask(masked2, kept_mask4, 'white', device,
args.debug)
device, id_objects4, obj_hierarchy4 = pcv.find_objects(
masked5, kept_mask4, device, args.debug)
device, roi4, roi_hierarchy4 = pcv.define_roi(masked2, 'rectangle', device,
None, 'default', args.debug,
False, 0, 0, 0, 0)
device, roi_objects4, hierarchy4, kept_mask4, obj_area = pcv.roi_objects(
img, 'partial', roi4, roi_hierarchy4, id_objects4, obj_hierarchy4,
device, args.debug)
# Object combine kept objects
device, obj, mask = pcv.object_composition(img, roi_objects4, hierarchy4,
device, args.debug)
############## Analysis ################
# Find shape properties, output shape image (optional)
device, shape_header, shape_data, shape_img = pcv.analyze_object(
img, args.image, obj, mask, device, args.debug,
args.outdir + '/' + filename)
# Shape properties relative to user boundary line (optional)
device, boundary_header, boundary_data, boundary_img1 = pcv.analyze_bound(
img, args.image, obj, mask, 330, device, args.debug,
args.outdir + '/' + filename)
# Tiller Tool Test
device, tillering_header, tillering_data, tillering_img = pcv.tiller_count(
img, args.image, obj, mask, 354, device, args.debug,
args.outdir + '/' + filename)
# Determine color properties: Histograms, Color Slices and Pseudocolored Images, output color analyzed images (optional)
device, color_header, color_data, norm_slice = pcv.analyze_color(
img, args.image, kept_mask4, 256, device, args.debug, 'all', 'rgb',
'v', args.outdir + '/' + filename)
# Output shape and color data
pcv.print_results(args.image, shape_header, shape_data)
pcv.print_results(args.image, color_header, color_data)
pcv.print_results(args.image, boundary_header, boundary_data)
pcv.print_results(args.image, tillering_header, tillering_data)
def main():
# Get options
args = options()
# Read image
img, path, filename = pcv.readimage(args.image)
#roi = cv2.imread(args.roi)
# Pipeline step
device = 0
# Convert RGB to HSV and extract the Saturation channel
device, s = pcv.rgb2gray_hsv(img, 's', device, args.debug)
# Threshold the Saturation image
device, s_thresh = pcv.binary_threshold(s, 36, 255, 'light', device, args.debug)
# Median Filter
device, s_mblur = pcv.median_blur(s_thresh, 5, device, args.debug)
device, s_cnt = pcv.median_blur(s_thresh, 5, device, args.debug)
# Fill small objects
device, s_fill = pcv.fill(s_mblur, s_cnt, 0, device, args.debug)
# Convert RGB to LAB and extract the Blue channel
device, b = pcv.rgb2gray_lab(img, 'b', device, args.debug)
# Threshold the blue image
device, b_thresh = pcv.binary_threshold(b, 138, 255, 'light', device, args.debug)
device, b_cnt = pcv.binary_threshold(b, 138, 255, 'light', device, args.debug)
# Fill small objects
device, b_fill = pcv.fill(b_thresh, b_cnt, 10, device, args.debug)
# Join the thresholded saturation and blue-yellow images
device, bs = pcv.logical_or(s_fill, b_fill, device, args.debug)
# Apply Mask (for vis images, mask_color=white)
device, masked = pcv.apply_mask(img, bs, 'white', device, args.debug)
# Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
device, masked_a = pcv.rgb2gray_lab(masked, 'a', device, args.debug)
device, masked_b = pcv.rgb2gray_lab(masked, 'b', device, args.debug)
# Threshold the green-magenta and blue images
device, maskeda_thresh = pcv.binary_threshold(masked_a, 125, 255, 'dark', device, args.debug)
device, maskedb_thresh = pcv.binary_threshold(masked_b, 133, 255, 'light', device, args.debug)
# Join the thresholded saturation and blue-yellow images (OR)
device, ab = pcv.logical_or(maskeda_thresh, maskedb_thresh, device, args.debug)
device, ab_cnt = pcv.logical_or(maskeda_thresh, maskedb_thresh, device, args.debug)
# Fill small objects
device, ab_fill = pcv.fill(ab, ab_cnt, 10, device, args.debug)
# Apply mask (for vis images, mask_color=white)
device, masked2 = pcv.apply_mask(masked, ab_fill, 'white', device, args.debug)
# Identify objects
device, id_objects,obj_hierarchy = pcv.find_objects(masked2, ab_fill, device, args.debug)
# Define ROI
device, roi1, roi_hierarchy= pcv.define_roi(masked2,'rectangle', device, None, 'default', args.debug,True, 0, 0,0,-925)
# Decide which objects to keep
device,roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(img,'partial',roi1,roi_hierarchy,id_objects,obj_hierarchy,device, args.debug)
# Object combine kept objects
device, obj, mask = pcv.object_composition(img, roi_objects, hierarchy3, device, args.debug)
############### Analysis ################
# Find shape properties, output shape image (optional)
device, shape_header,shape_data,shape_img = pcv.analyze_object(img, args.image, obj, mask, device,args.debug,args.outdir+'/'+filename)
# Shape properties relative to user boundary line (optional)
device, boundary_header,boundary_data, boundary_img1= pcv.analyze_bound(img, args.image,obj, mask, 900, device,args.debug,args.outdir+'/'+filename)
# Tiller Tool Test
device, tillering_header, tillering_data, tillering_img= pcv.tiller_count(img, args.image,obj, mask, 926, device,args.debug,args.outdir+'/'+filename)
# Determine color properties: Histograms, Color Slices and Pseudocolored Images, output color analyzed images (optional)
device, color_header,color_data,norm_slice= pcv.analyze_color(img, args.image, kept_mask, 256, device, args.debug,'all','rgb','v',args.outdir+'/'+filename)
# Output shape and color data
pcv.print_results(args.image, shape_header, shape_data)
pcv.print_results(args.image, color_header, color_data)
pcv.print_results(args.image, boundary_header, boundary_data)
pcv.print_results(args.image, tillering_header,tillering_data)