def main(): # Get options args = options() # Read image (converting fmax and track to 8 bit just to create a mask, use 16-bit for all the math) mask, path, filename = pcv.readimage(args.fmax) #mask = cv2.imread(args.fmax) track = cv2.imread(args.track) mask1, mask2, mask3= cv2.split(mask) # Pipeline step device = 0 # Mask pesky track autofluor device, track1= pcv.rgb2gray_hsv(track, 'v', device, args.debug) device, track_thresh = pcv.binary_threshold(track1, 0, 255, 'light', device, args.debug) device, track_inv=pcv.invert(track_thresh, device, args.debug) device, track_masked = pcv.apply_mask(mask1, track_inv, 'black', device, args.debug) # Threshold the Saturation image device, fmax_thresh = pcv.binary_threshold(track_masked, 20, 255, 'light', device, args.debug) # Median Filter device, s_mblur = pcv.median_blur(fmax_thresh, 0, device, args.debug) device, s_cnt = pcv.median_blur(fmax_thresh, 0, device, args.debug) # Fill small objects device, s_fill = pcv.fill(s_mblur, s_cnt, 5, device, args.debug) device, sfill_cnt = pcv.fill(s_mblur, s_cnt, 5, device, args.debug) # Identify objects device, id_objects,obj_hierarchy = pcv.find_objects(mask, sfill_cnt, device, args.debug) # Define ROI device, roi1, roi_hierarchy= pcv.define_roi(mask,'circle', device, None, 'default', args.debug,True, 0,0,-100,-100) # Decide which objects to keep device,roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(mask,'partial',roi1,roi_hierarchy,id_objects,obj_hierarchy,device, args.debug) # Object combine kept objects device, obj, masked = pcv.object_composition(mask, roi_objects, hierarchy3, device, args.debug) ################ Analysis ################ # Find shape properties, output shape image (optional) device, shape_header,shape_data,shape_img = pcv.analyze_object(mask, args.fmax, obj, masked, device,args.debug, args.outdir+'/'+filename) # Fluorescence Measurement (read in 16-bit images) fdark=cv2.imread(args.fdark, -1) fmin=cv2.imread(args.fmin, -1) fmax=cv2.imread(args.fmax, -1) device, fvfm_header, fvfm_data=pcv.fluor_fvfm(fdark,fmin,fmax,kept_mask, device, args.outdir+'/'+filename, 1000, args.debug) # Output shape and color data pcv.print_results(args.fmax, shape_header, shape_data) pcv.print_results(args.fmax, fvfm_header, fvfm_data)
def main(): # Get options args = options() # Read image (converting fmax and track to 8 bit just to create a mask, use 16-bit for all the math) mask, path, filename = pcv.readimage(args.fmax) #mask = cv2.imread(args.fmax) track = cv2.imread(args.track) mask1, mask2, mask3= cv2.split(mask) # Pipeline step device = 0 # Mask pesky track autofluor device, track1= pcv.rgb2gray_hsv(track, 'v', device, args.debug) device, track_thresh = pcv.binary_threshold(track1, 0, 255, 'light', device, args.debug) device, track_inv=pcv.invert(track_thresh, device, args.debug) device, track_masked = pcv.apply_mask(mask1, track_inv, 'black', device, args.debug) # Threshold the Saturation image device, fmax_thresh = pcv.binary_threshold(track_masked, 20, 255, 'light', device, args.debug) # Median Filter device, s_mblur = pcv.median_blur(fmax_thresh, 0, device, args.debug) device, s_cnt = pcv.median_blur(fmax_thresh, 0, device, args.debug) # Fill small objects device, s_fill = pcv.fill(s_mblur, s_cnt, 5, device, args.debug) device, sfill_cnt = pcv.fill(s_mblur, s_cnt, 5, device, args.debug) # Identify objects device, id_objects,obj_hierarchy = pcv.find_objects(mask, sfill_cnt, device, args.debug) # Define ROI device, roi1, roi_hierarchy= pcv.define_roi(mask,'circle', device, None, 'default', args.debug,True, 0,0,-100,-100) # Decide which objects to keep device,roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(mask,'partial',roi1,roi_hierarchy,id_objects,obj_hierarchy,device, args.debug) # Object combine kept objects device, obj, masked = pcv.object_composition(mask, roi_objects, hierarchy3, device, args.debug) ################ Analysis ################ # Find shape properties, output shape image (optional) device, shape_header,shape_data,shape_img = pcv.analyze_object(mask, args.fmax, obj, masked, device,args.debug, args.outdir+'/'+filename) # Fluorescence Measurement (read in 16-bit images) fdark=cv2.imread(args.fdark, -1) fmin=cv2.imread(args.fmin, -1) fmax=cv2.imread(args.fmax, -1) device, fvfm_header, fvfm_data=pcv.fluor_fvfm(fdark,fmin,fmax,kept_mask, device, args.outdir+'/'+filename, 1000, args.debug) # Output shape and color data pcv.print_results(args.fmax, shape_header, shape_data) pcv.print_results(args.fmax, fvfm_header, fvfm_data)
def test_plantcv_invert():
img = cv2.imread(os.path.join(TEST_DATA, TEST_INPUT_BINARY), -1)
device, inverted_img = pcv.invert(img=img, device=0, debug=None)
# Assert that the output image has the dimensions of the input image
if all([i == j] for i, j in zip(np.shape(inverted_img), TEST_BINARY_DIM)):
# Assert that the image is binary
if all([i == j] for i, j in zip(np.unique(inverted_img), [0, 255])):
assert 1
else:
assert 0
else:
assert 0
def test_plantcv_invert():
img = cv2.imread(os.path.join(TEST_DATA, TEST_INPUT_BINARY), -1)
device, inverted_img = pcv.invert(img=img, device=0, debug=None)
# Assert that the output image has the dimensions of the input image
if all([i == j] for i, j in zip(np.shape(inverted_img), TEST_BINARY_DIM)):
# Assert that the image is binary
if all([i == j] for i, j in zip(np.unique(inverted_img), [0, 255])):
assert 1
else:
assert 0
else:
assert 0
def main():
# Get options
args = options()
path_mask = '/home/mfeldman/tester/mask/mask_brass_tv_z1_L0.png'
# Read image
img, path, filename = pcv.readimage(args.image)
brass_mask = cv2.imread(path_mask)
# Pipeline step
device = 0
# Mask pesky brass piece
device, brass_mask1 = pcv.rgb2gray_hsv(brass_mask, 'v', device, args.debug)
device, brass_thresh = pcv.binary_threshold(brass_mask1, 0, 255, 'light', device, args.debug)
device, brass_inv=pcv.invert(brass_thresh, device, args.debug)
device, masked_image = pcv.apply_mask(img, brass_inv, 'white', device, args.debug)
# We can do a pretty good job of identifying the plant from the s channel
device, s = pcv.rgb2gray_hsv(masked_image, 's', device, args.debug)
s_thresh = cv2.inRange(s, 100, 190)
# Lets blur the result a bit to get rid of unwanted noise
s_blur = cv2.medianBlur(s_thresh,5)
# The a channel is good too
device, a = pcv.rgb2gray_lab(masked_image, 'a', device, args.debug)
a_thresh = cv2.inRange(a, 90, 120)
a_blur = cv2.medianBlur(a_thresh,5)
# Now lets set of a series of filters to remove unwanted background
plant_shape = cv2.bitwise_and(a_blur, s_blur)
# Lets remove all the crap on the sides of the image
plant_shape[:,:330] = 0
plant_shape[:,2100:] = 0
plant_shape[:200,:] = 0
# Now remove all remaining small points using erosion with a 3 x 3 kernel
kernel = np.ones((3,3),np.uint8)
erosion = cv2.erode(plant_shape ,kernel,iterations = 1)
# Now dilate to fill in small holes
kernel = np.ones((3,3),np.uint8)
dilation = cv2.dilate(erosion ,kernel,iterations = 1)
# Apply mask to the background image
device, masked = pcv.apply_mask(masked_image, plant_shape, 'white', device, args.debug)
# Identify objects
device, id_objects, obj_hierarchy = pcv.find_objects(masked, dilation, device, args.debug)
# Get ROI contours
device, roi, roi_hierarchy = pcv.define_roi(masked_image, 'circle', device, None, 'default', args.debug, True, x_adj=0, y_adj=0, w_adj=0, h_adj=-1200)
# ROI
device,roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(masked_image,'partial',roi, roi_hierarchy, id_objects,obj_hierarchy,device, args.debug)
# Get object contour and masked object
device, obj, mask = pcv.object_composition(img, roi_objects, hierarchy3, device, args.debug)
############## Landmarks ################
device, points = pcv.acute_vertex(obj, 40, 40, 40, img, device, args.debug)
boundary_line = 'NA'
# Use acute fxn to estimate tips
device, points_r, centroid_r, bline_r = pcv.scale_features(obj, mask, points, boundary_line, device, args.debug)
# Get number of points
tips = len(points_r)
# Use turgor_proxy fxn to get distances
device, vert_ave_c, hori_ave_c, euc_ave_c, ang_ave_c, vert_ave_b, hori_ave_b, euc_ave_b, ang_ave_b = pcv.turgor_proxy(points_r, centroid_r, bline_r, device, args.debug)
# Get pseudomarkers along the y-axis
device, left, right, center_h = pcv.y_axis_pseudolandmarks(obj, mask, img, device, args.debug)
# Re-scale the points
device, left_r, left_cr, left_br = pcv.scale_features(obj, mask, left, boundary_line, device, args.debug)
device, right_r, right_cr, right_br = pcv.scale_features(obj, mask, right, boundary_line, device, args.debug)
device, center_hr, center_hcr, center_hbr = pcv.scale_features(obj, mask, center_h, boundary_line, device, args.debug)
# Get pseudomarkers along the x-axis
device, top, bottom, center_v = pcv.x_axis_pseudolandmarks(obj, mask, img, device, args.debug)
# Re-scale the points
device, top_r, top_cr, top_br = pcv.scale_features(obj, mask, top, boundary_line, device, args.debug)
device, bottom_r, bottom_cr, bottom_br = pcv.scale_features(obj, mask, bottom, boundary_line, device, args.debug)
device, center_vr, center_vcr, center_vbr = pcv.scale_features(obj, mask, center_v, boundary_line, device, args.debug)
## Need to convert the points into a list of tuples format to match the scaled points
points = points.reshape(len(points),2)
points = points.tolist()
temp_out = []
for p in points:
p = tuple(p)
temp_out.append(p)
points = temp_out
left = left.reshape(20,2)
left = left.tolist()
temp_out = []
for l in left:
l = tuple(l)
temp_out.append(l)
left = temp_out
right = right.reshape(20,2)
right = right.tolist()
temp_out = []
for r in right:
r = tuple(r)
temp_out.append(r)
right = temp_out
center_h = center_h.reshape(20,2)
center_h = center_h.tolist()
temp_out = []
for ch in center_h:
ch = tuple(ch)
temp_out.append(ch)
center_h = temp_out
## Need to convert the points into a list of tuples format to match the scaled points
top = top.reshape(20,2)
top = top.tolist()
temp_out = []
for t in top:
t = tuple(t)
temp_out.append(t)
top = temp_out
bottom = bottom.reshape(20,2)
bottom = bottom.tolist()
temp_out = []
for b in bottom:
b = tuple(b)
temp_out.append(b)
bottom = temp_out
center_v = center_v.reshape(20,2)
center_v = center_v.tolist()
temp_out = []
for cvr in center_v:
cvr = tuple(cvr)
temp_out.append(cvr)
center_v = temp_out
#Store Landmark Data
landmark_header=(
'HEADER_LANDMARK',
'tip_points',
'tip_points_r',
'centroid_r',
'baseline_r',
'tip_number',
'vert_ave_c',
'hori_ave_c',
'euc_ave_c',
'ang_ave_c',
'vert_ave_b',
'hori_ave_b',
'euc_ave_b',
'ang_ave_b',
'left_lmk',
'right_lmk',
'center_h_lmk',
'left_lmk_r',
'right_lmk_r',
'center_h_lmk_r',
'top_lmk',
'bottom_lmk',
'center_v_lmk',
'top_lmk_r',
'bottom_lmk_r',
'center_v_lmk_r'
)
landmark_data = (
'LANDMARK_DATA',
points,
points_r,
centroid_r,
bline_r,
tips,
vert_ave_c,
hori_ave_c,
euc_ave_c,
ang_ave_c,
vert_ave_b,
hori_ave_b,
euc_ave_b,
ang_ave_b,
left,
right,
center_h,
left_r,
right_r,
center_hr,
top,
bottom,
center_v,
top_r,
bottom_r,
center_vr
)
############## VIS Analysis ################
outfile=False
#if args.writeimg==True:
# outfile=args.outdir+"/"+filename
# 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,outfile)
# 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,outfile)
# Determine color properties: Histograms, Color Slices and Pseudocolored Images, output color analyzed images (optional)
device, color_header,color_data,color_img= pcv.analyze_color(img, args.image, mask, 256, device, args.debug,None,'v','img',300,outfile)
# Output shape and color data
result=open(args.result,"a")
result.write('\t'.join(map(str,shape_header)))
result.write("\n")
result.write('\t'.join(map(str,shape_data)))
result.write("\n")
for row in shape_img:
result.write('\t'.join(map(str,row)))
result.write("\n")
result.write('\t'.join(map(str,color_header)))
result.write("\n")
result.write('\t'.join(map(str,color_data)))
result.write("\n")
result.write('\t'.join(map(str,boundary_header)))
result.write("\n")
result.write('\t'.join(map(str,boundary_data)))
result.write("\n")
result.write('\t'.join(map(str,boundary_img1)))
result.write("\n")
for row in color_img:
result.write('\t'.join(map(str,row)))
result.write("\n")
result.write('\t'.join(map(str,landmark_header)))
result.write("\n")
result.write('\t'.join(map(str,landmark_data)))
result.write("\n")
result.close()
def main():
# Get options
args = options()
# Read image
img, path, filename = pcv.readimage(args.image)
brass_mask = 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, 49, 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, 150, 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)
# Mask pesky brass piece
device, brass_mask1 = pcv.rgb2gray_hsv(brass_mask, "v", device, args.debug)
device, brass_thresh = pcv.binary_threshold(brass_mask1, 0, 255, "light", device, args.debug)
device, brass_inv = pcv.invert(brass_thresh, device, args.debug)
device, brass_masked = pcv.apply_mask(masked, brass_inv, "white", device, args.debug)
# Further mask soil and car
device, masked_a = pcv.rgb2gray_lab(brass_masked, "a", device, args.debug)
device, soil_car = pcv.binary_threshold(masked_a, 128, 255, "dark", device, args.debug)
device, soil_masked = pcv.apply_mask(brass_masked, soil_car, "white", device, args.debug)
# Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
device, soil_a = pcv.rgb2gray_lab(soil_masked, "a", device, args.debug)
device, soil_b = pcv.rgb2gray_lab(soil_masked, "b", device, args.debug)
# Threshold the green-magenta and blue images
device, soila_thresh = pcv.binary_threshold(soil_a, 118, 255, "dark", device, args.debug)
device, soilb_thresh = pcv.binary_threshold(soil_b, 150, 255, "light", device, args.debug)
# Join the thresholded saturation and blue-yellow images (OR)
device, soil_ab = pcv.logical_or(soila_thresh, soilb_thresh, device, args.debug)
device, soil_ab_cnt = pcv.logical_or(soila_thresh, soilb_thresh, device, args.debug)
# Fill small objects
device, soil_cnt = pcv.fill(soil_ab, soil_ab_cnt, 75, device, args.debug)
# Median Filter
# device, soil_mblur = pcv.median_blur(soil_fill, 5, device, args.debug)
# device, soil_cnt = pcv.median_blur(soil_fill, 5, device, args.debug)
# Apply mask (for vis images, mask_color=white)
device, masked2 = pcv.apply_mask(soil_masked, soil_cnt, "white", device, args.debug)
# Identify objects
device, id_objects, obj_hierarchy = pcv.find_objects(masked2, soil_cnt, device, args.debug)
# Define ROI
device, roi1, roi_hierarchy = pcv.define_roi(
img, "circle", device, None, "default", args.debug, True, 0, 0, -200, -200
)
# 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)
############## VIS Analysis ################
outfile = False
if args.writeimg == True:
outfile = args.outdir + "/" + filename
# 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, outfile
)
# Determine color properties: Histograms, Color Slices and Pseudocolored Images, output color analyzed images (optional)
device, color_header, color_data, color_img = pcv.analyze_color(
img, args.image, mask, 256, device, args.debug, None, "v", "img", 300, outfile
)
# Output shape and color data
result = open(args.result, "a")
result.write("\t".join(map(str, shape_header)))
result.write("\n")
result.write("\t".join(map(str, shape_data)))
result.write("\n")
for row in shape_img:
result.write("\t".join(map(str, row)))
result.write("\n")
result.write("\t".join(map(str, color_header)))
result.write("\n")
result.write("\t".join(map(str, color_data)))
result.write("\n")
for row in color_img:
result.write("\t".join(map(str, row)))
result.write("\n")
result.close()
############################# Use VIS image mask for NIR image#########################
# Find matching NIR image
device, nirpath = pcv.get_nir(path, filename, device, args.debug)
nir, path1, filename1 = pcv.readimage(nirpath)
nir2 = cv2.imread(nirpath, -1)
# Flip mask
device, f_mask = pcv.flip(mask, "horizontal", device, args.debug)
# Reize mask
device, nmask = pcv.resize(f_mask, 0.1304, 0.1304, device, args.debug)
# position, and crop mask
device, newmask = pcv.crop_position_mask(nir, nmask, device, 9, 12, "top", "left", args.debug)
# Identify objects
device, nir_objects, nir_hierarchy = pcv.find_objects(nir, newmask, device, args.debug)
# Object combine kept objects
device, nir_combined, nir_combinedmask = pcv.object_composition(nir, nir_objects, nir_hierarchy, device, args.debug)
####################################### Analysis #############################################
outfile1 = False
if args.writeimg == True:
outfile1 = args.outdir + "/" + filename1
device, nhist_header, nhist_data, nir_imgs = pcv.analyze_NIR_intensity(
nir2, filename1, nir_combinedmask, 256, device, False, args.debug, outfile1
)
device, nshape_header, nshape_data, nir_shape = pcv.analyze_object(
nir2, filename1, nir_combined, nir_combinedmask, device, args.debug, outfile1
)
coresult = open(args.coresult, "a")
coresult.write("\t".join(map(str, nhist_header)))
coresult.write("\n")
coresult.write("\t".join(map(str, nhist_data)))
coresult.write("\n")
for row in nir_imgs:
coresult.write("\t".join(map(str, row)))
coresult.write("\n")
coresult.write("\t".join(map(str, nshape_header)))
coresult.write("\n")
coresult.write("\t".join(map(str, nshape_data)))
coresult.write("\n")
coresult.write("\t".join(map(str, nir_shape)))
coresult.write("\n")
coresult.close()
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
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')
def main():
# Get options
args = options()
# Read image
img, path, filename = pcv.readimage(args.image)
brass_mask = 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, 49, 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, 150, 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)
# Mask pesky brass piece
device, brass_mask1 = pcv.rgb2gray_hsv(brass_mask, "v", device, args.debug)
device, brass_thresh = pcv.binary_threshold(brass_mask1, 0, 255, "light", device, args.debug)
device, brass_inv = pcv.invert(brass_thresh, device, args.debug)
device, brass_masked = pcv.apply_mask(masked, brass_inv, "white", device, args.debug)
# Further mask soil and car
device, masked_a = pcv.rgb2gray_lab(brass_masked, "a", device, args.debug)
device, soil_car1 = pcv.binary_threshold(masked_a, 128, 255, "dark", device, args.debug)
device, soil_car2 = pcv.binary_threshold(masked_a, 128, 255, "light", device, args.debug)
device, soil_car = pcv.logical_or(soil_car1, soil_car2, device, args.debug)
device, soil_masked = pcv.apply_mask(brass_masked, soil_car, "white", device, args.debug)
# Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
device, soil_a = pcv.rgb2gray_lab(soil_masked, "a", device, args.debug)
device, soil_b = pcv.rgb2gray_lab(soil_masked, "b", device, args.debug)
# Threshold the green-magenta and blue images
device, soila_thresh = pcv.binary_threshold(soil_a, 124, 255, "dark", device, args.debug)
device, soilb_thresh = pcv.binary_threshold(soil_b, 148, 255, "light", device, args.debug)
# Join the thresholded saturation and blue-yellow images (OR)
device, soil_ab = pcv.logical_or(soila_thresh, soilb_thresh, device, args.debug)
device, soil_ab_cnt = pcv.logical_or(soila_thresh, soilb_thresh, device, args.debug)
# Fill small objects
device, soil_cnt = pcv.fill(soil_ab, soil_ab_cnt, 250, device, args.debug)
# Median Filter
# device, soil_mblur = pcv.median_blur(soil_fill, 5, device, args.debug)
# device, soil_cnt = pcv.median_blur(soil_fill, 5, device, args.debug)
# Apply mask (for vis images, mask_color=white)
device, masked2 = pcv.apply_mask(soil_masked, soil_cnt, "white", device, args.debug)
# Identify objects
device, id_objects, obj_hierarchy = pcv.find_objects(masked2, soil_cnt, device, args.debug)
# Define ROI
device, roi1, roi_hierarchy = pcv.define_roi(
img, "rectangle", device, None, "default", args.debug, True, 600, 450, -600, -350
)
# 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)
############## VIS Analysis ################
outfile = False
if args.writeimg == True:
outfile = args.outdir + "/" + filename
# 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, outfile
)
# Determine color properties: Histograms, Color Slices and Pseudocolored Images, output color analyzed images (optional)
device, color_header, color_data, color_img = pcv.analyze_color(
img, args.image, mask, 256, device, args.debug, None, "v", "img", 300, outfile
)
# Output shape and color data
result = open(args.result, "a")
result.write("\t".join(map(str, shape_header)))
result.write("\n")
result.write("\t".join(map(str, shape_data)))
result.write("\n")
for row in shape_img:
result.write("\t".join(map(str, row)))
result.write("\n")
result.write("\t".join(map(str, color_header)))
result.write("\n")
result.write("\t".join(map(str, color_data)))
result.write("\n")
for row in color_img:
result.write("\t".join(map(str, row)))
result.write("\n")
def process_tv_images_core(vis_id, vis_img, nir_id, nir_rgb, nir_cv2, brass_mask, traits, debug=None):
device = 0
# Convert RGB to HSV and extract the Saturation channel
device, s = pcv.rgb2gray_hsv(vis_img, 's', device, debug)
# Threshold the Saturation image
device, s_thresh = pcv.binary_threshold(s, 75, 255, 'light', device, debug)
# Median Filter
device, s_mblur = pcv.median_blur(s_thresh, 5, device, debug)
device, s_cnt = pcv.median_blur(s_thresh, 5, device, debug)
# Fill small objects
device, s_fill = pcv.fill(s_mblur, s_cnt, 150, device, debug)
# Convert RGB to LAB and extract the Blue channel
device, b = pcv.rgb2gray_lab(vis_img, 'b', device, debug)
# Threshold the blue image
device, b_thresh = pcv.binary_threshold(b, 138, 255, 'light', device, debug)
device, b_cnt = pcv.binary_threshold(b, 138, 255, 'light', device, debug)
# Fill small objects
device, b_fill = pcv.fill(b_thresh, b_cnt, 100, device, debug)
# Join the thresholded saturation and blue-yellow images
device, bs = pcv.logical_and(s_fill, b_fill, device, debug)
# Apply Mask (for vis images, mask_color=white)
device, masked = pcv.apply_mask(vis_img, bs, 'white', device, debug)
# Mask pesky brass piece
device, brass_mask1 = pcv.rgb2gray_hsv(brass_mask, 'v', device, debug)
device, brass_thresh = pcv.binary_threshold(brass_mask1, 0, 255, 'light', device, debug)
device, brass_inv = pcv.invert(brass_thresh, device, debug)
device, brass_masked = pcv.apply_mask(masked, brass_inv, 'white', device, debug)
# Further mask soil and car
device, masked_a = pcv.rgb2gray_lab(brass_masked, 'a', device, debug)
device, soil_car1 = pcv.binary_threshold(masked_a, 128, 255, 'dark', device, debug)
device, soil_car2 = pcv.binary_threshold(masked_a, 128, 255, 'light', device, debug)
device, soil_car = pcv.logical_or(soil_car1, soil_car2, device, debug)
device, soil_masked = pcv.apply_mask(brass_masked, soil_car, 'white', device, debug)
# Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
device, soil_a = pcv.rgb2gray_lab(soil_masked, 'a', device, debug)
device, soil_b = pcv.rgb2gray_lab(soil_masked, 'b', device, debug)
# Threshold the green-magenta and blue images
device, soila_thresh = pcv.binary_threshold(soil_a, 124, 255, 'dark', device, debug)
device, soilb_thresh = pcv.binary_threshold(soil_b, 148, 255, 'light', device, debug)
# Join the thresholded saturation and blue-yellow images (OR)
device, soil_ab = pcv.logical_or(soila_thresh, soilb_thresh, device, debug)
device, soil_ab_cnt = pcv.logical_or(soila_thresh, soilb_thresh, device, debug)
# Fill small objects
device, soil_cnt = pcv.fill(soil_ab, soil_ab_cnt, 300, device, debug)
# Apply mask (for vis images, mask_color=white)
device, masked2 = pcv.apply_mask(soil_masked, soil_cnt, 'white', device, debug)
# Identify objects
device, id_objects, obj_hierarchy = pcv.find_objects(masked2, soil_cnt, device, debug)
# Define ROI
device, roi1, roi_hierarchy = pcv.define_roi(vis_img, 'rectangle', device, None, 'default', debug, True, 600, 450, -600,
-350)
# Decide which objects to keep
device, roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(vis_img, 'partial', roi1, roi_hierarchy,
id_objects, obj_hierarchy, device, debug)
# Object combine kept objects
device, obj, mask = pcv.object_composition(vis_img, roi_objects, hierarchy3, device, debug)
# Find shape properties, output shape image (optional)
device, shape_header, shape_data, shape_img = pcv.analyze_object(vis_img, vis_id, obj, mask, device, debug)
# Determine color properties
device, color_header, color_data, color_img = pcv.analyze_color(vis_img, vis_id, mask, 256, device, debug, None,
'v', 'img', 300)
# Output shape and color data
vis_traits = {}
for i in range(1, len(shape_header)):
vis_traits[shape_header[i]] = shape_data[i]
for i in range(2, len(color_header)):
vis_traits[color_header[i]] = serialize_color_data(color_data[i])
############################# Use VIS image mask for NIR image#########################
# Flip mask
device, f_mask = pcv.flip(mask, "horizontal", device, debug)
# Reize mask
device, nmask = pcv.resize(f_mask, 0.116148, 0.116148, device, debug)
# position, and crop mask
device, newmask = pcv.crop_position_mask(nir_rgb, nmask, device, 15, 5, "top", "right", debug)
# Identify objects
device, nir_objects, nir_hierarchy = pcv.find_objects(nir_rgb, newmask, device, debug)
# Object combine kept objects
device, nir_combined, nir_combinedmask = pcv.object_composition(nir_rgb, nir_objects, nir_hierarchy, device, debug)
####################################### Analysis #############################################
device, nhist_header, nhist_data, nir_imgs = pcv.analyze_NIR_intensity(nir_cv2, nir_id, nir_combinedmask, 256,
device, False, debug)
device, nshape_header, nshape_data, nir_shape = pcv.analyze_object(nir_cv2, nir_id, nir_combined, nir_combinedmask,
device, debug)
nir_traits = {}
for i in range(1, len(nshape_header)):
nir_traits[nshape_header[i]] = nshape_data[i]
for i in range(2, len(nhist_header)):
nir_traits[nhist_header[i]] = serialize_color_data(nhist_data[i])
# Add data to traits table
traits['tv_area'] = vis_traits['area']
return [vis_traits, nir_traits]
def process_tv_images(session, url, vis_id, nir_id, traits, debug=False):
"""Process top-view images.
Inputs:
session = requests session object
url = Clowder URL
vis_id = The Clowder ID of an RGB image
nir_img = The Clowder ID of an NIR grayscale image
traits = traits table (dictionary)
debug = None, print, or plot. Print = save to file, Plot = print to screen.
:param session: requests session object
:param url: str
:param vis_id: str
:param nir_id: str
:param traits: dict
:param debug: str
:return traits: dict
"""
# Read VIS image from Clowder
vis_r = session.get(posixpath.join(url, "api/files", vis_id), stream=True)
img_array = np.asarray(bytearray(vis_r.content), dtype="uint8")
img = cv2.imdecode(img_array, -1)
# Read the VIS top-view image mask for zoom = 1 from Clowder
mask_r = session.get(posixpath.join(url, "api/files/57451b28e4b0efbe2dc3d4d5"), stream=True)
mask_array = np.asarray(bytearray(mask_r.content), dtype="uint8")
brass_mask = cv2.imdecode(mask_array, -1)
device = 0
# Convert RGB to HSV and extract the Saturation channel
device, s = pcv.rgb2gray_hsv(img, 's', device, debug)
# Threshold the Saturation image
device, s_thresh = pcv.binary_threshold(s, 75, 255, 'light', device, debug)
# Median Filter
device, s_mblur = pcv.median_blur(s_thresh, 5, device, debug)
device, s_cnt = pcv.median_blur(s_thresh, 5, device, debug)
# Fill small objects
device, s_fill = pcv.fill(s_mblur, s_cnt, 150, device, debug)
# Convert RGB to LAB and extract the Blue channel
device, b = pcv.rgb2gray_lab(img, 'b', device, debug)
# Threshold the blue image
device, b_thresh = pcv.binary_threshold(b, 138, 255, 'light', device, debug)
device, b_cnt = pcv.binary_threshold(b, 138, 255, 'light', device, debug)
# Fill small objects
device, b_fill = pcv.fill(b_thresh, b_cnt, 100, device, debug)
# Join the thresholded saturation and blue-yellow images
device, bs = pcv.logical_and(s_fill, b_fill, device, debug)
# Apply Mask (for vis images, mask_color=white)
device, masked = pcv.apply_mask(img, bs, 'white', device, debug)
# Mask pesky brass piece
device, brass_mask1 = pcv.rgb2gray_hsv(brass_mask, 'v', device, debug)
device, brass_thresh = pcv.binary_threshold(brass_mask1, 0, 255, 'light', device, debug)
device, brass_inv = pcv.invert(brass_thresh, device, debug)
device, brass_masked = pcv.apply_mask(masked, brass_inv, 'white', device, debug)
# Further mask soil and car
device, masked_a = pcv.rgb2gray_lab(brass_masked, 'a', device, debug)
device, soil_car1 = pcv.binary_threshold(masked_a, 128, 255, 'dark', device, debug)
device, soil_car2 = pcv.binary_threshold(masked_a, 128, 255, 'light', device, debug)
device, soil_car = pcv.logical_or(soil_car1, soil_car2, device, debug)
device, soil_masked = pcv.apply_mask(brass_masked, soil_car, 'white', device, debug)
# Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
device, soil_a = pcv.rgb2gray_lab(soil_masked, 'a', device, debug)
device, soil_b = pcv.rgb2gray_lab(soil_masked, 'b', device, debug)
# Threshold the green-magenta and blue images
device, soila_thresh = pcv.binary_threshold(soil_a, 124, 255, 'dark', device, debug)
device, soilb_thresh = pcv.binary_threshold(soil_b, 148, 255, 'light', device, debug)
# Join the thresholded saturation and blue-yellow images (OR)
device, soil_ab = pcv.logical_or(soila_thresh, soilb_thresh, device, debug)
device, soil_ab_cnt = pcv.logical_or(soila_thresh, soilb_thresh, device, debug)
# Fill small objects
device, soil_cnt = pcv.fill(soil_ab, soil_ab_cnt, 300, device, debug)
# Apply mask (for vis images, mask_color=white)
device, masked2 = pcv.apply_mask(soil_masked, soil_cnt, 'white', device, debug)
# Identify objects
device, id_objects, obj_hierarchy = pcv.find_objects(masked2, soil_cnt, device, debug)
# Define ROI
device, roi1, roi_hierarchy = pcv.define_roi(img, 'rectangle', device, None, 'default', debug, True, 600, 450, -600,
-350)
# 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, debug)
# Object combine kept objects
device, obj, mask = pcv.object_composition(img, roi_objects, hierarchy3, device, debug)
# Find shape properties, output shape image (optional)
device, shape_header, shape_data, shape_img = pcv.analyze_object(img, vis_id, obj, mask, device, debug)
# Determine color properties
device, color_header, color_data, color_img = pcv.analyze_color(img, vis_id, mask, 256, device, debug, None,
'v', 'img', 300)
# Output shape and color data
vis_traits = {}
for i in range(1, len(shape_header)):
vis_traits[shape_header[i]] = shape_data[i]
for i in range(2, len(color_header)):
vis_traits[color_header[i]] = serialize_color_data(color_data[i])
#print(vis_traits)
add_plantcv_metadata(session, url, vis_id, vis_traits)
############################# Use VIS image mask for NIR image#########################
# Read NIR image from Clowder
nir_r = session.get(posixpath.join(url, "api/files", nir_id), stream=True)
nir_array = np.asarray(bytearray(nir_r.content), dtype="uint8")
nir = cv2.imdecode(nir_array, -1)
nir_rgb = cv2.cvtColor(nir, cv2.COLOR_GRAY2BGR)
# Flip mask
device, f_mask = pcv.flip(mask, "horizontal", device, debug)
# Reize mask
device, nmask = pcv.resize(f_mask, 0.116148, 0.116148, device, debug)
# position, and crop mask
device, newmask = pcv.crop_position_mask(nir_rgb, nmask, device, 15, 5, "top", "right", debug)
# Identify objects
device, nir_objects, nir_hierarchy = pcv.find_objects(nir_rgb, newmask, device, debug)
# Object combine kept objects
device, nir_combined, nir_combinedmask = pcv.object_composition(nir_rgb, nir_objects, nir_hierarchy, device, debug)
####################################### Analysis #############################################
device, nhist_header, nhist_data, nir_imgs = pcv.analyze_NIR_intensity(nir, nir_id, nir_combinedmask, 256,
device, False, debug)
device, nshape_header, nshape_data, nir_shape = pcv.analyze_object(nir, nir_id, nir_combined, nir_combinedmask,
device, debug)
nir_traits = {}
for i in range(1, len(nshape_header)):
nir_traits[nshape_header[i]] = nshape_data[i]
for i in range(2, len(nhist_header)):
nir_traits[nhist_header[i]] = serialize_color_data(nhist_data[i])
#print(nir_traits)
add_plantcv_metadata(session, url, nir_id, nir_traits)
# Add data to traits table
traits['tv_area'] = vis_traits['area']
return traits
def process_tv_images(vis_img, nir_img, debug=False):
"""Process top-view images.
Inputs:
vis_img = An RGB image.
nir_img = An NIR grayscale image.
debug = None, print, or plot. Print = save to file, Plot = print to screen.
:param vis_img: str
:param nir_img: str
:param debug: str
:return:
"""
# Read image
img, path, filename = pcv.readimage(vis_img)
brass_mask = cv2.imread('mask_brass_tv_z1_L1.png')
device = 0
# Convert RGB to HSV and extract the Saturation channel
device, s = pcv.rgb2gray_hsv(img, 's', device, debug)
# Threshold the Saturation image
device, s_thresh = pcv.binary_threshold(s, 75, 255, 'light', device, debug)
# Median Filter
device, s_mblur = pcv.median_blur(s_thresh, 5, device, debug)
device, s_cnt = pcv.median_blur(s_thresh, 5, device, debug)
# Fill small objects
device, s_fill = pcv.fill(s_mblur, s_cnt, 150, device, debug)
# Convert RGB to LAB and extract the Blue channel
device, b = pcv.rgb2gray_lab(img, 'b', device, debug)
# Threshold the blue image
device, b_thresh = pcv.binary_threshold(b, 138, 255, 'light', device, debug)
device, b_cnt = pcv.binary_threshold(b, 138, 255, 'light', device, debug)
# Fill small objects
device, b_fill = pcv.fill(b_thresh, b_cnt, 100, device, debug)
# Join the thresholded saturation and blue-yellow images
device, bs = pcv.logical_and(s_fill, b_fill, device, debug)
# Apply Mask (for vis images, mask_color=white)
device, masked = pcv.apply_mask(img, bs, 'white', device, debug)
# Mask pesky brass piece
device, brass_mask1 = pcv.rgb2gray_hsv(brass_mask, 'v', device, debug)
device, brass_thresh = pcv.binary_threshold(brass_mask1, 0, 255, 'light', device, debug)
device, brass_inv = pcv.invert(brass_thresh, device, debug)
device, brass_masked = pcv.apply_mask(masked, brass_inv, 'white', device, debug)
# Further mask soil and car
device, masked_a = pcv.rgb2gray_lab(brass_masked, 'a', device, debug)
device, soil_car1 = pcv.binary_threshold(masked_a, 128, 255, 'dark', device, debug)
device, soil_car2 = pcv.binary_threshold(masked_a, 128, 255, 'light', device, debug)
device, soil_car = pcv.logical_or(soil_car1, soil_car2, device, debug)
device, soil_masked = pcv.apply_mask(brass_masked, soil_car, 'white', device, debug)
# Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
device, soil_a = pcv.rgb2gray_lab(soil_masked, 'a', device, debug)
device, soil_b = pcv.rgb2gray_lab(soil_masked, 'b', device, debug)
# Threshold the green-magenta and blue images
device, soila_thresh = pcv.binary_threshold(soil_a, 124, 255, 'dark', device, debug)
device, soilb_thresh = pcv.binary_threshold(soil_b, 148, 255, 'light', device, debug)
# Join the thresholded saturation and blue-yellow images (OR)
device, soil_ab = pcv.logical_or(soila_thresh, soilb_thresh, device, debug)
device, soil_ab_cnt = pcv.logical_or(soila_thresh, soilb_thresh, device, debug)
# Fill small objects
device, soil_cnt = pcv.fill(soil_ab, soil_ab_cnt, 300, device, debug)
# Apply mask (for vis images, mask_color=white)
device, masked2 = pcv.apply_mask(soil_masked, soil_cnt, 'white', device, debug)
# Identify objects
device, id_objects, obj_hierarchy = pcv.find_objects(masked2, soil_cnt, device, debug)
# Define ROI
device, roi1, roi_hierarchy = pcv.define_roi(img, 'rectangle', device, None, 'default', debug, True, 600, 450, -600,
-350)
# 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, debug)
# Object combine kept objects
device, obj, mask = pcv.object_composition(img, roi_objects, hierarchy3, device, debug)
# Find shape properties, output shape image (optional)
device, shape_header, shape_data, shape_img = pcv.analyze_object(img, vis_img, obj, mask, device, debug)
# Determine color properties
device, color_header, color_data, color_img = pcv.analyze_color(img, vis_img, mask, 256, device, debug, None,
'v', 'img', 300)
print('\t'.join(map(str, shape_header)) + '\n')
print('\t'.join(map(str, shape_data)) + '\n')
for row in shape_img:
print('\t'.join(map(str, row)) + '\n')
print('\t'.join(map(str, color_header)) + '\n')
print('\t'.join(map(str, color_data)) + '\n')
for row in color_img:
print('\t'.join(map(str, row)) + '\n')
############################# Use VIS image mask for NIR image#########################
# Read NIR image
nir, path1, filename1 = pcv.readimage(nir_img)
nir2 = cv2.imread(nir_img, -1)
# Flip mask
device, f_mask = pcv.flip(mask, "horizontal", device, debug)
# Reize mask
device, nmask = pcv.resize(f_mask, 0.116148, 0.116148, device, debug)
# position, and crop mask
device, newmask = pcv.crop_position_mask(nir, nmask, device, 15, 5, "top", "right", debug)
# Identify objects
device, nir_objects, nir_hierarchy = pcv.find_objects(nir, newmask, device, debug)
# Object combine kept objects
device, nir_combined, nir_combinedmask = pcv.object_composition(nir, nir_objects, nir_hierarchy, device, debug)
####################################### Analysis #############################################
device, nhist_header, nhist_data, nir_imgs = pcv.analyze_NIR_intensity(nir2, filename1, nir_combinedmask, 256,
device, False, debug)
device, nshape_header, nshape_data, nir_shape = pcv.analyze_object(nir2, filename1, nir_combined, nir_combinedmask,
device, debug)
print('\t'.join(map(str,nhist_header)) + '\n')
print('\t'.join(map(str,nhist_data)) + '\n')
for row in nir_imgs:
print('\t'.join(map(str,row)) + '\n')
print('\t'.join(map(str,nshape_header)) + '\n')
print('\t'.join(map(str,nshape_data)) + '\n')
print('\t'.join(map(str,nir_shape)) + '\n')
def process_tv_images_core(vis_id,
vis_img,
nir_id,
nir_rgb,
nir_cv2,
brass_mask,
traits,
debug=None):
device = 0
# Convert RGB to HSV and extract the Saturation channel
device, s = pcv.rgb2gray_hsv(vis_img, 's', device, debug)
# Threshold the Saturation image
device, s_thresh = pcv.binary_threshold(s, 75, 255, 'light', device, debug)
# Median Filter
device, s_mblur = pcv.median_blur(s_thresh, 5, device, debug)
device, s_cnt = pcv.median_blur(s_thresh, 5, device, debug)
# Fill small objects
device, s_fill = pcv.fill(s_mblur, s_cnt, 150, device, debug)
# Convert RGB to LAB and extract the Blue channel
device, b = pcv.rgb2gray_lab(vis_img, 'b', device, debug)
# Threshold the blue image
device, b_thresh = pcv.binary_threshold(b, 138, 255, 'light', device,
debug)
device, b_cnt = pcv.binary_threshold(b, 138, 255, 'light', device, debug)
# Fill small objects
device, b_fill = pcv.fill(b_thresh, b_cnt, 100, device, debug)
# Join the thresholded saturation and blue-yellow images
device, bs = pcv.logical_and(s_fill, b_fill, device, debug)
# Apply Mask (for vis images, mask_color=white)
device, masked = pcv.apply_mask(vis_img, bs, 'white', device, debug)
# Mask pesky brass piece
device, brass_mask1 = pcv.rgb2gray_hsv(brass_mask, 'v', device, debug)
device, brass_thresh = pcv.binary_threshold(brass_mask1, 0, 255, 'light',
device, debug)
device, brass_inv = pcv.invert(brass_thresh, device, debug)
device, brass_masked = pcv.apply_mask(masked, brass_inv, 'white', device,
debug)
# Further mask soil and car
device, masked_a = pcv.rgb2gray_lab(brass_masked, 'a', device, debug)
device, soil_car1 = pcv.binary_threshold(masked_a, 128, 255, 'dark',
device, debug)
device, soil_car2 = pcv.binary_threshold(masked_a, 128, 255, 'light',
device, debug)
device, soil_car = pcv.logical_or(soil_car1, soil_car2, device, debug)
device, soil_masked = pcv.apply_mask(brass_masked, soil_car, 'white',
device, debug)
# Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
device, soil_a = pcv.rgb2gray_lab(soil_masked, 'a', device, debug)
device, soil_b = pcv.rgb2gray_lab(soil_masked, 'b', device, debug)
# Threshold the green-magenta and blue images
device, soila_thresh = pcv.binary_threshold(soil_a, 124, 255, 'dark',
device, debug)
device, soilb_thresh = pcv.binary_threshold(soil_b, 148, 255, 'light',
device, debug)
# Join the thresholded saturation and blue-yellow images (OR)
device, soil_ab = pcv.logical_or(soila_thresh, soilb_thresh, device, debug)
device, soil_ab_cnt = pcv.logical_or(soila_thresh, soilb_thresh, device,
debug)
# Fill small objects
device, soil_cnt = pcv.fill(soil_ab, soil_ab_cnt, 300, device, debug)
# Apply mask (for vis images, mask_color=white)
device, masked2 = pcv.apply_mask(soil_masked, soil_cnt, 'white', device,
debug)
# Identify objects
device, id_objects, obj_hierarchy = pcv.find_objects(
masked2, soil_cnt, device, debug)
# Define ROI
device, roi1, roi_hierarchy = pcv.define_roi(vis_img, 'rectangle', device,
None, 'default', debug, True,
600, 450, -600, -350)
# Decide which objects to keep
device, roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(
vis_img, 'partial', roi1, roi_hierarchy, id_objects, obj_hierarchy,
device, debug)
# Object combine kept objects
device, obj, mask = pcv.object_composition(vis_img, roi_objects,
hierarchy3, device, debug)
# Find shape properties, output shape image (optional)
device, shape_header, shape_data, shape_img = pcv.analyze_object(
vis_img, vis_id, obj, mask, device, debug)
# Determine color properties
device, color_header, color_data, color_img = pcv.analyze_color(
vis_img, vis_id, mask, 256, device, debug, None, 'v', 'img', 300)
# Output shape and color data
vis_traits = {}
for i in range(1, len(shape_header)):
vis_traits[shape_header[i]] = shape_data[i]
for i in range(2, len(color_header)):
vis_traits[color_header[i]] = serialize_color_data(color_data[i])
############################# Use VIS image mask for NIR image#########################
# Flip mask
device, f_mask = pcv.flip(mask, "horizontal", device, debug)
# Reize mask
device, nmask = pcv.resize(f_mask, 0.116148, 0.116148, device, debug)
# position, and crop mask
device, newmask = pcv.crop_position_mask(nir_rgb, nmask, device, 15, 5,
"top", "right", debug)
# Identify objects
device, nir_objects, nir_hierarchy = pcv.find_objects(
nir_rgb, newmask, device, debug)
# Object combine kept objects
device, nir_combined, nir_combinedmask = pcv.object_composition(
nir_rgb, nir_objects, nir_hierarchy, device, debug)
####################################### Analysis #############################################
device, nhist_header, nhist_data, nir_imgs = pcv.analyze_NIR_intensity(
nir_cv2, nir_id, nir_combinedmask, 256, device, False, debug)
device, nshape_header, nshape_data, nir_shape = pcv.analyze_object(
nir_cv2, nir_id, nir_combined, nir_combinedmask, device, debug)
nir_traits = {}
for i in range(1, len(nshape_header)):
nir_traits[nshape_header[i]] = nshape_data[i]
for i in range(2, len(nhist_header)):
nir_traits[nhist_header[i]] = serialize_color_data(nhist_data[i])
# Add data to traits table
traits['tv_area'] = vis_traits['area']
return [vis_traits, nir_traits]
def main():
# obtiene opciones de imagen
args = options()
#LINEA 22
if args.debug:
print("Debug mode turned on...")
# lee la imagen el flags=0 indica que se espera una imagen a escala de grises
img = cv2.imread(args.image, flags=0)
# cv2.imshow("imagen original",img)
# Get directory path and image name from command line arguments
path, img_name = os.path.split(args.image)
#LINEA 30
# Read in image which is the pixelwise average of background images
img_bkgrd = cv2.imread("background_average.jpg", flags=0)
#cv2.imshow("ventana del fondo",img_bkgrd)
# paso del procesamiento de imagenes
device = 0
######hasta qui bien
#linea 37
# Restar la imagen de fondo de la imagen con la planta.
device, bkg_sub_img = pcv.image_subtract(img, img_bkgrd, device,
args.debug)
#cv2.imshow("imagen resta",bkg_sub_img)
# Threshold the image of interest using the two-sided cv2.inRange function (keep what is between 50-190)
bkg_sub_thres_img = cv2.inRange(bkg_sub_img, 50, 190)
if args.debug:
cv2.imwrite('bkgrd_sub_thres.png', bkg_sub_thres_img)
#hasta qui todo bien
#linea 46
# Filtrado de Laplace (identificar bordes basados en la derivada 2)
device, lp_img = pcv.laplace_filter(img, 1, 1, device, args.debug)
#cv2.imshow("imagen de filtrado",lp_img)
if args.debug:
pcv.plot_hist(lp_img, 'histograma_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)
#cv2.imshow("imagen de borde lapacian",lp_shrp_img)
if args.debug:
pcv.plot_hist(lp_shrp_img, 'histograma_lp_shrp')
#hasta aqui todo bien linea 58
# Sobel filtering-filtrado de sobel
# 1ª derivada filtrado sobel a lo largo del eje horizontal, núcleo = 1, sin escala)
""" segun esta masl son siete,kito scale y me kedo con apertura k,chekar sobel en docs
device, sbx_img = pcv.sobel_filter(img, 1, 0, 1, 1, device, args.debug)
"""
device, sbx_img = pcv.sobel_filter(img, 1, 0, 1, device, args.debug)
#cv2.imshow("imagen sobel-eje horizontal",sbx_img)
if args.debug:
pcv.plot_hist(sbx_img, 'histograma_sbx')
# Filtrado de la primera derivada sobel a lo largo del eje vertical, núcleo = 1, sin escala)
device, sby_img = pcv.sobel_filter(img, 0, 1, 1, device, args.debug)
#cv2.imshow("imagen sobel-ejevertical",sby_img)
if args.debug:
pcv.plot_hist(sby_img, 'histograma_sby')
# Combina los efectos de ambos filtros x e y mediante la suma de matrizes
# Esto captura los bordes identificados dentro de cada plano y enfatiza los bordes encontrados en ambas imágenes
device, sb_img = pcv.image_add(sbx_img, sby_img, device, args.debug)
#cv2.imshow("imagen suma de sobel",sb_img)
if args.debug:
pcv.plot_hist(sb_img, 'histograma_sb_comb_img')
#hasta aqui todo bien linea 82
# usar filtro pasa bajo blur para suavizar la imagen de sobel
device, mblur_img = pcv.median_blur(sb_img, 1, device, args.debug)
#cv2.imshow("imagen blur",mblur_img)
device, mblur_invert_img = pcv.invert(mblur_img, device, args.debug)
#cv2.imshow("imagen blur-invertido",mblur_invert_img)
# Combinar la imagen suavizada del sobel con la imagen afilada del laplaciano
# combines the best features of both methods as described in "Digital Image Processing" by Gonzalez and Woods pg. 169
#Combina las mejores características de ambos métodos como se describe en "Digital Image Processing" por González y Woods pág. 169
device, edge_shrp_img = pcv.image_add(mblur_invert_img, lp_shrp_img,
device, args.debug)
#cv2.imshow("imagen-combinacion-sobel-laplacian",mblur_img)
if args.debug:
pcv.plot_hist(edge_shrp_img, 'hist_edge_shrp_img')
# Realizar el umbral para generar una imagen binaria
device, tr_es_img = pcv.binary_threshold(edge_shrp_img, 125, 255, 'dark',
device, args.debug)
#cv2.imshow("imagen binaria de combinacion",tr_es_img)
#hasta aqui todo bien linea 99
# Prepare a few small kernels for morphological filtering
#prepara nucleos pequeños para un filtrado moorfologico
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
# prepara un nucleo grande para la dilatacion
kern[1, 0:3] = 1
kern[0:3, 1] = 1
# Perform erosion with 4 small kernels
device, e1_img = pcv.erode(tr_es_img, 1, 1, device, args.debug)
#cv2.imshow("erosion 1",e1_img)
device, e2_img = pcv.erode(tr_es_img, 1, 1, device, args.debug)
#cv2.imshow("erosion 2",e2_img)
device, e3_img = pcv.erode(tr_es_img, 1, 1, device, args.debug)
#cv2.imshow("erosion 3",e3_img)
device, e4_img = pcv.erode(tr_es_img, 1, 1, device, args.debug)
#cv2.imshow("erosion 4",e4_img)
# Combine eroded images
device, c12_img = pcv.logical_or(e1_img, e2_img, device, args.debug)
#cv2.imshow("c12",c12_img)
device, c123_img = pcv.logical_or(c12_img, e3_img, device, args.debug)
#cv2.imshow("c123",c123_img)
device, c1234_img = pcv.logical_or(c123_img, e4_img, device, args.debug)
#cv2.imshow("c1234",c1234_img)
# Bring the two object identification approaches together.
# Using a logical OR combine object identified by background subtraction and the object identified by derivative filter.
device, comb_img = pcv.logical_or(c1234_img, bkg_sub_thres_img, device,
args.debug)
#cv2.imshow("comb_img",comb_img)
# Get masked image, Essentially identify pixels corresponding to plant and keep those.
device, masked_erd = pcv.apply_mask(img, comb_img, 'black', device,
args.debug)
#cv2.imshow("masked_erd",masked_erd)
#cv2.imshow("imagen original chkar",img)
# 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, im2, box1_img, rect_contour1, hierarchy1 = pcv.rectangle_mask(
img, (120, 184), (215, 252), device, args.debug, color='white')
#cv2.imshow("im2",box1_img)
# mask for the left side of the image
device, im3, box2_img, rect_contour2, hierarchy2 = pcv.rectangle_mask(
img, (1, 1), (85, 252), device, args.debug, color='white')
#cv2.imshow("im3",box2_img)
# mask for the right side of the image
device, im4, box3_img, rect_contour3, hierarchy3 = pcv.rectangle_mask(
img, (240, 1), (318, 252), device, args.debug, color='white')
#cv2.imshow("im4",box3_img)
# mask the edges
device, im5, box4_img, rect_contour4, hierarchy4 = pcv.rectangle_mask(
img, (1, 1), (318, 252), device, args.debug)
#cv2.imshow("im5",box4_img)
# 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)
#cv2.imshow("combinacion logica or",bx1234_img)
# invert this mask and then apply it the masked image.
device, inv_bx1234_img = pcv.invert(bx1234_img, device, args.debug)
# cv2.imshow("combinacion logica or invertida",inv_bx1234_img)
device, edge_masked_img = pcv.apply_mask(masked_erd, inv_bx1234_img,
'black', device, args.debug)
# cv2.imshow("edge_masked_img",edge_masked_img)
# assign the coordinates of an area of interest (rectangle around the area you expect the plant to be in)
device, im6, roi_img, roi_contour, roi_hierarchy = pcv.rectangle_mask(
img, (120, 75), (200, 184), device, args.debug)
#cv2.imshow("im6",roi_img)
# get the coordinates of the plant from the masked object
plant_objects, plant_hierarchy = cv2.findContours(edge_masked_img,
cv2.RETR_TREE,
cv2.CHAIN_APPROX_NONE)
# Obtain the coordinates of the plant object which are partially within the area of interest
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 to ensure no background
device, masked_img = pcv.apply_mask(kept_mask, inv_bx1234_img, 'black',
device, args.debug)
#cv2.imshow("mascara final",masked_img)
#/////////////////////////////////////////////////////////////
#device, masked_img = pcv.apply_mask(kept_mask, inv_bx1234_img, 'black', device, args.debug)
rgb = cv2.cvtColor(img, cv2.COLOR_GRAY2RGB)
#cv2.imshow("rgb",rgb)
# Generate a binary to send to the analysis function
device, mask = pcv.binary_threshold(masked_img, 1, 255, 'light', device,
args.debug)
#cv2.imshow("mask",mask)
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)
# Get final masked image
device, masked_img = pcv.apply_mask(kept_mask, inv_bx1234_img, 'black',
device, args.debug)
#cv2.imshow("maskara final2",masked_img)
################### copia lo de arriba esta mal el tutorial
# Obtain a 3 dimensional representation of this grayscale image (for pseudocoloring)
#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)
# Make a copy of this mask for pseudocoloring
#mask3d = np.copy(mask)
# Extract coordinates of plant for pseudocoloring of plant
#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)
# Extract coordinates of plant for pseudocoloring of plant
#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 ###
# Perform signal analysis
#################pruebas de que esta masl el tutorial""""""""""""""""
#ols=type(args.image)
#print ols
##############pruebas de que no agarro device, hist_header, hist_data, h_norm = pcv.analyze_NIR_intensity(img, args.image, mask, 256, device, args.debug, args.outdir + '/' + img_name)
#print(args.outdir+'/'+img_name)
#print(args.debug)
#al final si salio se agrego lo qyue esta debug= and filename=
##################################################### debug me marca True por ello puse pritn de mas
#device, hist_header, hist_data, h_norm = pcv.analyze_NIR_intensity(img, rgb, mask, 256, device, debug='print', filename=False)
device, hist_header, hist_data, h_norm = pcv.analyze_NIR_intensity(
img,
rgb,
mask,
256,
device,
debug=args.debug,
filename=args.outdir + '/' + img_name)
# Perform shape analysis
device, shape_header, shape_data, ori_img = pcv.analyze_object(
rgb,
args.image,
o,
m,
device,
debug=args.debug,
filename=args.outdir + '/' + img_name)
# Print the results to STDOUT
pcv.print_results(args.image, hist_header, hist_data)
pcv.print_results(args.image, shape_header, shape_data)
cv2.waitKey()
cv2.destroyAllWdindows()
def main():
# Get options
args = options()
# Read image
img, path, filename = pcv.readimage(args.image)
brass_mask = 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, 49, 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, 150, 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)
# Mask pesky brass piece
device, brass_mask1 = pcv.rgb2gray_hsv(brass_mask, 'v', device, args.debug)
device, brass_thresh = pcv.binary_threshold(brass_mask1, 0, 255, 'light',
device, args.debug)
device, brass_inv = pcv.invert(brass_thresh, device, args.debug)
device, brass_masked = pcv.apply_mask(masked, brass_inv, 'white', device,
args.debug)
# Further mask soil and car
device, masked_a = pcv.rgb2gray_lab(brass_masked, 'a', device, args.debug)
device, soil_car = pcv.binary_threshold(masked_a, 128, 255, 'dark', device,
args.debug)
device, soil_masked = pcv.apply_mask(brass_masked, soil_car, 'white',
device, args.debug)
# Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
device, soil_a = pcv.rgb2gray_lab(soil_masked, 'a', device, args.debug)
device, soil_b = pcv.rgb2gray_lab(soil_masked, 'b', device, args.debug)
# Threshold the green-magenta and blue images
device, soila_thresh = pcv.binary_threshold(soil_a, 118, 255, 'dark',
device, args.debug)
device, soilb_thresh = pcv.binary_threshold(soil_b, 155, 255, 'light',
device, args.debug)
# Join the thresholded saturation and blue-yellow images (OR)
device, soil_ab = pcv.logical_or(soila_thresh, soilb_thresh, device,
args.debug)
device, soil_ab_cnt = pcv.logical_or(soila_thresh, soilb_thresh, device,
args.debug)
# Fill small objects
device, soil_fill = pcv.fill(soil_ab, soil_ab_cnt, 200, device, args.debug)
# Median Filter
device, soil_mblur = pcv.median_blur(soil_fill, 5, device, args.debug)
device, soil_cnt = pcv.median_blur(soil_fill, 5, device, args.debug)
# Apply mask (for vis images, mask_color=white)
device, masked2 = pcv.apply_mask(soil_masked, soil_cnt, 'white', device,
args.debug)
# Identify objects
device, id_objects, obj_hierarchy = pcv.find_objects(
masked2, soil_cnt, device, args.debug)
# Define ROI
device, roi1, roi_hierarchy = pcv.define_roi(img, 'circle', device, None,
'default', args.debug, True,
0, 0, -50, -50)
# 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 ################
# output mask
device, maskpath, mask_images = pcv.output_mask(device, img, mask,
filename, args.outdir,
True, args.debug)
# 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)
# Determine color properties: Histograms, Color Slices and Pseudocolored Images,
# output color analyzed images (optional)
device, color_header, color_data, color_img = pcv.analyze_color(
img, args.image, mask, 256, device, args.debug, None, 'v', 'img', 300)
result = open(args.result, "a")
result.write('\t'.join(map(str, shape_header)))
result.write("\n")
result.write('\t'.join(map(str, shape_data)))
result.write("\n")
for row in mask_images:
result.write('\t'.join(map(str, row)))
result.write("\n")
result.write('\t'.join(map(str, color_header)))
result.write("\n")
result.write('\t'.join(map(str, color_data)))
result.write("\n")
result.close()
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():
# Initialize device
device = 0
# Parse command-line options
args = options()
# Read image
img, path, filename = pcv.readimage(filename=args.image, debug=args.debug)
# Convert RGB to LAB and extract the Green-Magenta channel
device, green_channel = pcv.rgb2gray_lab(img=img,
channel="a",
device=device,
debug=args.debug)
# Invert the Green-Magenta image because the plant is dark green
device, green_inv = pcv.invert(img=green_channel,
device=device,
debug=args.debug)
# Threshold the inverted Green-Magenta image to mostly isolate green pixels
device, green_thresh = pcv.binary_threshold(img=green_inv,
threshold=134,
maxValue=255,
object_type="light",
device=device,
debug=args.debug)
# Extract core plant region from the image to preserve delicate plant features during filtering
device += 1
plant_region = green_thresh[100:2000, 250:2250]
if args.debug is not None:
pcv.print_image(filename=str(device) + "_extract_plant_region.png",
img=plant_region)
# Use a Gaussian blur to disrupt the strong edge features in the cabinet
device, blur_gaussian = pcv.gaussian_blur(device=device,
img=green_thresh,
ksize=(7, 7),
sigmax=0,
sigmay=None,
debug=args.debug)
# Threshold the blurred image to remove features that were blurred
device, blur_thresholded = pcv.binary_threshold(img=blur_gaussian,
threshold=250,
maxValue=255,
object_type="light",
device=device,
debug=args.debug)
# Add the plant region back in to the filtered image
device += 1
blur_thresholded[100:2000, 250:2250] = plant_region
if args.debug is not None:
pcv.print_image(filename=str(device) + "_replace_plant_region.png",
img=blur_thresholded)
# Use a median blur to breakup the horizontal and vertical lines caused by shadows from the track edges
device, med_blur = pcv.median_blur(img=blur_thresholded,
ksize=5,
device=device,
debug=args.debug)
# Fill in small contours
device, green_fill_50 = pcv.fill(img=np.copy(med_blur),
mask=np.copy(med_blur),
size=50,
device=device,
debug=args.debug)
# Define an ROI for the brass stopper
device, stopper_roi, stopper_hierarchy = pcv.define_roi(
img=img,
shape="rectangle",
device=device,
roi=None,
roi_input="default",
debug=args.debug,
adjust=True,
x_adj=1420,
y_adj=890,
w_adj=-920,
h_adj=-1040)
# Identify all remaining contours in the binary image
device, contours, hierarchy = pcv.find_objects(img=img,
mask=np.copy(green_fill_50),
device=device,
debug=args.debug)
# Remove contours completely contained within the stopper region of interest
device, remove_stopper_mask = remove_countors_roi(mask=green_fill_50,
contours=contours,
hierarchy=hierarchy,
roi=stopper_roi,
device=device,
debug=args.debug)
# Define an ROI for a screw hole
device, screw_roi, screw_hierarchy = pcv.define_roi(img=img,
shape="rectangle",
device=device,
roi=None,
roi_input="default",
debug=args.debug,
adjust=True,
x_adj=1870,
y_adj=1010,
w_adj=-485,
h_adj=-960)
# Remove contours completely contained within the screw region of interest
device, remove_screw_mask = remove_countors_roi(mask=remove_stopper_mask,
contours=contours,
hierarchy=hierarchy,
roi=screw_roi,
device=device,
debug=args.debug)
# Identify objects
device, contours, contour_hierarchy = pcv.find_objects(
img=img, mask=remove_screw_mask, device=device, debug=args.debug)
# Define ROI
device, roi, roi_hierarchy = pcv.define_roi(img=img,
shape="rectangle",
device=device,
roi=None,
roi_input="default",
debug=args.debug,
adjust=True,
x_adj=565,
y_adj=200,
w_adj=-490,
h_adj=-250)
# Decide which objects to keep
device, roi_contours, roi_contour_hierarchy, _, _ = pcv.roi_objects(
img=img,
roi_type="partial",
roi_contour=roi,
roi_hierarchy=roi_hierarchy,
object_contour=contours,
obj_hierarchy=contour_hierarchy,
device=device,
debug=args.debug)
# If there are no contours left we cannot measure anything
if len(roi_contours) > 0:
# Object combine kept objects
device, plant_contour, plant_mask = pcv.object_composition(
img=img,
contours=roi_contours,
hierarchy=roi_contour_hierarchy,
device=device,
debug=args.debug)
outfile = False
if args.writeimg:
outfile = args.outdir + "/" + filename
# Find shape properties, output shape image (optional)
device, shape_header, shape_data, shape_img = pcv.analyze_object(
img=img,
imgname=args.image,
obj=plant_contour,
mask=plant_mask,
device=device,
debug=args.debug,
filename=outfile)
# Determine color properties: Histograms, Color Slices and Pseudocolored Images,
# output color analyzed images (optional)
device, color_header, color_data, color_img = pcv.analyze_color(
img=img,
imgname=args.image,
mask=plant_mask,
bins=256,
device=device,
debug=args.debug,
hist_plot_type=None,
pseudo_channel="v",
pseudo_bkg="img",
resolution=300,
filename=outfile)
# Output shape and color data
result = open(args.result, "a")
result.write('\t'.join(map(str, shape_header)) + "\n")
result.write('\t'.join(map(str, shape_data)) + "\n")
for row in shape_img:
result.write('\t'.join(map(str, row)) + "\n")
result.write('\t'.join(map(str, color_header)) + "\n")
result.write('\t'.join(map(str, color_data)) + "\n")
for row in color_img:
result.write('\t'.join(map(str, row)) + "\n")
result.close()
# Find matching NIR image
device, nirpath = pcv.get_nir(path=path,
filename=filename,
device=device,
debug=args.debug)
nir_rgb, nir_path, nir_filename = pcv.readimage(nirpath)
nir_img = cv2.imread(nirpath, 0)
# Make mask glovelike in proportions via dilation
device, d_mask = pcv.dilate(plant_mask,
kernel=1,
i=0,
device=device,
debug=args.debug)
# Resize mask
prop2, prop1 = conv_ratio()
device, nmask = pcv.resize(img=d_mask,
resize_x=prop1,
resize_y=prop2,
device=device,
debug=args.debug)
# Convert the resized mask to a binary mask
device, bmask = pcv.binary_threshold(img=nmask,
threshold=0,
maxValue=255,
object_type="light",
device=device,
debug=args.debug)
device, crop_img = crop_sides_equally(mask=bmask,
nir=nir_img,
device=device,
debug=args.debug)
# position, and crop mask
device, newmask = pcv.crop_position_mask(img=nir_img,
mask=crop_img,
device=device,
x=0,
y=1,
v_pos="bottom",
h_pos="right",
debug=args.debug)
# Identify objects
device, nir_objects, nir_hierarchy = pcv.find_objects(img=nir_rgb,
mask=newmask,
device=device,
debug=args.debug)
# Object combine kept objects
device, nir_combined, nir_combinedmask = pcv.object_composition(
img=nir_rgb,
contours=nir_objects,
hierarchy=nir_hierarchy,
device=device,
debug=args.debug)
if args.writeimg:
outfile = args.outdir + "/" + nir_filename
# Analyze NIR signal data
device, nhist_header, nhist_data, nir_imgs = pcv.analyze_NIR_intensity(
img=nir_img,
rgbimg=nir_rgb,
mask=nir_combinedmask,
bins=256,
device=device,
histplot=False,
debug=args.debug,
filename=outfile)
# Analyze the shape of the plant contour from the NIR image
device, nshape_header, nshape_data, nir_shape = pcv.analyze_object(
img=nir_img,
imgname=nir_filename,
obj=nir_combined,
mask=nir_combinedmask,
device=device,
debug=args.debug,
filename=outfile)
# Write NIR data to co-results file
coresult = open(args.coresult, "a")
coresult.write('\t'.join(map(str, nhist_header)) + "\n")
coresult.write('\t'.join(map(str, nhist_data)) + "\n")
for row in nir_imgs:
coresult.write('\t'.join(map(str, row)) + "\n")
coresult.write('\t'.join(map(str, nshape_header)) + "\n")
coresult.write('\t'.join(map(str, nshape_data)) + "\n")
coresult.write('\t'.join(map(str, nir_shape)) + "\n")
coresult.close()
def main():
# Get options
args = options()
# Read image
img, path, filename = pcv.readimage(args.image)
brass_mask = 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, 49, 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, 150, 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, 100, 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)
# Mask pesky brass piece
device, brass_mask1 = pcv.rgb2gray_hsv(brass_mask, 'v', device, args.debug)
device, brass_thresh = pcv.binary_threshold(brass_mask1, 0, 255, 'light', device, args.debug)
device, brass_inv=pcv.invert(brass_thresh, device, args.debug)
device, brass_masked = pcv.apply_mask(masked, brass_inv, 'white', device, args.debug)
# Further mask soil and car
device, masked_a = pcv.rgb2gray_lab(brass_masked, 'a', device, args.debug)
device, soil_car1 = pcv.binary_threshold(masked_a, 128, 255, 'dark', device, args.debug)
device, soil_car2 = pcv.binary_threshold(masked_a, 128, 255, 'light', device, args.debug)
device, soil_car=pcv.logical_or(soil_car1, soil_car2,device, args.debug)
device, soil_masked = pcv.apply_mask(brass_masked, soil_car, 'white', device, args.debug)
# Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
device, soil_a = pcv.rgb2gray_lab(soil_masked, 'a', device, args.debug)
device, soil_b = pcv.rgb2gray_lab(soil_masked, 'b', device, args.debug)
# Threshold the green-magenta and blue images
device, soila_thresh = pcv.binary_threshold(soil_a, 124, 255, 'dark', device, args.debug)
device, soilb_thresh = pcv.binary_threshold(soil_b, 148, 255, 'light', device, args.debug)
# Join the thresholded saturation and blue-yellow images (OR)
device, soil_ab = pcv.logical_or(soila_thresh, soilb_thresh, device, args.debug)
device, soil_ab_cnt = pcv.logical_or(soila_thresh, soilb_thresh, device, args.debug)
# Fill small objects
device, soil_cnt = pcv.fill(soil_ab, soil_ab_cnt, 200, device, args.debug)
# Median Filter
#device, soil_mblur = pcv.median_blur(soil_fill, 5, device, args.debug)
#device, soil_cnt = pcv.median_blur(soil_fill, 5, device, args.debug)
# Apply mask (for vis images, mask_color=white)
device, masked2 = pcv.apply_mask(soil_masked, soil_cnt, 'white', device, args.debug)
# Identify objects
device, id_objects,obj_hierarchy = pcv.find_objects(masked2, soil_cnt, device, args.debug)
# Define ROI
device, roi1, roi_hierarchy= pcv.define_roi(img,'rectangle', device, None, 'default', args.debug,True, 600,450,-600,-350)
# 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)
# 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','img',300,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)
def main():
# Get options
args = options()
# Read image
img, path, filename = pcv.readimage(args.image)
brass_mask = 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, 49, 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, 150, 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, 100, 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)
# Mask pesky brass piece
device, brass_mask1 = pcv.rgb2gray_hsv(brass_mask, 'v', device, args.debug)
device, brass_thresh = pcv.binary_threshold(brass_mask1, 0, 255, 'light',
device, args.debug)
device, brass_inv = pcv.invert(brass_thresh, device, args.debug)
device, brass_masked = pcv.apply_mask(masked, brass_inv, 'white', device,
args.debug)
# Further mask soil and car
device, masked_a = pcv.rgb2gray_lab(brass_masked, 'a', device, args.debug)
device, soil_car1 = pcv.binary_threshold(masked_a, 128, 255, 'dark',
device, args.debug)
device, soil_car2 = pcv.binary_threshold(masked_a, 128, 255, 'light',
device, args.debug)
device, soil_car = pcv.logical_or(soil_car1, soil_car2, device, args.debug)
device, soil_masked = pcv.apply_mask(brass_masked, soil_car, 'white',
device, args.debug)
# Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
device, soil_a = pcv.rgb2gray_lab(soil_masked, 'a', device, args.debug)
device, soil_b = pcv.rgb2gray_lab(soil_masked, 'b', device, args.debug)
# Threshold the green-magenta and blue images
device, soila_thresh = pcv.binary_threshold(soil_a, 124, 255, 'dark',
device, args.debug)
device, soilb_thresh = pcv.binary_threshold(soil_b, 148, 255, 'light',
device, args.debug)
# Join the thresholded saturation and blue-yellow images (OR)
device, soil_ab = pcv.logical_or(soila_thresh, soilb_thresh, device,
args.debug)
device, soil_ab_cnt = pcv.logical_or(soila_thresh, soilb_thresh, device,
args.debug)
# Fill small objects
device, soil_cnt = pcv.fill(soil_ab, soil_ab_cnt, 150, device, args.debug)
# Median Filter
#device, soil_mblur = pcv.median_blur(soil_fill, 5, device, args.debug)
#device, soil_cnt = pcv.median_blur(soil_fill, 5, device, args.debug)
# Apply mask (for vis images, mask_color=white)
device, masked2 = pcv.apply_mask(soil_masked, soil_cnt, 'white', device,
args.debug)
# Identify objects
device, id_objects, obj_hierarchy = pcv.find_objects(
masked2, soil_cnt, device, args.debug)
# Define ROI
device, roi1, roi_hierarchy = pcv.define_roi(img, 'rectangle', device,
None, 'default', args.debug,
True, 600, 450, -600, -350)
# 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)
############## VIS Analysis ################
outfile = False
if args.writeimg == True:
outfile = args.outdir + "/" + filename
# 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, outfile)
# Determine color properties: Histograms, Color Slices and Pseudocolored Images, output color analyzed images (optional)
device, color_header, color_data, color_img = pcv.analyze_color(
img, args.image, mask, 256, device, args.debug, None, 'v', 'img', 300,
outfile)
# Output shape and color data
result = open(args.result, "a")
result.write('\t'.join(map(str, shape_header)))
result.write("\n")
result.write('\t'.join(map(str, shape_data)))
result.write("\n")
for row in shape_img:
result.write('\t'.join(map(str, row)))
result.write("\n")
result.write('\t'.join(map(str, color_header)))
result.write("\n")
result.write('\t'.join(map(str, color_data)))
result.write("\n")
for row in color_img:
result.write('\t'.join(map(str, row)))
result.write("\n")
result.close()
############################# Use VIS image mask for NIR image#########################
# Find matching NIR image
device, nirpath = pcv.get_nir(path, filename, device, args.debug)
nir, path1, filename1 = pcv.readimage(nirpath)
nir2 = cv2.imread(nirpath, -1)
# Flip mask
device, f_mask = pcv.flip(mask, "horizontal", device, args.debug)
# Reize mask
device, nmask = pcv.resize(f_mask, 0.116148, 0.116148, device, args.debug)
# position, and crop mask
device, newmask = pcv.crop_position_mask(nir, nmask, device, 15, 5, "top",
"right", args.debug)
# Identify objects
device, nir_objects, nir_hierarchy = pcv.find_objects(
nir, newmask, device, args.debug)
# Object combine kept objects
device, nir_combined, nir_combinedmask = pcv.object_composition(
nir, nir_objects, nir_hierarchy, device, args.debug)
####################################### Analysis #############################################
outfile1 = False
if args.writeimg == True:
outfile1 = args.outdir + "/" + filename1
device, nhist_header, nhist_data, nir_imgs = pcv.analyze_NIR_intensity(
nir2, filename1, nir_combinedmask, 256, device, False, args.debug,
outfile1)
device, nshape_header, nshape_data, nir_shape = pcv.analyze_object(
nir2, filename1, nir_combined, nir_combinedmask, device, args.debug,
outfile1)
coresult = open(args.coresult, "a")
coresult.write('\t'.join(map(str, nhist_header)))
coresult.write("\n")
coresult.write('\t'.join(map(str, nhist_data)))
coresult.write("\n")
for row in nir_imgs:
coresult.write('\t'.join(map(str, row)))
coresult.write("\n")
coresult.write('\t'.join(map(str, nshape_header)))
coresult.write("\n")
coresult.write('\t'.join(map(str, nshape_data)))
coresult.write("\n")
coresult.write('\t'.join(map(str, nir_shape)))
coresult.write("\n")
coresult.close()