def average_all_img(directory, outdir):
allfiles = os.listdir(directory)
path = str(directory)
allpaths = []
for files in allfiles:
p = path + str(files)
allpaths.append(p)
img, path, filename = pcv.readimage(allpaths[0])
n = len(allpaths)
if len(np.shape(img)) == 3:
ix, iy, iz = np.shape(img)
arr = np.zeros((ix, iy, iz), np.float)
else:
ix, iy = np.shape(img)
arr = np.zeros((ix, iy), np.float)
# Build up average pixel intensities, casting each image as an array of floats
for i, paths in enumerate(allpaths):
img, path, filename = pcv.readimage(allpaths[i])
imarr = np.array(img, dtype=np.float)
arr = arr + imarr / n
# Round values in array and cast as 8-bit integer
arr = np.array(np.round(arr), dtype=np.uint8)
pcv.print_image(arr, (str(outdir)+"average_"+str(allfiles[0])))
def average_all_img(directory, outdir):
allfiles = os.listdir(directory)
path = str(directory)
allpaths = []
for files in allfiles:
p = path + str(files)
allpaths.append(p)
img, path, filename = pcv.readimage(allpaths[0])
n = len(allpaths)
if len(np.shape(img)) == 3:
ix, iy, iz = np.shape(img)
arr = np.zeros((ix, iy, iz), np.float)
else:
ix, iy = np.shape(img)
arr = np.zeros((ix, iy), np.float)
# Build up average pixel intensities, casting each image as an array of floats
for i, paths in enumerate(allpaths):
img, path, filename = pcv.readimage(allpaths[i])
imarr = np.array(img, dtype=np.float)
arr = arr + imarr / n
# Round values in array and cast as 8-bit integer
arr = np.array(np.round(arr), dtype=np.uint8)
pcv.print_image(arr, (str(outdir) + "average_" + str(allfiles[0])))
def get_fluor(imgfns, pn):
Fo_fn, Fm_fn, FsLss_fn, FmpLss_fn = imgfns
Fo = pcv.readimage(os.path.join(pn,Fo_fn))[0][:,:,0]
Fm = pcv.readimage(os.path.join(pn,Fm_fn))[0][:,:,0]
FsLss = pcv.readimage(os.path.join(pn,FsLss_fn))[0][:,:,0]
FmpLss = pcv.readimage(os.path.join(pn,FmpLss_fn))[0][:,:,0]
return(Fo, Fm, FsLss, FmpLss)
def main(path, imagename):
args = {'names': 'names.txt', 'outdir': './output-images'}
#Read image
img1, path, filename = pcv.readimage(path + imagename, "native")
#pcv.params.debug=args['debug']
#img1 = pcv.white_balance(img,roi=(400,800,200,200))
#img1 = cv2.resize(img1,(4000,2000))
shift1 = pcv.shift_img(img1, 10, 'top')
img1 = shift1
a = pcv.rgb2gray_lab(img1, 'a')
img_binary = pcv.threshold.binary(a, 120, 255, 'dark')
fill_image = pcv.fill(img_binary, 10)
dilated = pcv.dilate(fill_image, 1, 1)
id_objects, obj_hierarchy = pcv.find_objects(img1, dilated)
roi_contour, roi_hierarchy = pcv.roi.rectangle(4000, 2000, -2000, -4000,
img1)
#print(roi_contour)
roi_objects, roi_obj_hierarchy, kept_mask, obj_area = pcv.roi_objects(
img1, 'partial', roi_contour, roi_hierarchy, id_objects, obj_hierarchy)
clusters_i, contours, hierarchies = pcv.cluster_contours(
img1, roi_objects, roi_obj_hierarchy, 1, 4)
'''
pcv.params.debug = "print"'''
out = args['outdir']
names = args['names']
output_path = pcv.cluster_contour_splitimg(img1,
clusters_i,
contours,
hierarchies,
out,
file=filename,
filenames=names)
def main():
# Get options
args = options()
debug = args.debug
# Read image
img, path, filename = pcv.readimage(args.image)
# Pipeline step
device = 0
device, corrected_img = pcv.white_balance(device, img, debug,
(500, 1000, 500, 500))
img = corrected_img
device, img_gray_sat = pcv.rgb2gray_lab(img, 'a', device, debug)
device, img_binary = pcv.binary_threshold(img_gray_sat, 120, 255, 'dark',
device, debug)
mask = np.copy(img_binary)
device, fill_image = pcv.fill(img_binary, mask, 300, device, debug)
device, id_objects, obj_hierarchy = pcv.find_objects(
img, fill_image, device, debug)
device, roi, roi_hierarchy = pcv.define_roi(img, 'rectangle', device, None,
'default', debug, True, 1800,
1600, -1500, -500)
device, roi_objects, roi_obj_hierarchy, kept_mask, obj_area = pcv.roi_objects(
img, 'partial', roi, roi_hierarchy, id_objects, obj_hierarchy, device,
debug)
device, obj, mask = pcv.object_composition(img, roi_objects,
roi_obj_hierarchy, device,
debug)
outfile = os.path.join(args.outdir, filename)
device, color_header, color_data, color_img = pcv.analyze_color(
img, img, mask, 256, device, debug, None, 'v', 'img', 300, outfile)
device, shape_header, shape_data, shape_img = pcv.analyze_object(
img, "img", obj, mask, device, debug, outfile)
shapepath = outfile[:-4] + '_shapes.jpg'
shapepic = cv2.imread(shapepath)
plantsize = "The plant is " + str(np.sum(mask)) + " pixels large"
cv2.putText(shapepic, plantsize, (500, 500), cv2.FONT_HERSHEY_SIMPLEX, 5,
(0, 255, 0), 10)
pcv.print_image(shapepic, outfile[:-4] + '-out_shapes.jpg')
def main():
args = options()
h = np.load(args.matrix)
srcIm, path, filename = pcv.readimage(args.image, 'rgb')
height, width, channels = srcIm.shape
dstIm = cv2.warpPerspective(srcIm, h, (width, height))
destination = args.outdir + '/' + filename
cv2.imwrite(destination, dstIm)
def optical_xray_images(directory, filename):
# Read image
in_full_path = os.path.join(directory, filename)
img, path, filename = pcv.readimage(in_full_path, mode="rgb")
img_thermal = img.copy()
# record origial gray image
optical_org, pos = optical_image_org(img_thermal)
optical_org = smooth(optical_org, pos)
outfile = 'Gray_org_' + filename
out_full_path = os.path.join(directory, outfile)
cv2.imwrite(out_full_path, optical_org)
return
def main():
#Menangkap gambar IP Cam dengan opencv
##Ngosek, koding e wis ono tapi carane ngonek ning gcloud rung reti wkwk
#Mengambil gambar yang sudah didapatkan dari opencv untuk diproses di plantcv
path = 'Image test\capture (1).jpg'
gmbTumbuhanRaw, path, filename = pcv.readimage(path, mode='native')
#benarkan gambar yang miring
koreksiRot = pcv.rotate(gmbTumbuhanRaw, 2, True)
gmbKoreksi = koreksiRot
pcv.print_image(gmbKoreksi, 'Image test\Hasil\gambar_koreksi.jpg')
#Mengatur white balance dari gambar
#usahakan gambar rata (tanpa bayangan dari manapun!)!
#GANTI nilai dari region of intrest (roi) berdasarkan ukuran gambar!!
koreksiWhiteBal = pcv.white_balance(gmbTumbuhanRaw,
roi=(2, 100, 1104, 1200))
pcv.print_image(koreksiWhiteBal, 'Image test\Hasil\koreksi_white_bal.jpg')
#mengubah kontras gambar agar berbeda dengan warna background
#tips: latar jangan sama hijaunya
kontrasBG = pcv.rgb2gray_lab(koreksiWhiteBal, channel='a')
pcv.print_image(kontrasBG, 'Image test\Hasil\koreksi_kontras.jpg')
#binary threshol gambar
#sesuaikan thresholdnya
binthres = pcv.threshold.binary(gray_img=kontrasBG,
threshold=115,
max_value=255,
object_type='dark')
#hilangkan noise dengan fill noise
resiksitik = pcv.fill(binthres, size=10)
pcv.print_image(resiksitik, 'Image test\Hasil\\noiseFill.jpg')
#haluskan dengan dilate
dilasi = pcv.dilate(resiksitik, ksize=12, i=1)
#ambil objek dan set besar roi
id_objek, hirarki_objek = pcv.find_objects(gmbTumbuhanRaw, mask=dilasi)
roi_contour, roi_hierarchy = pcv.roi.rectangle(img=gmbKoreksi,
x=20,
y=96,
h=1100,
w=680)
#keluarkan gambar (untuk debug aja sih)
roicontour = cv2.drawContours(gmbKoreksi, roi_contour, -1, (0, 0, 255), 3)
pcv.print_image(roicontour, 'Image test\Hasil\\roicontour.jpg')
"""
def read_true_positive(true_positive_file):
class args:
#image = "C:\\Users\\RensD\\OneDrive\\studie\\Master\\The_big_project\\top_perspective\\0214_2018-03-07 08.55 - 26_true_positive.png"
image = true_positive_file
outdir = "C:\\Users\\RensD\\OneDrive\\studie\\Master\\The_big_project\\top_perspective\\output"
debug = "None"
result = "results.txt"
# Get options
pcv.params.debug = args.debug #set debug mode
pcv.params.debug_outdir = args.outdir #set output directory
# Read image (readimage mode defaults to native but if image is RGBA then specify mode='rgb')
# Inputs:
# filename - Image file to be read in
# mode - Return mode of image; either 'native' (default), 'rgb', 'gray', or 'csv'
img, path, filename = pcv.readimage(filename=args.image, mode='rgb')
s = pcv.rgb2gray_hsv(rgb_img=img, channel='s')
mask, masked_image = pcv.threshold.custom_range(rgb_img=s,
lower_thresh=[10],
upper_thresh=[255],
channel='gray')
masked = pcv.apply_mask(rgb_img=img, mask=mask, mask_color='white')
#new_im = Image.fromarray(mask)
#name = "positive_test.png"
#Recognizing objects
id_objects, obj_hierarchy = pcv.find_objects(masked, mask)
roi1, roi_hierarchy = pcv.roi.rectangle(img=masked,
x=0,
y=0,
h=960,
w=1280) # Currently hardcoded
with HiddenPrints():
roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(
img=img,
roi_contour=roi1,
roi_hierarchy=roi_hierarchy,
object_contour=id_objects,
obj_hierarchy=obj_hierarchy,
roi_type=roi_type)
obj, mask = pcv.object_composition(img=img,
contours=roi_objects,
hierarchy=hierarchy3)
#new_im.save(name)
return (mask)
def plot_hotspots(directory, filename):
# Read image
in_full_path = os.path.join(directory, filename)
outfile = 'Hotspot' + filename
out_full_path = os.path.join(directory, outfile)
img, path, filename = pcv.readimage(in_full_path, mode="rgb")
# Convert RGB to HSV and extract the saturation channel
s = pcv.rgb2gray_hsv(rgb_img=img, channel='s')
# Threshold the saturation image
s_thresh = pcv.threshold.binary(gray_img=s,
threshold=85,
max_value=255,
object_type='light')
# Median Blur
s_mblur = pcv.median_blur(gray_img=s_thresh, ksize=5)
edge = cv2.Canny(s_mblur, 60, 180)
fig, ax = plt.subplots(1, figsize=(12, 8))
plt.imshow(edge, cmap='Greys')
contours, hierarchy = cv2.findContours(edge.copy(), cv2.RETR_TREE,
cv2.CHAIN_APPROX_NONE)[-2:]
centroids = []
contours = sorted(contours, key=cv2.contourArea, reverse=True)
for i, cnt in enumerate(contours):
if (cv2.contourArea(cnt) > 10):
moment = cv2.moments(contours[i])
Cx = int(moment["m10"] / moment["m00"])
Cy = int(moment["m01"] / moment["m00"])
center = (Cx, Cy)
centroids.append((contours, center, moment["m00"], 0))
cv2.circle(img, (Cx, Cy), 5, (255, 255, 255), -1)
coordinate = '(' + str(Cx) + ',' + str(Cy) + ')'
cv2.putText(img, coordinate, (Cx, Cy), cv2.FONT_HERSHEY_SIMPLEX,
0.5, RED, 1, cv2.LINE_AA)
print(cv2.contourArea(cnt), Cx, Cy)
cv2.imwrite(out_full_path, img)
#cv2.imshow('canvasOutput', img);
#cv2.waitKey(0)
return
def main():
# Get options
args = options()
pcv.params.debug = args.debug # set debug mode
pcv.params.debug_outdir = args.outdir # set output directory
# Read image
img, path, filename = pcv.readimage(filename=args.image)
# Convert RGB to HSV and extract the saturation channel
h = pcv.rgb2gray_hsv(rgb_img=img, channel='h')
# Threshold the saturation image
h_thresh = pcv.threshold.binary(gray_img=h,
threshold=85,
max_value=255,
object_type='dark')
# Median Blur
h_mblur = pcv.median_blur(gray_img=h_thresh, ksize=20)
def main():
# Set variables
args = options()
pcv.params.debug = args.debug
# Read and rotate image
img, path, filename = pcv.readimage(filename=args.image)
img = pcv.rotate(img, -90, False)
# Create mask from LAB b channel
l = pcv.rgb2gray_lab(rgb_img=img, channel='b')
l_thresh = pcv.threshold.binary(gray_img=l,
threshold=115,
max_value=255,
object_type='dark')
l_mblur = pcv.median_blur(gray_img=l_thresh, ksize=5)
# Apply mask to image
masked = pcv.apply_mask(img=img, mask=l_mblur, mask_color='white')
ab_fill = pcv.fill(bin_img=l_mblur, size=50)
# Extract plant object from image
id_objects, obj_hierarchy = pcv.find_objects(img=img, mask=ab_fill)
roi1, roi_hierarchy = pcv.roi.rectangle(img=masked,
x=150,
y=270,
h=100,
w=100)
roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(
img=img,
roi_contour=roi1,
roi_hierarchy=roi_hierarchy,
object_contour=id_objects,
obj_hierarchy=obj_hierarchy,
roi_type='partial')
obj, mask = pcv.object_composition(img=img,
contours=roi_objects,
hierarchy=hierarchy3)
############### Analysis ################
# Analyze shape properties
analysis_image = pcv.analyze_object(img=img, obj=obj, mask=mask)
boundary_image2 = pcv.analyze_bound_horizontal(img=img,
obj=obj,
mask=mask,
line_position=370)
# Analyze colour properties
color_histogram = pcv.analyze_color(rgb_img=img,
mask=kept_mask,
hist_plot_type='all')
# Analyze shape independent of size
top_x, bottom_x, center_v_x = pcv.x_axis_pseudolandmarks(img=img,
obj=obj,
mask=mask)
top_y, bottom_y, center_v_y = pcv.y_axis_pseudolandmarks(img=img,
obj=obj,
mask=mask)
# Print results
pcv.print_results(filename='{}'.format(args.result))
pcv.print_image(img=color_histogram,
filename='{}_color_hist.jpg'.format(args.outdir))
pcv.print_image(img=kept_mask, filename='{}_mask.jpg'.format(args.outdir))
# Get options args = options() # Set debug to the global parameter pcv.params.debug = args.debug # In[3]: # Read image # Inputs: # filename - Image file to be read in # mode - How to read in the image; either 'native' (default), 'rgb', 'gray', or 'csv' img, path, filename = pcv.readimage(filename=args.image) # In[4]: # Convert RGB to HSV and extract the saturation channel # Inputs: # rgb_image - RGB image data # channel - Split by 'h' (hue), 's' (saturation), or 'v' (value) channel s = pcv.rgb2gray_hsv(rgb_img=img, channel='s') pcv.print_image(img=s, filename="upload/output_imgs/R2H.jpg") # In[5]: # Take a binary threshold to separate plant from background. # Threshold can be on either light or dark objects in the image.
import cv2
class options:
def __init__(self):
self.debug = "plot"
self.writeimg = False
args = options()
pcv.params.debug = args.debug
# Read in the image
nir_filename = ''
img, path, filename = pcv.readimage(nir_filename)
#----------------------------------------------------------------------------------------------------------------#
# This function takes an NIR image as input and returns two NDVI representations of it. One is a grayscale
# representation of the NDVI values, normalized from 0-255. The other returned image is the result of a specific
# LUT being applied to the grayscale. Ideally, objects coloured violet are possible plant material, while green,
# yellow, orange, and red objects represent plant material.
#---------------------------------------------------------------------------------------------------------------#
def NDVI_lin(image):
# Set up the colour mapped, and grayscale NDVI images
NDVI_img = np.zeros(shape=[image.shape[0], image.shape[1], 3],
dtype=np.uint8)
grayscale = np.zeros(shape=[image.shape[0], image.shape[1]],
dtype=np.uint8)
def image_avg(fundf):
# dn't understand why import suddently needs to be inside function
# import cv2 as cv2
# import numpy as np
# import pandas as pd
# import os
# from matplotlib import pyplot as plt
# from skimage import filters
# from skimage import morphology
# from skimage import segmentation
# Predefine some variables
global c, h, roi_c, roi_h, ilegend, mask_Fm, fn_Fm
# Get the filename for minimum and maximum fluoresence
fn_min = fundf.query('frame == "Fo" or frame == "Fp"').filename.values[0]
fn_max = fundf.query('frame == "Fm" or frame == "Fmp"').filename.values[0]
# Get the parameter name that links these 2 frames
param_name = fundf['parameter'].iloc[0]
# Create a new output filename that combines existing filename with parameter
outfn = os.path.splitext(os.path.basename(fn_max))[0]
outfn_split = outfn.split('-')
# outfn_split[2] = datetime.strptime(fundf.jobdate.values[0],'%Y-%m-%d').strftime('%Y%m%d')
outfn_split[2] = fundf.jobdate.dt.strftime('%Y%m%d').values[0]
basefn = "-".join(outfn_split[0:-1])
outfn_split[-1] = param_name
outfn = "-".join(outfn_split)
print(outfn)
# Make some directories based on sample id to keep output organized
plantbarcode = outfn_split[0]
fmaxdir = os.path.join(fluordir, plantbarcode)
os.makedirs(fmaxdir, exist_ok=True)
# If debug mode is 'print', create a specific debug dir for each pim file
if pcv.params.debug == 'print':
debug_outdir = os.path.join(debugdir, outfn)
os.makedirs(debug_outdir, exist_ok=True)
pcv.params.debug_outdir = debug_outdir
# read images and create mask from max fluorescence
# read image as is. only gray values in PSII images
imgmin, _, _ = pcv.readimage(fn_min)
img, _, _ = pcv.readimage(fn_max)
fdark = np.zeros_like(img)
out_flt = fdark.astype('float32') # <- needs to be float32 for imwrite
if param_name == 'FvFm':
# save max fluorescence filename
fn_Fm = fn_max
# create mask
# #create black mask over lower half of image to threshold upper plant only
# img_half, _, _, _ = pcv.rectangle_mask(img, p1=(0,321), p2=(480,640))
# # mask1 = pcv.threshold.otsu(img_half,255)
# algaethresh = filters.threshold_otsu(image=img_half)
# mask0 = pcv.threshold.binary(img_half, algaethresh, 255, 'light')
# # create black mask over upper half of image to threshold lower plant only
# img_half, _, _, _ = pcv.rectangle_mask(img, p1=(0, 0), p2=(480, 319), color='black')
# # mask0 = pcv.threshold.otsu(img_half,255)
# algaethresh = filters.threshold_otsu(image=img_half)
# mask1 = pcv.threshold.binary(img_half, algaethresh, 255, 'light')
# mask = pcv.logical_xor(mask0, mask1)
# # mask = pcv.dilate(mask, 2, 1)
# mask = pcv.fill(mask, 350)
# mask = pcv.erode(mask, 2, 2)
# mask = pcv.erode(mask, 2, 1)
# mask = pcv.fill(mask, 100)
# otsuT = filters.threshold_otsu(img)
# # sigma=(k-1)/6. This is because the length for 99 percentile of gaussian pdf is 6sigma.
# k = int(2 * np.ceil(3 * otsuT) + 1)
# gb = pcv.gaussian_blur(img, ksize = (k,k), sigma_x = otsuT)
# mask = img >= gb + 10
# pcv.plot_image(mask)
# local_otsu = filters.rank.otsu(img, pcv.get_kernel((9,9), 'rectangle'))#morphology.disk(2))
# thresh_image = img >= local_otsu
#_------>
elevation_map = filters.sobel(img)
# pcv.plot_image(elevation_map)
thresh = filters.threshold_otsu(image=img)
# thresh = 50
markers = np.zeros_like(img, dtype='uint8')
markers[img > thresh + 8] = 2
markers[img <= thresh + 8] = 1
# pcv.plot_image(markers,cmap=plt.cm.nipy_spectral)
mask = segmentation.watershed(elevation_map, markers)
mask = mask.astype(np.uint8)
# pcv.plot_image(mask)
mask[mask == 1] = 0
mask[mask == 2] = 1
# pcv.plot_image(mask, cmap=plt.cm.nipy_spectral)
# mask = pcv.erode(mask, 2, 1)
mask = pcv.fill(mask, 100)
# pcv.plot_image(mask, cmap=plt.cm.nipy_spectral)
# <-----------
roi_c, roi_h = pcv.roi.multi(img,
coord=(250, 200),
radius=70,
spacing=(0, 220),
ncols=1,
nrows=2)
if len(np.unique(mask)) == 1:
c = []
YII = mask
NPQ = mask
newmask = mask
else:
# find objects and setup roi
c, h = pcv.find_objects(img, mask)
# setup individual roi plant masks
newmask = np.zeros_like(mask)
# compute fv/fm and save to file
YII, hist_fvfm = pcv.photosynthesis.analyze_fvfm(fdark=fdark,
fmin=imgmin,
fmax=img,
mask=mask,
bins=128)
# YII = np.divide(Fv,
# img,
# out=out_flt.copy(),
# where=np.logical_and(mask > 0, img > 0))
# NPQ is 0
NPQ = np.zeros_like(YII)
# cv2.imwrite(os.path.join(fmaxdir, outfn + '-fvfm.tif'), YII)
# print Fm - will need this later
# cv2.imwrite(os.path.join(fmaxdir, outfn + '-fmax.tif'), img)
# NPQ will always be an array of 0s
else: # compute YII and NPQ if parameter is other than FvFm
newmask = mask_Fm
# use cv2 to read image becase pcv.readimage will save as input_image.png overwriting img
# newmask = cv2.imread(os.path.join(maskdir, basefn + '-FvFm-mask.png'),-1)
if len(np.unique(newmask)) == 1:
YII = np.zeros_like(newmask)
NPQ = np.zeros_like(newmask)
else:
# compute YII
YII, hist_yii = pcv.photosynthesis.analyze_fvfm(fdark,
fmin=imgmin,
fmax=img,
mask=newmask,
bins=128)
# make sure to initialize with out=. using where= provides random values at False pixels. you will get a strange result. newmask comes from Fm instead of Fm' so they can be different
#newmask<0, img>0 = FALSE: not part of plant but fluorescence detected.
#newmask>0, img<=0 = FALSE: part of plant in Fm but no fluorescence detected <- this is likely the culprit because pcv.apply_mask doesn't always solve issue.
# YII = np.divide(Fvp,
# img,
# out=out_flt.copy(),
# where=np.logical_and(newmask > 0, img > 0))
# compute NPQ
# Fm = cv2.imread(os.path.join(fmaxdir, basefn + '-FvFm-fmax.tif'), -1)
Fm = cv2.imread(fn_Fm, -1)
NPQ = np.divide(Fm,
img,
out=out_flt.copy(),
where=np.logical_and(newmask > 0, img > 0))
NPQ = np.subtract(NPQ,
1,
out=out_flt.copy(),
where=np.logical_and(NPQ >= 1, newmask > 0))
# cv2.imwrite(os.path.join(fmaxdir, outfn + '-yii.tif'), YII)
# cv2.imwrite(os.path.join(fmaxdir, outfn + '-npq.tif'), NPQ)
# end if-else Fv/Fm
# Make as many copies of incoming dataframe as there are ROIs so all results can be saved
outdf = fundf.copy()
for i in range(0, len(roi_c) - 1):
outdf = outdf.append(fundf)
outdf.frameid = outdf.frameid.astype('uint8')
# Initialize lists to store variables for each ROI and iterate through each plant
frame_avg = []
yii_avg = []
yii_std = []
npq_avg = []
npq_std = []
plantarea = []
ithroi = []
inbounds = []
if len(c) == 0:
for i, rc in enumerate(roi_c):
# each variable needs to be stored 2 x #roi
frame_avg.append(np.nan)
frame_avg.append(np.nan)
yii_avg.append(np.nan)
yii_avg.append(np.nan)
yii_std.append(np.nan)
yii_std.append(np.nan)
npq_avg.append(np.nan)
npq_avg.append(np.nan)
npq_std.append(np.nan)
npq_std.append(np.nan)
inbounds.append(False)
inbounds.append(False)
plantarea.append(0)
plantarea.append(0)
# Store iteration Number even if there are no objects in image
ithroi.append(int(i))
ithroi.append(int(i)) # append twice so each image has a value.
else:
i = 1
rc = roi_c[i]
for i, rc in enumerate(roi_c):
# Store iteration Number
ithroi.append(int(i))
ithroi.append(int(i)) # append twice so each image has a value.
# extract ith hierarchy
rh = roi_h[i]
# Filter objects based on being in the defined ROI
roi_obj, hierarchy_obj, submask, obj_area = pcv.roi_objects(
img,
roi_contour=rc,
roi_hierarchy=rh,
object_contour=c,
obj_hierarchy=h,
roi_type='partial')
if obj_area == 0:
print('!!! No plant detected in ROI ', str(i))
frame_avg.append(np.nan)
frame_avg.append(np.nan)
yii_avg.append(np.nan)
yii_avg.append(np.nan)
yii_std.append(np.nan)
yii_std.append(np.nan)
npq_avg.append(np.nan)
npq_avg.append(np.nan)
npq_std.append(np.nan)
npq_std.append(np.nan)
inbounds.append(False)
inbounds.append(False)
plantarea.append(0)
plantarea.append(0)
else:
# Combine multiple plant objects within an roi together
plant_contour, plant_mask = pcv.object_composition(
img=img, contours=roi_obj, hierarchy=hierarchy_obj)
#combine plant masks after roi filter
if param_name == 'FvFm':
newmask = pcv.image_add(newmask, plant_mask)
# Calc mean and std dev of fluoresence, YII, and NPQ and save to list
frame_avg.append(cppc.utils.mean(imgmin, plant_mask))
frame_avg.append(cppc.utils.mean(img, plant_mask))
# need double because there are two images per loop
yii_avg.append(cppc.utils.mean(YII, plant_mask))
yii_avg.append(cppc.utils.mean(YII, plant_mask))
yii_std.append(cppc.utils.std(YII, plant_mask))
yii_std.append(cppc.utils.std(YII, plant_mask))
npq_avg.append(cppc.utils.mean(NPQ, plant_mask))
npq_avg.append(cppc.utils.mean(NPQ, plant_mask))
npq_std.append(cppc.utils.std(NPQ, plant_mask))
npq_std.append(cppc.utils.std(NPQ, plant_mask))
plantarea.append(obj_area * cppc.pixelresolution**2)
plantarea.append(obj_area * cppc.pixelresolution**2)
# Check if plant is compeltely within the frame of the image
inbounds.append(pcv.within_frame(plant_mask))
inbounds.append(pcv.within_frame(plant_mask))
# Output a pseudocolor of NPQ and YII for each induction period for each image
imgdir = os.path.join(outdir, 'pseudocolor_images')
outfn_roi = outfn + '-roi' + str(i)
os.makedirs(imgdir, exist_ok=True)
npq_img = pcv.visualize.pseudocolor(NPQ,
obj=None,
mask=plant_mask,
cmap='inferno',
axes=False,
min_value=0,
max_value=2.5,
background='black',
obj_padding=0)
npq_img = cppc.viz.add_scalebar(
npq_img,
pixelresolution=cppc.pixelresolution,
barwidth=10,
barlabel='1 cm',
barlocation='lower left')
# If you change the output size and resolution you will need to adjust the timelapse video script
npq_img.set_size_inches(6, 6, forward=False)
npq_img.savefig(
os.path.join(imgdir, outfn_roi + '-NPQ.png'),
bbox_inches='tight',
dpi=100) #100 is default for matplotlib/plantcv
if ilegend == 1: #only need to print legend once
npq_img.savefig(os.path.join(imgdir, 'npq_legend.pdf'),
bbox_inches='tight')
npq_img.clf()
yii_img = pcv.visualize.pseudocolor(
YII,
obj=None,
mask=plant_mask,
cmap='gist_rainbow', #custom_colormaps.get_cmap(
# 'imagingwin')#
axes=False,
min_value=0,
max_value=1,
background='black',
obj_padding=0)
yii_img = cppc.viz.add_scalebar(
yii_img,
pixelresolution=cppc.pixelresolution,
barwidth=10,
barlabel='1 cm',
barlocation='lower left')
yii_img.set_size_inches(6, 6, forward=False)
yii_img.savefig(os.path.join(imgdir, outfn_roi + '-YII.png'),
bbox_inches='tight',
dpi=100)
if ilegend == 1: #print legend once and increment ilegend to stop in future iterations
yii_img.savefig(os.path.join(imgdir, 'yii_legend.pdf'),
bbox_inches='tight')
ilegend = ilegend + 1
yii_img.clf()
# end try-except-else
# end roi loop
# end if there are objects from roi filter
# save mask of all plants to file after roi filter
if param_name == 'FvFm':
mask_Fm = newmask.copy()
# pcv.print_image(newmask, os.path.join(maskdir, outfn + '-mask.png'))
# check YII values for uniqueness between all ROI. nonunique ROI suggests the plants grew into each other and can no longer be reliably separated in image processing.
# a single value isn't always robust. I think because there are small independent objects that fall in one roi but not the other that change the object within the roi slightly.
# also note, I originally designed this for trays of 2 pots. It will not detect if e.g. 2 out of 9 plants grow into each other
rounded_avg = [round(n, 3) for n in yii_avg]
rounded_std = [round(n, 3) for n in yii_std]
if len(roi_c) > 1:
isunique = not (rounded_avg.count(rounded_avg[0]) == len(yii_avg)
and rounded_std.count(rounded_std[0]) == len(yii_std))
else:
isunique = True
# save all values to outgoing dataframe
outdf['roi'] = ithroi
outdf['frame_avg'] = frame_avg
outdf['yii_avg'] = yii_avg
outdf['npq_avg'] = npq_avg
outdf['yii_std'] = yii_std
outdf['npq_std'] = npq_std
outdf['obj_in_frame'] = inbounds
outdf['unique_roi'] = isunique
return (outdf)
#!/usr/bin/env python
# coding: utf-8
# In[1]:
from plantcv import plantcv as pcv
# In[ ]:
# This command outputs all resulting images to the notebook.
pcv.params.debug = 'plot'
# In[6]:
# Importing the image. Including the path was necessary. Mode="native" by default.
img, path, img_filename = pcv.readimage(
filename="/users/jordanmanchengo/data/duckweed1.png")
# In[11]:
# Hue channel.
h = pcv.rgb2gray_hsv(rgb_img=img, channel='h')
# In[12]:
# Saturation channel.
s = pcv.rgb2gray_hsv(rgb_img=img, channel='s')
# In[13]:
# Value channel.
v = pcv.rgb2gray_hsv(rgb_img=img, channel='v')
def silhouette_top():
"First we draw the picture from the 3D data"
########################################################################################################################################################################
x = []
y = []
z = []
image_top = Image.new("RGB", (width, height), color='white')
draw = ImageDraw.Draw(image_top)
data_3d = open(args.image, "r")
orignal_file = args.image
for line in data_3d:
line = line.split(",")
y.append(int(line[0]))
x.append(int(line[1]))
z.append(int(line[2]))
i = 0
for point_x in x:
point_y = y[i]
draw.rectangle([point_x, point_y, point_x + 1, point_y + 1],
fill="black")
#rectange takes input [x0, y0, x1, y1]
i += 1
image_top.save("top_temp.png")
image_side = Image.new("RGB", (1280, 960), color='white')
draw = ImageDraw.Draw(image_side)
i = 0
for point_y in y:
point_z = z[i]
draw.rectangle([point_z, point_y, point_z + 1, point_y + 1],
fill="black")
#rectange takes input [x0, y0, x1, y1]
i += 1
image_side.save("side_temp.png")
########################################################################################################################################################################
args.image = "top_temp.png"
# Get options
pcv.params.debug = args.debug #set debug mode
pcv.params.debug_outdir = args.outdir #set output directory
pcv.params.debug = args.debug # set debug mode
pcv.params.debug_outdir = args.outdir # set output directory
# Read image
img, path, filename = pcv.readimage(filename=args.image)
v = pcv.rgb2gray_hsv(rgb_img=img, channel='v')
v_thresh, maskedv_image = pcv.threshold.custom_range(rgb_img=v,
lower_thresh=[0],
upper_thresh=[200],
channel='gray')
id_objects, obj_hierarchy = pcv.find_objects(img=maskedv_image,
mask=v_thresh)
# Define ROI
roi1, roi_hierarchy = pcv.roi.rectangle(img=maskedv_image,
x=0,
y=0,
h=height,
w=width)
# Decide which objects to keep
roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(
img=img,
roi_contour=roi1,
roi_hierarchy=roi_hierarchy,
object_contour=id_objects,
obj_hierarchy=obj_hierarchy,
roi_type='partial')
obj, mask = pcv.object_composition(img=img,
contours=roi_objects,
hierarchy=hierarchy3)
outfile = args.outdir + "/" + filename
# Shape properties relative to user boundary line (optional)
boundary_img1 = pcv.analyze_bound_horizontal(img=img,
obj=obj,
mask=mask,
line_position=1680)
new_im = Image.fromarray(boundary_img1)
new_im.save("output//" + args.filename + "_top_boundary.png")
# Find shape properties, output shape image (optional)
shape_img = pcv.analyze_object(img=img, obj=obj, mask=mask)
new_im = Image.fromarray(shape_img)
new_im.save("output//" + args.filename + "_top_shape.png")
new_im.save("output//" + args.filename + "shape_img.png")
GT = re.sub(pattern, replacement, files_names[file_counter])
pcv.outputs.add_observation(variable="genotype",
trait="genotype",
method="Regexed from the filename",
scale=None,
datatype=str,
value=int(GT),
label="GT")
# Write shape and color data to results file
pcv.print_results(filename=args.result)
##########################################################################################################################################
args.image = "side_temp.png"
# Get options
pcv.params.debug = args.debug #set debug mode
pcv.params.debug_outdir = args.outdir #set output directory
pcv.params.debug = args.debug # set debug mode
pcv.params.debug_outdir = args.outdir # set output directory
# Read image
img, path, filename = pcv.readimage(filename=args.image)
v = pcv.rgb2gray_hsv(rgb_img=img, channel='v')
v_thresh, maskedv_image = pcv.threshold.custom_range(rgb_img=v,
lower_thresh=[0],
upper_thresh=[200],
channel='gray')
id_objects, obj_hierarchy = pcv.find_objects(img=maskedv_image,
mask=v_thresh)
# Define ROI
roi1, roi_hierarchy = pcv.roi.rectangle(img=maskedv_image,
x=0,
y=0,
h=height,
w=width)
# Decide which objects to keep
roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(
img=img,
roi_contour=roi1,
roi_hierarchy=roi_hierarchy,
object_contour=id_objects,
obj_hierarchy=obj_hierarchy,
roi_type='partial')
obj, mask = pcv.object_composition(img=img,
contours=roi_objects,
hierarchy=hierarchy3)
outfile = args.outdir + "/" + filename
# Shape properties relative to user boundary line (optional)
boundary_img1 = pcv.analyze_bound_horizontal(img=img,
obj=obj,
mask=mask,
line_position=1680)
new_im = Image.fromarray(boundary_img1)
new_im.save("output//" + args.filename + "_side_boundary.png")
# Find shape properties, output shape image (optional)
shape_img = pcv.analyze_object(img=img, obj=obj, mask=mask)
new_im = Image.fromarray(shape_img)
new_im.save("output//" + args.filename + "_side_shape.png")
GT = re.sub(pattern, replacement, files_names[file_counter])
pcv.outputs.add_observation(variable="genotype",
trait="genotype",
method="Regexed from the filename",
scale=None,
datatype=str,
value=int(GT),
label="GT")
# Write shape and color data to results file
pcv.print_results(filename=args.result_side)
def main():
args = options()
os.chdir(args.outdir)
# Read RGB image
img, path, filename = pcv.readimage(args.image, mode="native")
# Get metadata from file name
geno_name = filename.split("}{")
geno_name = geno_name[5]
geno_name = geno_name.split("_")
geno_name = geno_name[1]
day = filename.split("}{")
day = day[7]
day = day.split("_")
day = day[1]
day = day.split("}")
day = day[0]
plot = filename.split("}{")
plot = plot[0]
plot = plot.split("_")
plot = plot[1]
exp_name = filename.split("}{")
exp_name = exp_name[1]
exp_name = exp_name.split("_")
exp_name = exp_name[1]
treat_name = filename.split("}{")
treat_name = treat_name[6]
# Create masks using Naive Bayes Classifier and PDFs file
masks = pcv.naive_bayes_classifier(img, args.pdfs)
# The following code will identify the racks in the image, find the top edge, and choose a line along the edge to pick a y coordinate to trim any soil/pot pixels identified as plant material.
# Convert RGB to HSV and extract the Value channel
v = pcv.rgb2gray_hsv(img, 'v')
# Threshold the Value image
v_thresh = pcv.threshold.binary(v, 98, 255, 'light')
# Dilate mask to fill holes
dilate_racks = pcv.dilate(v_thresh, 2, 1)
# Fill in small objects
mask = np.copy(dilate_racks)
fill_racks = pcv.fill(mask, 100000)
#edge detection
edges = cv2.Canny(fill_racks, 60, 180)
#write all the straight lines from edge detection
lines = cv2.HoughLinesP(edges,
rho=1,
theta=1 * np.pi / 180,
threshold=150,
minLineLength=50,
maxLineGap=15)
N = lines.shape[0]
for i in range(N):
x1 = lines[i][0][0]
y1 = lines[i][0][1]
x2 = lines[i][0][2]
y2 = lines[i][0][3]
cv2.line(img, (x1, y1), (x2, y2), (255, 0, 0), 2)
# keep only horizontal lines
N = lines.shape[0]
tokeep = []
for i in range(N):
want = (abs(lines[i][0][1] - lines[i][0][3])) <= 10
tokeep.append(want)
lines = lines[tokeep]
# keep only lines in lower half of image
N = lines.shape[0]
tokeep = []
for i in range(N):
want = 3100 > lines[i][0][1] > 2300
tokeep.append(want)
lines = lines[tokeep]
# assign lines to positions around plants
N = lines.shape[0]
tokeep = []
left = []
mid = []
right = []
for i in range(N):
leftones = lines[i][0][2] <= 2000
left.append(leftones)
midones = 3000 > lines[i][0][2] > 2000
mid.append(midones)
rightones = lines[i][0][0] >= 3300
right.append(rightones)
right = lines[right]
left = lines[left]
mid = lines[mid]
# choose y values for right left mid adding some pixels to go about the pot (subtract because of orientation of axis)
y_left = left[0][0][3] - 50
y_mid = mid[0][0][3] - 50
y_right = right[0][0][3] - 50
# reload original image to write new lines on
img, path, filename = pcv.readimage(args.image)
# write horizontal lines on image
cv2.line(img, (left[0][0][0], left[0][0][1]),
(left[0][0][2], left[0][0][3]), (255, 255, 51), 2)
cv2.line(img, (mid[0][0][0], mid[0][0][1]), (mid[0][0][2], mid[0][0][3]),
(255, 255, 51), 2)
cv2.line(img, (right[0][0][0], right[0][0][1]),
(right[0][0][2], right[0][0][3]), (255, 255, 51), 2)
# Add masks together
added = masks["healthy"] + masks["necrosis"] + masks["stem"]
# Dilate mask to fill holes
dilate_img = pcv.dilate(added, 2, 1)
# Fill in small objects
mask = np.copy(dilate_img)
fill_img = pcv.fill(mask, 400)
ret, inverted = cv2.threshold(fill_img, 75, 255, cv2.THRESH_BINARY_INV)
# Dilate mask to fill holes of plant
dilate_inv = pcv.dilate(inverted, 2, 1)
# Fill in small objects of plant
mask2 = np.copy(dilate_inv)
fill_plant = pcv.fill(mask2, 20)
inverted_img = pcv.invert(fill_plant)
# Identify objects
id_objects, obj_hierarchy = pcv.find_objects(img, inverted_img)
# Define ROIs
roi_left, roi_hierarchy_left = pcv.roi.rectangle(280, 1280, 1275, 1200,
img)
roi_mid, roi_hierarchy_mid = pcv.roi.rectangle(1900, 1280, 1275, 1200, img)
roi_right, roi_hierarchy_right = pcv.roi.rectangle(3600, 1280, 1275, 1200,
img)
# Decide which objects to keep
roi_objects_left, roi_obj_hierarchy_left, kept_mask_left, obj_area_left = pcv.roi_objects(
img, 'partial', roi_left, roi_hierarchy_left, id_objects,
obj_hierarchy)
roi_objects_mid, roi_obj_hierarchy_mid, kept_mask_mid, obj_area_mid = pcv.roi_objects(
img, 'partial', roi_mid, roi_hierarchy_mid, id_objects, obj_hierarchy)
roi_objects_right, roi_obj_hierarchy_right, kept_mask_right, obj_area_right = pcv.roi_objects(
img, 'partial', roi_right, roi_hierarchy_right, id_objects,
obj_hierarchy)
# Combine objects
obj_r, mask_r = pcv.object_composition(img, roi_objects_right,
roi_obj_hierarchy_right)
obj_m, mask_m = pcv.object_composition(img, roi_objects_mid,
roi_obj_hierarchy_mid)
obj_l, mask_l = pcv.object_composition(img, roi_objects_left,
roi_obj_hierarchy_left)
def analyze_bound_horizontal2(img,
obj,
mask,
line_position,
filename=False):
ori_img = np.copy(img)
# Draw line horizontal line through bottom of image, that is adjusted to user input height
if len(np.shape(ori_img)) == 3:
iy, ix, iz = np.shape(ori_img)
else:
iy, ix = np.shape(ori_img)
size = (iy, ix)
size1 = (iy, ix, 3)
background = np.zeros(size, dtype=np.uint8)
wback = np.zeros(size1, dtype=np.uint8)
x_coor = int(ix)
y_coor = int(iy) - int(line_position)
rec_corner = int(iy - 2)
rec_point1 = (1, rec_corner)
rec_point2 = (x_coor - 2, y_coor - 2)
cv2.rectangle(background, rec_point1, rec_point2, (255), 1)
below_contour, below_hierarchy = cv2.findContours(
background, cv2.RETR_TREE, cv2.CHAIN_APPROX_NONE)[-2:]
below = []
above = []
mask_nonzerox, mask_nonzeroy = np.nonzero(mask)
obj_points = np.vstack((mask_nonzeroy, mask_nonzerox))
obj_points1 = np.transpose(obj_points)
for i, c in enumerate(obj_points1):
xy = tuple(c)
pptest = cv2.pointPolygonTest(below_contour[0],
xy,
measureDist=False)
if pptest == 1:
below.append(xy)
cv2.circle(ori_img, xy, 1, (0, 0, 255))
cv2.circle(wback, xy, 1, (0, 0, 0))
else:
above.append(xy)
cv2.circle(ori_img, xy, 1, (0, 255, 0))
cv2.circle(wback, xy, 1, (255, 255, 255))
return wback
ori_img = np.copy(img)
# Draw line horizontal line through bottom of image, that is adjusted to user input height
if len(np.shape(ori_img)) == 3:
iy, ix, iz = np.shape(ori_img)
else:
iy, ix = np.shape(ori_img)
if obj_r is not None:
wback_r = analyze_bound_horizontal2(img, obj_r, mask_r, iy - y_right)
if obj_m is not None:
wback_m = analyze_bound_horizontal2(img, obj_m, mask_m, iy - y_mid)
if obj_l is not None:
wback_l = analyze_bound_horizontal2(img, obj_l, mask_l, iy - y_left)
threshold_light = pcv.threshold.binary(img, 1, 1, 'dark')
if obj_r is not None:
fgmask_r = pcv.background_subtraction(wback_r, threshold_light)
if obj_m is not None:
fgmask_m = pcv.background_subtraction(wback_m, threshold_light)
if obj_l is not None:
fgmask_l = pcv.background_subtraction(wback_l, threshold_light)
if obj_l is not None:
id_objects_left, obj_hierarchy_left = pcv.find_objects(img, fgmask_l)
if obj_m is not None:
id_objects_mid, obj_hierarchy_mid = pcv.find_objects(img, fgmask_m)
if obj_r is not None:
id_objects_right, obj_hierarchy_right = pcv.find_objects(img, fgmask_r)
# Combine objects
if obj_r is not None:
obj_r2, mask_r2 = pcv.object_composition(img, id_objects_right,
obj_hierarchy_right)
if obj_m is not None:
obj_m2, mask_m2 = pcv.object_composition(img, id_objects_mid,
obj_hierarchy_mid)
if obj_l is not None:
obj_l2, mask_l2 = pcv.object_composition(img, id_objects_left,
obj_hierarchy_left)
# Shape measurements
if obj_l is not None:
shape_header_left, shape_data_left, shape_img_left = pcv.analyze_object(
img, obj_l2, fgmask_l,
geno_name + '_' + plot + '_' + 'A' + '_' + day + '_' + 'shape.jpg')
if obj_r is not None:
shape_header_right, shape_data_right, shape_img_right = pcv.analyze_object(
img, obj_r2, fgmask_r,
geno_name + '_' + plot + '_' + 'C' + '_' + day + '_' + 'shape.jpg')
if obj_m is not None:
shape_header_mid, shape_data_mid, shape_img_mid = pcv.analyze_object(
img, obj_m2, fgmask_m,
geno_name + '_' + plot + '_' + 'B' + '_' + day + '_' + 'shape.jpg')
# Color data
if obj_r is not None:
color_header_right, color_data_right, norm_slice_right = pcv.analyze_color(
img, fgmask_r, 256, None, 'v', 'img',
geno_name + '_' + plot + '_' + 'C' + '_' + day + '_' + 'color.jpg')
if obj_m is not None:
color_header_mid, color_data_mid, norm_slice_mid = pcv.analyze_color(
img, fgmask_m, 256, None, 'v', 'img',
geno_name + '_' + plot + '_' + 'B' + '_' + day + '_' + 'color.jpg')
if obj_l is not None:
color_header_left, color_data_left, norm_slice_left = pcv.analyze_color(
img, fgmask_l, 256, None, 'v', 'img',
geno_name + '_' + plot + '_' + 'A' + '_' + day + '_' + 'color.jpg')
new_header = [
'experiment', 'day', 'genotype', 'treatment', 'plot', 'plant',
'percent.necrosis', 'area', 'hull-area', 'solidity', 'perimeter',
'width', 'height', 'longest_axis', 'center-of-mass-x',
'center-of-mass-y', 'hull_vertices', 'in_bounds', 'ellipse_center_x',
'ellipse_center_y', 'ellipse_major_axis', 'ellipse_minor_axis',
'ellipse_angle', 'ellipse_eccentricity', 'bin-number', 'bin-values',
'blue', 'green', 'red', 'lightness', 'green-magenta', 'blue-yellow',
'hue', 'saturation', 'value'
]
table = []
table.append(new_header)
added2 = masks["healthy"] + masks["stem"]
# Object combine kept objects
if obj_l is not None:
masked_image_healthy_left = pcv.apply_mask(added2, fgmask_l, 'black')
masked_image_necrosis_left = pcv.apply_mask(masks["necrosis"],
fgmask_l, 'black')
added_obj_left = masked_image_healthy_left + masked_image_necrosis_left
sample = "A"
# Calculations
necrosis_left = np.sum(masked_image_necrosis_left)
necrosis_percent_left = float(necrosis_left) / np.sum(added_obj_left)
table.append([
exp_name, day, geno_name, treat_name, plot, sample,
round(necrosis_percent_left, 5), shape_data_left[1],
shape_data_left[2], shape_data_left[3], shape_data_left[4],
shape_data_left[5], shape_data_left[6], shape_data_left[7],
shape_data_left[8], shape_data_left[9], shape_data_left[10],
shape_data_left[11], shape_data_left[12], shape_data_left[13],
shape_data_left[14], shape_data_left[15], shape_data_left[16],
shape_data_left[17], '"{}"'.format(color_data_left[1]),
'"{}"'.format(color_data_left[2]), '"{}"'.format(
color_data_left[3]), '"{}"'.format(color_data_left[4]),
'"{}"'.format(color_data_left[5]), '"{}"'.format(
color_data_left[6]), '"{}"'.format(color_data_left[7]),
'"{}"'.format(color_data_left[8]), '"{}"'.format(
color_data_left[9]), '"{}"'.format(color_data_left[10]),
'"{}"'.format(color_data_left[11])
])
# Object combine kept objects
if obj_m is not None:
masked_image_healthy_mid = pcv.apply_mask(added2, fgmask_m, 'black')
masked_image_necrosis_mid = pcv.apply_mask(masks["necrosis"], fgmask_m,
'black')
added_obj_mid = masked_image_healthy_mid + masked_image_necrosis_mid
sample = "B"
# Calculations
necrosis_mid = np.sum(masked_image_necrosis_mid)
necrosis_percent_mid = float(necrosis_mid) / np.sum(added_obj_mid)
table.append([
exp_name, day, geno_name, treat_name, plot, sample,
round(necrosis_percent_mid,
5), shape_data_mid[1], shape_data_mid[2], shape_data_mid[3],
shape_data_mid[4], shape_data_mid[5], shape_data_mid[6],
shape_data_mid[7], shape_data_mid[8], shape_data_mid[9],
shape_data_mid[10], shape_data_mid[11], shape_data_mid[12],
shape_data_mid[13], shape_data_mid[14], shape_data_mid[15],
shape_data_mid[16], shape_data_mid[17],
'"{}"'.format(color_data_mid[1]), '"{}"'.format(color_data_mid[2]),
'"{}"'.format(color_data_mid[3]), '"{}"'.format(color_data_mid[4]),
'"{}"'.format(color_data_mid[5]), '"{}"'.format(color_data_mid[6]),
'"{}"'.format(color_data_mid[7]), '"{}"'.format(color_data_mid[8]),
'"{}"'.format(color_data_mid[9]), '"{}"'.format(
color_data_mid[10]), '"{}"'.format(color_data_mid[11])
])
# Object combine kept objects
if obj_r is not None:
masked_image_healthy_right = pcv.apply_mask(added2, fgmask_r, 'black')
masked_image_necrosis_right = pcv.apply_mask(masks["necrosis"],
fgmask_r, 'black')
added_obj_right = masked_image_healthy_right + masked_image_necrosis_right
sample = "C"
# Calculations
necrosis_right = np.sum(masked_image_necrosis_right)
necrosis_percent_right = float(necrosis_right) / np.sum(
added_obj_right)
table.append([
exp_name, day, geno_name, treat_name, plot, sample,
round(necrosis_percent_right, 5), shape_data_right[1],
shape_data_right[2], shape_data_right[3], shape_data_right[4],
shape_data_right[5], shape_data_right[6], shape_data_right[7],
shape_data_right[8], shape_data_right[9], shape_data_right[10],
shape_data_right[11], shape_data_right[12], shape_data_right[13],
shape_data_right[14], shape_data_right[15], shape_data_right[16],
shape_data_right[17], '"{}"'.format(color_data_right[1]),
'"{}"'.format(color_data_right[2]), '"{}"'.format(
color_data_right[3]), '"{}"'.format(color_data_right[4]),
'"{}"'.format(color_data_right[5]), '"{}"'.format(
color_data_right[6]), '"{}"'.format(color_data_right[7]),
'"{}"'.format(color_data_right[8]), '"{}"'.format(
color_data_right[9]), '"{}"'.format(color_data_right[10]),
'"{}"'.format(color_data_right[11])
])
if obj_l is not None:
merged2 = cv2.merge([
masked_image_healthy_left,
np.zeros(np.shape(masks["healthy"]), dtype=np.uint8),
masked_image_necrosis_left
]) #blue, green, red
pcv.print_image(
merged2, geno_name + '_' + plot + '_' + 'A' + '_' + day + '_' +
'merged.jpg')
if obj_m is not None:
merged3 = cv2.merge([
masked_image_healthy_mid,
np.zeros(np.shape(masks["healthy"]), dtype=np.uint8),
masked_image_necrosis_mid
]) #blue, green, red
pcv.print_image(
merged3, geno_name + '_' + plot + '_' + 'B' + '_' + day + '_' +
'merged.jpg')
if obj_r is not None:
merged4 = cv2.merge([
masked_image_healthy_right,
np.zeros(np.shape(masks["healthy"]), dtype=np.uint8),
masked_image_necrosis_right
]) #blue, green, red
pcv.print_image(
merged4, geno_name + '_' + plot + '_' + 'C' + '_' + day + '_' +
'merged.jpg')
# Save area results to file (individual csv files for one image...)
file_name = filename.split("}{")
file_name = file_name[0] + "}{" + file_name[5] + "}{" + file_name[7]
outfile = str(file_name[:-4]) + 'csv'
with open(outfile, 'w') as f:
for row in table:
f.write(','.join(map(str, row)) + '\n')
print(filename)
def image_avg(fundf):
# dn't understand why import suddently needs to be inside function
# import cv2 as cv2
# import numpy as np
# import pandas as pd
# import os
# from matplotlib import pyplot as plt
# from skimage import filters
# from skimage import morphology
# from skimage import segmentation
# Predefine some variables
global c, h, roi_c, roi_h, ilegend, mask_Fm, fn_Fm
# Get the filename for minimum and maximum fluoresence
fn_min = fundf.query('frame == "Fo" or frame == "Fp"').filename.values[0]
fn_max = fundf.query('frame == "Fm" or frame == "Fmp"').filename.values[0]
# Get the parameter name that links these 2 frames
param_name = fundf['parameter'].iloc[0]
# Create a new output filename that combines existing filename with parameter
outfn = os.path.splitext(os.path.basename(fn_max))[0]
outfn_split = outfn.split('-')
# outfn_split[2] = datetime.strptime(fundf.jobdate.values[0],'%Y-%m-%d').strftime('%Y%m%d')
outfn_split[2] = fundf.jobdate.dt.strftime('%Y%m%d').values[0]
basefn = "-".join(outfn_split[0:-1])
outfn_split[-1] = param_name
outfn = "-".join(outfn_split)
print(outfn)
# Make some directories based on sample id to keep output organized
plantbarcode = outfn_split[0]
fmaxdir = os.path.join(fluordir, plantbarcode)
os.makedirs(fmaxdir, exist_ok=True)
# If debug mode is 'print', create a specific debug dir for each pim file
if pcv.params.debug == 'print':
debug_outdir = os.path.join(debugdir, outfn)
os.makedirs(debug_outdir, exist_ok=True)
pcv.params.debug_outdir = debug_outdir
# read images and create mask from max fluorescence
# read image as is. only gray values in PSII images
imgmin, _, _ = pcv.readimage(fn_min)
img, _, _ = pcv.readimage(fn_max)
fdark = np.zeros_like(img)
out_flt = fdark.astype('float32') # <- needs to be float32 for imwrite
if param_name == 'FvFm':
# save max fluorescence filename
fn_Fm = fn_max
# create mask
# #create black mask over lower half of image to threshold upper plant only
# img_half, _, _, _ = pcv.rectangle_mask(img, p1=(0,321), p2=(480,640))
# # mask1 = pcv.threshold.otsu(img_half,255)
# algaethresh = filters.threshold_otsu(image=img_half)
# mask0 = pcv.threshold.binary(img_half, algaethresh, 255, 'light')
# # create black mask over upper half of image to threshold lower plant only
# img_half, _, _, _ = pcv.rectangle_mask(img, p1=(0, 0), p2=(480, 319), color='black')
# # mask0 = pcv.threshold.otsu(img_half,255)
# algaethresh = filters.threshold_otsu(image=img_half)
# mask1 = pcv.threshold.binary(img_half, algaethresh, 255, 'light')
# mask = pcv.logical_xor(mask0, mask1)
# # mask = pcv.dilate(mask, 2, 1)
# mask = pcv.fill(mask, 350)
# mask = pcv.erode(mask, 2, 2)
# mask = pcv.erode(mask, 2, 1)
# mask = pcv.fill(mask, 100)
# otsuT = filters.threshold_otsu(img)
# # sigma=(k-1)/6. This is because the length for 99 percentile of gaussian pdf is 6sigma.
# k = int(2 * np.ceil(3 * otsuT) + 1)
# gb = pcv.gaussian_blur(img, ksize = (k,k), sigma_x = otsuT)
# mask = img >= gb + 10
# pcv.plot_image(mask)
# local_otsu = filters.rank.otsu(img, pcv.get_kernel((9,9), 'rectangle'))#morphology.disk(2))
# thresh_image = img >= local_otsu
#_------> start of mask
elevation_map = filters.sobel(img)
# pcv.plot_image(elevation_map)
thresh = filters.threshold_otsu(image=img)
# thresh = 50
markers = np.zeros_like(img, dtype='uint8')
markers[img > thresh + 8] = 2
markers[img <= thresh + 8] = 1
# pcv.plot_image(markers,cmap=plt.cm.nipy_spectral)
mask = segmentation.watershed(elevation_map, markers)
mask = mask.astype(np.uint8)
# pcv.plot_image(mask)
mask[mask == 1] = 0
mask[mask == 2] = 1
# pcv.plot_image(mask, cmap=plt.cm.nipy_spectral)
# mask = pcv.erode(mask, 2, 1)
if len(np.unique(mask))!=1:
mask = pcv.fill(mask, 100)
# pcv.plot_image(mask, cmap=plt.cm.nipy_spectral)
# <----------- end of masking
# roi needs to be defined regardless of mask
roi_c, roi_h = pcv.roi.multi(img,
coord=(250, 200),
radius=70,
spacing=(0, 220),
ncols=1,
nrows=2)
if len(np.unique(mask)) == 1:
c = []
YII = mask
NPQ = mask
newmask = mask
else:
# find objects and setup roi
c, h = pcv.find_objects(img, mask)
# setup individual roi plant masks
newmask = np.zeros_like(mask)
# compute fv/fm and save to file
YII, hist_fvfm = pcv.photosynthesis.analyze_fvfm(fdark=fdark,
fmin=imgmin,
fmax=img,
mask=mask,
bins=128)
# YII = np.divide(Fv,
# img,
# out=out_flt.copy(),
# where=np.logical_and(mask > 0, img > 0))
# NPQ is 0
NPQ = np.zeros_like(YII)
def test(true_positive_file, test_parameters):
hue_lower_tresh = test_parameters[0]
hue_higher_tresh = test_parameters[1]
saturation_lower_tresh = test_parameters[2]
saturation_higher_tresh = test_parameters[3]
value_lower_tresh = test_parameters[4]
value_higher_tresh = test_parameters[5]
green_lower_tresh = test_parameters[6]
green_higher_tresh = test_parameters[7]
red_lower_tresh = test_parameters[8]
red_higher_thresh = test_parameters[9]
blue_lower_tresh = test_parameters[10]
blue_higher_tresh = test_parameters[11]
blur_k = test_parameters[12]
fill_k = test_parameters[13]
class args:
#image = "C:\\Users\\RensD\\OneDrive\\studie\\Master\\The_big_project\\top_perspective\\0214_2018-03-07 08.55 - 26_cam9.png"
image = true_positive_file
outdir = "C:\\Users\\RensD\\OneDrive\\studie\\Master\\The_big_project\\top_perspective\\output"
debug = debug_setting
result = "results.txt"
# Get options
pcv.params.debug=args.debug #set debug mode
pcv.params.debug_outdir=args.outdir #set output directory
# Read image (readimage mode defaults to native but if image is RGBA then specify mode='rgb')
# Inputs:
# filename - Image file to be read in
# mode - Return mode of image; either 'native' (default), 'rgb', 'gray', or 'csv'
img, path, filename = pcv.readimage(filename=args.image, mode='rgb')
s = pcv.rgb2gray_hsv(rgb_img=img, channel='h')
mask, masked_image = pcv.threshold.custom_range(rgb_img=s, lower_thresh=[hue_lower_tresh], upper_thresh=[hue_higher_tresh], channel='gray')
masked = pcv.apply_mask(rgb_img=img, mask = mask, mask_color = 'white')
#print("filtered on hue")
s = pcv.rgb2gray_hsv(rgb_img=masked, channel='s')
mask, masked_image = pcv.threshold.custom_range(rgb_img=s, lower_thresh=[saturation_lower_tresh], upper_thresh=[saturation_higher_tresh], channel='gray')
masked = pcv.apply_mask(rgb_img=masked, mask = mask, mask_color = 'white')
#print("filtered on saturation")
s = pcv.rgb2gray_hsv(rgb_img=masked, channel='v')
mask, masked_image = pcv.threshold.custom_range(rgb_img=s, lower_thresh=[value_lower_tresh], upper_thresh=[value_higher_tresh], channel='gray')
masked = pcv.apply_mask(rgb_img=masked, mask = mask, mask_color = 'white')
#print("filtered on value")
mask, masked = pcv.threshold.custom_range(rgb_img=masked, lower_thresh=[0,green_lower_tresh,0], upper_thresh=[255,green_higher_tresh,255], channel='RGB')
masked = pcv.apply_mask(rgb_img=masked, mask = mask, mask_color = 'white')
#print("filtered on green")
mask, masked = pcv.threshold.custom_range(rgb_img=masked, lower_thresh=[red_lower_tresh,0,0], upper_thresh=[red_higher_thresh,255,255], channel='RGB')
masked = pcv.apply_mask(rgb_img=masked, mask = mask, mask_color = 'white')
#print("filtered on red")
mask_old, masked_old = pcv.threshold.custom_range(rgb_img=masked, lower_thresh=[0,0,blue_lower_tresh], upper_thresh=[255,255,blue_higher_tresh], channel='RGB')
masked = pcv.apply_mask(rgb_img=masked_old, mask = mask_old, mask_color = 'white')
#print("filtered on blue")
###____________________________________ Blur to minimize
try:
s_mblur = pcv.median_blur(gray_img = masked_old, ksize = blur_k)
s = pcv.rgb2gray_hsv(rgb_img=s_mblur, channel='v')
mask, masked_image = pcv.threshold.custom_range(rgb_img=s, lower_thresh=[0], upper_thresh=[254], channel='gray')
except:
print("failed blur step")
try:
mask = pcv.fill(mask, fill_k)
except:
pass
masked = pcv.apply_mask(rgb_img=masked, mask = mask, mask_color = 'white')
###_____________________________________ Now to identify objects
masked_a = pcv.rgb2gray_lab(rgb_img=masked, channel='a')
masked_b = pcv.rgb2gray_lab(rgb_img=masked, channel='b')
# Threshold the green-magenta and blue images
maskeda_thresh = pcv.threshold.binary(gray_img=masked_a, threshold=115,
max_value=255, object_type='dark')
maskeda_thresh1 = pcv.threshold.binary(gray_img=masked_a, threshold=135,
max_value=255, object_type='light')
maskedb_thresh = pcv.threshold.binary(gray_img=masked_b, threshold=128,
max_value=255, object_type='light')
ab1 = pcv.logical_or(bin_img1=maskeda_thresh, bin_img2=maskedb_thresh)
ab = pcv.logical_or(bin_img1=maskeda_thresh1, bin_img2=ab1)
# Fill small objects
# Inputs:
# bin_img - Binary image data
# size - Minimum object area size in pixels (must be an integer), and smaller objects will be filled
ab_fill = pcv.fill(bin_img=ab, size=200)
#print("filled")
# Apply mask (for VIS images, mask_color=white)
masked2 = pcv.apply_mask(rgb_img=masked, mask=ab_fill, mask_color='white')
id_objects, obj_hierarchy = pcv.find_objects(masked, ab_fill)
# Let's just take the largest
roi1, roi_hierarchy= pcv.roi.rectangle(img=masked, x=0, y=0, h=960, w=1280) # Currently hardcoded
with HiddenPrints():
roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(img=img, roi_contour=roi1,
roi_hierarchy=roi_hierarchy,
object_contour=id_objects,
obj_hierarchy=obj_hierarchy,
roi_type=roi_type)
obj, mask = pcv.object_composition(img=img, contours=roi_objects, hierarchy=hierarchy3)
if use_mask == True:
return(mask)
else:
masked2 = pcv.apply_mask(rgb_img=masked, mask=mask, mask_color='white')
return(masked2)
#!/usr/bin/env python
import numpy as np
from plantcv import plantcv as pcv
import json
import argparse
import os
parser = argparse.ArgumentParser(description='Analyse a job.')
parser.add_argument('job_file', metavar='job_file', type=str,
help='json job file')
parser.add_argument('image_base_dir', metavar='image_base_dir', type=str,
help='.')
args = parser.parse_args()
with open (args.job_file, 'r', encoding='utf-8') as f:
job = json.load(f)
os.symlink('{full_image_path}'.format(full_image_path=os.path.join(args.image_base_dir,job['path'])),'input_image.png')
img, path, filename = pcv.readimage(filename='input_image.png')
# if image is blank, error with specific code.
if np.count_nonzero(img) == 0:
exit(15)
def image_avg(fundf):
# Predefine some variables
global c, h, roi_c, roi_h
# Get the filename for minimum and maximum fluoresence
fn_min = fundf.query('frame == "Fo" or frame == "Fp"').filename.values[0]
fn_max = fundf.query('frame == "Fm" or frame == "Fmp"').filename.values[0]
# Get the parameter name that links these 2 frames
param_name = fundf['parameter'].iloc[0]
# Create a new output filename that combines existing filename with parameter
outfn = os.path.splitext(os.path.basename(fn_max))[0]
outfn_split = outfn.split('_')
# outfn_split[2] = datetime.strptime(fundf.jobdate.values[0],'%Y-%m-%d').strftime('%Y%m%d')
outfn_split[2] = fundf.jobdate.dt.strftime('%Y%m%d').values[0]
basefn = "-".join(outfn_split[0:-1])
outfn_split[-1] = param_name
outfn = "-".join(outfn_split)
print(outfn)
# Make some directories based on sample id to keep output organized
sampleid = outfn_split[0]
fmaxdir = os.path.join(fluordir, sampleid)
os.makedirs(fmaxdir, exist_ok=True)
# If debug mode is 'print', create a specific debug dir for each pim file
if pcv.params.debug == 'print':
debug_outdir = os.path.join(debugdir, outfn)
os.makedirs(debug_outdir, exist_ok=True)
pcv.params.debug_outdir = debug_outdir
# read images and create mask from max fluorescence
# read image as is. only gray values in PSII images
imgmin, _, _ = pcv.readimage(fn_min)
img, _, _ = pcv.readimage(fn_max)
fdark = np.zeros_like(img)
out_flt = fdark.astype('float32') # <- needs to be float32 for imwrite
if param_name == 'FvFm':
# create mask
mask = createmasks.psIImask(img)
# find objects and setup roi
c, h = pcv.find_objects(img, mask)
roi_c, roi_h = pcv.roi.multi(img,
coord=(250, 350),
radius=200,
spacing=(0, 0),
ncols=1,
nrows=1)
# setup individual roi plant masks
newmask = np.zeros_like(mask)
# compute fv/fm and save to file
Fv, hist_fvfm = pcv.fluor_fvfm(
fdark=fdark, fmin=imgmin, fmax=img, mask=mask, bins=128)
YII = np.divide(Fv, img, out=out_flt.copy(),
where=np.logical_and(mask > 0, img > 0))
cv2.imwrite(os.path.join(fmaxdir, outfn + '_fvfm.tif'), YII)
# NPQ is 0
NPQ = np.zeros_like(YII)
# print Fm
cv2.imwrite(os.path.join(fmaxdir, outfn + '_fmax.tif'), img)
# NPQ will always be an array of 0s
else: # compute YII and NPQ if parameter is other than FvFm
# use cv2 to read image becase pcv.readimage will save as input_image.png overwriting img
newmask = cv2.imread(os.path.join(
maskdir, basefn + '-FvFm_mask.png'), -1)
# compute YII
Fvp, hist_yii = pcv.fluor_fvfm(
fdark, fmin=imgmin, fmax=img, mask=newmask, bins=128)
# make sure to initialize with out=. using where= provides random values at False pixels. you will get a strange result. newmask comes from Fm instead of Fm' so they can be different
#newmask<0, img>0 = FALSE: not part of plant but fluorescence detected.
#newmask>0, img<=0 = FALSE: part of plant in Fm but no fluorescence detected <- this is likely the culprit because pcv.apply_mask doesn't always solve issue.
YII = np.divide(Fvp, img,
out=out_flt.copy(),
where=np.logical_and(newmask > 0, img > 0))
cv2.imwrite(os.path.join(fmaxdir, outfn + '_yii.tif'), YII)
# compute NPQ
Fm = cv2.imread(os.path.join(fmaxdir, basefn + '-FvFm_fmax.tif'), -1)
NPQ = np.divide(Fm, img,
out=out_flt.copy(),
where=np.logical_and(newmask > 0, img > 0))
NPQ = np.subtract(NPQ, 1, out=out_flt.copy(),
where=np.logical_and(NPQ >= 1, newmask > 0))
cv2.imwrite(os.path.join(fmaxdir, outfn + '_npq.tif'), NPQ)
# end if-else Fv/Fm
# Make as many copies of incoming dataframe as there are ROIs so all results can be saved
outdf = fundf.copy()
for i in range(0, len(roi_c)-1):
outdf = outdf.append(fundf)
outdf.imageid = outdf.imageid.astype('uint8')
# Initialize lists to store variables for each ROI and iterate through each plant
frame_avg = []
yii_avg = []
yii_std = []
npq_avg = []
npq_std = []
plantarea = []
ithroi = []
inbounds = []
i = 0
rc = roi_c[i]
for i, rc in enumerate(roi_c):
# Store iteration Number
ithroi.append(int(i))
ithroi.append(int(i)) # append twice so each image has a value.
# extract ith hierarchy
rh = roi_h[i]
# Filter objects based on being in the defined ROI
roi_obj, hierarchy_obj, submask, obj_area = pcv.roi_objects(
img,
roi_contour=rc,
roi_hierarchy=rh,
object_contour=c,
obj_hierarchy=h,
roi_type='partial')
if obj_area == 0:
print('!!! No plant detected in ROI ', str(i))
frame_avg.append(np.nan)
frame_avg.append(np.nan)
yii_avg.append(np.nan)
yii_avg.append(np.nan)
yii_std.append(np.nan)
yii_std.append(np.nan)
npq_avg.append(np.nan)
npq_avg.append(np.nan)
npq_std.append(np.nan)
npq_std.append(np.nan)
inbounds.append(np.nan)
inbounds.append(np.nan)
else:
# Combine multiple plant objects within an roi together
plant_contour, plant_mask = pcv.object_composition(
img=img, contours=roi_obj, hierarchy=hierarchy_obj)
#combine plant masks after roi filter
if param_name == 'FvFm':
newmask = pcv.image_add(newmask, plant_mask)
# Calc mean and std dev of fluoresence, YII, and NPQ and save to list
frame_avg.append(masked_stats.mean(imgmin, plant_mask))
frame_avg.append(masked_stats.mean(img, plant_mask))
# need double because there are two images per loop
yii_avg.append(masked_stats.mean(YII, plant_mask))
yii_avg.append(masked_stats.mean(YII, plant_mask))
yii_std.append(masked_stats.std(YII, plant_mask))
yii_std.append(masked_stats.std(YII, plant_mask))
npq_avg.append(masked_stats.mean(NPQ, plant_mask))
npq_avg.append(masked_stats.mean(NPQ, plant_mask))
npq_std.append(masked_stats.std(NPQ, plant_mask))
npq_std.append(masked_stats.std(NPQ, plant_mask))
# Check if plant is compeltely within the frame of the image
inbounds.append(pcv.within_frame(plant_mask))
inbounds.append(pcv.within_frame(plant_mask))
# end try-except-else
# end roi loop
# save mask of all plants to file after roi filter
if param_name == 'FvFm':
pcv.print_image(newmask, os.path.join(maskdir, outfn + '_mask.png'))
# Output a pseudocolor of NPQ and YII for each induction period for each image
imgdir = os.path.join(outdir, 'pseudocolor_images', sampleid)
os.makedirs(imgdir, exist_ok=True)
npq_img = pcv.visualize.pseudocolor(NPQ,
obj=None,
mask=newmask,
cmap='inferno',
axes=False,
min_value=0,
max_value=2.5,
background='black',
obj_padding=0)
npq_img = add_scalebar.add_scalebar(npq_img,
pixelresolution=pixelresolution,
barwidth=20,
barlocation='lower left')
# If you change the output size and resolution you will need to adjust the timelapse video script
npq_img.set_size_inches(6, 6, forward=False)
npq_img.savefig(os.path.join(imgdir, outfn + '_NPQ.png'),
bbox_inches='tight',
dpi=150)
npq_img.clf()
yii_img = pcv.visualize.pseudocolor(YII,
obj=None,
mask=newmask,
cmap=custom_colormaps.get_cmap(
'imagingwin'),
axes=False,
min_value=0,
max_value=1,
background='black',
obj_padding=0)
yii_img = add_scalebar.add_scalebar(yii_img,
pixelresolution=pixelresolution,
barwidth=20,
barlocation='lower left')
yii_img.set_size_inches(6, 6, forward=False)
yii_img.savefig(os.path.join(imgdir, outfn + '_YII.png'),
bbox_inches='tight',
dpi=150)
yii_img.clf()
# check YII values for uniqueness between all ROI. nonunique ROI suggests the plants grew into each other and can no longer be reliably separated in image processing.
# a single value isn't always robust. I think because there are small independent objects that fall in one roi but not the other that change the object within the roi slightly.
# also note, I originally designed this for trays of 2 pots. It will not detect if e.g. 2 out of 9 plants grow into each other
rounded_avg = [round(n, 3) for n in yii_avg]
rounded_std = [round(n, 3) for n in yii_std]
if len(roi_c) > 1:
isunique = not (rounded_avg.count(rounded_avg[0]) == len(yii_avg) and
rounded_std.count(rounded_std[0]) == len(yii_std))
else:
isunique = True
# save all values to outgoing dataframe
outdf['roi'] = ithroi
outdf['frame_avg'] = frame_avg
outdf['yii_avg'] = yii_avg
outdf['npq_avg'] = npq_avg
outdf['yii_std'] = yii_std
outdf['npq_std'] = npq_std
outdf['obj_in_frame'] = inbounds
outdf['unique_roi'] = isunique
return (outdf)
def main():
# Create input arguments object
args = options()
# Set debug mode
pcv.params.debug = args.debug
# Open a single image
img, imgpath, imgname = pcv.readimage(filename=args.image)
# Visualize colorspaces
all_cs = pcv.visualize.colorspaces(rgb_img=img)
# Extract the Blue-Yellow ("b") channel from the LAB colorspace
gray_img = pcv.rgb2gray_lab(rgb_img=img, channel="b")
# Plot a histogram of pixel values for the Blue-Yellow ("b") channel.
hist_plot = pcv.visualize.histogram(gray_img=gray_img)
# Apply a binary threshold to the Blue-Yellow ("b") grayscale image.
thresh_img = pcv.threshold.binary(gray_img=gray_img,
threshold=140,
max_value=255,
object_type="light")
# Apply a dilation with a 5x5 kernel and 3 iterations
dil_img = pcv.dilate(gray_img=thresh_img, ksize=5, i=3)
# Fill in small holes in the leaves
closed_img = pcv.fill_holes(bin_img=dil_img)
# Erode the plant pixels using a 5x5 kernel and 3 iterations
er_img = pcv.erode(gray_img=closed_img, ksize=5, i=3)
# Apply a Gaussian blur with a 5 x 5 kernel.
blur_img = pcv.gaussian_blur(img=er_img, ksize=(5, 5))
# Set pixel values less than 255 to 0
blur_img[np.where(blur_img < 255)] = 0
# Fill/remove objects less than 300 pixels in area
cleaned = pcv.fill(bin_img=blur_img, size=300)
# Create a circular ROI
roi, roi_str = pcv.roi.circle(img=img, x=1725, y=1155, r=400)
# Identify objects in the binary image
cnts, cnts_str = pcv.find_objects(img=img, mask=cleaned)
# Filter objects by region of interest
plant_cnt, plant_str, plant_mask, plant_area = pcv.roi_objects(
img=img,
roi_contour=roi,
roi_hierarchy=roi_str,
object_contour=cnts,
obj_hierarchy=cnts_str)
# Combine objects into one
plant, mask = pcv.object_composition(img=img,
contours=plant_cnt,
hierarchy=plant_str)
# Measure size and shape properties
shape_img = pcv.analyze_object(img=img, obj=plant, mask=mask)
if args.writeimg:
pcv.print_image(img=shape_img,
filename=os.path.join(args.outdir,
"shapes_" + imgname))
# Analyze color properties
color_img = pcv.analyze_color(rgb_img=img, mask=mask, hist_plot_type="hsv")
if args.writeimg:
pcv.print_image(img=color_img,
filename=os.path.join(args.outdir,
"histogram_" + imgname))
# Save the measurements to a file
pcv.print_results(filename=args.result)
def main():
# Get options
args = options()
# Read image
img, path, filename = pcv.readimage(args.image)
pcv.params.debug=args.debug #set debug mode
# STEP 1: Check if this is a night image, for some of these dataset's images were captured
# at night, even if nothing is visible. To make sure that images are not taken at
# night we check that the image isn't mostly dark (0=black, 255=white).
# if it is a night image it throws a fatal error and stops the workflow.
if np.average(img) < 50:
pcv.fatal_error("Night Image")
else:
pass
# STEP 2: Normalize the white color so you can later
# compare color between images.
# Inputs:
# img = image object, RGB colorspace
# roi = region for white reference, if none uses the whole image,
# otherwise (x position, y position, box width, box height)
# white balance image based on white toughspot
#img1 = pcv.white_balance(img=img,roi=(400,800,200,200))
img1 = pcv.white_balance(img=img, mode='hist', roi=None)
# STEP 3: Rotate the image
# Inputs:
# img = image object, RGB color space
# rotation_deg = Rotation angle in degrees, can be negative, positive values
# will move counter-clockwise
# crop = If True then image will be cropped to original image dimensions, if False
# the image size will be adjusted to accommodate new image dimensions
rotate_img = pcv.rotate(img=img1,rotation_deg=-1, crop=False)
# STEP 4: Shift image. This step is important for clustering later on.
# For this image it also allows you to push the green raspberry pi camera
# out of the image. This step might not be necessary for all images.
# The resulting image is the same size as the original.
# Inputs:
# img = image object
# number = integer, number of pixels to move image
# side = direction to move from "top", "bottom", "right","left"
shift1 = pcv.shift_img(img=img1, number=300, side='top')
img1 = shift1
# STEP 5: Convert image from RGB colorspace to LAB colorspace
# Keep only the green-magenta channel (grayscale)
# Inputs:
# img = image object, RGB colorspace
# channel = color subchannel ('l' = lightness, 'a' = green-magenta , 'b' = blue-yellow)
#a = pcv.rgb2gray_lab(img=img1, channel='a')
a = pcv.rgb2gray_lab(rgb_img=img1, channel='a')
# STEP 6: Set a binary threshold on the saturation channel image
# Inputs:
# img = img object, grayscale
# threshold = threshold value (0-255)
# max_value = value to apply above threshold (usually 255 = white)
# object_type = light or dark
# - If object is light then standard thresholding is done
# - If object is dark then inverse thresholding is done
img_binary = pcv.threshold.binary(gray_img=a, threshold=120, max_value=255, object_type='dark')
#img_binary = pcv.threshold.binary(gray_img=a, threshold=120, max_value=255, object_type'dark')
# ^
# |
# adjust this value
# STEP 7: Fill in small objects (speckles)
# Inputs:
# bin_img = image object, binary. img will be returned after filling
# size = minimum object area size in pixels (integer)
fill_image = pcv.fill(bin_img=img_binary, size=10)
# ^
# |
# adjust this value
# STEP 8: Dilate so that you don't lose leaves (just in case)
# Inputs:
# img = input image
# ksize = kernel size
# i = iterations, i.e. number of consecutive filtering passes
#dilated = pcv.dilate(img=fill_image, ksize=1, i=1)
dilated = pcv.dilate(gray_img=fill_image, ksize=2, i=1)
# STEP 9: Find objects (contours: black-white boundaries)
# Inputs:
# img = image that the objects will be overlayed
# mask = what is used for object detection
id_objects, obj_hierarchy = pcv.find_objects(img=img1, mask=dilated)
#id_objects, obj_hierarchy = pcv.find_objects(gray_img, mask)
# STEP 10: Define region of interest (ROI)
# Inputs:
# img = img to overlay roi
# x_adj = adjust center along x axis
# y_adj = adjust center along y axis
# h_adj = adjust height
# w_adj = adjust width
# roi_contour, roi_hierarchy = pcv.roi.rectangle(img1, 10, 500, -10, -100)
# ^ ^
# |________________|
# adjust these four values
roi_contour, roi_hierarchy = pcv.roi.rectangle(img=img1, x=200, y=190, h=2000, w=3000)
# STEP 11: Keep objects that overlap with the ROI
# Inputs:
# img = img to display kept objects
# roi_contour = contour of roi, output from any ROI function
# roi_hierarchy = contour of roi, output from any ROI function
# object_contour = contours of objects, output from "Identifying Objects" function
# obj_hierarchy = hierarchy of objects, output from "Identifying Objects" function
# roi_type = 'partial' (default, for partially inside), 'cutto', or 'largest' (keep only largest contour)
roi_objects, roi_obj_hierarchy, kept_mask, obj_area = pcv.roi_objects(img=img1, roi_contour=roi_contour,
roi_hierarchy=roi_hierarchy,
object_contour=id_objects,
obj_hierarchy=obj_hierarchy,
roi_type='partial')
# STEP 12: This function take a image with multiple contours and
# clusters them based on user input of rows and columns
# Inputs:
# img = An RGB image
# roi_objects = object contours in an image that are needed to be clustered.
# roi_obj_hierarchy = object hierarchy
# nrow = number of rows to cluster (this should be the approximate number of desired rows in the entire image even if there isn't a literal row of plants)
# ncol = number of columns to cluster (this should be the approximate number of desired columns in the entire image even if there isn't a literal row of plants)
# show_grid = if True then a grid gets displayed in debug mode (default show_grid=False)
clusters_i, contours, hierarchies = pcv.cluster_contours(img=img1, roi_objects=roi_objects,
roi_obj_hierarchy=roi_obj_hierarchy,
nrow=2, ncol=3)
# STEP 13: This function takes clustered contours and splits them into multiple images,
# also does a check to make sure that the number of inputted filenames matches the number
# of clustered contours. If no filenames are given then the objects are just numbered
# Inputs:
# img = ideally a masked RGB image.
# grouped_contour_indexes = output of cluster_contours, indexes of clusters of contours
# contours = contours to cluster, output of cluster_contours
# hierarchy = object hierarchy
# outdir = directory for output images
# file = the name of the input image to use as a base name , output of filename from read_image function
# filenames = input txt file with list of filenames in order from top to bottom left to right (likely list of genotypes)
# Set global debug behavior to None (default), "print" (to file), or "plot" (Jupyter Notebooks or X11)
pcv.params.debug = "print"
out = args.outdir
names = args.names
output_path, imgs, masks = pcv.cluster_contour_splitimg(rgb_img=img1, grouped_contour_indexes=clusters_i,
contours=contours, hierarchy=hierarchies,
outdir=out, file=filename, filenames=names)
def main():
# create options object for argument parsing
args = options()
# set device
device = 0
# set debug
pcv.params.debug = args.debug
outfile = False
if args.writeimg:
outfile = os.path.join(args.outdir, os.path.basename(args.image)[:-4])
# read in image
img, path, filename = pcv.readimage(filename=args.image, debug=args.debug)
# read in a background image for each zoom level
config_file = open(args.bkg, 'r')
config = json.load(config_file)
config_file.close()
if "z1500" in args.image:
bkg_image = config["z1500"]
elif "z2500" in args.image:
bkg_image = config["z2500"]
else:
pcv.fatal_error("Image {0} has an unsupported zoom level.".format(args.image))
bkg, bkg_path, bkg_filename = pcv.readimage(filename=bkg_image, debug=args.debug)
# Detect edges in the background image
device, bkg_sat = pcv.rgb2gray_hsv(img=bkg, channel="s", device=device, debug=args.debug)
device += 1
bkg_edges = feature.canny(bkg_sat)
if args.debug == "print":
pcv.print_image(img=bkg_edges, filename=str(device) + '_background_edges.png')
elif args.debug == "plot":
pcv.plot_image(img=bkg_edges, cmap="gray")
# Close background edge contours
bkg_edges_closed = ndi.binary_closing(bkg_edges)
device += 1
if args.debug == "print":
pcv.print_image(img=bkg_edges_closed, filename=str(device) + '_closed_background_edges.png')
elif args.debug == "plot":
pcv.plot_image(img=bkg_edges_closed, cmap="gray")
# Fill in closed contours in background
bkg_fill_contours = ndi.binary_fill_holes(bkg_edges_closed)
device += 1
if args.debug == "print":
pcv.print_image(img=bkg_fill_contours, filename=str(device) + '_filled_background_edges.png')
elif args.debug == "plot":
pcv.plot_image(img=bkg_fill_contours, cmap="gray")
# Naive Bayes image classification/segmentation
device, mask = pcv.naive_bayes_classifier(img=img, pdf_file=args.pdf, device=device, debug=args.debug)
# Do a light cleaning of the plant mask to remove small objects
cleaned = morphology.remove_small_objects(mask["plant"].astype(bool), 2)
device += 1
if args.debug == "print":
pcv.print_image(img=cleaned, filename=str(device) + '_cleaned_mask.png')
elif args.debug == "plot":
pcv.plot_image(img=cleaned, cmap="gray")
# Convert the input image to a saturation channel grayscale image
device, sat = pcv.rgb2gray_hsv(img=img, channel="s", device=device, debug=args.debug)
# Detect edges in the saturation image
edges = feature.canny(sat)
device += 1
if args.debug == "print":
pcv.print_image(img=edges, filename=str(device) + '_plant_edges.png')
elif args.debug == "plot":
pcv.plot_image(img=edges, cmap="gray")
# Combine pixels that are in both foreground edges and the filled background edges
device, combined_bkg = pcv.logical_and(img1=edges.astype(np.uint8) * 255,
img2=bkg_fill_contours.astype(np.uint8) * 255, device=device,
debug=args.debug)
# Remove background pixels from the foreground edges
device += 1
filtered = np.copy(edges)
filtered[np.where(combined_bkg == 255)] = False
if args.debug == "print":
pcv.print_image(img=filtered, filename=str(device) + '_filtered_edges.png')
elif args.debug == "plot":
pcv.plot_image(img=filtered, cmap="gray")
# Combine the cleaned naive Bayes mask and the filtered foreground edges
device += 1
combined = cleaned + filtered
if args.debug == "print":
pcv.print_image(img=combined, filename=str(device) + '_combined_foreground.png')
elif args.debug == "plot":
pcv.plot_image(img=combined, cmap="gray")
# Close off broken edges and other incomplete contours
device += 1
closed_features = ndi.binary_closing(combined, structure=np.ones((3, 3)))
if args.debug == "print":
pcv.print_image(img=closed_features, filename=str(device) + '_closed_features.png')
elif args.debug == "plot":
pcv.plot_image(img=closed_features, cmap="gray")
# Fill in holes in contours
# device += 1
# fill_contours = ndi.binary_fill_holes(closed_features)
# if args.debug == "print":
# pcv.print_image(img=fill_contours, filename=str(device) + '_filled_contours.png')
# elif args.debug == "plot":
# pcv.plot_image(img=fill_contours, cmap="gray")
# Use median blur to break horizontal and vertical thin edges (pot edges)
device += 1
blurred_img = ndi.median_filter(closed_features.astype(np.uint8) * 255, (3, 1))
blurred_img = ndi.median_filter(blurred_img, (1, 3))
# Remove small objects left behind by blurring
cleaned2 = morphology.remove_small_objects(blurred_img.astype(bool), 200)
if args.debug == "print":
pcv.print_image(img=cleaned2, filename=str(device) + '_cleaned_by_median_blur.png')
elif args.debug == "plot":
pcv.plot_image(img=cleaned2, cmap="gray")
# Define region of interest based on camera zoom level for masking the naive Bayes classified image
# if "z1500" in args.image:
# h = 1000
# elif "z2500" in args.image:
# h = 1050
# else:
# pcv.fatal_error("Image {0} has an unsupported zoom level.".format(args.image))
# roi, roi_hierarchy = pcv.roi.rectangle(x=300, y=150, w=1850, h=h, img=img)
# Mask the classified image to remove noisy areas prior to finding contours
# side_mask = np.zeros(np.shape(img)[:2], dtype=np.uint8)
# cv2.drawContours(side_mask, roi, -1, (255), -1)
# device, masked_img = pcv.apply_mask(img=cv2.merge([mask["plant"], mask["plant"], mask["plant"]]), mask=side_mask,
# mask_color="black", device=device, debug=args.debug)
# Convert the masked image back to grayscale
# masked_img = masked_img[:, :, 0]
# Close off contours at the base of the plant
# if "z1500" in args.image:
# pt1 = (1100, 1118)
# pt2 = (1340, 1120)
# elif "z2500" in args.image:
# pt1 = (1020, 1162)
# pt2 = (1390, 1166)
# else:
# pcv.fatal_error("Image {0} has an unsupported zoom level.".format(args.image))
# masked_img = cv2.rectangle(np.copy(masked_img), pt1, pt2, (255), -1)
# closed_mask = ndi.binary_closing(masked_img.astype(bool), iterations=3)
# Find objects in the masked naive Bayes mask
# device, objects, obj_hierarchy = pcv.find_objects(img=img, mask=np.copy(masked_img), device=device,
# debug=args.debug)
# objects, obj_hierarchy = cv2.findContours(np.copy(closed_mask.astype(np.uint8) * 255), cv2.RETR_CCOMP,
# cv2.CHAIN_APPROX_NONE)[-2:]
# Clean up the combined plant edges/mask image by removing filled in gaps/holes
# device += 1
# cleaned3 = np.copy(cleaned2)
# cleaned3 = cleaned3.astype(np.uint8) * 255
# # Loop over the contours from the naive Bayes mask
# for c, contour in enumerate(objects):
# # Calculate the area of each contour
# # area = cv2.contourArea(contour)
# # If the contour is a hole (i.e. it has no children and it has a parent)
# # And it is not a small hole in a leaf that was not classified
# if obj_hierarchy[0][c][2] == -1 and obj_hierarchy[0][c][3] > -1:
# # Then fill in the contour (hole) black on the cleaned mask
# cv2.drawContours(cleaned3, objects, c, (0), -1, hierarchy=obj_hierarchy)
# if args.debug == "print":
# pcv.print_image(img=cleaned3, filename=str(device) + '_gaps_removed.png')
# elif args.debug == "plot":
# pcv.plot_image(img=cleaned3, cmap="gray")
# Find contours using the cleaned mask
device, contours, contour_hierarchy = pcv.find_objects(img=img, mask=np.copy(cleaned2.astype(np.uint8)),
device=device, debug=args.debug)
# Define region of interest based on camera zoom level for contour filtering
if "z1500" in args.image:
h = 940
elif "z2500" in args.image:
h = 980
else:
pcv.fatal_error("Image {0} has an unsupported zoom level.".format(args.image))
roi, roi_hierarchy = pcv.roi.rectangle(x=300, y=150, w=1850, h=h, img=img)
# Filter contours in the region of interest
device, roi_objects, hierarchy, kept_mask, obj_area = 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)
# Analyze only images with plants present
if len(roi_objects) > 0:
# Object combine kept objects
device, plant_contour, plant_mask = pcv.object_composition(img=img, contours=roi_objects, hierarchy=hierarchy,
device=device, debug=args.debug)
if args.writeimg:
# Save the plant mask if requested
pcv.print_image(img=plant_mask, filename=outfile + "_mask.png")
# Find shape properties, output shape image
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)
# Set the boundary line based on the camera zoom level
if "z1500" in args.image:
line_position = 930
elif "z2500" in args.image:
line_position = 885
else:
pcv.fatal_error("Image {0} has an unsupported zoom level.".format(args.image))
# Shape properties relative to user boundary line
device, boundary_header, boundary_data, boundary_img = pcv.analyze_bound_horizontal(img=img, obj=plant_contour,
mask=plant_mask,
line_position=line_position,
device=device,
debug=args.debug,
filename=outfile)
# Determine color properties: Histograms, Color Slices and Pseudocolored Images,
# output color analyzed images
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")
result.write('\t'.join(map(str, boundary_header)) + "\n")
result.write('\t'.join(map(str, boundary_data)) + "\n")
result.write('\t'.join(map(str, boundary_img)) + "\n")
for row in color_img:
result.write('\t'.join(map(str, row)) + "\n")
result.close()
def main():
# Get options
args = options()
# Set variables
device = 0
pcv.params.debug = args.debug
img_file = args.image
# Read image
img, path, filename = pcv.readimage(filename=img_file, mode='rgb')
# Process saturation channel from HSV colour space
s = pcv.rgb2gray_hsv(rgb_img=img, channel='s')
lp_s = pcv.laplace_filter(s, 1, 1)
shrp_s = pcv.image_subtract(s, lp_s)
s_eq = pcv.hist_equalization(shrp_s)
s_thresh = pcv.threshold.binary(gray_img=s_eq,
threshold=215,
max_value=255,
object_type='light')
s_mblur = pcv.median_blur(gray_img=s_thresh, ksize=5)
# Process green-magenta channel from LAB colour space
b = pcv.rgb2gray_lab(rgb_img=img, channel='a')
b_lp = pcv.laplace_filter(b, 1, 1)
b_shrp = pcv.image_subtract(b, b_lp)
b_thresh = pcv.threshold.otsu(b_shrp, 255, object_type='dark')
# Create and apply mask
bs = pcv.logical_or(bin_img1=s_mblur, bin_img2=b_thresh)
filled = pcv.fill_holes(bs)
masked = pcv.apply_mask(img=img, mask=filled, mask_color='white')
# Extract colour channels from masked image
masked_a = pcv.rgb2gray_lab(rgb_img=masked, channel='a')
masked_b = pcv.rgb2gray_lab(rgb_img=masked, channel='b')
# Threshold the green-magenta and blue images
maskeda_thresh = pcv.threshold.binary(gray_img=masked_a,
threshold=115,
max_value=255,
object_type='dark')
maskeda_thresh1 = pcv.threshold.binary(gray_img=masked_a,
threshold=140,
max_value=255,
object_type='light')
maskedb_thresh = pcv.threshold.binary(gray_img=masked_b,
threshold=128,
max_value=255,
object_type='light')
# Join the thresholded saturation and blue-yellow images (OR)
ab1 = pcv.logical_or(bin_img1=maskeda_thresh, bin_img2=maskedb_thresh)
ab = pcv.logical_or(bin_img1=maskeda_thresh1, bin_img2=ab1)
# Produce and apply a mask
opened_ab = pcv.opening(gray_img=ab)
ab_fill = pcv.fill(bin_img=ab, size=200)
closed_ab = pcv.closing(gray_img=ab_fill)
masked2 = pcv.apply_mask(img=masked, mask=bs, mask_color='white')
# Identify objects
id_objects, obj_hierarchy = pcv.find_objects(img=masked2, mask=ab_fill)
# Define region of interest (ROI)
roi1, roi_hierarchy = pcv.roi.rectangle(img=masked2,
x=250,
y=100,
h=200,
w=200)
# Decide what objects to keep
roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(
img=img,
roi_contour=roi1,
roi_hierarchy=roi_hierarchy,
object_contour=id_objects,
obj_hierarchy=obj_hierarchy,
roi_type='partial')
# Object combine kept objects
obj, mask = pcv.object_composition(img=img,
contours=roi_objects,
hierarchy=hierarchy3)
############### Analysis ################
outfile = False
if args.writeimg == True:
outfile = args.outdir + "/" + filename
# Analyze the plant
analysis_image = pcv.analyze_object(img=img, obj=obj, mask=mask)
color_histogram = pcv.analyze_color(rgb_img=img,
mask=kept_mask,
hist_plot_type='all')
top_x, bottom_x, center_v_x = pcv.x_axis_pseudolandmarks(img=img,
obj=obj,
mask=mask)
top_y, bottom_y, center_v_y = pcv.y_axis_pseudolandmarks(img=img,
obj=obj,
mask=mask)
# Print results of the analysis
pcv.print_results(filename=args.result)
pcv.output_mask(img,
kept_mask,
filename,
outdir=args.outdir,
mask_only=True)
def main():
# Get options
args = options()
debug = args.debug
# Read image
img, path, filename = pcv.readimage(args.image)
# Pipeline step
device = 0
device, img1 = pcv.white_balance(device, img, debug,
(100, 100, 1000, 1000))
img = img1
#seedmask, path1, filename1 = pcv.readimage(args.mask)
#device, seedmask = pcv.rgb2gray(seedmask, device, debug)
#device, inverted = pcv.invert(seedmask, device, debug)
#device, masked_img = pcv.apply_mask(img, inverted, 'white', device, debug)
device, img_gray_sat = pcv.rgb2gray_hsv(img1, 's', device, debug)
device, img_binary = pcv.binary_threshold(img_gray_sat, 70, 255, 'light',
device, debug)
img_binary1 = np.copy(img_binary)
device, fill_image = pcv.fill(img_binary1, img_binary, 300, device, debug)
device, seed_objects, seed_hierarchy = pcv.find_objects(
img, fill_image, device, debug)
device, roi1, roi_hierarchy1 = pcv.define_roi(img, 'rectangle', device,
None, 'default', debug, True,
1500, 1000, -1000, -500)
device, roi_objects, roi_obj_hierarchy, kept_mask, obj_area = pcv.roi_objects(
img, 'partial', roi1, roi_hierarchy1, seed_objects, seed_hierarchy,
device, debug)
img_copy = np.copy(img)
for i in range(0, len(roi_objects)):
rand_color = pcv.color_palette(1)
cv2.drawContours(img_copy,
roi_objects,
i,
rand_color[0],
-1,
lineType=8,
hierarchy=roi_obj_hierarchy)
pcv.print_image(
img_copy,
os.path.join(args.outdir, filename[:-4]) + "-seed-confetti.jpg")
shape_header = [] # Store the table header
table = [] # Store the PlantCV measurements for each seed in a table
for i in range(0, len(roi_objects)):
if roi_obj_hierarchy[0][i][
3] == -1: # Only continue if the object is an outermost contour
# Object combine kept objects
# Inputs:
# contours = object list
# device = device number. Used to count steps in the pipeline
# debug = None, print, or plot. Print = save to file, Plot = print to screen.
device, obj, mask = pcv.object_composition(
img, [roi_objects[i]], np.array([[roi_obj_hierarchy[0][i]]]),
device, None)
if obj is not None:
# Measure the area and other shape properties of each seed
# Inputs:
# img = image object (most likely the original), color(RGB)
# imgname = name of image
# obj = single or grouped contour object
# device = device number. Used to count steps in the pipeline
# debug = None, print, or plot. Print = save to file, Plot = print to screen.
# filename = False or image name. If defined print image
device, shape_header, shape_data, shape_img = pcv.analyze_object(
img, "img", obj, mask, device, None)
if shape_data is not None:
table.append(shape_data[1])
data_array = np.array(table)
maxval = np.argmax(data_array)
maxseed = np.copy(img)
cv2.drawContours(maxseed, roi_objects, maxval, (0, 255, 0), 10)
imgtext = "This image has " + str(len(data_array)) + " seeds"
sizeseed = "The largest seed is in green and is " + str(
data_array[maxval]) + " pixels"
cv2.putText(maxseed, imgtext, (500, 300), cv2.FONT_HERSHEY_SIMPLEX, 5,
(0, 0, 0), 10)
cv2.putText(maxseed, sizeseed, (500, 600), cv2.FONT_HERSHEY_SIMPLEX, 5,
(0, 0, 0), 10)
pcv.print_image(maxseed,
os.path.join(args.outdir, filename[:-4]) + "-maxseed.jpg")
# Get options args = options() # Set debug to the global parameter pcv.params.debug = args.debug # In[106]: # Read image (sometimes you need to run this line twice to see the image) # Inputs: # filename - Image file to be read in # mode - How to read in the image; either 'native' (default), 'rgb', 'gray', or 'csv' img, path, filename = pcv.readimage(filename=args.image) # In[107]: #crop Image from plantcv import plantcv as pcv # Set global debug behavior to None (default), "print" (to file), # or "plot" (Jupyter Notebooks or X11) pcv.params.debug = "plot" # Crop image crop_img = pcv.crop(img=img, x=400, y=20, h=100, w=100)
def main():
# Get options
args = options()
# Set variables
pcv.params.debug = args.debug # Replace the hard-coded debug with the debug flag
img_file = args.image # Replace the hard-coded input image with image flag
############### Image read-in ################
# Read target image
img, path, filename = pcv.readimage(filename = img_file, mode = "rgb")
############### Find scale and crop ################
# find colour card in the image to be analysed
df, start, space = pcv.transform.find_color_card(rgb_img = img)
if int(start[0]) < 2000:
img = imutils.rotate_bound(img, -90)
rotated = 1
df, start, space = pcv.transform.find_color_card(rgb_img = img)
else: rotated = 0
#if img.shape[0] > 6000:
# rotated = 1
#else: rotated = 0
img_mask = pcv.transform.create_color_card_mask(rgb_img = img, radius = 10, start_coord = start, spacing = space, ncols = 4, nrows = 6)
# write the spacing of the colour card to file as size marker
with open(r'size_marker.csv', 'a') as f:
writer = csv.writer(f)
writer.writerow([filename, space[0]])
# define a bounding rectangle around the colour card
x_cc,y_cc,w_cc,h_cc = cv2.boundingRect(img_mask)
x_cc = int(round(x_cc - 0.3 * w_cc))
y_cc = int(round(y_cc - 0.3 * h_cc))
h_cc = int(round(h_cc * 1.6))
w_cc = int(round(w_cc * 1.6))
# crop out colour card
start_point = (x_cc, y_cc)
end_point = (x_cc+w_cc, y_cc+h_cc)
colour = (0, 0, 0)
thickness = -1
crop_img = cv2.rectangle(img, start_point, end_point, colour, thickness)
############### Fine segmentation ################
# Threshold A and B channels of the LAB colourspace and the Hue channel of the HSV colourspace
l_thresh, _ = pcv.threshold.custom_range(img=crop_img, lower_thresh=[70,0,0], upper_thresh=[255,255,255], channel='LAB')
a_thresh, _ = pcv.threshold.custom_range(img=crop_img, lower_thresh=[0,0,0], upper_thresh=[255,145,255], channel='LAB')
b_thresh, _ = pcv.threshold.custom_range(img=crop_img, lower_thresh=[0,0,123], upper_thresh=[255,255,255], channel='LAB')
h_thresh_low, _ = pcv.threshold.custom_range(img=crop_img, lower_thresh=[0,0,0], upper_thresh=[130,255,255], channel='HSV')
h_thresh_high, _ = pcv.threshold.custom_range(img=crop_img, lower_thresh=[150,0,0], upper_thresh=[255,255,255], channel='HSV')
h_thresh = pcv.logical_or(h_thresh_low, h_thresh_high)
# Join the thresholded images to keep only consensus pixels
ab = pcv.logical_and(b_thresh, a_thresh)
lab = pcv.logical_and(l_thresh, ab)
labh = pcv.logical_and(lab, h_thresh)
# Fill small objects
labh_clean = pcv.fill(labh, 200)
# Dilate to close broken borders
#labh_dilated = pcv.dilate(labh_clean, 4, 1)
labh_dilated = labh_clean
# Apply mask (for VIS images, mask_color=white)
masked = pcv.apply_mask(crop_img, labh_dilated, "white")
# Identify objects
contours, hierarchy = pcv.find_objects(crop_img, labh_dilated)
# Define ROI
if rotated == 1:
roi_height = 3000
roi_lwr_bound = y_cc + (h_cc * 0.5) - roi_height
roi_contour, roi_hierarchy= pcv.roi.rectangle(x=1000, y=roi_lwr_bound, h=roi_height, w=2000, img=crop_img)
else:
roi_height = 1500
roi_lwr_bound = y_cc + (h_cc * 0.5) - roi_height
roi_contour, roi_hierarchy= pcv.roi.rectangle(x=2000, y=roi_lwr_bound, h=roi_height, w=2000, img=crop_img)
# Decide which objects to keep
filtered_contours, filtered_hierarchy, mask, area = pcv.roi_objects(img = crop_img,
roi_type = 'partial',
roi_contour = roi_contour,
roi_hierarchy = roi_hierarchy,
object_contour = contours,
obj_hierarchy = hierarchy)
# Combine kept objects
obj, mask = pcv.object_composition(crop_img, filtered_contours, filtered_hierarchy)
############### Analysis ################
outfile=False
if args.writeimg==True:
outfile_black=args.outdir+"/"+filename+"_black"
outfile_white=args.outdir+"/"+filename+"_white"
outfile_analysed=args.outdir+"/"+filename+"_analysed"
# analyse shape
shape_img = pcv.analyze_object(crop_img, obj, mask)
pcv.print_image(shape_img, outfile_analysed)
# analyse colour
colour_img = pcv.analyze_color(crop_img, mask, 'hsv')
# keep the segmented plant for visualisation
picture_mask = pcv.apply_mask(crop_img, mask, "black")
pcv.print_image(picture_mask, outfile_black)
picture_mask = pcv.apply_mask(crop_img, mask, "white")
pcv.print_image(picture_mask, outfile_white)
# print out results
pcv.outputs.save_results(filename=args.result, outformat="json")
P[:, i] = img[xs, ys, i].reshape((-1))
return P
@staticmethod
def restore_image(flatten, shape):
img = np.zeros(shape)
for i in range(shape[2]):
img[:, :, i] = flatten[:, i].reshape(shape[:2])
return img
if __name__ == '__main__':
sharp_img, _, _ = pcv.readimage(
filename="res/colorboard/sharp.png"
)
blur_img, _, _ = pcv.readimage(
filename="res/colorboard/blur.png"
)
mask = np.zeros(shape=np.shape(sharp_img)[:2], dtype=np.uint8())
mask = utils.create_mask(sharp_img, mask, 85, 115, 40, 42, 1, [23])
mask = utils.create_mask(sharp_img, mask, 300, 113, 41, 42, 1,
[22, 21, 20, 18, 17, 14])
mask = mask * 10
solver = MyColorCorrection(blur_img, sharp_img, np.ones((480, 480)), 1)
img_corrected = solver.transform(blur_img)
cv2.imwrite('corrected_all.png', img_corrected)
def main():
# Initialize options
args = options()
# Set PlantCV debug mode to input debug method
pcv.params.debug = args.debug
# Use PlantCV to read in the input image. The function outputs an image as a NumPy array, the path to the file,
# and the image filename
img, path, filename = pcv.readimage(filename=args.image)
# ## Segmentation
# ### Saturation channel
# Convert the RGB image to HSV colorspace and extract the saturation channel
s = pcv.rgb2gray_hsv(rgb_img=img, channel='s')
# Use a binary threshold to set an inflection value where all pixels in the grayscale saturation image below the
# threshold get set to zero (pure black) and all pixels at or above the threshold get set to 255 (pure white)
s_thresh = pcv.threshold.binary(gray_img=s, threshold=80, max_value=255, object_type='light')
# ### Blue-yellow channel
# Convert the RGB image to LAB colorspace and extract the blue-yellow channel
b = pcv.rgb2gray_lab(rgb_img=img, channel='b')
# Use a binary threshold to set an inflection value where all pixels in the grayscale blue-yellow image below the
# threshold get set to zero (pure black) and all pixels at or above the threshold get set to 255 (pure white)
b_thresh = pcv.threshold.binary(gray_img=b, threshold=134, max_value=255, object_type='light')
# ### Green-magenta channel
# Convert the RGB image to LAB colorspace and extract the green-magenta channel
a = pcv.rgb2gray_lab(rgb_img=img, channel='a')
# In the green-magenta image the plant pixels are darker than the background. Setting object_type="dark" will
# invert the image first and then use a binary threshold to set an inflection value where all pixels in the
# grayscale green-magenta image below the threshold get set to zero (pure black) and all pixels at or above the
# threshold get set to 255 (pure white)
a_thresh = pcv.threshold.binary(gray_img=a, threshold=122, max_value=255, object_type='dark')
# Combine the binary images for the saturation and blue-yellow channels. The "or" operator returns a binary image
# that is white when a pixel was white in either or both input images
bs = pcv.logical_or(bin_img1=s_thresh, bin_img2=b_thresh)
# Combine the binary images for the combined saturation and blue-yellow channels and the green-magenta channel.
# The "or" operator returns a binary image that is white when a pixel was white in either or both input images
bsa = pcv.logical_or(bin_img1=bs, bin_img2=a_thresh)
# The combined binary image labels plant pixels well but the background still has pixels labeled as foreground.
# Small white noise (salt) in the background can be removed by filtering white objects in the image by size and
# setting a size threshold where smaller objects can be removed
bsa_fill1 = pcv.fill(bin_img=bsa, size=15) # Fill small noise
# Before more stringent size filtering is done we want to connect plant parts that may still be disconnected from
# the main plant. Use a dilation to expand the boundary of white regions. Ksize is the size of a box scanned
# across the image and i is the number of times a scan is done
bsa_fill2 = pcv.dilate(gray_img=bsa_fill1, ksize=3, i=3)
# Remove small objects by size again but use a higher threshold
bsa_fill3 = pcv.fill(bin_img=bsa_fill2, size=250)
# Use the binary image to identify objects or connected components.
id_objects, obj_hierarchy = pcv.find_objects(img=img, mask=bsa_fill3)
# Because the background still contains pixels labeled as foreground, the object list contains background.
# Because these images were collected in an automated system the plant is always centered in the image at the
# same position each time. Define a region of interest (ROI) to set the area where we expect to find plant
# pixels. PlantCV can make simple ROI shapes like rectangles, circles, etc. but here we use a custom ROI to fit a
# polygon around the plant area
roi_custom, roi_hier_custom = pcv.roi.custom(img=img, vertices=[[1085, 1560], [1395, 1560], [1395, 1685],
[1890, 1744], [1890, 25], [600, 25], [615, 1744],
[1085, 1685]])
# Use the ROI to filter out objects found outside the ROI. When `roi_type = "cutto"` objects outside the ROI are
# cropped out. The default `roi_type` is "partial" which allows objects to overlap the ROI and be retained
roi_objects, hierarchy, kept_mask, obj_area = pcv.roi_objects(img=img, roi_contour=roi_custom,
roi_hierarchy=roi_hier_custom,
object_contour=id_objects,
obj_hierarchy=obj_hierarchy, roi_type='cutto')
# Filter remaining objects by size again to remove any remaining background objects
filled_mask1 = pcv.fill(bin_img=kept_mask, size=350)
# Use a closing operation to first dilate (expand) and then erode (shrink) the plant to fill in any additional
# gaps in leaves or stems
filled_mask2 = pcv.closing(gray_img=filled_mask1)
# Remove holes or dark spot noise (pepper) in the plant binary image
filled_mask3 = pcv.fill_holes(filled_mask2)
# With the clean binary image identify the contour of the plant
id_objects, obj_hierarchy = pcv.find_objects(img=img, mask=filled_mask3)
# Because a plant or object of interest may be composed of multiple contours, it is required to combine all
# remaining contours into a single contour before measurements can be done
obj, mask = pcv.object_composition(img=img, contours=id_objects, hierarchy=obj_hierarchy)
# ## Measurements PlantCV has several built-in measurement or analysis methods. Here, basic measurements of size
# and shape are done. Additional typical modules would include plant height (`pcv.analyze_bound_horizontal`) and
# color (`pcv.analyze_color`)
shape_img = pcv.analyze_object(img=img, obj=obj, mask=mask)
# Save the shape image if requested
if args.writeimg:
outfile = os.path.join(args.outdir, filename[:-4] + "_shapes.png")
pcv.print_image(img=shape_img, filename=outfile)
# ## Morphology workflow
# Update a few PlantCV parameters for plotting purposes
pcv.params.text_size = 1.5
pcv.params.text_thickness = 5
pcv.params.line_thickness = 15
# Convert the plant mask into a "skeletonized" image where each path along the stem and leaves are a single pixel
# wide
skel = pcv.morphology.skeletonize(mask=mask)
# Sometimes wide parts of leaves or stems are skeletonized in the direction perpendicular to the main path. These
# "barbs" or "spurs" can be removed by pruning the skeleton to remove small paths. Pruning will also separate the
# individual path segments (leaves and stem parts)
pruned, segmented_img, segment_objects = pcv.morphology.prune(skel_img=skel, size=30, mask=mask)
pruned, segmented_img, segment_objects = pcv.morphology.prune(skel_img=pruned, size=3, mask=mask)
# Leaf and stem segments above are separated but only into individual paths. We can sort the segments into stem
# and leaf paths by identifying primary segments (stems; those that end in a branch point) and secondary segments
# (leaves; those that begin at a branch point and end at a tip point)
leaf_objects, other_objects = pcv.morphology.segment_sort(skel_img=pruned, objects=segment_objects, mask=mask)
# Label the segment unique IDs
segmented_img, labeled_id_img = pcv.morphology.segment_id(skel_img=pruned, objects=leaf_objects, mask=mask)
# Measure leaf insertion angles. Measures the angle between a line fit through the stem paths and a line fit
# through the first `size` points of each leaf path
labeled_angle_img = pcv.morphology.segment_insertion_angle(skel_img=pruned, segmented_img=segmented_img,
leaf_objects=leaf_objects, stem_objects=other_objects,
size=22)
# Save leaf angle image if requested
if args.writeimg:
outfile = os.path.join(args.outdir, filename[:-4] + "_leaf_insertion_angles.png")
pcv.print_image(img=labeled_angle_img, filename=outfile)
# ## Other potential morphological measurements There are many other functions that extract data from within the
# morphology sub-package of PlantCV. For our purposes, we are most interested in the relative angle between each
# leaf and the stem which we measure with `plantcv.morphology.segment_insertion_angle`. However, the following
# cells show some of the other traits that we are able to measure from images that can be succesfully sorted into
# primary and secondary segments.
# Segment the plant binary mask using the leaf and stem segments. Allows for the measurement of individual leaf
# areas
# filled_img = pcv.morphology.fill_segments(mask=mask, objects=leaf_objects)
# Measure the path length of each leaf (geodesic distance)
# labeled_img2 = pcv.morphology.segment_path_length(segmented_img=segmented_img, objects=leaf_objects)
# Measure the straight-line, branch point to tip distance (Euclidean) for each leaf
# labeled_img3 = pcv.morphology.segment_euclidean_length(segmented_img=segmented_img, objects=leaf_objects)
# Measure the curvature of each leaf (Values closer to 1 indicate that a segment is a straight line while larger
# values indicate the segment has more curvature)
# labeled_img4 = pcv.morphology.segment_curvature(segmented_img=segmented_img, objects=leaf_objects)
# Measure absolute leaf angles (angle of linear regression line fit to each leaf object) Note: negative values
# signify leaves to the left of the stem, positive values signify leaves to the right of the stem
# labeled_img5 = pcv.morphology.segment_angle(segmented_img=segmented_img, objects=leaf_objects)
# Measure leaf curvature in degrees
# labeled_img6 = pcv.morphology.segment_tangent_angle(segmented_img=segmented_img, objects=leaf_objects, size=35)
# Measure stem characteristics like stem angle and length
# stem_img = pcv.morphology.analyze_stem(rgb_img=img, stem_objects=other_objects)
# Remove unneeded observations (hack)
_ = pcv.outputs.observations.pop("tips")
_ = pcv.outputs.observations.pop("branch_pts")
angles = pcv.outputs.observations["segment_insertion_angle"]["value"]
remove_indices = []
for i, value in enumerate(angles):
if value == "NA":
remove_indices.append(i)
remove_indices.sort(reverse=True)
for i in remove_indices:
_ = pcv.outputs.observations["segment_insertion_angle"]["value"].pop(i)
# ## Save the results out to file for downsteam analysis
pcv.print_results(filename=args.result)
