def test_plantcv_naive_bayes_classifier():
img = cv2.imread(os.path.join(TEST_DATA, TEST_INPUT_COLOR))
device, mask = pcv.naive_bayes_classifier(img=img, pdf_file=os.path.join(TEST_DATA, TEST_PDFS),
device=0, debug=None)
# Assert that the output image has the dimensions of the input image
if all([i == j] for i, j in zip(np.shape(mask), TEST_GRAY_DIM)):
# Assert that the image is binary
if all([i == j] for i, j in zip(np.unique(mask), [0, 255])):
assert 1
else:
assert 0
else:
assert 0
def test_plantcv_naive_bayes_classifier():
img = cv2.imread(os.path.join(TEST_DATA, TEST_INPUT_COLOR))
device, mask = pcv.naive_bayes_classifier(img=img,
pdf_file=os.path.join(
TEST_DATA, TEST_PDFS),
device=0,
debug=None)
# Assert that the output image has the dimensions of the input image
if all([i == j] for i, j in zip(np.shape(mask), TEST_GRAY_DIM)):
# Assert that the image is binary
if all([i == j] for i, j in zip(np.unique(mask), [0, 255])):
assert 1
else:
assert 0
else:
assert 0
def naive_bayes():
if request.method == 'POST':
imagefile = request.files['image']
pdffile = request.files['pdf']
i = os.path.join(app.config['UPLOAD_FOLDER'], imagefile.filename)
imagefile.save(i)
p = os.path.join(app.config['UPLOAD_FOLDER'], pdffile.filename)
pdffile.save(p)
print("Files uploaded successfully")
img, path, filename = pcv.readimage(i)
#Creating the mask from the base image and the model
device, mask = pcv.naive_bayes_classifier(img,
pdf_file=pdffile.filename,
device=0,
debug="print")
#Applying the mask to the colour image
device, masked_image = pcv.apply_mask(img,
mask['plant'],
'white',
device,
debug="print")
#Converting the image from a Numpy array to a Base64 string to allow the website to render it properly
im = Image.fromarray(masked_image.astype("uint8"))
b, g, r = im.split()
im = Image.merge("RGB", (r, g, b))
rawBytes = io.BytesIO()
im.save(rawBytes, "PNG")
rawBytes.seek(0)
outimage = base64.b64encode(rawBytes.read())
#Returning the template and image
return render_template("result.html", image=outimage)
def main():
# Get options
args = options()
# Read image
img, path, filename = pcv.readimage(args.image)
# roi = cv2.imread(args.roi)
# Pipeline step
device = 0
device, mask = pcv.naive_bayes_classifier(img, "naive_bayes.pdf.txt",
device, args.debug)
mask1 = np.uint8(mask)
mask_copy = np.copy(mask1)
# Fill small objects
device, soil_fill = pcv.fill(mask1, mask_copy, 200, device, args.debug)
# Median Filter
device, soil_mblur = pcv.median_blur(soil_fill, 5, device, args.debug)
device, soil_cnt = pcv.median_blur(soil_fill, 5, device, args.debug)
# Apply mask (for vis images, mask_color=white)
device, masked2 = pcv.apply_mask(img, soil_cnt, 'white', device,
args.debug)
# Identify objects
device, id_objects, obj_hierarchy = pcv.find_objects(
masked2, soil_cnt, device, args.debug)
# Define ROI
device, roi1, roi_hierarchy = pcv.define_roi(img, 'rectangle', device,
None, 'default', args.debug,
True, 0, 0, 0, -925)
# Decide which objects to keep
device, roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(
img, 'partial', roi1, roi_hierarchy, id_objects, obj_hierarchy, device,
args.debug)
# Object combine kept objects
device, obj, mask = pcv.object_composition(img, roi_objects, hierarchy3,
device, args.debug)
# ############## Analysis ################
# output mask
device, maskpath, mask_images = pcv.output_mask(device, img, mask,
filename, args.outdir,
True, args.debug)
# Find shape properties, output shape image (optional)
device, shape_header, shape_data, shape_img = pcv.analyze_object(
img, args.image, obj, mask, device, args.debug)
# Shape properties relative to user boundary line (optional)
device, boundary_header, boundary_data, boundary_img1 = pcv.analyze_bound(
img, args.image, obj, mask, 900, device)
# Determine color properties: Histograms, Color Slices and Pseudocolored Images,
# output color analyzed images (optional)
device, color_header, color_data, color_img = pcv.analyze_color(
img, args.image, mask, 256, device, args.debug, None, 'v', 'img', 300)
result = open(args.result, "a")
result.write('\t'.join(map(str, shape_header)))
result.write("\n")
result.write('\t'.join(map(str, shape_data)))
result.write("\n")
for row in mask_images:
result.write('\t'.join(map(str, row)))
result.write("\n")
result.write('\t'.join(map(str, color_header)))
result.write("\n")
result.write('\t'.join(map(str, color_data)))
result.write("\n")
result.write('\t'.join(map(str, boundary_header)))
result.write("\n")
result.write('\t'.join(map(str, boundary_data)))
result.write("\n")
result.close()
def get_feature(img):
print("step one")
"""
Step one: Background forground substraction
"""
# Get options
args = options()
debug = args.debug
# Read image
filename = args.result
# img, path, filename = pcv.readimage(args.image)
# Pipeline step
device = 0
device, resize_img = pcv.resize(img, 0.4, 0.4, device, debug)
# Classify the pixels as plant or background
device, mask_img = pcv.naive_bayes_classifier(
resize_img,
pdf_file=
"/home/matthijs/PycharmProjects/SMR1/src/vision/ML_background/Trained_models/model_3/naive_bayes_pdfs.txt",
device=0,
debug='print')
# Median Filter
device, blur = pcv.median_blur(mask_img.get('plant'), 5, device, debug)
print("step two")
"""
Step one: Identifiy the objects, extract and filter the objects
"""
# Identify objects
device, id_objects, obj_hierarchy = pcv.find_objects(resize_img,
blur,
device,
debug=None)
# Define ROI
device, roi1, roi_hierarchy = pcv.define_roi(resize_img,
'rectangle',
device,
roi=True,
roi_input='default',
debug=True,
adjust=True,
x_adj=50,
y_adj=10,
w_adj=-100,
h_adj=0)
# Decide which objects to keep
device, roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(
resize_img, 'cutto', roi1, roi_hierarchy, id_objects, obj_hierarchy,
device, debug)
# print(roi_objects[0])
# cv2.drawContours(resize_img, [roi_objects[0]], 0, (0, 255, 0), 3)
# cv2.imshow("img",resize_img)
# cv2.waitKey(0)
area_oud = 0
i = 0
index = 0
object_list = []
# a = np.array([[hierarchy3[0][0]]])
hierarchy = []
for cnt in roi_objects:
area = cv2.contourArea(cnt)
M = cv2.moments(cnt)
if M["m10"] or M["m01"]:
cX = int(M["m10"] / M["m00"])
cY = int(M["m01"] / M["m00"])
# check if the location of the contour is between the constrains
if cX > 200 and cX < 500 and cY > 25 and cY < 400:
# cv2.circle(resize_img, (cX, cY), 5, (255, 0, 255), thickness=1, lineType=1, shift=0)
# check if the size of the contour is bigger than 250
if area > 450:
obj = np.vstack(roi_objects)
object_list.append(roi_objects[i])
hierarchy.append(hierarchy3[0][i])
print(i)
i = i + 1
a = np.array([hierarchy])
# a = [[[-1,-1,-1,-1][-1,-1,-1,-1][-1,-1,-1,-1]]]
# Object combine kept objects
# device, obj, mask_2 = pcv.object_composition(resize_img, object_list, a, device, debug)
mask_contours = np.zeros(resize_img.shape, np.uint8)
cv2.drawContours(mask_contours, object_list, -1, (255, 255, 255), -1)
gray_image = cv2.cvtColor(mask_contours, cv2.COLOR_BGR2GRAY)
ret, mask_contours = cv2.threshold(gray_image, 127, 255, cv2.THRESH_BINARY)
# Identify objects
device, id_objects, obj_hierarchy = pcv.find_objects(resize_img,
mask_contours,
device,
debug=None)
# Decide which objects to keep
device, roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(
resize_img,
'cutto',
roi1,
roi_hierarchy,
id_objects,
obj_hierarchy,
device,
debug=None)
# Object combine kept objects
device, obj, mask = pcv.object_composition(resize_img,
roi_objects,
hierarchy3,
device,
debug=None)
############### Analysis ################
masked = mask.copy()
outfile = False
if args.writeimg == True:
outfile = args.outdir + "/" + filename
print("step three")
"""
Step three: Calculate all the features
"""
# Find shape properties, output shape image (optional)
device, shape_header, shape_data, shape_img = pcv.analyze_object(
resize_img, args.image, obj, mask, device, debug, filename="/file")
print(shape_img)
# Shape properties relative to user boundary line (optional)
device, boundary_header, boundary_data, boundary_img1 = pcv.analyze_bound(
resize_img, args.image, obj, mask, 1680, device)
# Determine color properties: Histograms, Color Slices and Pseudocolored Images, output color analyzed images (optional)
device, color_header, color_data, color_img = pcv.analyze_color(
resize_img, args.image, kept_mask, 256, device, debug, 'all', 'v',
'img', 300)
maks_watershed = mask.copy()
kernel = np.zeros((5, 5), dtype=np.uint8)
device, mask_watershed, = pcv.erode(maks_watershed, 5, 1, device, debug)
device, watershed_header, watershed_data, analysis_images = pcv.watershed_segmentation(
device, resize_img, mask, 50, './examples', debug)
device, list_of_acute_points = pcv.acute_vertex(obj, 30, 60, 10,
resize_img, device, debug)
device, top, bottom, center_v = pcv.x_axis_pseudolandmarks(
obj, mask, resize_img, device, debug)
device, left, right, center_h = pcv.y_axis_pseudolandmarks(
obj, mask, resize_img, device, debug)
device, points_rescaled, centroid_rescaled, bottomline_rescaled = pcv.scale_features(
obj, mask, list_of_acute_points, 225, device, debug)
# Identify acute vertices (tip points) of an object
# Results in set of point values that may indicate tip points
device, vert_ave_c, hori_ave_c, euc_ave_c, ang_ave_c, vert_ave_b, hori_ave_b, euc_ave_b, ang_ave_b = pcv.landmark_reference_pt_dist(
points_rescaled, centroid_rescaled, bottomline_rescaled, device, debug)
landmark_header = [
'HEADER_LANDMARK', 'tip_points', 'tip_points_r', 'centroid_r',
'baseline_r', 'tip_number', 'vert_ave_c', 'hori_ave_c', 'euc_ave_c',
'ang_ave_c', 'vert_ave_b', 'hori_ave_b', 'euc_ave_b', 'ang_ave_b',
'left_lmk', 'right_lmk', 'center_h_lmk', 'left_lmk_r', 'right_lmk_r',
'center_h_lmk_r', 'top_lmk', 'bottom_lmk', 'center_v_lmk', 'top_lmk_r',
'bottom_lmk_r', 'center_v_lmk_r'
]
landmark_data = [
'LANDMARK_DATA', 0, 0, 0, 0,
len(list_of_acute_points), vert_ave_c, hori_ave_c, euc_ave_c,
ang_ave_c, vert_ave_b, hori_ave_b, euc_ave_b, ang_ave_b, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0
]
shape_data_train = list(shape_data)
shape_data_train.pop(0)
shape_data_train.pop(10)
watershed_data_train = list(watershed_data)
watershed_data_train.pop(0)
landmark_data_train = [
len(list_of_acute_points), vert_ave_c, hori_ave_c, euc_ave_c,
ang_ave_c, vert_ave_b, hori_ave_b, euc_ave_b, ang_ave_b
]
X = shape_data_train + watershed_data_train + landmark_data_train
print("len X", len(X))
print(X)
# Write shape and color data to results fil
result = open(args.result, "a")
result.write('\t'.join(map(str, shape_header)))
result.write("\n")
result.write('\t'.join(map(str, shape_data)))
result.write("\n")
result.write('\t'.join(map(str, watershed_header)))
result.write("\n")
result.write('\t'.join(map(str, watershed_data)))
result.write("\n")
result.write('\t'.join(map(str, landmark_header)))
result.write("\n")
result.write('\t'.join(map(str, landmark_data)))
result.write("\n")
for row in shape_img:
result.write('\t'.join(map(str, row)))
result.write("\n")
result.write('\t'.join(map(str, color_header)))
result.write("\n")
result.write('\t'.join(map(str, color_data)))
result.write("\n")
for row in color_img:
result.write('\t'.join(map(str, row)))
result.write("\n")
result.close()
print("done")
print(shape_img)
return X, shape_img, masked
def get_height(img):
# print("step one")
"""
Step one: Background forground substraction
"""
# Get options
args = options()
debug = args.debug
# Read image
filename = args.result
# img, path, filename = pcv.readimage(args.image)
# Pipeline step
device = 0
device, resize_img = pcv.resize(img, 0.4, 0.4, device, debug)
# Classify the pixels as plant or background
device, mask_img = pcv.naive_bayes_classifier(
resize_img,
pdf_file=
"./../ML_background/Trained_models/model_6/naive_bayes_pdfs.txt",
device=0,
debug='print')
# Median Filter
device, blur = pcv.median_blur(mask_img.get('plant'), 5, device, debug)
# print("step two")
"""
Step one: Identifiy the objects, extract and filter the objects
"""
# Identify objects
device, id_objects, obj_hierarchy = pcv.find_objects(resize_img,
blur,
device,
debug=None)
# Define ROI
device, roi1, roi_hierarchy = pcv.define_roi(resize_img,
'rectangle',
device,
roi=True,
roi_input='default',
debug=None,
adjust=True,
x_adj=50,
y_adj=10,
w_adj=0,
h_adj=0)
# Decide which objects to keep
device, roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(
resize_img, 'cutto', roi1, roi_hierarchy, id_objects, obj_hierarchy,
device, debug)
# print(roi_objects[0])
# cv2.drawContours(resize_img, [roi_objects[0]], 0, (0, 255, 0), 3)
# cv2.imshow("img",resize_img)
# cv2.waitKey(0)
area_oud = 0
i = 0
index = 0
object_list = []
# a = np.array([[hierarchy3[0][0]]])
hierarchy = []
for cnt in roi_objects:
area = cv2.contourArea(cnt)
M = cv2.moments(cnt)
if M["m10"] or M["m01"]:
cX = int(M["m10"] / M["m00"])
cY = int(M["m01"] / M["m00"])
# check if the location of the contour is between the constrains
# cv2.circle(resize_img, (cX, cY), 5, (255, 0, 255), thickness=1, lineType=1, shift=0)
# check if the size of the contour is bigger than 250
if area > 200:
obj = np.vstack(roi_objects)
object_list.append(roi_objects[i])
hierarchy.append(hierarchy3[0][i])
# print(i)
i = i + 1
a = np.array([hierarchy])
# a = [[[-1,-1,-1,-1][-1,-1,-1,-1][-1,-1,-1,-1]]]
# Object combine kept objects
# device, obj, mask_2 = pcv.object_composition(resize_img, object_list, a, device, debug)
mask_contours = np.zeros(resize_img.shape, np.uint8)
cv2.drawContours(mask_contours, object_list, -1, (255, 255, 255), -1)
gray_image = cv2.cvtColor(mask_contours, cv2.COLOR_BGR2GRAY)
ret, mask_contours = cv2.threshold(gray_image, 127, 255, cv2.THRESH_BINARY)
# Identify objects
device, id_objects, obj_hierarchy = pcv.find_objects(resize_img,
mask_contours,
device,
debug=None)
# Decide which objects to keep
device, roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(
resize_img,
'cutto',
roi1,
roi_hierarchy,
id_objects,
obj_hierarchy,
device,
debug=None)
# Object combine kept objects
device, obj, mask = pcv.object_composition(resize_img,
roi_objects,
hierarchy3,
device,
debug=None)
############### Analysis ################
try:
if len(obj) > 0:
# Find shape properties, output shape image (optional)
device, shape_header, shape_data, shape_img = pcv.analyze_object(
resize_img, args.image, obj, mask, device, debug)
# cv2.waitKey(10000)
return shape_data[6]
else:
return -1
except:
return -1
import glob
import cv2
import plantcv as pcv
cv_img = []
for img in glob.glob("Data_set/Foto's/*.jpg"):
n = cv2.imread(img)
device = 0
device, n = pcv.resize(n, 0.2, 0.2, device)
# Classify the pixels as plant or background
device, mask = pcv.naive_bayes_classifier(n, pdf_file="Trained_models/model_2/naive_bayes_pdfs.txt", device=0,
debug=None)
cv2.imshow("mask", mask.get('plant'))
cv2.waitKey(2000)
def main():
# Parse command-line options
args = options()
device = 0
# Open output file
out = open(args.outfile, "w")
# Open the image file
img, path, fname = pcv.readimage(filename=args.image, debug=args.debug)
# Classify healthy and unhealthy plant pixels
device, masks = pcv.naive_bayes_classifier(img=img,
pdf_file=args.pdfs,
device=device)
# Use the identified blue mesh area to build a mask for the pot area
# First errode the blue mesh region to remove background
device, mesh_errode = pcv.erode(img=masks["Background_Blue"],
kernel=9,
i=3,
device=device,
debug=args.debug)
# Define a region of interest for blue mesh contours
device, pot_roi, pot_hierarchy = pcv.define_roi(img=img,
shape='rectangle',
device=device,
roi=None,
roi_input='default',
debug=args.debug,
adjust=True,
x_adj=0,
y_adj=500,
w_adj=0,
h_adj=-650)
# Find blue mesh contours
device, mesh_objects, mesh_hierarchy = pcv.find_objects(img=img,
mask=mesh_errode,
device=device,
debug=args.debug)
# Keep blue mesh contours in the region of interest
device, kept_mesh_objs, kept_mesh_hierarchy, kept_mask_mesh, _ = pcv.roi_objects(
img=img,
roi_type='partial',
roi_contour=pot_roi,
roi_hierarchy=pot_hierarchy,
object_contour=mesh_objects,
obj_hierarchy=mesh_hierarchy,
device=device,
debug=args.debug)
# Flatten the blue mesh contours into a single object
device, mesh_flattened, mesh_mask = pcv.object_composition(
img=img,
contours=kept_mesh_objs,
hierarchy=kept_mesh_hierarchy,
device=device,
debug=args.debug)
# Initialize a pot mask
pot_mask = np.zeros(np.shape(masks["Background_Blue"]), dtype=np.uint8)
# Find the minimum bounding rectangle for the blue mesh region
rect = cv2.minAreaRect(mesh_flattened)
# Create a contour for the minimum bounding box
box = cv2.boxPoints(rect)
box = np.int0(box)
# Create a mask from the bounding box contour
cv2.drawContours(pot_mask, [box], 0, (255), -1)
# If the bounding box area is too small then the plant has likely occluded too much of the pot for us to use this
# as a marker for the pot area
if np.sum(pot_mask) / 255 < 2900000:
print(np.sum(pot_mask) / 255)
# Create a new pot mask
pot_mask = np.zeros(np.shape(masks["Background_Blue"]), dtype=np.uint8)
# Set the mask area to the ROI area
box = np.array([[0, 500], [0, 2806], [2304, 2806], [2304, 500]])
cv2.drawContours(pot_mask, [box], 0, (255), -1)
# Dialate the blue mesh area to include the ridge of the pot
device, pot_mask_dilated = pcv.dilate(img=pot_mask,
kernel=3,
i=60,
device=device,
debug=args.debug)
# Mask the healthy mask
device, healthy_masked = pcv.apply_mask(img=cv2.merge(
[masks["Healthy"], masks["Healthy"], masks["Healthy"]]),
mask=pot_mask_dilated,
mask_color="black",
device=device,
debug=args.debug)
# Mask the unhealthy mask
device, unhealthy_masked = pcv.apply_mask(img=cv2.merge(
[masks["Unhealthy"], masks["Unhealthy"], masks["Unhealthy"]]),
mask=pot_mask_dilated,
mask_color="black",
device=device,
debug=args.debug)
# Convert the masks back to binary
healthy_masked, _, _ = cv2.split(healthy_masked)
unhealthy_masked, _, _ = cv2.split(unhealthy_masked)
# Fill small objects
device, fill_image_healthy = pcv.fill(img=np.copy(healthy_masked),
mask=np.copy(healthy_masked),
size=300,
device=device,
debug=args.debug)
device, fill_image_unhealthy = pcv.fill(img=np.copy(unhealthy_masked),
mask=np.copy(unhealthy_masked),
size=1000,
device=device,
debug=args.debug)
# Define a region of interest
device, roi1, roi_hierarchy = pcv.define_roi(img=img,
shape='rectangle',
device=device,
roi=None,
roi_input='default',
debug=args.debug,
adjust=True,
x_adj=450,
y_adj=1000,
w_adj=-400,
h_adj=-1000)
# Filter objects that overlap the ROI
device, id_objects, obj_hierarchy_healthy = pcv.find_objects(
img=img, mask=fill_image_healthy, device=device, debug=args.debug)
device, _, _, kept_mask_healthy, _ = pcv.roi_objects(
img=img,
roi_type='partial',
roi_contour=roi1,
roi_hierarchy=roi_hierarchy,
object_contour=id_objects,
obj_hierarchy=obj_hierarchy_healthy,
device=device,
debug=args.debug)
device, id_objects, obj_hierarchy_unhealthy = pcv.find_objects(
img=img, mask=fill_image_unhealthy, device=device, debug=args.debug)
device, _, _, kept_mask_unhealthy, _ = pcv.roi_objects(
img=img,
roi_type='partial',
roi_contour=roi1,
roi_hierarchy=roi_hierarchy,
object_contour=id_objects,
obj_hierarchy=obj_hierarchy_unhealthy,
device=device,
debug=args.debug)
# Combine the healthy and unhealthy mask
device, mask = pcv.logical_or(img1=kept_mask_healthy,
img2=kept_mask_unhealthy,
device=device,
debug=args.debug)
# Output a healthy/unhealthy image
classified_img = cv2.merge([
np.zeros(np.shape(mask), dtype=np.uint8), kept_mask_healthy,
kept_mask_unhealthy
])
pcv.print_image(img=classified_img,
filename=os.path.join(
args.outdir,
os.path.basename(args.image)[:-4] + ".classified.png"))
# Output a healthy/unhealthy image overlaid on the original image
overlayed = cv2.addWeighted(src1=np.copy(classified_img),
alpha=0.5,
src2=np.copy(img),
beta=0.5,
gamma=0)
pcv.print_image(img=overlayed,
filename=os.path.join(
args.outdir,
os.path.basename(args.image)[:-4] + ".overlaid.png"))
# Extract hue values from the image
device, h = pcv.rgb2gray_hsv(img=img,
channel="h",
device=device,
debug=args.debug)
# Extract the plant hue values
plant_hues = h[np.where(mask == 255)]
# Initialize hue histogram
hue_hist = {}
for i in range(0, 180):
hue_hist[i] = 0
# Store all hue values
hue_values = []
# Populate histogram
total_px = len(plant_hues)
for hue in plant_hues:
hue_hist[hue] += 1
hue_values.append(hue)
# Parse the filename
genotype, treatment, replicate, timepoint = os.path.basename(
args.image)[:-4].split("_")
replicate = replicate.replace("#", "")
if timepoint[-3:] == "dbi":
timepoint = -1
else:
timepoint = timepoint.replace("dpi", "")
# Output results
for i in range(0, 180):
out.write("\t".join(
map(str, [
genotype, treatment, timepoint, replicate, total_px, i,
hue_hist[i]
])) + "\n")
out.close()
# Calculate basic statistics
healthy_sum = int(np.sum(kept_mask_healthy))
unhealthy_sum = int(np.sum(kept_mask_unhealthy))
healthy_total_ratio = healthy_sum / float(healthy_sum + unhealthy_sum)
unhealthy_total_ratio = unhealthy_sum / float(healthy_sum + unhealthy_sum)
stats = open(args.outfile[:-4] + ".stats.txt", "w")
stats.write("%s, %f, %f, %f, %f" %
(os.path.basename(args.image), healthy_sum, unhealthy_sum,
healthy_total_ratio, unhealthy_total_ratio) + '\n')
stats.close()
# Fit a 3-component Gaussian Mixture Model
gmm = mixture.GaussianMixture(n_components=3,
covariance_type="full",
tol=0.001)
gmm.fit(np.expand_dims(hue_values, 1))
gmm3 = open(args.outfile[:-4] + ".gmm3.txt", "w")
gmm3.write("%s, %f, %f, %f, %f, %f, %f, %f, %f, %f" %
(os.path.basename(args.image), gmm.means_.ravel()[0],
gmm.means_.ravel()[1], gmm.means_.ravel()[2],
np.sqrt(gmm.covariances_.ravel()[0]),
np.sqrt(gmm.covariances_.ravel()[1]),
np.sqrt(gmm.covariances_.ravel()[2]), gmm.weights_.ravel()[0],
gmm.weights_.ravel()[1], gmm.weights_.ravel()[2]) + '\n')
gmm3.close()
# Fit a 2-component Gaussian Mixture Model
gmm = mixture.GaussianMixture(n_components=2,
covariance_type="full",
tol=0.001)
gmm.fit(np.expand_dims(hue_values, 1))
gmm2 = open(args.outfile[:-4] + ".gmm2.txt", "w")
gmm2.write("%s, %f, %f, %f, %f, %f, %f" %
(os.path.basename(args.image), gmm.means_.ravel()[0],
gmm.means_.ravel()[1], np.sqrt(gmm.covariances_.ravel()[0]),
np.sqrt(gmm.covariances_.ravel()[1]), gmm.weights_.ravel()[0],
gmm.weights_.ravel()[1]) + '\n')
gmm2.close()
# Fit a 1-component Gaussian Mixture Model
gmm = mixture.GaussianMixture(n_components=1,
covariance_type="full",
tol=0.001)
gmm.fit(np.expand_dims(hue_values, 1))
gmm1 = open(args.outfile[:-4] + ".gmm1.txt", "w")
gmm1.write(
"%s, %f, %f, %f" %
(os.path.basename(args.image), gmm.means_.ravel()[0],
np.sqrt(gmm.covariances_.ravel()[0]), gmm.weights_.ravel()[0]) + '\n')
gmm1.close()
