8/12/2020 Lab07-Object Segmentation

LAB07 - Image Segmentation

Dr. Tran Anh Tuan,

Faculty of Mathematics and Computer Science,

University of Science, HCMC

In [197]: import numpy as np
import cv2
from matplotlib import pyplot as plt
from skimage.color import rgb2gray
from skimage.filters import threshold_otsu
from skimage.measure import label, regionprops
from skimage.segmentation import mark_boundaries
from scipy import ndimage as ndi
import pandas as pd
import json
import os
import timeit
import random

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In [198]: def ShowImage(ImageList, nRows = 1, nCols = 2, WidthSpace = 0.00, HeightSpace = 0.00):

from matplotlib import pyplot as plt
import matplotlib.gridspec as gridspec

gs = gridspec.GridSpec(nRows, nCols)
gs.update(wspace=WidthSpace, hspace=HeightSpace) # set the spacing between axes.
plt.figure(figsize=(20,20))
for i in range(len(ImageList)):
ax1 = plt.subplot(gs[i])
ax1.set_xticklabels([])
ax1.set_yticklabels([])
ax1.set_aspect('equal')

plt.subplot(nRows, nCols,i+1)

image = ImageList[i].copy()
if (len(image.shape) < 3):
plt.imshow(image, plt.cm.gray)
else:
plt.imshow(image)
plt.title("Image " + str(i))
plt.axis('off')

plt.show()

In [199]: def FillHoles(Mask):

Result = ndi.binary_fill_holes(Mask)
return Result

def morphology(Mask, Size):

from skimage.morphology import erosion, dilation, opening, closing, white_tophat
from skimage.morphology import disk
selem = disk(abs(Size))
if(Size > 0):
result = dilation(Mask, selem)
else:
result = erosion(Mask, selem)
return result

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In [200]: import os
import pandas as pd

def get_subfiles(dir):
"Get a list of immediate subfiles"
return next(os.walk(dir))[2]

In [201]: def SegmentColorImageByMask(IM, Mask):

Mask = Mask.astype(np.uint8)
result = cv2.bitwise_and(IM, IM, mask = Mask)
return result

In [202]: def SegmentationByOtsu(image, mask):

image_process = image.copy()
image_mask = mask.copy()

image_process[image_mask == 0] = 0
ListPixel = image_process.ravel()
ListPixel = ListPixel[ListPixel > 0]

from skimage.filters import threshold_otsu

otsu_thresh = threshold_otsu(ListPixel)

return otsu_thresh

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In [203]: def ResizeImage(IM, DesiredWidth, DesiredHeight):

from skimage.transform import rescale, resize

OrigWidth = float(IM.shape[1])
OrigHeight = float(IM.shape[0])
Width = DesiredWidth
Height = DesiredHeight

if((Width == 0) & (Height == 0)):

return IM

if(Width == 0):
Width = int((OrigWidth * Height)/OrigHeight)

if(Height == 0):
Height = int((OrigHeight * Width)/OrigWidth)

dim = (Width, Height)

# print(dim)
resizedIM = cv2.resize(IM, dim, interpolation = cv2.INTER_NEAREST)
# imshows([IM, resizedIM], ["Image", "resizedIM"],1,2)
return resizedIM

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In [204]: def SegmentByKmeans(image_orig, nClusters = 3):

img = image_orig.copy()
Z = img.reshape((-1,3))

# convert to np.float32
Z = np.float32(Z)

# define criteria, number of clusters(K) and apply kmeans()

criteria = (cv2.TERM_CRITERIA_EPS + cv2.TERM_CRITERIA_MAX_ITER, 100, 1.0)
K = nClusters
ret,labellist,center=cv2.kmeans(Z,K,None,criteria,10,cv2.KMEANS_RANDOM_CENTERS)

# Now convert back into uint8, and make original image

center = np.uint8(center)
res = center[labellist.flatten()]
res2 = res.reshape((img.shape))
label2 = labellist.reshape((img.shape[:2]))

image_index = label2
image_kmeans = res2

# Sort to make sure the index is stable

AreaList = []
for idx in range(image_index.max() + 1):
mask = image_index == idx
AreaList.append(mask.sum().sum())

sort_index = np.argsort(AreaList)[::-1]
index = 0
image_index1 = image_index * 0
for idx in sort_index:
image_index1[image_index == idx] = index
index = index + 1

image_index = image_index1.copy()

return image_index, image_kmeans

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In [205]: def LabelObjectByMask(image_input, image_mask, type = "BBox", color = (0,255,0), thick = 2):
# image_input = image_orig.copy()
image_output = image_input.copy()

label_img = label(image_mask)
regions = regionprops(label_img)
for props in regions:
minr, minc, maxr, maxc = props.bbox
left_top = (minc, minr)
right_bottom = (maxc, maxr)
at_row, at_col = props.centroid

if(type == "Center"):
cv2.drawMarker(image_output, (int(at_col), int(at_row)),color, markerType=cv2.MARKER_STAR, marker
Size=15, thickness= 1, line_type=cv2.LINE_AA)
if(type == "BBox"):
cv2.rectangle(image_output,left_top, right_bottom, color ,thick)

if(type == "Boundary"):
color = [(number / 255) for number in color]
image_mask = morphology(image_mask, 1)
image_output = mark_boundaries(image_output, image_mask, color = color, mode='thick')

if(type == "Fill"):
image_output[image_mask > 0] = color

return image_output

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In [206]: def SelectMaskByThreshArea(Mask, minArea = 300, maxArea = 100000):

import pandas as pd
from skimage.measure import label, regionprops

mask = Mask.copy()
mask_output = mask * 0
bboxList = []

label_img = label(mask)
regions = regionprops(label_img)
for props in regions:
area = props.area
label = props.label
if((area > minArea) and (area < maxArea)):
mask_output = mask_output + (label_img == label).astype(int)

return mask_output

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In [207]: def ConvertGrayToIndex(image_gray):

PixelList = list(np.unique(image_gray.flatten()))

random_color = lambda: (int(random()*255), int(random()*255), int(random()*255))

colors = [random_color() for i in range(len(PixelList))]

image_index = image_gray.copy()
for idx, value in enumerate(PixelList):
image_index = np.where(image_index==PixelList[idx], -(idx + 1), image_index)
image_index = -image_index

image_color = np.dstack((image_gray,image_gray,image_gray))
rows, cols = image_color.shape[:2]
for x in range(rows):
for y in range(cols):
index = PixelList.index(image_gray[x,y])
image_color[x, y, :] = colors[index]

# Sort to make sure the index is stable

AreaList = []
for idx in range(image_index.max() + 1):
mask = image_index == idx
AreaList.append(mask.sum().sum())

sort_index = np.argsort(AreaList)[::-1]
index = 0
image_index1 = image_index * 0
for idx in sort_index:
image_index1[image_index == idx] = index
index = index + 1
image_index = image_index1.copy()

return image_index, image_color

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In [208]: def pointsList(new_mask, n):

gray = (new_mask*255).astype(np.uint8)

thresh, im_bw = cv2.threshold(gray, 127, 255, cv2.THRESH_BINARY)

contours, hierarchy = cv2.findContours(im_bw, cv2.RETR_TREE, cv2.CHAIN_APPROX_NONE)

step = int(len(contours[0])/n)
points = np.array(contours[0][0])

if step == 0:
step = 5
for i in range (0, len(contours[0]), step):
points = np.append((points), (contours[0][i]), axis=0)
if len(points) > n:
np.delete(points, 0)

return points

In [209]: DataPath = "D:\\MSI DATA (Previous Computer)\\Teaching And Training\\Image Segmentation\\Image Segnemtation D
ataSet\\"

path = DataPath
all_names = get_subfiles(path)
print("Number of Images:", len(all_names))
IMG = []
for i in range(len(all_names)):
tmp = cv2.imread(path + all_names[i])
IMG.append(tmp)

SegDataIMG1 = IMG.copy()
SegDataName1 = all_names

Number of Images: 60

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In [210]: FileName = 'Skin 01.jpg'

idx = SegDataName1.index(FileName)
print("Selected Image : ", "\nIndex ", idx, "\nName ", SegDataName1[idx])

image = SegDataIMG1[idx]
image = ResizeImage(image, DesiredWidth = 300, DesiredHeight = 0)

image_orig = cv2.cvtColor(image, cv2.COLOR_BGR2RGB)

image_gray = cv2.cvtColor(image,cv2.COLOR_BGR2GRAY)
image_hsv = cv2.cvtColor(image, cv2.COLOR_BGR2HSV)
image_ycbcr = cv2.cvtColor(image, cv2.COLOR_BGR2YCR_CB)
ShowImage([image_orig, image_gray, image_hsv, image_ycbcr], 1, 4)

Selected Image :
Index 55
Name Skin 01.jpg

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In [211]: image_output = image_orig.copy()

rows,cols = image_orig.shape[:2]
at_row = 120;
at_col = 140;
mouse_click = (int(at_col), int(at_row))
cv2.drawMarker(image_output, mouse_click ,color = (0, 255, 0),
markerType=cv2.MARKER_STAR, markerSize=10, thickness= 1, line_type=cv2.LINE_AA)
ShowImage([image_output], 1, 2)

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In [212]: # import the necessary packages

from skimage.segmentation import slic
from skimage.segmentation import mark_boundaries
from skimage.util import img_as_float
from skimage import io
import matplotlib.pyplot as plt

# load the image and convert it to a floating point data type

image = img_as_float(image_orig)
# loop over the number of segments
SegmentIndexList = []
SegmentColorList = []
numSegments = 100
# apply SLIC and extract (approximately) the supplied number
# of segments
segments = slic(image, n_segments = numSegments, sigma = 7)
image_color = mark_boundaries(image, segments)

ShowImage([segments, image_color], 1, 3)

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In [213]: def GetPointsLabelling(image, image_mask, nPoints = 10):

image_label = label(image_mask)
XList = []
YList = []

for idx in range(image_label.max()):

image_mask = image_label == (idx + 1)
n_points_polygon = round(nPoints)
points = pointsList(image_mask, n_points_polygon)
X = [i[0].item() for i in points]
Y = [i[1].item() for i in points]
XList = XList + X
YList = YList + Y

print("XList : ", XList)

print("YList : ", YList)
image_points = image.copy()
cv2.polylines(image_points,[points],True,(0,255,0))
for col_idx, row_idx in zip(XList, YList):
cv2.drawMarker(image_points, (col_idx, row_idx),(0,0,255), markerType=cv2.MARKER_STAR, markerSize=2,
thickness=1, line_type=cv2.LINE_AA)

return image_points, XList, YList

In [214]: image_output = image_orig.copy()

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In [215]: at_row = 95;

at_col = 195;
image_mask = (segments == segments[at_row, at_col])

mouse_click = (int(at_col), int(at_row))

cv2.drawMarker(image_output, mouse_click ,color = (0, 255, 0),
markerType=cv2.MARKER_STAR, markerSize=10, thickness= 1, line_type=cv2.LINE_AA)
image_output, XList, YList = GetPointsLabelling(image_output, image_mask, nPoints = 10)

ShowImage([image_mask], 1, 1)
ShowImage([image_output], 1, 1)

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XList : [189, 189, 184, 182, 185, 190, 196, 202, 206, 206, 202, 196, 190]
YList : [87, 87, 92, 98, 104, 108, 110, 107, 101, 95, 89, 87, 87]

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In [216]: at_row = 120;

at_col = 140;
image_mask = (segments == segments[at_row, at_col])

mouse_click = (int(at_col), int(at_row))

cv2.drawMarker(image_output, mouse_click ,color = (0, 255, 0),
markerType=cv2.MARKER_STAR, markerSize=10, thickness= 1, line_type=cv2.LINE_AA)
image_output, XList, YList = GetPointsLabelling(image_output, image_mask, nPoints = 10)

ShowImage([image_mask], 1, 1)
ShowImage([image_output], 1, 1)

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XList : [139, 139, 130, 121, 120, 128, 137, 146, 155, 159, 153, 144]
YList : [113, 113, 115, 121, 130, 135, 138, 138, 132, 123, 116, 113]

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In [217]: FileName = 'Hand Gesture 05.jpg'

idx = SegDataName1.index(FileName)
print("Selected Image : ", "\nIndex ", idx, "\nName ", SegDataName1[idx])

image = SegDataIMG1[idx]
image = ResizeImage(image, DesiredWidth = 300, DesiredHeight = 0)

image_orig = cv2.cvtColor(image, cv2.COLOR_BGR2RGB)

image_gray = cv2.cvtColor(image,cv2.COLOR_BGR2GRAY)
image_hsv = cv2.cvtColor(image, cv2.COLOR_BGR2HSV)
image_ycbcr = cv2.cvtColor(image, cv2.COLOR_BGR2YCR_CB)
ShowImage([image_orig, image_gray, image_hsv, image_ycbcr], 1, 4)

Selected Image :
Index 44
Name Hand Gesture 05.jpg

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In [218]: # import the necessary packages

from skimage.segmentation import slic
from skimage.segmentation import mark_boundaries
from skimage.util import img_as_float
from skimage import io
import matplotlib.pyplot as plt

# load the image and convert it to a floating point data type

image = img_as_float(image_orig)
# loop over the number of segments
SegmentIndexList = []
SegmentColorList = []
numSegments = 100
# apply SLIC and extract (approximately) the supplied number
# of segments
segments = slic(image, n_segments = numSegments, sigma = 7)
image_color = mark_boundaries(image, segments)

ShowImage([segments, image_color], 1, 3)

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In [219]: def doClick(image_check, image_mask, mouse_click, MaskList, ImageList):

image_mask = (image_mask + (segments == segments[at_row, at_col])) > 0
mouse_click = (int(at_col), int(at_row))
cv2.drawMarker(image_check, mouse_click ,color = (0, 255, 0),
markerType=cv2.MARKER_STAR, markerSize=10, thickness= 1, line_type=cv2.LINE_AA)

MaskList.append(image_mask)
ImageList.append(image_check)

return image_check, image_mask, MaskList, ImageList

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In [220]: ImageList = []
MaskList = []
image_check = image_color.copy()
image_mask = image_gray * 0

at_row = 85; at_col = 170;

image_check, image_mask, MaskList, ImageList = doClick(image_check, image_mask,
mouse_click, MaskList, ImageList)

at_row = 60; at_col = 165;

image_check, image_mask, MaskList, ImageList = doClick(image_check, image_mask,
mouse_click, MaskList, ImageList)

at_row = 50; at_col = 150;

image_check, image_mask, MaskList, ImageList = doClick(image_check, image_mask,
mouse_click, MaskList, ImageList)

at_row = 70; at_col = 150;

image_check, image_mask, MaskList, ImageList = doClick(image_check, image_mask,
mouse_click, MaskList, ImageList)

at_row = 100; at_col = 170;

image_check, image_mask, MaskList, ImageList = doClick(image_check, image_mask,
mouse_click, MaskList, ImageList)

at_row = 30; at_col = 180;

image_check, image_mask, MaskList, ImageList = doClick(image_check, image_mask,
mouse_click, MaskList, ImageList)

ShowImage(MaskList, 2, 3)
ShowImage(ImageList, 2, 3)

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Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).
Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).
Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).
Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).
Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).
Clipping input data to the valid range for imshow with RGB data ([0..1] for floats or [0..255] for integers).

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In [221]: image_output = image_orig.copy()

image_output, XList, YList = GetPointsLabelling(image_output, image_mask, nPoints = 10)

ShowImage([image_output], 1, 1)

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XList : [167, 167, 164, 138, 133, 141, 157, 184, 190, 196, 197, 171]
YList : [22, 22, 38, 28, 56, 88, 120, 132, 101, 69, 37, 22]

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