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Commit 52070a1

Browse files 
2 parents 4d9d86e + 67be536 commit 52070a1

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7 files changed

+51
-31
lines changed

7 files changed

+51
-31
lines changed

‎ActiveContour.py

Lines changed: 6 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -13,6 +13,8 @@
1313
import cv2
1414
from scipy import ndimage
1515
import Image_preperation as prep
16+
import FileManager as fm
17+
import Image_preperation as prep
1618

1719
def calc_internal(p1,p2):
1820
if (np.array_equal(p1,p2)):
@@ -256,15 +258,15 @@ def resolution_downscale(img, resize):
256258
if __name__ == "__main__":
257259

258260
dir_radiographs = "_Data\Radiographs\*.tif"
259-
radiographs = ActiveShapeModel.load_files(dir_radiographs)
261+
radiographs = fm.load_files(dir_radiographs)
260262
radiograph = radiographs[0]
261263
init = np.load("initial_position.npy")
262264

263265
down_sample = 5
264266
tooth = init[0,4,:,:]/0.3
265267
#tooth = tooth/down_sample
266268

267-
radiograph_pre = pre_processing(radiograph)
269+
radiograph_pre = prep.pre_processing(radiograph)
268270
img = resolution_downscale(radiograph_pre,down_sample)
269271

270272
fig, ax = plt.subplots(figsize=(15, 15))
@@ -276,7 +278,7 @@ def resolution_downscale(img, resize):
276278
# In[196]:
277279

278280

279-
smooth = gaussian_smooth1(radiograph,10)
281+
smooth = prep.gaussian_smooth1(radiograph,10)
280282
grad = calc_external_img2(smooth)
281283
grad2 = calc_external_img2(radiograph)
282284
fig, ax = plt.subplots(figsize=(15, 15))
@@ -343,7 +345,7 @@ def resolution_downscale(img, resize):
343345
# In[141]:
344346

345347

346-
new_tooth = active_contour(tooth2, gausian(piece,1.5), 2, 2, 25)
348+
new_tooth = active_contour(tooth2, prep.gaussian(piece,1.5), 2, 2, 25)
347349
fig, ax = plt.subplots(figsize=(7, 7))
348350
plt.imshow(piece)
349351
plt.plot(new_tooth[:,0], new_tooth[:,1], 'ro', markersize=2)

‎ActiveShapeModel.py

Lines changed: 27 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -32,7 +32,7 @@ def active_shape_scale(img, tooth_points, pca_tooth, length, scale):
3232

3333
scaled_img , scaled_tooth_points = scaling(img, tooth_points, 1/scale)
3434
edge_img = prep.calc_external_img_active_contour(scaled_img)
35-
new_points = active_shape(edge_img, scaled_tooth_points, pca_tooth, length)
35+
new_points = active_shape(edge_img, scaled_tooth_points, pca_tooth, length,20)
3636
new_img, new_scaled_points = scaling(scaled_img, new_points, scale)
3737

3838
return new_scaled_points
@@ -44,6 +44,7 @@ def active_shape(edge_img, tooth_points, pca_tooth, length, alfa):
4444
b, pose_param = match.match_model_points(new_points, pca_tooth)
4545

4646
x = match.generate_model_point(b, pca_tooth)
47+
print(match.inv_transform(x.reshape(40,2),pose_param))
4748
return match.inv_transform(x.reshape(40,2),pose_param)
4849

4950
def active_shape_n_times(edge_img, tooth_points, pca_tooth, length,alfa, n_times):
@@ -110,53 +111,55 @@ def show_evolution(img, points_list):
110111
plt.show()
111112

112113

113-
# In[95]:
114+
# In[95]:
115+
114116

117+
points = active_shape_n_times(edge_img, tooth, pca_tooth, 5, 10,1)
118+
print(tooth.shape)
115119

116-
points = active_shape_n_times(edge_img, tooth, pca_tooth, 5, 10)
117120

118121

119-
# In[102]:
122+
# In[102]:
120123

121124

122-
new_points = points[1]
125+
new_points = points[1]
123126

124127

125-
# In[103]:
128+
# In[103]:
126129

127130

128-
fig, ax = plt.subplots(figsize=(15, 15))
129-
plt.imshow(radiograph)
130-
plt.plot(new_points[:,0], new_points[:,1], 'ro', markersize=1)
131-
plt.show()
131+
fig, ax = plt.subplots(figsize=(15, 15))
132+
plt.imshow(radiograph)
133+
plt.plot(new_points[:,0], new_points[:,1], 'ro', markersize=1)
134+
plt.show()
132135

133136

134-
# In[3]:
137+
# In[3]:
135138

136139

137-
img = fm.load_img_piece()
138-
tooth = fm.load_tooth_of_piece(4)
139-
landmarks = fm.load_landmarks_std()
140-
tooth_variations = landmarks[:,4]
141-
edge_img, pca_tooth = preperation(img, tooth_variations)
142-
fm.show_with_points(img, tooth)
140+
img = fm.load_img_piece()
141+
tooth = fm.load_tooth_of_piece(4)
142+
landmarks = fm.load_landmarks_std()
143+
tooth_variations = landmarks[:,4]
144+
edge_img, pca_tooth = preperation(img, tooth_variations)
145+
fm.show_with_points(img, tooth)
143146

144147

145-
# In[38]:
148+
# In[38]:
146149

147150

148-
#points_array = active_shape_scale_n_times(img, tooth, pca_tooth, 15, 4, 10)
149-
points_array = active_shape_n_times(edge_img, tooth, pca_tooth, 10, 20 ,9)
151+
#points_array = active_shape_scale_n_times(img, tooth, pca_tooth, 15, 4, 10)
152+
points_array = active_shape_n_times(edge_img, tooth, pca_tooth, 10, 20 ,9)
150153

151154

152-
# In[39]:
155+
# In[39]:
153156

154157

155-
show_evolution(img, points_array)
158+
show_evolution(img, points_array)
156159

157160

158-
# In[22]:
161+
# In[22]:
159162

160163

161-
points_array[0].shape
164+
points_array[0].shape
162165

‎Image_preperation.py

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -7,6 +7,7 @@
77
import cv2
88
import numpy as np
99
import math
10+
import matplotlib
1011
from scipy import ndimage, signal
1112
import matplotlib.pyplot as plt
1213
import matplotlib
@@ -17,6 +18,7 @@
1718

1819
from skimage.util.dtype import dtype_range
1920
from skimage.util import img_as_ubyte
21+
from skimage.util import img_as_float
2022
from skimage.morphology import disk
2123
from skimage.filters import rank
2224
from skimage import exposure

‎Initial_pose_estimator.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -183,5 +183,5 @@ def active_contour_match(img, init):
183183
# In[19]:
184184

185185

186-
radiograph.shape
186+
# radiograph.shape
187187

‎Initialisation.py

Lines changed: 15 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,6 +2,7 @@
22
import FileManager
33
import numpy as np
44
import Initial_pose_estimator as ipe
5+
import ActiveShapeModel as asm
56

67
def showControls():
78
popup = np.ones((220,355), np.uint8)
@@ -13,11 +14,12 @@ def showControls():
1314
cv2.putText(popup,'Pageup/down: Bottom/top tooth distance',(10,55), font, 0.5,(240,255,255),1,cv2.LINE_AA)
1415
cv2.putText(popup,'" / ": Save current position to file',(10,100), font, 0.5,(240,255,255),1,cv2.LINE_AA)
1516
cv2.putText(popup,'" . ": Activate automatic initialisation',(10,115), font, 0.5,(240,255,255),1,cv2.LINE_AA)
16-
cv2.putText(popup,'" \' ": Activate automatic initialisation',(10,130), font, 0.5,(240,255,255),1,cv2.LINE_AA)
17+
cv2.putText(popup,'" \' ": Do segmentation',(10,130), font, 0.5,(240,255,255),1,cv2.LINE_AA)
1718
cv2.putText(popup,'" , ": Change to next radiograph',(10,145), font, 0.5,(240,255,255),1,cv2.LINE_AA)
1819
cv2.putText(popup,'" m ": Reset model',(10,160), font, 0.5,(240,255,255),1,cv2.LINE_AA)
1920
cv2.putText(popup,'" esc ": Close program',(10,175), font, 0.5,(240,255,255),1,cv2.LINE_AA)
2021
cv2.putText(popup,'" k ": Show/hide this popup',(10,190), font, 0.5,(240,255,255),1,cv2.LINE_AA)
22+
cv2.putText(popup,'" o ": ASM iteration',(10,205), font, 0.5,(240,255,255),1,cv2.LINE_AA)
2123
saved = cv2.namedWindow( "Controls", cv2.WINDOW_AUTOSIZE )
2224
cv2.imshow("Controls",popup)
2325

@@ -260,7 +262,18 @@ def InitializeASM(directory = "_Data\\Radiographs\\*.tif"):
260262
segmentation = cv2.bitwise_and(grays, grays, mask=mask)
261263
cv2.namedWindow("Segmentation",cv2.WINDOW_AUTOSIZE)
262264
cv2.imshow("Segmentation", segmentation)
263-
265+
elif k == 111:
266+
landmarks = FileManager.load_landmarks_std()
267+
grays = cv2.cvtColor(backdrop, cv2.COLOR_BGR2GRAY)
268+
tooth_variations = landmarks[:,0]
269+
tooth_points = np.empty((40,2))
270+
tooth_points = output[0,0,:,:]
271+
edge_img, pca_tooth = asm.preperation(grays, tooth_variations)
272+
points = asm.active_shape_scale(edge_img, tooth_points, pca_tooth, 5, scale)
273+
all_landmarks_std[0,0,:,:] = points
274+
drawTeeth(all_landmarks_std, backdrop, tooth_size, image_center, tooth_gap, top_bottom_separation)
275+
cv2.setMouseCallback('Radiograph',moveTeeth,(resized_image,all_landmarks_std,tooth_size,image_center,tooth_gap,top_bottom_separation))
276+
print("done")
264277
elif k == 47:
265278
# print(output)
266279
np.save("initial_position", output)

‎Report.docx

-891 KB
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‎initial_position.npy

0 Bytes
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