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Commit 4d9d86e

Browse files
fit function angle fix
better image preperation filemanager some update
1 parent 26e25bf commit 4d9d86e

13 files changed

+1230
-953
lines changed

‎.ipynb_checkpoints/ActiveContour-checkpoint.ipynb

Lines changed: 47 additions & 580 deletions
Large diffs are not rendered by default.

‎.ipynb_checkpoints/FileManager-checkpoint.ipynb

Lines changed: 47 additions & 11 deletions
Large diffs are not rendered by default.

‎.ipynb_checkpoints/FitFunction-checkpoint.ipynb

Lines changed: 228 additions & 53 deletions
Large diffs are not rendered by default.

‎.ipynb_checkpoints/Image_preperation-checkpoint.ipynb

Lines changed: 195 additions & 85 deletions
Large diffs are not rendered by default.

‎ActiveContour.ipynb

Lines changed: 101 additions & 38 deletions
Large diffs are not rendered by default.

‎ActiveFitContour.ipynb

Lines changed: 124 additions & 19 deletions
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‎FileManager.ipynb

Lines changed: 9 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
"cells": [
33
{
44
"cell_type": "code",
5-
"execution_count": 4,
5+
"execution_count": 3,
66
"metadata": {},
77
"outputs": [],
88
"source": [
@@ -12,6 +12,12 @@
1212
"import matplotlib.pyplot as plt\n",
1313
"from scipy.spatial import procrustes\n",
1414
"import numpy as np\n",
15+
"import Image_preperation as prep\n",
16+
"\n",
17+
"def pre_pocess(img):\n",
18+
" median = prep.median_filter(img)\n",
19+
" contrast = prep.contrast_stretching(median)\n",
20+
" return contrast\n",
1521
"\n",
1622
"def resolution_scale(img, points, scale):\n",
1723
" new_points = resolution_scale_points(points, scale)\n",
@@ -46,7 +52,8 @@
4652
"\n",
4753
"def load_img_piece():\n",
4854
" img = load_radiograph()\n",
49-
" return img[700:1300,1200:1800]\n",
55+
" new_img = pre_pocess(img)\n",
56+
" return new_img[700:1300,1200:1800]\n",
5057
"\n",
5158
"def show_with_points(img, points):\n",
5259
" fig, ax = plt.subplots(figsize=(7, 7))\n",

‎FileManager.py

Lines changed: 16 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11

22
# coding: utf-8
33

4-
# In[2]:
4+
# In[3]:
55

66

77
import os
@@ -10,6 +10,12 @@
1010
import matplotlib.pyplot as plt
1111
from scipy.spatial import procrustes
1212
import numpy as np
13+
import Image_preperation as prep
14+
15+
def pre_pocess(img):
16+
median = prep.median_filter(img)
17+
contrast = prep.contrast_stretching(median)
18+
return contrast
1319

1420
def resolution_scale(img, points, scale):
1521
new_points = resolution_scale_points(points, scale)
@@ -35,16 +41,17 @@ def load_tooth(i):
3541
init = np.load("initial_position.npy")
3642
return init[0,i,:,:]/0.3
3743

38-
def load_tooth_of_piece(i=4):
39-
tooth = load_tooth(i)
44+
def load_tooth_of_piece():
45+
tooth = load_tooth(4)
4046
tooth_of_piece = tooth
4147
tooth_of_piece[:,0]=tooth[:,0]-1200
4248
tooth_of_piece[:,1]=tooth[:,1]-700
4349
return tooth_of_piece
4450

4551
def load_img_piece():
4652
img = load_radiograph()
47-
return img[700:1300,1200:1800]
53+
new_img = pre_pocess(img)
54+
return new_img[700:1300,1200:1800]
4855

4956
def show_with_points(img, points):
5057
fig, ax = plt.subplots(figsize=(7, 7))
@@ -142,13 +149,15 @@ def show_teeth_points(landmarks):
142149
plt.figure()
143150
n = len(landmarks)
144151
hn = int(n/2)
152+
fig, ax = plt.subplots(figsize=(15, 7))
145153

146154
print('Showing Teeth Landmarks')
147155

148156
for i, landmark in enumerate(landmarks):
149157
plt.subplot(2, hn, i+1)
150-
plt.xticks(())
151-
plt.yticks(())
158+
if(i!=hn):
159+
plt.xticks(())
160+
plt.yticks(())
152161
plt.plot(landmark[:,0], landmark[:,1], 'ro')
153162

154163
plt.show()
@@ -164,7 +173,7 @@ def load_segmentations():
164173
return load_files(dir_segmentations)
165174

166175

167-
# In[9]:
176+
# In[5]:
168177

169178

170179
if __name__ == "__main__":

‎FitFunction.ipynb

Lines changed: 135 additions & 23 deletions
Large diffs are not rendered by default.

‎FitFunction.py

Lines changed: 73 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11

22
# coding: utf-8
33

4-
# In[7]:
4+
# In[2]:
55

66

77
import Image_preperation as prep
@@ -68,13 +68,50 @@ def is_vertical(a,b,c):
6868
def is_equal(b_proj , b):
6969
return np.array_equal(b_proj, b)
7070

71+
7172
def get_normal_angle(a,b,c):
7273
if( is_horizontal(a,b,c) ):
7374
return math.pi/2
7475
if( is_vertical(a,b,c) ):
7576
return 0
7677

7778
b_proj = project_on(b, a,c)
79+
80+
#is linear
81+
if(is_equal(b_proj , b)):
82+
83+
c_norm = np.add(c,[2,0])
84+
if(is_equal(a,b)):
85+
a_corr = np.add(a,[-5,0])
86+
a_proj = project_on(a_corr, b ,c)
87+
rad = calc_angle(a_proj,b,c_norm)
88+
else:
89+
rad = calc_angle(a,b,c_norm)
90+
91+
#not linear
92+
else:
93+
b_norm = np.add(b, [2,0])
94+
rad = calc_angle(b_proj, b, b_norm)
95+
96+
#rad given back relative to x-axis
97+
if( b_norm[0] > b[0]):
98+
if (b_proj[1] > b_norm[1]):
99+
return rad
100+
else:
101+
return -rad
102+
else:
103+
if( b_proj[1] > b_norm[1]):
104+
return -rad
105+
else:
106+
return rad
107+
108+
def get_normal_angle2(a,b,c):
109+
if( is_horizontal(a,b,c) ):
110+
return math.pi/2
111+
if( is_vertical(a,b,c) ):
112+
return 0
113+
114+
b_proj = project_on(b, a,c)
78115

79116
if(is_equal(b_proj , b)):
80117
c_norm = np.add(c,[2,0])
@@ -86,7 +123,7 @@ def get_normal_angle(a,b,c):
86123

87124
b_norm = np.add(b, [2,0])
88125

89-
return calc_angle(b, b_proj, b_norm)
126+
return calc_angle(b_proj, b, b_norm)
90127

91128
def project_on(x, a,c):
92129
n = np.subtract(a, c)
@@ -214,7 +251,7 @@ def test_normal_on_edge():
214251

215252

216253

217-
# In[14]:
254+
# In[3]:
218255

219256

220257
if __name__ == "__main__":
@@ -232,6 +269,7 @@ def test_normal_on_edge():
232269
new_points[:,1]=points[:,1]-300
233270

234271
a,b,c = new_points[0:3]
272+
235273
rad = get_normal_angle(a,b,c)
236274
p1 = get_point_at_distance(b, 20, rad)
237275
p2 = get_point_at_distance(b, -20, rad)
@@ -240,17 +278,17 @@ def test_normal_on_edge():
240278
p2 = np.array(p2,dtype=int)
241279
make_line(img_copy, p1,p2)
242280

243-
visualize_points = new_points.take([38,39,0,1,2,3],axis=0)
281+
visualize_points = new_points.take([38,39,0,1,2,3,4,5],axis=0)
244282
proj = project_on(b, a,c)
245-
visualize_points = np.append(visualize_points,proj).reshape(-1,2)
283+
#new_visualize_points = np.append(visualize_points,proj).reshape(-1,2)
246284

247285
show_with_points(img_copy,visualize_points)
248286

249287
edges = get_points_on_angle_normal(b, rad, 20)
250-
edge_img = prep.edge_detection_high(new_pice)
288+
edge_img = prep.sobel(new_pice)
251289
strength = edge_strength_at_points(edges ,edge_img)
252290

253-
show_with_points(new_pice,edges)
291+
#show_with_points(new_pice,np.append(edges,visualize_points).reshape(-1,2))
254292

255293
fig, ax = plt.subplots(figsize=(7, 7))
256294
plt.plot(np.arange(-20,21),strength)
@@ -274,3 +312,31 @@ def test_normal_on_edge():
274312
# new_points, error = fit_measure(tooth, 30, edge_img)
275313
# fm.show_with_points(piece, new_points)
276314

315+
316+
# In[11]:
317+
318+
319+
math.degrees(rad)
320+
321+
322+
# In[14]:
323+
324+
325+
math.degrees(calc_angle(c,b,a))
326+
327+
328+
# In[4]:
329+
330+
331+
edge_img = prep.calc_external_img_active_contour(new_pice)
332+
p = strongest_edge_point_on_normal(a,b,c,20, edge_img)
333+
show_with_points(edge_img,np.append(visualize_points,p).reshape(-1,2))
334+
335+
336+
# In[8]:
337+
338+
339+
edge_img = prep.canny(new_pice)
340+
p = strongest_edge_point_on_normal(a,b,c,20, edge_img)
341+
show_with_points(edge_img,np.append(visualize_points,p).reshape(-1,2))
342+

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