/
move_embryo_fov_new_new_thresh_pressureold.py
400 lines (392 loc) · 21.5 KB
/
move_embryo_fov_new_new_thresh_pressureold.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
# -*- coding: utf-8 -*-
"""
Created on Wed Feb 9 09:49:36 2022
@author: User
"""
from XYZ_Stage.XYZ_Position import XYZ_Location
from Delta_XY_FOV_1_lin import Delta_XY_FOV_1_lin
from Delta_XY_FOV_2_lin import Delta_XY_FOV_2_lin
from Delta_Z_FOV_1_lin import Delta_Z_FOV_1_lin
from Delta_Z_FOV_2_lin import Delta_Z_FOV_2_lin
from Delta_px_y_FOV_1 import Delta_px_y_FOV_1
from Delta_px_y_FOV_2 import Delta_px_y_FOV_2
from ML.ml_injection_point_estimation_new import ml_injection_point_estimation_new
import time
# from matplotlib import pyplot as plt
from Pressure_Control.Continuous_Pressure import continuous_pressure
from stream_image import stream_image
import numpy as np
import cv2
from detect_injection import detect_injection
from ML.transform_points import transform_points
def move_embryo_fov_new_new_thresh_pressure(fov,action,X_est,Y_est,Z_est,inj_depth,inj_speed,back_pressure_value,pressure_value,pressure_time,arduino,current_x,current_y,current_z,view_1_x,view_1_y,view_2_x,view_2_y,footage_socket_1,footage_socket_2,inj_num,y1_1_crop,y2_1_crop,x1_1_crop,x2_1_crop,y1_2_crop,y2_2_crop,x1_2_crop,x2_2_crop,im_height_1,im_width_1,im_height_2,im_width_2,graph,sess,ser,time_wait,next_z,post_z,current_z_new,move_num,pic,thresh_1,thresh_2,resize,sum_image_thresh_min,target_pixel,x_coord_emb_1,y_coord_emb_1,x_coord_emb_2,y_coord_emb_2,send_num):
end=0
end_1=0
end_2=0
injection_list_num=0
injected=2
sum_image=0
x_coord_tip_1=view_1_x
y_coord_tip_1=view_1_y
x_coord_tip_2=view_2_x
y_coord_tip_2=view_2_y
x_post_1=0
y_post_1=0
x_post_2=0
y_post_2=0
back_pressure_value_new=pressure_value
pressure_value=pressure_value
im_width_1_old=im_width_1
im_height_1_old=im_height_1
im_width_2_old=im_width_2
im_height_2_old=im_height_2
sum_image=-20
if fov==1 and action=='centroid':
current_z_new=current_z
# FOV 1 Center
img1,img2=stream_image(footage_socket_1,footage_socket_2,pic,1)
img1_crop=img1[y1_1_crop:y2_1_crop,x1_1_crop:x2_1_crop]
if resize==1:
img1_crop=cv2.resize(img1_crop,(400,400))
im_height_1=400
im_width_1=400
output_dict_detection_boxes_stored,output_dict_detection_classes_stored,output_dict_detection_scores_stored,y1a_rc,y2a_rc,x1a_rc,x2a_rc,xc_rc,yc_rc=ml_injection_point_estimation_new([img1_crop],thresh_1,im_height_1,im_width_1,graph,sess,1)
list_classes=output_dict_detection_classes_stored[0].tolist()
if 1 not in list_classes:
print('No centroid detected FOV1')
# cv2.imwrite('C:/Users/User/Downloads/Andrew_files/Amey Code-20190710T183750Z-001/Amey Code/ML/Centroid_FOV_1_No_Work/{}.jpg'.format(inj_num),img1_crop)
current_x=X_est
current_y=Y_est
current_z=Z_est
end=2
else:
list_classes_index=list_classes.index(1)
if resize==1:
xc_rc[0][list_classes_index],yc_rc[0][list_classes_index]=transform_points(im_width_1,im_height_1,im_width_1_old,im_height_1_old,xc_rc[0][list_classes_index],yc_rc[0][list_classes_index])
# plt.figure(1)
# plt.title('Detected Centroid FOV1')
# plt.xlabel('x coordinate (px)')
# plt.ylabel('y coordinate (px)')
# plt.plot(xc_rc[0][list_classes_index]+x1_1_crop,yc_rc[0][list_classes_index]+y1_1_crop,'ro',markersize=3)
# plt.plot(view_1_x,view_1_y,'bo',markersize=3)
# plt.imshow(img1,cmap='gray')
# plt.show()
dx,dy=Delta_XY_FOV_1_lin(view_1_x,xc_rc[0][list_classes_index]+x1_1_crop)
dx=dx
dy=dy
print('Move up half z for FOV_1')
dz=int(float(Delta_Z_FOV_1_lin(view_1_y,yc_rc[0][list_classes_index]+y1_1_crop-135)))
# dz=int(float(Delta_Z_FOV_1_lin(view_1_y,yc_rc[0][list_classes_index]+y1_1_crop-130)))
current_z=current_z+dz
print('Current Z = ',current_z)
print('Moving embryo center under needle FOV1')
XYZ_Location(5000,5000,2000,current_x,current_y,current_z,ser)
time.sleep(.25)
current_x=current_x+dx
current_y=current_y+dy
x_coord_emb_1=xc_rc[0][list_classes_index]+x1_1_crop
y_coord_emb_1=yc_rc[0][list_classes_index]+y1_1_crop
x_coord_tip_1=view_1_x
y_coord_tip_1=view_1_y
print('Current X = ',current_x)
print('Current Y = ',current_y)
XYZ_Location(5000,5000,2000,current_x,current_y,current_z,ser)
time.sleep(.25)
next_z=current_z
elif fov==2 and action=='centroid':
current_z_new=current_z
# time.sleep(.15)
img1,img2=stream_image(footage_socket_1,footage_socket_2,pic,0)
img2_crop=img2[y1_2_crop:y2_2_crop,x1_2_crop:x2_2_crop]
if resize==2:
img2_crop=cv2.resize(img2_crop,(400,400))
im_height_2=400
im_width_2=400
output_dict_detection_boxes_stored,output_dict_detection_classes_stored,output_dict_detection_scores_stored,y1a_rc,y2a_rc,x1a_rc,x2a_rc,xc_rc,yc_rc=ml_injection_point_estimation_new([img2_crop],thresh_2,im_height_2,im_width_2,graph,sess,2)
list_classes=output_dict_detection_classes_stored[0].tolist()
if 1 not in list_classes:
print('No centroid detected FOV2')
# cv2.imwrite('C:/Users/User/Downloads/Andrew_files/Amey Code-20190710T183750Z-001/Amey Code/ML/Centroid_FOV_2_No_Work/{}.jpg'.format(inj_num),img2_crop)
current_x=current_x
current_y=current_y
current_z=current_z
end=1
print('Done centroid FOV2')
else:
list_classes_index=list_classes.index(1)
if resize==2:
xc_rc[0][list_classes_index],yc_rc[0][list_classes_index]=transform_points(im_width_2,im_height_2,im_width_2_old,im_height_2_old,xc_rc[0][list_classes_index],yc_rc[0][list_classes_index])
# plt.figure(2)
# plt.title('Detected Centroid FOV2')
# plt.xlabel('x coordinate (px)')
# plt.ylabel('y coordinate (px)')
# plt.plot(xc_rc[0][list_classes_index]+x1_2_crop,yc_rc[0][list_classes_index]+y1_2_crop,'ro',markersize=3)
# plt.plot(view_2_x,view_2_y,'bo',markersize=3)
# plt.imshow(img2,cmap='gray')
# plt.show()
dx,dy=Delta_XY_FOV_2_lin(view_2_x,xc_rc[0][list_classes_index]+x1_2_crop)
print('Move up half z for FOV_2')
dz=int(float(Delta_Z_FOV_2_lin(view_2_y,yc_rc[0][list_classes_index]+y1_2_crop-120)))
# dz=int(float(Delta_Z_FOV_2_lin(view_2_y,yc_rc[0][list_classes_index]+y1_2_crop-115)))
current_z=current_z+dz
print('Current Z = ',current_z)
print('Moving embryo center under needle FOV2')
XYZ_Location(5000,5000,2000,current_x,current_y,current_z,ser)
time.sleep(.25)
current_x=current_x+dx
current_y=current_y+dy
x_coord_emb_2=xc_rc[0][list_classes_index]+x1_2_crop
y_coord_emb_2=yc_rc[0][list_classes_index]+y1_2_crop
x_coord_tip_2=view_2_x
y_coord_tip_2=view_2_y
print('Current X = ',current_x)
print('Current Y = ',current_y)
XYZ_Location(5000,5000,2000,current_x,current_y,current_z,ser)
time.sleep(.25)
injection_list_num=2
next_z=current_z
elif action=='no move':
next_z=next_z
# time.sleep(.15)
img1,img2=stream_image(footage_socket_1,footage_socket_2,pic,send_num)
img1_crop=img1[y1_1_crop:y2_1_crop,x1_1_crop:x2_1_crop]
if resize==1:
img1_crop=cv2.resize(img1_crop,(400,400))
im_height_1=400
im_width_1=400
output_dict_detection_boxes_stored,output_dict_detection_classes_stored,output_dict_detection_scores_stored,y1a_rc,y2a_rc,x1a_rc,x2a_rc,xc_rc,yc_rc=ml_injection_point_estimation_new([img1_crop],thresh_1,im_height_1,im_width_1,graph,sess,3)
list_classes=output_dict_detection_classes_stored[0].tolist()
current_z_new=current_z
if 3 in list_classes:
print('Posterior detected FOV1')
list_classes_index=list_classes.index(3)
if resize==1:
xc_rc[0][list_classes_index],yc_rc[0][list_classes_index]=transform_points(im_width_1,im_height_1,im_width_1_old,im_height_1_old,xc_rc[0][list_classes_index],yc_rc[0][list_classes_index])
# plt.figure(3)
# plt.title('Detected Injection Point FOV1')
# plt.xlabel('x coordinate (px)')
# plt.ylabel('y coordinate (px)')
# plt.plot(xc_rc[0][list_classes_index]+x1_1_crop,yc_rc[0][list_classes_index]+y1_1_crop,'ro',markersize=3)
# plt.plot(view_1_x,view_1_y,'bo',markersize=3)
# plt.imshow(img1,cmap='gray')
# plt.show()
dx,dy=Delta_XY_FOV_1_lin(view_1_x,xc_rc[0][list_classes_index]+x1_1_crop)
current_x_new=current_x+dx
current_y_new=current_y+dy
dz_1=int(float(Delta_Z_FOV_1_lin(view_1_y,yc_rc[0][list_classes_index]+y1_1_crop-70)))
x_coord_emb_1=xc_rc[0][list_classes_index]+x1_1_crop
y_coord_emb_1=yc_rc[0][list_classes_index]+y1_1_crop
x_coord_tip_1=view_1_x
y_coord_tip_1=view_1_y
img2_crop=img2[y1_2_crop:y2_2_crop,x1_2_crop:x2_2_crop]
if resize==2:
img2_crop=cv2.resize(img2_crop,(400,400))
im_height_2=400
im_width_2=400
output_dict_detection_boxes_stored,output_dict_detection_classes_stored,output_dict_detection_scores_stored,y1a_rc,y2a_rc,x1a_rc,x2a_rc,xc_rc,yc_rc=ml_injection_point_estimation_new([img2_crop],thresh_2,im_height_2,im_width_2,graph,sess,6)
list_classes=output_dict_detection_classes_stored[0].tolist()
if 3 in list_classes:
print('Posterior detected FOV2')
list_classes_index_2=list_classes.index(3)
if resize==2:
xc_rc[0][list_classes_index_2],yc_rc[0][list_classes_index_2]=transform_points(im_width_2,im_height_2,im_width_2_old,im_height_2_old,xc_rc[0][list_classes_index_2],yc_rc[0][list_classes_index_2])
# plt.figure(6)
# plt.title('Detected Injection Point FOV2')
# plt.xlabel('x coordinate (px)')
# plt.ylabel('y coordinate (px)')
# plt.plot(xc_rc[0][list_classes_index_2]+x1_2_crop,yc_rc[0][list_classes_index_2]+y1_2_crop,'ro',markersize=3)
# plt.plot(view_2_x,view_2_y,'bo',markersize=3)
# plt.imshow(img2,cmap='gray')
# plt.show()
dx,dy=Delta_XY_FOV_2_lin(view_2_x,xc_rc[0][list_classes_index_2]+x1_2_crop)
current_x_new=current_x_new+dx
current_y_new=current_y_new+dy
dz_2=int(float(Delta_Z_FOV_2_lin(view_2_y,yc_rc[0][list_classes_index_2]+y1_2_crop-70)))
current_z_new=current_z+int(np.mean([dz_1,dz_2]))
x_coord_emb_2=xc_rc[0][list_classes_index_2]+x1_2_crop
y_coord_emb_2=yc_rc[0][list_classes_index_2]+y1_2_crop
x_coord_tip_2=view_2_x
y_coord_tip_2=view_2_y
# if abs(x_coord_emb_1-x_coord_tip_1)<=5*move_num and abs(x_coord_emb_2-x_coord_tip_2)<=5*move_num:
if abs(x_coord_emb_1-x_coord_tip_1)<=15 and abs(x_coord_emb_2-x_coord_tip_2)<=15:
current_x=current_x
current_y=current_y
else:
current_x=current_x_new
current_y=current_y_new
else:
print('Done posterior FOV2')
end_2=1
else:
end_1=1
print('Done posterior FOV1')
elif action=='just move':
next_z=next_z
print('Current X = ',current_x)
print('Current Y = ',current_y)
print('Current Z = ',current_z)
print('Moving embryo injecion point under needle')
XYZ_Location(5000,5000,2000,current_x,current_y,current_z,ser)
# time.sleep(.25)
time.sleep(.5)
elif action=='inject new':
XYZ_Location(5000,5000,2000,current_x,current_y,current_z,ser)
time.sleep(.5)
next_z=next_z
current_z_new=current_z
# time.sleep(.15)
img1,img2=stream_image(footage_socket_1,footage_socket_2,pic,0)
img1_crop=img1[y1_1_crop:y2_1_crop,x1_1_crop:x2_1_crop]
if resize==1:
img1_crop=cv2.resize(img1_crop,(400,400))
im_height_1=400
im_width_1=400
output_dict_detection_boxes_stored,output_dict_detection_classes_stored,output_dict_detection_scores_stored,y1a_rc_1,y2a_rc_1,x1a_rc_1,x2a_rc_1,xc_rc_1,yc_rc_1=ml_injection_point_estimation_new([img1_crop],thresh_1,im_height_1,im_width_1,graph,sess,3)
list_classes_1=output_dict_detection_classes_stored[0].tolist()
img2_crop=img2[y1_2_crop:y2_2_crop,x1_2_crop:x2_2_crop]
if resize==2:
img2_crop=cv2.resize(img2_crop,(400,400))
im_height_2=400
im_width_2=400
output_dict_detection_boxes_stored,output_dict_detection_classes_stored,output_dict_detection_scores_stored,y1a_rc_2,y2a_rc_2,x1a_rc_2,x2a_rc_2,xc_rc_2,yc_rc_2=ml_injection_point_estimation_new([img2_crop],thresh_2,im_height_2,im_width_2,graph,sess,2)
list_classes_2=output_dict_detection_classes_stored[0].tolist()
if 3 in list_classes_1 and 3 in list_classes_2:
print('Posterior detected FOV1')
list_classes_index_1=list_classes_1.index(3)
if resize==1:
xc_rc_1[0][list_classes_index_1],yc_rc_1[0][list_classes_index_1]=transform_points(im_width_1,im_height_1,im_width_1_old,im_height_1_old,xc_rc_1[0][list_classes_index_1],yc_rc_1[0][list_classes_index_1])
x_post_1=xc_rc_1[0][list_classes_index_1]
y_post_1=yc_rc_1[0][list_classes_index_1]
print('Posterior detected FOV2')
list_classes_index_2=list_classes_2.index(3)
if resize==2:
xc_rc_2[0][list_classes_index_2],yc_rc_2[0][list_classes_index_2]=transform_points(im_width_2,im_height_2,im_width_2_old,im_height_2_old,xc_rc_2[0][list_classes_index_2],yc_rc_2[0][list_classes_index_2])
x_post_2=xc_rc_2[0][list_classes_index_2]
y_post_2=yc_rc_2[0][list_classes_index_2]
# cv2.imwrite('C:/Users/User/Downloads/Andrew_files/Amey Code-20190710T183750Z-001/Amey Code/ML/Surface_injection/images/post_fov_1_{}.jpg'.format(inj_num),img1_crop)
# cv2.imwrite('C:/Users/User/Downloads/Andrew_files/Amey Code-20190710T183750Z-001/Amey Code/ML/Surface_injection/images/post_fov_2_{}.jpg'.format(inj_num),img2_crop)
injection_list_num=1
dz=int(np.mean([float(Delta_Z_FOV_1_lin(view_1_y,y_post_1+y1_1_crop)),float(Delta_Z_FOV_2_lin(view_2_y,y_post_2+y1_2_crop))]))+inj_depth
print('Injection Depth = ',dz)
dy_1=Delta_px_y_FOV_1(float(Delta_Z_FOV_1_lin(view_1_y,y_post_1+y1_1_crop)))
dy_2=Delta_px_y_FOV_2(float(Delta_Z_FOV_2_lin(view_2_y,y_post_2+y1_2_crop)))
y_post_1_new=y_post_1-dy_1
y_post_2_new=y_post_2-dy_2
# plt.figure(7)
# plt.title('Detected Injection Point FOV1')
# plt.xlabel('x coordinate (px)')
# plt.ylabel('y coordinate (px)')
# plt.plot(x_post_1+x1_1_crop,y_post_1+y1_1_crop,'ro',markersize=3)
# plt.plot(view_1_x,view_1_y,'bo',markersize=3)
# plt.imshow(img1,cmap='gray')
# plt.figure(8)
# plt.title('Detected Injection Point FOV2')
# plt.xlabel('x coordinate (px)')
# plt.ylabel('y coordinate (px)')
# plt.plot(x_post_2+x1_2_crop,y_post_2+y1_2_crop,'ro',markersize=3)
# plt.plot(view_2_x,view_2_y,'bo',markersize=3)
# plt.imshow(img2,cmap='gray')
# plt.show()
current_z=current_z+dz
print('Current Z = ',current_z)
print('Piercing through embryo')
# change from 2000 to 5000
XYZ_Location(5000,5000,inj_speed,current_x,current_y,current_z,ser)
# Pressure
print('Injecting embryo')
#comment
while pressure_value<=40 and injected==2:
correct=0
o=0
# while correct==0:
while correct==0 and injected==2:
print('Try ',o+1)
signal=continuous_pressure(back_pressure_value_new,pressure_value,'inj')
arduino.write(signal.encode())
# time.sleep(.1)
time.sleep(.05)
# arduino.flush()
q_=arduino.readline()
q_=q_.decode()
s=q_.find('Received')
if pressure_value>5:
# if pressure_value>9:
img1,img2=stream_image(footage_socket_1,footage_socket_2,pic,0)
sum_image_1=detect_injection(img1,int(x_post_1+x1_1_crop),int(y_post_1_new+y1_1_crop),inj_num,1)
sum_image_2=detect_injection(img2,int(x_post_2+x1_2_crop),int(y_post_2_new+y1_2_crop),inj_num,2)
sum_image=np.max([sum_image_1,sum_image_2])
print('Max of blue px = ',sum_image)
if sum_image_thresh_min<=sum_image<=target_pixel or sum_image>=target_pixel:
injected=1
if pressure_value>5:
press_num=int((pressure_value + 43.6279)/0.9535)
else:
press_num=int((pressure_value + 0.35)/0.107)
if pressure_value>5:
if press_num>99:
if q_[s+9]=='P' and q_[s+10:s+13]==str(int((pressure_value + 43.6279)/0.9535)) and q_[s+13]=='p' and q_[s+14]=='\r':
correct=1
else:
o+=1
else:
if q_[s+9]=='P' and q_[s+10:s+12]==str(int((pressure_value + 43.6279)/0.9535)) and q_[s+12]=='p' and q_[s+13]=='\r':
correct=1
else:
o+=1
else:
if press_num>9:
if q_[s+9]=='P' and q_[s+10:s+12]==str(int((pressure_value + 0.35)/0.107)) and q_[s+12]=='p' and q_[s+13]=='\r':
correct=1
else:
o+=1
else:
if q_[s+9]=='P' and q_[s+10:s+11]==str(int((pressure_value + 0.35)/0.107)) and q_[s+11]=='p' and q_[s+12]=='\r':
correct=1
else:
o+=1
if sum_image_thresh_min<=sum_image<=target_pixel or sum_image>=target_pixel:
injected=1
else:
pressure_value+=1
# img1,img2=stream_image(footage_socket_1,footage_socket_2,pic,0)
# img1_crop=img1[y1_1_crop:y2_1_crop,x1_1_crop:x2_1_crop]
# img2_crop=img2[y1_2_crop:y2_2_crop,x1_2_crop:x2_2_crop]
# sum_image_1=detect_injection(img1,view_1_x,view_1_y,y2_1_crop)
# sum_image_2=detect_injection(img2,view_2_x,view_2_y,y2_2_crop)
# sum_image=np.max([sum_image_1,sum_image_2])
# print('Max of blue px = ',sum_image)
# if sum_image_thresh_min<=sum_image<=target_pixel or sum_image>=target_pixel:
# injected=1
# else:
# pressure_value+=1
#new
print('Pressure done')
correct=0
o=0
while correct==0:
print('Try ',o+1)
arduino.write("P0p".encode())
arduino.flush()
q_=arduino.readline()
q_=q_.decode()
s=q_.find('Received')
if q_[s+9]=='P' and q_[s+10]=='0' and q_[s+11]=='p' and q_[s+12]=='\r':
correct=1
else:
o+=1
current_z=current_z-inj_depth-300
# Come out
#comment
XYZ_Location(20000,20000,500,current_x,current_y,current_z,ser)
time.sleep(2.5)
#comment
end=3
elif 3 not in list_classes_1:
print('no injection because FOV 1')
end_1=1
else:
print('no injection because FOV 2')
end_2=1
else:
print('Doing nothing')
return end,current_x,current_y,current_z,next_z,injection_list_num,x_coord_emb_1,y_coord_emb_1,x_coord_tip_1,y_coord_tip_1,x_coord_emb_2,y_coord_emb_2,x_coord_tip_2,y_coord_tip_2,y1_1_crop,y2_1_crop,x1_1_crop,x2_1_crop,y1_2_crop,y2_2_crop,x1_2_crop,x2_2_crop,im_width_1_old,im_height_1_old,im_width_2_old,im_height_2_old,current_z_new,move_num,injected,end_1,end_2,injected,sum_image,pressure_value