~gcg/splithopkinsontools/trunk : revision 9

6

import numpy as np

7

import os, sys

8

from scipy import misc, signal, stats

9

import glob

9

import glob, pickle

10

import copy

11

from pyqtgraph.Qt import QtGui, QtCore

12

import numpy as np

13

import pyqtgraph as pg

14

from pyqtgraph.parametertree import Parameter, ParameterTree

15

from trackROI_OpenCV import TrackROI # produces same data as Timo

15

16

17

# only edit lines below:

17

path = "/home/gcg/SHTB/20171005_PP"

18

path = "/home/gcg/SHTB/Probe6.2"

18

19

params = [{'name': 'px2mm', 'type': 'float', 'value': 0.02439, 'step': 1.0e-3, 'siPrefix': False, 'suffix': 'mm/px'},

20

{'name': 'scan rate', 'type': 'float', 'value': 200, 'step': 1, 'suffix': 'kHz'},

20

params = [{'name': 'px2mm', 'type': 'float', 'value': 0.021277, 'step': 1.0e-3, 'siPrefix': False, 'suffix': 'mm/px'},

21

{'name': 'scan rate', 'type': 'float', 'value': 200.0, 'step': 1, 'suffix': 'kHz'},

21

22

{'name': 'width ROI 1 in px', 'type': 'float', 'value': 1, 'suffix': ' px'},

22

23

{'name': 'width ROI 1 in mm', 'type': 'float', 'value': 1, 'suffix': ' mm'},

23

24

{'name': 'velocity ROI 1', 'type': 'float', 'value': 0, 'suffix': ' m/s'},

24

25

{'name': 'width ROI 2 in px', 'type': 'float', 'value': 1, 'suffix': ' px'},

25

26

{'name': 'width ROI 2 in mm', 'type': 'float', 'value': 1, 'suffix': ' mm'},

26

27

{'name': "distance ROI1 -- ROI2", 'type': 'float', 'value': 0, 'suffix': ' mm'},

28

{'name': "ROI1 start", 'type': 'float', 'value': 2564.0448385397744, 'suffix': ' px'},

29

{'name': "ROI1 stop", 'type': 'float', 'value': 2600.7122370880443, 'suffix': ' px'},

30

{'name': "ROI2 start", 'type': 'float', 'value': 2644.9711630257034, 'suffix': ' px'},

31

{'name': "ROI2 stop", 'type': 'float', 'value': 2685.8212880711058, 'suffix': ' px'},

27

32

]

28

33

29

34

33

38

34

39

os.chdir(path)

35

40

files = glob.glob("*.bmp")

41

print(files)

36

42

if not (len(files) == 1):

37

print "There are have multiple .bmp files in the working directory."

38

print "This program expects only a single .bmp image file containing linescan data."

43

print("There are have multiple .bmp files in the working directory.")

44

print("This program expects only a single .bmp image file containing linescan data.")

39

45

sys.exit(1)

40

46

41

print files[0]

47

print(files[0])

42

48

43

49

image_data = misc.imread(os.path.join(path,files[0]), flatten=1)

44

print np.shape(image_data)

50

print(np.shape(image_data))

51

return image_data

45

52

46

53

# average every two subsequent lines

47

nx, ny = np.shape(image_data)

48

new_data = np.zeros((nx/2, ny))

49

for i in xrange(nx/2 - 1):

50

j = 2*i

51

k = j + 1

52

new_data[i,:] = 0.5 * (image_data[j,:] + image_data[k,:])

53

54

print "*** AVERAGED EVERY TWO LINES ***"

55

56

#return image_data

54

# nx, ny = np.shape(image_data)

55

# new_data = np.zeros((int(nx/2), ny))

56

# for i in xrange(nx/2 - 1):

57

# j = 2*i

58

# k = j + 1

59

# new_data[i,:] = 0.5 * (image_data[j,:] + image_data[k,:])

60

#

61

# print("*** AVERAGED EVERY TWO LINES ***")

62

63

57

64

return new_data

58

65

59

66

def updatePlot():

60

67

global x

61

start1, end1 = ROI1.getRegion()

62

width1 = end1 - start1

63

start2, end2 = ROI2.getRegion()

64

width2 = end2 - start2

65

p["width ROI 1 in px"] = width1

66

p["width ROI 1 in mm"] = width1 * p["px2mm"]

67

p["width ROI 2 in px"] = width2

68

p["width ROI 2 in mm"] = width2 * p["px2mm"]

68

p["ROI1 start"], p["ROI1 stop"] = ROI1.getRegion()

69

p["width ROI 1 in px"] = p["ROI1 stop"] - p["ROI1 start"]

70

p["width ROI 1 in mm"] = p["width ROI 1 in px"] * p["px2mm"]

71

72

p["ROI2 start"], p["ROI2 stop"] = ROI2.getRegion()

73

p["width ROI 2 in px"] = p["ROI2 stop"] - p["ROI2 start"]

74

p["width ROI 2 in mm"] = p["width ROI 2 in px"] * p["px2mm"]

69

75

70

76

p["distance ROI1 -- ROI2"] = (np.mean(ROI2.getRegion()) - np.mean(ROI1.getRegion())) * p["px2mm"]

71

77

87

93

layoutVL.addWidget(btnROI1) # button goes in upper-left

88

94

layoutVL.addWidget(btnROI2) # button goes in upper-left

89

95

layoutVL.addWidget(btnSave)

96

layoutVL.addWidget(btnSaveConfig)

97

layoutVL.addWidget(btnRestoreConfig)

90

98

#layout.addWidget(listw) # list widget goes in bottom-left

91

99

layoutVR.addWidget(plotAll)

92

100

layoutVR.addWidget(plot) # plot goes on right side, spanning 3 rows

96

104

97

105

def clickedBtnROI1(btnROI1):

98

106

print("button clicked!", ROI1.getRegion())

99

from trackROI import TrackROI

107

#from trackROI_OpenCV import TrackROI

100

108

with pg.BusyCursor():

101

109

t1 = TrackROI(data, int(ROI1.getRegion()[0]), int(ROI1.getRegion()[1]))

102

110

global curve1

103

111

curve1.setData(x, t1.displacements * p["px2mm"])

104

112

113

114

# --- indicate the path of displaced ROI1 on image ---

115

global checkROI1

116

x0 = np.mean(ROI1.getRegion())

117

checkROI1.clear()

118

checkROI1 = pg.ScatterPlotItem(size=2, pen=pg.mkPen(None), brush=pg.mkBrush(0, 255, 0, 120))

119

120

spots = []

121

for i in xrange(numFrames):

122

spot = {'pos': (x0 + t1.displacements[i], i)}

123

spots.append(spot)

124

125

checkROI1.addPoints(spots)

126

plotAll.addItem(checkROI1)

127

105

128

xmin, xmax = velRange1.getRegion()

106

129

indices = np.where(np.logical_and(x > xmin, x < xmax))

107

130

slope, intercept, r_value, p_value, std_err = stats.linregress(x[indices],t1.displacements[indices]* p["px2mm"])

108

print "linear velocity of ROI1 in selected range is ", slope

131

print("linear velocity of ROI1 in selected range is ", slope)

109

132

p["velocity ROI 1"] = slope

110

133

plotTrack1.plot((xmin, xmax), (intercept + slope * xmin, intercept + slope * xmax))

111

134

112

135

# also update difference of ROI1 and ROI2

113

136

x1, y1 = curve1.getData()

114

137

x2, y2 = curve2.getData()

115

curve3.setData(x, y2 - y1)

138

curve3.setData(x, (y2 - y1))

116

139

117

140

def clickedBtnROI2(btnROI2):

118

141

print("button 2 clicked!", ROI2.getRegion())

119

from trackROI import TrackROI

142

#from trackROI import TrackROI

120

143

with pg.BusyCursor():

121

144

t2 = TrackROI(data, int(ROI2.getRegion()[0]), int(ROI2.getRegion()[1]))

122

145

global curve2

126

149

x1, y1 = curve1.getData()

127

150

x2, y2 = curve2.getData()

128

151

curve3.setData(x, (y2 - y1))

152

153

# --- indicate the path of displaced ROI1 on image ---

154

global checkROI2

155

x0 = np.mean(ROI2.getRegion())

156

checkROI2.clear()

157

checkROI2 = pg.ScatterPlotItem(size=2, pen=pg.mkPen(None), brush=pg.mkBrush(255, 255, 0, 120))

158

159

spots = []

160

for i in xrange(numFrames):

161

spot = {'pos': (x0 + t2.displacements[i], i)}

162

spots.append(spot)

163

164

checkROI2.addPoints(spots)

165

plotAll.addItem(checkROI2)

166

129

167

130

168

def saveToFile(btn):

131

169

x1, y1 = curve1.getData() # displacement of ROI1

134

172

135

173

#print x

136

174

137

L0 = np.mean(ROI2.getRegion()) - np.mean(ROI1.getRegion())

175

L0 = p["distance ROI1 -- ROI2"]

176

print "Saving with L0 = ", L0

138

177

strain = (y2 - y1) / L0

139

178

140

179

header = "linescan frequency = %f kHz\npixel length = %f mm\ngauge length = %f\ntime [msec], ROI1 displacement [mm], ROI2 displacement [mm], relative displacement [mm], strain [-]" % (p["scan rate"], p["px2mm"], L0*p["px2mm"])

141

np.savetxt(os.path.join(path, "linescan_analysis.dat"), np.column_stack((2*x, y1, y2, y3, strain)),

180

np.savetxt(os.path.join(path, "linescan_analysis.dat"), np.column_stack((x, y1, y2, y3, strain)),

142

181

header=header)

143

print "wrote output file linescan_analysis.dat to directory [%s]" % (path)

182

print("wrote output file linescan_analysis.dat to directory [%s]" % (path))

183

184

def saveState():

185

state = p.saveState()

186

outfile = os.path.join(path, "configuration.pkl")

187

output = open(outfile, 'wb')

188

pickle.dump(state, output)

189

output.close()

190

print "saved configuration state to file %s" % (outfile)

191

192

def loadState():

193

#global p

194

global ROI1

195

infile = os.path.join(path, "configuration.pkl")

196

pkl_file = open(infile, 'rb')

197

state = pickle.load(pkl_file)

198

p.restoreState(state) #, addChildren=False, removeChildren=False)

199

pkl_file.close()

200

print "restored configuration state from file %s" % (infile)

201

print p["ROI1 start"]

202

ROI1.setRegion([p["ROI1 start"], p["ROI1 stop"]])

203

print ROI1.getRegion()

204

updatePlot()

205

206

207

#def restore():

208

# global state

209

# p.restoreState(state, addChildren=add)

144

210

145

211

def change(param, changes):

146

212

""" called whenever a value in the parameter tree is changed

148

214

global x

149

215

x = np.arange(N) * (1.0 / p["scan rate"])

150

216

151

updatePlot()

217

#updatePlot() # ... does not seem to work

152

218

153

219

for param, change, data in changes:

154

220

path = p.childPath(param)

156

222

childName = '.'.join(path)

157

223

else:

158

224

childName = param.name()

159

print(' path: %s' % path)

160

print(' parameter: %s' % childName)

161

print(' change: %s' % change)

162

print(' data: %s' % str(data))

225

print('* path: %s' % path)

226

print('* parameter: %s' % childName)

227

print('* change: %s' % change)

228

print('* data: %s' % str(data))

163

229

print(' ----------')

164

230

165

231

if childName == "Save Stress/Strain":

197

263

btnROI2 = QtGui.QPushButton('track ROI 2')

198

264

btnROI2.clicked.connect(clickedBtnROI2)

199

265

200

btnSave = QtGui.QPushButton('save to file')

266

btnSave = QtGui.QPushButton('save results to file')

201

267

btnSave.clicked.connect(saveToFile)

202

268

269

btnSaveConfig = QtGui.QPushButton('save config to file')

270

btnSaveConfig.clicked.connect(saveState)

271

272

btnRestoreConfig = QtGui.QPushButton('load config to file')

273

btnRestoreConfig.clicked.connect(loadState)

274

203

275

plotAll = pg.PlotWidget(title="all linescan frames")

204

276

imgAll = pg.ImageItem(np.transpose(data))

277

checkROI1 = pg.ScatterPlotItem(size=2, pen=pg.mkPen(None), brush=pg.mkBrush(0, 255, 0, 120))

278

checkROI2 = pg.ScatterPlotItem(size=2, pen=pg.mkPen(None), brush=pg.mkBrush(0, 255, 0, 120))

205

279

plotAll.addItem(imgAll)

206

280

plotAll.setLabel('left', "frame no.")

207

281

plotAll.setLabel('bottom', "pixel no.")

210

284

plot.setLabel('left', "no unit")

211

285

plot.setLabel('bottom', "pixel no.")

212

286

213

ROI1 = pg.LinearRegionItem([2413,2580])

214

ROI2 = pg.LinearRegionItem([3476,3800])

287

ROI1 = pg.LinearRegionItem([p["ROI1 start"],p["ROI1 stop"]])

288

ROI2 = pg.LinearRegionItem([p["ROI2 start"],p["ROI2 stop"]])

215

289

ROI1.setZValue(10)

216

290

ROI2.setZValue(10)

217

291

plot.addItem(ROI1)