towards fiducial detection
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@@ -4,91 +4,135 @@ Demonstrate a simple data-slicing task: given 3D data (displayed at top), select
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a 2D plane and interpolate data along that plane to generate a slice image
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(displayed at bottom).
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https://www.hindawi.com/journals/js/2021/5643054/
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https://www.hindawi.com/journals/mpe/2021/8243072/
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"""
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## Add path to library (just for examples; you do not need this)
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import logging
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import numpy as np
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_log=logging.getLogger(__name__)
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import numpy as np
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import PIL.Image
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from scipy import ndimage,signal
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import glob
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from pyqtgraph.Qt import QtCore, QtGui
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import pyqtgraph as pg
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app=QtGui.QApplication([])
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## Create window with two ImageView widgets
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win=QtGui.QMainWindow()
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win.resize(800, 800)
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win.setWindowTitle('pyqtgraph example: DataSlicing')
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cw=QtGui.QWidget()
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win.setCentralWidget(cw)
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l=QtGui.QGridLayout()
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cw.setLayout(l)
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imv1=pg.ImageView()
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imv2=pg.ImageView()
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l.addWidget(imv1, 0, 0)
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l.addWidget(imv2, 1, 0)
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sld=QtGui.QSlider(QtCore.Qt.Horizontal)
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sld.setMinimum(10)
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sld.setMaximum(30)
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sld.setValue(20)
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sld.setTickPosition(QtGui.QSlider.TicksBelow)
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sld.setTickInterval(5)
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class autofocus(QtGui.QMainWindow):
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def __init__(self, parent = None):
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super(autofocus, self).__init__(parent)
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self.resize(800, 1500)
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self.setWindowTitle('pyqtgraph example: DataSlicing')
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cw=QtGui.QWidget()
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self.setCentralWidget(cw)
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l=QtGui.QGridLayout()
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cw.setLayout(l)
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l.addWidget(sld, 2, 0)
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win.show()
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#self._imgLst=imgLst=sorted(glob.glob("../scratch/autofocus1/image*.png"))
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self._imgLst=imgLst=sorted(glob.glob("../scratch/autofocus2/image*.png"))
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self._metrics=mtr=np.ndarray(shape=(len(imgLst), 5))
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mtr[:]=0
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self._sld=sld=QtGui.QSlider(QtCore.Qt.Horizontal)
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sld.setMinimum(0)
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sld.setMaximum(len(imgLst)-1)
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sld.setValue(0)
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sld.setTickPosition(QtGui.QSlider.TicksBelow)
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sld.setTickInterval(1)
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sld.valueChanged.connect(self.cb_sld_change)
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roi=pg.LineSegmentROI([[10, 64], [120, 64]], pen='r')
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imv1.addItem(roi)
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self._imv1=imv1=pg.ImageView()
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self._imv2=imv2=pg.ImageView()
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x1=np.linspace(-30, 10, 128)[:, np.newaxis, np.newaxis]
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x2=np.linspace(-20, 20, 128)[:, np.newaxis, np.newaxis]
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y=np.linspace(-30, 10, 128)[np.newaxis, :, np.newaxis]
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z=np.linspace(-20, 20, 128)[np.newaxis, np.newaxis, :]
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d1=np.sqrt(x1**2+y**2+z**2)
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d2=2*np.sqrt(x1[::-1]**2+y**2+z**2)
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d3=4*np.sqrt(x2**2+y[:, ::-1]**2+z**2)
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data=(np.sin(d1)/d1**2)+(np.sin(d2)/d2**2)+(np.sin(d3)/d3**2)
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#spl=QtGui.QSplitter(QtCore.Qt.Horizontal)
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self._pw=pw=pg.PlotWidget(name='Plot1') ## giving the plots names allows us to link
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import PIL.Image
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from scipy import ndimage
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import glob
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imgLst=sorted(glob.glob("image*.png"))
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v=np.ndarray(shape=(len(imgLst), 2))
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#for i, fn in enumerate(imgLst):
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# img=PIL.Image.open(fn)
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# img=np.asarray(img)
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# s=ndimage.sobel(img)
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# v[i, 0]=s.sum()
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# v[i, 1]=s.std()
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#fig, ax=plt.subplots()
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#mx=v.max(0)
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#mn=v.min(0)
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#v=(v-mn)/(mx-mn)
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# ax.plot(v[:,0])
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#ax.plot(v)
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#plt.show()
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# pass
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self._plt=plt=[]
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for c in ('rgbcy'):
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plt.append(pw.plot(pen=c))
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def update():
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global data, imv1, imv2, imgLst
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d2=roi.getArrayRegion(data, imv1.imageItem, axes=(1, 2))
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imv2.setImage(d2)
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pw.resize(100,100)
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pw.setMaximumSize(2000,200)
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l.addWidget(sld, 0, 0)
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l.addWidget(imv1, 1, 0)
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l.addWidget(imv2, 2, 0)
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l.addWidget(pw, 3, 0)
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## Display the data
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self.cb_sld_change(0,True)
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mtr[1:,:]=mtr[0,:]
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self._imv1.setHistogramRange(0, 100)
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self._imv1.setLevels(0, 40)
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self._imv2.setHistogramRange(0, 100)
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self._imv2.setLevels(0, 40)
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def cb_sld_change(self,val,auto=False):
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i=self._sld.value()
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_log.debug(f'{i}')
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fn= self._imgLst[i]
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img=PIL.Image.open(fn)
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img=np.asarray(img)
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#slb=ndimage.sobel(img)
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img16=np.array(img,np.int16)
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s1=np.array(((1,0,-1),(2,0,-2),(1,0,-1)),np.int16)
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sb1=signal.convolve2d(img16, s1, mode='same', boundary='fill', fillvalue=0)
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sb2=signal.convolve2d(img16, s1.T, mode='same', boundary='fill', fillvalue=0)
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sb=np.abs(sb1)+np.abs(sb2)
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#remove irrelevant low values
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idx=sb[:]<20
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sbLut=sb*1
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sbLut[idx]=0
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#import numpy as np
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#import matplotlib.pyplot as plt
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mx=sb.max()+1
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lut=(np.sin(np.arange(mx)/mx*np.pi-np.pi/2)+1)*128
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#lut=((np.arcsin(np.arange(mx)/(mx-1)*2-1)/np.pi)+.5)*255
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#lut=np.array(lut*255,np.uint16)
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#sbLut=lut[sb]
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#import matplotlib.pyplot as plt
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#plt.plot(lut);plt.show()
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#img2=ndimage.grey_dilation(sb,size=(5,5)) #, size=None, footprint=None, structure=None, output=None, mode='reflect', cval=0.0, origin=0)
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img2=ndimage.grey_closing(sb,size=(25,25)) #, size=None, footprint=None, structure=None, output=None, mode='reflect', cval=0.0, origin=0)
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roi.sigRegionChanged.connect(update)
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#fft=np.log(np.abs(np.fft.fft2(sb)))
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#fft=np.fft.fftshift(fft)
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# fft[300:700,400:800]=0
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# v[i,1]=fft.sum()
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## Display the data
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imv1.setImage(data)
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imv1.setHistogramRange(-0.01, 0.01)
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imv1.setLevels(-0.003, 0.003)
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self._imv1.setImage(sb,autoRange=auto,autoLevels=auto,autoHistogramRange=auto)
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#self._imv2.setImage(sb,autoRange=auto,autoLevels=auto,autoHistogramRange=auto)
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self._imv2.setImage(sbLut,autoRange=auto,autoLevels=auto,autoHistogramRange=auto)
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mtr=self._metrics
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update()
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mtr[i, 0]=img.std()
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mtr[i, 1]=sb.sum()
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mtr[i, 2]=sb.std()
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mtr[i, 3]=sbLut.sum()#sb.std()
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mtr[i, 4]=sbLut.std()#img2.sum()
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mx=mtr.max(0)
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mn=mtr.min(0)
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mtr=(mtr-mn)/(mx-mn)
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_log.debug(f'{i} {mtr[i,:]}')
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for i in range(mtr.shape[1]):
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self._plt[i].setData(mtr[:,i])
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## Start Qt event loop unless running in interactive mode.
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if __name__=='__main__':
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import sys
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logging.basicConfig(level=logging.DEBUG, format='%(levelname)s:%(module)s:%(lineno)d:%(funcName)s:%(message)s ')
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app=QtGui.QApplication([])
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af=autofocus()
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af.show()
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if (sys.flags.interactive!=1) or not hasattr(QtCore, 'PYQT_VERSION'):
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QtGui.QApplication.instance().exec_()
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