232 lines
6.8 KiB
Python
232 lines
6.8 KiB
Python
# -*- coding: utf-8 -*-
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"""
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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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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 cv2 as cv
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import PIL.Image
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from scipy import ndimage,signal
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import glob, os
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from pyqtgraph.Qt import QtCore, QtGui
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import pyqtgraph as pg
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pg.setConfigOptions(imageAxisOrder='row-major')
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def set_fiducial(pic):
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# fiducial test
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f=np.array(((0, 0, 0, 0, 0),
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(0, 1, 1, 1, 0),
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(0, 1, 0, 0, 0),
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(0, 1, 1, 0, 0),
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(0, 1, 0, 0, 0),
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(0, 0, 0, 0, 0),), pic.dtype)
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pic[0:6, 0:5]=f*pic.max()
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def wtestimages():
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#fn=os.path.expanduser('~/Documents/prj/SwissFEL/epics_ioc_modules/ESB_MX/python/SwissMX/scratch/fiducial/image{idx:03d}.png')
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fn=os.path.expanduser('../scratch/fiducial/image{idx:03d}.png')
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img=np.kron(np.array([[1, 0] * 5, [0, 1] * 5] * 6,dtype=np.uint8), np.ones((100, 100),dtype=np.uint8)*255)
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set_fiducial(img)
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pil_img=PIL.Image.fromarray(img)
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pil_img.save(fn.format(idx=2))
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img=np.ndarray((1000,1200),dtype=np.uint8)
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img[:]=255
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#img=np.zeros((1200,1000),dtype=np.uint8)
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fid=np.array([[0, 1] * 2, [1, 0] * 2] * 2,dtype=np.uint8)[:3,:3]
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fid=np.kron(fid, np.ones((210, 210),dtype=np.uint8)*255)
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img[100:100+fid.shape[0],200:200+fid.shape[1]]=fid
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set_fiducial(img)
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pil_img=PIL.Image.fromarray(img)
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pil_img.save(fn.format(idx=3))
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img=np.ndarray((1200,1000))
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#wtestimages()
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class fiducial(QtGui.QMainWindow):
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def __init__(self, parent = None):
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super(fiducial, 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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#self._imgLst=imgLst=sorted(glob.glob("../scratch/autofocus1/image*.png"))
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self._imgLst=imgLst=sorted(glob.glob("../scratch/fiducial/*.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._sldImgIdx=sld1=QtGui.QSlider(QtCore.Qt.Horizontal)
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sld1.setMinimum(0)
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sld1.setMaximum(len(imgLst)-1)
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sld1.setValue(0)
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sld1.setTickPosition(QtGui.QSlider.TicksBelow)
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sld1.setTickInterval(1)
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sld1.valueChanged.connect(self.cb_sld_change)
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self._sldTplSz=sld2=QtGui.QSlider(QtCore.Qt.Horizontal)
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sld2.setMinimum(0)
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sld2.setMaximum(300)
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sld2.setValue(90)
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sld2.valueChanged.connect(self.cb_sld_change)
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self._sldTplBrd=sld3=QtGui.QSlider(QtCore.Qt.Horizontal)
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sld3.setMinimum(3)
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sld3.setMaximum(50)
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sld3.setValue(20)
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sld3.valueChanged.connect(self.cb_sld_change)
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self._imv1=imv1=pg.ImageView()
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self._imv2=imv2=pg.ImageView()
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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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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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pw.resize(100,100)
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pw.setMaximumSize(2000,200)
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l.addWidget(sld1, 0, 0)
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l.addWidget(sld2, 1, 0)
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l.addWidget(sld3, 2, 0)
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l.addWidget(imv1, 3, 0)
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l.addWidget(imv2, 4, 0)
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l.addWidget(pw, 5, 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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self._imv2.setHistogramRange(0, 1)
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self._imv2.setLevels(0, 1)
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def cb_sld_change(self,val,auto=False):
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i=self._sldImgIdx.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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#pil_img=PIL.Image.fromarray(img)
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#pil_img.save('../scratch/fiducial/image002.png')
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#fn='/home/zamofing_t/Documents/prj/SwissFEL/epics_ioc_modules/ESB_MX/python/SwissMX/scratch/fiducial/zoom0400.png'
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#pil_img=PIL.Image.open(fn+'_')
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#img=np.asarray(pil_img)
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#img=np.array(img,dtype=np.uint8)
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#pil_img=PIL.Image.fromarray(img)
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#pil_img.save(fn)
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#img16=np.array(img,np.int16)
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#fft=np.log(np.abs(np.fft.fft2(img)))
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#fft=np.fft.fftshift(fft)
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fid=np.array([[0, 1]*2, [1, 0]*2]*2, dtype=np.uint8)[:3, :3]
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fid=np.kron(fid, np.ones((100, 100), dtype=np.uint8)*255)
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#res = cv.matchTemplate(img,fid,cv.TM_CCORR_NORMED )
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#fid=np.ones((250,250),dtype=np.uint8)*255
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#fid[20:230,20:230]=0
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#sz=( 84, 84); brd=( 7, 7) # zoom 001
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#sz=(128, 128); brd=( 9, 9) # zoom 200
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#sz=(200, 200); brd=(13, 13) # zoom 400
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v=self._sldTplSz.value(); sz=(v,v)
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v=self._sldTplBrd.value(); brd=(v,v)
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fid=np.ones((sz[1]+2*brd[1],sz[0]+2*brd[0]),dtype=np.uint8)*255
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fid[brd[1]:sz[1]+brd[1],brd[0]:sz[0]+brd[0]]=0
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mask=np.ones((sz[1]+2*brd[1],sz[0]+2*brd[0]),dtype=np.uint8)*255
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mask[2*brd[1]:sz[1],2*brd[0]:sz[0]]=0
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#https://docs.opencv.org/4.5.2/d4/dc6/tutorial_py_template_matching.html
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#res = cv.matchTemplate(img,fid,cv.TM_CCORR_NORMED )
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res = cv.matchTemplate(img,fid,cv.TM_CCORR_NORMED,mask=mask)
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corr_u8=np.array(res*255,np.uint8)
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h,w=img.shape
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fh2,fw2=fid.shape
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fw2//=2
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fh2//=2
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mtr=np.ndarray((5,2),np.uint16)
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corr=np.ndarray((5,),np.float32)
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for i in range(5):
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p=np.unravel_index(res.argmax(), res.shape)
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corr[i]=res[p]
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mtr[i,:]=p
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y0=max(p[0]-fh2,0)
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y1=min(p[0]+fh2,h)
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x0=max(p[1]-fw2,0)
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x1=min(p[1]+fw2,w)
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res[y0:y1,x0:x1]*=.5
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res[p[0],p[1]]=0
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corr_u8=np.array(res*255,np.uint8)
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ctr=mtr.mean(0,dtype=np.int32)+(fw2,fh2)
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try:
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img=img*1
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img[ctr[0]-5:ctr[0]+5,ctr[1]-5:ctr[1]+5]=255
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img[ctr[0],:]=0
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img[:,ctr[1]]=0
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except IndexError as e:
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pass
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self._imv1.setImage(img,autoRange=auto,autoLevels=auto,autoHistogramRange=auto)
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self._imv2.setImage(res,autoRange=auto,autoLevels=auto,autoHistogramRange=auto)
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pos=mtr.mean(0)[::-1]+(fw2,fh2)
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print(fid)
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print(mask)
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print(corr)
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print(mtr)
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print(f'TplSz:{sz} TplBrd:{brd}')
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_log.debug(f'position: {pos} correlation:{corr.mean()}')
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#mtr=self._metrics
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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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fd=fiducial()
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fd.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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