automatic extraction of line profiles from scaled images

[klaus.ha...@gmail.com]

Hello,
I would like to generate lineprofiles through scaled images

I can generate a

LineROI((20, 20), (40, 0), .1)    though it goes from 20 20 to 40 40 in user coordinates  ,  ?

I would like to click programmatically the ROI button
and then retrieve the XY data array from the ROI plotwidget , what do I need for this ?
get arrayregion is in weird units...... and the x axis misses

thank you,
yours,

Klaus


last pyqtgraph version from macport



#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import division
from PyQt4.QtCore import *
from PyQt4.QtGui import *
#changer les chemins
import numpy as np
import scipy.ndimage as ndi
import pyqtgraph as pg
from pyqtgraph.Point import Point
from  open_SQUID_image import open_image_file
from  open_SQUID_image import three_points_plain
from  open_SQUID_image import slider

from os import path as pt

## Create image to display



class Cross(QDialog):
    def __init__(self,parent = None):
        QWidget.__init__(self)
        self.Form = QWidget()
        layout = QVBoxLayout()
        self.Form.setLayout(layout)
   

        self.plt = pg.PlotItem()
        self.plt.setTitle("swapaxes_scaled")
        self.p1 = pg.ImageView(view=self.plt)
       
       
       
        # Disconnect old ROI
        #imv = pg.image(pg.np.random.normal(size=(100, 100)))

        self.p1.roi.sigRegionChanged.disconnect(self.p1.roiChanged)
# Create new ROI and install exactly as done in ImageView.__init__
        self.p1.roi = pg.LineROI((20, 20), (40, 0), .1)
        self.p1.roi.setZValue(20)
        self.p1.view.addItem(self.p1.roi)
        self.p1.roi.hide()
        self.p1.roi.sigRegionChanged.connect(self.p1.roiChanged)
       
       
       
       
       
        #self.p2 = pg.PlotWidget()


        layout.addWidget(self.p1, 1)
        #layout.addWidget(self.p2, 2)


        self.data = np.ones((100, 100), dtype=float)
        self.data[45:55, 45:55] = 0
        self.data[25, :] = 5
        self.data[:, 25] = 5
        self.data[75, :] = 5
        self.data[:, 75] = 5
        self.data[50, :] = 10
        self.data[:, 50] = 10
        self.data += np.sin(np.linspace(0, 20, 100)).reshape(1, 100)
        self.data += np.random.normal(size=(100,100))
        self.x_length=100
        self.y_length=100
        self.start_x_mu=1
        self.delta_x_mu=0.8
        self.start_y_mu=1
        self.delta_y_mu=0.5


        self.x0, self.x1 = (self.start_x_mu,self.start_x_mu+ self.x_length*self.delta_x_mu)
        self.y0, self.y1 = (self.start_y_mu, self.start_y_mu+self.y_length*self.delta_y_mu)
        print "return=X1= {} Y1= {}".format(self.x1,self.y1)

        self.xscale, self.yscale = (self.x1-self.x0) / self.data.shape[0], (self.y1-self.y0) / self.data.shape[1]
        print "xscale= {} yscale= {}".format(self.xscale,self.yscale)

        print "self.data shape before plotting",self.data.shape
        self.p1.setImage(self.data,pos=[self.x0, self.y0], scale=[self.xscale, self.yscale])
        self.plt.setAspectLocked(True)


      
   

        self.p1.roi.sigRegionChangeFinished.connect(self.updateFromROI)

        titi=self.p1.getRoiPlot()
        print type(titi)
        titi.setVisible(True)


        #proxy = pg.SignalProxy(self.plt.scene().sigMouseMoved, rateLimit=60, slot=self.mouseMoved)

        self.Form.show()
       
       

    def updateFromROI(self):
     
        data, coords=self.p1.roi.getArrayRegion(self.data,self.plt,(0,1),returnMappedCoords=True)
       
       
        print "data=", data
        print "coord=",coords

[klaus.ha...@gmail.com]

Le dimanche 24 juillet 2016 03:38:57 UTC+2, klaus.ha...@gmail.com a écrit :

Hello,
I would like to generate lineprofiles through scaled images

I can generate a

LineROI((20, 20), (40, 0), .1)    though it goes from 20 20 to 40 40 in user coordinates  ,  ?

I would like to click programmatically the ROI button

 

Now I can  retrieve the XY data array from the ROI plotwidget , with the csv exporter

thank you,
yours,

Klaus


last pyqtgraph version from macport

#!/usr/bin/env python

# -*- coding: utf-8 -*-

from __future__ import division

from PyQt4.QtCore import *

from PyQt4.QtGui import *

#changer les chemins

import numpy as np

import scipy.ndimage as ndi

import pyqtgraph as pg

import pyqtgraph.exporters

from pyqtgraph.Point import Point

from  open_SQUID_image import open_image_file

from  open_SQUID_image import three_points_plain

from  open_SQUID_image import slider

from os import path as pt

## Create image to display

class Cross(QDialog):

    def __init__(self,parent = None):

        QWidget.__init__(self)

        self.Form = QWidget()

        layout = QVBoxLayout()

        self.Form.setLayout(layout)

        #le plotitem contien ROI button

        self.titi=self.p1.getRoiPlot()

        print type(self.titi)

        self.titi.setVisible(True)

        self.Plot_Item=self.titi.getPlotItem()

        #proxy = pg.SignalProxy(self.plt.scene().sigMouseMoved, rateLimit=60, slot=self.mouseMoved)

        self.Form.show()

        

        

    def updateFromROI(self):

      

        data, coords=self.p1.roi.getArrayRegion(self.data,self.plt,(0,1),returnMappedCoords=True)

        

        

        print "data=", data

        print "coord=",coords

        print self.Plot_Item.listDataItems()

        exporter=pg.exporters.CSVExporter(self.Plot_Item)

        

        exporter.export('tst.csv')

        

## Start Qt event loop unless running in interactive mode or using pyside.

if __name__=="__main__":

    import math

    import sys

    app=QApplication(sys.argv)

    mine_cross=Cross()

    app.exec_()