ramanscanui.py 12.2 KB
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# -*- coding: utf-8 -*-
"""
GEPARD - Gepard-Enabled PARticle Detection
Copyright (C) 2018  Lars Bittrich and Josef Brandt, Leibniz-Institut für 
Polymerforschung Dresden e. V. <bittrich-lars@ipfdd.de>    

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program, see COPYING.  
If not, see <https://www.gnu.org/licenses/>.
"""

from PyQt5 import QtCore, QtWidgets
import numpy as np
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from multiprocessing import Process, Queue, Event
import queue
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from time import time
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from external import tsp
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import datetime
import sys
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import os
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def reorder(points, N=20):
    y0, y1 = points[:,1].min(), points[:,1].max()
    y = np.linspace(y0,y1+.1,N+1)
    allind = np.arange(points.shape[0])
    newind = []
    for i, yi in enumerate(y[:-1]):
        yi1 = y[i+1]
        indy = allind[(points[:,1]>=yi)&(points[:,1]<yi1)]
        p = points[indy,:]
        indx = p[:,0].argsort()
        if i%2==1:
            newind.append(indy[indx])
        else:
            newind.append(indy[indx[::-1]])
    newind = np.concatenate(newind, axis=0)
    assert np.unique(newind).shape[0]==allind.shape[0]
    return newind

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def scan(ramanSettings, positions, controlclass, dataqueue, stopevent, 
         logpath=''):
    fp = None
    if logpath != '':
        try:
            fp = open(os.path.join(logpath, 'ramanscanlog.txt'), 'a')
            sys.stderr = fp
            sys.stdout = fp
        except IOError:
            print('separate loging failed', flush=True)
            pass
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    ramanctrl = controlclass()
    ramanctrl.connect()
    print("connected:", time(), flush=True)
    ramanctrl.initiateMeasurement(ramanSettings)
    for i, p in enumerate(positions):
        x, y, z = p
        print("time:", time(), flush=True)
        print("position:", x, y, z, flush=True)
        ramanctrl.moveToAbsolutePosition(x, y, z, measurementRunning=True)
        print("move done", flush=True)
        ramanctrl.triggerMeasurement(i)
        print("trigger done", flush=True)
        
        if stopevent.is_set():
            ramanctrl.disconnect()
            return
        
        dataqueue.put(i)
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    ramanctrl.disconnect()
    if fp is not None:
        fp.close()
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class RamanScanUI(QtWidgets.QWidget):
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    imageUpdate = QtCore.pyqtSignal(str, name='imageUpdate')    #str = 'df' (= darkfield) or 'bf' (=bright field)
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    ramanscanUpdate = QtCore.pyqtSignal()
    
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    def __init__(self, ramanctrl, dataset, logpath='', parent=None):
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        super().__init__(parent, QtCore.Qt.Window)
        self.view = parent
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        self.logpath = logpath
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        self.ramanctrl = ramanctrl
        self.dataset = dataset
        self.process = None
        
        vbox = QtWidgets.QVBoxLayout()
        hbox = QtWidgets.QHBoxLayout()
        
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        self.params = []
        for param in self.ramanctrl.ramanParameters:
#            if param.dtype == 'selectBtn':
#                self.params.append(QtWidgets.QPushButton(str(param.value)))   
#                self.params[-1].released.connect(self.makeGetFnameLambda('Select template file', self.ramanctrl.measTemplatePath, param.openFileType, self.params[-1]))
            if param.dtype == 'int':
                self.params.append(QtWidgets.QSpinBox())
                self.params[-1].setMinimum(param.minVal)
                self.params[-1].setMaximum(param.maxVal)
                self.params[-1].setValue(param.value)
            if param.dtype == 'double':
                self.params.append(QtWidgets.QDoubleSpinBox())
                self.params[-1].setMinimum(param.minVal)
                self.params[-1].setMaximum(param.maxVal)
                self.params[-1].setValue(param.value)
            if param.dtype  == 'combobox':
                self.params.append(QtWidgets.QComboBox())
                self.params[-1].addItems([str(i) for i in param.valList])

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        self.group2 = QtWidgets.QGroupBox("Raman settings", self)
        grid2 = QtWidgets.QFormLayout()
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        for index, param in enumerate(self.params):
            param.setMinimumWidth(70)
            grid2.addRow(QtWidgets.QLabel(self.ramanctrl.ramanParameters[index].name), param)

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        self.prun = QtWidgets.QPushButton("Raman scan", self)
        self.prun.released.connect(self.run)
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        grid2.addRow(self.prun)
        self.group2.setLayout(grid2)
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        self.pexit = QtWidgets.QPushButton("Cancel", self)
        self.pexit.released.connect(self.stopScan)
        self.prun.setEnabled(False)
        self.progressbar = QtWidgets.QProgressBar(self)
        self.timelabeltext = "Estimated time to finish: "
        self.progresstime = QtWidgets.QLabel(self.timelabeltext, self)
        self.progresstime.setEnabled(False)
        self.progressbar.setEnabled(False)
        
        hbox.addStretch()
        hbox.addWidget(self.pexit)
        
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        vbox.addWidget(self.group2)
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        vbox.addLayout(hbox)
        vbox.addWidget(self.progresstime)
        vbox.addWidget(self.progressbar)
        
        self.setLayout(vbox)
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        self.setWindowTitle("Raman Scan")
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        #self.show()
        self.setVisible(False)
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    def makeGetFnameLambda(self, msg, path, fileType, btn):
        return lambda : self.getFName(msg, path, fileType, btn)
    
    def getFName(self, msg, path, filetype, btn):
        fname = QtWidgets.QFileDialog.getOpenFileName(self, msg, path, filetype)[0]
        btn.setText(fname.split('\\')[-1])
        btn.setMinimumSize(btn.sizeHint())

    
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    def resetDataset(self, ds):
        self.dataset = ds
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        numParticles = self.dataset.particleContainer.getNumberOfParticles()
        if len(numParticles)>0:
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            self.prun.setEnabled(True)
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            self.setWindowTitle(str(numParticles) + " Particles")
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    @QtCore.pyqtSlot()
    def stopScan(self):
        if self.process is not None and self.process.is_alive():
            reply = QtWidgets.QMessageBox.question(self, 'Stop raman scan?',
                                "Do you want to terminate the running scan?",
                                QtWidgets.QMessageBox.Yes | 
                                QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.No)
            if reply == QtWidgets.QMessageBox.Yes:
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                self.ramanctrl.finishMeasurement()
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                self.timer.stop()
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                self.processstopevent.set()
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                self.process.join()
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                self.dataqueue.close()
                self.dataqueue.join_thread()
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                self.view.unblockUI()
            else:
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                QtWidgets.QMessageBox.about(self, 'Stopping', 'Stopping without acive process...')
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                return
        self.close()
        
    @QtCore.pyqtSlot()
    def run(self):
        if self.dataset.readin:
            reply = QtWidgets.QMessageBox.critical(self, 'Dataset is newly read from disk!',
                "Coordinate systems might have changed since. Do you want to continue with saved coordinates?", 
                QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.No)

            if reply == QtWidgets.QMessageBox.Yes:
                self.dataset.readin = False
            else:
                return
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        self.view.imparent.ramanSwitch.hide()
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        self.view.setMicroscopeMode()
        
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        points = np.asarray(self.dataset.particleContainer.getMeasurementPixelCoords())
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        ramanSettings = {'filename': self.dataset.name,
                         'numPoints': len(points),
                         'path': self.dataset.path}
        for index, param in enumerate(self.params):
            try: ramanSettings[self.ramanctrl.ramanParameters[index].name] = self.ramanctrl.ramanParameters[index].value_of(param)
            except: print(param)
            
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        lmin = None
        for i in range(20,41):
            c = reorder(points, i)
            l = np.sum(np.sqrt(np.sum(np.diff(points[c,:],axis=0)**2,axis=1)))
            if lmin is None or l<lmin:
                lmin = l
                cmin = c
        if len(points)<20000:
            cmin, T = tsp.tspcomp(np.double(points), np.int32(cmin))
        assert np.all(np.sort(cmin)==np.arange(len(points), dtype=np.int32))
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        scanpoints = np.array([self.dataset.mapToLengthRaman(p, microscopeMode=self.view.microscopeMode) for p in points[cmin,:]])
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        zmin, zmax = scanpoints[:,2].min(), scanpoints[:,2].max()
        softwarez = self.ramanctrl.getSoftwareZ()  # get current software z
        zmin -= softwarez
        zmax -= softwarez
        reply = QtWidgets.QMessageBox.question(self, 'Starting raman scan',
            "Please switch to Raman laser. Microscope will move"\
            " (%4.0f,%4.0f) µm relative to current position. Proceed?"%(zmin,zmax), 
            QtWidgets.QMessageBox.Yes | 
            QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.No)

        if reply == QtWidgets.QMessageBox.Yes:
            self.dataset.mode = "ramanscan"
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            measurements2particles = [[int(np.where(cmin == i)[0])] for i in range(len(cmin))]   #i.e., list of scanIndicesPerParticle
            for particleIndex, listOfScanIndices in enumerate(measurements2particles):
                
#                curParticle = self.particleContainer.getParticleOfIndex(particleIndex)
                for scanIndex in listOfScanIndices:
                    
                    
                    self.particleContainer.setMeasurementScanIndex(indexOfNewMeas, scanIndex)
            
            
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#            self.dataset.ramanscansortindex = cmin
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            self.dataset.saveParticleData()
            self.view.saveDataSet()
            self.view.prepareAnalysis()
            self.view.scaleImage(2.0)
            self.view.highLightRamanIndex(0)
            self.view.blockUI()
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            self.group2.setEnabled(False)
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            self.progresstime.setEnabled(True)
            self.progressbar.setEnabled(True)
            self.progressbar.setRange(0, len(scanpoints))
            self.progressbar.setValue(0)
            self.ramanctrl.disconnect()
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            self.processstopevent = Event()
            self.dataqueue = Queue()
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            self.process = Process(target=scan, args=(ramanSettings, scanpoints, 
                                                      self.ramanctrl.__class__, 
                                                      self.dataqueue, 
                                                      self.processstopevent,
                                                      self.logpath))
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            self.process.start()
            self.starttime = time()
            self.timer = QtCore.QTimer(self)
            self.timer.timeout.connect(self.checkOnScan)
            self.timer.setSingleShot(True)
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            self.timer.start(10000.)
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    @QtCore.pyqtSlot()      
    def checkOnScan(self):
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        try:
            i = self.dataqueue.get_nowait()
        except queue.Empty:
            i = -1
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        if i>=0:
        
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            self.progressbar.setValue(i+1)
            self.view.highLightRamanIndex(i+1)
            Npoints = len(self.dataset.ramanpoints)
            if i>3:
                timerunning = time()-self.starttime
                ttot = timerunning*Npoints/(i+1)
                time2go = ttot - timerunning
                self.progresstime.setText(self.timelabeltext + str(datetime.timedelta(seconds=round(time2go))))
            if i==Npoints-1:
                self.process.join()
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                self.dataqueue.close()
                self.dataqueue.join_thread()
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                self.dataset.ramanscandone = True
                self.view.saveDataSet()
                self.view.unblockUI()
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#                self.view.switchMode("ParticleAnalysis")    #directly going to analysis is not feasible... We first have to export spectra etc...
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                self.progressbar.setValue(0)
                self.progressbar.setEnabled(False)
                self.progresstime.setEnabled(False)
                self.close()
                return
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        self.timer.start(100.)
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