ramanscanui.py

# -*- 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
from multiprocessing import Process, Queue, Event
import queue
from time import sleep, time
from external import tsp
import datetime
import sys
import os
from pathlib import Path

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

def scan(ramanSettings, positions, controlclass, dataqueue, stopevent):
    logpath = os.path.join(Path.home(),'gepard', 'ramanscanlog.txt')    
    with open(logpath, "a") as fp:
        sys.stderr = fp
        sys.stdout = fp
        
        ramanctrl = controlclass()
        ramanctrl.connect()
        print("connected:", time())
        ramanctrl.initiateMeasurement(ramanSettings)
        for i, p in enumerate(positions):
            x, y, z = p
            print("time:", time())
            print("position:", x, y, z)
            sys.stdout.flush()          #remove this line after testing
            ramanctrl.moveToAbsolutePosition(x, y, z)
            print("move done")
            sys.stdout.flush()
            ramanctrl.triggerMeasurement(i)
            print("trigger done")
            sys.stdout.flush()
            
            if stopevent.is_set():
                ramanctrl.disconnect()
                return
            
            dataqueue.put(i)

        ramanctrl.disconnect()


class RamanScanUI(QtWidgets.QWidget):
    imageUpdate = QtCore.pyqtSignal(str, name='imageUpdate')    #str = 'df' (= darkfield) or 'bf' (=bright field)
    ramanscanUpdate = QtCore.pyqtSignal()
    
    def __init__(self, ramanctrl, dataset, parent=None):
        super().__init__(parent, QtCore.Qt.Window)
        self.view = parent
        self.ramanctrl = ramanctrl
        self.dataset = dataset
        self.process = None
        
        vbox = QtWidgets.QVBoxLayout()
        hbox = QtWidgets.QHBoxLayout()
        
        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])

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

        self.prun = QtWidgets.QPushButton("Raman scan", self)
        self.prun.released.connect(self.run)
        grid2.addRow(self.prun)
        self.group2.setLayout(grid2)
        
        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)
        
        vbox.addWidget(self.group2)
        vbox.addLayout(hbox)
        vbox.addWidget(self.progresstime)
        vbox.addWidget(self.progressbar)
        
        self.setLayout(vbox)
        self.setWindowTitle("Raman Scan")
        #self.show()
        self.setVisible(False)
    
    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())

    
    def resetDataset(self, ds):
        self.dataset = ds
        if len(self.dataset.ramanpoints)>0:
            self.prun.setEnabled(True)
            self.setWindowTitle(str(len(ds.ramanpoints)) + " Particles")
        
    @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:
                self.timer.stop()
                self.processstopevent.set()
                self.process.join()
                self.dataqueue.close()
                self.dataqueue.join_thread()
                self.view.unblockUI()
            else:
                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
        self.view.imparent.ramanSwitch.hide()
        points = np.asarray(self.dataset.ramanpoints)
        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)
            
        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))
        scanpoints = np.array([self.dataset.mapToLengthRaman(p, microscopeMode=self.view.microscopeMode) for p in points[cmin,:]])
        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"
            self.dataset.ramanscansortindex = cmin
            self.dataset.saveParticleData()
            self.view.saveDataSet()
            self.view.prepareAnalysis()
            self.view.scaleImage(2.0)
            self.view.highLightRamanIndex(0)
            self.view.blockUI()
            self.group2.setEnabled(False)
            self.progresstime.setEnabled(True)
            self.progressbar.setEnabled(True)
            self.progressbar.setRange(0, len(scanpoints))
            self.progressbar.setValue(0)
            self.ramanctrl.disconnect()
            self.processstopevent = Event()
            self.dataqueue = Queue()
            self.process = Process(target=scan, args=(ramanSettings, scanpoints, self.ramanctrl.__class__, self.dataqueue, self.processstopevent))
            self.process.start()
            self.starttime = time()
            self.timer = QtCore.QTimer(self)
            self.timer.timeout.connect(self.checkOnScan)
            self.timer.setSingleShot(True)
            self.timer.start(10000.)
    
    @QtCore.pyqtSlot()      
    def checkOnScan(self):
        try:
            i = self.dataqueue.get_nowait()
        except queue.Empty:
            i = -1
            
        if i>=0:
        
            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()
                self.dataqueue.close()
                self.dataqueue.join_thread()
                self.dataset.ramanscandone = True
                self.view.saveDataSet()
                self.view.unblockUI()
                self.view.switchMode("ParticleAnalysis")
                self.progressbar.setValue(0)
                self.progressbar.setEnabled(False)
                self.progresstime.setEnabled(False)
                self.close()
                return
        self.timer.start(100.)