opticalscan.py 32.6 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 .imagestitch import imageStacking
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import os, sys
import logging
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import logging.handlers
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import cv2
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from .helperfunctions import cv2imread_fix, cv2imwrite_fix
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from time import time, localtime, strftime
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from .opticalbackground import BackGroundManager
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from .uielements import TimeEstimateProgressbar
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from .zlevelsetter import ZLevelSetter
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from .scenePyramid import ScenePyramid
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from .gepardlogging import setDefaultLoggingConfig
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def scan(path, sol, zpositions, grid, controlclass, dataqueue,
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         stopevent, logpath, ishdr=False):
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    if ishdr:
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        merge_mertens = cv2.createMergeMertens()

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    logger = logging.getLogger()    
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    logger.addHandler(
        logging.handlers.RotatingFileHandler(
            logpath, maxBytes=5 * (1 << 20), backupCount=10)
    )
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    setDefaultLoggingConfig(logger)
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    logger.info('starting new optical scan')
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    try:
        ramanctrl = controlclass(logger)
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        ramanctrl.updateImageConfig(os.path.dirname(logpath))
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        ramanctrl.connect()
        zlist = list(enumerate(zpositions))
        for i, p in enumerate(grid):
            x, y = p
            z = sol[0]*x + sol[1]*y + sol[2]
            for k, zk in (zlist if i%2==0 else zlist[::-1]):
                name = f"image_{i}_{k}.bmp"
                logger.info(f'taking image {name}, time: ' + strftime("%d %b %Y %H:%M:%S", localtime()))
                zik = z+zk
                assert not np.isnan(zik)
                logger.info(f"moving to: {x}, {y}, {zik}, time: " + strftime("%d %b %Y %H:%M:%S", localtime()))
                ramanctrl.moveToAbsolutePosition(x, y, zik)
                if ishdr:
                    img_list = []
                    fname = os.path.join(path, f"tmp.bmp")
                    values = [5.,25.,100.] 
                    for j, val in enumerate(values if (i%2+k%2)%2==0 else reversed(values)):
                        ramanctrl.setBrightness(val)
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                        logger.info(f'writing hdr image to {fname}')
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                        ramanctrl.saveImage(fname)
                        img_list.append(cv2imread_fix(fname))
                    res_mertens = merge_mertens.process(img_list)
                    res_mertens_8bit = np.clip(res_mertens*255, 0, 255).astype('uint8')
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                    cv2imwrite_fix(os.path.join(path, name), res_mertens_8bit)
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                else:
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                    img_path = os.path.join(path, name)
                    logger.info(f'writing non hdr image to {img_path}')
                    ramanctrl.saveImage(img_path)
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                if stopevent.is_set():
                    ramanctrl.disconnect()
                    return
            dataqueue.put(i)
        ramanctrl.disconnect()
    except:
        logger.exception('Fatal error in optical scan')
        from .errors import showErrorMessageAsWidget
        showErrorMessageAsWidget('See opticalScanLog in project directory for information')
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def subtractBackground(image, background):
    avg = np.mean(background)
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    subtracted = np.clip(np.array(image - background + avg, dtype=np.uint8), 0, 255)
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    return subtracted
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def legacyLoadAndPasteImage(srcnames, fullimage, fullzval, width, height,
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                            rotationvalue, p0, p1, p, background=None):
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    colimgs = []
    for name in srcnames:
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        if os.path.isfile(name):
            curImg = cv2imread_fix(name)
            if background is not None:
                curImg = subtractBackground(curImg, background)
            colimgs.append(curImg)

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    img, zval = imageStacking(colimgs)

    x, y = p
    Nx, Ny = int((p1[0] - p0[0] + width) / width * img.shape[1]), int((p0[1] - p1[1] + height) / height * img.shape[
        0]) + 10  # + 10 because of rotation and hopefully it will be small
    c, s = np.cos(np.radians(rotationvalue)), np.sin(np.radians(rotationvalue))
    dx, dy = (x - p0[0]) / width * img.shape[1], (p0[1] - y) / height * img.shape[0]

    M = np.float32([[c, s, dx], [-s, c, dy]])
    if fullimage is not None:
        cv2.warpAffine(img, M, (Nx, Ny), fullimage, borderMode=cv2.BORDER_TRANSPARENT)
        cv2.warpAffine(zval, M, (Nx, Ny), fullzval, borderMode=cv2.BORDER_TRANSPARENT)
        dst = fullimage
        zval = fullzval
    else:
        dst = cv2.warpAffine(img, M, (Nx, Ny))
        zval = cv2.warpAffine(zval, M, (Nx, Ny))
    return dst, zval

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def removeSrcTiles(names, path):
    files = os.listdir(path)
    for fpath in names:
        file = os.path.basename(fpath)
        if file in files:
            os.remove(fpath)


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def loadAndPasteImage(srcnames, pyramid, fullzval, width, height,
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                      rotationvalue, p0, p1, p, logger, background=None):
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    """
    :param list of str srcnames: list of stacked scan files to merge
    :param ScenePyramid pyramid: the scene pyramid
    :param numpy.ndarray fullzval: full size zval image
    :param float width: width of camera
    :param float height: height camera
    :param float rotationvalue: angle of camera
    :param list of float p0: (min x; max y) of scan tile positions
    :param list of float p1: (max x; min y) of scan tile positions
    :param list of float p: position of current scan tile
    :param numpy.ndarray background:
    :return:
    """
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    colimgs = []
    for name in srcnames:
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        if os.path.isfile(name):
            curImg = cv2imread_fix(name)
            if background is not None:
                curImg = subtractBackground(curImg, background)
            colimgs.append(curImg)

    if 0 == len(colimgs):
        logger.warning(f'no src image(s) found to paste in loadAndPasteImage()')
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        return None, fullzval
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    img, zval = imageStacking(colimgs)
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    x, y = p
    Nx, Ny = int((p1[0]-p0[0]+width)/width*img.shape[1]), int((p0[1]-p1[1]+height)/height*img.shape[0]) + 10  # + 10 because of rotation and hopefully it will be small
    c, s = np.cos(np.radians(rotationvalue)), np.sin(np.radians(rotationvalue))
    dx, dy = (x-p0[0])/width*img.shape[1], (p0[1]-y)/height*img.shape[0]
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    M = np.float32([[c, s, dx], [-s, c, dy]])
    dst = None

    if pyramid is not None:
        if fullzval is not None:
            cv2.warpAffine(zval, M, (Nx, Ny), fullzval, borderMode=cv2.BORDER_TRANSPARENT)
            zval = fullzval
        else:
            zval = cv2.warpAffine(zval, M, (Nx, Ny))

        pyramid.addSrcTile(
            img,
            np.float32([[c, s, 0], [-s, c, 0]]),
            (dx, dy),
            (Nx, Ny)
        )
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    return dst, zval
    

class PointCoordinates(QtWidgets.QGridLayout):
    readPoint = QtCore.pyqtSignal(float, float, float, name='readPoint')
    
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    def __init__(self, N, ramanctrl, parent=None, names=None):
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        super().__init__(parent)
        self.dswidgets = []
        self.N = 0
        self.ramanctrl = ramanctrl
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        self.names = names
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        self.pimageOnly = QtWidgets.QPushButton("Image")
        self.addWidget(self.pimageOnly, 0, 6, QtCore.Qt.AlignRight)
        self.pimageOnly.released.connect(QtCore.pyqtSlot()(lambda : self.read(-1)))
        self.createWidgets(N)
    
    @QtCore.pyqtSlot()    
    def createWidgets(self, N, pointsgiven=[]):
        self.validpoints = [False]*N
        points = np.zeros((N,3))
            
        def connect(button, index):
            button.released.connect(QtCore.pyqtSlot()(lambda : self.read(index)))
        
        for i in range(self.N,min(N,len(self.dswidgets))):
            self.itemAtPosition(i+1,0).setVisible(True)
            self.itemAtPosition(i+1,1).setVisible(True)
            self.itemAtPosition(i+1,2).setVisible(True)
            self.itemAtPosition(i+1,3).setVisible(True)
            self.itemAtPosition(i+1,4).setVisible(True)
            self.itemAtPosition(i+1,5).setVisible(True)
            self.itemAtPosition(i+1,6).setVisible(True)
        for i in range(self.N, N):
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            if self.names is not None:
                lx = QtWidgets.QLabel(f"{self.names[i]} -> x:")
            else:
                lx = QtWidgets.QLabel(f"{i+1} -> x:")
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            ly = QtWidgets.QLabel("y:")
            lz = QtWidgets.QLabel("z:")
            wx = QtWidgets.QDoubleSpinBox()
            wy = QtWidgets.QDoubleSpinBox()
            wz = QtWidgets.QDoubleSpinBox()
            wx.setDecimals(1)
            wy.setDecimals(1)
            wz.setDecimals(1)
            wx.setRange(-500_000, 500_000)
            wy.setRange(-500_000, 500_000)
            wz.setRange(-500_000, 500_000)
            wx.setValue(points[i,0])
            wy.setValue(points[i,1])
            wz.setValue(points[i,2])
            self.addWidget(lx, i+1, 0, QtCore.Qt.AlignLeft)
            self.addWidget(wx, i+1, 1, QtCore.Qt.AlignRight)
            self.addWidget(ly, i+1, 2, QtCore.Qt.AlignLeft)
            self.addWidget(wy, i+1, 3, QtCore.Qt.AlignRight)
            self.addWidget(lz, i+1, 4, QtCore.Qt.AlignLeft)
            self.addWidget(wz, i+1, 5, QtCore.Qt.AlignRight)
            pread = QtWidgets.QPushButton("read")
            connect(pread, i)
            self.addWidget(pread, i+1, 6, QtCore.Qt.AlignRight)
            
            self.dswidgets.append([wx,wy,wz])
        for i in range(N, len(self.dswidgets)):
            self.itemAtPosition(i+1,0).setVisible(False)
            self.itemAtPosition(i+1,1).setVisible(False)
            self.itemAtPosition(i+1,2).setVisible(False)
            self.itemAtPosition(i+1,3).setVisible(False)
            self.itemAtPosition(i+1,4).setVisible(False)
            self.itemAtPosition(i+1,5).setVisible(False)
            self.itemAtPosition(i+1,6).setVisible(False)
        self.N = N
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        for i, p in pointsgiven:
            wx, wy, wz = self.dswidgets[i]
            x, y, z = p
            wx.setValue(x)
            wy.setValue(y)        
            wz.setValue(z)
            self.validpoints[i] = True
        for i in range(len(pointsgiven), N):
            wx, wy, wz = self.dswidgets[i]
            wx.setValue(0)
            wy.setValue(0)        
            wz.setValue(0)
        
        self.update()
        
    def read(self, index):
        x, y, z = self.ramanctrl.getPosition()
        z = self.ramanctrl.getUserZ()
        if index>=0:
            wx, wy, wz = self.dswidgets[index]
            wx.setValue(x)
            wy.setValue(y)        
            wz.setValue(z)
            self.validpoints[index] = True
        self.readPoint.emit(x,y,z)
        
    def getPoints(self):
        points = np.zeros((self.N, 3), dtype=np.double)
        for i in range(self.N):
            if self.validpoints[i]:
                wx, wy, wz = self.dswidgets[i]
                points[i,0] = wx.value()
                points[i,1] = wy.value()
                points[i,2] = wz.value()
            else:
                points[i,:] = np.nan
        return points
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class OpticalScan(QtWidgets.QWidget):
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    imageUpdate = QtCore.pyqtSignal(str, name='imageUpdate')    #str = 'df' (= darkfield) or 'bf' (=bright field)
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    boundaryUpdate = QtCore.pyqtSignal()
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    backGroundSavedToPath = QtCore.pyqtSignal(int, str)
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    def __init__(self, ramanctrl, dataset, logger, parent=None):
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        super().__init__(parent, QtCore.Qt.Window)
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        self.logger = logger
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        self.view: QtWidgets.QGraphicsView = parent
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        mainLayout = QtWidgets.QVBoxLayout()

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        pointgroup = QtWidgets.QGroupBox("Point coordinates [µm]", self)
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        self.ramanctrl = ramanctrl
        self.dataset = dataset
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        self.pyramid: ScenePyramid = None
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        self.positions = []
        self.process = None
        self.points = PointCoordinates(5, self.ramanctrl, self)
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        pointgroup.setLayout(self.points)
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        self.points.readPoint.connect(self.takePoint)
        
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        bkggroup = QtWidgets.QGroupBox('Manage Background Images')
        self.enableBackGround = QtWidgets.QCheckBox('Enable BackgroundSubtraction')
        self.enableBackGround.setChecked(False)
        self.enableBackGround.stateChanged.connect(self.enableDisableBackground)
        self.backGroundManager = BackGroundManager(self)
        self.backGroundManager.managerClosed.connect(self.managerWasClosed)
        self.backGroundManager.readBackground.connect(self.readBackground)
        self.showBgkManagerBtn = QtWidgets.QPushButton('Show Background Manager Window')
        self.showBgkManagerBtn.setDisabled(True)
        self.showBgkManagerBtn.clicked.connect(self.showHideBackgroundWindow)
        
        bkglayout = QtWidgets.QVBoxLayout()
        bkglayout.addWidget(self.enableBackGround)
        bkglayout.addWidget(self.showBgkManagerBtn)
        bkggroup.setLayout(bkglayout)
        
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        self.pareaselect = QtWidgets.QPushButton("Area select", self)
        label = QtWidgets.QLabel("Size increase:", self)
        self.radiusincreaseedit = QtWidgets.QDoubleSpinBox(self)
        self.radiusincreaseedit.setMinimum(-1000)
        self.radiusincreaseedit.setMaximum(1000)
        self.radiusincreaseedit.setDecimals(0)
        self.radiusincreaseedit.setSingleStep(20)
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        self.radiusincreaseedit.setMaximumWidth(100)
        self.radiusincreaseedit.valueChanged.connect(self.areaSelect)
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        self.hdrcheck = QtWidgets.QCheckBox("High dynamic range", self)
        self.hdrcheck.setChecked(False)
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        self.zLevelSetter = ZLevelSetter()
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        self.zLevelSetter.sizeChanged.connect(self._updateSize)
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        self.prun = QtWidgets.QPushButton("Run", self)
        self.pexit = QtWidgets.QPushButton("Cancel", self)
        self.pareaselect.released.connect(self.areaSelect)
        self.prun.released.connect(self.run)
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        self.pexit.released.connect(self.cancelScan)
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        self.prun.setEnabled(False)
        
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        self.progressbar = TimeEstimateProgressbar()
        self.progressbar.disable()
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        radioGroup = QtWidgets.QGroupBox('Shape')
        radioLayout = QtWidgets.QHBoxLayout()
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        self.circlerad = QtWidgets.QRadioButton("Circle")
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        self.circlerad.clicked.connect(self.areaSelect)
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        self.rectanglerad = QtWidgets.QRadioButton("Rectangle")
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        self.rectanglerad.setChecked(True)
        self.rectanglerad.clicked.connect(self.areaSelect)
        radioLayout.addWidget(self.circlerad)
        radioLayout.addWidget(self.rectanglerad)
        radioGroup.setLayout(radioLayout)

        micModeGroup = QtWidgets.QGroupBox('Mode for Image Acquisition')
        micModeLayout = QtWidgets.QHBoxLayout()
        self.df_btn = QtWidgets.QRadioButton('Darkfield')
        self.df_btn.setChecked(True)
        self.df_btn.clicked.connect(self.areaSelect)
        self.bf_btn = QtWidgets.QRadioButton('Brightfield')
        self.bf_btn.clicked.connect(self.areaSelect)
        micModeLayout.addWidget(self.df_btn)
        micModeLayout.addWidget(self.bf_btn)
        micModeGroup.setLayout(micModeLayout)
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        self.areaOptionsGroup = QtWidgets.QGroupBox('Area Select Options')
        areaLayout = QtWidgets.QFormLayout()
        areaLayout.addRow(radioGroup)
        areaLayout.addRow(label, self.radiusincreaseedit)
        areaLayout.addRow(micModeGroup)
        if not self.view.ramanSwitchNeeded:
            micModeGroup.setDisabled(True)
        areaLayout.addRow(self.pareaselect)
        self.areaOptionsGroup.setLayout(areaLayout)
        self.areaOptionsGroup.setDisabled(True)
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        furtherOptionsGroup = QtWidgets.QGroupBox('Further Options')
        furtherOptionsLayout = QtWidgets.QFormLayout()
        furtherOptionsLayout.addRow(self.hdrcheck)
        furtherOptionsGroup.setLayout(furtherOptionsLayout)
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        btnLayout = QtWidgets.QHBoxLayout()
        btnLayout.addWidget(self.prun)
        btnLayout.addWidget(self.pexit)
        btnLayout.addStretch()
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        vbox1 = QtWidgets.QVBoxLayout()
        vbox2 = QtWidgets.QVBoxLayout()

        vbox1.addWidget(pointgroup)
        vbox1.addWidget(self.zLevelSetter)
        vbox1.addStretch()

        vbox2.addWidget(self.areaOptionsGroup)
        vbox2.addWidget(bkggroup)
        vbox2.addWidget(furtherOptionsGroup)
        vbox2.addStretch()

        optionsLayout = QtWidgets.QHBoxLayout()
        optionsLayout.addLayout(vbox1)
        optionsLayout.addLayout(vbox2)

        mainLayout.addLayout(optionsLayout)
        mainLayout.addWidget(self.progressbar)
        mainLayout.addLayout(btnLayout)
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        self.setLayout(mainLayout)
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        self.setVisible(False)
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    def enableDisableBackground(self):
        self.showBgkManagerBtn.setEnabled(self.enableBackGround.isChecked())
        if self.enableBackGround.isChecked():
            self.backGroundManager.calculateAverageImage()
        else:
            self.deleteBackGroundImage()
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    def showHideBackgroundWindow(self):
        if self.backGroundManager.isHidden():
            self.backGroundManager.show()
            self.showBgkManagerBtn.setText('Hide Background Manager Window')
        else:
            self.backGroundManager.hide()
            self.showBgkManagerBtn.setText('Show Background Manager Window')
        
    def managerWasClosed(self):
        self.showBgkManagerBtn.setText('Show Background Manager Window')
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    @QtCore.pyqtSlot()
    def _updateSize(self):
        self.adjustSize()

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    @QtCore.pyqtSlot()
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    def cancelScan(self):
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        if self.process is not None and self.process.is_alive():
            reply = QtWidgets.QMessageBox.question(self, 'Stop optical 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.progressbar.resetTimerAndCounter()
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                self.timer.stop()
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                self.processstopevent.set()
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                self.process.terminate()
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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()
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                self.close()

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    @QtCore.pyqtSlot()
    def areaSelect(self):
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        magn = self.ramanctrl.magn
        
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        if self.circlerad.isChecked() == True:
            xym, r = cv2.minEnclosingCircle(np.array([p[:2] for p in self.dataset.fitpoints], 
                                                     dtype=np.float32))
            r += self.radiusincreaseedit.value()
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            phi = np.linspace(0, 2*np.pi, magn, endpoint=False)
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            self.dataset.boundary = [[xym[0]+r*np.cos(phii), xym[1]+r*np.sin(phii)] for phii in phi]
        else:
            da = self.radiusincreaseedit.value()
            x0, x1 = self.dataset.fitpoints[:,0].min()-da, self.dataset.fitpoints[:,0].max()+da
            y0, y1 = self.dataset.fitpoints[:,1].min()-da, self.dataset.fitpoints[:,1].max()+da
            a = 2*(y1-y0 + x1-x0)
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            nx, ny = max(int(np.round((x1-x0)/a*magn)),2), max(int(np.round((y1-y0)/a*magn)),2)
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            x, dx = np.linspace(x0, x1, nx, endpoint=False, retstep=True)
            y, dy = np.linspace(y0, y1, ny, endpoint=False, retstep=True)
            self.dataset.boundary = [[xi, yi] for xi, yi in zip(x,y0*np.ones_like(x))] + \
                                    [[xi, yi] for xi, yi in zip(x1*np.ones_like(y),y)] + \
                                    [[xi, yi] for xi, yi in zip(x[::-1]+dx,y1*np.ones_like(x))] + \
                                    [[xi, yi] for xi, yi in zip(x0*np.ones_like(y),y[::-1]+dy)]
            
        self.boundaryUpdate.emit()
        self.prun.setEnabled(True)
    
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    def setPyramid(self, pyramid):
        self.pyramid = pyramid

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    def resetDataset(self, ds):
        self.dataset = ds
        self.points.createWidgets(5, list(zip(ds.fitindices,ds.fitpoints)))
        if len(self.dataset.fitindices)>1:
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            self.areaOptionsGroup.setEnabled(True)
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        softwarez = self.ramanctrl.getSoftwareZ()
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        if abs(softwarez) > 0.1 and self.ramanctrl.name == 'WITecCOM':
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            reply = QtWidgets.QMessageBox.critical(self, 'Software z position nonzero',
            "The software z position needs to be set to zero."\
            " Moving z for %4.0f µm relative to current position. Counteract manually before proceeding!"%(-softwarez), 
            QtWidgets.QMessageBox.Yes | 
            QtWidgets.QMessageBox.Abort, QtWidgets.QMessageBox.Abort)

            if reply == QtWidgets.QMessageBox.Yes:
                self.ramanctrl.moveZto(0.0)
            else:
                QtWidgets.QMessageBox.information(self, "Information", 'Scan may stop if the software z position gets to high!',
                                                  QtWidgets.QMessageBox.Ok)
        
    @QtCore.pyqtSlot(float, float, float) 
    def takePoint(self, x, y, z):
        if self.dataset.heightmap is not None:
            reply = QtWidgets.QMessageBox.critical(self, 'Dataset already contains optical scan data',
                "Continuation will invalidate all previous results! Continue anyway?", 
                QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.No)

            if reply != QtWidgets.QMessageBox.Yes:
                return
        self.ramanctrl.saveImage(self.dataset.getTmpImageName())
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        width, height, rotationvalue = self.ramanctrl.getImageDimensions(self.view.microscopeMode)
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        pshift = self.ramanctrl.getRamanPositionShift()
        self.dataset.pshift = pshift
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        img = cv2imread_fix(self.dataset.getTmpImageName())
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        self.dataset.imagedim_bf = self.ramanctrl.getImageDimensions('bf')
        self.dataset.pixelscale_bf = self.dataset.imagedim_bf[0]/img.shape[1]          #=imagedim_width/shape[1]
        self.dataset.imagedim_df = self.ramanctrl.getImageDimensions('df')
        self.dataset.pixelscale_df = self.dataset.imagedim_df[0]/img.shape[1]          #=imagedim_width/shape[1]
        
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        points = self.points.getPoints()
        ind = np.isfinite(points[:,0])
        self.dataset.fitindices = np.arange(points.shape[0])[ind]
        points = points[ind,:].copy()
        self.dataset.fitpoints = points
        if len(points)>1:
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            self.areaOptionsGroup.setEnabled(True)
        
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        points = np.concatenate(([[x,y,z]], points), axis=0)
        p0 = [points[:,0].min(), points[:,1].max()]
        p1 = [points[:,0].max(), points[:,1].min()]
        if self.dataset.maxdim is not None:
            p0 = [min(p0[0], self.dataset.maxdim[0]), max(p0[1], self.dataset.maxdim[1])]
            p1 = [max(p1[0], self.dataset.maxdim[2]), min(p1[1], self.dataset.maxdim[3])]
            
        Nx, Ny = int((p1[0]-p0[0]+width)/width*img.shape[1]), int((p0[1]-p1[1]+height)/height*img.shape[0]) + 10  # + 10 because of rotation and hopefully it will be small
        c, s = np.cos(np.radians(rotationvalue)), np.sin(np.radians(rotationvalue))
        dx, dy = (x-p0[0])/width*img.shape[1], (p0[1]-y)/height*img.shape[0]
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        M = np.float32([[c, s, dx], [-s, c, dy]])
        #dst = cv2.warpAffine(img, M, (Nx, Ny))
        M_rot = np.float32([[c, s, 0], [-s, c, 0]])
        img_rot = cv2.warpAffine(img, M_rot, (img.shape[1], img.shape[0] + 10))
        # calc new pixel start coords for tile
        # @see https://stackoverflow.com/a/43166421/9880753
        c_dest = cv2.transform(np.float32([[(0, 0)]]), np.float32([[c, s, dx], [-s, c, dy]]))

        self.pyramid.addSrcTileSimple(
            img_rot,
            (c_dest[0][0][0], c_dest[0][0][1]),
            p0
        )

        #if self.view.imgdata is not None and self.dataset.lastpos is not None:
        #    lp = self.dataset.lastpos
        #    dx, dy = (lp[0]-p0[0])/width*img.shape[1], (p0[1]-lp[1])/height*img.shape[0]
        #    full = self.view.imgdata
        #    M = np.float32([[1,0,dx],[0,1,dy]])
        #    try:
        #        full = cv2.warpAffine(full, M, (Nx, Ny))            #fails, if image dimensions are >32767x32767px...
        #        dst = cv2.max(full, dst)
        #    except:
        #        QtWidgets.QMessageBox.critical(self, 'Error', 'Image is too large\nSelect smaller region.')
        #        raise
        #        return
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        #self.view.imgdata = dst
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        self.dataset.lastpos = p0
        self.dataset.maxdim = p0 + p1
        self.dataset.readin = False
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        self.imageUpdate.emit(self.view.microscopeMode)
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    @QtCore.pyqtSlot(int) 
    def readBackground(self, indexOfCallingImage):
        tmp_path = self.dataset.getTmpImageName()
        self.ramanctrl.saveImage(tmp_path)
        self.backGroundSavedToPath.emit(indexOfCallingImage, tmp_path)
    
    def writeBackGroundImage(self, backgroundImg):
        cv2imwrite_fix(self.dataset.getBackgroundImageName(), cv2.cvtColor(backgroundImg, cv2.COLOR_RGB2BGR))
    
    def deleteBackGroundImage(self):
        if os.path.exists(self.dataset.getBackgroundImageName()):
            os.remove(self.dataset.getBackgroundImageName())
        
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    @QtCore.pyqtSlot() 
    def run(self):
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        ramanPoints = self.dataset.particleContainer.getMeasurementPixelCoords()
        if len(ramanPoints) != 0:
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            reply = QtWidgets.QMessageBox.critical(self, 'Dataset already contains raman scan points',
                "Continuation will invalidate all previous results! Continue anyway?", 
                QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.No)

            if reply != QtWidgets.QMessageBox.Yes:
                return
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        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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        if os.path.exists(self.dataset.getBackgroundImageName()):
            reply = QtWidgets.QMessageBox.critical(self, 'Background correction info.',
                "A background image was saved. All acquired images will be corrected. Continue?\nOtherwise delete images in background manager", 
                QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.Yes)

            if reply != QtWidgets.QMessageBox.Yes:
                return
        
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        self.view.imparent.ramanSwitch.df_btn.setChecked(self.df_btn.isChecked())
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        self.view.imparent.ramanSwitch.setDisabled(True)
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        self.view.setMicroscopeMode()
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        if self.df_btn.isChecked():
            self.view.dataset.imagescanMode = 'df'
        else:
            self.view.dataset.imagescanMode = 'bf'
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        points = np.float32(self.dataset.fitpoints)
        # convert z to software z, which is relative to current user z
        softwarez = self.ramanctrl.getSoftwareZ()  # get current software z
        points[:,2] += softwarez-self.ramanctrl.getUserZ()
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        try:
            zrange = self.zLevelSetter.getZLevels()
        except ValueError:
            return

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        zmaxstack = max(zrange)
        if len(zrange) == 1:
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            zmaxstack = 0.0
            self.dataset.zpositions = np.array([0.0])
        else:
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            # self.dataset.zpositions = np.linspace(0, zmaxstack, Nz)
            self.dataset.zpositions = zrange

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        width, height, rotationvalue = self.dataset.imagedim_df
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        self.logger.debug(f"Width: {width}, height: {height}, rotation: {rotationvalue}")
        self.logger.debug(f"Points x: {points[:,0].min(), points[:,0].max()}")
        self.logger.debug(f"Points y: {points[:,1].min(), points[:,1].max()}")
        self.logger.debug(f"Points z: {points[:,2].min(), points[:,2].max()}")
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        A = np.ones((points.shape[0],3))
        A[:,:2] = points[:,:2]
        b = points[:,2]
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        sol = np.linalg.lstsq(A, b, rcond=None)[0]
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        self.dataset.heightmap = sol
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        self.logger.info(f"Fit deviation: {sol[0]*points[:,0]+sol[1]*points[:,1]+sol[2] -points[:,2]}")
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        path = self.dataset.getScanPath()
        # get zmin and zmax in absolut software z coordinates
        zmin, zmax = None, None
        for i, p in enumerate(self.dataset.grid):
            x, y = p
            z = sol[0]*x + sol[1]*y + sol[2]
            if i==0:
                zmin, zmax = z, z
            else:
                if zmin>z: zmin = z
                if zmax<z: zmax = z
        zmax += zmaxstack        
        # convert to relative movements for user info:
        zmin -= softwarez
        zmax -= softwarez
        reply = QtWidgets.QMessageBox.question(self, 'Starting optical scan',
            "Please switch to dark field optics. 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.prun.setEnabled(False)
            self.ramanctrl.disconnect()
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            self.processstopevent = Event()
            self.dataqueue = Queue()
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            logpath = os.path.join(self.dataset.path, 'opticalScanLog.txt')
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            self.process = Process(target=scan, args=(path, sol, self.dataset.zpositions, 
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                                self.dataset.grid, self.ramanctrl.__class__,
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                                self.dataqueue, self.processstopevent, 
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                                logpath, self.hdrcheck.isChecked()))
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            self.process.start()
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            self.progressbar.enable()
            self.progressbar.resetTimerAndCounter()
            self.progressbar.setMaxValue(len(self.dataset.grid))
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            self.pyramid.resetScene()
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            self.view.blockUI()
            grid = np.asarray(self.dataset.grid)
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            p0 = [grid[:, 0].min(), grid[:, 1].max()]
            p1 = [grid[:, 0].max(), grid[:, 1].min()]
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            self.dataset.lastpos = p0
            self.dataset.maxdim = p0 + p1
            self.dataset.mode = "opticalscan"
            self.dataset.save()
            self.timer = QtCore.QTimer(self)
            self.timer.timeout.connect(self.checkOnScan)
            self.timer.setSingleShot(True)
            self.timer.start(1000.)
    
    @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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            Ngrid = len(self.dataset.grid)
            names = []
            for k in range(len(self.dataset.zpositions)):
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                names.append(os.path.join(self.dataset.getScanPath(), f"image_{i}_{k}.bmp"))
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            width, height, rotationvalue = (self.dataset.imagedim_df if self.view.imparent.ramanSwitch.df_btn.isChecked() else self.dataset.imagedim_bf)
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            p = self.dataset.grid[i]
            p0, p1 = self.dataset.maxdim[:2], self.dataset.maxdim[2:]
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            if os.path.exists(self.dataset.getBackgroundImageName()):
                background_img = cv2imread_fix(self.dataset.getBackgroundImageName())
            else:
                background_img = None
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            self.view.imgdata, self.dataset.zvalimg = loadAndPasteImage(
                names, self.pyramid, self.dataset.zvalimg, width, height,
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                rotationvalue, p0, p1, p, self.logger, background=background_img
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            )

            removeSrcTiles(names, self.dataset.getScanPath())

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            self.progressbar.setValue(i+1)
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            self.imageUpdate.emit(self.view.microscopeMode)
            
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            if i==Ngrid-1:
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                # cv2imwrite_fix(self.dataset.getImageName(), cv2.cvtColor(self.view.imgdata, cv2.COLOR_RGB2BGR))
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                self.dataset.saveZvalImg()
                self.process.join()
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                self.dataqueue.close()
                self.dataqueue.join_thread()
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                self.pyramid.toDataset()

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                self.ramanctrl.connect()
                self.view.saveDataSet()
                self.view.unblockUI()
                self.view.switchMode("ParticleDetection")
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                self.progressbar.resetTimerAndCounter()
                self.progressbar.disable()
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                self.close()
                return
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        self.timer.start(100.)
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    def closeEvent(self, event):
        self.backGroundManager.close()
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        event.accept()