Merge branch 'Thresholding,Background' into RefactoringAnalysisModules

analysis/particleContainer.py

@@ -43,6 +43,12 @@ class ParticleContainer(object):
         indexOfNewMeas = len(self.measurements)-1
         return indexOfNewMeas
     
+    def clearParticles(self):
+        self.particles = []
+    
+    def clearMeasurements(self):
+        self.measurements = []
+
     def setMeasurementScanIndex(self, indexOfMeasurment, scanIndex):
         self.measurements[indexOfMeasurment].ramanScanIndex = scanIndex
     

dataset.py

@@ -149,6 +149,7 @@ class DataSet(object):
 #        self.particlestats = []
 #        self.ramanscansortindex = None
         self.particleContainer = ParticleContainer(self)
+        self.particleDetectionDone = False
         self.ramanscandone = False
         
 #        self.results = {'polymers': None,
@@ -247,34 +248,24 @@ class DataSet(object):
                 self.imagedim_df = self.imagedim
                 del self.imagedim
             
+            
+            if not hasattr(self, 'particles2spectra'):
+                self.particles2spectra = [[int(np.where(self.ramanscansortindex == i)[0])] for i in range(len(self.ramanscansortindex))]
+            
             self.version = 2
         
         if self.version == 2:
             self.particleContainer = ParticleContainer(self)
-            def recreateMeasurement2ParticleFromScanIndices():
-                measurements2particles = [[int(np.where(self.ramanscansortindex == i)[0])] for i in range(len(self.ramanscansortindex))]
-                return measurements2particles
-
  
             self.particleContainer.initializeParticles(len(self.particlestats))
             self.particleContainer.setParticleContours(self.particlecontours)
             self.particleContainer.setParticleStats(self.particlestats)
             self.particleContainer.applyPixelScaleToParticleStats(self.getPixelScale())
             
-            if hasattr(self, 'particles2spectra'):
-                if self.particles2spectra is not None:
-                    measurements2particles = self.particles2spectra
-                else:
-                    measurements2particles = recreateMeasurement2ParticleFromScanIndices()
-            else:    
-                measurements2particles = recreateMeasurement2ParticleFromScanIndices()
-                
-            for particleIndex, listOfScanIndices in enumerate(measurements2particles):
+            if len(self.particlestats) > 0:   #i.e., particle detection was completed and particle data is there 
+                for particleIndex, listOfScanIndices in enumerate(self.particles2spectra):
                     curParticle = self.particleContainer.getParticleOfIndex(particleIndex)
                     for scanIndex in listOfScanIndices:
-#                    curParticle.addEmptyMeasurement()
-#                    curParticle.setMeasurementPixelCoords(measIndex, x, y)
-#                    curParticle.setMeasurementScanIndex(measIndex, scanIndex)
                         indexOfNewMeas = self.particleContainer.addEmptyMeasurement()
                         x, y = self.ramanpoints[particleIndex][0], self.ramanpoints[particleIndex][1]
                         self.particleContainer.setMeasurementPixelCoords(indexOfNewMeas, x, y)
@@ -292,8 +283,6 @@ class DataSet(object):
 #            self.version = 3
         # add later conversion for higher version numbers here
     
-    
-    
     def getSubImage(self, img, index, draw=True):
         contour = self.particlecontours[index]
         x0, x1 = contour[:,0,0].min(), contour[:,0,0].max()
@@ -395,29 +384,15 @@ class DataSet(object):
     def getLegacyDetectImageName(self):
         return os.path.join(self.path, "detectimage.png")
     
+    def getBackgroundImageName(self):
+        return os.path.join(self.path, "background.bmp")
+    
     def getDetectImageName(self):
         raise NotImplementedError("No longer implemented due to change in API")
     
     def getTmpImageName(self):
         return os.path.join(self.path, "tmp.bmp")
             
-    def saveParticleData(self):
-        print('Not saving ParticleData into text file...:\nThe current output format might be wrong, if multiple spectra per particle are present...')
-#        if len(self.ramanscansortindex)>0:
-#            data = []
-#            pixelscale = (self.pixelscale_df if self.imagescanMode == 'df' else self.pixelscale_bf)
-#            for i in self.ramanscansortindex:
-#                data.append(list(self.ramanpoints[i])+list(self.particlestats[i]))
-#            data = np.array(data)
-#            data[:,0], data[:,1], z = self.mapToLengthRaman((data[:,0], data[:,1]), microscopeMode=self.imagescanMode, noz=True)
-#            data[:,2:7] *= pixelscale
-#            header = "x [µm], y [µm], length [µm], height [µm], length_ellipse [µm], height_ellipse [µm]"
-#            if data.shape[1]>6:
-#                header = header + ", area [µm^2]"
-#                data[:,6] *= pixelscale
-#            np.savetxt(os.path.join(self.path, "particledata.txt"), data, 
-#                       header=header)
-            
     def save(self):
         saveData(self, self.fname)
     

detectionview.py

@@ -20,7 +20,7 @@ If not, see <https://www.gnu.org/licenses/>.
 """
 import numpy as np
 from PyQt5 import QtCore, QtWidgets, QtGui
-from segmentation import Segmentation
+from segmentation import Segmentation, MeasurementPoint
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg
 import matplotlib.pyplot as plt
 from threading import Thread
@@ -248,7 +248,9 @@ class ImageView(QtWidgets.QLabel):
             painter.setPen(QtCore.Qt.red)
             painter.setBrush(QtCore.Qt.red)
             for p in self.measpoints:
-                painter.drawEllipse(p[0]-2, p[1]-2, 5, 5)
+                for point in self.measpoints[p]:
+#                painter.drawEllipse(p[0]-2, p[1]-2, 5, 5)
+                    painter.drawEllipse(point.x-2, point.y-2, 5, 5)
 
         if self.showseedpoints:
             painter.setPen(QtCore.Qt.white)
@@ -581,10 +583,9 @@ class ParticleDetectionView(QtWidgets.QWidget):
     @QtCore.pyqtSlot()
     def clearDetection(self):
         if self.dataset is not None:
-            self.dataset.ramanpoints = []
-            self.dataset.particlecontours = []
-            self.dataset.particlestats = []
-            self.dataset.ramanscansortindex = []
+            self.dataset.particleContainer.clearParticles()
+            self.dataset.particleContainer.clearMeasurements()
+            self.dataset.particleDetectionDone = False
             self.dataset.ramanscandone = False
             self.dataset.mode = "opticalscan"
             self.dataset.save()
@@ -676,7 +677,7 @@ class ParticleDetectionView(QtWidgets.QWidget):
                     curParticle.addMeasurement(particleContainer.measurements[indexOfNewMeas])
                     
                     
-                
+            self.dataset.particleDetectionDone = True
 #            self.dataset.ramanpoints = measurementPoints    #consider moving that to particleContainer
 #            self.dataset.particlecontours = contours
 #            self.dataset.particlestats = particlestats

gepard.py

@@ -102,12 +102,13 @@ class GEPARDMainWindow(QtWidgets.QMainWindow):
         if fileName:
             isValid, msg = self.testFilename(fileName)
             if isValid:
-                self.fname = str(fileName)   #TODO: No spaces for Renishaw Interface!!
+                self.fname = str(fileName)
                 self.view.new(self.fname)  
                 self.scalingChanged(1.)
             else:
                 QtWidgets.QMessageBox.critical(self, "Error", msg)
             
+    @QtCore.pyqtSlot()  
     def testFilename(self, fileName):
         if self.view.ramanctrl.name == 'RenishawCOM':   #the renishawCom does not allow Spaces within filePath
             if fileName.find(' ') == 0:

imagestitch.py

@@ -48,15 +48,17 @@ def imageStacking(colimgs):
     return im, zval
 
 def combineImages(path, nx, ny, nk, width, height, angle):
-    imgs = []
     full = None
     for i in range(nx):
         for j in range(ny):
+            if nk > 1:
                 colimgs = []
                 for k in range(nk):
                     colimgs.append(cv2.imread(path + f'test_{i}_{j}_{k}.bmp'))
                 img = imageStacking(colimgs)
-            imgs.append(img)
+            else:
+                img = cv2.imread(path + f'test_{i}_{j}_1.bmp')
+
             dx = i*.9*img.shape[1]
             dy = j*.8*img.shape[0]
             c, s = np.cos(np.radians(angle)), np.sin(np.radians(angle))
@@ -67,6 +69,7 @@ def combineImages(path, nx, ny, nk, width, height, angle):
                 full = dst
             else:
                 full = cv2.max(full,dst)
+
     cv2.imwrite("full_dunkel.png", full)
     
     

opticalbackground.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, QtGui
+import cv2
+import numpy as np
+import os
+
+from helperfunctions import cv2imread_fix
+
+class BackGroundManager(QtWidgets.QWidget):
+    managerClosed = QtCore.pyqtSignal()
+    readBackground = QtCore.pyqtSignal(int)
+    
+    def __init__(self, parentOSwidget):
+        super(BackGroundManager, self).__init__()
+        self.setFixedSize(1500, 900)
+        self.setWindowTitle('Optical Background Manager')
+        self.parentOSwidget = parentOSwidget
+        self.parentOSwidget.backGroundSavedToPath.connect(self.updateChildImage)
+        self.ramanctrl = self.parentOSwidget.ramanctrl
+        
+        layout = QtWidgets.QHBoxLayout()
+        self.setLayout(layout)
+        
+        self.imagesGroup = QtWidgets.QGroupBox('Current Background Images')
+        self.imagesLayout = QtWidgets.QGridLayout()        
+        
+        self.imgContainers = []
+        self.avgImg = None
+        self.presetIndividualImages()
+        
+        self.previewImage = QtWidgets.QGraphicsView()
+        self.setupGraphicsView(self.previewImage, scaleFactor=0.8)
+        
+        previewGroup = QtWidgets.QGroupBox()
+        previewLayout = QtWidgets.QVBoxLayout()
+        self.blurspinbox = QtWidgets.QSpinBox(self)
+        self.blurspinbox.setMinimum(3)
+        self.blurspinbox.setMaximum(99)
+        self.blurspinbox.setSingleStep(2)
+        self.blurspinbox.setValue(5)
+        self.blurspinbox.valueChanged.connect(self.calculateAverageImage)
+        self.blurspinbox.setMaximumWidth(150)
+        
+        self.previewCurrentViewBtn = QtWidgets.QPushButton('Acquire 3x3 area and preview subtracted result')
+        self.previewCurrentViewBtn.clicked.connect(self.previewStitchedArea)
+        self.previewArea = QtWidgets.QGraphicsView()
+        self.setupGraphicsView(self.previewArea, scaleFactor=0.5)
+        
+        previewLayout.addWidget(QtWidgets.QLabel('Radius for blur'))
+        previewLayout.addWidget(self.blurspinbox)
+        previewLayout.addWidget(QtWidgets.QLabel('Preview of averaged and smoothed image'))
+        previewLayout.addWidget(self.previewImage)
+        previewLayout.addWidget(self.previewCurrentViewBtn)
+        previewLayout.addWidget(self.previewArea)
+        
+        previewGroup.setLayout(previewLayout)
+        
+        layout.addWidget(self.imagesGroup)
+        layout.addWidget(previewGroup)
+        
+    def presetIndividualImages(self, nrows=3, ncols=2):
+        index = 0
+        for row in range(nrows):
+            for col in range(ncols):
+                self.imgContainers.append(SingleImageContainer(self, index))
+                self.imagesLayout.addWidget(self.imgContainers[-1], row, col)
+                index += 1
+                
+        self.imagesGroup.setLayout(self.imagesLayout)
+    
+    def previewStitchedArea(self):
+        if self.avgImg is None:
+            QtWidgets.QMessageBox.about(self, 'Warning', 'No Background Image is aquired')
+            return
+        else:
+            from opticalscan import loadAndPasteImage
+            self.dataset = self.parentOSwidget.dataset
+            
+            #acquire images in 3x3 area to preview quality of background subtraction
+            x, y, z = self.ramanctrl.getPosition()
+            micMode = self.parentOSwidget.view.microscopeMode
+            width, height, angle = self.ramanctrl.getImageDimensions(micMode)
+            startPoint = [x-width, y-height]
+            endPoint = [x+width, y+height]
+            points = np.concatenate(([startPoint], [endPoint]), axis=0)
+            p0 = [points[:,0].min(), points[:,1].max()]
+            p1 = [points[:,0].max(), points[:,1].min()]
+            
+            reply = QtWidgets.QMessageBox.question(self, 'Message',f"The stage will move {round(3*width)} in x and {round(3*height)} in y.\nContinue?", 
+                                                   QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.No)
+            if reply == QtWidgets.QMessageBox.Yes:
+                fullimg = None
+                zimg = None
+         
+                for row in range(3):
+                    for col in range(3):
+                        curPoint = [startPoint[0] + row*width, startPoint[1] + col*height]
+                        self.ramanctrl.moveToAbsolutePosition(curPoint[0], curPoint[1])
+                        self.ramanctrl.saveImage(self.dataset.getTmpImageName())
+                        
+                        fullimg, zimg = loadAndPasteImage([self.dataset.getTmpImageName()], fullimg, zimg, width, height, angle, p0, p1, curPoint, background=self.avgImg)
+                        self.updateGraphicsView(self.previewArea, fullimg, convertColors=True)
+
+
+    def setupGraphicsView(self, graphView, scaleFactor=1.):
+        graphView.item = QtWidgets.QGraphicsPixmapItem()
+        scene = QtWidgets.QGraphicsScene(graphView)
+        scene.addItem(graphView.item)
+        graphView.setScene(scene)
+        graphView.scale(scaleFactor, scaleFactor)
+    
+    def updateGraphicsView(self, graphView, img, convertColors=False):
+        if img is not None:
+            prevImg = img
+        else:
+            prevImg = np.zeros((300, 300))
+        
+        if convertColors:
+            prevImg = cv2.cvtColor(img, cv2.COLOR_RGB2BGR)
+            
+        height, width = prevImg.shape[:2]
+        bytesPerLine = 3 * width
+        pix = QtGui.QPixmap()
+        pix.convertFromImage(QtGui.QImage(prevImg, width, height, bytesPerLine, QtGui.QImage.Format_RGB888))
+        graphView.item.setPixmap(pix)
+    
+    @QtCore.pyqtSlot(int, str) 
+    def updateChildImage(self, index, path):
+        self.imgContainers[index].updateImage(path)
+        self.calculateAverageImage()
+    
+    def calculateAverageImage(self):
+        curImgs = [i.getImage() for i in self.imgContainers if i.getImage() is not None]
+                
+        if len(curImgs) > 0:
+            curImgs = np.array(curImgs)
+            self.avgImg = np.sum(curImgs, axis=0)/len(curImgs)
+            radius = self.blurspinbox.value()
+            if radius %2 == 0:
+                radius += 1
+            if radius < 0:
+                radius = 1    
+            self.avgImg = cv2.GaussianBlur(self.avgImg, (radius, radius), 0)
+            self.avgImg = np.uint8(self.avgImg)
+            self.parentOSwidget.writeBackGroundImage(self.avgImg)
+        else:
+            self.avgImg = None
+            self.parentOSwidget.deleteBackGroundImage()
+            
+        self.updateGraphicsView(self.previewImage, self.avgImg)
+        
+    def closeEvent(self, event):
+        self.managerClosed.emit()
+        event.accept()
+    
+    
+class SingleImageContainer(QtWidgets.QGroupBox):
+    def __init__(self, parent, index):
+        super(SingleImageContainer, self).__init__()
+        self.index = index
+        self.parent = parent
+        
+        layout = QtWidgets.QVBoxLayout()
+        layout.addWidget(QtWidgets.QLabel(f'Background {index+1}'))
+        
+        readBtn = QtWidgets.QPushButton('ReadImage')
+        readBtn.clicked.connect(self.readImage)
+        
+        self.image = ImagePixmap()
+        
+        delBtn = QtWidgets.QPushButton('Delete Image')
+        delBtn.clicked.connect(self.clearImage)
+        
+        layout.addWidget(readBtn)
+        layout.addWidget(self.image)
+        layout.addWidget(delBtn)
+        
+        self.setLayout(layout)
+    
+    def readImage(self):
+        self.parent.readBackground.emit(self.index)
+    
+    def updateImage(self, path):
+        self.image.updateImage(path)
+    
+    def clearImage(self):
+        self.image.clearImage()
+        self.parent.calculateAverageImage()
+        
+    def getImage(self):
+        return self.image.imgdata
+
+
+class ImagePixmap(QtWidgets.QGraphicsView):
+    def __init__(self):
+        super(ImagePixmap, self).__init__()
+        self.item = QtWidgets.QGraphicsPixmapItem()
+        self.item.setPos(0, 0)
+        self.item.setAcceptedMouseButtons(QtCore.Qt.NoButton)
+        self.imgdata = None
+        
+        scene = QtWidgets.QGraphicsScene(self)
+        scene.addItem(self.item)
+        self.setScene(scene)
+        
+        self.scale(0.4, 0.4)
+        self.updateImage()
+        
+    def updateImage(self, img_path=None):
+        if img_path is None:
+            self.loadImageIntoPixmap(self.createBlancImage())
+            
+        elif os.path.exists(img_path):
+            self.imgdata = cv2.cvtColor(cv2imread_fix(img_path), cv2.COLOR_BGR2RGB)
+            self.loadImageIntoPixmap(self.imgdata)
+
+    def createBlancImage(self):
+        blancImg = np.zeros((300, 500, 3))
+        cv2.putText(blancImg, 'None selected', (150, 150), cv2.FONT_HERSHEY_COMPLEX, 1, (255, 255, 255), 2)
+        return blancImg
+    
+    def loadImageIntoPixmap(self, img):
+        height, width = img.shape[:2]
+        bytesPerLine = 3 * width
+        pix = QtGui.QPixmap()
+        pix.convertFromImage(QtGui.QImage(img, width, height, bytesPerLine, QtGui.QImage.Format_RGB888))
+        self.item.setPixmap(pix)
+    
+    def clearImage(self):
+        self.imgdata = None
+        self.updateImage()

opticalscan.py

@@ -30,6 +30,7 @@ from helperfunctions import cv2imread_fix, cv2imwrite_fix
 from time import time
 import datetime
 import sys
+from opticalbackground import BackGroundManager
 
 def scan(path, sol, zpositions, grid, controlclass, dataqueue, 
          stopevent, logpath='', ishdr=False):
@@ -81,18 +82,21 @@ def scan(path, sol, zpositions, grid, controlclass, dataqueue,
     if fp is not None:
         fp.close()
 
+def subtractBackground(image, background):
+    avg = np.mean(background)
+    subtracted = np.clip(np.array(image - background + avg, dtype = np.uint8), 0, 255)
+    return subtracted
     
 def loadAndPasteImage(srcnames, fullimage, fullzval, width, height, 
-                      rotationvalue, p0, p1, p, halfResolution = False):
+                      rotationvalue, p0, p1, p, background=None):
     colimgs = []
     for name in srcnames:
-        colimgs.append(cv2.cvtColor(cv2imread_fix(name), cv2.COLOR_BGR2RGB))
+        curImg = cv2imread_fix(name)
+        if background is not None:
+            curImg = subtractBackground(curImg, background)
+        colimgs.append(cv2.cvtColor(curImg, cv2.COLOR_BGR2RGB))
     img, zval = imageStacking(colimgs)
 
-    if halfResolution:              #halve resolution, if fullimage would become too large otherwise
-        img = cv2.resize(img, None, fx = 0.5, fy = 0.5, interpolation = cv2.INTER_CUBIC)
-        zval= cv2.resize(zval, None, fx = 0.5, fy = 0.5, interpolation = cv2.INTER_CUBIC)
-
     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))
@@ -179,6 +183,7 @@ class PointCoordinates(QtWidgets.QGridLayout):
             self.itemAtPosition(i+1,5).setVisible(False)
             self.itemAtPosition(i+1,6).setVisible(False)
         self.N = N
+        
         for i, p in pointsgiven:
             wx, wy, wz = self.dswidgets[i]
             x, y, z = p
@@ -217,9 +222,11 @@ class PointCoordinates(QtWidgets.QGridLayout):
                 points[i,:] = np.nan
         return points
     
+
 class OpticalScan(QtWidgets.QWidget):
     imageUpdate = QtCore.pyqtSignal(str, name='imageUpdate')    #str = 'df' (= darkfield) or 'bf' (=bright field)
     boundaryUpdate = QtCore.pyqtSignal()
+    backGroundSavedToPath = QtCore.pyqtSignal(int, str)
     
     def __init__(self, ramanctrl, dataset, logpath='', parent=None):
         super().__init__(parent, QtCore.Qt.Window)
@@ -235,6 +242,22 @@ class OpticalScan(QtWidgets.QWidget):