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StripesCounter_v10.py
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StripesCounter_v10.py
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#!/usr/bin/env python
#=================================================================
# Author: Patrick Brockmann CEA/DRF/LSCE - April 2021
#=================================================================
import sys, os
#======================================================
try:
import re
from PyQt5.Qt import Qt
from PyQt5.QtCore import *
from PyQt5.QtGui import *
from PyQt5.QtWidgets import *
import matplotlib
matplotlib.use('Qt5Agg')
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
from matplotlib.figure import Figure
import matplotlib.patches as patches
from matplotlib.lines import Line2D
import matplotlib.pyplot as plt
from skimage.measure import profile_line
import peakutils
import numpy as np
import cv2
from shapely.geometry import Point, LineString
import text_line
except:
print("Some modules have not been found:")
print("---> re, matplotlib, PyQt5, skimage, peakutils, numpy, cv2, shapely")
sys.exit()
#======================================================
version = "v10.93"
maximumWidth = 250
#======================================================
class MainWindow(QMainWindow):
#------------------------------------------------------------------
def __init__(self):
QMainWindow.__init__(self)
self.initValues()
#-------------------------------
self.setMinimumSize(QSize(1100, 800))
self.setWindowTitle("StripesCounter " + version)
# Create new action
openAction = QAction(QIcon('open.png'), '&Open', self)
openAction.setShortcut('Ctrl+O')
openAction.setStatusTip('Open document')
openAction.triggered.connect(self.openCall)
# Create exit action
exitAction = QAction(QIcon('exit.png'), '&Exit', self)
exitAction.setShortcut('Ctrl+Q')
exitAction.setStatusTip('Exit application')
exitAction.triggered.connect(self.exitCall)
# Create about action
aboutAction = QAction(QIcon('about.png'), '&About', self)
aboutAction.setShortcut('F1')
aboutAction.setStatusTip('About the application')
aboutAction.triggered.connect(self.aboutCall)
# Create menu bar and add action
self.menuBar = self.menuBar()
fileMenu = self.menuBar.addMenu('&File')
fileMenu.addAction(openAction)
fileMenu.addAction(exitAction)
fileMenu = self.menuBar.addMenu('&About')
fileMenu.addAction(aboutAction)
self.cboxInverseImage = QCheckBox("Inverse image")
self.cboxInverseImage.setChecked(False)
self.cboxInverseImage.toggled.connect(self.toggled_cboxInverseImage)
self.labelAlpha = QLabel("Contrast level: 1.0")
self.labelAlpha.setAlignment(Qt.AlignLeft)
self.labelBeta = QLabel("Brightness level: 0")
self.labelBeta.setAlignment(Qt.AlignLeft)
self.labelKernelSize = QLabel("Kernel size: " + str(self.kernelSize))
self.labelKernelSize.setAlignment(Qt.AlignLeft)
self.labelProfileLinewidth = QLabel("Profile linewidth: " + str(self.profileLinewidth))
self.labelProfileLinewidth.setAlignment(Qt.AlignLeft)
self.labelPeakUtils_minDist = QLabel("PeakUtils - Minimum distance: " + str(self.peakutils_minDist))
self.labelPeakUtils_minDist.setAlignment(Qt.AlignLeft)
self.labelPeakUtils_thres = QLabel("PeakUtils - Threshold: %d" % self.peakutils_thres)
self.labelPeakUtils_thres.setAlignment(Qt.AlignLeft)
self.mySliderAlpha = QSlider(Qt.Horizontal, self)
self.mySliderAlpha.setMaximumWidth(maximumWidth)
self.mySliderAlpha.setMinimum(10)
self.mySliderAlpha.setMaximum(30)
self.mySliderAlpha.setValue(1)
self.mySliderAlpha.setTickInterval(1)
self.mySliderAlpha.setTickPosition(QSlider.TicksBelow)
self.mySliderAlpha.valueChanged[int].connect(self.changeValueAlpha)
self.mySliderBeta = QSlider(Qt.Horizontal, self)
self.mySliderBeta.setMaximumWidth(maximumWidth)
self.mySliderBeta.setMinimum(-100)
self.mySliderBeta.setMaximum(100)
self.mySliderBeta.setValue(0)
self.mySliderBeta.setTickInterval(5)
self.mySliderBeta.setTickPosition(QSlider.TicksBelow)
self.mySliderBeta.valueChanged[int].connect(self.changeValueBeta)
self.mySliderKernelSize = QSlider(Qt.Horizontal, self)
self.mySliderKernelSize.setMaximumWidth(maximumWidth)
self.mySliderKernelSize.setMinimum(1)
self.mySliderKernelSize.setMaximum(51)
self.mySliderKernelSize.setValue(self.kernelSize)
self.mySliderKernelSize.setTickInterval(2)
self.mySliderKernelSize.setSingleStep(2)
self.mySliderKernelSize.setTickPosition(QSlider.TicksBelow)
self.mySliderKernelSize.valueChanged[int].connect(self.changeValueKernelSize)
self.mySliderProfileLinewidth = QSlider(Qt.Horizontal, self)
self.mySliderProfileLinewidth.setMaximumWidth(maximumWidth)
self.mySliderProfileLinewidth.setMinimum(1)
self.mySliderProfileLinewidth.setMaximum(50)
self.mySliderProfileLinewidth.setValue(self.profileLinewidth)
self.mySliderProfileLinewidth.setTickInterval(1)
self.mySliderProfileLinewidth.setTickPosition(QSlider.TicksBelow)
self.mySliderProfileLinewidth.valueChanged[int].connect(self.changeValueProfileLinewidth)
self.mySliderPeakUtils_minDist = QSlider(Qt.Horizontal, self)
self.mySliderPeakUtils_minDist.setMaximumWidth(maximumWidth)
self.mySliderPeakUtils_minDist.setMinimum(1)
self.mySliderPeakUtils_minDist.setMaximum(30)
self.mySliderPeakUtils_minDist.setValue(self.peakutils_minDist)
self.mySliderPeakUtils_minDist.setTickInterval(1)
self.mySliderPeakUtils_minDist.setTickPosition(QSlider.TicksBelow)
self.mySliderPeakUtils_minDist.valueChanged[int].connect(self.changeValuePeakUtils_minDist)
self.mySliderPeakUtils_thres = QSlider(Qt.Horizontal, self)
self.mySliderPeakUtils_thres.setMaximumWidth(maximumWidth)
self.mySliderPeakUtils_thres.setMinimum(0)
self.mySliderPeakUtils_thres.setMaximum(255)
self.mySliderPeakUtils_thres.setValue(self.peakutils_thres)
self.mySliderPeakUtils_thres.setTickInterval(5)
self.mySliderPeakUtils_thres.setTickPosition(QSlider.TicksBelow)
self.mySliderPeakUtils_thres.valueChanged[int].connect(self.changeValuePeakUtils_thres)
self.cboxPeaks = QCheckBox("Display peaks on current profile")
self.cboxPeaks.setChecked(False)
self.cboxPeaks.toggled.connect(self.toggled_cboxPeaks)
self.cboxReverseProfile = QCheckBox("Reverse profile")
self.cboxReverseProfile.setChecked(False)
self.cboxReverseProfile.toggled.connect(self.toggled_cboxReverseProfile)
#-----------------------
#self.fig, self.ax = plt.subplots(nrows=2, figsize=(8,8), gridspec_kw={'height_ratios': [2, 1]})
self.fig, self.ax = plt.subplots(nrows=2, figsize=(8,8))
self.fig.tight_layout()
self.fig.subplots_adjust(top=0.9, bottom=0.15)
self.canvas = FigureCanvas(self.fig)
# https://github.com/matplotlib/matplotlib/issues/707/
self.canvas.setFocusPolicy(Qt.ClickFocus)
self.canvas.setFocus()
self.canvas.mpl_connect('button_press_event', self.on_press)
self.canvas.mpl_connect('button_release_event', self.on_release)
self.canvas.mpl_connect('pick_event', self.on_pick)
self.canvas.mpl_connect('motion_notify_event', self.on_motion)
self.canvas.mpl_connect('scroll_event', self.zoom)
#-----------------------
# Create toolbar, passing canvas as first parament, parent (self, the MainWindow) as second.
#self.toolbar = NavigationToolbar(self.canvas, self)
#self.toolbar.pan()
self.buttonDefineScaleValue = QPushButton('Define scale value')
self.buttonDefineScaleValue.setMaximumWidth(maximumWidth)
self.buttonDefineScaleValue.clicked.connect(self.defineScaleValue)
self.buttonDefineScale = QPushButton('Define scale')
self.buttonDefineScale.setMaximumWidth(maximumWidth)
self.buttonDefineScale.clicked.connect(self.defineScale)
self.buttonSave = QPushButton('Save data as CSV and image as PNG')
self.buttonSave.setMaximumWidth(maximumWidth)
self.buttonSave.clicked.connect(self.save)
layoutH = QHBoxLayout()
layoutV1 = QVBoxLayout()
layoutV1.addWidget(self.canvas)
#layoutV1.addWidget(self.toolbar)
layoutV2 = QVBoxLayout()
layoutV2.setAlignment(Qt.AlignTop)
layoutV2.addWidget(self.cboxInverseImage)
layoutV2.addSpacing(1)
layoutV2.addWidget(self.labelAlpha)
layoutV2.addWidget(self.mySliderAlpha)
layoutV2.addSpacing(1)
layoutV2.addWidget(self.labelBeta)
layoutV2.addWidget(self.mySliderBeta)
layoutV2.addSpacing(1)
layoutV2.addWidget(self.labelKernelSize)
layoutV2.addWidget(self.mySliderKernelSize)
layoutV2.addSpacing(1)
layoutV2.addWidget(self.labelProfileLinewidth)
layoutV2.addWidget(self.mySliderProfileLinewidth)
layoutV2.addSpacing(1)
layoutV2.addWidget(self.labelPeakUtils_minDist)
layoutV2.addWidget(self.mySliderPeakUtils_minDist)
layoutV2.addSpacing(1)
layoutV2.addWidget(self.labelPeakUtils_thres)
layoutV2.addWidget(self.mySliderPeakUtils_thres)
layoutV2.addWidget(self.cboxPeaks)
layoutV2.addWidget(self.cboxReverseProfile)
layoutV2.addSpacing(5)
layoutV2.addWidget(self.buttonDefineScaleValue)
layoutV2.addWidget(self.buttonDefineScale)
layoutV2.addWidget(self.buttonSave)
layoutH.addLayout(layoutV1)
layoutH.addLayout(layoutV2)
#layoutH.addStretch(1)
# Create a placeholder widget to hold our toolbar and canvas.
widget = QWidget()
widget.setLayout(layoutH)
self.setCentralWidget(widget)
self.initInterface()
#------------------------------------------------------------------
def initValues(self):
self.alpha_default = 0.3
self.line_object = None
self.lineWithWidthList = []
self.scale_object = None
self.scaleValue_object = None
self.scaleValue = 0.
self.scaleLength = 0
self.offset = [0,0]
self.n = 0
self.mousepress = None
self.listLabelPoints = []
self.current_artist = None
self.press = False
self.xpress = 0
self.ypress = 0
self.cur_xlim = 0
self.cur_ylim = 0
self.kernelSize = 3
self.kernelOffset = 0
self.profileLinewidth = 1
self.peakutils_minDist = 1
self.peakutils_thres = 125
self.dist_profile = None
self.profile = None
self.profile_convolved = None
self.indexes = None
self.peaksCurve = None
self.peaks = None
self.peakHover0 = None
self.peakHover1 = None
self.line1 = self.line2 = self.line3 = None
self.counterFilename = 1
self.radius = 25
#------------------------------------------------------------------
def initInterface(self):
self.cboxInverseImage.setChecked(False)
self.cboxInverseImage.setEnabled(False)
self.labelAlpha.setEnabled(False)
self.mySliderAlpha.setEnabled(False)
self.labelBeta.setEnabled(False)
self.mySliderBeta.setEnabled(False)
self.labelKernelSize.setEnabled(False)
self.mySliderKernelSize.setEnabled(False)
self.labelProfileLinewidth.setEnabled(False)
self.mySliderProfileLinewidth.setEnabled(False)
self.labelPeakUtils_thres.setEnabled(False)
self.mySliderPeakUtils_thres.setEnabled(False)
self.labelPeakUtils_minDist.setEnabled(False)
self.cboxPeaks.setEnabled(False)
self.cboxReverseProfile.setEnabled(False)
self.mySliderPeakUtils_minDist.setEnabled(False)
self.cboxPeaks.setChecked(False)
self.cboxReverseProfile.setChecked(False)
self.buttonDefineScale.setEnabled(False)
self.buttonDefineScaleValue.setEnabled(False)
self.buttonSave.setEnabled(False)
self.mySliderKernelSize.setValue(self.kernelSize)
self.mySliderProfileLinewidth.setValue(self.profileLinewidth)
self.mySliderPeakUtils_minDist.setValue(self.peakutils_minDist)
self.mySliderPeakUtils_thres.setValue(self.peakutils_thres)
self.ax[0].set_visible(False)
self.ax[1].set_visible(False)
#------------------------------------------------------------------
def changeValueAlpha(self, value):
self.alphaLevel = value/10.
self.labelAlpha.setText("Contrast level: " + str(self.alphaLevel))
self.adjusted = cv2.convertScaleAbs(self.gray, alpha=self.alphaLevel, beta=self.betaLevel)
self.image_object.set_data(self.adjusted)
self.drawProfile()
self.canvas.draw()
#------------------------------------------------------------------
def toggled_cboxInverseImage(self):
self.gray = cv2.bitwise_not(self.gray)
self.adjusted = cv2.convertScaleAbs(self.gray, alpha=self.alphaLevel, beta=self.betaLevel)
self.image_object.set_data(self.adjusted)
self.drawProfile()
self.canvas.draw()
#------------------------------------------------------------------
def changeValueBeta(self, value):
self.betaLevel = value
self.labelBeta.setText("Brighness level: " + str(self.betaLevel))
self.adjusted = cv2.convertScaleAbs(self.gray, alpha=self.alphaLevel, beta=self.betaLevel)
self.image_object.set_data(self.adjusted)
self.drawProfile()
self.canvas.draw()
#------------------------------------------------------------------
def changeValueKernelSize(self, value):
if value % 2 != 0:
self.kernelSize = value
self.labelKernelSize.setText("Kernel size: " + str(self.kernelSize))
self.drawProfile()
#------------------------------------------------------------------
def changeValueProfileLinewidth(self, value):
self.profileLinewidth= value
self.labelProfileLinewidth.setText("Profile linewidth: " + str(self.profileLinewidth))
self.update_lineWithWidthList()
self.canvas.draw()
self.drawProfile()
#------------------------------------------------------------------
def changeValuePeakUtils_minDist(self, value):
self.peakutils_minDist = value
self.labelPeakUtils_minDist.setText("PeakUtils - Minimum distance: " + str(self.peakutils_minDist))
self.drawProfile()
#------------------------------------------------------------------
def changeValuePeakUtils_thres(self, value):
self.peakutils_thres = value
self.labelPeakUtils_thres.setText("PeakUtils - Threshold: %d" % self.peakutils_thres)
self.drawProfile()
#------------------------------------------------------------------
def toggled_cboxPeaks(self):
self.drawProfile()
#------------------------------------------------------------------
def toggled_cboxReverseProfile(self):
self.drawProfile()
#------------------------------------------------------------------
def zoom(self, event):
if event.inaxes == self.ax[0]: # to zoom and pan in ax[0]
# https://stackoverflow.com/questions/11551049/matplotlib-plot-zooming-with-scroll-wheel
scale_zoom = 1.2
cur_xlim = self.ax[0].get_xlim()
cur_ylim = self.ax[0].get_ylim()
xdata = event.xdata # get event x location
ydata = event.ydata # get event y location
if event.button == 'up':
# deal with zoom in
scale_factor = 1 / scale_zoom
elif event.button == 'down':
# deal with zoom out
scale_factor = scale_zoom
else:
# deal with something that should never happen
scale_factor = 1
#print(event.button)
new_width = (cur_xlim[1] - cur_xlim[0]) * scale_factor
new_height = (cur_ylim[1] - cur_ylim[0]) * scale_factor
relx = (cur_xlim[1] - xdata)/(cur_xlim[1] - cur_xlim[0])
rely = (cur_ylim[1] - ydata)/(cur_ylim[1] - cur_ylim[0])
self.ax[0].set_xlim([xdata - new_width * (1-relx), xdata + new_width * (relx)])
self.ax[0].set_ylim([ydata - new_height * (1-rely), ydata + new_height * (rely)])
self.canvas.draw()
#------------------------------------------------------------------
def on_release(self, event):
self.current_artist = None
self.press = False
if self.line_object != None:
self.line_object.set_alpha(self.alpha_default)
for p in list(self.ax[0].patches):
p.set_alpha(self.alpha_default)
self.canvas.draw()
#------------------------------------------------------------------
def on_pick(self, event):
# https://stackoverflow.com/questions/29086662/matplotlib-pick-event-functionality
# filter because the scroll wheel is registered as a button
if event.mouseevent.button == 'down' or event.mouseevent.button == 'up':
#print("pick", event.mouseevent.button)
return
if self.current_artist is None:
self.current_artist = event.artist
#print("pick ", self.current_artist)
if isinstance(event.artist, patches.Circle):
if event.mouseevent.dblclick:
if self.mousepress == "right":
#print("double click right")
if len(self.ax[0].patches) > 2:
#print("\ndelete", event.artist.get_label())
event.artist.remove()
xdata = list(self.line_object.get_xdata())
ydata = list(self.line_object.get_ydata())
for i in range(0,len(xdata)):
if event.artist.get_label() == self.listLabelPoints[i]:
xdata.pop(i)
ydata.pop(i)
self.listLabelPoints.pop(i)
break
#print('--->', self.listLabelPoints)
self.line_object.set_data(xdata, ydata)
self.update_lineWithWidthList()
self.drawProfile()
self.canvas.draw()
else:
x0, y0 = self.current_artist.center
x1, y1 = event.mouseevent.xdata, event.mouseevent.ydata
self.offset = [(x0 - x1), (y0 - y1)]
event.artist.set_alpha(1.0)
self.canvas.draw()
elif isinstance(event.artist, Line2D):
if event.mouseevent.dblclick:
if self.mousepress == "left":
#print("double click left")
self.n = self.n+1
x, y = event.mouseevent.xdata, event.mouseevent.ydata
newPointLabel = "point"+str(self.n)
point_object = patches.Circle([x, y], radius=self.radius, color='red', fill=False, lw=2,
alpha=self.alpha_default, transform=self.ax[0].transData, label=newPointLabel)
point_object.set_picker(5)
self.ax[0].add_patch(point_object)
xdata = list(self.line_object.get_xdata())
ydata = list(self.line_object.get_ydata())
#print('\ninit', self.listLabelPoints)
pointInserted = False
for i in range(0,len(xdata)-1):
#print("--> testing inclusion %s in [%s-%s]"
# %(newPointLabel, self.listLabelPoints[i], self.listLabelPoints[i+1]))
line = LineString([(xdata[i], ydata[i]), (xdata[i+1], ydata[i+1])])
point = Point(x,y)
if line.distance(point) < 20: # 20 = minimum distance in pixel for point inclusion on line
xdata.insert(i+1, x)
ydata.insert(i+1, y)
self.listLabelPoints.insert(i+1, newPointLabel)
pointInserted = True
#print("include", newPointLabel)
break
self.line_object.set_data(xdata, ydata)
self.update_lineWithWidthList()
#print('final', listLabelPoints)
#if not pointInserted:
#print("Error: point not inserted, too far from line")
#point_object.remove()
self.drawProfile()
self.canvas.draw()
else:
xdata = event.artist.get_xdata()
ydata = event.artist.get_ydata()
x1, y1 = event.mouseevent.xdata, event.mouseevent.ydata
self.offset = xdata[0] - x1, ydata[0] - y1
event.artist.set_alpha(1.0)
self.canvas.draw()
#------------------------------------------------------------------
def on_motion(self, event):
#----------------------------------------------
# display hover scatter points when mouse passes over a peak
if self.peakHover0 != None:
self.peakHover0.remove()
self.peakHover0 = None
self.canvas.draw()
if self.peakHover1 != None:
self.peakHover1.remove()
self.peakHover1 = None
self.canvas.draw()
cont = False
if event.inaxes == self.ax[0] and self.peaks != None and self.cboxPeaks.isChecked():
cont, ind = self.peaks.contains(event)
elif event.inaxes == self.ax[1]:
cont, ind = self.peaksCurve.contains(event)
if cont and self.peaks != None:
i = ind["ind"][0]
pos = self.peaks.get_offsets()[i]
self.peakHover0 = self.ax[0].scatter(pos[0], pos[1],
c='yellow', s=10, zorder=12)
pos = self.peaksCurve.get_offsets()[i]
self.peakHover1 = self.ax[1].scatter(pos[0], pos[1],
c='yellow', s=200, edgecolors='b', lw=1, alpha=0.8, zorder=0)
self.canvas.draw()
#----------------------------------------------
if not self.press: return
if event.xdata == None or event.ydata == None: return
#----------------------------------------------
if self.current_artist != None:
dx, dy = self.offset
if isinstance(self.current_artist, patches.Circle):
cx, cy = event.xdata + dx, event.ydata + dy
self.current_artist.center = cx, cy
#print("moving", self.current_artist.get_label())
xdata = list(self.line_object.get_xdata())
ydata = list(self.line_object.get_ydata())
for i in range(0,len(xdata)):
if self.listLabelPoints[i] == self.current_artist.get_label():
xdata[i] = cx
ydata[i] = cy
break
self.line_object.set_data(xdata, ydata)
elif isinstance(self.current_artist, Line2D):
xdata = list(self.line_object.get_xdata())
ydata = list(self.line_object.get_ydata())
xdata0 = xdata[0]
ydata0 = ydata[0]
for i in range(0,len(xdata)):
xdata[i] = event.xdata + dx + xdata[i] - xdata0
ydata[i] = event.ydata + dy + ydata[i] - ydata0
self.line_object.set_data(xdata, ydata)
for p in list(self.ax[0].patches):
pointLabel = p.get_label()
i = self.listLabelPoints.index(pointLabel)
p.center = xdata[i], ydata[i]
self.update_lineWithWidthList()
self.canvas.draw()
self.drawProfile()
elif event.inaxes == self.ax[0]: # to zoom and pan in ax[0]
dx = event.xdata - self.xpress
dy = event.ydata - self.ypress
self.cur_xlim -= dx
self.cur_ylim -= dy
self.ax[0].set_xlim(self.cur_xlim)
self.ax[0].set_ylim(self.cur_ylim)
self.canvas.draw()
#------------------------------------------------------------------
def on_press(self, event):
self.press = True
if event.button == 3:
self.mousepress = "right"
elif event.button == 1:
self.mousepress = "left"
if event.inaxes == self.ax[0]: # to zoom and pan in ax[0]
self.cur_xlim = self.ax[0].get_xlim()
self.cur_ylim = self.ax[0].get_ylim()
self.xpress = event.xdata
self.ypress = event.ydata
if event and event.dblclick:
if len(self.listLabelPoints) < 2:
self.n = self.n+1
x, y = event.xdata, event.ydata
newPointLabel = "point"+str(self.n)
point_object = patches.Circle([x, y], radius=self.radius, color='red', fill=False, lw=2,
alpha=self.alpha_default, transform=self.ax[0].transData, label=newPointLabel)
point_object.set_picker(5)
self.ax[0].add_patch(point_object)
self.listLabelPoints.append(newPointLabel)
if len(self.listLabelPoints) == 2:
xdata = []
ydata = []
for p in list(self.ax[0].patches):
cx, cy = p.center
xdata.append(cx)
ydata.append(cy)
self.line_object, = self.ax[0].plot(xdata, ydata, alpha=self.alpha_default, c='red', lw=2, picker=True)
self.line_object.set_pickradius(5)
self.update_lineWithWidthList()
self.canvas.draw()
self.drawProfile()
#------------------------------------------------------------------
def drawProfile(self):
if self.line_object is None:
return
try:
if self.scaleValue != 0. and self.scaleLength != 0:
self.scalePixel = self.scaleValue / self.scaleLength
else:
self.scalePixel = 1
xdata = list(self.line_object.get_xdata())
ydata = list(self.line_object.get_ydata())
line = LineString(list(zip(xdata,ydata)))
listEndSegment = [0]
self.profile = np.array([])
self.profile_mx = np.array([])
self.profile_my = np.array([])
self.profile_segment = np.array([])
self.dist_profile = np.array([])
for i in range(0,len(xdata)-1):
#print("---", i, xdata[i], xdata[i+1])
profile_tmp = profile_line(self.adjusted, (ydata[i], xdata[i]), (ydata[i+1], xdata[i+1]),
order=0, mode='constant', cval=0, linewidth=self.profileLinewidth)
profile_mx_tmp = profile_line(self.mx, (ydata[i], xdata[i]), (ydata[i+1], xdata[i+1]),
order=0, mode='constant', cval=0, linewidth=self.profileLinewidth)
profile_my_tmp = profile_line(self.my, (ydata[i], xdata[i]), (ydata[i+1], xdata[i+1]),
order=0, mode='constant', cval=0, linewidth=self.profileLinewidth)
self.profile = np.concatenate((self.profile, profile_tmp))
self.profile_mx = np.concatenate((self.profile_mx, profile_mx_tmp))
self.profile_my = np.concatenate((self.profile_my, profile_my_tmp))
self.profile_segment = np.concatenate((self.profile_segment, profile_mx_tmp*0 + i+1)) # store segment number
dist_profile_tmp = np.linspace(0, self.scalePixel*len(profile_tmp), num=len(profile_tmp))
if i > 0:
# add last point of previous segment
self.dist_profile = np.concatenate((self.dist_profile, dist_profile_tmp + self.dist_profile[-1]))
else:
self.dist_profile = np.concatenate((self.dist_profile, dist_profile_tmp))
listEndSegment.append(self.dist_profile[-1])
self.ax[1].set_visible(True)
self.ax[1].clear()
self.ax[1].set_facecolor('whitesmoke')
if self.cboxReverseProfile.isChecked():
self.profile = 255 - self.profile
self.ax[1].plot(self.dist_profile, self.profile, c='red', lw=1, alpha=0.8)
for x in listEndSegment:
self.ax[1].axvline(x=x, linestyle='dashed', color='red', alpha=0.8)
kernel = np.ones(self.kernelSize) / self.kernelSize
self.kernelOffset = int(self.kernelSize/2)
# use mode='same' and put boundaries values to np.nan
self.profile_convolved = np.convolve(self.profile, kernel, mode='same')
self.profile_convolved[0:self.kernelOffset] = self.profile_convolved[-self.kernelOffset:] = np.nan
self.ax[1].plot(self.dist_profile, self.profile_convolved, c='b', lw=1, alpha=0.8)
# https://peakutils.readthedocs.io/en/latest/reference.html
self.indexes = peakutils.indexes(self.profile_convolved, thres=self.peakutils_thres, thres_abs=True, min_dist=self.peakutils_minDist)
self.peaksCurve = self.ax[1].scatter(self.dist_profile[self.indexes], self.profile_convolved[self.indexes], c='b', s=10)
if self.peaks != None:
self.peaks.remove()
self.peaks = None
if self.cboxPeaks.isChecked():
points = []
for i in self.indexes:
point = Point(self.profile_mx[i], self.profile_my[i])
# Closest point on the line
newPoint = line.interpolate(line.project(point))
points.append(newPoint)
xs = [point.x for point in points]
ys = [point.y for point in points]
self.peaks = self.ax[0].scatter(xs, ys, c='b', s=5, zorder=10)
stripesNb = len(self.indexes)
self.line1 = "Number of peaks: %3d" %(stripesNb)
if stripesNb > 1:
stripesDist = self.dist_profile[self.indexes[-1]]-self.dist_profile[self.indexes[0]]
self.line2 = "Length of stripes: %.5f (first: %.5f, last: %.5f)" \
%(stripesDist, self.dist_profile[self.indexes[0]], self.dist_profile[self.indexes[-1]])
self.line3 = "Growth stripe rate (μm/stripe): %.5f" %(1000*stripesDist/(stripesNb-1))
else:
self.line2 = ""
self.line3 = ""
self.ax[1].text(0.2, 0.1, self.line1 + '\n' + self.line2 + '\n' + self.line3,
va="top", transform=self.fig.transFigure)
self.ax[1].grid(linestyle='dotted')
self.ax[1].axhline(self.peakutils_thres, color="b", lw=1, linestyle='solid', alpha=0.8)
self.labelKernelSize.setEnabled(True)
self.mySliderKernelSize.setEnabled(True)
self.labelProfileLinewidth.setEnabled(True)
self.mySliderProfileLinewidth.setEnabled(True)
self.labelPeakUtils_minDist.setEnabled(True)
self.mySliderPeakUtils_minDist.setEnabled(True)
self.labelPeakUtils_thres.setEnabled(True)
self.mySliderPeakUtils_thres.setEnabled(True)
self.cboxPeaks.setEnabled(True)
self.cboxReverseProfile.setEnabled(True)
self.buttonDefineScaleValue.setEnabled(True)
self.buttonDefineScale.setEnabled(True)
self.buttonSave.setEnabled(True)
self.canvas.draw()
except:
#print("Error in drawProfile")
return
#------------------------------------------------------------------
def openCall(self):
self.openFileNameDialog()
#------------------------------------------------------------------
def detectScale(self):
try:
fld = cv2.ximgproc.createFastLineDetector()
lines = fld.detect(self.mask)
self.scaleLength = 0
for line in lines:
pt1 = np.array((line[0][0],line[0][1]))
pt2 = np.array((line[0][2],line[0][3]))
length = np.linalg.norm(pt1 - pt2)
#print(pt1, pt2, dist)
if (length > self.scaleLength):
self.scaleLength = int(length)
point1Scale = pt1
point2Scale = pt2
#print("Detected scale length in pixel: ", scaleLength)
if self.scaleLength > 0:
self.scale_object = self.ax[0].plot([point1Scale[0], point2Scale[0]],
[point1Scale[1], point2Scale[1]],
alpha=1.0, c='purple', lw=2)
except:
self.scaleLength = 0
try:
self.scaleValue_object = self.ax[0].text(
min(point1Scale[0], point2Scale[0]),
min(point1Scale[1], point2Scale[1]),
" %.3f mm" %(self.scaleValue),
alpha=1.0, c='purple', horizontalalignment='left', verticalalignment='bottom', clip_on=True)
except:
self.scaleValue_object = self.ax[0].text(
200, 200, # Set a default scaleValue_object at 200,200
" %.3f mm" %(self.scaleValue),
alpha=1.0, c='purple', horizontalalignment='left', verticalalignment='bottom', clip_on=True)
try:
import pytesseract
scaleDetected = pytesseract.image_to_string(self.mask)
matchObj = re.match(r'[^0-9]*([0-9]*)mm', scaleDetected.strip())
self.scaleValue = float(matchObj.group(1))
#print("Detected scale value: ", self.scaleValue)
self.scaleValue_object.set_text(" %.3f mm" %(self.scaleValue))
except:
self.scaleValue = 0.
#------------------------------------------------------------------
def defineScaleValue(self):
#value, okPressed = QInputDialog.getDouble(self, "Get scale value","Value:", self.scaleValue, 0, 100, 1)
# --> get comma instead of dot
dialog = QInputDialog()
dialog.setInputMode(QInputDialog.DoubleInput)
dialog.setLocale(QLocale(QLocale.English, QLocale.UnitedStates))
dialog.setLabelText("Value: ")
dialog.setDoubleMinimum(0)
dialog.setDoubleMaximum(100)
dialog.setIntStep(1)
dialog.setDoubleDecimals(3)
dialog.setDoubleValue(self.scaleValue)
dialog.setWindowTitle("Get scale value")
okPressed = dialog.exec_()
if okPressed:
self.scaleValue = dialog.doubleValue()
else:
return
self.ax[0].set_title(os.path.basename(self.imageFileName) + '\n'
+ " Scale length [pixels]: %s" %(self.scaleLength) + '\n'
+ " Scale value [mm]: %.3f" %(self.scaleValue),
loc='left', fontsize=10)
self.scaleValue_object.set_text(" %.3f mm" %(self.scaleValue))
self.drawProfile()
#------------------------------------------------------------------
def defineScale(self):
xdata = self.line_object.get_xdata()
ydata = self.line_object.get_ydata()
point1Scale = [xdata[0], ydata[0]] # Scale from the 1st segment
point2Scale = [xdata[1], ydata[1]]
self.scaleLength = int(np.linalg.norm(np.array(point1Scale) - np.array(point2Scale)))
self.ax[0].set_title(os.path.basename(self.imageFileName) + '\n'
+ " Scale length [pixels]: %s" %(self.scaleLength) + '\n'
+ " Scale value [mm]: %.3f" %(self.scaleValue),
loc='left', fontsize=10)
if self.scale_object == None:
self.scale_object = self.ax[0].plot([point1Scale[0], point2Scale[0]],
[point1Scale[1], point2Scale[1]],
alpha=1.0, c='purple', lw=2)
else:
self.scale_object[0].set_data([point1Scale[0], point2Scale[0]],
[point1Scale[1], point2Scale[1]])
self.scaleValue_object.set_position((point1Scale[0], point1Scale[1]))
self.drawProfile()
#------------------------------------------------------------------
def update_lineWithWidthList(self):
for line in self.lineWithWidthList:
line.remove()
self.lineWithWidthList = []
if self.profileLinewidth > 1:
xdata = list(self.line_object.get_xdata())
ydata = list(self.line_object.get_ydata())
for i in range(len(xdata)-1):
line = LineString([(xdata[i], ydata[i]), (xdata[i+1], ydata[i+1])])
dilated = line.buffer(self.profileLinewidth/2., cap_style=2, join_style=1)
line1, = self.ax[0].plot(*dilated.exterior.xy, alpha=self.alpha_default, c='red', lw=2)
self.lineWithWidthList.append(line1)
#------------------------------------------------------------------
def displayImage(self):
self.initValues()
self.initInterface()
self.ax[0].set_visible(True)
self.ax[0].clear()
img = cv2.imread(self.imageFileName)
(self.mx, self.my) = np.meshgrid(np.arange(img.shape[1]), np.arange(img.shape[0]))
self.gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
mask0 = cv2.inRange(self.gray, 0, 0)
self.mask = cv2.bitwise_not(mask0)
self.alphaLevel = self.mySliderAlpha.value()/10.
self.betaLevel = self.mySliderBeta.value()
self.adjusted = cv2.convertScaleAbs(self.gray, alpha=self.alphaLevel, beta=self.betaLevel)
self.image_object = self.ax[0].imshow(self.adjusted, cmap='gray', aspect='equal')
self.detectScale()
self.ax[0].set_title(os.path.basename(self.imageFileName) + '\n'
+ " Scale length [pixels]: %s" %(self.scaleLength) + '\n'
+ " Scale value [mm]: %.3f" %(self.scaleValue),
loc='left', fontsize=10)
self.ax[0].set_adjustable('datalim')
self.cboxInverseImage.setEnabled(True)
self.labelAlpha.setEnabled(True)
self.mySliderAlpha.setEnabled(True)
self.labelBeta.setEnabled(True)
self.mySliderBeta.setEnabled(True)
self.canvas.draw()
#------------------------------------------------------------------
def save(self):
base=os.path.basename(self.imageFileName)
file1Name = os.path.splitext(base)[0] + "_StripesCounterFile_{}.csv"
while os.path.isfile(file1Name.format("%02d" %self.counterFilename)):
self.counterFilename += 1
file1NameCSV = file1Name.format("%02d" %self.counterFilename)
file1 = open(file1NameCSV, "w")
file1.write("#================================================\n")
file1.write("# StripesCounter " + version + "\n")
file1.write("# File: %s\n" %(self.imageFileName))
file1.write("# Detected scale value: %.3f\n" %(self.scaleValue))
file1.write("# Detected scale length in pixel: %d\n" %(self.scaleLength))
file1.write("# Inverse image: %s\n" %(self.cboxInverseImage.isChecked()))
file1.write("# Contrast level: %.1f\n" %(self.alphaLevel))
file1.write("# Brightness level: %d\n" %(self.betaLevel))
file1.write("# Kernel size: %d\n" %(self.kernelSize))
file1.write("# Profile linewidth: %d\n" %(self.profileLinewidth))
file1.write("# PeakUtils - Minimum distance: %d\n" %(self.peakutils_minDist))
file1.write("# PeakUtils - Threshold: %d\n" %(self.peakutils_thres))
xdata = list(self.line_object.get_xdata())
ydata = list(self.line_object.get_ydata())
file1.write("# Number of segments: %d\n" %(len(xdata)-1))
for i in range(0,len(xdata)):
file1.write("# Point%d: [%d, %d]\n" %(i+1, xdata[i], ydata[i]))
file1.write("# " + self.line1 + '\n# ' + self.line2 + '\n# ' + self.line3 + '\n')
file1.write("#================================================\n")
file1.write("n,xpos,ypos1,ypos2,peak,segment\n")
profile_convolvedFilled = np.nan_to_num(self.profile_convolved , nan=-999)
for i,v in enumerate(self.dist_profile):
if i in self.indexes:
file1.write("%d,%.7f,%.7f,%.7f,%d,%d\n"
%(i+1, self.dist_profile[i], self.profile[i], profile_convolvedFilled[i], 1, self.profile_segment[i]))
else:
file1.write("%d,%.7f,%.7f,%.7f,%d,%d\n"
%(i+1, self.dist_profile[i], self.profile[i], profile_convolvedFilled[i], 0, self.profile_segment[i]))
file1.close()
file1NamePNG = os.path.splitext(file1NameCSV)[0] + ".png"
plt.savefig(file1NamePNG)
print("---------------------------")
print("Saved csv file: " + file1NameCSV)
print("Saved png file: " + file1NamePNG)
# draw the line to keep a record of what has been saved so far.
self.ax[0].plot(xdata, ydata, alpha=0.5, c='blue', lw=2)
text_line.CurvedText(
x=[xdata[0], xdata[-1]],
y=[ydata[0], ydata[-1]],
text="File %02d"%self.counterFilename,
va='bottom',
axes=self.ax[0],
alpha=0.5,
color="blue"
)
self.canvas.draw()
#------------------------------------------------------------------
def openFileNameDialog(self):
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
self.imageFileName, _ = QFileDialog.getOpenFileName(self, "QFileDialog.getOpenFileName()",
"","PNG, JPG, TIF Files (*.png *.jpg *.tif);;PNG Files (*.png);;JPG Files (*.jpg);;TIF Files (*.tif);;All Files (*)", options=options)
if self.imageFileName:
self.displayImage()
#------------------------------------------------------------------
def exitCall(self):
self.close()
#------------------------------------------------------------------
def aboutCall(self):
msg = " StripesCounter " + version + """
* Open an image, optionnaly with a scale and value scale annotation
* Pan the image from a mouse click
* Zoom in or out with wheel zoom (or 2 fingers pad actions)
* Enhance the image from brightness and contrast sliders
* Create a profile line by double clicking
* At the 2nd point, the profile to be extracted is drawn as a red line
* The profile of the image is drawn corresponding to the profile line
* Add segments to the profile line by double clicking on it
- left double clicking to add a control point
- right double clicking to remove a control point
* Number of peaks (stripes) are counted from the smoothed profile
* Adapt various parameters for peak dectection and smoothing
* Move, modify the profile line and control points if needed
* Control the width of the profile line
* Inspect detected peaks with a mouse over from image or profile
* Define new scale and scale value if needed
* Save the image and the data points, visualize the extracted profile
* Developped by Patrick Brockmann (LSCE)
"""
QMessageBox.about(self, "About the StripesCounter", msg.strip())
#======================================================
if __name__ == "__main__":
app = QApplication(sys.argv)
mainWin = MainWindow()
mainWin.show()
sys.exit( app.exec_() )