# -- coding: utf-8 --
# Copyright 2018 Olivier Scholder <o.scholder@gmail.com>
"""
This is a standalone script which allows the user to perfome cross-section on ToF-SIMS images on different channels
"""
import sys
from PyQt5.QtWidgets import QApplication, QMainWindow, QTableWidgetItem, QFileDialog, QWidget, QAction, QProgressBar, QStatusBar
from PyQt5.QtGui import QPixmap
from PyQt5.QtCore import Qt, QCoreApplication
from slicer import Ui_slicer
import os
import re
import pySPM
import numpy as np
from pySPM.utils import CDF
from scipy import optimize as opt
class SlicerApp(QWidget):
def __init__(self, filename=None):
super(QWidget, self).__init__()
self.ui = Ui_slicer()
self.ui.setupUi(self)
self.canvas = self.ui.mpl.canvas
self.fig = self.ui.mpl.canvas.fig
self.initPlotLayout()
self.level = None
if filename is None:
if len(sys.argv) < 2:
self.path, _ = QFileDialog.getOpenFileName(self,"ITA Image", "","(*.ITA)")
else:
# If an argument is sent to the script, the first argument will be used as a Path. Very usefull for debugging the script without having to selectr the folder each time with window dialog
self.path = sys.argv[1]
else:
self.path = filename
if not os.path.exists(self.path):
raise Exception("File \"{}\" is not found".format(self.path))
if os.path.exists(self.path+".level.npy"):
self.level = np.load(self.path+".level.npy")
self.curs = [0,0,0]
self.volume = None
self.ITA = pySPM.ITA(self.path)
for i,x in enumerate(self.ITA.get_masses()):
self.ui.peakList.setRowCount(i+1)
self.ui.peakList.setItem(i, 0, QTableWidgetItem(x['assign']))
self.ui.peakList.setItem(i, 1, QTableWidgetItem("{:.2f}u".format((x['cmass']))))
self.ui.peakList.setItem(i, 2, QTableWidgetItem("{:.2f}u".format(x['umass'] - x['lmass'])))
self.ui.peakList.show()
self.ui.cmap.currentIndexChanged.connect(self.plot)
self.ui.prof1daxis.currentIndexChanged.connect(self.plot)
self.ui.peakList.cellClicked.connect(self.load_channel)
self.canvas.mpl_connect('button_press_event', self.on_pick)
self.flatAction = QAction("Flatten substrate from this channel")
self.flatAction.triggered.connect(self.flatten)
self.ui.correction.stateChanged.connect(self.plot)
self.ui.peakList.addAction(self.flatAction)
self.ui.status.setText("IDLE")
def flatline(self, y):
for x in range(self.volume.shape[1]):
popt, pcov = opt.curve_fit(CDF, np.arange(self.volume.shape[2]), self.volume[y,x,:], (10, self.volume.shape[2]/2, 1))
self.level[y, x] = popt[1]
def flatten(self):
from scipy import optimize as opt
self.ui.status.setText("Start the flattening...")
self.level = np.zeros(self.volume.shape[:2])
self.ui.pb.setMaximum(self.volume.shape[0])
for y in range(self.volume.shape[0]):
self.ui.pb.setValue(y)
self.flatline(y)
QCoreApplication.processEvents()
self.ax.clear()
self.ax.imshow(self.level)
self.canvas.draw()
self.ui.pb.setValue(0)
self.ui.status.setText("Flattening finished")
np.save(self.path+".level", self.level)
def load_channel(self, row, col):
self.ui.status.setText("Loading channel...")
id = row
vol = []
for i in range(self.ITA.Nscan):
x = self.ITA.getImage(id, i)
vol.append(x)
self.volume = np.stack([x for x in vol], axis=2)
if not self.level is None:
self.corrected = np.zeros(self.volume.shape)
z = np.arange(self.ITA.Nscan)
self.ui.pb.setMaximum(self.level.shape[0])
for y in np.arange(self.level.shape[0]):
self.ui.pb.setValue(y)
for x in np.arange(self.level.shape[1]):
dz = int(-self.level[y,x] + np.max(self.level))
self.corrected[y,x,dz:] = self.volume[y,x,:self.volume.shape[2]-dz]
self.ui.pb.setValue(0)
self.plot()
self.ui.status.setText("IDLE")
def plot(self):
if self.ui.correction.isChecked():
A = self.corrected
else:
A = self.volume
cmap = self.ui.cmap.currentText()
self.axXY.clear()
self.axXZ.clear()
self.axYZ.clear()
self.ax.clear()
if self.volume is None:
return
self.axXY.imshow(A[:,:,self.curs[2]],cmap=cmap)
self.axXZ.imshow(A[self.curs[1],:,:].T,cmap=cmap)
self.axYZ.imshow(A[:,self.curs[0],:].T,cmap=cmap)
self.axXY.axhline(self.curs[1])
self.axXY.axvline(self.curs[0])
self.axXZ.axhline(self.curs[2])
self.axXZ.axvline(self.curs[0])
self.axYZ.axhline(self.curs[2])
self.axYZ.axvline(self.curs[1])
self.axXY.set_title("XY")
self.axXZ.set_title("XZ")
self.axYZ.set_title("YZ")
if self.ui.prof1daxis.currentText() in 'XYZ':
i = 'XYZ'.index(self.ui.prof1daxis.currentText())
self.ax.set_xlabel("XYZ"[i])
if i==0:
self.ax.plot(A[:,self.curs[0],self.curs[2]])
elif i==1:
self.ax.plot(A[self.curs[1],:,self.curs[2]])
elif i==2:
self.ax.plot(A[self.curs[1],self.curs[0],:])
self.canvas.draw()
def on_pick(self, event):
if not event.inaxes in [self.axYZ,self.axXZ,self.axXY]:
return
x = event.xdata
y = event.ydata
axis = [self.axYZ,self.axXZ,self.axXY].index(event.inaxes)
xdata = int(x)
ydata = int(y)
if event.inaxes == self.axXY:
self.curs[0] = xdata
self.curs[1] = ydata
elif event.inaxes == self.axYZ:
self.curs[1] = xdata
self.curs[2] = ydata
elif event.inaxes == self.axXZ:
self.curs[0] = xdata
self.curs[2] = ydata
else:
print("Click event not handled")
self.curs = [np.clip(0,self.curs[i],self.volume.shape[i]-1) for i in range(3)]
self.plot()
def initPlotLayout(self):
"""
Setup the plotting layout.
"""
self.axXY = self.fig.add_subplot(2,2,1)
self.axYZ = self.fig.add_subplot(2,2,2)
self.axXZ = self.fig.add_subplot(2,2,3)
self.ax = self.fig.add_subplot(2,2,4)
self.fig.tight_layout()
app = QApplication(sys.argv)
window = SlicerApp()
window.show()
sys.exit(app.exec_())
