zcetools.py

from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
from PyQt5 import QtCore
from PyQt5 import QtWidgets
from PyQt5 import QtPrintSupport
import numpy as np
import prasopes.graphtools as gt
import prasopes.filetools as ft
import os.path
import pkg_resources
import logging


logger = logging.getLogger('zceLogger')


def pop_dial(zcespec, gradspect, data_set, coff_d, grad_d,
             textfield, fn, parent):
    logger.debug("populating ZCE dialog")
    if fn[0] is None:
        QtWidgets.QMessageBox.warning(
            parent, "ZCE calculation",
            "No spectrum opened, nothing to display")
        return
    zcespec.clear()
    gradspect.clear()

    coff_d['x'] = data_set['masses'] - 196
    coff_d['y'] = np.mean(data_set['matrix'], axis=0)
    grad_d['x'] = coff_d['x']
    grad_d['y'] = -np.gradient(coff_d['y'])
    gradspect.axhline(0, color="#FF000088", linestyle=":")
    zcespec.axhline(0, color="#0000FF88", linestyle=":")
    gt.pop_plot(zcespec, coff_d)
    gt.pop_plot(gradspect, grad_d)
    grad_d['line'][0].set_color("red")
    gradspect.set_ylim(bottom=gradspect.get_ylim()[1] * -0.1)
    zcespec.set_title("COFF", loc="center")

    maxarg = np.argmax(grad_d['y'])
    grad_d['gmax'] = coff_d['x'][maxarg]
    halfmax = np.max(grad_d['y']) / 2
    peakargs = np.where(grad_d['y'] > halfmax)[0]
    start = [peakargs[0]-1, peakargs[0]]
    end = [peakargs[-1]+1, peakargs[-1]]
    grad_d['fwhm_y'] = [halfmax, halfmax]
    grad_d['fwhm_x'] = [
        np.interp(halfmax, grad_d['y'][start], grad_d['x'][start]),
        np.interp(halfmax, grad_d['y'][end], grad_d['x'][end])]
    grad_d['fwhm'] = grad_d['fwhm_x'][1] - grad_d['fwhm_x'][0]

    gradspect.plot(grad_d['fwhm_x'], grad_d['fwhm_y'], "#880088")
    textfield.setText(
        "ZCE = {:.2f}\nFWHM = {:.2f}\nCenter(HM) = {:.2f}".format(
            grad_d['gmax'], grad_d['fwhm'],
            np.mean(grad_d['fwhm_x'])))
    gradspect.annotate(' FWHM = {:.2f}'.format(grad_d['fwhm']),
                       xy=(grad_d['fwhm_x'][1], grad_d['fwhm_y'][1]))
    gradspect.annotate('{:.2f}'.format(grad_d['gmax']),
                       xy=(grad_d['x'][maxarg], grad_d['y'][maxarg]))
    zcespec.figure.canvas.draw()


def exp_zce(zce_spec, zcegrad_spec, fn, parent):
    """export the ZCE graph into the .dat file format"""
    if fn[0] is None:
        QtWidgets.QMessageBox.warning(
            parent, "Export ZCE spectrum",
            "Nothing to export, cancelling request")
        return
    exp_f_name = ft.get_save_filename(
        "Export ZCE spectrum", "dat table (*.dat)", "dat", parent)
    if exp_f_name is not '':
        expf = open(exp_f_name, 'w')
        expf.write("mass ion_count ion_count_gradient fwhm_x fwhm_y\n"
                   "m/z\n"
                   "{} zce={} fwhm={} hmcenter={}\n".format(
                       os.path.basename(fn[0]), zcegrad_spec['gmax'],
                       zcegrad_spec['fwhm'],
                       np.mean(zcegrad_spec['fwhm_x'])))
        for i in range(len(zce_spec['x'])):
            fwhm = ["", ""]
            if i <= 1:
                fwhm = [zcegrad_spec['fwhm_x'][i],
                        zcegrad_spec['fwhm_y'][i]]
            expf.write("{} {} {} {} {}\n".format(
                zce_spec['x'][i], zce_spec['y'][i], zcegrad_spec['y'][i],
                fwhm[0], fwhm[1]))
        expf.close()


def help_msg(pw):
    path = pkg_resources.resource_filename(__name__, 'zcetools_help')
    with open(path, 'r') as helpfile:
        helpcontent = helpfile.read()
        QtWidgets.QMessageBox.information(
            pw, "TSQ zce tool help", "{}".format(helpcontent))


def print_graph(ds, coff, coffgrad, filename):
    printfig = Figure(figsize=(5, 2), dpi=100)
    printplot = printfig.add_subplot(111)
    printplot_overlay = printplot.twinx()
    printcanvas = FigureCanvas(printfig)
    textfield = QtWidgets.QLabel()
    pop_dial(printplot, printplot_overlay, ds, coff, coffgrad,
             textfield, filename, None)
    widget = QtWidgets.QDialog(None, windowTitle='Print preview')
    layout = QtWidgets.QVBoxLayout(widget)
    layout.addWidget(printcanvas)
    widget.resize(600, 400)
    widget.show()
    dialog = QtPrintSupport.QPrintDialog()
    if dialog.exec_() == QtWidgets.QDialog.Accepted:
        printcanvas.render(dialog.printer())
    widget.close()


def dialog(parent, ds, filename, update_signal):
    coff = dict(x=[0], y=[0], line=None, name="",
                xlabel="Voltage (V)", ylabel="ion count")
    coffgrad = dict(x=[0], y=[0], c_ymin=-0.1, line=None, name="",
                    xlabel="", ylabel="ion count gradient", gmax=None,
                    fwhm_x=None, fwhm_y=None, fwhm=None)

    def onclose(widget, event, update_fnc):
        logger.debug("ZCE window custom close routine called")
        update_signal.signal.disconnect(update_fnc)
        QtWidgets.QDialog.closeEvent(widget, event)

    def update_fnc():
        pop_dial(coffspect, coffspect_grad, ds, coff, coffgrad,
                 textfield, filename, parent)

    dial_widget = QtWidgets.QDialog(
            parent, windowTitle='TSQ zero collision energy calculator')
    dial_widget.closeEvent = lambda event: onclose(
        dial_widget, event, update_fnc)
    update_signal.signal.connect(update_fnc)

    dial_graph = Figure(figsize=(5, 2), dpi=100, facecolor="None")
    coffspect = dial_graph.add_subplot(111, facecolor=(1, 1, 1, 0.8))
    coffspect_grad = coffspect.twinx()
    graph_canvas = FigureCanvas(dial_graph)
    graph_canvas.setStyleSheet("background-color:transparent;")
    graph_canvas.setAutoFillBackground(False)
    graph_canvas.setFocusPolicy(QtCore.Qt.ClickFocus)

    gt.zoom_factory(coffspect_grad, 1.15, coffgrad)
    gt.pan_factory(coffspect_grad, coffgrad)

    zce_export = QtWidgets.QPushButton("Export ZCE")
    zce_export.clicked.connect(lambda: exp_zce(
        coff, coffgrad, filename, parent))
    zce_print = QtWidgets.QPushButton("Print ZCE")
    zce_print.clicked.connect(lambda: print_graph(
        ds, coff, coffgrad, filename))
    zce_help = QtWidgets.QPushButton("Help")
    zce_help.clicked.connect(lambda: help_msg(parent))
    close_button = QtWidgets.QPushButton("Close")
    close_button.clicked.connect(dial_widget.close)

    butt_layout = QtWidgets.QHBoxLayout()
    butt_layout.addWidget(zce_help)
    butt_layout.addStretch(1)
    textfield = QtWidgets.QLabel(coffgrad['gmax'])
    butt_layout.addWidget(textfield)
    butt_layout.addStretch(1)
    butt_layout.addWidget(zce_print)
    butt_layout.addWidget(zce_export)
    butt_layout.addWidget(close_button)

    dial_layout = QtWidgets.QVBoxLayout(dial_widget)
    dial_layout.addWidget(graph_canvas)
    dial_layout.addLayout(butt_layout)
    dial_widget.show()
    pop_dial(coffspect, coffspect_grad, ds, coff, coffgrad,
             textfield, filename, parent)