Merge branch 'master' pt 2/2

prasopes/zcetools.py

+import numpy as np
+import prasopes.graphtools as gt
+import os.path
+from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
+from matplotlib.figure import Figure
+from PyQt5 import QtCore
+from PyQt5 import QtWidgets
+
+
+def pop_dial(zcespec, gradspect, data_set, widget, coff_d, grad_d,
+             textfield, fn, parent):
+    if fn[0] is None:
+        QtWidgets.QMessageBox.warning(
+            parent, "ZCE calculation",
+            "No spectrum opened, cancelling request")
+        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'])
+    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]
+    climb = np.argsort(grad_d['y'][:maxarg])
+    fall = np.argsort(grad_d['y'][maxarg:]) + maxarg
+    halfmax = np.max(grad_d['y']) / 2
+    grad_d['fwhm_y'] = [halfmax, halfmax]
+    grad_d['fwhm_x'] = [
+        np.interp(halfmax, grad_d['y'][climb], grad_d['x'][climb]),
+        np.interp(halfmax, grad_d['y'][fall], grad_d['x'][fall])]
+    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()
+    widget.show()
+
+
+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 = QtWidgets.QFileDialog.getSaveFileName(
+            caption="Export ZCE spectrum",
+            filter="dat table format (*.dat)")[0]
+    if exp_f_name is not '':
+        # fix for Qt5 "Feature"
+        if exp_f_name[-4:] != '.dat':
+            exp_f_name = exp_f_name + ".dat"
+            if os.path.isfile(exp_f_name):
+                quest = QtWidgets.QMessageBox.warning(
+                    parent, "Export spectrum",
+                    "{} already exists.\n Do you want to replace it?"
+                    .format(os.path.basename(exp_f_name)),
+                    QtWidgets.QMessageBox.Yes, QtWidgets.QMessageBox.No)
+                if(hex(quest)) == "0x10000":
+                    return
+        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 dialog(parent, ds, filename):
+    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)
+
+    dial_widget = QtWidgets.QDialog(parent)
+    dial_widget.setWindowTitle('TSQ zero collision energy calculator')
+
+    dial_graph = Figure(figsize=(5, 2), dpi=100)
+    dial_graph.patch.set_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_help = QtWidgets.QPushButton("Help")
+    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_export)
+    butt_layout.addWidget(close_button)
+
+    dial_layout = QtWidgets.QVBoxLayout(dial_widget)
+    dial_layout.addWidget(graph_canvas)
+    dial_layout.addLayout(butt_layout)
+    pop_dial(coffspect, coffspect_grad, ds, dial_widget, coff, coffgrad,
+             textfield, filename, parent)
+