Initial reactivity support

* code is WIP, just proof of concept

prasopes/__init__.py

@@ -10,11 +10,12 @@ from . import predictmz
 from . import tangoicons
 from . import zcetools
 from . import zcetools_help
+from . import reactivitytools
 
 
-__version__ = "0.0.18"
+__version__ = "0.0.19"
 
 
 __all__ = ['config', 'datatools', 'docks', 'drltools', 'filetools',
            'graphtools', 'imagetools', 'predictmz', 'tangoicons', 'zcetools',
-           'zcetools_help']
+           'zcetools_help', 'reactivitytools']

prasopes/__main__.py

@@ -74,7 +74,8 @@ def load_file(parent, augCanvas, update, settings, loadthread, filename=None):
             if autoparams:
                 try:
                     (augCanvas.ms['params'], rawheaders,
-                        augCanvas.chrom['machtype']) = load_params(filename)
+                        augCanvas.chrom['machtype']) = load_params(
+                                filename, settings.value("tmp_location"))
                     segments = [len(subset['chrom_dat'][0])
                                 for subset in augCanvas.ds]
                     indicies = [sum(segments[:i+1])

prasopes/drltools.py

@@ -6,13 +6,13 @@ from PyQt5 import QtCore
 from PyQt5 import QtWidgets
 from PyQt5 import QtGui
 from PyQt5 import QtPrintSupport
-from copy import copy
 import matplotlib
 import numpy as np
 import prasopes.datatools as dt
 import prasopes.graphtools as gt
 import prasopes.filetools as ft
 import prasopes.config as cf
+import prasopes.reactivitytools as rt
 import os.path
 import logging
 matplotlib.use("Qt5Agg")
@@ -342,7 +342,7 @@ def add_line(ds, drls, drlspectrum):
     drls['dt'].setCellWidget(newrow, 0, checkbox)
 
     for i in range(drls['cors'].value()):
-        col = copy(1+i*2)
+        col = 1+i*2
         drls['dt'].setCellWidget(newrow, col, QtWidgets.QComboBox())
         drls['dt'].cellWidget(newrow, col).setFocusPolicy(QtCore.Qt.NoFocus)
         drls['dt'].cellWidget(newrow, col).setFrame(False)
@@ -694,6 +694,7 @@ def main_window(parent, augCanvas, update_signal):
     drl_load = QtWidgets.QPushButton("&Load")
     drl_save = QtWidgets.QPushButton("&Save")
     drl_export = QtWidgets.QPushButton("&Export")
+    drl_reactivity = QtWidgets.QPushButton("&Reactivity")
     drl_print = QtWidgets.QPushButton("&Print")
     close = QtWidgets.QPushButton("&Close")
     close.clicked.connect(window.close)
@@ -715,6 +716,8 @@ def main_window(parent, augCanvas, update_signal):
     drl_print.clicked.connect(lambda: print_graph(ds, drls))
     drl_export.clicked.connect(lambda: export_drlspectrum(
         main_widget, filename, ds, drls))
+    drl_reactivity.clicked.connect(lambda: rt.main_window(parent,
+        augCanvas, update_signal, drls))
 
     drls['pt'].itemChanged.connect(lambda item: ptable_changed(
         item.row(), item.column(), ds, drls, chromplot))
@@ -740,6 +743,8 @@ def main_window(parent, augCanvas, update_signal):
     actionBar.addWidget(drl_save)
     actionBar.addWidget(drl_print)
     actionBar.addWidget(StretchWidget())
+    actionBar.addWidget(drl_reactivity)
+    actionBar.addWidget(StretchWidget())
     actionBar.addWidget(drl_export)
     actionBar.addWidget(close)
 

prasopes/reactivitytools.py

+#!/usr/bin/env python3
+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 QtGui
+from PyQt5 import QtPrintSupport
+import matplotlib
+import numpy as np
+import prasopes.datatools as dt
+import prasopes.graphtools as gt
+import prasopes.filetools as ft
+import prasopes.config as cf
+import prasopes.drltools as drl
+import os.path
+import logging
+matplotlib.use("Qt5Agg")
+
+
+logger = logging.getLogger('drlLogger')
+
+
+def pop_dial(augCanvas, drls, graph, labels):
+    logger.debug("populating reactivity dialog")
+    # Do not do anything when data set is not populated
+    if len(augCanvas.ds) == 0:
+        return
+    graph.clear()
+    gt.pop_plot([0], [0], graph, labels)
+    names, times, intensities = drl.get_daughterset(augCanvas.ds, drls)
+    if len(names) < 2:
+        return
+    params = augCanvas.ms['params']
+    pressures = []
+    for time in times:
+        toavg = []
+        for param in params[1]:
+            if param[0] == time:
+                toavg.append(param[36])
+        if len(toavg) != 0:
+            pressures.append([time, np.average(toavg)])
+    goodtimes = np.where([t in np.asarray(pressures).T[0] for t in times])
+    for i in range(1,len(intensities)):
+        relint = np.divide(intensities[i], np.clip(np.sum(
+            intensities, 0), np.finfo(np.float32).eps, None),
+            dtype=np.float64)
+        graph.plot(np.asarray(pressures).T[1], relint[goodtimes], label=names[i],
+                color=(gt.colors[i % len(gt.colors)] / 255), marker=".",
+                markersize=2, linestyle="None")
+
+
+def main_window(parent, augCanvas, update_signal, drls):
+    """constructs a dialog window"""
+    reactlabels = dict(name="", xlabel="pressure (mT)", ylabel="rel intensity")
+    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(augCanvas, drls, dialspect, reactlabels)
+
+    dial_widget = QtWidgets.QDialog(
+            parent, windowTitle='TSQ reactivity interpreter')
+    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")
+    dialspect = dial_graph.add_subplot(111, facecolor=(1, 1, 1, 0.8))
+    graph_canvas = FigureCanvas(dial_graph)
+    graph_canvas.setStyleSheet("background-color:transparent;")
+    graph_canvas.setAutoFillBackground(False)
+
+    gt.zoom_factory(dialspect, 1.15, reactlabels)
+    gt.pan_factory(dialspect, reactlabels)
+
+    dial_layout = QtWidgets.QVBoxLayout(dial_widget)
+    dial_layout.addWidget(graph_canvas)
+    dial_widget.setFocus()
+    dial_widget.show()
+    pop_dial(augCanvas, drls, dialspect, reactlabels)