Added more Qsettings for modifying GUI

* changed layout of the QSettings
* added functions for intensity annotation and some memory of user
  preferences

prasopes/__main__.py

@@ -108,7 +108,7 @@ def main():
     ds = dict(chrom_dat=None, masses=None, matrix=None)
     ms = dict(x=[0], y=[0], line=None, annotation=[],
               name="Spectrum", xlabel="m/z", ylabel="ion count",
-              xtics=20, autoy=True, predict=None)
+              xtics=20, predict=None)
     chrom = dict(x=[0], y=[0], line=None, t_start=None, t_end=None,
                  name="Chromatogram", xlabel="time(min)",
                  ylabel="total ion count", timesarg=None)
@@ -190,11 +190,23 @@ def main():
     aboutact = QtWidgets.QAction("&About Prasopes", None)
     aboutact.triggered.connect(lambda: about(main_window))
     autozoomy = QtWidgets.QAction(QtGui.QIcon.fromTheme(
-        "zoom-original"), "Auto Zoom Y", None, checkable=True, checked=True)
-    autozoomy.triggered.connect(lambda: gt.autozoomy(
-        autozoomy.isChecked(), spectrum, ms))
-    filebrowseract = QtWidgets.QAction("&File browser", None,
-                                       checkable=True, checked=True)
+        "zoom-original"), "Auto Zoom Y", None, checkable=True,
+        checked=config.value("view/autozoomy", type=bool))
+    autozoomy.triggered.connect(lambda: config.setValue(
+                                "view/autozoomy", autozoomy.isChecked()))
+    autozoomy.triggered.connect(lambda: gt.autozoomy(spectrum, ms))
+    intensities = QtWidgets.QAction(
+            "&Show intensities", None, checkable=True,
+            checked=config.value("view/intensities", type=bool))
+    intensities.triggered.connect(lambda: config.setValue(
+        "view/intensities", intensities.isChecked()))
+    intensities.triggered.connect(lambda: gt.ann_spec(spectrum, ms))
+    intensities.triggered.connect(lambda: spectrum.figure.canvas.draw())
+    filebrowseract = QtWidgets.QAction(
+            "&File browser", None, checkable=True,
+            checked=config.value("view/filebrowservisible", type=bool))
+    filebrowseract.triggered.connect(lambda: config.setValue(
+        "view/filebrowservisible", filebrowseract.isChecked()))
     filebrowseract.triggered.connect(
         lambda: treedock.show() if filebrowseract.isChecked() == True
                 else treedock.hide())
@@ -216,7 +228,11 @@ def main():
     tools_menu.addAction(zceact)
     tools_menu.addAction(drlact)
     tools_menu.addSeparator()
-    tools_menu.addAction(filebrowseract)
+    view_menu = QtWidgets.QMenu('&View', main_window)
+    view_menu.addAction(filebrowseract)
+    view_menu.addAction(autozoomy)
+    view_menu.addAction(intensities)
+    main_window.menuBar().addMenu(view_menu)
     help_menu = QtWidgets.QMenu('&Help', main_window)
     main_window.menuBar().addMenu(help_menu)
     help_menu.addAction(aboutact)
@@ -233,13 +249,13 @@ def main():
     toolBar.addAction(openact)
     toolBar.addAction(exportact)
     toolBar.addSeparator()
+    toolBar.addWidget(QtWidgets.QLabel("Predict Formula:"))
+    toolBar.addWidget(predictform)
+    toolBar.addSeparator()
     toolBar.addAction(zceact)
     toolBar.addAction(drlact)
     toolBar.addSeparator()
     toolBar.addAction(autozoomy)
-    toolBar.addSeparator()
-    toolBar.addWidget(QtWidgets.QLabel("Predict Formula:"))
-    toolBar.addWidget(predictform)
 
 
     fileModel = QtWidgets.QFileSystemModel()
@@ -252,6 +268,8 @@ def main():
     dirview = QtWidgets.QListView()
     dirview.setModel(fileModel)
     treedock = QtWidgets.QDockWidget()
+    if not config.value("view/filebrowservisible",type=bool):
+        treedock.hide()
     treedock.setWidget(QtWidgets.QWidget())
     treedock_layout = QtWidgets.QVBoxLayout(treedock.widget())
     treedock_layout.addWidget(treeview)

prasopes/config.py

@@ -7,6 +7,10 @@ from PyQt5 import QtPrintSupport
 
 def settings():
     settings = QtCore.QSettings("Yansoft","Prasopes")
+    defvals = {("view/autozoomy", True),
+               ("view/filebrowservisible", True),
+               ("view/intensities", False)}
+    [settings.setValue(i[0], i[1]) for i in defvals if settings.value(i[0]) == None]
     return settings
 
 

prasopes/graphtools.py

 import numpy as np
 import prasopes.datatools as dt
+import prasopes.config as cf
 
 
 def zoom_factory(axis, base_scale, plot_data=None):
@@ -86,7 +87,7 @@ def pan_factory(axis, plot=None):
 def pick_masses(x_min, x_max, ms_spec, msdata):
     """zoom the spectrum in x axis by mass range"""
     ms_spec.set_xlim(x_min, x_max)
-    autozoomy(msdata['autoy'], ms_spec, msdata)
+    autozoomy(ms_spec, msdata)
     ann_spec(ms_spec, msdata)
 
 
@@ -101,10 +102,10 @@ def plot_subtime(mpl_spectrum, mpl_chromatogram, data_set, mass_spect,
         data_set['matrix'][chrom_spect['timesarg']], axis=0)
     pop_plot(mpl_spectrum, mass_spect)
     mpl_spectrum.set_xlim(slims[0])
-    if mass_spect['autoy'] is False:
+    if not cf.settings().value("view/autozoomy", type=bool):
         mpl_spectrum.set_ylim(slims[1])
     else:
-        autozoomy(mass_spect['autoy'], mpl_spectrum, mass_spect)
+        autozoomy(mpl_spectrum, mass_spect)
 
     mpl_chromatogram.clear()
     pop_plot(mpl_chromatogram, chrom_spect)
@@ -144,9 +145,8 @@ def arrow_factory(spectrum, chromatogram, ds, mass_spect,
     fig.canvas.mpl_connect('key_press_event', lambda event: arrow_fun(
         event, spectrum, chromatogram, ds, mass_spect, chrom_spect))
 
-def autozoomy(state, ms_spec, msdata):
-    if state is True:
-        msdata['autoy'] = True
+def autozoomy(ms_spec, msdata):
+    if cf.settings().value("view/autozoomy", type=bool):
         ms_spec.autoscale(True, 'y')
         ymin = -0.01
         argvis = dt.argsubselect(msdata['x'], *ms_spec.get_xlim())
@@ -155,8 +155,6 @@ def autozoomy(state, ms_spec, msdata):
             ms_spec.set_ylim(ymax*ymin,
                              ymax*1.1)
             ms_spec.figure.canvas.draw()
-    else:
-        msdata['autoy'] = False
 
 
 def ann_spec(ms_spec, msdata, ann_limit=0.01):
@@ -208,12 +206,16 @@ def ann_spec(ms_spec, msdata, ann_limit=0.01):
     msdata['annotation'].clear()
 
     for i in s_peaks:
-        msdata['annotation'].append(ms_spec.annotate(
-            #annotation with peak-height
-            #'{0:.2f}\n{1: .2e}'.format(msdata['x'][i], msdata['y'][i]), xy=(msdata['x'][i], msdata['y'][i]),
-            '{0:.2f}'.format(msdata['x'][i]), xy=(msdata['x'][i], msdata['y'][i]),
-            textcoords='data'))
-
+        print(cf.settings().value("view/intensities", type=bool))
+        if cf.settings().value("view/intensities", type=bool):
+            annotation = '{0:.2f}\n{1: .2e}'.format(msdata['x'][i],
+                                                    msdata['y'][i])
+            print("ifim")
+        else:
+            annotation = '{0:.2f}'.format(msdata['x'][i])
+            print("elsim")
+        msdata['annotation'].append(ms_spec.annotate(annotation,
+            xy=(msdata['x'][i], msdata['y'][i]), textcoords='data'))
 
 def pop_plot(plot, plot_data):
     """Define and populate plot"""