Constrained layout, intensity selector

* modded code to accept constrained layout in main GUI without major
issues
* added intensity selector - in a dirty way for now

prasopes/__main__.py

@@ -174,7 +174,11 @@ def oddeven_changed(chromatogram, spectrum, ds, ms, filename, chrom, config,
     update_spectrum(chromatogram, spectrum, ds, ms, filename, chrom, config)
 
 
-def key_pressed(event, chrom, spect, ds, ms_ds, fn, chrom_ds, config):
+def key_pressed(event, chrom, spect, ds, ms_ds, fn, chrom_ds, config,
+        mass_selector, intensity_selector):
+    if event.modifiers() == QtCore.Qt.ShiftModifier:
+        mass_selector.active = False
+        intensity_selector.active = True
     if event.key() == QtCore.Qt.Key_F5:
         update_spectrum(chrom, spect, ds, ms_ds, fn, chrom_ds, config)
     if event.key() == QtCore.Qt.Key_C:
@@ -187,6 +191,12 @@ def key_pressed(event, chrom, spect, ds, ms_ds, fn, chrom_ds, config):
         gt.shift_times(event, spect, chrom, ds, ms_ds, chrom_ds)
 
 
+def key_released(event, spect, mass_selector, intensity_selector):
+    if event.key() == QtCore.Qt.Key_Shift:
+        mass_selector.active = True
+        intensity_selector.active = False
+
+
 def about(parent):
     """constructs window with "about" info"""
     QtWidgets.QMessageBox.information(
@@ -237,11 +247,10 @@ def main():
     paramstable = dt.table(["","name","value"], 100)
     paramstable.horizontalHeader().setSectionResizeMode(
             0, QtWidgets.QHeaderView.ResizeToContents)
-    graph = Figure(figsize=(5, 4), dpi=100, facecolor="None")
+    graph = Figure(figsize=(5, 4), dpi=100, facecolor="None", constrained_layout=True)
     grid = graph.add_gridspec(2, 1)
     chromatogram = graph.add_subplot(grid[0,0], facecolor=(1, 1, 1, 0.8))
     spectrum = graph.add_subplot(grid[1,0], facecolor=(1, 1, 1, 0.8))
-    graph.tight_layout()
     mpl_canvas = FigureCanvas(graph)
     mpl_canvas.setStyleSheet("background-color:transparent;")
     mpl_canvas.setAutoFillBackground(False)
@@ -256,6 +265,12 @@ def main():
             x_min, x_max, spectrum, ms), 'horizontal', minspan=0.01,
         useblit=True, rectprops=dict(alpha=0.15, facecolor='purple'),
         button=3)
+    intensity_selector = SpanSelector(
+        spectrum, lambda y_min, y_max: gt.pick_intensities(
+            y_max, spectrum, ms), 'vertical', minspan=0.01,
+        useblit=True, rectprops=dict(alpha=0.15, facecolor='purple'),
+        button=3)
+    intensity_selector.active=False
     time_selector = SpanSelector(
          chromatogram, lambda x_min, x_max: gt.pick_times(
              x_min, x_max, spectrum, ds, chromatogram, ms, chrom, paramstable),
@@ -426,7 +441,10 @@ def main():
         chrom, update, config)
     main_window.setAcceptDrops(True)
     main_window.keyPressEvent = lambda event: key_pressed(event, chromatogram,
-            spectrum, ds, ms, filename, chrom, config)
+            spectrum, ds, ms, filename, chrom, config,
+            mass_selector, intensity_selector)
+    main_window.keyReleaseEvent = lambda event: key_released(event, spectrum,
+            mass_selector, intensity_selector)
 
     main_window.addToolBar(QtCore.Qt.TopToolBarArea, toolBar)
     main_window.addDockWidget(QtCore.Qt.LeftDockWidgetArea, treedock)

prasopes/graphtools.py

+from PyQt5 import QtWidgets
+from PyQt5 import QtCore
+from matplotlib.widgets import SpanSelector
 import numpy as np
 import prasopes.datatools as dt
 import prasopes.config as cf
 import matplotlib
-from PyQt5 import QtWidgets
-from PyQt5 import QtCore
 
 
 colors = np.array([[0, 0, 0], [255, 0, 0], [0, 255, 0], [0, 0, 255],
@@ -13,6 +14,20 @@ colors = np.array([[0, 0, 0], [255, 0, 0], [0, 255, 0], [0, 0, 255],
 
 ann_bbox = dict(boxstyle="round", fc="w", ec="0.5", alpha=0.5)
 
+
+def pick_masses(vmin, vmax, ax, data):
+    """zoom the spectrum in x axis by mass range"""
+    ax.set_xlim(vmin, vmax)
+    autozoomy(ax)
+    ann_spec(ax, data)
+
+
+def pick_intensities(vmax, ax, data):
+    """zoom the spectrum in y axis by top intensity from range"""
+    ax.set_ylim(-vmax*0.01, vmax)
+    ann_spec(ax, data)
+
+
 def zoom_factory(axis, base_scale, plot_data=None):
     """returns zooming functionality to axis"""
     def zoom_fun(event, pd, ax, scale):
@@ -78,6 +93,7 @@ def pan_factory(axis, plot=None):
                     action, id_drag, id_release, pd, ax))
 
     def drag_fun(event, ax):
+        ax.figure.set_constrained_layout(False)
         ax.drag_pan(1, 'x', event.x, event.y)
         ax.figure.canvas.draw()
 
@@ -88,6 +104,7 @@ def pan_factory(axis, plot=None):
             if type(pd) is dict and "annotation" in pd:
                 ann_spec(ax, pd)
             ax.figure.canvas.draw()
+            ax.figure.set_constrained_layout(True)
 
     fig = axis.get_figure()
     fig.canvas.mpl_connect('button_press_event',
@@ -115,13 +132,6 @@ def textedit_factory(axis, plot_data):
     axis.figure.canvas.mpl_connect('pick_event', annpicked)
 
 
-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(ms_spec)
-    ann_spec(ms_spec, msdata)
-
-
 def plot_subtime(mpl_spectrum, mpl_chromatogram, ds, ms_data, chrom_data):
     """plot averaged spectrum of subselected part of the chromatogram"""
     slims = [mpl_spectrum.get_xlim(), mpl_spectrum.get_ylim()]
@@ -221,9 +231,9 @@ def autozoomy(ms_spec):
         ms_spec.autoscale(True, 'y')
         gap = 0.01
         ymax = np.max([np.max(line.get_data()[1][dt.argsubselect(
-            line.get_data()[0], *ms_spec.get_xlim())])
+            line.get_data()[0], *ms_spec.get_xlim())])*1.1
             for line in ms_spec.lines])
-        ms_spec.set_ylim(-ymax*gap, ymax*1.1)
+        ms_spec.set_ylim(-ymax*gap, ymax)
         ms_spec.figure.canvas.draw()
 
 def ann_spec(ms_spec, msdata, ann_limit=0.01):
@@ -373,6 +383,7 @@ def populate(mpl_chromatogram, mpl_spectrum, data_set,
     for ax in (mpl_spectrum, mpl_chromatogram):
         if not ms_data['headers'] == []:
             ax.legend(loc=2)
+            ax.get_legend().set_in_layout(False)
         ax.autoscale(True)
         ax.set_ylim(ax.get_ylim()[1]*-0.01, ax.get_ylim()[1]*1.1)
         ax.figure.canvas.draw()