More fixes, copying of parameters working

* sw is still haunted by bugs after uniting but its workable

prasopes/__main__.py

@@ -78,8 +78,9 @@ class AugFigureCanvas(FigureCanvas):
         self.mass_selector = gt.AugSpanSelector(self.spectplot, self.ms)
         #TODO: rewrite timeSelector to better shape when I'm done
         self.time_selector = SpanSelector(self.chromplot, lambda x_min, x_max:
-                gt.pick_times(x_min, x_max, self.spectplot, self.ds, self.chromplot, self.ms, self.chrom, self.paramstable), 'horizontal', useblit=True, rectprops=dict(
-                        alpha=0.15, facecolor='purple'), button=3)
+                gt.pick_times(x_min, x_max, self), 'horizontal',
+                useblit=True, rectprops=dict(alpha=0.15, facecolor='purple'),
+                button=3)
 
 
 def load_file(parent, augCanvas, update, settings, loadthread, filename=None):
@@ -215,6 +216,9 @@ def key_pressed(event, augCanvas, config):
         update_spectrum(augCanvas, config)
     if event.key() == QtCore.Qt.Key_C:
         if event.modifiers().__int__() == QtCore.Qt.ControlModifier:
+            if augCanvas.paramstable.underMouse():
+                dt.clip_tablestr(augCanvas)
+            else:
                 imgt.clip_spect_img(augCanvas.ms, augCanvas.spectplot,
                                     augCanvas.filename)
         if event.modifiers().__int__() == QtCore.Qt.ControlModifier+\

prasopes/datatools.py

@@ -40,6 +40,15 @@ def clip_spectstr(augCanvas):
     [QtWidgets.QApplication.clipboard().setText(string, i) for i in range(2)]
 
 
+def clip_tablestr(augCanvas):
+        pairs = [" ".join((augCanvas.paramstable.item(row, 1).text(),
+                           augCanvas.paramstable.item(row, 2).text()))
+                 for row in range(augCanvas.paramstable.rowCount())
+                 if augCanvas.paramstable.cellWidget(row, 0).checkState()]
+        text = ", ".join(pairs)
+        [QtWidgets.QApplication.clipboard().setText(text, i) for i in range(2)]
+
+
 def table(labels, minsizex=600, minsizey=0):
     """creates a reasonable table"""
     table = QtWidgets.QTableWidget(columnCount=len(labels))

prasopes/graphtools.py

@@ -183,83 +183,86 @@ def textedit_factory(axis, plot_data):
     axis.figure.canvas.mpl_connect('pick_event', annpicked)
 
 
-def plot_subtime(mpl_spectrum, mpl_chromatogram, ds, ms_data, chrom_data):
+#def plot_subtime(mpl_spectrum, mpl_chromatogram, ds, ms_data, chrom_data):
+def plot_subtime(augCanvas):
     """plot averaged spectrum of subselected part of the chromatogram"""
-    slims = [mpl_spectrum.get_xlim(), mpl_spectrum.get_ylim()]
-    chlims = [mpl_chromatogram.get_xlim(), mpl_chromatogram.get_ylim()]
-    ms_data['annotation'].clear()
-    mpl_spectrum.clear()
-    mpl_chromatogram.clear()
-
-    for i,subset in enumerate(ds):
-        selection = chrom_data['timesarg'][i]
-        if len(ms_data['headers']) == len(ds):
-            legend = legendize(ms_data['headers'][i][selection], chrom_data)
+    slims = [augCanvas.spectplot.get_xlim(), augCanvas.spectplot.get_ylim()]
+    chlims = [augCanvas.chromplot.get_xlim(), augCanvas.chromplot.get_ylim()]
+    augCanvas.ms['annotation'].clear()
+    augCanvas.spectplot.clear()
+    augCanvas.chromplot.clear()
+
+    for i,subset in enumerate(augCanvas.ds):
+        selection = augCanvas.chrom['timesarg'][i]
+        if len(augCanvas.ms['headers']) == len(augCanvas.ds):
+            legend = legendize(augCanvas.ms['headers'][i][selection],
+                               augCanvas.chrom)
         else:
             legend = None
         if cf.settings().value("view/oddeven", type=bool):
             for j in range(2):
                 chromx = subset['chrom_dat'][0, :][j::2]
                 chromy = subset['chrom_dat'][1, :][j::2]
-                pop_plot(chromx, chromy, mpl_chromatogram, chrom_data, i*2+j,
-                         legend)
+                pop_plot(chromx, chromy, augCanvas.chromplot,
+                         augCanvas.chrom, i*2+j, legend)
                 if not np.array_equal(selection[j::2], []):
                     clr = i*2+j if selection[0] % 2 == 0\
                             else i*2+(1-j)
                     ms_x = subset['masses']
                     ms_y = np.mean(subset['matrix'][selection[j::2]], axis=0)
-                    pop_plot(ms_x, ms_y, mpl_spectrum, ms_data, clr, legend)
+                    pop_plot(ms_x, ms_y, augCanvas.spectplot,
+                             augCanvas.ms, clr, legend)
                     dots_x = subset['chrom_dat'][0, selection[j::2]]
                     dots_y = subset['chrom_dat'][1, selection[j::2]]
-                    mpl_chromatogram.plot(dots_x, dots_y, '.', color=(
+                    augCanvas.chromplot.plot(dots_x, dots_y, '.', color=(
                         colors[(clr) % len(colors)]/255))
         else:
             chromx = subset['chrom_dat'][0, :]
             chromy = subset['chrom_dat'][1, :]
-            pop_plot(chromx, chromy, mpl_chromatogram, chrom_data, i, legend)
+            pop_plot(chromx, chromy, augCanvas.chromplot,
+                     augCanvas.chrom, i, legend)
             if not np.array_equal(selection, []):
                 ms_x = subset['masses']
                 ms_y = np.mean(subset['matrix'][selection], axis=0)
-                pop_plot(ms_x, ms_y, mpl_spectrum, ms_data, i, legend)
+                pop_plot(ms_x, ms_y, augCanvas.spectplot,
+                         augCanvas.ms, i, legend)
                 dots_x = subset['chrom_dat'][0, selection]
                 dots_y = subset['chrom_dat'][1, selection]
-                mpl_chromatogram.plot(dots_x, dots_y, '.', color=(
+                augCanvas.chromplot.plot(dots_x, dots_y, '.', color=(
                     colors[i % len(colors)]/255))
 
-    mpl_spectrum.set_xlim(slims[0])
+    augCanvas.spectplot.set_xlim(slims[0])
     if not cf.settings().value("view/autozoomy", type=bool):
-        mpl_spectrum.set_ylim(slims[1])
-    if not ms_data['headers'] == []:
-        mpl_spectrum.legend(loc=2)
-        mpl_spectrum.get_legend().set_in_layout(False)
-        mpl_chromatogram.legend(loc=2)
-        mpl_chromatogram.get_legend().set_in_layout(False)
+        augCanvas.spectplot.set_ylim(slims[1])
+    if not augCanvas.ms['headers'] == []:
+        augCanvas.spectplot.legend(loc=2)
+        augCanvas.spectplot.get_legend().set_in_layout(False)
+        augCanvas.chromplot.legend(loc=2)
+        augCanvas.chromplot.get_legend().set_in_layout(False)
     else:
-        autozoomy(mpl_spectrum)
-    ann_spec(mpl_spectrum, ms_data)
-    mpl_chromatogram.set_xlim(chlims[0])
-    mpl_chromatogram.set_ylim(chlims[1])
-    mpl_chromatogram.get_figure().canvas.draw()
+        autozoomy(augCanvas.spectplot)
+    ann_spec(augCanvas.spectplot, augCanvas.ms)
+    augCanvas.chromplot.set_xlim(chlims[0])
+    augCanvas.chromplot.set_ylim(chlims[1])
+    augCanvas.chromplot.get_figure().canvas.draw()
 
 
-def pick_times(x_min, x_max, mpl_spectrum, data_set, mpl_chromatogram,
-               mass_spect, chrom_spect, table):
+def pick_times(x_min, x_max, augCanvas):
     """subselect part of the chromatogram and plot it"""
-    chrom_spect['t_start'] = x_min
-    chrom_spect['t_end'] = x_max
+    augCanvas.chrom['t_start'] = x_min
+    augCanvas.chrom['t_end'] = x_max
     times = dt.argsubselect(np.concatenate(
-        [subset['chrom_dat'][0] for subset in data_set]), x_min, x_max)
-    chrom_spect['timesarg'].clear()
-    for subset in data_set:
+        [subset['chrom_dat'][0] for subset in augCanvas.ds]), x_min, x_max)
+    augCanvas.chrom['timesarg'].clear()
+    for subset in augCanvas.ds:
         goodtimes = np.where((times < len(subset['chrom_dat'][0])) & ~(times < 0))[0]
-        chrom_spect['timesarg'].append(times[goodtimes])
+        augCanvas.chrom['timesarg'].append(times[goodtimes])
         times = times - len(subset['chrom_dat'][0])
-    update_paramstable(table, mass_spect, chrom_spect)
-    plot_subtime(mpl_spectrum, mpl_chromatogram, data_set, mass_spect,
-                 chrom_spect)
+    update_paramstable(augCanvas)
+    plot_subtime(augCanvas)
 
 
-def shift_times(event, spect, chrom, ds, ms_ds, chrom_ds):
+def shift_times(event, augCanvas):
     """shifts times when arrow is pressed"""
     if event.key() == QtCore.Qt.Key_Left:
         move = -1
@@ -267,14 +270,15 @@ def shift_times(event, spect, chrom, ds, ms_ds, chrom_ds):
         move = +1
     else:
         return
-    if not np.array_equal(chrom_ds['timesarg'], []):
-        x_min, x_max = chrom_ds['t_start'], chrom_ds['t_end']
-        alltimes = np.concatenate([subset['chrom_dat'][0] for subset in ds])
+    if not np.array_equal(augCanvas.chrom['timesarg'], []):
+        x_min, x_max = augCanvas.chrom['t_start'], augCanvas.chrom['t_end']
+        alltimes = np.concatenate([subset['chrom_dat'][0] for subset
+                                   in augCanvas.ds])
         times = dt.argsubselect(alltimes, x_min, x_max) + move
         goodtimes = np.where((times < len(alltimes)) & ~(times <0))[0]
         if not np.array_equal(goodtimes, []):
             x_min, x_max = alltimes[times[goodtimes[[0,-1]]]]
-            pick_times(x_min, x_max, spect, ds, chrom, ms_ds, chrom_ds)
+            pick_times(x_min, x_max, augCanvas)
 
 
 def autozoomy(ms_spec):