Support for timsTOF - pt2

* fixed selection of times
* fixed complex spectra
* odd/even support better (still not fixed completely)
* lost of things still broken

prasopes/datasets.py

@@ -23,6 +23,17 @@ class Dataset():
         self.timemin = -np.inf
         self.timemax = np.inf
 
+    def get_chromargs(self):
+        times = dt.argsubselect(np.concatenate(
+             [subset[0] for subset in self.chromatograms]),
+             self.timemin, self.timemax)
+        args = []
+        for subset in self.chromatograms:
+            goodtimes = np.where((times < len(subset[0])) & ~(times < 0))[0]
+            args.append(times[goodtimes])
+            times -= len(subset[0])
+        return args
+
     def refresh(self):
         """implement per-case"""
         return None
@@ -71,24 +82,22 @@ class ThermoRawDataset(Dataset):
         return chroms
 
     def get_spectra(self):
-        times = dt.argsubselect(np.concatenate(
-             [subset[0][0] for subset in self.dataset]),
-             self.timemin, self.timemax)
-        args = []
-        for subset in self.dataset:
-            goodtimes = np.where((times < len(subset[0][0]))
-                             & ~(times < 0))[0]
-            args.append(times[goodtimes])
-            times =- len(subset[0][0])
-            spectra = []
-            for i,subset in enumerate(self.dataset):
-                if cf.settings().value("view/oddeven", type=bool):
-                    for j in (0,1):
-                        yvalz = np.mean(subset[2][args[i][j::2]], axis=0)
+        args = self.get_chromargs()
+        spectra = []
+        for i,subset in enumerate(self.dataset):
+            if cf.settings().value("view/oddeven", type=bool):
+                for j in (0,1):
+                    if len(subset[2][args[i*2+j][j::2]]):
+                        yvalz = np.mean(subset[2][args[i*2+j][j::2]], axis=0)
                         spectra.append([subset[1], yvalz])
-                else:
+                    else:
+                        spectra.append([[],[]])
+            else:
+                if len(subset[2][args[i]]):
                     yvalz = np.mean(subset[2][args[i]], axis=0)
                     spectra.append([subset[1], yvalz])
+                else:
+                    spectra.append([[],[]])
         return spectra
 
 
@@ -109,8 +118,9 @@ class BrukerTimsDataset(Dataset):
     def get_chromatograms(self):
         keys = ('retention_time', 'intensity')
         times = self.dataset.retention_times / 60
-        intensities = [np.sum(i['intensity']) for i in self.dataset.query_iter(
-                       self.dataset.ms1_frames, columns=('intensity',))]
+        intensities = np.asarray([
+            np.sum(i['intensity']) for i in self.dataset.query_iter(
+            self.dataset.ms1_frames, columns=('intensity',))])
         return [[times,intensities]]
 
     def get_spectra(self):

prasopes/graphtools.py

@@ -238,44 +238,15 @@ def plot_subtime(augCanvas):
     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, 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, augCanvas.spectplot,
-                             augCanvas.ms, clr, legend)
-                    dots_x = subset['chrom_dat'][0, selection[j::2]]
-                    dots_y = subset['chrom_dat'][1, selection[j::2]]
-                    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, 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, augCanvas.spectplot,
-                         augCanvas.ms, i, legend)
-                dots_x = subset['chrom_dat'][0, selection]
-                dots_y = subset['chrom_dat'][1, selection]
-                augCanvas.chromplot.plot(dots_x, dots_y, '.', color=(
-                    colors[i % len(colors)]/255))
+    chromargs = augCanvas.ds.get_chromargs()
+    populate(augCanvas)
+    chromxy = augCanvas.ds.get_chromatograms()
+
+    for i, args in enumerate(chromargs):
+        if len(args):
+            dots_x, dots_y = [chromxy[i][j][args] for j in (0,1)]
+            augCanvas.chromplot.plot(dots_x, dots_y, '.', color=(
+            colors[i % len(colors)]/255))
 
     augCanvas.spectplot.set_xlim(slims[0])
     if not cf.settings().value("view/autozoomy", type=bool):
@@ -298,19 +269,7 @@ def pick_times(x_min, x_max, augCanvas):
     """subselect part of the chromatogram and plot it"""
     augCanvas.ds.timemin = x_min
     augCanvas.ds.timemax = x_max
-    populate(augCanvas)
-    """augCanvas.chrom['t_start'] = x_min
-    augCanvas.chrom['t_end'] = x_max
-    times = dt.argsubselect(np.concatenate(
-        [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]
-        augCanvas.chrom['timesarg'].append(times[goodtimes])
-        times = times - len(subset['chrom_dat'][0])
-    update_paramstable(augCanvas)
-    plot_subtime(augCanvas)"""
+    plot_subtime(augCanvas)
 
 
 def shift_times(event, augCanvas):
@@ -411,7 +370,6 @@ def ann_spec(ms_spec, msdata, ann_limit=0.01):
 def pop_plot(xdata, ydata, plot, plot_data, colornum=0, legend=None, annotate=True):
     """Define and populate plot"""
     if len(xdata):
-        print(colornum)
         plot.plot(xdata, ydata, linewidth=1, color=(
             colors[colornum % len(colors)]/255), label=legend)
     plot.set_title(plot_data['name'], loc="right")
@@ -501,24 +459,6 @@ def populate(augCanvas):
         pop_plot(msxy[i][0], msxy[i][1], augCanvas.spectplot, augCanvas.ms, i, legend)
         pop_plot(chromxy[i][0], chromxy[i][1], augCanvas.chromplot,
                 augCanvas.chrom, i, legend)
-        """if cf.settings().value("view/oddeven", type=bool):
-            msx = subset['masses']
-            for j in range(2):
-                msy = np.mean(subset['matrix'][j::2], axis=0)
-                chromx = subset['chrom_dat'][0, :][j::2]
-                chromy = subset['chrom_dat'][1, :][j::2]
-                pop_plot(msx, msy, augCanvas.spectplot, augCanvas.ms,
-                         i*2+j, legend)
-                pop_plot(chromx, chromy, augCanvas.chromplot,
-                         augCanvas.chrom, i*2+j, legend)
-        else:
-            msx = subset['masses']
-            msy = np.mean(subset['matrix'], axis=0)
-            chromx = subset['chrom_dat'][0, :]
-            chromy = subset['chrom_dat'][1, :]
-            pop_plot(msx, msy, augCanvas.spectplot, augCanvas.ms, i, legend)
-            pop_plot(chromx, chromy, augCanvas.chromplot, augCanvas.chrom,
-                     i, legend)"""
     for ax in (augCanvas.spectplot, augCanvas.chromplot):
         if not augCanvas.ms['headers'] == []:
             ax.legend(loc=2)