TimsTof - big files support

* introduced sampling (to be refined!)

prasopes/datasets.py

@@ -134,6 +134,7 @@ class BrukerTimsDataset(Dataset):
     def get_chromatograms(self):
         keys = ('retention_time', 'intensity')
         times = self.dataset.retention_times / 60
+        #devNote - summing is fast, asarray is fast, iterating is slow.
         intensities = np.asarray([
             np.sum(i['intensity']) for i in self.dataset.query_iter(
             self.dataset.ms1_frames, columns=('intensity',))])
@@ -142,15 +143,20 @@ class BrukerTimsDataset(Dataset):
     def get_spectra(self, mint=None, maxt=None):
         mint = mint or self.mintime
         maxt = maxt or self.maxtime
-        massints = self.dataset.rt_query(mint*60, maxt*60,
-                                               columns=('mz', 'intensity'))
+        #TODO: set in config
+        frames = dt.argsubselect(self.dataset.retention_times,
+                                 mint*60, maxt*60) + 1
+        timescap = 500
+        framessel = frames if timescap >= len(frames) else np.linspace(
+                frames[0], frames[-1], timescap).astype('int')
+        massints = self.dataset.query(framessel, columns=('mz', 'intensity'))
         sortmasses = np.sort(massints['mz'])
         masssteps = sortmasses[1:] - sortmasses[:-1]
         binspos = np.where(masssteps > 0.001)[0]
         bins = sortmasses[:-1][binspos] + (masssteps[binspos]/2)
         binpos = np.digitize(massints['mz'], bins)
         masses = np.bincount(binpos, massints['mz']) / np.bincount(binpos)
-        ints = np.bincount(binpos, massints['intensity']) / self.dataset.max_frame
+        ints = np.bincount(binpos, massints['intensity']) / len(framessel)
         return [[masses, ints]]
 
     def get_peakchrom(self, startm, endm):

prasopes/graphtools.py

@@ -239,11 +239,11 @@ def plot_subtime(augCanvas):
 
     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)]
+            dots_x, dots_y = [augCanvas.ds.chromatograms[i][j][args]
+                              for j in (0,1)]
             augCanvas.chromplot.plot(dots_x, dots_y, '.', color=(
             colors[i % len(colors)]/255))