Parameters change support - pt6

* drltools roughly fixed
* not tested!!

prasopes/drltools.py

@@ -44,41 +44,45 @@ def floatize(table, row, column, nonneg=True):
     return outfloat
 
 
-def get_massargs(pt, row, ds):
+def get_massargs(pt, row, subset):
     startm = floatize(pt, row, 1) - (floatize(pt, row, 2) / 2)
     endm = floatize(pt, row, 1) + (floatize(pt, row, 2) / 2)
-    massargs = dt.argsubselect(ds['masses'], startm, endm)
+    massargs = dt.argsubselect(subset['masses'], startm, endm)
     return massargs
 
 
 def update_profile(pt, row, dataset):
     """parent table profile spectrum updating procedure"""
-    # Dont do anything to graph when the spectrum is not populated
     logger.debug("updating parent table row {} profile".format(row))
-    if isinstance(dataset['masses'], type(None)):
+    # Dont do anything to graph when the spectrum is not populated
+    if len(dataset) == 0:
         return
-
     spectrum = pt.cellWidget(row, 3).figure.get_axes()[0]
-    masses = dataset['masses']
-    massargs = get_massargs(pt, row, dataset)
-    yshape = np.mean(dataset['matrix'], axis=0)
     spectrum.clear()
-    spectrum.plot(masses, yshape, ':', color='gray')
-    spectrum.plot(masses[massargs], yshape[massargs], 'r')
-    xex = max((masses[massargs[-1]]-masses[massargs[0]])*0.25, 0.20)
-    spectrum.set_xlim(masses[massargs[0]]-xex,
-                      masses[massargs[-1]]+xex)
-    ymax = max(yshape[massargs])
+    limits = []
+    for i,subset in enumerate(dataset):
+        masses = subset['masses']
+        massargs = get_massargs(pt, row, subset)
+        yshape = np.mean(subset['matrix'], axis=0)
+        spectrum.plot(masses, yshape, ':', color='gray')
+        spectrum.plot(masses[massargs], yshape[massargs], color=
+                gt.colors[i % len(gt.colors)]/255)
+        limits.append((masses[massargs[[0,-1]]],max(yshape[massargs])))
+    widest = np.argmax([abs(lim[0][1]-lim[0][0]) for lim in limits])
+    xmin, xmax = limits[widest][0]
+    xex = max((xmax-xmin)*0.25,0.20)
+    spectrum.set_xlim(xmin-xex, xmax+xex)
+    ymax = max([lim[1] for lim in limits])
     spectrum.set_ylim(ymax*-0.1, ymax*1.2)
     spectrum.figure.canvas.draw()
 
 
 def get_intensity(row, ds, drls):
-    massargs = get_massargs(drls['pt'], row, ds)
     #prevent division by 0
-    intensity = np.divide(np.sum( ds['matrix'].T[massargs].T, axis=1),
-            np.clip(ds['chrom_dat'][1], np.nextafter(
-                0, 1, dtype=np.float32), None))
+    intensity = np.concatenate([np.divide(np.sum(subset['matrix'].T[
+        get_massargs(drls['pt'],row,subset)].T, axis=1),
+        np.clip(subset['chrom_dat'][1], np.finfo(np.float32).eps, None))
+        for subset in ds])
     return intensity
 
 
@@ -86,7 +90,7 @@ def get_daughterset(ds, drls):
     """Fuction to acquire the curves of the daugher ions"""
     logger.info("getting set of the daughter ions")
     names = []
-    times = ds['chrom_dat'][0, :] - drls['tshift'].value()
+    times = np.concatenate([sub['chrom_dat'][0, :] - drls['tshift'].value() for sub in ds])
     intensities = []
     for row in range(drls['dt'].rowCount()):
         if drls['dt'].cellWidget(row, 0).checkState() == 2:
@@ -104,14 +108,13 @@ def get_daughterset(ds, drls):
             cortext = " + ".join(corlist)
             intensities.append(intensity)
             names.append("{} - ({})".format(
-                drls['dt'].item(row, 0).text(),
-                cortext))
+                drls['dt'].item(row, 0).text(), cortext))
     return names, times, intensities
 
 
 def get_parentset(ds, drls):
     names = []
-    times = ds['chrom_dat'][0, :]
+    times = np.concatenate([sub['chrom_dat'][0, :] for sub in ds])
     intensities = []
     rowlist = []
     for row in range(drls['dt'].rowCount()):
@@ -134,12 +137,12 @@ def update_drlspectrum(ds, drls, drlspectrum):
     """Generic DRL spectrum updating procedure"""
     logger.info("updating DRL spectrum")
     # Do not do anything when the data set is not populated.
-    if isinstance(ds['masses'], type(None)):
+    if len(ds) == 0:
         return
 
     names, times, intensities = get_daughterset(ds, drls)
     drlspectrum.clear()
-    gt.pop_plot(drlspectrum, drls['graphlabels'])
+    gt.pop_plot(0, 0, drlspectrum, drls['graphlabels'])
     drlspectrum.axvline(0, 0, 0.9, color="#FF000088", linestyle=":")
 
     if drls['cutoff'].value() != 0:
@@ -158,8 +161,8 @@ def update_drlspectrum(ds, drls, drlspectrum):
             if drls['rel'].checkState() == 2:
                 #Do not divide by 0
                 intensity = np.divide(intensity, np.clip(np.sum(
-                    intensities, 0), np.nextafter(
-                        0, 1, dtype=np.float32), None), dtype=np.float64)
+                    intensities, 0), np.finfo(np.float32).eps, None),
+                    dtype=np.float64)
             drlspectrum.plot(times, intensity, label=label,
                              color=(gt.colors[row % len(gt.colors)] / 255))
             i += 1
@@ -661,8 +664,7 @@ def main_window(parent, ds, filename, cache, update_signal):
         drls['checkAll'] = QtWidgets.QCheckBox("Select all")
         drls['cors'] = QtWidgets.QSpinBox(minimum=0)
         drls['cors'].setValue(3)
-        drls['graphlabels'] = dict(x=[0], y=[0], line=None, name="",
-                                   xlabel="time(min)",
+        drls['graphlabels'] = dict(line=None, name="", xlabel="time(min)",
                                    ylabel="relative intensity")
 
         dial_graph = Figure(figsize=(5, 2), dpi=100, facecolor="None")
@@ -672,7 +674,7 @@ def main_window(parent, ds, filename, cache, update_signal):
         graph_canvas.setAutoFillBackground(False)
         gt.pan_factory(chromplot)
         gt.zoom_factory(chromplot, 1.15)
-        gt.pop_plot(chromplot, drls['graphlabels'])
+        gt.pop_plot(0, 0, chromplot, drls['graphlabels'])
 
         dcolums = ["Name"]
         for i in range(drls['cors'].value()):

prasopes/imagetools.py

@@ -24,7 +24,7 @@ def paint_image(mass_spec, spect, painttarget=None):
     printplot.set_xlim(spect.get_xlim())
     printplot.set_ylim(spect.get_ylim())
     data = [line.get_data() for line in spect.lines]
-    [gt.pop_plot(*line, printplot, mass_spec) for line in data]
+    [gt.pop_plot(*line, printplot, mass_spec, i) for i,line in enumerate(data)]
     printplot.locator_params(nbins=xtics, axis='x')
     cache_file = BytesIO()
     paintfig.savefig(cache_file)