Merge pull request #34 from michaelmarty/v3

V3

.gitignore

@@ -128,5 +128,7 @@ unidec_bin/Example Data/POPC_Nanodiscs_unidecfiles/POPC_Nanodiscs_Total_2D_Mass_
 unidec_bin/Example Data/BSA_unidecfiles/BSA_chargedata.dat
 unidec_bin/Example Data/BSA_unidecfiles/BSA_chargedata_areas.dat
 unidec_bin/Example Data/BSA_unidecfiles/BSA_peakparam.dat
+ /__pycache__/
+unidec_bin/Example Data/GroEL HCD UniDec_unidecfiles/GroEL HCD UniDec_peak_areas.dat
 
 

GUniDec.py

@@ -13,7 +13,7 @@
 import unidec_modules.IM_functions as IM_func
 from unidec_modules import Extract2D, peakwidthtools, masstools, miscwindows, \
     MassDefects, mainwindow, nativez, ManualSelectionWindow, AutocorrWindow, fft_window, GridDecon, isotopetools
-from unidec_modules.isolated_packages import FileDialogs, texmaker
+from unidec_modules.isolated_packages import FileDialogs, texmaker, score_window
 import datacollector
 import import_wizard
 import unidec_modules.IM_windows as IM_wind
@@ -126,6 +126,8 @@ def on_open_file(self, filename, directory, skipengine=False, **kwargs):
         :param skipengine: Boolean, Whether to skip running the engine (used when loading state)
         :return: None
         """
+        # tstart =time.perf_counter()
+
         # Clear other plots and panels
         self.view.peakpanel.clear_list()
         self.view.clear_all_plots()
@@ -145,6 +147,7 @@ def on_open_file(self, filename, directory, skipengine=False, **kwargs):
         if self.eng.config.batchflag != 1:
             self.view.controls.ctlminmz.SetValue(str(np.amin(self.eng.data.data2[:, 0])))
             self.view.controls.ctlmaxmz.SetValue(str(np.amax(self.eng.data.data2[:, 0])))
+
         # Plot 1D
         if self.eng.config.batchflag == 0:
             self.view.plot1.plotrefreshtop(self.eng.data.data2[:, 0], self.eng.data.data2[:, 1], "Data", "m/z",
@@ -156,17 +159,20 @@ def on_open_file(self, filename, directory, skipengine=False, **kwargs):
             if self.eng.config.batchflag == 0:
                 self.view.plot1im.contourplot(self.eng.data.rawdata3, self.eng.config, xlab="m/z (Th)",
                                               ylab="Arrival Time (ms)", title="IM-MS Data")
+        #tstart = time.perf_counter()
         # Load Config to GUI
         self.import_config()
         self.view.SetStatusText("Ready", number=5)
-
+        #print("ImportConfig: %.2gs" % (time.perf_counter() - tstart))
         if False:
             try:
-                self.eng.unidec_imports(everything=True)
+                self.eng.unidec_imports(everything=False)
                 self.after_unidec_run()
             except:
                 pass
 
+        #print("ImportData: %.2gs" % (time.perf_counter() - tstart))
+
     def on_save_state(self, e=None, filenew=None):
         """
         Saves the state by running self.eng.save_state. If no file is specified, opens a file dialog.
@@ -301,7 +307,7 @@ def on_paste_spectrum(self, e=None):
                 os.chdir(newdir)
                 np.savetxt(fname, data)
                 print("Saved Pasted Spectrum as File:", fname, " in directory:", newdir)
-                self.on_open_file(fname, newdir)
+                self.on_open_file(fname, newdir, pasted=True)
             else:
                 print("Paste failed, got: ", data)
         except Exception as e:
@@ -324,6 +330,7 @@ def on_dataprep_button(self, e=None):
         self.view.SetStatusText("Data Prep", number=5)
         self.export_config(self.eng.config.confname)
         self.eng.process_data()
+        self.eng.get_auto_peak_width(set=False)
         self.import_config()
         self.view.clear_all_plots()
         self.view.plot1.plotrefreshtop(self.eng.data.data2[:, 0], self.eng.data.data2[:, 1], "Data Sent to UniDec",
@@ -343,7 +350,7 @@ def on_dataprep_button(self, e=None):
         self.view.SetStatusText("R\u00B2 ", number=3)
         self.view.SetStatusText("Data Prep Done", number=5)
         tend = time.perf_counter()
-        # print "Data Prep Done. Time: %.2gs" % (tend - tstart)
+        print("Data Prep Done. Time: %.2gs" % (tend - tstart))
         pass
 
     def on_unidec_button(self, e=None):
@@ -491,6 +498,7 @@ def makeplot1(self, e=None):
                                            "m/z (Th)", "Normalized Intensity", "Data", self.eng.config, nopaint=True)
             try:
                 self.view.plot1.plotadd(self.eng.data.data2[:, 0], self.eng.data.fitdat, 'red', "Fit Data")
+                pass
             except:
                 pass
             if self.eng.config.aggressiveflag != 0 and len(self.eng.data.baseline) == len(self.eng.data.fitdat):
@@ -1658,6 +1666,9 @@ def on_score2(self, e=0):
         self.on_score_window()
 
     def on_score_window(self, e=0):
+        self.on_score()
+        sw = score_window.ScoreFrame(self.view)
+        sw.populate(self.eng.pks)
         pass
 
     # def on_remove_noise_points(self, e=0):

metaunidec/gui_elements/list_ctrls.py

@@ -16,10 +16,11 @@
 
 
 class YValueListCtrl(wx.ListCtrl, listmix.ListCtrlAutoWidthMixin, listmix.TextEditMixin):
-    def __init__(self, parent, id_value, pos=wx.DefaultPosition, size=wx.DefaultSize, style=0):
+    def __init__(self, parent, id_value, config=None, pos=wx.DefaultPosition, size=wx.DefaultSize, style=0):
         wx.ListCtrl.__init__(self, parent, id_value, pos, size, style)
         listmix.ListCtrlAutoWidthMixin.__init__(self)
         listmix.TextEditMixin.__init__(self)
+        self.config = config
         self.InsertColumn(0, "Index")
         self.InsertColumn(1, "Variable 1")
         self.InsertColumn(2, "Variable 2")
@@ -28,10 +29,16 @@ def __init__(self, parent, id_value, pos=wx.DefaultPosition, size=wx.DefaultSize
         self.SetColumnWidth(1, width=75)
         self.SetColumnWidth(2, width=75)
         self.SetColumnWidth(3, width=75)
+        self.freeze_reorder = False
+        self.parent = parent
 
     def populate(self, dataset, colors=None):
         self.DeleteAllItems()
-        colormap = cm.get_cmap('rainbow', dataset.len)
+        try:
+            colormap = cm.get_cmap(self.config.spectracmap, dataset.len)
+        except:
+            print("Failed to get spectra cmap", self.config)
+            colormap = cm.get_cmap('rainbow', dataset.len)
         peakcolors = colormap(np.arange(dataset.len))
         if colors is None:
             colors = peakcolors
@@ -69,9 +76,38 @@ def populate(self, dataset, colors=None):
         self.colors = colors
         self.rename_column(1, dataset.v1name)
         self.rename_column(2, dataset.v2name)
+        self.freeze_reorder = False
+
+    def recolor(self):
+        dataset = self.data
+        try:
+            colormap = cm.get_cmap(self.config.spectracmap, dataset.len)
+        except:
+            print("Failed to get spectra cmap", self.config)
+            colormap = cm.get_cmap('rainbow', dataset.len)
+        peakcolors = colormap(np.arange(dataset.len))
+        colors = peakcolors
+        for i in range(0, dataset.len):
+            s = dataset.spectra[i]
+            index = int(s.index)
+            # print(s.index, s.var1)
+            if colors is not None:
+                color = wx.Colour(int(round(colors[i][0] * 255)), int(round(colors[i][1] * 255)),
+                                  int(round(colors[i][2] * 255)), alpha=255)
+                self.SetItemBackgroundColour(index, col=color)
+
+                luminance = ud.get_luminance(color, type=2)
+                # print(wx.Colour(colout), luminance)
+                if luminance < luminance_cutoff:
+                    self.SetItemTextColour(index, col=white_text)
+                else:
+                    self.SetItemTextColour(index, col=black_text)
+                s.color = colors[i]
+        self.colors = colors
 
     def clear_list(self):
         self.DeleteAllItems()
+        self.freeze_reorder = False
 
     def add_line(self, var1="count", var2=0):
         if var1 == "count":
@@ -83,8 +119,8 @@ def add_line(self, var1="count", var2=0):
 
     def get_list(self):
         count = self.GetItemCount()
-        #colormap = cm.get_cmap('rainbow', count)
-        #peakcolors = colormap(np.arange(count))
+        # colormap = cm.get_cmap('rainbow', count)
+        # peakcolors = colormap(np.arange(count))
         peakcolors = self.get_colors()
         list_output = []
         for i in range(0, count):
@@ -105,11 +141,12 @@ def get_list(self):
             list_output.append(sublist)
 
         indexes = np.array([i[0] for i in list_output])
-        if np.any(indexes != np.arange(0, len(list_output))):
+        if np.any(indexes != np.arange(0, len(list_output))) and not self.freeze_reorder:
             list_output = self.reorder(list_output)
         return list_output
 
     def reorder(self, list):
+        print("Reordering...")
         newlist = []
         indexes = np.array([i[0] for i in list])
         sind = np.sort(indexes)
@@ -122,10 +159,12 @@ def reorder(self, list):
             newlist.append(list[index])
         self.data.spectra = newspectra
         self.repopulate()
+        self.parent.pres.eng.data.export_hdf5()
         return newlist
 
     def repopulate(self):
         self.populate(self.data, self.colors)
+        self.freeze_reorder = False
         pass
 
     def rename_column(self, num, text):
@@ -148,9 +187,10 @@ def __init__(self, parent, pres, size=(200, 400)):
         id_value = wx.ID_ANY
         self.selection = []
         self.pres = pres
+        self.config = self.pres.eng.config
         sizer = wx.BoxSizer(wx.VERTICAL)
 
-        self.list = YValueListCtrl(self, id_value, size=size, style=wx.LC_REPORT | wx.BORDER_NONE)
+        self.list = YValueListCtrl(self, id_value, config=self.config, size=size, style=wx.LC_REPORT | wx.BORDER_NONE)
 
         sizer.Add(self.list, 1, wx.EXPAND)
         self.SetSizer(sizer)
@@ -233,8 +273,13 @@ def on_popup_four(self, event):
             self.selection.append(item)
         for i in range(0, num):
             self.list.DeleteItem(self.selection[num - i - 1])
+        self.list.freeze_reorder = True
         self.pres.on_ignore(self.selection)
 
+        if self.list.GetItemCount() < 1:
+            print("Ignored everything; repopulating...")
+            self.on_popup_six()
+
     def on_popup_five(self, event):
         item = self.list.GetFirstSelected()
         num = self.list.GetSelectedItemCount()
@@ -247,9 +292,11 @@ def on_popup_five(self, event):
         for i in range(tot - 1, -1, -1):
             if not np.any(np.array(self.selection) == i):
                 self.list.DeleteItem(i)
+        self.list.freeze_reorder = True
         self.pres.on_isolate(self.selection)
 
-    def on_popup_six(self, event):
+    def on_popup_six(self, event=None):
+        self.list.get_list()
         self.list.repopulate()
         self.pres.on_repopulate()