Merge pull request #38 from michaelmarty/v3

Version 4.1.2

datacollector.py

@@ -670,7 +670,7 @@ def on_save(self, e):
         dlg = wx.FileDialog(self, "Save Collection in JSON Format", self.directory, self.savename, "*.json")
         if dlg.ShowModal() == wx.ID_OK:
             self.savename = dlg.GetPath()
-            with open(self.savename, "w") as outfile:
+            with open(self.savename, "w+") as outfile:
                 json.dump(outdict, outfile)
             print("Saved: ", self.savename)
         dlg.Destroy()

metaunidec/gui_elements/ud_menu_meta.py

@@ -221,6 +221,8 @@ def __init__(self, parent, config, pres):
         self.experimentalmenu.AppendSeparator()
         self.menulinreg = self.experimentalmenu.Append(wx.ID_ANY, "Linear Regression")
         self.parent.Bind(wx.EVT_MENU, self.pres.on_linreg, self.menulinreg)
+        self.menusubdiv = self.experimentalmenu.Append(wx.ID_ANY, "Subtract and Divide")
+        self.parent.Bind(wx.EVT_MENU, self.pres.sub_div, self.menusubdiv)
         #self.menuAdditionalParameters = self.experimentalmenu.Append(wx.ID_ANY, "Additional Parameters",
         #                                                             "Adjust some experimental parameters")
         # self.parent.Bind(wx.EVT_MENU, self.pres.on_additional_parameters, self.menuAdditionalParameters)

metaunidec/mudeng.py

@@ -162,7 +162,7 @@ def export_spectra(self, e=None):
             outfile = self.config.outfname + "_" + str(s.var1) + ".txt"
             np.savetxt(outfile, s.rawdata)
             print(outfile)
-            self.config.config_export(self.config.outfname + "_config.dat")
+            self.config.config_export(self.config.outfname + "_conf.dat")
 
     def batch_set_config(self, paths):
         for p in paths:

metaunidec/ultrameta.py

@@ -361,7 +361,7 @@ def on_save(self, e):
         dlg = wx.FileDialog(self, "Save Collection in JSON Format", self.directory, self.savename, "*.json", wx.FD_SAVE)
         if dlg.ShowModal() == wx.ID_OK:
             self.savename = dlg.GetPath()
-            with open(self.savename, "w") as outfile:
+            with open(self.savename, "w+") as outfile:
                 json.dump(outdict, outfile)
             print("Saved: ", self.savename)
         dlg.Destroy()
@@ -461,7 +461,7 @@ def run_hdf5(self, path):
             print("Error3: File Not Found:", path)
             return
         out = mudeng.metaunidec_call(self.config, "-ultraextract", path=path)
-        if out is not 0:
+        if out != 0:
             self.SetStatusText("ERROR with File: " + path, number=2)
             print("ERROR C: File", path, out)
 

readme.md

@@ -194,6 +194,16 @@ The main GUI class is GUniDec.UniDecApp.
 
 ## Change Log
 
+v.4.1.2
+
+**Added button in UniDec to turn off data normalization.** Note: the beta values will be automatically scaled to match this. 
+
+Renamed the parameter ZScore in the UniScore calculation to CSScore. Added R squared to the UniScore calculation.
+
+Added several experimental subtract and divide features. Tweaks to linear regression experimental feature. 
+
+Bug fixes and compatibility updates.
+
 v.4.1.1
 
 Added right click feature to color peaks by their scores.

unidec.py

@@ -310,7 +310,7 @@ def run_unidec(self, silent=False, efficiency=False):
         if out == 0:
             self.unidec_imports(efficiency)
             if not silent:
-                print("File Name: ", self.config.filename, "R Sqaured: ", self.config.error)
+                print("File Name: ", self.config.filename, "R Squared: ", self.config.error)
             return out
         else:
             print("UniDec Run Error:", out)
@@ -1177,7 +1177,7 @@ def pks_mscore(self, xfwhm=2, pow=2):
             # print("Peak Mass:", p.mass, "Peak Shape Score", avg, p.mscore)
             p.mscore = avg
 
-    def pks_zscore(self, xfwhm=2):
+    def pks_csscore(self, xfwhm=2):
         try:
             if len(self.pks.peaks[0].zstack) < 1:
                 self.get_zstack(xfwhm=xfwhm)
@@ -1219,8 +1219,8 @@ def pks_zscore(self, xfwhm=2):
                 else:
                     badarea += val - low
 
-            p.z_score = 1 - ud.safedivide1(badarea, zs)
-            # print(badarea, zs, p.z_score)
+            p.cs_score = 1 - ud.safedivide1(badarea, zs)
+            # print(badarea, zs, p.cs_score)
 
     def get_mzstack(self, xfwhm=2):
         zarr = np.reshape(self.data.mzgrid[:, 2], (len(self.data.data2), len(self.data.ztab)))
@@ -1344,6 +1344,15 @@ def pks_fscore(self):
                     fscore2 = self.score_minimum(height, umin)
                     # print("Fscore5", fscore2, umin, height)
                     p.fscore *= fscore2
+    '''
+    def tscore(self):
+        try:
+            tscore = 1 - np.sum(np.abs(self.data.fitdat - self.data.data2[:, 1])) / np.sum(self.data.data2[:, 1])
+        except Exception as e:
+            print("Error in Tscore: ", e)
+            tscore = 0
+        self.data.tscore = tscore
+        return tscore'''
 
     def dscore(self, xfwhm=2, pow=2):
         """
@@ -1362,27 +1371,32 @@ def dscore(self, xfwhm=2, pow=2):
 
         self.pks_mscore(xfwhm=xfwhm, pow=pow)
         self.pks_uscore(pow=pow, xfwhm=xfwhm)
-        self.pks_zscore(xfwhm=xfwhm)
+        self.pks_csscore(xfwhm=xfwhm)
         self.pks_fscore()
+        #self.tscore()
         tscores = []
         ints = []
         for p in self.pks.peaks:
-            scores = np.array([p.mscore, p.uscore, p.z_score, p.fscore])  # p.rsquared,
+            scores = np.array([p.mscore, p.uscore, p.fscore, p.cs_score])  # p.rsquared,
             p.dscore = np.product(scores)
+            p.lscore = np.product(scores[:-1])
             tscores.append(p.dscore)
             ints.append(p.height)
             print("Mass:", p.mass,
                   "Peak Shape:", round(p.mscore * 100, 2),
                   "Uniqueness:", round(p.uscore * 100, 2),
                   # "Fitting R^2", round(p.rsquared * 100, 2),
-                  "Charge:", round(p.z_score * 100, 2),
+                  "Charge:", round(p.cs_score * 100, 2),
                   "FWHM:", round(p.fscore * 100, 2),
                   "Combined:", round(p.dscore * 100, 2))
             # print(p.intervalFWHM)
         ints = np.array(ints)
-        self.pks.uniscore = ud.weighted_avg(tscores, ints ** pow)
+        self.pks.uniscore = ud.weighted_avg(tscores, ints ** pow) * self.config.error
+        print("R Squared:", self.config.error)
+        #print("TScore:", self.data.tscore)
         print("Average Peaks Score (UniScore):", self.pks.uniscore)
 
+
     def filter_peaks(self, minscore=0.4):
         # w = deepcopy(self.config.peakwindow)
         # t = deepcopy(self.config.peakthresh)

unidec_bin/Example Data/ADH_unidecfiles/ADH_conf.dat

@@ -45,6 +45,7 @@ spectracmap rainbow
 publicationmode 1
 isotopemode 0
 peaknorm 1
+datanorm 1
 baselineflag 1.0
 orbimode 0
 integratelb -1000.0

unidec_bin/Example Data/BSA_unidecfiles/BSA_conf.dat

@@ -23,8 +23,8 @@ subbuff 0.0
 subtype 2
 smooth 0.0
 mzbins 0.0
-peakwindow 50.0
-peakthresh 0.025
+peakwindow 500.0
+peakthresh 0.01
 peakplotthresh 0.1
 plotsep 0.025
 intthresh 0.0
@@ -45,6 +45,7 @@ spectracmap rainbow
 publicationmode 1
 isotopemode 0
 peaknorm 1
+datanorm 1
 baselineflag 1.0
 orbimode 0
 integratelb -1000.0

unidec_bin/Example Data/GroEL UniDec_unidecfiles/GroEL UniDec_conf.dat

@@ -20,7 +20,7 @@ mtabsig 0.0
 minmz 10079.027219759617
 maxmz 13777.256263028847
 subbuff 0.0
-subtype 0
+subtype 2
 smooth 0.0
 mzbins 0.0
 peakwindow 50000.0
@@ -45,6 +45,7 @@ spectracmap rainbow
 publicationmode 1
 isotopemode 0
 peaknorm 1
+datanorm 1
 baselineflag 1.0
 orbimode 0
 integratelb -1000.0

unidec_bin/Example Data/POPC_Nanodiscs_unidecfiles/POPC_Nanodiscs_conf.dat

@@ -15,7 +15,7 @@ massub 160000.0
 masslb 80000.0
 msig 1.0
 molig 760.0
-massbins 10.0
+massbins 1.0
 mtabsig 0.0
 minmz 8761.430704083608
 maxmz 12864.965623887581

unidec_modules/gui_elements/ud_controls.py

@@ -191,6 +191,8 @@ def __init__(self, parent, config, pres, panel, iconfile):
         gbox1b.Add(wx.StaticText(panel1b, label="Intensity Threshold: "), (i, 0), flag=wx.ALIGN_CENTER_VERTICAL)
         i += 1
 
+
+
         self.ctladductmass = wx.TextCtrl(panel1b, value='', size=size1)
         gbox1b.Add(self.ctladductmass, (i, 1), span=(1, 1))
         gbox1b.Add(wx.StaticText(panel1b, label="Adduct Mass (Da): "), (i, 0), flag=wx.ALIGN_CENTER_VERTICAL)
@@ -202,16 +204,27 @@ def __init__(self, parent, config, pres, panel, iconfile):
         i += 1
 
         if self.config.imflag == 0:
+
+
             self.ctldatareductionpercent = wx.TextCtrl(panel1b, value="", size=size1)
             gbox1b.Add(self.ctldatareductionpercent, (i, 1), span=(1, 1))
             gbox1b.Add(wx.StaticText(panel1b, label="Data Reduction (%): "), (i, 0), flag=wx.ALIGN_CENTER_VERTICAL)
             i += 1
+
+            self.ctldatanorm = wx.CheckBox(panel1b, label="Normalize Data")
+            self.ctldatanorm.SetValue(True)
+            gbox1b.Add(self.ctldatanorm, (i, 0), span=(1, 2))
+            i += 1
+
             self.ctlbintype = wx.Choice(panel1b, -1, size=(240, 50),
                                         choices=["Linear m/z (Constant " + '\N{GREEK CAPITAL LETTER DELTA}' + "m/z)",
                                                  "Linear resolution (Constant (m/z)/(" + '\N{GREEK CAPITAL LETTER DELTA}' + "m/z))",
                                                  "Nonlinear", "Linear Interpolated", "Linear Resolution Interpolated"])
             gbox1b.Add(self.ctlbintype, (i, 0), span=(1, 2))
             i += 1
+
+
+
         else:
             self.ctlconvertflag = wx.CheckBox(panel1b, label="Compress when converting to .txt")
             self.ctlconvertflag.SetValue(True)
@@ -697,6 +710,7 @@ def import_config_to_gui(self):
                 self.ctlmanualassign.SetValue(self.config.manualfileflag)
                 self.ctlisotopemode.SetSelection(self.config.isotopemode)
                 self.ctlorbimode.SetValue(self.config.orbimode)
+                self.ctldatanorm.SetValue(self.config.datanorm)
                 self.ctlbintype.SetSelection(int(self.config.linflag))
                 self.ctlpsig.SetValue(str(self.config.psig))
                 self.ctlbeta.SetValue(str(self.config.beta))
@@ -827,6 +841,7 @@ def export_gui_to_config(self, e=None):
             self.config.reductionpercent = ud.string_to_value(self.ctldatareductionpercent.GetValue())
             self.config.isotopemode = int(self.ctlisotopemode.GetSelection())
             self.config.orbimode = int(self.ctlorbimode.GetValue())
+            self.config.datanorm = int(self.ctldatanorm.GetValue())
             self.config.psig = ud.string_to_value(self.ctlpsig.GetValue())
             self.config.beta = ud.string_to_value(self.ctlbeta.GetValue())
             self.config.manualfileflag = int(self.ctlmanualassign.GetValue())
@@ -957,6 +972,7 @@ def setup_tool_tips(self):
         self.ctlminnativez.SetToolTip(wx.ToolTip("Minimum offset from a native charge state"))
         self.ctlmaxnativez.SetToolTip(wx.ToolTip("Maximum offset from a native charge state"))
         if self.config.imflag == 0:
+            self.ctldatanorm.SetToolTip(wx.ToolTip("Normalize Data and Results"))
             self.ctldatareductionpercent.SetToolTip(
                 wx.ToolTip(
                     "Reduces the amount of data by removing everything below a threshold.\nSets the threshold to fit the percentage of data to remove."))

unidec_modules/gui_elements/ud_menu.py

@@ -244,6 +244,13 @@ def __init__(self, parent, config, pres, tabbed):
             self.experimentalmenu.AppendSeparator()
             self.menuAdditionalParameters = self.experimentalmenu.Append(wx.ID_ANY, "Additional Parameters",
                                                                          "Adjust some experimental parameters")
+
+            self.experimentalmenu.AppendSeparator()
+            self.menulinreg = self.experimentalmenu.Append(wx.ID_ANY, "Linear Regression")
+            self.parent.Bind(wx.EVT_MENU, self.pres.on_linreg, self.menulinreg)
+            self.menusubdiv = self.experimentalmenu.Append(wx.ID_ANY, "Subtract and Divide")
+            self.parent.Bind(wx.EVT_MENU, self.pres.sub_div, self.menusubdiv)
+
             self.experimentalmenu.AppendSeparator()
 
             self.menuscore1 = self.experimentalmenu.Append(wx.ID_ANY, "Show Peak Scores", "Show Peak Scores")
@@ -325,9 +332,7 @@ def __init__(self, parent, config, pres, tabbed):
         self.menutheomass = self.experimentalmenu.Append(wx.ID_ANY, "Plot Theoretical Mass")
         self.parent.Bind(wx.EVT_MENU, self.pres.plot_theo_mass, self.menutheomass)
 
-        self.experimentalmenu.AppendSeparator()
-        self.menulinreg = self.experimentalmenu.Append(wx.ID_ANY, "Linear Regression")
-        self.parent.Bind(wx.EVT_MENU, self.pres.on_linreg, self.menulinreg)
+
 
         # self.menucentroid = self.experimentalmenu.Append(wx.ID_ANY, "Get Centroid at FWHM")
         # self.parent.Bind(wx.EVT_MENU, self.pres.on_centroid, self.menucentroid)

unidec_modules/isolated_packages/score_window.py

@@ -19,7 +19,7 @@ def scr(score):
 
 
 def scr2(p):
-    scores = [p.dscore, p.uscore, p.mscore, p.z_score, p.fscore]
+    scores = [p.dscore, p.uscore, p.mscore, p.cs_score, p.fscore]
     strings = [scr(s) for s in scores]
     out = ""
     for s in strings:
@@ -40,7 +40,7 @@ def score_plots(eng):
         plt.figure()
         plt.subplot(131)
         plt.title(
-            "Combined Score: " + str(round(p.dscore * 100, 2)) + "\nCharge Score: " + str(round(p.z_score * 100, 2))
+            "Combined Score: " + str(round(p.dscore * 100, 2)) + "\nCharge Score: " + str(round(p.cs_score * 100, 2))
         )
         plt.plot(ztab, sumz)
         plt.plot(p.zdist[:, 0], p.zdist[:, 1], color="k")
@@ -147,7 +147,7 @@ def populate(self, pks):
         l = len(pks.peaks)
 
         collabels = ["Mass", "Intensity", "DScore", "Uniqueness/Fit", "Peak Shape",
-                     "Charge Dist.", "FWHM Penalties"]
+                     "Charge Dist.", "FWHM Penalties", "Limited Score (DScore without CSScore)"]
 
         cl = len(collabels)
         self.CreateGrid(l + 1, cl)
@@ -168,7 +168,7 @@ def populate(self, pks):
             self.SetCellFont(i, 0, wx.Font(10, wx.FONTFAMILY_DEFAULT, wx.FONTSTYLE_NORMAL, wx.FONTWEIGHT_BOLD))
             self.SetCellValue(i, 1, str(p.height))
 
-            scores = [p.dscore, p.uscore, p.mscore, p.z_score, p.fscore]
+            scores = [p.dscore, p.uscore, p.mscore, p.cs_score, p.fscore, p.lscore]
             scores = deepcopy(scores)
             cindex = 2
             for s in scores:

unidec_modules/isolated_packages/texmaker.py

@@ -21,7 +21,7 @@ def MakeTexReport(fname, config, path, peaks, labels, names, color, figureflags)
                                   ['$\\bigcirc$', '$\\bigtriangledown$', '$\\bigtriangleup$', '$\\triangleright$',
                                    '$\\square$', '$\\lozenge$', '$\\bigstar$']]))
 
-    f = open(fname, 'w')
+    f = open(fname, 'w+')
     f.write("\\documentclass{article}\n")
     f.write("\\usepackage{graphicx}\n")
     f.write("\\usepackage{amsmath}\n")

unidec_modules/peakstructure.py

@@ -62,17 +62,18 @@ def __init__(self):
         self.mzstack = []
         self.mscore = 0
         self.uscore = 0
-        self.z_score = 0
+        self.cs_score = 0
         self.rsquared = 0
         self.fscore = 0
         self.dscore = 0
+        self.lscore = 0
         self.mdist = None
         self.zdist = None
 
     def line_out(self, type="Full"):
         if type == "Full":
             outputs = [self.mass, self.centroid, self.height, self.area, self.textmarker, self.match, self.matcherror,
-                       self.integral, self.diff, self.avgcharge, self.dscore]
+                       self.integral, self.diff, self.avgcharge, self.dscore, self.lscore]
         elif type == "Basic":
             outputs = [self.mass, self.height, self.integral]
         else:

unidec_modules/tims_import_wizard/data_importer.py

@@ -92,7 +92,7 @@ def auto_from_wizard(lines, exedir):
             for index in mapper:
                 if l[index] == "None":
                     l[index] = None
-                if mapper[index] is not '':
+                if mapper[index] != '':
                     try:
                         parse[conv[mapper[index]]] = l[index]
                     except Exception as e:
@@ -201,7 +201,7 @@ def MakeUniDecConfig(job_kwargs):
     else:
         twaveflag = 1
 
-    f = open(filename, 'w')
+    f = open(filename, 'w+')
     f.write("twaveflag " + str(twaveflag) + "\n")
     f.write("mzbins " + str(job_kwargs[tt.BIN]) + "\n")
     if job_kwargs[tt.PUSHER] is not None:
@@ -412,7 +412,7 @@ def parse_file(file_path, exp_type='linear', collision=None, debug=False, dir=No
 
             out[tt.DRIFT_V] = search_extern(file_path, 'Transfer Collision Energy')
 
-        if out[tt.TYPE] is not 'ms':
+        if out[tt.TYPE] != 'ms':
             # try to grab the pusher frequency from the stat code
             # pusher = get_stat_code(file_path, 76, dir=exedir)
             pusher = get_stat_name(file_path, "Transport RF")