Merge pull request #31 from michaelmarty/v3

Update to v.3.2. Build now with Python 3.7. Added logo to main screen…
michaelmarty · Mar 11, 2019 · faf0d40 · faf0d40
2 parents e0c13a7 + eaa3a11
commit faf0d40
Show file tree

Hide file tree

Showing 8 changed files with 43 additions and 7 deletions.
diff --git a/GUniDec.spec b/GUniDec.spec
@@ -104,6 +104,7 @@ a.datas += [('mass_table.csv', 'unidec_bin\\mass_table.csv', 'DATA')]
 a.datas += [('metaunidec/images/allButton.png', 'metaunidec\\images\\allButton.png', 'DATA')]
 a.datas += [('metaunidec/images/peakRightClick.png', 'metaunidec\\images\\peakRightClick.png', 'DATA')]
 a.datas += [('metaunidec/images/rightClick.png', 'metaunidec\\images\\rightClick.png', 'DATA')]
+a.datas += [('UniDecLogoMR.png', 'UniDecLogoMR.png', 'DATA')]
 
 
 a.datas.extend(dir_files(os.path.join(os.path.dirname(pymzml.__file__), 'obo'), 'obo'))

diff --git a/Launcher.py b/Launcher.py
@@ -14,7 +14,7 @@
 from metaunidec.ultrameta import DataCollector as UMDC
 import wx.py as py
 import sys
-
+import os
 
 class UniDecLauncher(UniDecPres):
     """
@@ -58,13 +58,27 @@ def __init__(self, parent):
         button6 = wx.Button(panel, -1, "HDF5 Import Wizard\n\nImport Data into HDF5 for MetaUniDec")
         button7 = wx.Button(panel, -1, "UltraMeta Data Collector\n\nVisualize Multiple HDF5 Data Sets\nFit Trends")
 
+        html = wx.html.HtmlWindow(panel, -1, size=(330,260))
+        pathtofile = os.path.dirname(os.path.abspath(__file__))
+        self.imagepath = os.path.join(pathtofile, "UniDecLogoMR.png")
+        #print(self.imagepath)
+        html.SetPage(
+            "<html><body>"
+            #"<h1>UniDec</h1>"
+            "<img src=\"" + self.imagepath +"\" alt=\"PNG Icon\" height=\"200\" width=\"290\">"
+            "<p>Please Cite: Marty et al. Anal. Chem. 2015. " 
+            "DOI: 10.1021/acs.analchem.5b00140.</p>"
+            "</body></html>"
+        )
+
         sizer.Add(button1, (0, 0), flag=wx.EXPAND)
         sizer.Add(button2, (1, 0), flag=wx.EXPAND)
         sizer.Add(button3, (2, 0), flag=wx.EXPAND)
         sizer.Add(button4, (0, 1), flag=wx.EXPAND)
         sizer.Add(button6, (2, 1), flag=wx.EXPAND)
         sizer.Add(button7, (1, 1), flag=wx.EXPAND)
         sizer.Add(button5, (3, 0), span=(1, 2), flag=wx.EXPAND)
+        sizer.Add(html, (0, 2), span=(4, 2))
 
         self.Bind(wx.EVT_BUTTON, self.button1, button1)
         self.Bind(wx.EVT_BUTTON, self.button2, button2)

diff --git a/UniDecLogoMR.png b/UniDecLogoMR.png
diff --git a/readme.md b/readme.md
@@ -192,6 +192,16 @@ The main GUI class is GUniDec.UniDecApp.
 
 ## Change Log
 
+v.3.2
+
+Added a logo to the start screen.
+
+Update to the latest mzML specification.
+
+Build update to Python 3.7 and latest libraries.
+
+Bug fixes.
+
 v.3.1.1
 
 Expanded isotope mode to either output monoisotopic masses or average masses. 

diff --git a/unidec.py b/unidec.py
@@ -372,8 +372,11 @@ def pick_peaks(self):
         # Generate Intensities of Each Charge State for Each Peak
         mztab = ud.make_peaks_mztab(self.data.mzgrid, self.pks, self.config.adductmass)
         #Calculate errors for peaks with FWHM
-        ud.peaks_error_FWHM(self.pks, self.data.massdat)
-        ud.peaks_error_mean(self.pks, self.data.massgrid, self.data.ztab, self.data.massdat, self.config)
+        try:
+            ud.peaks_error_FWHM(self.pks, self.data.massdat)
+            ud.peaks_error_mean(self.pks, self.data.massgrid, self.data.ztab, self.data.massdat, self.config)
+        except Exception as e:
+            print("Error in error calculations:", e)
         if self.config.batchflag == 0:
             ud.make_peaks_mztab_spectrum(self.data.mzgrid, self.pks, self.data.data2, mztab)
             self.export_config()

diff --git a/unidec_modules/isolated_packages/ZoomBox.py b/unidec_modules/isolated_packages/ZoomBox.py
@@ -1,6 +1,6 @@
 from matplotlib.patches import Rectangle
 
-from pubsub import setupkwargs
+#from pubsub import setupkwargs
 from pubsub import pub
 
 import numpy as np

diff --git a/unidec_modules/unidec_enginebase.py b/unidec_modules/unidec_enginebase.py
@@ -14,7 +14,7 @@ def __init__(self):
 
         :return: None
         """
-        self.version = "3.1.1"
+        self.version = "3.2.0"
         print("\nUniDec Engine v." + self.version)
         self.config = None
         self.config_history = []

diff --git a/unidec_modules/unidectools.py b/unidec_modules/unidectools.py
@@ -2212,8 +2212,16 @@ def peaks_error_FWHM(pks, data):
                 else:
                     rightwidth += 1
             counter += 1
-        pk.errorFWHM = data[index + rightwidth, 0] - data[index - leftwidth, 0]
-        pk.intervalFWHM = [data[index - leftwidth, 0], data[index + rightwidth, 0]]
+
+        indexstart = index - leftwidth
+        indexend = index + rightwidth
+        if indexstart < 0:
+            indexstart = 0
+        if indexend >= len(data):
+            indexend = len(data) - 1
+
+        pk.errorFWHM = data[indexend, 0] - data[indexstart, 0]
+        pk.intervalFWHM = [data[indexstart, 0], data[indexend, 0]]
         start = pk.intervalFWHM[0]
         end = pk.intervalFWHM[1]
         pk.centroid = center_of_mass(data, start, end)[0]