Merge pull request #45 from michaelmarty/v3

V3

.gitignore

@@ -135,7 +135,27 @@ __pycache__/
 unidec_bin/Example Data/ADH_unidecfiles/ADH_peak_areas.dat
 unidec_bin/Example Data/POPC_Nanodiscs_unidecfiles/POPC_Nanodiscs_1D_Mass_Defects.txt
 unidec_bin/Example Data/POPC_Nanodiscs_unidecfiles/POPC_Nanodiscs_2D_Mass_Defects.txt
-unidec_modules/thermo_reader/
+unidec_modules/thermo_reader/greparam.py
 unidec_bin/Presets/Marius/
-
+MANIFEST.in
+desktop.ini
+setup.py
+unidec_bin/Example Data/BSA_unidecfiles/BSA_Figure1.pdf
+unidec_bin/Example Data/BSA_unidecfiles/BSA_Figure2.pdf
+unidec_bin/Example Data/BSA_unidecfiles/BSA_Figure3.pdf
+unidec_bin/Example Data/BSA_unidecfiles/BSA_Figure4.pdf
+unidec_bin/Example Data/BSA_unidecfiles/BSA_Figure5.pdf
+unidec_bin/Example Data/BSA_unidecfiles/BSA_Figure6.pdf
+unidec_bin/Example Data/BSA_unidecfiles/BSA_manualfile.dat
+unidec_bin/Example Data/BSA_unidecfiles/BSA_report.aux
+unidec_bin/Example Data/BSA_unidecfiles/BSA_report.log
+unidec_bin/Example Data/BSA_unidecfiles/BSA_report.pdf
+unidec_bin/recent.txt
+unidec_bin/Example Data/BSA_unidecfiles/BSA_chargepeaks.txt
+unidec_bin/Example Data/POPC_Nanodiscs_unidecfiles/Extract_grid_2D_Extract.txt
+unidec_bin/Example Data/POPC_Nanodiscs_unidecfiles/Extract_total_2D_Extract.txt
+ExtractFull2D_Da.txt
+extracts.txt
+sums.txt
+unidec_bin/Example Data/POPC_Nanodiscs_unidecfiles/POPC_Nanodiscs_chargepeaks.txt
 

UniChrom.py

@@ -201,7 +201,11 @@ def on_unidec_run(self, e=None):
         savefile = self.export_mz_file()
         if self.udwin is None:
             self.udwin = GUniDec.UniDecApp()
-        self.udwin.on_open_file(savefile, self.eng.dirname)
+        try:
+            self.udwin.on_open_file(savefile, self.eng.dirname)
+        except:
+            self.udwin = GUniDec.UniDecApp()
+            self.udwin.on_open_file(savefile, self.eng.dirname)
         pass
 
     def export_mz_file(self, e=None, append=None, directory=None):

datacollector.py

@@ -8,12 +8,12 @@
 import matplotlib.cm as cm
 from matplotlib.pyplot import colormaps
 from matplotlib import rcParams
-
+from matplotlib.patches import Rectangle
 from pubsub import pub
 
 import multiprocessing
 from unidec_modules import UniFit, Extract2D, unidecstructure, PlotAnimations, plot1d, plot2d, miscwindows, \
-    MassDefects, nativez, IM_functions
+    MassDefects, nativez, IM_functions, DoubleDec
 from unidec_modules.PlottingWindow import PlottingWindow
 import unidec_modules.unidectools as ud
 from unidec_modules.AutocorrWindow import AutocorrWindow
@@ -169,7 +169,7 @@ def get_list(self, fcmap='rainbow'):
 class ListCtrlPanel(wx.Panel):
     def __init__(self, parent, list_type="X", size=(200, 400)):
         wx.Panel.__init__(self, parent, -1, style=wx.WANTS_CHARS)
-        id_value = wx.NewId()
+        id_value = wx.NewIdRef()
         self.selection = []
         self.list_type = list_type
         self.parent=parent
@@ -186,11 +186,11 @@ def __init__(self, parent, list_type="X", size=(200, 400)):
         self.SetAutoLayout(True)
         self.Bind(wx.EVT_LIST_ITEM_RIGHT_CLICK, self.on_right_click, self.list)
 
-        self.popupID1 = wx.NewId()
-        self.popupID2 = wx.NewId()
+        self.popupID1 = wx.NewIdRef()
+        self.popupID2 = wx.NewIdRef()
         if list_type == "Y":
-            self.popupID3 = wx.NewId()
-            self.popupID4 = wx.NewId()
+            self.popupID3 = wx.NewIdRef()
+            self.popupID4 = wx.NewIdRef()
 
         self.Bind(wx.EVT_MENU, self.on_popup_one, id=self.popupID1)
         self.Bind(wx.EVT_MENU, self.on_popup_two, id=self.popupID2)
@@ -251,7 +251,7 @@ def clear_frame(self):
         self.repaint()
 
 
-datachoices = {0: "Raw Data", 1: "Processed Data", 2: "Zero Charge Mass Spectrum", 3: "CCS (Experimental)"}
+datachoices = {0: "Raw Data", 1: "Processed Data", 2: "Zero Charge Mass Spectrum", 3: "CCS (Experimental)", 4: "DoubleDec (Experimental)"}
 extractchoices = {0: "Height", 1: "Local Max", 2: "Area", 3: "Center of Mass", 4: "Local Max Position",
                   5: "Center of Mass 50%", 6: "Center of Mass 10%"}
 extractlabels = {0: "Intensity", 1: "Intensity", 2: "Area", 3: "Mass", 4: "Mass", 5: "Mass", 6: "Mass"}
@@ -327,13 +327,19 @@ def __init__(self, parent, title, config=None, pks=None, *args, **kwargs):
         self.menumsmsnorm = self.experimentalmenu.Append(wx.ID_ANY, "Normalize to MSMS",
                                                          "Normalizes mass deconvolutions to MS1 scan for variable 1 +/- variable 2")
         self.Bind(wx.EVT_MENU, self.on_msms_norm, self.menumsmsnorm)
+        self.menudd = self.experimentalmenu.Append(wx.ID_ANY, "Batch DoubleDec",
+                                                         "Run DoubleDec on All Files")
+        self.Bind(wx.EVT_MENU, self.on_doubledec, self.menudd)
         self.menuautocorr = self.experimentalmenu.Append(wx.ID_ANY, "View Autocorrelation of Sum",
                                                          "Shows autocorelation plot of sum")
         self.Bind(wx.EVT_MENU, self.on_autocorr, self.menuautocorr)
         self.toolsmenu.AppendSeparator()
         self.menuylabel = self.toolsmenu.Append(wx.ID_ANY, "Specify Var. 1 Label", "Adds Var. 1 axis label to plot")
         self.Bind(wx.EVT_MENU, self.on_ylabel, self.menuylabel)
 
+        self.menuplotx = self.toolsmenu.Append(wx.ID_ANY, "Plot X Ranges", "Plot X Ranges")
+        self.Bind(wx.EVT_MENU, self.shade_plots, self.menuplotx)
+
         self.toolsmenu.AppendSeparator()
 
         ### CMap drop down menu
@@ -528,8 +534,10 @@ def __init__(self, parent, title, config=None, pks=None, *args, **kwargs):
         self.ylabel = ""
         self.fcmap = "rainbow"
         self.xcmap = "rainbow"
+        self.offsets = []
         self.check_cmaps()
         self.hdf5_file = ""
+        self.kernelfile=""
         self.filetype = 0
         self.update_set(0)
         self.Centre()
@@ -828,6 +836,7 @@ def update_set(self, e):
             self.ctlmin.SetValue(str(self.range[0]))
             self.ctlmax.SetValue(str(self.range[1]))
 
+
     def on_run(self, e, vals=None):
         tstart = time.perf_counter()
         self.update_get(e)
@@ -932,6 +941,14 @@ def on_run(self, e, vals=None):
                     data = np.loadtxt(filename)
                 self.xlabel = "CCS (A^2)"
 
+            elif self.datachoice == 4:
+                self.xlabel = "Mass (Da)"
+                filename = os.path.join(header + "_unidecfiles", subheader + "_massdd.txt")
+                if self.filetype == 1:
+                    data = get_dataset(msdata, "mass_data_dd")
+                else:
+                    data = np.loadtxt(filename)
+
             if not ud.isempty(self.range):
                 bool1 = data[:, 0] >= self.range[0]
                 bool2 = data[:, 0] <= self.range[1]
@@ -961,7 +978,14 @@ def on_run(self, e, vals=None):
                     window = float(self.window)
                 except (ValueError, TypeError):
                     window = None
-                val = ud.data_extract(data, float(s), self.extractchoice, window=window)
+
+                if ";" not in s:
+                    val = ud.data_extract(data, float(s), self.extractchoice, window=window)
+                else:
+                    xs = s.split(';')
+                    val = 0
+                    for xval in xs:
+                        val += ud.data_extract(data, float(xval), self.extractchoice, window=window)
                 xext.append(val)
             self.extract.append(xext)
         self.ypanel.list.populate(self.yvals, colors=ycolors)
@@ -988,6 +1012,40 @@ def on_run(self, e, vals=None):
             hdf.close()
         print("Extraction Complete")
 
+    def shade_plots(self, e):
+        self.update_get(e)
+        for i in range(0, len(self.xvals)):
+            color = self.xcolors[i]
+
+            s = self.xvals[i][0]
+            try:
+                window = float(self.window)
+            except (ValueError, TypeError):
+                window = None
+
+            if ";" not in s:
+                val = float(s)
+                self.make_shade_plot(val, window, color)
+            else:
+                xs = s.split(';')
+                val = 0
+                for xval in xs:
+                    val += float(xval)
+                    self.make_shade_plot(val,  window, color)
+        self.plot1.repaint()
+
+    def make_shade_plot(self, val, window, color):
+        y0 = np.amin(self.data[0][:, 1])
+        ywidth = np.amax(self.data[0][:, 1]) - y0
+        if self.plot1.kdnorm == 1000:
+            val = val/self.plot1.kdnorm
+            window = window/self.plot1.kdnorm
+
+        print(val, window)
+        self.plot1.subplot1.add_patch(
+            Rectangle((val - window, y0), window * 2., ywidth, alpha=0.5, facecolor=color, edgecolor='black',
+                      fill=True))
+
     def make_grid_plots(self, e):
         self.grid = np.array(self.grid)
         if not ud.isempty(self.grid):
@@ -1298,6 +1356,41 @@ def on_msms_norm(self, e):
             print(vals)
             self.on_run(0, vals=vals)
 
+    def on_doubledec(self, e):
+        self.update_get(e)
+        if self.filetype == 1:
+            hdf = h5py.File(self.hdf5_file)
+        self.paths = []
+        self.headers = []
+        for k, l in enumerate(self.yvals):
+            if self.filetype == 1:
+                msdata = hdf.get(self.topname + "/" + str(l[0]))
+            filename = l[0]
+            header = os.path.splitext(filename)[0]
+            if self.localpath == 1 or not os.path.isabs(filename):
+                header = os.path.join(self.directory, header)
+                filename = os.path.join(self.directory, filename)
+            subheader = os.path.split(header)[1]
+
+            filename = os.path.join(header + "_unidecfiles", subheader + "_mass.txt")
+            if self.filetype == 1:
+                data = get_dataset(msdata, "mass_data")
+            else:
+                data = np.loadtxt(filename)
+
+            self.paths.append(filename)
+            self.headers.append(header)
+        print(self.paths)
+
+        dlg = wx.FileDialog(self, "Open Kernel Text File", self.directory, self.kernelfile, "*.txt")
+        if dlg.ShowModal() == wx.ID_OK:
+            self.kernelfile = dlg.GetPath()
+        dlg.Destroy()
+        print(self.kernelfile)
+        DoubleDec.batch_dd(self.paths, self.kernelfile)
+
+
+
     def on_ylabel(self, e):
         dlg = miscwindows.SingleInputDialog(self)
         dlg.initialize_interface(title="Set Variable 1 Label", message="Variable 1 axis label:", defaultvalue="")

iFAMS/wxiFAMS.py

@@ -85,18 +85,18 @@ def __init__(self, parent, inputdata=None, config=None, directory=""):
         controlsizer2.Add(self.ctlwindow, 0, wx.ALIGN_CENTER_VERTICAL)
         controlsizer2.Add(wx.StaticText(panel, label="Delta"), 0, wx.ALIGN_CENTER_VERTICAL)
         controlsizer2.Add(self.ctlwindow1, 0, wx.ALIGN_CENTER_VERTICAL)
-        controlsizer4.Add(wx.StaticText(panel, label="# of zero frequency data"), 0, wx.ALIGN_RIGHT)
-        controlsizer4.Add(self.zerodata, 0, wx.ALIGN_RIGHT)
-        controlsizer4.Add(wx.StaticText(panel, label="# of harmonics for filter"), 0, wx.ALIGN_RIGHT)
-        controlsizer4.Add(self.overtone, 0, wx.ALIGN_RIGHT)
-        controlsizer3.Add(wx.StaticText(panel, label="# of harmonics for average"), 0, wx.ALIGN_RIGHT)
-        controlsizer3.Add(self.harmavg, 0, wx.ALIGN_RIGHT)
-        controlsizer5.Add(wx.StaticText(panel, label="lowest charge state"), 0, wx.ALIGN_RIGHT)
-        controlsizer5.Add(self.lowcharge, 0, wx.ALIGN_RIGHT)
-        controlsizer5.Add(wx.StaticText(panel, label="highest charge state"), 0, wx.ALIGN_RIGHT)
-        controlsizer5.Add(self.highcharge, 0, wx.ALIGN_RIGHT)
-        controlsizer5.Add(wx.StaticText(panel, label="subunit mass"), 0, wx.ALIGN_RIGHT)
-        controlsizer5.Add(self.mansub, 0, wx.ALIGN_RIGHT)
+        controlsizer4.Add(wx.StaticText(panel, label="# of zero frequency data"), 0)
+        controlsizer4.Add(self.zerodata, 0)
+        controlsizer4.Add(wx.StaticText(panel, label="# of harmonics for filter"), 0)
+        controlsizer4.Add(self.overtone, 0)
+        controlsizer3.Add(wx.StaticText(panel, label="# of harmonics for average"), 0)
+        controlsizer3.Add(self.harmavg, 0)
+        controlsizer5.Add(wx.StaticText(panel, label="lowest charge state"), 0)
+        controlsizer5.Add(self.lowcharge, 0)
+        controlsizer5.Add(wx.StaticText(panel, label="highest charge state"), 0)
+        controlsizer5.Add(self.highcharge, 0)
+        controlsizer5.Add(wx.StaticText(panel, label="subunit mass"), 0)
+        controlsizer5.Add(self.mansub, 0)
 
         recalcbutton = wx.Button(panel, label="Recalc. Maxima Finder")
         controlsizer2.Add(recalcbutton, 0, wx.EXPAND)

metaunidec/gui_elements/list_ctrls.py

@@ -197,15 +197,15 @@ def __init__(self, parent, pres, size=(200, 400)):
         self.SetAutoLayout(True)
         self.Bind(wx.EVT_LIST_ITEM_RIGHT_CLICK, self.on_right_click, self.list)
 
-        self.popupID1 = wx.NewId()
-        self.popupID2 = wx.NewId()
-        self.popupID3 = wx.NewId()
-        self.popupID4 = wx.NewId()
-        self.popupID5 = wx.NewId()
-        self.popupID6 = wx.NewId()
-        self.popupID7 = wx.NewId()
-        self.popupID10 = wx.NewId()
-        self.popupID11 = wx.NewId()
+        self.popupID1 = wx.NewIdRef()
+        self.popupID2 = wx.NewIdRef()
+        self.popupID3 = wx.NewIdRef()
+        self.popupID4 = wx.NewIdRef()
+        self.popupID5 = wx.NewIdRef()
+        self.popupID6 = wx.NewIdRef()
+        self.popupID7 = wx.NewIdRef()
+        self.popupID10 = wx.NewIdRef()
+        self.popupID11 = wx.NewIdRef()
 
         self.Bind(wx.EVT_MENU, self.on_popup_one, id=self.popupID1)
         self.Bind(wx.EVT_MENU, self.on_popup_two, id=self.popupID2)

metaunidec/gui_elements/ud_cont_meta.py

@@ -103,7 +103,7 @@ def __init__(self, parent, config, pres, panel, iconfile):
         self.ctlminmz = wx.TextCtrl(panel1, value="", size=(50, -1))
         self.ctlmaxmz = wx.TextCtrl(panel1, value="", size=(60, -1))
         mzrange = wx.BoxSizer(wx.HORIZONTAL)
-        mzrange.Add(wx.StaticText(panel1, label="m/z: "), 0, wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
+        mzrange.Add(wx.StaticText(panel1, label="m/z: "), 0, wx.ALIGN_CENTER_VERTICAL)
         mzrange.Add(self.ctlminmz)
         mzrange.Add(wx.StaticText(panel1, label=" to "), 0, wx.ALIGN_CENTER_VERTICAL)
         mzrange.Add(self.ctlmaxmz)
@@ -271,9 +271,9 @@ def __init__(self, parent, config, pres, panel, iconfile):
         sbs = wx.StaticBoxSizer(sb, orient=wx.HORIZONTAL)
         self.ctlminnativez = wx.TextCtrl(panel2b, value='', size=(75, -1))
         self.ctlmaxnativez = wx.TextCtrl(panel2b, value='', size=(75, -1))
-        sbs.Add(self.ctlminnativez, flag=wx.LEFT | wx.ALIGN_CENTER_VERTICAL | wx.EXPAND, border=5)
-        sbs.Add(wx.StaticText(panel2b, label=' to '), 0, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
-        sbs.Add(self.ctlmaxnativez, flag=wx.LEFT | wx.ALIGN_CENTER_VERTICAL | wx.EXPAND, border=5)
+        sbs.Add(self.ctlminnativez, flag=wx.LEFT | wx.EXPAND, border=5)
+        sbs.Add(wx.StaticText(panel2b, label=' to '), 0, wx.EXPAND)
+        sbs.Add(self.ctlmaxnativez, flag=wx.LEFT | wx.EXPAND, border=5)
         gbox2b.Add(sbs, (i, 0), span=(1, 2), flag=wx.EXPAND)
         i += 1
 
@@ -397,16 +397,15 @@ def __init__(self, parent, config, pres, panel, iconfile):
         self.ctlspeccm = wx.ComboBox(panel3b, wx.ID_ANY, style=wx.CB_READONLY)
         self.parent.Bind(wx.EVT_COMBOBOX, self.on_spectra_color_change, self.ctlspeccm)
 
-        #for mp in self.config.cmaps2:
+        # for mp in self.config.cmaps2:
         #    self.ctl2dcm.Append(mp)
-        #for mp in self.config.cmaps:
+        # for mp in self.config.cmaps:
         #    self.ctlpeakcm.Append(mp)
         #    self.ctlspeccm.Append(mp)
         self.ctl2dcm.AppendItems(self.config.cmaps2)
         self.ctlpeakcm.AppendItems(self.config.cmaps)
         self.ctlspeccm.AppendItems(self.config.cmaps)
 
-
         i = 0
         gbox3b.Add(wx.StaticText(panel3b, label='2D Color Map: '), (i, 0), flag=wx.ALIGN_CENTER_VERTICAL)
         gbox3b.Add(self.ctl2dcm, (i, 1), flag=wx.ALIGN_CENTER_VERTICAL)
@@ -440,21 +439,21 @@ def __init__(self, parent, config, pres, panel, iconfile):
         sbs2 = wx.StaticBoxSizer(sb2, orient=wx.HORIZONTAL)
         self.ctlintlb = wx.TextCtrl(panel3b, value='', size=(75, -1))
         self.ctlintub = wx.TextCtrl(panel3b, value='', size=(75, -1))
-        sbs2.Add(self.ctlintlb, flag=wx.LEFT | wx.ALIGN_CENTER_VERTICAL | wx.EXPAND, border=5)
-        sbs2.Add(wx.StaticText(panel3b, label=' to '), 0, flag=wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
-        sbs2.Add(self.ctlintub, flag=wx.LEFT | wx.ALIGN_CENTER_VERTICAL | wx.EXPAND, border=5)
-        sbs2.Add(wx.StaticText(panel3b, label=' Da '), 0, flag=wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
+        sbs2.Add(self.ctlintlb, flag=wx.LEFT | wx.EXPAND, border=5)
+        sbs2.Add(wx.StaticText(panel3b, label=' to '), 0, flag=wx.EXPAND)
+        sbs2.Add(self.ctlintub, flag=wx.LEFT | wx.EXPAND, border=5)
+        sbs2.Add(wx.StaticText(panel3b, label=' Da '), 0, flag=wx.EXPAND)
         gbox3b.Add(sbs2, (i, 0), span=(1, 2), flag=wx.EXPAND)
         i += 1
 
         sb3 = wx.StaticBox(panel3b, label='Limits on # of Spectra')
         sbs3 = wx.StaticBoxSizer(sb3, orient=wx.HORIZONTAL)
         self.ctlcrossover = wx.TextCtrl(panel3b, value='', size=(75, -1))
         self.ctlnumtot = wx.TextCtrl(panel3b, value='', size=(75, -1))
-        sbs3.Add(wx.StaticText(panel3b, label='If over'), 0, flag=wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
-        sbs3.Add(self.ctlcrossover, flag=wx.LEFT | wx.ALIGN_CENTER_VERTICAL | wx.EXPAND, border=5)
-        sbs3.Add(wx.StaticText(panel3b, label=' plot only'), 0, flag=wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
-        sbs3.Add(self.ctlnumtot, flag=wx.LEFT | wx.ALIGN_CENTER_VERTICAL | wx.EXPAND, border=5)
+        sbs3.Add(wx.StaticText(panel3b, label='If over'), 0, flag=wx.EXPAND)
+        sbs3.Add(self.ctlcrossover, flag=wx.LEFT | wx.EXPAND, border=5)
+        sbs3.Add(wx.StaticText(panel3b, label=' plot only'), 0, flag=wx.EXPAND)
+        sbs3.Add(self.ctlnumtot, flag=wx.LEFT | wx.EXPAND, border=5)
         gbox3b.Add(sbs3, (i, 0), span=(1, 2), flag=wx.EXPAND)
         i += 1
 
@@ -966,9 +965,9 @@ def update_quick_controls(self, e=None):
             except:
                 value = -1
             psval = self.ctlpsfun.GetSelection()
-            #try:
+            # try:
             #    fwhm, psfun, mid = ud.auto_peak_width(self.pres.eng.data.data2)
-            #except:
+            # except:
             #    fwhm = -1
             #    psfun = -1
             if value == 0: