Update importSpectra, include version number from branch Development

__init__.py

+__version__ = "1.0.0"

__main__.py

@@ -18,63 +18,36 @@ You should have received a copy of the GNU General Public License
 along with this program, see COPYING.  
 If not, see <https://www.gnu.org/licenses/>.
 """
-import logging
-import logging.handlers
-import traceback
 import os
-from io import StringIO
-from typing import List
 from PyQt5 import QtCore, QtWidgets, QtGui
 from .sampleview import SampleView
-from .gui.scalebar import ScaleBar
-from .instrumentcom.instrumentConfig import defaultPath
-from .instrumentcom.lightModeSwitch import LightModeSwitch
-from .gui.colorlegend import ColorLegend
-from .gepardlogging import setDefaultLoggingConfig
-from .workmodes import ModeHandler
-from .unittests.test_gepard import testGepard
-from .helperfunctions import getAppFolder
-
-
-def excepthook(excType, excValue, tracebackobj):
-    """
-    Global function to catch unhandled exceptions.
-
-    @param excType exception type
-    @param excValue exception value
-    @param tracebackobj traceback object
-    :return:
-    """
-    tbinfofile = StringIO()
-    traceback.print_tb(tracebackobj, None, tbinfofile)
-    tbinfofile.seek(0)
-    tbinfo = tbinfofile.read()
-    logging.critical("Fatal error in program excecution!")
-    logging.critical(tbinfo)
-    from .errors import showErrorMessageAsWidget
-    showErrorMessageAsWidget(tbinfo)
-
-
+from .scalebar import ScaleBar
+from .ramancom.ramancontrol import defaultPath
+from .ramancom.ramanSwitch import RamanSwitch
+from .analysis.colorlegend import ColorLegend
+from gepard import __version__
+            
 class GEPARDMainWindow(QtWidgets.QMainWindow):
-    def __init__(self, logger):
+    def __init__(self, logpath):
         super(GEPARDMainWindow, self).__init__()
 
-        self.setWindowTitle("GEPARD")
-        self.fname: str = ''
+        self.setWindowTitle("GEPARD " + __version__)
         self.resize(900, 700)
+        
+        self.view = SampleView(logpath)
+        self.view.imparent = self
+        self.view.ScalingChanged.connect(self.scalingChanged)
         self.scalebar = ScaleBar(self)
         self.legend = ColorLegend(self)
-        self.lightModeSwitch = LightModeSwitch(self)
-        self.view = SampleView(self, logger)
-        self.view.ScalingChanged.connect(self.scalingChanged)
+        self.ramanSwitch = RamanSwitch(self)
         self.view.ScalingChanged.connect(self.scalebar.updateScale)
         
         mdiarea = QtWidgets.QMdiArea(self)
         mdiarea.addSubWindow(self.scalebar)
         mdiarea.addSubWindow(self.legend)
-        mdiarea.addSubWindow(self.lightModeSwitch)
+        mdiarea.addSubWindow(self.ramanSwitch)
         self.legend.hide()
-        self.lightModeSwitch.hide()
+        self.ramanSwitch.hide()
         
         subview = mdiarea.addSubWindow(self.view)
         subview.showMaximized()

analysis/importSpectra.py

@@ -3,7 +3,7 @@
 """
 Created on Tue May 28 20:33:14 2019
 
-@author: brandt
+@author: brandt, kanaki
 """
 import numpy as np
 
@@ -11,7 +11,21 @@ import numpy as np
 and names for all in file contained spectra'''
 
 
-#TODO: Include sanity checks for correct file format?
+def listInstruments():
+    instruments = ["WiTec", "PerkinElmer", "Renishaw"]
+    return instruments
+
+
+def chooseInstrument(instrument, fname):
+    if instrument == "WiTec":
+        spectra, names = importWITecSpectra(fname)
+    elif instrument == "PerkinElmer":
+        spectra, names = importPerkinElmerSpectra(fname)
+    elif instrument == "Renishaw":
+        spectra, names = importRenishawSpectra(fname)
+
+    return spectra, names
+
 
 def importWITecSpectra(fname):
     def firstColumnOnlyHasUniqueNumbers(data):
@@ -28,7 +42,8 @@ def importWITecSpectra(fname):
         return data, names
     else:
         raise ImportError
-    
+
+
 def importRenishawSpectra(fname):
     data = np.loadtxt(fname)
     rawSpectra = data[:, 2:4]
@@ -54,16 +69,32 @@ def importRenishawSpectra(fname):
     return spectra, names
 #    return np.transpose(np.hstack((wavenumbers, spectra))), names
 
+
 def importPerkinElmerSpectra(fname):
+    """Import Spotlight spectra from csv-file created with the PerkingElmer convert-tool."""
     names = []
-    spectra = []
+    rawSpectra = []
+    spectraIndices = []
     with open(fname) as fp:
+        # First line contains spectra file names.  The first name is Marker.sp, the rest Marker_xxx.sp, starting with
+        # 001.  Spectra start in third line
         for index, line in enumerate(fp.readlines()):
             if index == 0:
                 for name in line.split(';'):
-                    names.append(name.split('.sp')[0])
-                    
+                    try:
+                        specIndex = int(name.split('.sp')[0].split('_')[1])
+                    except IndexError:
+                        specIndex = int(0)
+
+                    names.append(name.split('.sp')[0] + ' (' + str(specIndex)+ ')')
+                    spectraIndices.append(specIndex)
             elif index > 1:
-                spectra.append(line.split(';'))
-    
-    return np.array(spectra, dtype=np.float), names[1:]
+                rawSpectra.append(line.split(';'))
+
+        # Spectra in csv are sorted alphabetically by filename, causing incorrect order when 1000 spectra are
+        # exceeded.  Sort numerically by spectrum index:
+        sortingIndex = np.argsort(spectraIndices)
+        namesSorted = [names[ii] for ii in sortingIndex]
+        spectra = np.array(rawSpectra, dtype=np.float)[:,sortingIndex]
+
+    return spectra, namesSorted[1:]