Initial commit of current project status. Some modification will be needed...

Initial commit of current project status. Some modification will be needed before this will work without manual adaptations…

README.md

 # GEPARD
 
 GEPARD - Gepard-Enabled PARticle Detection for Raman microscopes.
+
+Copyright (C) 2018  Lars Bittrich and Josef Brandt, Leibniz-Institut für 
+Polymerforschung Dresden e. V. <bittrich-lars@ipfdd.de> 
+
+Requirements:
+
+* python 3.6, PyQt5, OpenCV 3.4.1, numpy 1.14, scikit-image 0.13.1, scipy 1.1.0,
+  win32com, pythoncom, cython 0.28
+  
+* we advise the use of Anaconda (python 3.6): https://www.anaconda.com/download
+  this package contains most of the python libraries
+  however, opencv and scikit-image are missing
+  start anaconda prompt and install opencv:
+  pip install opencv-python
+  conda install scikit-image
+
+* we recommend working with a 64bit OS and also a python interpreter compiled 
+  for 64bit as many use cases require a lot of memory (16 GB better 32 GB 
+  recommended)
+  
+* the tsp module in externalmodules can be built with
+  python setuptsp.py
+  please note: for this step a valid compiler needs to be installed in the 
+  system; Otherwise use the precompiled tsp-module
+  
+If you plan on using the WITec Raman interface to control your device, please
+note: You use this interface at your OWN RISK! Make sure, that no obstacles
+block the objective and that you UNDERSTAND and VALIDATE the code, that controls
+the microscope! Start with "witectesting.py", which should read and move within
+small margins.
+  
+At the moment the program is an executable python script. Copy the folder with 
+all its content to some place and run (e.g. using anaconda prompt):
+python gepard.py
+
+It is possible to create a windows link file, that executes python with the
+gepard script as an argument and the working directory pointing to the folder
+containing gepard for convenience.

WITecCOM.py

+# -*- coding: utf-8 -*-
+"""
+GEPARD - Gepard-Enabled PARticle Detection
+Copyright (C) 2018  Lars Bittrich and Josef Brandt, Leibniz-Institut für 
+Polymerforschung Dresden e. V. <bittrich-lars@ipfdd.de>    
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+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 os
+import sys
+try:
+    import pythoncom
+    import win32com.client
+except ImportError:
+    os.environ["NO_WITEC_CONTROL"] = "True"
+    
+from time import sleep, time
+from ramanbase import RamanBase
+from socket import gethostname
+
+
+class WITecCOM(RamanBase):
+    CLSID = "{C45E77CE-3D66-489A-B5E2-159F443BD1AA}"
+    hostname = "unknown"
+    def __init__(self, hostname=None):
+        super().__init__()
+        if hostname is None:
+            hostname = gethostname()
+        self.IBUCSAccess = win32com.client.DispatchEx(self.CLSID, machine=hostname, 
+                                                      clsctx=pythoncom.CLSCTX_REMOTE_SERVER)
+        
+    def connect(self):
+        if not self.IBUCSAccess.RequestWriteAccess(True):
+            self.connected = False
+            return False
+        
+        IBUCSCore = win32com.client.CastTo(self.IBUCSAccess, 'IBUCSCore')
+        self.PosXInterface = IBUCSCore.GetSubSystemDefaultInterface("UserParameters|SamplePositioning|AbsolutePositionX")
+        self.PosYInterface = IBUCSCore.GetSubSystemDefaultInterface("UserParameters|SamplePositioning|AbsolutePositionY")
+        self.PosZInterface = IBUCSCore.GetSubSystemDefaultInterface("UserParameters|ScanTable|PositionMicroscopeZ")
+        self.GoToInterface = IBUCSCore.GetSubSystemDefaultInterface("UserParameters|SamplePositioning|GoToPosition")
+        self.PosXCurInterface = IBUCSCore.GetSubSystemDefaultInterface("Status|Software|SamplePositioner|CurrentPositionX")
+        self.PosYCurInterface = IBUCSCore.GetSubSystemDefaultInterface("Status|Software|SamplePositioner|CurrentPositionY")
+        self.PosZCurInterface = IBUCSCore.GetSubSystemDefaultInterface("Status|Software|SamplePositioner|CurrentPositionZ")
+        self.PosZCurUserInterface = IBUCSCore.GetSubSystemDefaultInterface("Status|Hardware|Controller|DataChannels|StepperMotorPosition")
+        # Get Float Manipulators
+        self.PosXFloatMan = win32com.client.CastTo(self.PosXInterface, 'IBUCSFloat')
+        self.PosYFloatMan = win32com.client.CastTo(self.PosYInterface, 'IBUCSFloat')
+        self.PosZFloatMan = win32com.client.CastTo(self.PosZInterface, 'IBUCSFloat')
+        self.PosXCurFloatMan = win32com.client.CastTo(self.PosXCurInterface, 'IBUCSStatusContainer')
+        self.PosYCurFloatMan = win32com.client.CastTo(self.PosYCurInterface, 'IBUCSStatusContainer')
+        self.PosZCurFloatMan = win32com.client.CastTo(self.PosZCurInterface, 'IBUCSStatusContainer')
+        self.PosZCurUserFloatMan = win32com.client.CastTo(self.PosZCurUserInterface, 'IBUCSStatusContainer')
+        self.GoToTrigger = win32com.client.CastTo(self.GoToInterface, 'IBUCSTrigger')
+        
+        self.ImageNameInterface = IBUCSCore.GetSubSystemDefaultInterface("MultiComm|MultiCommVideoSystem|BitmapFileName")
+        self.ImageNameMan = win32com.client.CastTo(self.ImageNameInterface, 'IBUCSString')
+        self.ImageSaveInterface = IBUCSCore.GetSubSystemDefaultInterface("MultiComm|MultiCommVideoSystem|SaveColorBitmapToFile")
+        self.ImageSaveMan = win32com.client.CastTo(self.ImageSaveInterface, 'IBUCSTrigger')
+        
+        self.ImageHeightInterface = IBUCSCore.GetSubSystemDefaultInterface("MultiComm|MicroscopeControl|Video|Calibration|ImageHeightMicrons")
+        self.ImageHeightMan = win32com.client.CastTo(self.ImageHeightInterface, 'IBUCSFloat')
+        self.ImageWidthInterface = IBUCSCore.GetSubSystemDefaultInterface("MultiComm|MicroscopeControl|Video|Calibration|ImageWidthMicrons")
+        self.ImageWidthMan = win32com.client.CastTo(self.ImageWidthInterface, 'IBUCSFloat')
+        self.ImageRotationInterface = IBUCSCore.GetSubSystemDefaultInterface("MultiComm|MicroscopeControl|Video|Calibration|RotationDegrees")
+        self.ImageRotationMan = win32com.client.CastTo(self.ImageRotationInterface, 'IBUCSFloat')
+        
+        self.SequencerStartInterface = IBUCSCore.GetSubSystemDefaultInterface("UserParameters|SequencerSingleSpectrum|Start")
+        self.SequencerStartTrigger = win32com.client.CastTo(self.SequencerStartInterface, 'IBUCSTrigger')
+        
+        self.SequencerBusyInterface = IBUCSCore.GetSubSystemDefaultInterface("Status|Software|Sequencers|IsASequencerActive")
+        self.SequencerBusyStatus = win32com.client.CastTo(self.SequencerBusyInterface, 'IBUCSStatusContainer') 
+        
+        self.TimeSeriesSlowNumMeasurementsInterface = IBUCSCore.GetSubSystemDefaultInterface("UserParameters|SequencerTimeSeriesSlow|AmountOfMeasurements")
+        self.TimeSeriesSlowNumMeasurementsMan = win32com.client.CastTo(self.TimeSeriesSlowNumMeasurementsInterface, 'IBUCSInt')
+        self.TimeSeriesSlowNameInterface = IBUCSCore.GetSubSystemDefaultInterface("UserParameters|SequencerTimeSeriesSlow|Naming|DataName")
+        self.TimeSeriesSlowNameMan = win32com.client.CastTo(self.TimeSeriesSlowNameInterface, 'IBUCSString')
+        self.TimeSeriesSlowNumAccumulationsInterface = IBUCSCore.GetSubSystemDefaultInterface("UserParameters|SequencerTimeSeriesSlow|SpectrumAcquisition|Accumulations")
+        self.TimeSeriesSlowNumAccumulationsMan = win32com.client.CastTo(self.TimeSeriesSlowNumAccumulationsInterface, 'IBUCSInt')
+        self.TimeSeriesSlowIntTimeInterface = IBUCSCore.GetSubSystemDefaultInterface("UserParameters|SequencerTimeSeriesSlow|SpectrumAcquisition|IntegrationTime")
+        self.TimeSeriesSlowIntTimeMan = win32com.client.CastTo(self.TimeSeriesSlowIntTimeInterface, 'IBUCSFloat')
+        self.TimeSeriesSlowNumInterface = IBUCSCore.GetSubSystemDefaultInterface("UserParameters|SequencerTimeSeriesSlow|Naming|DataNumber")
+        self.TimeSeriesSlowNumMan = win32com.client.CastTo(self.TimeSeriesSlowNumInterface, 'IBUCSInt')
+        self.TimeSeriesSlowModeInterface = IBUCSCore.GetSubSystemDefaultInterface("UserParameters|SequencerTimeSeriesSlow|MeasurementMode")
+        self.TimeSeriesSlowModeMan = win32com.client.CastTo(self.TimeSeriesSlowModeInterface, 'IBUCSEnum')
+        self.TimeSeriesSlowNextInterface = IBUCSCore.GetSubSystemDefaultInterface("UserParameters|SequencerTimeSeriesSlow|NextMeasurement")
+        self.TimeSeriesSlowNextMan = win32com.client.CastTo(self.TimeSeriesSlowNextInterface, 'IBUCSTrigger')
+        
+        self.TimeSeriesSlowStartInterface = IBUCSCore.GetSubSystemDefaultInterface("UserParameters|SequencerTimeSeriesSlow|Start")
+        self.TimeSeriesSlowStartMan = win32com.client.CastTo(self.TimeSeriesSlowStartInterface, 'IBUCSTrigger')
+        
+        self.TimeSeriesSlowStopInterface = IBUCSCore.GetSubSystemDefaultInterface("UserParameters|StopSequencer")
+        self.TimeSeriesSlowStopMan = win32com.client.CastTo(self.TimeSeriesSlowStopInterface, 'IBUCSTrigger')
+        
+        self.TimeSeriesSlowIndNextInterface = IBUCSCore.GetSubSystemDefaultInterface("UserParameters|SequencerTimeSeriesSlow|IndexOfNextMeasurement")
+        self.TimeSeriesSlowIndNextMan = win32com.client.CastTo(self.TimeSeriesSlowIndNextInterface, 'IBUCSInt')
+        
+        self.TimeSeriesSlowActivityInterface = IBUCSCore.GetSubSystemDefaultInterface("Status|Software|Sequencers|ActiveSequencer|CurrentActivity")
+        self.TimeSeriesSlowActivityMan = win32com.client.CastTo(self.TimeSeriesSlowActivityInterface, 'IBUCSStatusContainer')
+        
+        self.RamanRelativeXInterface = IBUCSCore.GetSubSystemDefaultInterface("MultiComm|MicroscopeControl|Video|ProbePosition|RelativeX")
+        self.RamanRelativeXMan = win32com.client.CastTo(self.RamanRelativeXInterface, 'IBUCSFloat')
+        self.RamanRelativeYInterface = IBUCSCore.GetSubSystemDefaultInterface("MultiComm|MicroscopeControl|Video|ProbePosition|RelativeY")
+        self.RamanRelativeYMan = win32com.client.CastTo(self.RamanRelativeYInterface, 'IBUCSFloat')
+        
+        self.BrightnessInterface = IBUCSCore.GetSubSystemDefaultInterface("MultiComm|MicroscopeControl|WhiteLight|Top|BrightnessPercentage")
+        self.BrightnessMan = win32com.client.CastTo(self.BrightnessInterface, 'IBUCSFloat')
+        
+        self.connected = True
+        return True
+    
+    def getBrightness(self):
+        assert self.connected
+        return self.BrightnessMan.GetValue()
+    
+    def setBrightness(self, newval):
+        if newval<0: 
+            newval = 0.0
+        elif newval>100.:
+            newval = 100.0
+        self.BrightnessMan.SetValue(newval)
+        sleep(.1)
+    
+    def getRamanPositionShift(self):
+        rx = .5-self.RamanRelativeXMan.GetValue() # current assumption is, that image center is current position
+        ry = self.RamanRelativeYMan.GetValue()-.5
+        width, height = self.ImageWidthMan.GetValue(), self.ImageHeightMan.GetValue()
+        return rx*width, ry*height
+        
+    
+    def disconnect(self):
+        if self.connected:
+            self.IBUCSAccess.RequestWriteAccess(False)
+        self.connected = False
+    
+    def getPosition(self):
+        assert self.connected
+        self.PosXCurFloatMan.Update()
+        x = self.PosXCurFloatMan.GetSingleValueAsDouble()[1]
+        self.PosYCurFloatMan.Update()
+        y = self.PosYCurFloatMan.GetSingleValueAsDouble()[1]
+        self.PosZCurFloatMan.Update()
+        z = self.PosZCurFloatMan.GetSingleValueAsDouble()[1]
+        return x, y, z
+    
+    def getSoftwareZ(self):
+        self.PosZCurFloatMan.Update()
+        z = self.PosZCurFloatMan.GetSingleValueAsDouble()[1]
+        return z
+    
+    def getUserZ(self):
+        assert self.connected
+        self.PosZCurUserFloatMan.Update()
+        z = self.PosZCurUserFloatMan.GetSingleValueAsDouble()[1]
+        return z
+        
+    def moveToAbsolutePosition(self, x, y, z=None, epsxy=0.11, epsz=0.011):
+        assert self.connected
+        initpos = self.getPosition()
+        # move only if new position is really different; repeat if new position is ignored (happens some times)
+        while max(abs(initpos[0]-x), abs(initpos[1]-y))>epsxy:
+            t0 = time()
+            self.PosXFloatMan.SetValue(x)
+            self.PosYFloatMan.SetValue(y)
+            self.GoToTrigger.OperateTrigger()
+            
+            # wait till position is found within accuracy of epsxy; check if position changes at all
+            distance = 2*epsxy
+            while distance > epsxy:# and (lastpos is None or lastpos!=curpos):
+                curpos = self.getPosition()
+                distance = max(abs(curpos[0]-x), abs(curpos[1]-y))
+                if ((time()-t0>0.5) and max(abs(curpos[0]-initpos[0]), abs(curpos[1]-initpos[1]))<epsxy) or (time()-t0>10.):
+                    print("WARNING: signal ignored:", time()-t0, x, y, curpos, initpos)
+                    sys.stdout.flush()
+                    break
+                sleep(.01)
+            sleep(.1)
+            initpos = self.getPosition()
+        if z is not None:
+            self.moveZto(z, epsz)
+            
+    def moveZto(self, z, epsz=0.011):
+        assert self.connected
+        #z = round(z,2)
+        while abs(self.PosZCurFloatMan.GetSingleValueAsDouble()[1]-z)>epsz:
+            initpos = self.PosZCurFloatMan.GetSingleValueAsDouble()[1]
+            t0 = time()
+            self.PosZFloatMan.SetValue(z)
+            distance = 2*epsz
+            while distance > epsz:
+                self.PosZCurFloatMan.Update()
+                curpos = self.PosZCurFloatMan.GetSingleValueAsDouble()[1]
+                distance = abs(curpos-z)
+                if ((time()-t0>0.5) and abs(curpos-initpos)<epsz)  or (time()-t0>10.):
+                    print("WARNING: signal z ignored:", time()-t0)
+                    sys.stdout.flush()
+                    break
+                sleep(.01)
+            sleep(.1)
+        
+    def saveImage(self, fname):
+        assert self.connected
+        self.ImageNameMan.SetValue(fname)
+        self.ImageSaveMan.OperateTrigger()
+        sleep(.1)
+        
+    def getImageDimensions(self):
+        """ Get the image width and height in um and the orientation angle in degrees.
+        """
+        assert self.connected
+        width, height = self.ImageWidthMan.GetValue(), self.ImageHeightMan.GetValue()
+        angle = self.ImageRotationMan.GetValue()
+        return width, height, angle
+    
+    def startSinglePointScan(self):
+        assert self.connected
+        self.SequencerStartTrigger.OperateTrigger()
+        # Wait until sequencer has finished
+        while True:
+            self.SequencerBusyStatus.Update()
+            Busy = self.SequencerBusyStatus.GetSingleValueAsInt()[1]
+            if not Busy:
+                break
+            
+    def initiateTimeSeriesScan(self, label, numberofscans, accumulations, integrtime):
+        assert self.connected
+        self.timeseries = numberofscans
+        self.TimeSeriesSlowNameMan.SetValue(label)
+        self.TimeSeriesSlowNumMeasurementsMan.SetValue(numberofscans)
+        self.TimeSeriesSlowNumAccumulationsMan.SetValue(accumulations)
+        self.TimeSeriesSlowIntTimeMan.SetValue(integrtime)
+        self.TimeSeriesSlowModeMan.SetValueNumeric(0)
+        self.TimeSeriesSlowNumMan.SetValue(0)
+        self.TimeSeriesSlowStartMan.OperateTrigger()
+        sleep(0.1)
+        t1 = time()
+        while True:
+            self.TimeSeriesSlowActivityMan.Update()
+            valid, act = self.TimeSeriesSlowActivityMan.GetSingleValueAsString()
+            if act=="Waiting for next Measurement":
+                break
+            else:
+                sleep(0.02)
+                if time()-t1>3.:
+                    print("Waiting for measurement ready...")
+                    t1 = time()
+        
+        
+    def nextTimeSeriesScan(self, num):
+        assert self.timeseries
+        self.TimeSeriesSlowNextMan.OperateTrigger()
+        # Wait until sequencer has finished
+        sleep(0.1)
+        t1 = time()
+        while True:
+            ind = self.TimeSeriesSlowIndNextMan.GetValue()
+            if ind>num:
+                break
+            else:
+                sleep(0.02)
+                if time()-t1>3.:
+                    print("Waiting for next index...")
+                    t1 = time()
+        while True:
+            valid, act = self.TimeSeriesSlowActivityMan.GetSingleValueAsString()
+            if act=="Waiting for next Measurement":
+                break
+            else:
+                sleep(0.02)
+                if time()-t1>3.:
+                    print("Waiting for measurement ready...")
+                    t1 = time()
+        if num==self.timeseries-1:
+            self.timeseries = False
+
+        
\ No newline at end of file

dataset.py

+# -*- coding: utf-8 -*-
+"""
+GEPARD - Gepard-Enabled PARticle Detection
+Copyright (C) 2018  Lars Bittrich and Josef Brandt, Leibniz-Institut für 
+Polymerforschung Dresden e. V. <bittrich-lars@ipfdd.de>    
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+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 os
+import pickle
+import numpy as np
+import cv2
+from helperfunctions import cv2imread_fix, cv2imwrite_fix
+from copy import copy
+
+currentversion = 1
+
+def loadData(fname):
+    retds = None
+    with open(fname, "rb") as fp:
+        ds = pickle.load(fp)
+        ds.fname = fname
+        ds.readin = True
+        ds.updatePath()
+        retds = DataSet(fname)
+        retds.version = 0
+        retds.__dict__.update(ds.__dict__)
+        if retds.version < currentversion:
+            retds.legacyConversion()
+        elif retds.zvalimg=="saved":
+            retds.loadZvalImg()
+    return retds
+
+def saveData(dataset, fname):
+    with open(fname, "wb") as fp:
+        # zvalimg is rather large and thus it is saved separately in a tif file 
+        # only onces after its creation
+        zvalimg = dataset.zvalimg
+        if zvalimg is not None:
+            dataset.zvalimg = "saved"
+        pickle.dump(dataset, fp, protocol=-1)
+        dataset.zvalimg = zvalimg
+
+class DataSet(object):
+    def __init__(self, fname, newProject=False):
+        self.fname = fname
+        # parameters specifically for optical scan
+        self.version = currentversion
+        self.lastpos = None
+        self.maxdim = None
+        self.pixelscale = None # µm / pixel
+        self.imagedim = None  # width, height, angle
+        self.fitpoints = []   # manually adjusted positions aquired to define the specimen geometry
+        self.fitindices = []  # which of the five positions in the ui are already known
+        self.boundary = []    # scan boundary computed by a circle around the fitpoints + manual adjustments
+        self.grid = []        # scan grid positions for optical scan
+        self.zpositions = []  # z-positions for optical scan
+        self.heightmap = None
+        self.zvalimg = None
+        
+        # parameters specifically for raman scan
+        self.pshift = None    # shift of raman scan position relative to image center
+        self.seedpoints = np.array([])
+        self.seeddeletepoints = np.array([])
+        self.ramanpoints = []
+        self.particlecontours = []
+        self.particlestats = []
+        self.ramanscansortindex = None
+        self.ramanscandone = False
+        
+        self.readin = True    # a value that is always set to True at loadData 
+                              # and mark that the coordinate system might be changed in the meantime
+        self.mode = "prepare"
+        if newProject:
+            self.fname = self.newProject(fname)
+        self.updatePath()
+        
+    def saveZvalImg(self):
+        if self.zvalimg is not None:
+            cv2imwrite_fix(self.getZvalImageName(), self.zvalimg)
+            
+    def loadZvalImg(self):
+        if os.path.exists(self.getZvalImageName()):
+            self.zvalimg = cv2imread_fix(self.getZvalImageName(), cv2.IMREAD_GRAYSCALE)
+        
+    def legacyConversion(self, recreatefullimage=False):
+        if self.version==0:
+            print("Converting legacy version 0 to 1")
+            print("This may take some time")
+            
+            # local imports as these functions are only needed for the rare occasion of legacy conversion
+            from opticalscan import loadAndPasteImage
+            
+            # try to load png and check for detection contours
+            buggyimage = recreatefullimage
+            if not buggyimage and os.path.exists(self.getLegacyImageName()):
+                img = cv2imread_fix(self.getLegacyImageName())
+                Nc = len(self.particlecontours)
+                if Nc>0:
+                    contour = self.particlecontours[Nc//2]
+                    contpixels = img[contour[:,0,1],contour[:,0,0]]
+                    if np.all(contpixels[:,1]==255) and np.all(contpixels[:,2]==0) \
+                        and np.all(contpixels[:,0]==0):
+                        buggyimage = True
+                if not buggyimage:
+                    cv2imwrite_fix(self.getImageName(), img)
+                del img
+            
+            if buggyimage:
+                print("recreating fullimage from grid data")
+                imgdata = None
+                zvalimg = None
+                Ngrid = len(self.grid)
+                
+                width, height, rotationvalue = self.imagedim
+                p0, p1 = self.maxdim[:2], self.maxdim[2:]
+                for i in range(Ngrid):
+                    print(f"Processing image {i+1} of {Ngrid}")
+                    names = []
+                    for k in range(len(self.zpositions)):
+                        names.append(os.path.join(self.getScanPath(), f"image_{i}_{k}.bmp"))
+                    p = self.grid[i]
+                    imgdata, zvalimg = loadAndPasteImage(names, imgdata, zvalimg, width, 
+                                                            height, rotationvalue, p0, p1, p)
+                self.zvalimg = zvalimg
+                cv2imwrite_fix(self.getImageName(), cv2.cvtColor(imgdata, cv2.COLOR_RGB2BGR))
+                del imgdata
+            self.saveZvalImg()
+            if "particleimgs" in self.__dict__:
+                del self.particleimgs
+            
+            self.version = 1
+            #os.remove(self.getLegacyImageName())
+            #os.remove(self.getLegacyDetectImageName())
+            #self.save()
+        # add later conversion for higher version numbers here
+        
+    def getSubImage(self, img, index, draw=True):
+        contour = self.particlecontours[index]
+        x0, x1 = contour[:,0,0].min(), contour[:,0,0].max()
+        y0, y1 = contour[:,0,1].min(), contour[:,0,1].max()
+        subimg = img[y0:y1+1,x0:x1+1].copy()
+        if draw:
+            cv2.drawContours(subimg, [contour], -1, (0,255,0), 1)
+        return subimg
+        
+    def getZval(self, pixelpos):
+        assert self.zvalimg is not None
+        zp = self.zvalimg[round(pixelpos[1]), round(pixelpos[0])]
+        z0, z1 = self.zpositions.min(), self.zpositions.max()
+        return zp/255.*(z1-z0) + z0
+        
+    def mapHeight(self, x, y):
+        assert not self.readin
+        assert self.heightmap is not None
+        return self.heightmap[0]*x + self.heightmap[1]*y + self.heightmap[2]
+        
+    def mapToPixel(self, p, force=False):
+        if not force:
+            assert not self.readin
+        p0 = copy(self.lastpos)
+        p0[0] -= self.imagedim[0]/2
+        p0[1] += self.imagedim[1]/2
+        return (p[0] - p0[0])/self.pixelscale, (p0[1] - p[1])/self.pixelscale
+    
+    def mapToLength(self, pixelpos, force=False):
+        if not force:
+            assert not self.readin
+        p0 = copy(self.lastpos)
+        p0[0] -= self.imagedim[0]/2
+        p0[1] += self.imagedim[1]/2
+        return (pixelpos[0]*self.pixelscale + p0[0]), (p0[1] - pixelpos[1]*self.pixelscale)
+    
+    def mapToLengthRaman(self, pixelpos, noz=False):
+        p0x, p0y = self.mapToLength(pixelpos)
+        x, y = p0x + self.pshift[0], p0y + self.pshift[1]
+        z = None
+        if not noz:
+            z = self.mapHeight(x, y)
+            z += self.getZval(pixelpos)
+        return x, y, z
+        
+    def newProject(self, fname):
+        path = os.path.split(fname)[0]
+        name = os.path.splitext(os.path.basename(fname))[0]
+        newpath = os.path.join(path, name)
+        fname = os.path.join(newpath, name + ".pkl")
+        if not os.path.exists(newpath):
+            os.mkdir(newpath)        # for new projects a directory will be created
+        elif os.path.exists(fname):  # if this project is already there, load it instead
+            self.__dict__.update(loadData(fname).__dict__)
+        return fname
+    
+    def getScanPath(self):
+        scandir = os.path.join(self.path, "scanimages")
+        if not os.path.exists(scandir):
+            os.mkdir(scandir)
+        return scandir
+        
+    def updatePath(self):
+        self.path = os.path.split(self.fname)[0]
+        self.name = os.path.splitext(os.path.basename(self.fname))[0]
+        
+    def getImageName(self):
+        return os.path.join(self.path, "fullimage.tif")
+    
+    def getZvalImageName(self):
+        return os.path.join(self.path, "zvalues.tif")
+    
+    def getLegacyImageName(self):
+        return os.path.join(self.path, "fullimage.png")
+    
+    def getLegacyDetectImageName(self):
+        return os.path.join(self.path, "detectimage.png")
+    
+    def getDetectImageName(self):
+        raise NotImplementedError("No longer implemented due to change in API")
+    
+    def getTmpImageName(self):
+        return os.path.join(self.path, "tmp.bmp")
+    
+    def saveParticleData(self):
+        if len(self.ramanscansortindex)>0:
+            data = []
+            for i in self.ramanscansortindex:
+                data.append(list(self.ramanpoints[i])+list(self.particlestats[i]))
+            data = np.array(data)
+            data[:,0], data[:,1], z = self.mapToLengthRaman((data[:,0], data[:,1]), noz=True)
+            data[:,2:7] *= self.pixelscale
+            header = "x [µm], y [µm], length [µm], height [µm], length_ellipse [µm], height_ellipse [µm]"
+            if data.shape[1]>6:
+                header = header + ", area [µm^2]"
+                data[:,6] *= self.pixelscale
+            np.savetxt(os.path.join(self.path, "particledata.txt"), data, 
+                       header=header)
+            
+    def save(self):
+        saveData(self, self.fname)
+        
\ No newline at end of file

externalmodules/setuptsp.py

+# -*- coding: utf-8 -*-
+"""
+GEPARD - Gepard-Enabled PARticle Detection
+Copyright (C) 2018  Lars Bittrich and Josef Brandt, Leibniz-Institut für 
+Polymerforschung Dresden e. V. <bittrich-lars@ipfdd.de>    
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+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/>.
+"""
+
+try:
+    from setuptools import setup
+    from setuptools import Extension
+except ImportError:
+    from distutils.core import setup
+    from distutils.extension import Extension
+from Cython.Build import cythonize
+import numpy as np
+import sys
+
+if len(sys.argv)==1:
+    sys.argv.append("build_ext")
+    sys.argv.append("--inplace")
+
+ext = Extension("tsp", ["tsp.pyx"],
+        extra_compile_args=['-O3'],)
+
+setup(
+    name = "optimized tsp-module",
+    ext_modules = cythonize([ext]), # accepts a glob pattern
+    include_dirs=[np.get_include()]
+)
\ No newline at end of file