relative import fix. Gepard can now be imported as a module.

IMPORTANT: start Gepard by: "python -m gepard" outside of the module directory

gepard.py → __main__.py

@@ -18,13 +18,13 @@ 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/>.
 """
-from PyQt5 import QtCore, QtWidgets, QtGui
-from sampleview import SampleView
-from scalebar import ScaleBar
-from ramancom.ramancontrol import defaultPath
-from ramancom.ramanSwitch import RamanSwitch
-from colorlegend import ColorLegend
 import os
+from PyQt5 import QtCore, QtWidgets, QtGui
+from .sampleview import SampleView
+from .scalebar import ScaleBar
+from .ramancom.ramancontrol import defaultPath
+from .ramancom.ramanSwitch import RamanSwitch
+from .colorlegend import ColorLegend
             
 class MeasureParticleWindow(QtWidgets.QMainWindow):
     
@@ -116,7 +116,7 @@ class MeasureParticleWindow(QtWidgets.QMainWindow):
 
     def createActions(self):
         fname = os.path.join(os.path.split(__file__)[0],
-                             os.path.join("data","brand.png"))
+                             os.path.join('data', 'brand.png'))
         self.aboutAct = QtWidgets.QAction(QtGui.QIcon(fname),
                                           "About Particle Measurment", self)
         self.aboutAct.triggered.connect(self.about)
@@ -330,4 +330,4 @@ if __name__ == '__main__':
     meas.showMaximized()
     ret = app.exec_()
     if fp is not None:
-        fp.close()
\ No newline at end of file
+        fp.close()

analysis/datastats.py

@@ -21,7 +21,7 @@ If not, see <https://www.gnu.org/licenses/>.
 import os
 import numpy as np
 import operator
-from dataset import loadData, recursiveDictCompare
+from ..dataset import loadData, recursiveDictCompare
 
 
 def readDataStats(fname):
@@ -215,4 +215,4 @@ class DataStats(object):
     def testRead(self):
         statsread = readDataStats(self.dataset.fname)
         return recursiveDictCompare(self.__dict__, statsread.__dict__)
-        
\ No newline at end of file
+        

dataset.py

@@ -22,7 +22,7 @@ import os
 import pickle
 import numpy as np
 import cv2
-from helperfunctions import cv2imread_fix, cv2imwrite_fix
+from .helperfunctions import cv2imread_fix, cv2imwrite_fix
 from copy import copy
 
 currentversion = 2

detectionview.py

@@ -20,7 +20,7 @@ If not, see <https://www.gnu.org/licenses/>.
 """
 import numpy as np
 from PyQt5 import QtCore, QtWidgets, QtGui
-from segmentation import Segmentation
+from .segmentation import Segmentation
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg
 import matplotlib.pyplot as plt
 from threading import Thread
@@ -690,4 +690,4 @@ if __name__ == "__main__":
     view = ParticleDetectionView(img, ds, None)    
     view.setDataSet(ds)
     view.show()
-    app.exec_()
\ No newline at end of file
+    app.exec_()

opticalscan.py

@@ -23,10 +23,10 @@ from PyQt5 import QtCore, QtWidgets
 import numpy as np
 from multiprocessing import Process, Queue, Event
 import queue
-from imagestitch import imageStacking
+from .imagestitch import imageStacking
 import os
 import cv2
-from helperfunctions import cv2imread_fix, cv2imwrite_fix
+from .helperfunctions import cv2imread_fix, cv2imwrite_fix
 from time import time
 import datetime
 import sys
@@ -636,4 +636,4 @@ if __name__ == "__main__":
     ds = DataSet('Test')
     optscan = OpticalScan(SimulatedRaman(), ds)
     optscan.show()
-    sys.exit(app.exec_())
\ No newline at end of file
+    sys.exit(app.exec_())

ramancom/ramancontrol.py

@@ -43,19 +43,19 @@ except KeyError:
     pass
 
 if interface == "SIMULATED_RAMAN_CONTROL":
-    from ramancom.simulatedraman import SimulatedRaman
+    from .simulatedraman import SimulatedRaman
     RamanControl = SimulatedRaman
     print("WARNING: using only simulated raman control!")
     simulatedRaman = True
     
 elif interface == "WITEC_CONTROL":
-    from ramancom.WITecCOM import WITecCOM
+    from .WITecCOM import WITecCOM
     RamanControl = WITecCOM
     RamanControl.magn = int(config["General Microscope Setup"]["magnification"])    # not yet implemented in WITecCOM, but would probably be a good idea...
     simulatedRaman = False
     
 elif interface == "RENISHAW_CONTROL":
-    from ramancom.renishawcom import RenishawCOM
+    from .renishawcom import RenishawCOM
     RamanControl = RenishawCOM
     RamanControl.magn = int(config["General Microscope Setup"]["magnification"])
     try:

ramancom/simulatedraman.py

@@ -24,7 +24,7 @@ Simualted Raman interface module for testing without actual raman system connect
 from time import sleep
 import numpy as np
 from shutil import copyfile
-from ramancom.ramanbase import RamanBase
+from .ramanbase import RamanBase
 
 
 class SimulatedRaman(RamanBase):
@@ -117,4 +117,4 @@ class SimulatedRaman(RamanBase):
         print("Scan number:", num)
         sleep(.1)
         if num==self.timeseries-1:
-            self.timeseries = False
\ No newline at end of file
+            self.timeseries = False

ramanscanui.py

@@ -24,7 +24,7 @@ import numpy as np
 from multiprocessing import Process, Queue, Event
 import queue
 from time import time
-from external import tsp
+from .external import tsp
 import datetime
 import sys
 import os
@@ -289,4 +289,4 @@ class RamanScanUI(QtWidgets.QWidget):
                 self.close()
                 return
         self.timer.start(100.)
-        
\ No newline at end of file
+        

sampleview.py

@@ -21,17 +21,17 @@ If not, see <https://www.gnu.org/licenses/>.
 from PyQt5 import QtCore, QtGui, QtWidgets
 import numpy as np
 import os
-from dataset import DataSet, loadData
-from ramancom.ramancontrol import RamanControl, simulatedRaman
-from opticalscan import OpticalScan
-from ramanscanui import RamanScanUI
-from detectionview import ParticleDetectionView
-from analysis.analysisview import ParticleAnalysis
-from zeissimporter import ZeissImporter
-from viewitems import FitPosIndicator, Node, Edge, ScanIndicator, RamanScanIndicator, SegmentationContours
-from helperfunctions import polygoncovering, cv2imread_fix
+from .dataset import DataSet, loadData
+from .ramancom.ramancontrol import RamanControl, simulatedRaman
+from .opticalscan import OpticalScan
+from .ramanscanui import RamanScanUI
+from .detectionview import ParticleDetectionView
+from .analysis.analysisview import ParticleAnalysis
+from .zeissimporter import ZeissImporter
+from .viewitems import FitPosIndicator, Node, Edge, ScanIndicator, RamanScanIndicator, SegmentationContours
+from .helperfunctions import polygoncovering, cv2imread_fix
 import cv2
-from ramancom.configRaman import RamanConfigWin
+from .ramancom.configRaman import RamanConfigWin
 
 class SampleView(QtWidgets.QGraphicsView):
     ScalingChanged = QtCore.pyqtSignal(float)
@@ -168,10 +168,12 @@ class SampleView(QtWidgets.QGraphicsView):
         if mode is None:
             return
         assert mode in ["OpticalScan", "ParticleDetection", "RamanScan", "ParticleAnalysis"]
+        print("switching to mode:", mode, flush=True)
         self.oscanwidget.setVisible(False)
         if self.detectionwidget is not None:
             self.detectionwidget.close()
             self.detectionwidget.destroy()
+            self.detectionwidget = None
         self.ramanwidget.setVisible(False)
         self.contouritem.resetContours([])
         self.mode = mode
@@ -186,6 +188,7 @@ class SampleView(QtWidgets.QGraphicsView):
                 self.detectionwidget.show()
                 self.detectionwidget.imageUpdate.connect(self.detectionUpdate)
                 self.detectionwidget.detectionFinished.connect(self.activateMaxMode)
+                self.detectionwidget.setVisible(True)
             
         elif mode == "RamanScan":
             self.ramanwidget.resetDataset(self.dataset)
@@ -313,8 +316,8 @@ class SampleView(QtWidgets.QGraphicsView):
                 x, y, z = self.dataset.mapToLengthRaman([p0.x(), p0.y()], 
                                                          microscopeMode=self.microscopeMode,
                                                          noz=(False if self.mode=="RamanScan" else True))
-                if z is not None:
-                    assert z>-100.
+                #if z is not None:
+                #    assert z>-100.
                 self.ramanctrl.moveToAbsolutePosition(x, y, z)
         elif event.button()==QtCore.Qt.LeftButton and self.mode=="ParticleDetection":
             p0 = self.mapToScene(event.pos())
@@ -534,4 +537,4 @@ class SampleView(QtWidgets.QGraphicsView):
             self.scene().removeItem(item)
         self.ramanscanitems = []
 
-        
\ No newline at end of file
+        

zeissimporter.py

@@ -20,11 +20,11 @@ If not, see <https://www.gnu.org/licenses/>.
 """
 import os
 from PyQt5 import QtCore, QtWidgets
-from zeissxml import ZeissHandler, make_parser
-from opticalscan import PointCoordinates
-from helperfunctions import cv2imread_fix, cv2imwrite_fix
-from ramancom.ramancontrol import defaultPath
-from dataset import DataSet
+from .zeissxml import ZeissHandler, make_parser
+from .opticalscan import PointCoordinates
+from .helperfunctions import cv2imread_fix, cv2imwrite_fix
+from .ramancom.ramancontrol import defaultPath
+from .dataset import DataSet
 from scipy.optimize import least_squares
 from itertools import permutations
 import cv2