Several Bugfixes

analysis/analysisWidgets.py

@@ -19,7 +19,6 @@ along with this program, see COPYING.
 If not, see <https://www.gnu.org/licenses/>.
 """
 from PyQt5 import QtCore, QtWidgets, QtGui
-from PIL import ImageFont
 import numpy as np
 
 
@@ -60,14 +59,13 @@ class Legend(QtWidgets.QMdiSubWindow):
         if numEntries > 0:
             
             def getSize(fontsize, text, tileSize, spacer):
-#                font = ImageFont.truetype('arial.ttf', fontsize)
-#                size = font.getsize(text)
-                size = 5*len(text), fontsize+2
-                width, height = size[0]*1.5 + tileSize + spacer, numEntries * (tileSize+1*spacer) + 2*spacer
-                
+                font = QtGui.QFont()
+                font.setPixelSize(fontSize)
+                fm = QtGui.QFontMetrics(font)
+                pixelwidth = fm.width(text)
+                width, height = pixelwidth + tileSize + 3*spacer, numEntries * (tileSize+1*spacer) + 2*spacer
                 return width, height
             
-            
             fontSize, tileSize, spacer = self.fontSize, self.tileSize, self.spacer
             longestEntry = max([i[0] for i in self.items], key=len)
             width, height = getSize(fontSize, longestEntry, tileSize, spacer)

analysis/analysisview.py

@@ -40,8 +40,12 @@ from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as Navigatio
 
 import pandas as pd
 from analysis.loadresults import LoadWITecResults
-from analysis.sqlexport import SQLExport
 from analysis.editParticles import ParticleEditor
+try:
+    from analysis.sqlexport import SQLExport
+    sqlEnabled = True
+except:
+    sqlEnabled = False
 
 
 class ParticleAnalysis(QtWidgets.QWidget):
@@ -263,7 +267,6 @@ class ParticleAnalysis(QtWidgets.QWidget):
         self.layout_SArea.addWidget(self.resultCheckBoxes)
 #        self.layout_SArea.addStretch(1)
         
-        
         self.exportbtn= QtWidgets.QPushButton('Export Results')
         self.exportbtn.clicked.connect(self.exportData)
         self.exportbtn.setDisabled(True)
@@ -286,7 +289,23 @@ class ParticleAnalysis(QtWidgets.QWidget):
          
     def loadSpectra(self, fname):
         try:
-            return np.loadtxt(fname)
+            specs = np.loadtxt(fname)
+            #if spectra are already in correct format (WITec, first column: wavenumbers, other columns, intensities), 
+            #we take them, otherwise we have to convert from Renishaw export format...
+            if len(np.unique(specs[:, 0])) == len(specs[:, 0]): #--> only unique numbers -> this is the wavenumber column, we have the witec format
+                return specs
+            else:        
+                #columns 0 and 1 are x and y coordinates. We dont need them...
+                startWavenumber = specs[0, 2]
+                startIndices = np.where(specs[:, 2] == startWavenumber)[0]
+                
+                spectra = np.zeros((startIndices[1], len(startIndices)+1))   #create array with shape (numWavenumbers, numSpectra+1) (first column holds wavenumbers)
+                spectra[:, 0] = specs[startIndices[0]:startIndices[1], 2]
+                for i in range(len(startIndices)-1):
+                    spectra[:, i+1] = specs[startIndices[i]:startIndices[i+1], 3]
+                #aaand the last spectrum:
+                spectra[:, -1] = specs[startIndices[-1]:, 3]
+                return np.flip(spectra, 0)    #Renishaw goes from highest to lowest wavenumber, out of whatever reason...
         except:
             return None
         
@@ -295,21 +314,32 @@ class ParticleAnalysis(QtWidgets.QWidget):
         self.additiveResults = self.parent.dataset.results['additives']
         self.hqis = self.parent.dataset.results['hqis']
         self.addhqis = self.parent.dataset.results['additive_hqis']
-            
+                
         self.colorSeed = self.parent.dataset.colorSeed
         if type(self.colorSeed) != str:
             self.colorSeed = 'default'
         
         #load Spectra
-        self.spectra = self.loadSpectra(os.path.join(self.parent.dataset.path, self.parent.dataset.name + '_000_Spec.Data 1.txt'))
+        if self.parent.dataset.spectraPath is None:
+            fname = os.path.join(self.parent.dataset.path, self.parent.dataset.name + '_000_Spec.Data 1.txt')
+        else:
+            fname = self.parent.dataset.spectraPath
+        self.spectra = self.loadSpectra(fname)
         if self.spectra is None:
             fname = QtWidgets.QFileDialog.getOpenFileName(self, 'Select Spectra File', self.parent.dataset.path, 'text file (*.txt)')[0]
             self.spectra = self.loadSpectra(fname)
             if self.spectra is None:
                 QtWidgets.QMessageBox.critical(self, 'ERROR!', 'spectra file could not be opened with np.loadtxt...')
                 return
+        self.parent.dataset.spectraPath = fname
         self.spec_ax.set_xbound(100, (3400 if self.spectra[-1, 0] > 3400 else self.spectra[-1, 0]))
-
+        self.specCanvas.draw()
+        
+        ####fake data!!!
+        if self.spectraResults is None:
+            self.spectraResults = ['empty']*(self.spectra.shape[1]-1)
+            self.hqis = [100]*(self.spectra.shape[1]-1)
+        
         self.loadParticleData()
         
     def loadParticleData(self):
@@ -380,7 +410,9 @@ class ParticleAnalysis(QtWidgets.QWidget):
         self.particleResults = [None]*len(self.particlestats)
         self.typehistogram = {i: 0 for i in self.uniquePolymers}
         
-        assert len(self.particles2spectra) == len(self.particlestats), 'inconsistent data!!'
+        if len(self.particles2spectra) != len(self.particlestats):
+            QtWidgets.QMessageBox.critical(self, 'Error', 'Inconsistent particle data. Please restore backup!')
+            return
         
         for particleID, specList in enumerate(self.particles2spectra):
             assignment = self.currentPolymers[specList[0]]   #we take the first result as particle result. Hence, all spectra per particle have to have the same result
@@ -498,6 +530,7 @@ class ParticleAnalysis(QtWidgets.QWidget):
         self.spec_ax.set_xlabel('Wavenumber (cm-1)', fontsize = 15)
         self.spec_ax.set_ylabel('Counts', fontsize = 15)
         self.spec_ax.set_title('ScanPoint Number {}, Size = {} µm'.format(specIndex+1, np.round(self.particlestats[self.currentParticleIndex][2], 1)))
+        self.spec_ax.set_xbound(100, (3400 if self.spectra[-1, 0] > 3400 else self.spectra[-1, 0]))
         self.spec_ax.figure.canvas.draw()
         self.parent.centerOnRamanIndex(specIndex, centerOn=centerOn, highlightContour=highlightContour)
         self.parent.highLightRamanIndex(specIndex)
@@ -805,7 +838,10 @@ class ExportDialog(QtWidgets.QWidget):
 
         self.sqlbtn = QtWidgets.QPushButton('Export to SQL Database')
         self.sqlbtn.resize(self.sqlbtn.sizeHint()) 
-        self.sqlbtn.clicked.connect(self.toSQL)
+        if sqlEnabled:
+            self.sqlbtn.clicked.connect(self.toSQL)
+        else:
+            self.sqlbtn.setDisabled(True)
         
         self.sqlExport = None
 

analysis/editParticles.py

@@ -26,16 +26,33 @@ If not, see <https://www.gnu.org/licenses/>.
 """
 import numpy as np
 import cv2
+from PyQt5 import QtWidgets
 #import matplotlib.pyplot as plt
 
 class ParticleEditor(object):
     def __init__(self, parent):
         self.parent = parent    #the assigned analysis widget
+        self.backupFreq = 3     #save a backup every n actions
+        self.neverBackedUp = True
+        self.actionCounter = 0
 
     def createSafetyBackup(self):
-        self.parent.parent.dataset.saveBackup()
-
+        self.actionCounter += 1
+        if self.actionCounter == self.backupFreq-1 or self.neverBackedUp:            
+            print('backing up')
+            self.parent.parent.dataset.saveBackup()
+            self.neverBackedUp = False
+            self.actionCounter = 0
+        
+    def getNewEntry(self):
+        text, okClicked = QtWidgets.QInputDialog.getText(self.parent.parent, "Custom assignment", "Enter new assignment")
+        if okClicked and text != '':
+            return text
+    
     def combineParticles(self, contourIndices, new_assignment):
+        if new_assignment == 'other':
+            new_assignment = self.getNewEntry()
+        
         contourIndices = sorted(contourIndices)   #we want to keep the contour with lowest index
         print('selected contours:', contourIndices)
         self.createSafetyBackup()
@@ -76,7 +93,6 @@ class ParticleEditor(object):
             sortindices = self.parent.parent.dataset.ramanscansortindex
             self.parent.parent.dataset.particles2spectra = [[int(np.where(sortindices == i)[0])] for i in range(len(sortindices))]
         
-        
         #Contour indices are the same as the original particlestats, which are contained in the dataset. 
         #We have to modify that and reload in the analysisview
         #first, overwrite first index with new particlestats
@@ -89,7 +105,6 @@ class ParticleEditor(object):
         self.parent.parent.dataset.particlecontours[contourIndices[0]] = newContour
         self.parent.parent.dataset.particlecontours = [i for ind, i in enumerate(self.parent.parent.dataset.particlecontours) if ind not in contourIndices[1:]]
         
-        
         #update particle2spectra_list
         #what is the current particle index??
         specIndices = []
@@ -98,13 +113,12 @@ class ParticleEditor(object):
             specIndices.append(self.parent.particles2spectra[index])
         
         #flatten index list (in case, that a nested list was created...)
-        specIndices = list(np.unique(np.array(specIndices)))
+        specIndices = list(np.concatenate(specIndices))
         for i in specIndices:
             self.parent.spectraResults[i] = new_assignment
             self.parent.hqis[i] = 100   #avoid sorting them out again by hqi-filter...
             print(f'spectrum {i} of particle{contourIndices[0]} is now {new_assignment}')
         
-        
         #modify particles2spectra..         
         self.parent.parent.dataset.particles2spectra[contourIndices[0]] = specIndices
         for index in reversed(contourIndices[1:]):
@@ -116,11 +130,13 @@ class ParticleEditor(object):
         
         #update contours in sampleview
         self.parent.parent.contouritem.resetContours(self.parent.parent.dataset.particlecontours)
-        
         self.parent.loadParticleData()
        
     
     def reassignParticles(self, contourindices, new_assignment):
+        if new_assignment == 'other':
+            new_assignment = self.getNewEntry()
+            
         self.createSafetyBackup()
         for partIndex in contourindices:
             for specIndex in self.parent.particles2spectra[partIndex]:
@@ -128,7 +144,7 @@ class ParticleEditor(object):
                 self.parent.spectraResults[specIndex] = new_assignment
                 self.parent.hqis[specIndex] = 100
 
-        self.parent.createHistogramData()
+        self.parent.loadParticleData()
             
     
     def deleteParticles(self):

dataset.py

@@ -102,7 +102,7 @@ class DataSet(object):
 
         self.resultParams = {'minHQI': None,
                              'compHQI': None}
-        
+        self.spectraPath = None
         self.particles2spectra = None    #links idParticle to corresponding idSpectra (i.e., first measured particle (ID=0) is linked to spectra indices 0 and 1)
         self.colorSeed = 'default'
         self.resultsUploadedToSQL = []
@@ -177,13 +177,13 @@ class DataSet(object):
                 print('pixelscale was', self.pixelscale)
                 self.pixelscale_bf = self.pixelscale
                 self.pixelscale_df = self.pixelscale
-#                del self.pixelscale
+                del self.pixelscale
             
             if hasattr(self, 'imagedim'):
                 self.imagedim_bf = self.imagedim
                 self.imagedim_df = self.imagedim
-#                del self.imagedim
-            
+                del self.imagedim
+
             self.version = 2
             
         # add later conversion for higher version numbers here

gepard.py

@@ -25,6 +25,7 @@ from ramancom.ramancontrol import defaultPath
 from ramancom.ramanSwitch import RamanSwitch
 from analysis.analysisWidgets import Legend
 import os
+from pathlib import Path
             
 class MeasureParticleWindow(QtWidgets.QMainWindow):
     
@@ -287,12 +288,17 @@ if __name__ == '__main__':
 
     import sys
     from time import localtime, strftime
+    logpath = os.path.join(Path.home(),'gepard')
+    if not os.path.exists(logpath):
+        os.mkdir(logpath)
+    logname = os.path.join(logpath, 'logfile.txt')
 #    logname = os.path.join(os.path.split(__file__)[0], os.path.join("logfile.txt"))
-#    fp = open(logname, "a")
-#    sys.stderr = fp
-#    sys.stdout = fp
+    fp = open(logname, "a")
+    sys.stderr = fp
+    sys.stdout = fp
     
     print("starting GEPARD at: " + strftime("%d %b %Y %H:%M:%S", localtime()))
+    sys.stdout.flush()
     app = QtWidgets.QApplication(sys.argv)
     meas = MeasureParticleWindow()
     meas.showMaximized()

opticalscan.py

@@ -30,6 +30,7 @@ from helperfunctions import cv2imread_fix, cv2imwrite_fix
 from time import sleep, time
 import datetime
 import sys
+from pathlib import Path
 
 #def scan(path, sol, zpositions, grid, controlclass, connection, ishdr=False):
 def scan(path, sol, zpositions, grid, controlclass, dataqueue, stopevent, ishdr=False):
@@ -37,7 +38,9 @@ def scan(path, sol, zpositions, grid, controlclass, dataqueue, stopevent, ishdr=
     sys.stdout.flush()
     if ishdr:
         merge_mertens = cv2.createMergeMertens()
-    with open("scanlog.txt", "a") as fp:
+    
+    logpath = os.path.join(Path.home(),'gepard', 'scanlog.txt')        
+    with open(logpath, "a") as fp:
         sys.stderr = fp
         sys.stdout = fp
         

ramancom/WITecCOM.py

@@ -35,8 +35,6 @@ except:
     from ramanbase import RamanBase
     from configRaman import RamanSettingParam
 from socket import gethostname
-from PyQt5 import QtWidgets
-
 
 
 class WITecCOM(RamanBase):

ramanscanui.py

@@ -27,6 +27,8 @@ from time import sleep, time
 from external import tsp
 import datetime
 import sys
+import os
+from pathlib import Path
 
 def reorder(points, N=20):
     y0, y1 = points[:,1].min(), points[:,1].max()
@@ -47,7 +49,8 @@ def reorder(points, N=20):
     return newind
 
 def scan(ramanSettings, positions, controlclass, dataqueue, stopevent):
-    with open("ramanscanlog.txt", "a") as fp:
+    logpath = os.path.join(Path.home(),'gepard', 'ramanscanlog.txt')    
+    with open(logpath, "a") as fp:
         sys.stderr = fp
         sys.stdout = fp
         

viewitems.py

@@ -63,15 +63,22 @@ class SegmentationContours(QtWidgets.QGraphicsItem):
     
     def paint(self, painter, option, widget):           
         painter.setPen(QtCore.Qt.green)
-        
+        lenColorList = len(self.colorList)
         for index, c in enumerate(self.contours):
             if index not in self.selectedContours:
-                color = self.colorList[index]
+                if lenColorList > 0:
+                    color = self.colorList[index]
+                    painter.setPen(QtGui.QColor(int(color.red()*0.7), int(color.green()*0.7), int(color.blue()*0.7), color.alpha()))
+                else:
+                    color = QtCore.Qt.green
+                    painter.setPen(color)
                 painter.setBrush(color)
-                painter.setPen(QtGui.QColor(int(color.red()*0.7), int(color.green()*0.7), int(color.blue()*0.7), color.alpha()))
                 painter.drawPolygon(c)
             else:
-                alpha = self.colorList[index].alpha()
+                if lenColorList > 0:
+                    alpha = self.colorList[index].alpha()
+                else:
+                    alpha = 255
                 painter.setBrush(QtGui.QColor(200, 200, 200, alpha))
                 painter.setPen(QtCore.Qt.white)
                 painter.drawPolygon(c)
@@ -136,17 +143,17 @@ class SegmentationContours(QtWidgets.QGraphicsItem):
             print('deleting')
         elif action in combineActs:
             newAssignment = action.text()
-            if newAssignment == "other":
-                QtWidgets.QMessageBox.about(self.parent, "Not yet implemented", "we are getting there...")
-                return
+#            if newAssignment == "other":
+#                QtWidgets.QMessageBox.about(self.parent, "Not yet implemented", "we are getting there...")
+#                return
 
             self.parent.analysiswidget.editor.combineParticles(self.selectedContours, newAssignment)
             
         elif action in reassignActs:
             newAssignment = action.text()
-            if newAssignment == "other":
-                QtWidgets.QMessageBox.about(self.parent, "Not yet implemented", "we are getting there...")
-                return
+#            if newAssignment == "other":
+#                QtWidgets.QMessageBox.about(self.parent, "Not yet implemented", "we are getting there...")
+#                return
                 
             self.parent.analysiswidget.editor.reassignParticles(self.selectedContours, newAssignment)