Automated Test until Spectrum Scan

__main__.py

@@ -79,7 +79,7 @@ class GEPARDMainWindow(QtWidgets.QMainWindow):
         closeAll()
         
     @QtCore.pyqtSlot(float) 
-    def scalingChanged(self, scale):
+    def scalingChanged(self):
         self.zoomInAct.setEnabled(self.view.scaleFactor < 20.0)
         self.zoomOutAct.setEnabled(self.view.scaleFactor > .01)
         self.normalSizeAct.setEnabled(self.view.scaleFactor != 1.)
@@ -91,7 +91,7 @@ class GEPARDMainWindow(QtWidgets.QMainWindow):
         if fileName:
             self.fname = str(fileName)
             self.view.open(self.fname)  
-            self.scalingChanged(1.)
+            self.scalingChanged()
     
     @QtCore.pyqtSlot()         
     def importProject(self, fileName=False):
@@ -101,7 +101,7 @@ class GEPARDMainWindow(QtWidgets.QMainWindow):
         if fileName:
             self.fname = str(fileName)
             self.view.importProject(self.fname)  
-            self.scalingChanged(1.)
+            self.scalingChanged()
             
     @QtCore.pyqtSlot() 
     def new(self, fileName=False):
@@ -113,7 +113,7 @@ class GEPARDMainWindow(QtWidgets.QMainWindow):
             if isValid:
                 self.fname = str(fileName)
                 self.view.new(self.fname)  
-                self.scalingChanged(1.)
+                self.scalingChanged()
             else:
                 QtWidgets.QMessageBox.critical(self, "Error", msg)
             

gui/detectionview.py

@@ -299,7 +299,7 @@ class ParticleDetectionView(QtWidgets.QWidget):
         self.seg = Segmentation(self.dataset, self)
         self.seg.detectionState.connect(self.updateDetectionState)
         self.thread = None
-        self.threadrunning = False
+        self.detectThreadRunning = False
 
         logPath = os.path.join(self.dataset.path, 'detectionlog.txt')
         self.logger = logging.getLogger('detection')
@@ -397,8 +397,7 @@ class ParticleDetectionView(QtWidgets.QWidget):
                     grid.addWidget(paramui, i, 1, QtCore.Qt.AlignLeft)
                 else:
                     grid.addWidget(paramui, i, 0, 1, 2, QtCore.Qt.AlignLeft) 
-                    
-                
+
             if label is not None:
                 grid.addWidget(label, i, 0, QtCore.Qt.AlignLeft)
                 
@@ -448,7 +447,7 @@ class ParticleDetectionView(QtWidgets.QWidget):
         vbox.addWidget(self.hideSeedsInSampleViewBtn)
             
         self.slider = QtWidgets.QSlider(self)
-        self.slider.setRange(0,100)
+        self.slider.setRange(0, 100)
         self.slider.setValue(80)
         self.slider.setOrientation(QtCore.Qt.Horizontal)
         self.slider.sliderMoved.connect(self.imglabel.resetAlpha)
@@ -654,7 +653,7 @@ class ParticleDetectionView(QtWidgets.QWidget):
         self.updateImageSeeds()
         
     def detectShow(self, showname):
-        if not self.threadrunning:
+        if not self.detectThreadRunning:
             self.saveDetectParams(self.dataset)
             img = self.subimg.copy()
             kwargs = {}
@@ -699,7 +698,7 @@ class ParticleDetectionView(QtWidgets.QWidget):
         self.seg.cancelcomputation = True
         self.thread.join()
         self.seg.cancelcomputation = False
-        self.threadrunning = False
+        self.detectThreadRunning = False
         
     def blockUI(self):
         self.pdetectsub.setEnabled(False)
@@ -731,7 +730,7 @@ class ParticleDetectionView(QtWidgets.QWidget):
             return
         self.blockUI()
         self.pdetectall.setText("Cancel")
-        self.threadrunning = True
+        self.detectThreadRunning = True
         self.img = self.pyramid.getFullImage()
         self.thread = Thread(target=self._worker)
         self.thread.start()
@@ -743,7 +742,7 @@ class ParticleDetectionView(QtWidgets.QWidget):
     @QtCore.pyqtSlot()      
     def checkOnComputation(self):
         if self.thread is not None:
-            if not self.threadrunning:
+            if not self.detectThreadRunning:
                 self.thread = None
                 self.progressbar.disable()
                 self.unBlockUI()
@@ -794,7 +793,7 @@ class ParticleDetectionView(QtWidgets.QWidget):
         seedradius = self.seedradiusedit.value()
         self.seg.setParameters(**kwargs)
         try:
-            measurementPoints, contours= self.seg.apply2Image(self.img, seedpoints, deletepoints, seedradius, self.dataset, detectLogger)
+            measurementPoints, contours = self.seg.apply2Image(self.img, seedpoints, deletepoints, seedradius, self.dataset, detectLogger)
         except:
             showErrorMessageAsWidget('Fatal error in particle detection, see detectionlog for info')
             detectLogger.exception('Fatal error in particle detection')
@@ -804,7 +803,7 @@ class ParticleDetectionView(QtWidgets.QWidget):
         
         if self.dataset is not None:
             self.applyResultsToDataset(measurementPoints, contours)
-        self.threadrunning = False
+        self.detectThreadRunning = False
     
     def applyResultsToDataset(self, measurementPoints, contours):
         self.dataset.ramanscandone = False

gui/opticalscanui.py

@@ -62,7 +62,7 @@ def scan(path, sol, zpositions, grid, controlclass, dataqueue,
         for i, p in enumerate(grid):
             x, y = p
             z = sol[0]*x + sol[1]*y + sol[2]
-            for k, zk in (zlist if i%2==0 else zlist[::-1]):
+            for k, zk in (zlist if i % 2 == 0 else zlist[::-1]):
                 name = f"image_{i}_{k}.bmp"
                 logger.info(f'taking image {name}, time: ' + strftime("%d %b %Y %H:%M:%S", localtime()))
                 zik = z+zk
@@ -72,7 +72,7 @@ def scan(path, sol, zpositions, grid, controlclass, dataqueue,
                 if ishdr:
                     img_list = []
                     fname = os.path.join(path, f"tmp.bmp")
-                    values = [5.,25.,100.] 
+                    values = [5., 25., 100.]
                     for j, val in enumerate(values if (i%2+k%2)%2==0 else reversed(values)):
                         ramanctrl.setBrightness(val)
                         logger.info(f'writing hdr image to {fname}')
@@ -309,6 +309,7 @@ class OpticalScanUI(QtWidgets.QWidget):
     # def __init__(self, ramanctrl, dataset, logger, parent=None):
     def __init__(self, sampleview: 'SampleView'):
         super().__init__(sampleview, QtCore.Qt.Window)
+        self.timer = QtCore.QTimer(self)
         self.logger = sampleview.logger
         self.view: QtWidgets.QGraphicsView = sampleview
         mainLayout = QtWidgets.QVBoxLayout()
@@ -715,10 +716,9 @@ class OpticalScanUI(QtWidgets.QWidget):
             self.dataset.maxdim = p0 + p1
             self.dataset.mode = "opticalscan"
             self.dataset.save()
-            self.timer = QtCore.QTimer(self)
             self.timer.timeout.connect(self.checkOnScan)
             self.timer.setSingleShot(True)
-            self.timer.start(1000.)
+            self.timer.start(1000)
     
     @QtCore.pyqtSlot()      
     def checkOnScan(self):

helperfunctions.py

@@ -22,6 +22,8 @@ If not, see <https://www.gnu.org/licenses/>.
 import numpy as np
 import cv2
 import os
+import sys
+from PyQt5 import QtWidgets, QtCore
 
 try:
     from skimage.io import imread as skimread
@@ -123,3 +125,7 @@ def hasFTIRControl(sampleview) -> bool:
     """
     ramanName: str = sampleview.ramanctrl.name.lower()
     return ramanName.find('ftir') != -1
+
+
+def getAppFolder() -> str:
+    return QtCore.QStandardPaths.writableLocation(QtCore.QStandardPaths.AppLocalDataLocation)

ramancom/simulated/imageGenerator.py

@@ -21,14 +21,13 @@ If not, see <https://www.gnu.org/licenses/>.
 Image Generator for fake images for testing with simulated instrument interfaces
 """
 import os
-import sys
-from PyQt5 import QtWidgets, QtCore
 import cv2
 import numpy as np
 import noise
 from copy import deepcopy
 import pickle
 from typing import Tuple, List
+from ...helperfunctions import getAppFolder
 
 
 def particleIsVisible(particle: np.ndarray, full: np.ndarray, pos: Tuple[int, int]) -> bool:
@@ -133,8 +132,6 @@ class FakeCamera:
 
     def close(self) -> None:
         self.fakeFilter.saveToFile()
-        if self.fakeFilter.app is not None:
-            self.fakeFilter.app.deleteLater()
 
     def updateImageAtPosition(self, position: List[float]) -> None:
         """
@@ -205,7 +202,6 @@ class FakeFilter:
         self.presetParticles: List[dict] = []
         self.particles: List[FakeParticle] = []
         self.filePath: str = ''
-        self.app: QtWidgets.QApplication = None
         self._updateFromFile()
 
     def _updateFromFile(self) -> None:
@@ -238,20 +234,12 @@ class FakeFilter:
 
     def saveToFile(self) -> None:
         fpath: str = self._getFilePath()
-        # QApplication cannot be pickled, so we replace it temporarily with None
-        origApp = self.app
-        self.app = None
         with open(fpath, "wb") as fp:
             pickle.dump(self, fp, protocol=-1)
-        self.app = origApp
 
     def _getFilePath(self) -> str:
         if self.filePath == '':
-            if self.app is None:
-                self.app = QtWidgets.QApplication(sys.argv)  # has to be an instance attribute :/
-                self.app.setApplicationName("GEPARD")
-            path: str = QtCore.QStandardPaths.writableLocation(QtCore.QStandardPaths.AppLocalDataLocation)
-            self.filePath = os.path.join(path, 'fakeFilter.pkl')
+            self.filePath = os.path.join(getAppFolder(), 'fakeFilter.pkl')
         return self.filePath
 
     def getParticleImage(self, particle: FakeParticle, blurRadius: int = 0) -> np.ndarray:

ramancom/simulated/simulatedStage.py

@@ -21,16 +21,13 @@ If not, see <https://www.gnu.org/licenses/>.
 Simulates a Microscope Stage with Camera.
 """
 import os
-import sys
 from PyQt5 import QtWidgets, QtGui, QtCore
 import cv2
 import json
 import numpy as np
 from typing import List
-try:
-    from .imageGenerator import FakeCamera
-except ImportError:
-    from imageGenerator import FakeCamera
+from .imageGenerator import FakeCamera
+from ...helperfunctions import getAppFolder
 
 
 class SimulatedStage(object):
@@ -91,9 +88,7 @@ class SimulatedStage(object):
                 json.dump(self._configToDict(), fp)
 
     def _getFilePath(self) -> str:
-        self.app: QtWidgets.QApplication = QtWidgets.QApplication(sys.argv)  # has to be an instance attribute :/
-        self.app.setApplicationName("GEPARD")
-        path: str = QtCore.QStandardPaths.writableLocation(QtCore.QStandardPaths.AppLocalDataLocation)
+        path: str = getAppFolder()
         return os.path.join(path, 'simulatedStageConfig.txt')
 
     def _configToDict(self) -> dict:

ramanscanui.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/>.
-"""
-
-from PyQt5 import QtCore, QtWidgets
-import numpy as np
-from multiprocessing import Process, Queue, Event
-import queue
-import os
-import logging
-import logging.handlers
-from .external import tsp
-from .uielements import TimeEstimateProgressbar
-from .gepardlogging import setDefaultLoggingConfig
-from .analysis.particleCharacterization import FTIRAperture
-from .helperfunctions import getRamanControl
-
-
-def reorder(points, N=20):
-    """
-    Finds an efficient reordering of scan points in meandering horizontal 
-    stripes.
-    
-    Parameters
-    ----------
-    points : list of scan points in 2D
-    N : integer, optional
-        The number of horizontal stripes in which the points should be aranged. 
-        The default is 20.
-
-    Returns
-    -------
-    newind : index array
-        The new index array to reorder the scan points for efficient travel 
-        between points.
-
-    """
-    y0, y1 = points[:,1].min(), points[:,1].max()
-    y = np.linspace(y0,y1+.1,N+1)
-    allind = np.arange(points.shape[0])
-    newind = []
-    for i, yi in enumerate(y[:-1]):
-        yi1 = y[i+1]
-        indy = allind[(points[:,1]>=yi)&(points[:,1]<yi1)]
-        p = points[indy,:]
-        indx = p[:,0].argsort()
-        if i%2==1:
-            newind.append(indy[indx])
-        else:
-            newind.append(indy[indx[::-1]])
-    newind = np.concatenate(newind, axis=0)
-    assert np.unique(newind).shape[0]==allind.shape[0]
-    return newind
-
-
-def scan(ramanSettings, positions, controlclass, dataqueue, stopevent, 
-         logpath=''):
-    if logpath != '':
-        logger = logging.getLogger('RamanScanLogger')
-        logger.addHandler(
-            logging.handlers.RotatingFileHandler(
-                logpath, maxBytes=5 * (1 << 20), backupCount=10)
-        )
-        setDefaultLoggingConfig(logger)
-    
-    try:
-        ramanctrl = getRamanControl(controlclass, logger)
-        ramanctrl.connect()
-        if ramanctrl.name == 'ThermoFTIRCom':
-            ramanSettings['Apertures'] = positions
-
-        ramanctrl.initiateMeasurement(ramanSettings)
-        logger.info(ramanctrl.name)
-        for i, p in enumerate(positions):
-            if not ramanctrl.name == 'ThermoFTIRCom':
-                x, y, z = p
-            else:
-                x, y, z = p.centerX, p.centerY, p.centerZ
-                width, height, angle = p.width, p.height, p.angle
-                logger.info(f'{width}, {height}, {angle}')
-                ramanctrl.setAperture(width, height, angle)
-
-            logger.info(f"position: {x}, {y}, {z}")
-            ramanctrl.moveToAbsolutePosition(x, y, z)
-            logger.info("move done")
-            ramanctrl.triggerMeasurement(i)
-            logger.info("trigger done")
-            
-            if stopevent.is_set():
-                ramanctrl.disconnect()
-                return
-            
-            dataqueue.put(i)
-            
-        ramanctrl.finishMeasurement()
-        ramanctrl.disconnect()
-    except:
-        logger.exception('Fatal error in ramanscan')
-        from .errors import showErrorMessageAsWidget
-        showErrorMessageAsWidget('See ramanscanlog in project directory for information')
-
-
-class RamanScanUI(QtWidgets.QWidget):
-    imageUpdate = QtCore.pyqtSignal(str, name='imageUpdate')    #str = 'df' (= darkfield) or 'bf' (=bright field)
-    ramanscanUpdate = QtCore.pyqtSignal()
-    
-    def __init__(self, ramanctrl, dataset, logger, parent=None):
-        super().__init__(parent, QtCore.Qt.Window)
-        self.view = parent
-        self.logger = logger
-        self.ramanctrl = ramanctrl
-        self.dataset = dataset
-        self.process = None
-        self.processstopevent = Event()
-        self.dataqueue = Queue()
-        self.timer = QtCore.QTimer(self)
-        
-        vbox = QtWidgets.QVBoxLayout()
-        hbox = QtWidgets.QHBoxLayout()
-        
-        self.params = []
-        self.paramsGroup = QtWidgets.QGroupBox("Raman settings")
-        self.paramsLayout = QtWidgets.QFormLayout()
-
-        self.prun = QtWidgets.QPushButton("Raman scan", self)
-        self.prun.released.connect(self.run)
-        self.paramsGroup.setLayout(self.paramsLayout)
-        self.updateRamanParameters()
-        
-        self.pexit = QtWidgets.QPushButton("Cancel", self)
-        self.pexit.released.connect(self.cancelScan)
-        self.prun.setEnabled(False)
-
-        self.progressbar = TimeEstimateProgressbar()
-        self.progressbar.disable()
-        
-        hbox.addStretch()
-        hbox.addWidget(self.pexit)
-        
-        vbox.addWidget(self.paramsGroup)
-        vbox.addLayout(hbox)
-        vbox.addWidget(self.progressbar)
-        
-        self.setLayout(vbox)
-        self.setWindowTitle("Raman Scan")
-        self.setVisible(False)
-    
-    def updateRamanParameters(self):
-        """
-        Update the raman parameters in the layout
-        :return:
-        """
-        for index in reversed(range(self.paramsLayout.count())):
-            widget = self.paramsLayout.itemAt(index).widget()
-            self.paramsLayout.removeWidget(widget)
-            widget.setParent(None)
-            
-        self.params = []
-        for param in self.ramanctrl.ramanParameters:
-            if param.dtype == 'int':
-                self.params.append(QtWidgets.QSpinBox())
-                self.params[-1].setMinimum(param.minVal)
-                self.params[-1].setMaximum(param.maxVal)
-                self.params[-1].setValue(param.value)
-            if param.dtype == 'double':
-                self.params.append(QtWidgets.QDoubleSpinBox())
-                self.params[-1].setMinimum(param.minVal)
-                self.params[-1].setMaximum(param.maxVal)
-                self.params[-1].setValue(param.value)
-            if param.dtype == 'combobox':
-                self.params.append(QtWidgets.QComboBox())
-                self.params[-1].addItems([str(i) for i in param.valList])
-            if param.dtype == 'checkBox':
-                self.params.append(QtWidgets.QCheckBox())
-                self.params[-1].setChecked(param.value)
-        
-        for index, param in enumerate(self.params):
-            param.setMinimumWidth(70)
-            self.paramsLayout.addRow(QtWidgets.QLabel(self.ramanctrl.ramanParameters[index].name), param)
-            
-        self.paramsLayout.addRow(self.prun)
-        self.paramsGroup.setLayout(self.paramsLayout)
-            
-    def makeGetFnameLambda(self, msg, path, fileType, btn):
-        return lambda: self.getFName(msg, path, fileType, btn)
-    
-    def getFName(self, msg, path, filetype, btn):
-        fname = QtWidgets.QFileDialog.getOpenFileName(self, msg, path, filetype)[0]
-        btn.setText(fname.split('\\')[-1])
-        btn.setMinimumSize(btn.sizeHint())
-    
-    def resetDataset(self, ds):
-        self.dataset = ds
-        numParticles = self.dataset.particleContainer.getNumberOfParticles()
-        numMeasurements = self.dataset.particleContainer.getNumberOfMeasurements()
-        if numParticles>0:
-            self.prun.setEnabled(True)
-            self.setWindowTitle(f'{numParticles} Particles ({numMeasurements}  Measurements)')
-        
-    @QtCore.pyqtSlot()