#/usr/bin/env python import sys #import readline try: from akvo.gui.main_ui import Ui_MainWindow uicerr = False except: # Fallback from akvo.gui.mainui import Ui_MainWindow uicerr = """ USING THE DEFAULT GUI FILES, AKVO MAY NOT WORK CORRECTLY! See INSTALL.txt for details regarding GUI configuration if you are encountering problems. Clicking ignore will prevent this warning from showing each time you launch Akvo. """ import matplotlib #matplotlib.use("QT4Agg") from PyQt5 import QtCore, QtGui, QtWidgets import numpy as np import time import os from copy import deepcopy from matplotlib.backends.backend_qt4 import NavigationToolbar2QT #as NavigationToolbar import datetime, time from akvo.tressel import mrsurvey #from akvo.lemma import pyLemmaCore # Looking ahead! import pkg_resources # part of setuptools version = pkg_resources.require("Akvo")[0].version import yaml # Writes out numpy arrays into Eigen vectors as serialized by Lemma class MatrixXr(yaml.YAMLObject): yaml_tag = u'MatrixXr' def __init__(self, rows, cols, data): self.rows = rows self.cols = cols self.data = np.zeros((rows,cols)) def __repr__(self): return "%s(rows=%r, cols=%r, data=%r)" % (self.__class__.__name__, self.rows, self.cols, self.data) class VectorXr(yaml.YAMLObject): yaml_tag = r'VectorXr' def __init__(self, array): self.size = np.shape(array)[0] self.data = array.tolist() def __repr__(self): # Converts to numpy array on import return "np.array(%r)" % (self.data) from collections import OrderedDict #def represent_ordereddict(dumper, data): # print("representing IN DA HOUSE!!!!!!!!!!!!!!!!!!!!!") # value = [] # for item_key, item_value in data.items(): # node_key = dumper.represent_data(item_key) # node_value = dumper.represent_data(item_value) # value.append((node_key, node_value)) # return yaml.nodes.MappingNode(u'tag:yaml.org,2002:map', value) #yaml.add_representer(OrderedDict, represent_ordereddict) def setup_yaml(): """ https://stackoverflow.com/a/8661021 """ represent_dict_order = lambda self, data: self.represent_mapping('tag:yaml.org,2002:map', data.items()) yaml.add_representer(OrderedDict, represent_dict_order) setup_yaml() class AkvoYamlNode(yaml.YAMLObject): yaml_tag = u'AkvoData' def __init__(self): self.Akvo_VERSION = version self.Import = OrderedDict() # {} self.Processing = OrderedDict() #def __init__(self, node): # self.Akvo_VERSION = node["version"] # self.Import = OrderedDict( node["Import"] ) # {} # self.Processing = OrderedDict( node["Processing"] ) def __repr__(self): return "%s(name=%r, Akvo_VESION=%r, Import=%r, Processing=%r)" % ( #self.__class__.__name__, self.Akvo_VERSION, self.Import, self.Processing ) self.__class__.__name__, self.Akvo_VERSION, self.Import, OrderedDict(self.Processing) ) #self.__class__.__name__, self.Akvo_VERSION, self.Import, OrderedDict(self.Processing)) try: import thread except ImportError: import _thread as thread #Py3K compatibility class MyPopup(QtWidgets.QWidget): def __init__(self, name): super().__init__() self.name = name self.initUI() def initUI(self): lblName = QtWidgets.QLabel(self.name, self) class ApplicationWindow(QtWidgets.QMainWindow): def __init__(self): QtWidgets.QMainWindow.__init__(self) self.setAttribute(QtCore.Qt.WA_DeleteOnClose) akvohome = os.path.expanduser("~") + "/.akvo" if not os.path.exists(akvohome): os.makedirs(akvohome) self.ui = Ui_MainWindow() self.ui.setupUi(self) if uicerr != False and not os.path.exists(akvohome+"/pyuic-warned"): reply = QtGui.QMessageBox.warning(self, 'Warning', uicerr, QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ignore) if reply == 1024: # "0x400" in hex pass elif reply == 1048576: # "0x100000" in hex warn = open( akvohome+"/pyuic-warned" ,"w" ) warn.write("Gui files were not compiled locally using pyuic! Further warnings have been supressed") warn.close() self.RAWDataProc = None self.YamlNode = AkvoYamlNode() # initialise some stuff self.ui.lcdNumberTauPulse2.setEnabled(0) self.ui.lcdNumberTauPulse1.setEnabled(0) self.ui.lcdNumberNuTx.setEnabled(0) self.ui.lcdNumberTuneuF.setEnabled(0) self.ui.lcdNumberSampFreq.setEnabled(0) self.ui.lcdNumberTauDelay.setEnabled(0) self.ui.lcdNumberNQ.setEnabled(0) #MAK 20170126: add in a list to hold processing steps self.logText = [] #################### # Make connections # #################### # Menu items self.ui.actionOpen_GMR.triggered.connect(self.openGMRRAWDataset) self.ui.actionSave_Preprocessed_Dataset.triggered.connect(self.SavePreprocess) self.ui.actionExport_Preprocessed_Dataset.triggered.connect(self.ExportPreprocess) self.ui.actionExport_Preprocessed_Dataset.setEnabled(False) self.ui.actionOpen_Preprocessed_Dataset.triggered.connect(self.OpenPreprocess) self.ui.actionAboutAkvo.triggered.connect(self.about) # Buttons # #QtCore.QObject.connect(self.ui.fullWorkflowPushButton, QtCore.SIGNAL("clicked()"), self.preprocess ) self.ui.loadDataPushButton.pressed.connect(self.loadRAW) self.ui.sumDataGO.pressed.connect( self.sumDataChans ) self.ui.bandPassGO.pressed.connect( self.bandPassFilter ) self.ui.filterDesignPushButton.pressed.connect( self.designFilter ) self.ui.fdDesignPushButton.pressed.connect( self.designFDFilter ) self.ui.downSampleGO.pressed.connect( self.downsample ) self.ui.windowFilterGO.pressed.connect( self.windowFilter ) # self.ui.despikeGO.pressed.connect( self.despikeFilter ) # use smart stack instead self.ui.adaptGO.pressed.connect( self.adaptFilter ) self.ui.adaptFDGO.pressed.connect( self.adaptFilterFD ) self.ui.qdGO.pressed.connect( self.quadDet ) self.ui.gateIntegrateGO.pressed.connect( self.gateIntegrate ) self.ui.calcQGO.pressed.connect( self.calcQ ) self.ui.FDSmartStackGO.pressed.connect( self.FDSmartStack ) self.ui.harmonicGO.pressed.connect( self.harmonicModel ) self.ui.plotQD.setEnabled(False) self.ui.plotQD.pressed.connect( self.plotQD ) self.ui.plotGI.setEnabled(False) self.ui.plotGI.pressed.connect( self.plotGI ) # hide header info box #self.ui.headerFileBox.setVisible(False) self.ui.headerFileBox.clicked.connect( self.headerBoxShrink ) self.ui.headerBox2.setVisible(False) # Clean up the tab widget self.ui.actionPreprocessing.triggered.connect(self.addPreProc) self.ui.actionModelling.triggered.connect(self.addModelling) self.ui.actionInversion.triggered.connect(self.addInversion) # tabs #self.ui.ProcTabs.tabCloseRequested.connect( self.closeTabs ) #self.ui.ProcTabs.tabBar().setTabButton(7, QtWidgets.QTabBar.RightSide,None) self.ui.ProcTabs.removeTab(4) self.ui.ProcTabs.removeTab(4) self.ui.ProcTabs.removeTab(4) self.ui.ProcTabs.removeTab(4) #self.ui.LoadTab.close( ) # Add progressbar to statusbar self.ui.barProgress = QtWidgets.QProgressBar() self.ui.statusbar.addPermanentWidget(self.ui.barProgress, 0); self.ui.barProgress.setMaximumSize(100, 16777215); self.ui.barProgress.hide(); self.ui.mplwidget_navigator.setCanvas(self.ui.mplwidget) #self.ui.mplwidget_navigator_2.setCanvas(self.ui.mplwidget) ########################################################################## # Loop Table self.ui.loopTableWidget.setRowCount(80) self.ui.loopTableWidget.setColumnCount(6) self.ui.loopTableWidget.setHorizontalHeaderLabels( ["ch. tag", \ "Northing [m]","Easting [m]","Height [m]", "Radius","Tx"] ) for ir in range(0, self.ui.loopTableWidget.rowCount() ): for ic in range(1, self.ui.loopTableWidget.columnCount() ): pCell = QtWidgets.QTableWidgetItem() #pCell.setFlags(QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable) pCell.setFlags(QtCore.Qt.NoItemFlags) # not selectable pCell.setBackground( QtGui.QColor("lightgrey").lighter(110) ) self.ui.loopTableWidget.setItem(ir, ic, pCell) self.ui.loopTableWidget.cellChanged.connect(self.loopCellChanged) #self.ui.loopTableWidget.cellPressed.connect(self.loopCellChanged) self.ui.loopTableWidget.itemClicked.connect(self.loopCellClicked) #self.ui.loopTableWidget.cellPressed.connect(self.loopCellClicked) self.ui.loopTableWidget.setDragDropOverwriteMode(False) self.ui.loopTableWidget.setDragEnabled(False) #self.ui.loopTableWidget.setDragDropMode(QtWidgets.QAbstractItemView.InternalMove) self.loops = {} ########################################################################## # layer Table self.ui.layerTableWidget.setRowCount(80) self.ui.layerTableWidget.setColumnCount(3) self.ui.layerTableWidget.setHorizontalHeaderLabels( [r"top [m]", r"bottom [m]", "σ [ Ωm]" ] ) # do we want this self.ui.layerTableWidget.setDragDropOverwriteMode(False) self.ui.layerTableWidget.setDragEnabled(True) self.ui.layerTableWidget.setDragDropMode(QtWidgets.QAbstractItemView.InternalMove) pCell = QtWidgets.QTableWidgetItem() pCell.setFlags(QtCore.Qt.NoItemFlags) # not selectable pCell.setBackground( QtGui.QColor("lightgrey").lighter(110) ) self.ui.layerTableWidget.setItem(0, 1, pCell) for ir in range(1, self.ui.layerTableWidget.rowCount() ): for ic in range(0, self.ui.layerTableWidget.columnCount() ): pCell = QtWidgets.QTableWidgetItem() #pCell.setFlags(QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable) pCell.setFlags(QtCore.Qt.NoItemFlags) # not selectable pCell.setBackground( QtGui.QColor("lightgrey").lighter(110) ) self.ui.layerTableWidget.setItem(ir, ic, pCell) self.ui.layerTableWidget.cellChanged.connect(self.sigmaCellChanged) def closeTabs(self): #self.ui.ProcTabs.removeTab(idx) self.ui.ProcTabs.clear( ) def addPreProc(self): if self.ui.actionPreprocessing.isChecked(): self.ui.actionModelling.setChecked(False) self.ui.actionInversion.setChecked(False) self.ui.ProcTabs.clear( ) self.ui.ProcTabs.insertTab( 0, self.ui.LoadTab, "Load" ) self.ui.ProcTabs.insertTab( 1, self.ui.NCTab, "NC" ) self.ui.ProcTabs.insertTab( 2, self.ui.QCTab, "QC" ) self.ui.ProcTabs.insertTab( 3, self.ui.METATab, "META" ) self.ui.ProcTabs.insertTab( 4, self.ui.LogTab, "Log" ) else: self.ui.ProcTabs.removeTab(0) self.ui.ProcTabs.removeTab(0) self.ui.ProcTabs.removeTab(0) self.ui.ProcTabs.removeTab(0) def addModelling(self): if self.ui.actionModelling.isChecked(): self.ui.actionPreprocessing.setChecked(False) self.ui.actionInversion.setChecked(False) self.ui.ProcTabs.clear( ) self.ui.ProcTabs.insertTab( 0, self.ui.KernTab, "Kernel" ) self.ui.ProcTabs.insertTab( 1, self.ui.ModelTab, "Modelling" ) self.ui.ProcTabs.insertTab( 2, self.ui.LogTab, "Log" ) else: self.ui.ProcTabs.removeTab(0) self.ui.ProcTabs.removeTab(0) def addInversion(self, idx): if self.ui.actionInversion.isChecked(): self.ui.actionPreprocessing.setChecked(False) self.ui.actionModelling.setChecked(False) self.ui.ProcTabs.clear( ) self.ui.ProcTabs.insertTab( 0, self.ui.InvertTab, "Inversion" ) self.ui.ProcTabs.insertTab( 1, self.ui.AppraiseTab, "Appraisal" ) self.ui.ProcTabs.insertTab( 2, self.ui.LogTab, "Log" ) else: self.ui.ProcTabs.removeTab(0) self.ui.ProcTabs.removeTab(0) def headerBoxShrink(self): #self.ui.headerFileBox.setVisible(False) if self.ui.headerFileBox.isChecked( ): #self.ui.headerFileBox.setMinimumSize(460,250) self.ui.headerBox2.setVisible(True) else: #self.ui.headerFileBox.setMinimumSize(460,50) self.ui.headerBox2.setVisible(False) def sigmaCellChanged(self): self.ui.layerTableWidget.cellChanged.disconnect(self.sigmaCellChanged) # TODO consider building the model whenever this is called. Would be nice to be able to # do that. Would require instead dist of T2 I guess. jj = self.ui.layerTableWidget.currentColumn() ii = self.ui.layerTableWidget.currentRow() val = "class 'NoneType'>" try: val = eval (str( self.ui.layerTableWidget.item(ii, jj).text() )) except: #if jj != 0: # Error = QtWidgets.QMessageBox() # Error.setWindowTitle("Error!") # Error.setText("Non-numeric value encountered") self.ui.layerTableWidget.cellChanged.connect(self.sigmaCellChanged) return if jj == 1: #item.setFlags(QtCore.Qt.ItemIsEnabled) pCell = self.ui.layerTableWidget.item(ii, jj) pCell.setBackground( QtGui.QColor("white")) pCell = self.ui.layerTableWidget.item(ii+1, jj-1) if str(type(pCell)) == "": pCell = QtWidgets.QTableWidgetItem() pCell.setFlags(QtCore.Qt.ItemIsEnabled) self.ui.layerTableWidget.setItem(ii+1, jj-1, pCell) if ii == 0: pCell.setText(str(val)) #pCell3 = self.ui.layerTableWidget.item(ii+1, jj) #print ("setting", ii, jj, type(pCell3)) #print ( "setting", ii, jj, type(pCell3)) #pCell3.setFlags( QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEditable | QtCore.Qt.ItemIsEnabled ) #pCell3.setFlags( QtCore.Qt.ItemIsEditable ) elif ii > 0: val2 = eval (str( self.ui.layerTableWidget.item(ii-1, jj).text() )) #print ("val2", val2, val, type(val)) #if str(type(pCell)) == "": if type(val) == str or val > val2: pCell.setText(str(val)) else: Error = QtWidgets.QMessageBox() Error.setWindowTitle("Error!") Error.setText("Non-increasing layer detected") Error.setDetailedText("Each layer interface must be below the one above it.") Error.exec_() pCell2 = self.ui.layerTableWidget.item(ii, jj) pCell2.setText(str("")) self.ui.layerTableWidget.cellChanged.connect(self.sigmaCellChanged) return # enable next layer pCell4 = self.ui.layerTableWidget.item(ii+1, jj) pCell4.setBackground( QtGui.QColor("lightblue") ) #.lighter(110)) pCell4.setFlags( QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEditable | QtCore.Qt.ItemIsEnabled ) pCell5 = self.ui.layerTableWidget.item(ii+1, jj+1) pCell5.setBackground( QtGui.QColor("white")) pCell5.setFlags( QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEditable | QtCore.Qt.ItemIsEnabled ) print("ii", ii, "jj", jj) if ii == 0 and jj == 0: pCell = self.ui.layerTableWidget.item(0, 1) pCell.setBackground( QtGui.QColor("lightblue")) #.lighter(110) ) pCell.setFlags( QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEditable | QtCore.Qt.ItemIsEnabled ) self.ui.layerTableWidget.cellChanged.connect(self.sigmaCellChanged) def loopCellClicked(self, item): print("checkstate", item.checkState(),item.row()) #self.ui.loopTableWidget.itemClicked.disconnect(self.loopCellClicked) jj = item.column() ii = item.row() tp = type(self.ui.loopTableWidget.item(ii, 0)) print("tp", tp, ii, jj) if str(tp) == "": return #print("Clicked", ii, jj) if jj == 5 and self.ui.loopTableWidget.item(ii, 0).text() in self.loops.keys(): #print("jj=5") self.loops[ self.ui.loopTableWidget.item(ii, 0).text() ]["Tx"] = self.ui.loopTableWidget.item(ii, 5).checkState() # update surrogates print("updating surrogates") for point in self.loops[ self.ui.loopTableWidget.item(ii, 0).text() ]["points"][1:]: pCell = self.ui.loopTableWidget.item(point, 5) if self.ui.loopTableWidget.item(ii, 5).checkState(): pCell.setCheckState(QtCore.Qt.Checked); else: pCell.setCheckState(QtCore.Qt.Unchecked); #print( "loops", self.loops[ self.ui.loopTableWidget.item(ii, 0).text() ]["Tx"]) #self.ui.loopTableWidget.itemClicked.connect(self.loopCellClicked) def loopCellChanged(self): self.ui.loopTableWidget.cellChanged.disconnect(self.loopCellChanged) jj = self.ui.loopTableWidget.currentColumn() ii = self.ui.loopTableWidget.currentRow() if jj == 0 and len( self.ui.loopTableWidget.item(ii, jj).text().strip()) == 0: for jjj in range(jj+1,jj+6): pCell = self.ui.loopTableWidget.item(ii, jjj) pCell.setBackground( QtGui.QColor("white") ) pCell.setFlags( QtCore.Qt.NoItemFlags | QtCore.Qt.ItemIsUserCheckable ) # not selectable elif jj == 0 and len( self.ui.loopTableWidget.item(ii, jj).text().strip() ): # ch. tag modified for jjj in range(jj+1,jj+5): pCell = self.ui.loopTableWidget.item(ii, jjj) pCell.setFlags( QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEditable | QtCore.Qt.ItemIsEnabled ) pCell.setBackground( QtGui.QColor("lightblue") ) if self.ui.loopTableWidget.item(ii, jj).text() not in self.loops.keys(): # This is a new loop ID self.loops[ self.ui.loopTableWidget.item(ii, jj).text() ] = {} self.loops[ self.ui.loopTableWidget.item(ii, jj).text() ]["Tx"] = self.ui.loopTableWidget.item(ii, 5).checkState() self.loops[ self.ui.loopTableWidget.item(ii, jj).text() ]["points"] = [ii] # Transmitter cell pCell = self.ui.loopTableWidget.item(ii, jj+5) pCell.setCheckState(QtCore.Qt.Unchecked) pCell.setFlags( QtCore.Qt.ItemIsUserCheckable | QtCore.Qt.ItemIsEnabled ) pCell.setBackground( QtGui.QColor("lightblue") ) else: # This is an existing loop ID self.loops[ self.ui.loopTableWidget.item(ii, jj).text() ]["points"].append( ii ) pCell = self.ui.loopTableWidget.item(ii, jj+5) pCell.setFlags(QtCore.Qt.NoItemFlags) # not selectable if self.loops[ self.ui.loopTableWidget.item(ii, 0).text() ]["Tx"]: pCell.setCheckState(QtCore.Qt.Checked); else: pCell.setCheckState(QtCore.Qt.Unchecked); #pCell.setFlags( ) pCell.setBackground( QtGui.QColor("lightblue") ) self.plotLoops() self.ui.loopTableWidget.cellChanged.connect(self.loopCellChanged) def plotLoops(self): print("Plotting loopz") self.ui.mplwidget.reAxH(1) #self.ui.mplwidget.ax1.clear() #self.ui.mplwidget.ax2.clear() nor = dict() eas = dict() dep = dict() for ii in range( self.ui.loopTableWidget.rowCount() ): for jj in range( self.ui.loopTableWidget.columnCount() ): tp = type(self.ui.loopTableWidget.item(ii, jj)) if str(tp) == "": pass elif not len(self.ui.loopTableWidget.item(ii, jj).text()): pass else: if jj == 0: idx = self.ui.loopTableWidget.item(ii, 0).text() if idx not in nor.keys(): nor[idx] = list() eas[idx] = list() dep[idx] = list() if jj == 1: nor[idx].append( eval(self.ui.loopTableWidget.item(ii, 1).text()) ) elif jj == 2: eas[idx].append( eval(self.ui.loopTableWidget.item(ii, 2).text()) ) elif jj == 3: dep[idx].append( eval(self.ui.loopTableWidget.item(ii, 3).text()) ) for ii in nor.keys(): try: self.ui.mplwidget.ax1.plot( np.array(nor[ii]), np.array(eas[ii]) ) except: pass #self.ui.mplwidget.figure.axes().set self.ui.mplwidget.ax1.set_aspect('equal') #, adjustable='box') self.ui.mplwidget.draw() def about(self): # TODO proper popup with info #self.w = MyPopup("""About Akvo \n # Akvo is an open source project developed primarily by Trevor Irons. #""") #self.w.setGeometry(100, 100, 400, 200) #self.w.show() # Just a splash screen for now logo = pkg_resources.resource_filename(__name__, 'akvo_about.png') pixmap = QtGui.QPixmap(logo) self.splash = QtWidgets.QSplashScreen(pixmap, QtCore.Qt.WindowStaysOnTopHint) self.splash.show() def connectGMRDataProcessor(self): self.RAWDataProc = mrsurvey.GMRDataProcessor() self.RAWDataProc.progressTrigger.connect(self.updateProgressBar) self.RAWDataProc.enableDSPTrigger.connect(self.enableDSP) self.RAWDataProc.doneTrigger.connect(self.doneStatus) self.RAWDataProc.updateProcTrigger.connect(self.updateProc) def openGMRRAWDataset(self): """ Opens a GMR header file """ try: with open('.gmr.last.path') as f: fpath = f.readline() pass except IOError as e: fpath = '.' self.headerstr = QtWidgets.QFileDialog.getOpenFileName(self, 'Open File', fpath)[0] # arg2 = File Type 'All Files (*)' self.ui.headerFileTextBrowser.clear() self.ui.headerFileTextBrowser.append(self.headerstr) if len(self.headerstr) == 0: return # clear the processing log self.ui.logTextBrowser.clear() self.logText = [] #MAK 20170126 path,filen=os.path.split(str(self.headerstr)) f = open('.gmr.last.path', 'w') f.write( str(self.headerstr) ) # prompt last file self.connectGMRDataProcessor() self.RAWDataProc.readHeaderFile(str(self.headerstr)) # If we got this far, enable all the widgets self.ui.lcdNumberTauPulse1.setEnabled(True) self.ui.lcdNumberNuTx.setEnabled(True) self.ui.lcdNumberTuneuF.setEnabled(True) self.ui.lcdNumberSampFreq.setEnabled(True) self.ui.lcdNumberNQ.setEnabled(True) self.ui.headerFileBox.setEnabled(True) self.ui.headerFileBox.setChecked( True ) self.ui.headerBox2.setVisible(True) self.ui.inputRAWParametersBox.setEnabled(True) self.ui.loadDataPushButton.setEnabled(True) # make plots as you import the dataset self.ui.plotImportCheckBox.setEnabled(True) self.ui.plotImportCheckBox.setChecked(True) # Update info from the header into the GUI self.ui.pulseTypeTextBrowser.clear() self.ui.pulseTypeTextBrowser.append(self.RAWDataProc.pulseType) self.ui.lcdNumberNuTx.display(self.RAWDataProc.transFreq) self.ui.lcdNumberTauPulse1.display(1e3*self.RAWDataProc.pulseLength[0]) self.ui.lcdNumberTuneuF.display(self.RAWDataProc.TuneCapacitance) self.ui.lcdNumberSampFreq.display(self.RAWDataProc.samp) self.ui.lcdNumberNQ.display(self.RAWDataProc.nPulseMoments) self.ui.DeadTimeSpinBox.setValue(1e3*self.RAWDataProc.deadTime) self.ui.CentralVSpinBox.setValue( self.RAWDataProc.transFreq ) if self.RAWDataProc.pulseType != "FID": self.ui.lcdNumberTauPulse2.setEnabled(1) self.ui.lcdNumberTauPulse2.display(1e3*self.RAWDataProc.pulseLength[1]) self.ui.lcdNumberTauDelay.setEnabled(1) self.ui.lcdNumberTauDelay.display(1e3*self.RAWDataProc.interpulseDelay) self.ui.FIDProcComboBox.clear() if self.RAWDataProc.pulseType == "4PhaseT1": self.ui.FIDProcComboBox.insertItem(0, "Pulse 1") self.ui.FIDProcComboBox.insertItem(1, "Pulse 2") self.ui.FIDProcComboBox.insertItem(2, "Both") self.ui.FIDProcComboBox.setCurrentIndex (1) elif self.RAWDataProc.pulseType == "FID": self.ui.FIDProcComboBox.insertItem(0, "Pulse 1") self.ui.FIDProcComboBox.setCurrentIndex (0) def ExportPreprocess(self): """ This method export to YAML """ try: with open('.akvo.last.yaml.path') as f: fpath = f.readline() pass except IOError as e: fpath = '.' fdir = os.path.dirname(fpath) # Pickle the preprocessed data dictionary SaveStr = QtWidgets.QFileDialog.getSaveFileName(self, "Save as", fdir, r"Processed data (*.yaml)")[0] spath,filen=os.path.split(str(SaveStr)) f = open('.akvo.last.yaml.path', 'w') f.write( str(spath) ) # prompt last file INFO = {} INFO["headerstr"] = str(self.headerstr) INFO["pulseType"] = self.RAWDataProc.pulseType INFO["transFreq"] = self.RAWDataProc.transFreq.tolist() INFO["pulseLength"] = self.RAWDataProc.pulseLength.tolist() INFO["TuneCapacitance"] = self.RAWDataProc.TuneCapacitance.tolist() #INFO["samp"] = self.RAWDataProc.samp INFO["nPulseMoments"] = self.RAWDataProc.nPulseMoments #INFO["deadTime"] = self.RAWDataProc.deadTime INFO["processed"] = "Akvo v. 1.0, on " + time.strftime("%d/%m/%Y") # Pulse current info ip = 0 INFO["Pulses"] = {} for pulse in self.RAWDataProc.DATADICT["PULSES"]: qq = [] qv = [] for ipm in range(self.RAWDataProc.DATADICT["nPulseMoments"]): #for istack in self.RAWDataProc.DATADICT["stacks"]: # print ("stack q", self.RAWDataProc.DATADICT[pulse]["Q"][ipm,istack-1]) qq.append(np.mean( self.RAWDataProc.DATADICT[pulse]["Q"][ipm,:]) ) qv.append(np.std( self.RAWDataProc.DATADICT[pulse]["Q"][ipm,:]/self.RAWDataProc.pulseLength[ip] )) INFO["Pulses"][pulse] = {} INFO["Pulses"][pulse]["units"] = "A" INFO["Pulses"][pulse]["current"] = VectorXr(np.array(qq)/self.RAWDataProc.pulseLength[ip]) INFO["Pulses"][pulse]["variance"] = VectorXr(np.array(qv)) ip += 1 # Data if self.RAWDataProc.gated == True: INFO["Gated"] = {} INFO["Gated"]["abscissa units"] = "ms" INFO["Gated"]["data units"] = "nT" for pulse in self.RAWDataProc.DATADICT["PULSES"]: INFO["Gated"][pulse] = {} INFO["Gated"][pulse]["abscissa"] = VectorXr( self.RAWDataProc.GATEDABSCISSA ) INFO["Gated"][pulse]["windows"] = VectorXr( self.RAWDataProc.GATEDWINDOW ) for ichan in self.RAWDataProc.DATADICT[pulse]["chan"]: INFO["Gated"][pulse]["Chan. " + str(ichan)] = {} INFO["Gated"][pulse]["Chan. " + str(ichan)]["STD"] = VectorXr( np.std(self.RAWDataProc.GATED[ichan]["NR"], axis=0) ) for ipm in range(self.RAWDataProc.DATADICT["nPulseMoments"]): INFO["Gated"][pulse]["Chan. " + str(ichan)]["Q-"+str(ipm) + " CA"] = VectorXr(self.RAWDataProc.GATED[ichan]["CA"][ipm]) INFO["Gated"][pulse]["Chan. " + str(ichan)]["Q-"+str(ipm) + " RE"] = VectorXr(self.RAWDataProc.GATED[ichan]["RE"][ipm]) INFO["Gated"][pulse]["Chan. " + str(ichan)]["Q-"+str(ipm) + " IM"] = VectorXr(self.RAWDataProc.GATED[ichan]["IM"][ipm]) #INFO["Gated"][pulse]["Chan. " + str(ichan)]["Q-"+str(ipm) + " IP"] = VectorXr(self.RAWDataProc.GATED[ichan]["IP"][ipm]) #INFO["Gated"][pulse]["Chan. " + str(ichan)]["Q-"+str(ipm) + " NR"] = VectorXr(self.RAWDataProc.GATED[ichan]["NR"][ipm]) #INFO["Gated"][pulse]["Chan. " + str(ichan)]["Q-"+str(ipm) + " STD" ] = VectorXr(self.RAWDataProc.GATED[ichan]["SIGMA"][ipm]) # we have gated data # Window edges # Window centres with open(SaveStr, 'w') as outfile: #for line in self.logText: # outfile.write(line+"\n") yaml.dump(self.YamlNode, outfile) yaml.dump(INFO, outfile, default_flow_style=False) def SavePreprocess(self): #if "Saved" not in self.YamlNode.Processing.keys(): # self.YamlNode.Processing["Saved"] = [] #self.YamlNode.Processing["Saved"].append(datetime.datetime.now().isoformat()) #self.Log() import pickle, os try: with open('.akvo.last.path') as f: fpath = f.readline() pass except IOError as e: fpath = '.' fdir = os.path.dirname(fpath) # Pickle the preprocessed data dictionary SaveStr = QtWidgets.QFileDialog.getSaveFileName(self, "Save as", fdir, r"Pickle (*.dmp)") print(SaveStr) spath,filen=os.path.split(str(SaveStr[0])) f = open('.akvo.last.path', 'w') f.write( str(spath) ) # prompt last file save = open(SaveStr[0], 'wb') # Add some extra info INFO = {} INFO["pulseType"] = self.RAWDataProc.pulseType INFO["transFreq"] = self.RAWDataProc.transFreq INFO["pulseLength"] = self.RAWDataProc.pulseLength INFO["TuneCapacitance"] = self.RAWDataProc.TuneCapacitance INFO["samp"] = self.RAWDataProc.samp INFO["nPulseMoments"] = self.RAWDataProc.nPulseMoments INFO["deadTime"] = self.RAWDataProc.deadTime INFO["transFreq"] = self.RAWDataProc.transFreq INFO["headerstr"] = str(self.headerstr) INFO["log"] = yaml.dump( self.YamlNode ) #self.logText #MAK 20170127 self.RAWDataProc.DATADICT["INFO"] = INFO pickle.dump(self.RAWDataProc.DATADICT, save) save.close() # Export XML file suitable for USGS ScienceBase Data Release def ExportXML(self): """ This is a filler function for use by USGS collaborators """ return 42 def OpenPreprocess(self): import pickle try: with open('.akvo.last.path') as f: fpath = f.readline() pass except IOError as e: fpath = '.' #filename = QtWidgets.QFileDialog.getOpenFileName(self, 'Open File', '.') fpath = QtWidgets.QFileDialog.getOpenFileName(self, 'Open preprocessed file', fpath, r"Pickle Files (*.dmp)")[0] f = open('.akvo.last.path', 'w') f.write( str(fpath) ) # prompt last file self.ui.logTextBrowser.clear() self.logText = [] if len(fpath) == 0: return pfile = open(fpath,'rb') unpickle = pickle.Unpickler(pfile) self.connectGMRDataProcessor() self.RAWDataProc.DATADICT = unpickle.load() # This line causes Akvo to crash, if the header file is no longer there. We don't need to load the # file. TODO, need to disable "Load Data" in Load command though, as that is no longer possible. #self.RAWDataProc.readHeaderFile(self.RAWDataProc.DATADICT["INFO"]["headerstr"]) self.headerstr = self.RAWDataProc.DATADICT["INFO"]["headerstr"] self.RAWDataProc.pulseType = self.RAWDataProc.DATADICT["INFO"]["pulseType"] self.RAWDataProc.transFreq = self.RAWDataProc.DATADICT["INFO"]["transFreq"] self.RAWDataProc.pulseLength = self.RAWDataProc.DATADICT["INFO"]["pulseLength"] self.RAWDataProc.TuneCapacitance = self.RAWDataProc.DATADICT["INFO"]["TuneCapacitance"] self.RAWDataProc.samp = self.RAWDataProc.DATADICT["INFO"]["samp"] self.RAWDataProc.nPulseMoments = self.RAWDataProc.DATADICT["INFO"]["nPulseMoments"] self.RAWDataProc.deadTime = self.RAWDataProc.DATADICT["INFO"]["deadTime"] self.RAWDataProc.transFreq = self.RAWDataProc.DATADICT["INFO"]["transFreq"] self.RAWDataProc.dt = 1./self.RAWDataProc.samp self.dataChan = self.RAWDataProc.DATADICT[ self.RAWDataProc.DATADICT["PULSES"][0] ]["chan"] # Keep backwards compatibility with prior saved pickles??? #self.ui.logTextBrowser.clear() #self.ui.logTextBrowser.append( yaml.dump(self.YamlNode)) #, default_flow_style=False) ) #for a in self.logText: # self.ui.logTextBrowser.append(str(a)) #self.ui.logTextBrowser #self.ui.logTextBrowser.clear() #print ( self.RAWDataProc.DATADICT["INFO"]["log"] ) self.logText = self.RAWDataProc.DATADICT["INFO"]["log"] # YAML self.YamlNode = AkvoYamlNode( ) #self.logText ) self.YamlNode.Akvo_VERSION = (yaml.load( self.logText )).Akvo_VERSION self.YamlNode.Import = OrderedDict((yaml.load( self.logText )).Import) self.YamlNode.Processing = OrderedDict((yaml.load( self.logText )).Processing) #self.YamlNode.Akvo_VERSION = 2 #yaml.load( self.logText )["Akvo_VERSION"] #, Loader=yaml.RoundTripLoader) # offending line! #self.YamlNode = AkvoYamlNode( self.logText ) # offending line! #print("import type", type( self.YamlNode.Processing )) self.Log() #self.ui.logTextBrowser.append( yaml.dump(self.YamlNode)) #, default_flow_style=False) ) #except KeyError: # pass # Remove "Saved" and "Loaded" from processing flow #if "Loaded" not in self.YamlNode.Processing.keys(): # self.YamlNode.Processing["Loaded"] = [] #self.YamlNode.Processing["Loaded"].append(datetime.datetime.now().isoformat()) #self.Log() # If we got this far, enable all the widgets self.ui.lcdNumberTauPulse1.setEnabled(True) self.ui.lcdNumberNuTx.setEnabled(True) self.ui.lcdNumberTuneuF.setEnabled(True) self.ui.lcdNumberSampFreq.setEnabled(True) self.ui.lcdNumberNQ.setEnabled(True) self.ui.headerFileBox.setEnabled(True) self.ui.headerFileBox.setChecked( False ) #self.ui.headerBox2.setVisible(True) self.ui.inputRAWParametersBox.setEnabled(True) self.ui.loadDataPushButton.setEnabled(True) # make plots as you import the dataset self.ui.plotImportCheckBox.setEnabled(True) self.ui.plotImportCheckBox.setChecked(True) # Update info from the header into the GUI self.ui.pulseTypeTextBrowser.clear() self.ui.pulseTypeTextBrowser.append(self.RAWDataProc.pulseType) self.ui.lcdNumberNuTx.display(self.RAWDataProc.transFreq) self.ui.lcdNumberTauPulse1.display(1e3*self.RAWDataProc.pulseLength[0]) self.ui.lcdNumberTuneuF.display(self.RAWDataProc.TuneCapacitance) self.ui.lcdNumberSampFreq.display(self.RAWDataProc.samp) self.ui.lcdNumberNQ.display(self.RAWDataProc.nPulseMoments) self.ui.DeadTimeSpinBox.setValue(1e3*self.RAWDataProc.deadTime) self.ui.CentralVSpinBox.setValue( self.RAWDataProc.transFreq ) if self.RAWDataProc.pulseType != "FID": self.ui.lcdNumberTauPulse2.setEnabled(1) self.ui.lcdNumberTauPulse2.display(1e3*self.RAWDataProc.pulseLength[1]) self.ui.lcdNumberTauDelay.setEnabled(1) self.ui.lcdNumberTauDelay.display(1e3*self.RAWDataProc.interpulseDelay) self.ui.FIDProcComboBox.clear() if self.RAWDataProc.pulseType == "4PhaseT1": self.ui.FIDProcComboBox.insertItem(0, "Pulse 1") #, const QVariant & userData = QVariant() ) self.ui.FIDProcComboBox.insertItem(1, "Pulse 2") #, const QVariant & userData = QVariant() ) self.ui.FIDProcComboBox.insertItem(2, "Both") #, const QVariant & userData = QVariant() ) if len( self.RAWDataProc.DATADICT["PULSES"]) == 2: self.ui.FIDProcComboBox.setCurrentIndex (2) elif self.RAWDataProc.DATADICT["PULSES"][0] == "Pulse 1": self.ui.FIDProcComboBox.setCurrentIndex (0) else: self.ui.FIDProcComboBox.setCurrentIndex (1) elif self.RAWDataProc.pulseType == "FID": self.ui.FIDProcComboBox.insertItem(0, "Pulse 1") #, const QVariant & userData = QVariant() ) self.ui.FIDProcComboBox.setCurrentIndex (0) # QtCore.QObject.connect(self.RAWDataProc, QtCore.SIGNAL("updateProgress(int)"), self.updateProgressBar) # QtCore.QObject.connect(self.RAWDataProc, QtCore.SIGNAL("enableDSP()"), self.enableDSP) # QtCore.QObject.connect(self.RAWDataProc, QtCore.SIGNAL("doneStatus()"), self.doneStatus) self.RAWDataProc.progressTrigger.connect(self.updateProgressBar) self.RAWDataProc.enableDSPTrigger.connect(self.enableDSP) self.RAWDataProc.doneTrigger.connect(self.doneStatus) self.enableAll() def loadRAW(self): ################################################# # Check to make sure we are ready to process # Header if self.RAWDataProc == None: err_msg = "You need to load a header first." reply = QtGui.QMessageBox.critical(self, 'Error', err_msg) #, QtGui.QMessageBox.Yes, QtGui.QMessageBox.No) return # Stacks try: self.procStacks = np.array(eval(str("np.r_["+self.ui.stacksLineEdit.text())+"]")) except: err_msg = "You need to set your stacks correctly.\n" + \ "This should be a Python Numpy interpretable list\n" + \ "of stack indices. For example 1:24 or 1:4,8:24" QtGui.QMessageBox.critical(self, 'Error', err_msg) return # Data Channels #Chan = np.arange(0,9,1) try: self.dataChan = np.array(eval(str("np.r_["+self.ui.dataChanLineEdit.text())+"]")) except: #QMessageBox messageBox; #messageBox.critical(0,"Error","An error has occured !"); #messageBox.setFixedSize(500,200); #quit_msg = "Are you sure you want to exit the program?" #reply = QtGui.QMessageBox.question(self, 'Message', # quit_msg, QtGui.QMessageBox.Yes, QtGui.QMessageBox.No) err_msg = "You need to set your data channels correctly.\n" + \ "This should be a Python Numpy interpretable list\n" + \ "of indices. For example 1 or 1:3 or 1:3 5\n\n" + \ "valid GMR data channels fall between 1 and 8. Note that\n" +\ "1:3 is not inclusive of 3 and is the same as 1,2 " reply = QtGui.QMessageBox.critical(self, 'Error', err_msg) #, QtGui.QMessageBox.Yes, QtGui.QMessageBox.No) return ############################# # Reference Channels # TODO make sure no overlap between data and ref channels self.refChan = np.array( () ) if str(self.ui.refChanLineEdit.text()): # != "none": try: self.refChan = np.array(eval(str("np.r_["+self.ui.refChanLineEdit.text())+"]")) except: err_msg = "You need to set your reference channels correctly.\n" + \ "This should be a Python Numpy interpretable list\n" + \ "of indices. For example 1 or 1:3 or 1:3 5\n\n" + \ "valid GMR data channels fall between 1 and 8. Note that\n" +\ "1:3 is not inclusive of 3 and is the same as 1,2 " QtGui.QMessageBox.critical(self, 'Error', err_msg) return ##################################################### # Load data self.lock("loading RAW GMR dataset") if self.RAWDataProc.pulseType == "FID": self.procThread = thread.start_new_thread(self.RAWDataProc.loadFIDData, \ (str(self.headerstr), self.procStacks, self.dataChan, self.refChan, \ str(self.ui.FIDProcComboBox.currentText()), self.ui.mplwidget, \ 1e-3 * self.ui.DeadTimeSpinBox.value( ), self.ui.plotImportCheckBox.isChecked() )) #, self)) elif self.RAWDataProc.pulseType == "4PhaseT1": self.procThread = thread.start_new_thread(self.RAWDataProc.load4PhaseT1Data, \ (str(self.headerstr), self.procStacks, self.dataChan, self.refChan, \ str(self.ui.FIDProcComboBox.currentText()), self.ui.mplwidget, \ 1e-3 * self.ui.DeadTimeSpinBox.value( ), self.ui.plotImportCheckBox.isChecked() )) #, self)) self.YamlNode.Import["GMR Header"] = self.headerstr self.YamlNode.Import["opened"] = datetime.datetime.now().isoformat() self.YamlNode.Import["pulse Type"] = str(self.RAWDataProc.pulseType) self.YamlNode.Import["stacks"] = self.procStacks.tolist() self.YamlNode.Import["data channels"] = self.dataChan.tolist() self.YamlNode.Import["reference channels"] = self.refChan.tolist() self.YamlNode.Import["pulse records"] = str(self.ui.FIDProcComboBox.currentText()) self.YamlNode.Import["instrument dead time"] = (1e-3 * self.ui.DeadTimeSpinBox.value( )) self.Log ( ) # should be already done # QtCore.QObject.connect(self.RAWDataProc, QtCore.SIGNAL("updateProgress(int)"), self.updateProgressBar) # QtCore.QObject.connect(self.RAWDataProc, QtCore.SIGNAL("enableDSP()"), self.enableDSP) # QtCore.QObject.connect(self.RAWDataProc, QtCore.SIGNAL("doneStatus()"), self.doneStatus) #self.ui.ProcessedBox.setEnabled(True) self.ui.lcdNumberFID1Length.setEnabled(1) self.ui.lcdNumberFID2Length.setEnabled(1) self.ui.lcdNumberResampFreq.setEnabled(1) self.ui.lcdTotalDeadTime.setEnabled(1) self.ui.lcdTotalDeadTime.display( self.ui.DeadTimeSpinBox.value( ) ) #self.ui.lcdNumberFID1Length.display(0) #self.ui.lcdNumberFID2Length.display(0) #self.ui.lcdNumberResampFreq.display( self.RAWDataProc.samp ) self.mpl_toolbar = NavigationToolbar2QT(self.ui.mplwidget, self.ui.mplwidget) self.ui.mplwidget.draw() def Log(self): #for line in yaml.dump(self.YamlNode, default_flow_style=False): #for line in nlogText: # self.ui.logTextBrowser.append( line ) # self.logText.append( line ) self.ui.logTextBrowser.clear() self.ui.logTextBrowser.append( yaml.dump(self.YamlNode)) #, default_flow_style=False) ) def disable(self): self.ui.BandPassBox.setEnabled(False) self.ui.downSampleGroupBox.setEnabled(False) self.ui.windowFilterGroupBox.setEnabled(False) # self.ui.despikeGroupBox.setEnabled(False) self.ui.adaptBox.setEnabled(False) self.ui.adaptFDBox.setEnabled(False) self.ui.qCalcGroupBox.setEnabled(False) self.ui.FDSmartStackGroupBox.setEnabled(False) self.ui.sumDataBox.setEnabled(False) self.ui.qdGroupBox.setEnabled(False) self.ui.gateBox.setEnabled(False) def enableAll(self): self.enableDSP() self.enableQC() def enableDSP(self): # Bandpass filter self.ui.BandPassBox.setEnabled(True) self.ui.BandPassBox.setChecked(True) self.ui.bandPassGO.setEnabled(False) # need to design first self.ui.plotBP.setEnabled(True) self.ui.plotBP.setChecked(True) # downsample self.ui.downSampleGroupBox.setEnabled(True) self.ui.downSampleGroupBox.setChecked(True) # window self.ui.windowFilterGroupBox.setEnabled(True) self.ui.windowFilterGroupBox.setChecked(True) # Despike # self.ui.despikeGroupBox.setEnabled(True) # self.ui.despikeGroupBox.setChecked(False) # Adaptive filtering self.ui.adaptBox.setEnabled(True) self.ui.adaptBox.setChecked(True) # FD Adaptive filtering self.ui.adaptFDBox.setEnabled(True) self.ui.adaptFDBox.setChecked(True) # sum group box try: if len(self.dataChan) > 1: self.ui.sumDataBox.setEnabled(True) self.ui.sumDataBox.setChecked(True) except: pass # Quadrature Detect self.ui.qdGroupBox.setEnabled(True) self.ui.qdGroupBox.setChecked(True) self.enableQC() def enableQC(self): # Q calc self.ui.qCalcGroupBox.setEnabled(True) self.ui.qCalcGroupBox.setChecked(True) # FD SmartStack self.ui.FDSmartStackGroupBox.setEnabled(True) self.ui.FDSmartStackGroupBox.setChecked(True) # Quadrature detect try: for pulse in self.RAWDataProc.DATADICT["PULSES"]: np.shape(self.RAWDataProc.DATADICT[pulse]["Q"]) self.RAWDataProc.DATADICT["stack"] self.ui.qdGroupBox.setEnabled(True) self.ui.qdGroupBox.setChecked(True) except: self.ui.qdGroupBox.setEnabled(False) self.ui.qdGroupBox.setChecked(False) # Gating try: self.RAWDataProc.DATADICT["CA"] self.ui.gateBox.setEnabled(True) self.ui.gateBox.setChecked(True) except: self.ui.gateBox.setEnabled(False) self.ui.gateBox.setChecked(False) def despikeFilter(self): self.lock("despike filter") thread.start_new_thread(self.RAWDataProc.despike, \ (self.ui.windowSpinBox.value(), \ self.ui.thresholdSpinBox.value(), \ str(self.ui.replComboBox.currentText()), \ self.ui.rollOnSpinBox.value(), \ self.ui.despikeInterpWinSpinBox.value(), self.ui.mplwidget)) def calcQ(self): if "Calc Q" not in self.YamlNode.Processing.keys(): #print("In CalcQ", yaml.dump(self.YamlNode.Processing) ) self.YamlNode.Processing["Calc Q"] = True #print( yaml.dump(self.YamlNode.Processing) ) self.Log() else: err_msg = "Q values have already been calculated" reply =QtWidgets.QMessageBox.critical(self, 'Error', err_msg) return self.lock("pulse moment calculation") thread.start_new_thread(self.RAWDataProc.effectivePulseMoment, \ (self.ui.CentralVSpinBox.value(), \ self.ui.mplwidget)) def harmonicModel(self): self.lock("harmonic noise modelling") thread.start_new_thread(self.RAWDataProc.harmonicModel, \ (self.ui.f0Spin.value(), \ self.ui.mplwidget)) def FDSmartStack(self): if "TD stack" not in self.YamlNode.Processing.keys(): self.YamlNode.Processing["TD stack"] = {} self.YamlNode.Processing["TD stack"]["outlier"] = str( self.ui.outlierTestCB.currentText() ) self.YamlNode.Processing["TD stack"]["cutoff"] = str( self.ui.MADCutoff.value() ) self.Log() else: err_msg = "TD noise cancellation has already been applied!" reply =QtWidgets.QMessageBox.critical(self, 'Error', err_msg) return self.lock("time-domain smart stack") thread.start_new_thread(self.RAWDataProc.TDSmartStack, \ (str(self.ui.outlierTestCB.currentText()), \ self.ui.MADCutoff.value(), self.ui.mplwidget)) def adaptFilter(self): if "TD noise cancellation" not in self.YamlNode.Processing.keys(): self.YamlNode.Processing["TD noise cancellation"] = {} self.YamlNode.Processing["TD noise cancellation"]["n_Taps"] = str(self.ui.MTapsSpinBox.value()) self.YamlNode.Processing["TD noise cancellation"]["lambda"] = str(self.ui.adaptLambdaSpinBox.value()) self.YamlNode.Processing["TD noise cancellation"]["truncate"] = str(self.ui.adaptTruncateSpinBox.value()) self.YamlNode.Processing["TD noise cancellation"]["mu"] = str(self.ui.adaptMuSpinBox.value()) self.YamlNode.Processing["TD noise cancellation"]["PCA"] = str(self.ui.PCAComboBox.currentText()) self.Log() else: err_msg = "TD noise cancellation has already been applied!" reply =QtWidgets.QMessageBox.critical(self, 'Error', err_msg) #return self.lock("TD noise cancellation filter") thread.start_new_thread(self.RAWDataProc.adaptiveFilter, \ (self.ui.MTapsSpinBox.value(), \ self.ui.adaptLambdaSpinBox.value(), \ self.ui.adaptTruncateSpinBox.value(), \ self.ui.adaptMuSpinBox.value(), \ str(self.ui.PCAComboBox.currentText()), \ self.ui.mplwidget)) def sumDataChans(self): if "Data sum" not in self.YamlNode.Processing.keys(): self.YamlNode.Processing["Data sum"] = True self.Log() else: err_msg = "Data channels have already been summed!" reply =QtWidgets.QMessageBox.critical(self, 'Error', err_msg) return self.lock("Summing data channels") self.dataChan = [self.dataChan[0]] self.ui.sumDataBox.setEnabled(False) thread.start_new_thread( self.RAWDataProc.sumData, ( self.ui.mplwidget, 7 ) ) def adaptFilterFD(self): self.lock("FD noise cancellation filter") thread.start_new_thread(self.RAWDataProc.adaptiveFilterFD, \ (str(self.ui.windowTypeComboBox.currentText()), \ self.ui.windowBandwidthSpinBox.value(), \ self.ui.CentralVSpinBox.value(), \ self.ui.mplwidget)) def bandPassFilter(self): if "Bandpass filter" not in self.YamlNode.Processing.keys(): self.YamlNode.Processing["Bandpass filter"] = {} self.YamlNode.Processing["Bandpass filter"]["central_nu"] = str(self.ui.CentralVSpinBox.value()) self.YamlNode.Processing["Bandpass filter"]["passband"] = str(self.ui.passBandSpinBox.value()) self.YamlNode.Processing["Bandpass filter"]["stopband"] = str(self.ui.stopBandSpinBox.value()) self.YamlNode.Processing["Bandpass filter"]["gpass"] = str(self.ui.gpassSpinBox.value()) self.YamlNode.Processing["Bandpass filter"]["gstop"] = str(self.ui.gstopSpinBox.value()) self.YamlNode.Processing["Bandpass filter"]["type"] = str(self.ui.fTypeComboBox.currentText()) self.Log() else: err_msg = "Bandpass filter has already been applied!" reply =QtWidgets.QMessageBox.critical(self, 'Error', err_msg) return self.lock("bandpass filter") nv = self.ui.lcdTotalDeadTime.value( ) + self.ui.lcdNumberFTauDead.value() self.ui.lcdTotalDeadTime.display( nv ) thread.start_new_thread(self.RAWDataProc.bandpassFilter, \ (self.ui.mplwidget, 0, self.ui.plotBP.isChecked() )) def downsample(self): self.lock("resampling") if "Resample" not in self.YamlNode.Processing.keys(): self.YamlNode.Processing["Resample"] = {} self.YamlNode.Processing["Resample"]["downsample factor"] = [] self.YamlNode.Processing["Resample"]["truncate length"] = [] self.YamlNode.Processing["Resample"]["downsample factor"].append( str(self.ui.downSampleSpinBox.value() ) ) self.YamlNode.Processing["Resample"]["truncate length"].append( str( self.ui.truncateSpinBox.value() ) ) self.Log( ) thread.start_new_thread(self.RAWDataProc.downsample, \ (self.ui.truncateSpinBox.value(), \ self.ui.downSampleSpinBox.value(), self.ui.mplwidget)) def quadDet(self): if "Quadrature detection" not in self.YamlNode.Processing.keys(): self.YamlNode.Processing["Quadrature detection"] = {} self.YamlNode.Processing["Quadrature detection"]["trim"] = str( self.ui.trimSpin.value() ) self.Log() else: err_msg = "Quadrature detection has already been done!" reply =QtWidgets.QMessageBox.critical(self, 'Error', err_msg) return self.lock("quadrature detection") thread.start_new_thread(self.RAWDataProc.quadDet, \ (self.ui.trimSpin.value(), int(self.ui.QDType.currentIndex()), self.ui.mplwidget)) self.ui.plotQD.setEnabled(True) def plotQD(self): self.lock("plot QD") thread.start_new_thread(self.RAWDataProc.plotQuadDet, \ (self.ui.trimSpin.value(), int(self.ui.QDType.currentIndex()), self.ui.mplwidget)) def gateIntegrate(self): if "Gate integrate" not in self.YamlNode.Processing.keys(): self.YamlNode.Processing["Gate integrate"] = {} self.YamlNode.Processing["Gate integrate"]["gpd"] = str(self.ui.GPDspinBox.value( ) ) self.Log() self.lock("gate integration") thread.start_new_thread(self.RAWDataProc.gateIntegrate, \ (self.ui.GPDspinBox.value(), self.ui.trimSpin.value(), self.ui.mplwidget)) self.ui.actionExport_Preprocessed_Dataset.setEnabled(True) self.ui.plotGI.setEnabled(True) def plotGI(self): self.lock("plot gate integrate") thread.start_new_thread(self.RAWDataProc.plotGateIntegrate, \ (self.ui.GPDspinBox.value(), self.ui.trimSpin.value(), \ self.ui.QDType_2.currentIndex(), self.ui.mplwidget)) def designFilter(self): [bord, fe] = self.RAWDataProc.designFilter( \ self.ui.CentralVSpinBox.value(), \ self.ui.passBandSpinBox.value(), \ self.ui.stopBandSpinBox.value(), \ self.ui.gpassSpinBox.value(), \ self.ui.gstopSpinBox.value(), \ str(self.ui.fTypeComboBox.currentText()), self.ui.mplwidget) self.ui.lcdNumberFilterOrder.display(bord) self.ui.lcdNumberFTauDead.display(1e3*fe) #self.ui.lcdNumberFilterOrder.display(bord) self.ui.bandPassGO.setEnabled(1) # self.ui.lcdNumberTauPulse2.display(1e3*self.RAWDataProc.pulseLength[1]) def windowFilter(self): if "Window filter" not in self.YamlNode.Processing.keys(): self.YamlNode.Processing["Window filter"] = {} self.YamlNode.Processing["Window filter"]["type"] = str(self.ui.windowTypeComboBox.currentText()) self.YamlNode.Processing["Window filter"]["width"] = str(self.ui.windowBandwidthSpinBox.value()) self.YamlNode.Processing["Window filter"]["centre"] = str(self.ui.CentralVSpinBox.value() ) self.Log() else: err_msg = "FD window has already been applied!" reply =QtWidgets.QMessageBox.critical(self, 'Error', err_msg) return self.lock("window filter") thread.start_new_thread(self.RAWDataProc.windowFilter, \ (str(self.ui.windowTypeComboBox.currentText()), \ self.ui.windowBandwidthSpinBox.value(), \ self.ui.CentralVSpinBox.value(), \ self.ui.mplwidget)) def designFDFilter(self): # thread.start_new_thread(self.RAWDataProc.computeWindow, ( \ # "Pulse 1", # self.ui.windowBandwidthSpinBox.value(), \ # self.ui.CentralVSpinBox.value(), \ # str(self.ui.windowTypeComboBox.currentText()), \ # self.ui.mplwidget )) a,b,c,d,dead = self.RAWDataProc.computeWindow( \ "Pulse 1", self.ui.windowBandwidthSpinBox.value(), \ self.ui.CentralVSpinBox.value(), \ str(self.ui.windowTypeComboBox.currentText()), \ self.ui.mplwidget ) self.ui.lcdWinDead.display(dead) def updateProgressBar(self, percent): self.ui.barProgress.setValue(percent) def updateProc(self): if str(self.ui.FIDProcComboBox.currentText()) == "Pulse 1": self.ui.lcdNumberFID1Length.display(self.RAWDataProc.DATADICT["Pulse 1"]["TIMES"][-1]- self.RAWDataProc.DATADICT["Pulse 1"]["TIMES"][0]) elif str(self.ui.FIDProcComboBox.currentText()) == "Pulse 2": self.ui.lcdNumberFID2Length.display(self.RAWDataProc.DATADICT["Pulse 2"]["TIMES"][-1]- self.RAWDataProc.DATADICT["Pulse 2"]["TIMES"][0]) else: self.ui.lcdNumberFID1Length.display(self.RAWDataProc.DATADICT["Pulse 1"]["TIMES"][-1]- self.RAWDataProc.DATADICT["Pulse 1"]["TIMES"][0]) self.ui.lcdNumberFID2Length.display(self.RAWDataProc.DATADICT["Pulse 2"]["TIMES"][-1]- self.RAWDataProc.DATADICT["Pulse 2"]["TIMES"][0]) self.ui.lcdNumberResampFreq.display( self.RAWDataProc.samp ) def doneStatus(self): # unlocks GUI self.ui.statusbar.clearMessage ( ) self.ui.barProgress.hide() self.updateProc() self.enableAll() def lock(self, string): self.ui.statusbar.showMessage ( string ) self.ui.barProgress.show() self.ui.barProgress.setValue(0) self.disable() def unlock(self): self.ui.statusbar.clearMessage ( ) self.ui.barProgress.hide() self.enableAll() def done(self): self.ui.statusbar.showMessage ( "" ) ################################################################ ################################################################ # Boiler plate main function import pkg_resources from pkg_resources import resource_string import matplotlib.image as mpimg import matplotlib.pyplot as plt def main(): # splash screen logo logo = pkg_resources.resource_filename(__name__, 'akvo.png') logo2 = pkg_resources.resource_filename(__name__, 'akvo2.png') qApp = QtWidgets.QApplication(sys.argv) ssplash = False if ssplash: pixmap = QtGui.QPixmap(logo) splash = QtWidgets.QSplashScreen(pixmap, QtCore.Qt.WindowStaysOnTopHint) splash.show() aw = ApplicationWindow() img=mpimg.imread(logo) for ax in [ aw.ui.mplwidget ]: ax.fig.clear() subplot = ax.fig.add_subplot(111) #ax.fig.patch.set_facecolor( None ) #ax.fig.patch.set_alpha( .0 ) subplot.imshow(img) subplot.xaxis.set_major_locator(plt.NullLocator()) subplot.yaxis.set_major_locator(plt.NullLocator()) ax.draw() if ssplash: splash.showMessage("Loading modules") splash.finish(aw) #time.sleep(1) aw.setWindowTitle("Akvo v"+str(version)) aw.show() qApp.setWindowIcon(QtGui.QIcon(logo2)) sys.exit(qApp.exec_()) if __name__ == "__main__": main()