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- #/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
- 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.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)) == "<class 'NoneType'>":
- 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)) == "<class 'NoneType'>":
- 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) == "<class 'NoneType'>":
- 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) == "<class 'NoneType'>":
- 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()
-
- 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 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()
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