Surface NMR processing and inversion GUI
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akvoGUI.py 72KB

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  1. #/usr/bin/env python
  2. import sys
  3. import matplotlib
  4. matplotlib.use("QT5Agg")
  5. from PyQt5 import QtCore, QtGui, QtWidgets #, uic
  6. import numpy as np
  7. import time
  8. import os
  9. from copy import deepcopy
  10. from matplotlib.backends.backend_qt4 import NavigationToolbar2QT #as NavigationToolbar
  11. import datetime, time
  12. import pkg_resources # part of setuptools
  13. from collections import OrderedDict
  14. from ruamel import yaml
  15. from akvo.gui.main_ui import Ui_MainWindow
  16. from akvo.gui.addCircularLoop_ui import Ui_circularLoopAdd
  17. from akvo.gui.addFigure8Loop_ui import Ui_figure8LoopAdd
  18. from akvo.gui.addPolygonalLoop_ui import Ui_polygonalLoopAdd
  19. from akvo.tressel import mrsurvey
  20. from pyLemma import LemmaCore
  21. from pyLemma import FDEM1D
  22. from pyLemma import Merlin
  23. VERSION = pkg_resources.require("Akvo")[0].version
  24. # Writes out numpy arrays into Eigen vectors as serialized by Lemma
  25. class MatrixXr(yaml.YAMLObject):
  26. yaml_tag = u'MatrixXr'
  27. def __init__(self, rows, cols, data):
  28. self.rows = rows
  29. self.cols = cols
  30. self.data = np.zeros((rows,cols))
  31. def __repr__(self):
  32. return "%s(rows=%r, cols=%r, data=%r)" % (self.__class__.__name__, self.rows, self.cols, self.data)
  33. class VectorXr(yaml.YAMLObject):
  34. yaml_tag = r'VectorXr'
  35. def __init__(self, array):
  36. self.size = np.shape(array)[0]
  37. self.data = array.tolist()
  38. def __repr__(self):
  39. # Converts to numpy array on import
  40. return "np.array(%r)" % (self.data)
  41. def setup_yaml():
  42. """ https://stackoverflow.com/a/8661021 """
  43. represent_dict_order = lambda self, data: self.represent_mapping('tag:yaml.org,2002:map', data.items())
  44. yaml.add_representer(OrderedDict, represent_dict_order)
  45. setup_yaml()
  46. class AkvoYamlNode(yaml.YAMLObject):
  47. yaml_tag = u'AkvoData'
  48. def __init__(self):
  49. self.Akvo_VERSION = VERSION
  50. self.Import = OrderedDict() # {}
  51. self.Processing = [] # OrderedDict()
  52. self.Stacking = OrderedDict()
  53. self.META = OrderedDict()
  54. def __repr__(self):
  55. return "%s(name=%r, Akvo_VERSION=%r, Import=%r, Processing=%r, self.Stacking=%r, self.META=%r)" % (
  56. self.__class__.__name__, self.Akvo_VERSION, self.Import, self.Processing, self.Stacking, self.META )
  57. try:
  58. import thread
  59. except ImportError:
  60. import _thread as thread #Py3K compatibility
  61. class MyPopup(QtWidgets.QWidget):
  62. def __init__(self, name):
  63. super().__init__()
  64. self.name = name
  65. self.initUI()
  66. def initUI(self):
  67. lblName = QtWidgets.QLabel(self.name, self)
  68. class ApplicationWindow(QtWidgets.QMainWindow):
  69. def __init__(self):
  70. super().__init__()
  71. #QtWidgets.QMainWindow.__init__(self)
  72. self.setAttribute(QtCore.Qt.WA_DeleteOnClose)
  73. # alternative to calling pyuic
  74. #self.ui = uic.loadUi('main.ui', self)
  75. self.ui = Ui_MainWindow()
  76. self.ui.setupUi(self)
  77. self.RAWDataProc = None
  78. self.YamlNode = AkvoYamlNode()
  79. # initialise some stuff
  80. self.ui.lcdNumberTauPulse2.setEnabled(0)
  81. self.ui.lcdNumberTauPulse1.setEnabled(0)
  82. self.ui.lcdNumberNuTx.setEnabled(0)
  83. self.ui.lcdNumberTuneuF.setEnabled(0)
  84. self.ui.lcdNumberSampFreq.setEnabled(0)
  85. self.ui.lcdNumberTauDelay.setEnabled(0)
  86. self.ui.lcdNumberNQ.setEnabled(0)
  87. self.logText = []
  88. #######################
  89. ##################### #
  90. ## Make connections # #
  91. ##################### #
  92. #######################
  93. ##############
  94. # Menu items #
  95. ##############
  96. self.ui.actionOpen_GMR.triggered.connect(self.openGMRRAWDataset)
  97. self.ui.actionSave_Preprocessed_Dataset.triggered.connect(self.SavePreprocess)
  98. self.ui.actionExport_Preprocessed_Dataset.triggered.connect(self.ExportPreprocess)
  99. self.ui.actionExport_Preprocessed_Dataset.setEnabled(False)
  100. self.ui.actionOpen_Preprocessed_Dataset.triggered.connect(self.OpenPreprocess)
  101. self.ui.actionAboutAkvo.triggered.connect(self.about)
  102. ###########
  103. # Buttons #
  104. ###########
  105. self.ui.loadDataPushButton.pressed.connect(self.loadRAW)
  106. self.ui.sumDataGO.pressed.connect( self.sumDataChans )
  107. self.ui.bandPassGO.pressed.connect( self.bandPassFilter )
  108. self.ui.filterDesignPushButton.pressed.connect( self.designFilter )
  109. self.ui.fdDesignPushButton.pressed.connect( self.designFDFilter )
  110. self.ui.downSampleGO.pressed.connect( self.downsample )
  111. self.ui.windowFilterGO.pressed.connect( self.windowFilter )
  112. self.ui.adaptGO.pressed.connect( self.adaptFilter )
  113. self.ui.adaptFDGO.pressed.connect( self.adaptFilterFD )
  114. self.ui.qdGO.pressed.connect( self.quadDet )
  115. self.ui.gateIntegrateGO.pressed.connect( self.gateIntegrate )
  116. self.ui.calcQGO.pressed.connect( self.calcQ )
  117. self.ui.FDSmartStackGO.pressed.connect( self.FDSmartStack )
  118. self.ui.harmonicGO.pressed.connect( self.harmonicModel )
  119. self.ui.f0K1Spin.valueChanged.connect( self.LCDHarmonics )
  120. self.ui.f0KNSpin.valueChanged.connect( self.LCDHarmonics )
  121. self.ui.f0KsSpin.valueChanged.connect( self.LCDHarmonics )
  122. self.ui.f0Spin.valueChanged.connect( self.LCDHarmonics )
  123. self.ui.NHarmonicsFreqsSpin.valueChanged.connect( self.LCDHarmonics2 )
  124. self.ui.f1K1Spin.valueChanged.connect( self.LCDHarmonics2 )
  125. self.ui.f1KNSpin.valueChanged.connect( self.LCDHarmonics2 )
  126. self.ui.f1KsSpin.valueChanged.connect( self.LCDHarmonics2 )
  127. self.ui.f1Spin.valueChanged.connect( self.LCDHarmonics2 )
  128. self.ui.plotQD.setEnabled(False)
  129. self.ui.plotQD.pressed.connect( self.plotQD )
  130. self.ui.plotGI.setEnabled(False)
  131. self.ui.plotGI.pressed.connect( self.plotGI )
  132. # META
  133. self.ui.locEdit.editingFinished.connect( self.logSite )
  134. self.ui.UTMzone.currentIndexChanged.connect( self.logSite )
  135. self.ui.latBand.currentIndexChanged.connect( self.logSite )
  136. self.ui.ellipsoid.currentIndexChanged.connect( self.logSite )
  137. self.ui.incSpinBox.valueChanged.connect( self.logSite )
  138. self.ui.decSpinBox.valueChanged.connect( self.logSite )
  139. self.ui.intensitySpinBox.valueChanged.connect( self.logSite )
  140. self.ui.tempSpinBox.valueChanged.connect( self.logSite )
  141. self.ui.timeEdit.timeChanged.connect( self.logSite )
  142. self.ui.dateEdit.dateChanged.connect( self.logSite )
  143. # this may call the yaml stuff too often...
  144. self.ui.txtComments.textChanged.connect( self.logSite )
  145. self.ui.plotLoops.pressed.connect( self.plotLoops2 )
  146. self.ui.removeLoopButton.pressed.connect( self.removeLoop )
  147. # Loops
  148. self.ui.addLoopButton.pressed.connect( self.loopAdd )
  149. self.loops = {}
  150. # hide header info box
  151. #self.ui.headerFileBox.setVisible(False)
  152. self.ui.headerFileBox.clicked.connect( self.headerBoxShrink )
  153. self.ui.headerBox2.setVisible(False)
  154. # Clean up the tab widget
  155. self.ui.actionPreprocessing.triggered.connect(self.addPreProc)
  156. self.ui.actionModelling.triggered.connect(self.addModelling)
  157. self.ui.actionInversion.triggered.connect(self.addInversion)
  158. # tabs
  159. #self.ui.ProcTabs.tabCloseRequested.connect( self.closeTabs )
  160. #self.ui.ProcTabs.tabBar().setTabButton(7, QtWidgets.QTabBar.RightSide,None)
  161. self.ui.ProcTabs.removeTab(4)
  162. self.ui.ProcTabs.removeTab(4)
  163. self.ui.ProcTabs.removeTab(4)
  164. self.ui.ProcTabs.removeTab(4)
  165. #self.ui.LoadTab.close( )
  166. # Add progressbar to statusbar
  167. self.ui.barProgress = QtWidgets.QProgressBar()
  168. self.ui.statusbar.addPermanentWidget(self.ui.barProgress, 0);
  169. self.ui.barProgress.setMaximumSize(100, 16777215);
  170. self.ui.barProgress.hide();
  171. self.ui.mplwidget_navigator.setCanvas(self.ui.mplwidget)
  172. #self.ui.mplwidget_navigator_2.setCanvas(self.ui.mplwidget)
  173. self.ui.txRxTable.setColumnCount(4)
  174. self.ui.txRxTable.setRowCount(0)
  175. self.ui.txRxTable.setHorizontalHeaderLabels( ["Label", "Geom.","Turns","Tx/Rx"] )
  176. ##########################################################################
  177. # layer Table
  178. self.ui.layerTableWidget.setRowCount(80)
  179. self.ui.layerTableWidget.setColumnCount(3)
  180. self.ui.layerTableWidget.setHorizontalHeaderLabels( [r"top [m]", r"bottom [m]", "σ [ Ωm]" ] )
  181. # do we want this
  182. self.ui.layerTableWidget.setDragDropOverwriteMode(False)
  183. self.ui.layerTableWidget.setDragEnabled(True)
  184. self.ui.layerTableWidget.setDragDropMode(QtWidgets.QAbstractItemView.InternalMove)
  185. pCell = QtWidgets.QTableWidgetItem()
  186. pCell.setFlags(QtCore.Qt.NoItemFlags) # not selectable
  187. pCell.setBackground( QtGui.QColor("lightgrey").lighter(110) )
  188. self.ui.layerTableWidget.setItem(0, 1, pCell)
  189. for ir in range(1, self.ui.layerTableWidget.rowCount() ):
  190. for ic in range(0, self.ui.layerTableWidget.columnCount() ):
  191. pCell = QtWidgets.QTableWidgetItem()
  192. #pCell.setFlags(QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
  193. pCell.setFlags(QtCore.Qt.NoItemFlags) # not selectable
  194. pCell.setBackground( QtGui.QColor("lightgrey").lighter(110) )
  195. self.ui.layerTableWidget.setItem(ir, ic, pCell)
  196. self.ui.layerTableWidget.cellChanged.connect(self.sigmaCellChanged)
  197. def LCDHarmonics(self):
  198. self.ui.lcdH1F.setEnabled(True)
  199. self.ui.lcdH1F.display( self.ui.f0Spin.value() * self.ui.f0K1Spin.value() )
  200. self.ui.lcdHNF.setEnabled(True)
  201. self.ui.lcdHNF.display( self.ui.f0Spin.value() * self.ui.f0KNSpin.value() )
  202. self.ui.lcdf0NK.setEnabled(True)
  203. self.ui.lcdf0NK.display( (self.ui.f0KNSpin.value()+1-self.ui.f0K1Spin.value()) * self.ui.f0KsSpin.value() )
  204. def LCDHarmonics2(self):
  205. if self.ui.NHarmonicsFreqsSpin.value() == 2:
  206. self.ui.lcdH1F2.setEnabled(True)
  207. self.ui.lcdH1F2.display( self.ui.f1Spin.value() * self.ui.f1K1Spin.value() )
  208. self.ui.lcdHNF2.setEnabled(True)
  209. self.ui.lcdHNF2.display( self.ui.f1Spin.value() * self.ui.f1KNSpin.value() )
  210. self.ui.lcdf0NK2.setEnabled(True)
  211. self.ui.lcdf0NK2.display( (self.ui.f1KNSpin.value()+1-self.ui.f1K1Spin.value()) * self.ui.f1KsSpin.value() )
  212. else:
  213. self.ui.lcdH1F2.setEnabled(False)
  214. self.ui.lcdHNF2.setEnabled(False)
  215. self.ui.lcdf0NK2.setEnabled(False)
  216. def closeTabs(self):
  217. #self.ui.ProcTabs.removeTab(idx)
  218. self.ui.ProcTabs.clear( )
  219. def addPreProc(self):
  220. if self.ui.actionPreprocessing.isChecked():
  221. self.ui.actionModelling.setChecked(False)
  222. self.ui.actionInversion.setChecked(False)
  223. self.ui.ProcTabs.clear( )
  224. self.ui.ProcTabs.insertTab( 0, self.ui.LoadTab, "Load" )
  225. self.ui.ProcTabs.insertTab( 1, self.ui.NCTab, "NC" )
  226. self.ui.ProcTabs.insertTab( 2, self.ui.QCTab, "QC" )
  227. self.ui.ProcTabs.insertTab( 3, self.ui.METATab, "META" )
  228. self.ui.ProcTabs.insertTab( 4, self.ui.LogTab, "Log" )
  229. else:
  230. self.ui.ProcTabs.removeTab(0)
  231. self.ui.ProcTabs.removeTab(0)
  232. self.ui.ProcTabs.removeTab(0)
  233. self.ui.ProcTabs.removeTab(0)
  234. def addModelling(self):
  235. if self.ui.actionModelling.isChecked():
  236. self.ui.actionPreprocessing.setChecked(False)
  237. self.ui.actionInversion.setChecked(False)
  238. self.ui.ProcTabs.clear( )
  239. self.ui.ProcTabs.insertTab( 0, self.ui.KernTab, "Kernel" )
  240. self.ui.ProcTabs.insertTab( 1, self.ui.ModelTab, "Modelling" )
  241. self.ui.ProcTabs.insertTab( 2, self.ui.LogTab, "Log" )
  242. else:
  243. self.ui.ProcTabs.removeTab(0)
  244. self.ui.ProcTabs.removeTab(0)
  245. def addInversion(self, idx):
  246. if self.ui.actionInversion.isChecked():
  247. self.ui.actionPreprocessing.setChecked(False)
  248. self.ui.actionModelling.setChecked(False)
  249. self.ui.ProcTabs.clear( )
  250. self.ui.ProcTabs.insertTab( 0, self.ui.InvertTab, "Inversion" )
  251. self.ui.ProcTabs.insertTab( 1, self.ui.AppraiseTab, "Appraisal" )
  252. self.ui.ProcTabs.insertTab( 2, self.ui.LogTab, "Log" )
  253. else:
  254. self.ui.ProcTabs.removeTab(0)
  255. self.ui.ProcTabs.removeTab(0)
  256. def loopAdd(self):
  257. #print(self.ui.loopLabel.text())
  258. #print(self.ui.loopGeom.currentText())
  259. #print(self.ui.loopType.currentText())
  260. #print( "label len", len(self.ui.loopLabel.text()) )
  261. if len(self.ui.loopLabel.text().strip()) == 0:
  262. Error = QtWidgets.QMessageBox()
  263. Error.setWindowTitle("Error!")
  264. Error.setText("Loop label cannot be blank or repeated")
  265. Error.setDetailedText("Each loop label must be unique and comprise at least one character. Leading and trailing whitespace will be trimmed.")
  266. Error.exec_()
  267. else:
  268. ### Circular loop
  269. if self.ui.loopGeom.currentText() == "Circular":
  270. dialog = QtWidgets.QDialog()
  271. dialog.ui = Ui_circularLoopAdd()
  272. dialog.ui.setupUi(dialog)
  273. dialog.exec_()
  274. dialog.show()
  275. if dialog.result():
  276. cn = dialog.ui.centreNorth.value()
  277. ce = dialog.ui.centreEast.value()
  278. ht = dialog.ui.loopHeight.value()
  279. rad = dialog.ui.loopRadius.value()
  280. turns = dialog.ui.loopTurns.value()
  281. ns = dialog.ui.segments.value()
  282. cwise = dialog.ui.cwiseBox.currentIndex()
  283. print("cwise", cwise)
  284. #dip = dialog.ui.dip.value()
  285. #azimuth = dialog.ui.az.value()
  286. self.loops[self.ui.loopLabel.text()] = FDEM1D.PolygonalWireAntenna()
  287. self.loops[self.ui.loopLabel.text()].SetNumberOfPoints( dialog.ui.segments.value() + 1 )
  288. self.loops[self.ui.loopLabel.text()].SetNumberOfTurns( dialog.ui.loopTurns.value() )
  289. points = np.linspace(0, 2*np.pi, dialog.ui.segments.value()+1)
  290. for iseg, ipt in enumerate(points):
  291. if cwise == 0:
  292. self.loops[self.ui.loopLabel.text()].SetPoint(iseg, ( cn+rad*np.sin(ipt), ce+rad*np.cos(ipt), ht) )
  293. else:
  294. self.loops[self.ui.loopLabel.text()].SetPoint(iseg, ( -cn+rad*np.sin(ipt), ce+rad*np.cos(ipt), ht) )
  295. self.loops[self.ui.loopLabel.text()].SetNumberOfFrequencies(1)
  296. self.loops[self.ui.loopLabel.text()].SetCurrent(1.)
  297. if self.ui.loopGeom.currentText() == "figure-8":
  298. dialog = QtWidgets.QDialog()
  299. dialog.ui = Ui_figure8LoopAdd()
  300. dialog.ui.setupUi(dialog)
  301. dialog.exec_()
  302. dialog.show()
  303. if dialog.result():
  304. cn1 = dialog.ui.centreNorth1.value()
  305. ce1 = dialog.ui.centreEast1.value()
  306. cn2 = dialog.ui.centreNorth2.value()
  307. ce2 = dialog.ui.centreEast2.value()
  308. ht = dialog.ui.loopHeight.value()
  309. rad = dialog.ui.loopRadius.value()
  310. turns = dialog.ui.loopTurns.value()
  311. ns = dialog.ui.segments.value()
  312. #cwise = dialog.ui.cwiseBox.currentIndex()
  313. print(cn1, ce1, cn2, ce2, ht, rad, turns, ns)
  314. if self.ui.loopGeom.currentText() == "polygon":
  315. dialog = QtWidgets.QDialog()
  316. dialog.ui = Ui_polygonalLoopAdd()
  317. dialog.ui.setupUi(dialog)
  318. ##########################################################################
  319. # Loop Table
  320. dialog.ui.loopTableWidget.setRowCount(80)
  321. dialog.ui.loopTableWidget.setColumnCount(3)
  322. #dialog.ui.loopTableWidget.horizontalHeader().setSectionResizeMode(0, QtGui.Qt.QHeaderView.Stretch)
  323. dialog.ui.loopTableWidget.setHorizontalHeaderLabels( \
  324. ["Northing [m]","Easting [m]","Height [m]"])
  325. for ir in range(0, dialog.ui.loopTableWidget.rowCount() ):
  326. for ic in range(0, 3): #dialog.ui.loopTableWidget.columnCount() ):
  327. pCell = QtWidgets.QTableWidgetItem()
  328. #pCell.setFlags(QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
  329. #pCell.setFlags(QtCore.Qt.NoItemFlags) # not selectable
  330. #pCell.setBackground( QtGui.QColor("lightgrey").lighter(110) )
  331. dialog.ui.loopTableWidget.setItem(ir, ic, pCell)
  332. #dialog.ui.loopTableWidget.cellChanged.connect(self.loopCellChanged)
  333. #dialog.ui.loopTableWidget.itemClicked.connect(self.loopCellClicked)
  334. #self.ui.loopTableWidget.cellPressed.connect(self.loopCellChanged)
  335. #self.ui.loopTableWidget.cellPressed.connect(self.loopCellClicked)
  336. dialog.ui.loopTableWidget.setDragDropOverwriteMode(False)
  337. dialog.ui.loopTableWidget.setDragEnabled(False)
  338. #self.ui.loopTableWidget.setDragDropMode(QtWidgets.QAbstractItemView.InternalMove)
  339. dialog.ui.loopTableWidget.resizeColumnsToContents()
  340. dialog.exec_()
  341. dialog.show()
  342. if dialog.result():
  343. self.loops[self.ui.loopLabel.text()] = FDEM1D.PolygonalWireAntenna()
  344. self.loops[self.ui.loopLabel.text()].SetNumberOfTurns( dialog.ui.loopTurns.value() )
  345. npts = 0
  346. for ir in range(0, dialog.ui.loopTableWidget.rowCount() ):
  347. if len(dialog.ui.loopTableWidget.item(ir, 0).text()) == 0:
  348. break
  349. npts += 1
  350. self.loops[self.ui.loopLabel.text()].SetNumberOfPoints( npts )
  351. for ir in range( 0, npts ):
  352. self.loops[self.ui.loopLabel.text()].SetPoint(ir, eval(dialog.ui.loopTableWidget.item(ir, 0).text()), \
  353. eval(dialog.ui.loopTableWidget.item(ir, 1).text()), \
  354. eval(dialog.ui.loopTableWidget.item(ir, 2).text()) \
  355. )
  356. self.loops[self.ui.loopLabel.text()].SetNumberOfFrequencies(1)
  357. self.loops[self.ui.loopLabel.text()].SetCurrent(1.)
  358. # general across all types
  359. if dialog.result():
  360. yml = open( self.ui.loopLabel.text() + ".yml", 'w' )
  361. print( self.loops[self.ui.loopLabel.text()], file=yml)
  362. # update the table
  363. self.ui.txRxTable.setRowCount( len(self.loops.keys()) )
  364. pCell = QtWidgets.QTableWidgetItem()
  365. pCell.setText( self.ui.loopLabel.text() )
  366. pCell.setFlags( QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEnabled )
  367. self.ui.txRxTable.setItem( len(self.loops.keys())-1, 0, pCell)
  368. gCell = QtWidgets.QTableWidgetItem()
  369. gCell.setText( self.ui.loopGeom.currentText() )
  370. gCell.setFlags( QtCore.Qt.ItemIsEnabled )
  371. self.ui.txRxTable.setItem( len(self.loops.keys())-1, 1, gCell)
  372. tCell = QtWidgets.QTableWidgetItem()
  373. tCell.setText( str(dialog.ui.loopTurns.value()) )
  374. tCell.setFlags( QtCore.Qt.ItemIsEnabled )
  375. self.ui.txRxTable.setItem( len(self.loops.keys())-1, 2, tCell)
  376. txCell = QtWidgets.QTableWidgetItem()
  377. txCell.setText( str(self.ui.loopType.currentText()) )
  378. txCell.setFlags( QtCore.Qt.ItemIsEnabled )
  379. self.ui.txRxTable.setItem( len(self.loops.keys())-1, 3, txCell)
  380. def headerBoxShrink(self):
  381. #self.ui.headerFileBox.setVisible(False)
  382. if self.ui.headerFileBox.isChecked( ):
  383. #self.ui.headerFileBox.setMinimumSize(460,250)
  384. self.ui.headerBox2.setVisible(True)
  385. else:
  386. #self.ui.headerFileBox.setMinimumSize(460,50)
  387. self.ui.headerBox2.setVisible(False)
  388. def sigmaCellChanged(self):
  389. self.ui.layerTableWidget.cellChanged.disconnect(self.sigmaCellChanged)
  390. # TODO consider building the model whenever this is called. Would be nice to be able to
  391. # do that. Would require instead dist of T2 I guess.
  392. jj = self.ui.layerTableWidget.currentColumn()
  393. ii = self.ui.layerTableWidget.currentRow()
  394. val = "class 'NoneType'>"
  395. try:
  396. val = eval (str( self.ui.layerTableWidget.item(ii, jj).text() ))
  397. except:
  398. #if jj != 0:
  399. # Error = QtWidgets.QMessageBox()
  400. # Error.setWindowTitle("Error!")
  401. # Error.setText("Non-numeric value encountered")
  402. self.ui.layerTableWidget.cellChanged.connect(self.sigmaCellChanged)
  403. return
  404. if jj == 1:
  405. #item.setFlags(QtCore.Qt.ItemIsEnabled)
  406. pCell = self.ui.layerTableWidget.item(ii, jj)
  407. pCell.setBackground( QtGui.QColor("white"))
  408. pCell = self.ui.layerTableWidget.item(ii+1, jj-1)
  409. if str(type(pCell)) == "<class 'NoneType'>":
  410. pCell = QtWidgets.QTableWidgetItem()
  411. pCell.setFlags(QtCore.Qt.ItemIsEnabled)
  412. self.ui.layerTableWidget.setItem(ii+1, jj-1, pCell)
  413. if ii == 0:
  414. pCell.setText(str(val))
  415. #pCell3 = self.ui.layerTableWidget.item(ii+1, jj)
  416. #print ("setting", ii, jj, type(pCell3))
  417. #print ( "setting", ii, jj, type(pCell3))
  418. #pCell3.setFlags( QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEditable | QtCore.Qt.ItemIsEnabled )
  419. #pCell3.setFlags( QtCore.Qt.ItemIsEditable )
  420. elif ii > 0:
  421. val2 = eval (str( self.ui.layerTableWidget.item(ii-1, jj).text() ))
  422. #print ("val2", val2, val, type(val))
  423. #if str(type(pCell)) == "<class 'NoneType'>":
  424. if type(val) == str or val > val2:
  425. pCell.setText(str(val))
  426. else:
  427. Error = QtWidgets.QMessageBox()
  428. Error.setWindowTitle("Error!")
  429. Error.setText("Non-increasing layer detected")
  430. Error.setDetailedText("Each layer interface must be below the one above it.")
  431. Error.exec_()
  432. #err_msg = "Quadrature detection has already been done!"
  433. #reply =QtWidgets.QMessageBox.critical(self, 'Error',
  434. # err_msg)
  435. pCell2 = self.ui.layerTableWidget.item(ii, jj)
  436. pCell2.setText(str(""))
  437. self.ui.layerTableWidget.cellChanged.connect(self.sigmaCellChanged)
  438. return
  439. # enable next layer
  440. pCell4 = self.ui.layerTableWidget.item(ii+1, jj)
  441. pCell4.setBackground( QtGui.QColor("lightblue") ) #.lighter(110))
  442. pCell4.setFlags( QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEditable | QtCore.Qt.ItemIsEnabled )
  443. pCell5 = self.ui.layerTableWidget.item(ii+1, jj+1)
  444. pCell5.setBackground( QtGui.QColor("white"))
  445. pCell5.setFlags( QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEditable | QtCore.Qt.ItemIsEnabled )
  446. print("ii", ii, "jj", jj)
  447. if ii == 0 and jj == 0:
  448. pCell = self.ui.layerTableWidget.item(0, 1)
  449. pCell.setBackground( QtGui.QColor("lightblue")) #.lighter(110) )
  450. pCell.setFlags( QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEditable | QtCore.Qt.ItemIsEnabled )
  451. self.ui.layerTableWidget.cellChanged.connect(self.sigmaCellChanged)
  452. def plotLoops2(self):
  453. self.ui.mplwidget.reAxH(1)
  454. for loop in self.loops:
  455. POINTS = self.loops[loop].GetPoints().T
  456. self.ui.mplwidget.ax1.plot( POINTS[:,1], POINTS[:,0], label=loop )
  457. self.ui.mplwidget.ax1.spines['right'].set_visible(False)
  458. self.ui.mplwidget.ax1.spines['top'].set_visible(False)
  459. self.ui.mplwidget.ax1.set_xlabel("easting (m)")
  460. self.ui.mplwidget.ax1.set_ylabel("northing (m)")
  461. self.ui.mplwidget.ax1.legend()
  462. self.ui.mplwidget.ax1.set_aspect('equal') #, adjustable='box')
  463. self.ui.mplwidget.draw()
  464. def removeLoop(self):
  465. del self.loops[ self.ui.txRxTable.item( self.ui.txRxTable.currentRow(), 0).text() ]
  466. self.ui.txRxTable.removeRow(self.ui.txRxTable.currentRow())
  467. def about(self):
  468. # TODO proper popup with info
  469. #self.w = MyPopup("""About Akvo \n
  470. # Akvo is an open source project developed primarily by Trevor Irons.
  471. #""")
  472. #self.w.setGeometry(100, 100, 400, 200)
  473. #self.w.show()
  474. #print("ABOUT")
  475. # Just a splash screen for now
  476. logo = pkg_resources.resource_filename(__name__, 'akvo-about.png')
  477. pixmap = QtGui.QPixmap(logo)
  478. self.splash = QtWidgets.QSplashScreen(pixmap, QtCore.Qt.WindowStaysOnTopHint)
  479. self.splash.show()
  480. def connectGMRDataProcessor(self):
  481. self.RAWDataProc = mrsurvey.GMRDataProcessor()
  482. self.RAWDataProc.progressTrigger.connect(self.updateProgressBar)
  483. self.RAWDataProc.enableDSPTrigger.connect(self.enableDSP)
  484. self.RAWDataProc.doneTrigger.connect(self.doneStatus)
  485. self.RAWDataProc.updateProcTrigger.connect(self.updateProc)
  486. def openGMRRAWDataset(self):
  487. """ Opens a GMR header file
  488. """
  489. try:
  490. with open('.gmr.last.path') as f:
  491. fpath = f.readline()
  492. pass
  493. except IOError as e:
  494. fpath = '.'
  495. self.headerstr = QtWidgets.QFileDialog.getOpenFileName(self, 'Open File', fpath)[0] # arg2 = File Type 'All Files (*)'
  496. self.ui.headerFileTextBrowser.clear()
  497. self.ui.headerFileTextBrowser.append(self.headerstr)
  498. if len(self.headerstr) == 0:
  499. return
  500. # clear the processing log
  501. self.ui.logTextBrowser.clear()
  502. self.logText = [] #MAK 20170126
  503. path,filen=os.path.split(str(self.headerstr))
  504. f = open('.gmr.last.path', 'w')
  505. f.write( str(self.headerstr) ) # prompt last file
  506. self.connectGMRDataProcessor()
  507. self.RAWDataProc.readHeaderFile(str(self.headerstr))
  508. # If we got this far, enable all the widgets
  509. self.ui.lcdNumberTauPulse1.setEnabled(True)
  510. self.ui.lcdNumberNuTx.setEnabled(True)
  511. self.ui.lcdNumberTuneuF.setEnabled(True)
  512. self.ui.lcdNumberSampFreq.setEnabled(True)
  513. self.ui.lcdNumberNQ.setEnabled(True)
  514. self.ui.headerFileBox.setEnabled(True)
  515. self.ui.headerFileBox.setChecked( True )
  516. self.ui.headerBox2.setVisible(True)
  517. self.ui.inputRAWParametersBox.setEnabled(True)
  518. self.ui.loadDataPushButton.setEnabled(True)
  519. # make plots as you import the dataset
  520. self.ui.plotImportCheckBox.setEnabled(True)
  521. self.ui.plotImportCheckBox.setChecked(True)
  522. # Update info from the header into the GUI
  523. self.ui.pulseTypeTextBrowser.clear()
  524. self.ui.pulseTypeTextBrowser.append(self.RAWDataProc.pulseType)
  525. self.ui.lcdNumberNuTx.display(self.RAWDataProc.transFreq)
  526. self.ui.lcdNumberTauPulse1.display(1e3*self.RAWDataProc.pulseLength[0])
  527. self.ui.lcdNumberTuneuF.display(self.RAWDataProc.TuneCapacitance)
  528. self.ui.lcdNumberSampFreq.display(self.RAWDataProc.samp)
  529. self.ui.lcdNumberNQ.display(self.RAWDataProc.nPulseMoments)
  530. self.ui.DeadTimeSpinBox.setValue(1e3*self.RAWDataProc.deadTime)
  531. self.ui.CentralVSpinBox.setValue( self.RAWDataProc.transFreq )
  532. if self.RAWDataProc.pulseType != "FID":
  533. self.ui.lcdNumberTauPulse2.setEnabled(1)
  534. self.ui.lcdNumberTauPulse2.display(1e3*self.RAWDataProc.pulseLength[1])
  535. self.ui.lcdNumberTauDelay.setEnabled(1)
  536. self.ui.lcdNumberTauDelay.display(1e3*self.RAWDataProc.interpulseDelay)
  537. self.ui.FIDProcComboBox.clear()
  538. if self.RAWDataProc.pulseType == "4PhaseT1" or self.RAWDataProc.pulseType == "T1":
  539. self.ui.FIDProcComboBox.insertItem(0, "Pulse 1")
  540. self.ui.FIDProcComboBox.insertItem(1, "Pulse 2")
  541. self.ui.FIDProcComboBox.insertItem(2, "Both")
  542. self.ui.FIDProcComboBox.setCurrentIndex (1)
  543. elif self.RAWDataProc.pulseType == "FID":
  544. self.ui.FIDProcComboBox.insertItem(0, "Pulse 1")
  545. self.ui.FIDProcComboBox.setCurrentIndex (0)
  546. def ExportPreprocess(self):
  547. """ This method exports to YAML
  548. """
  549. try:
  550. with open('.akvo.last.yaml.path') as f:
  551. fpath = f.readline()
  552. pass
  553. except IOError as e:
  554. fpath = '.'
  555. fdir = os.path.dirname(fpath)
  556. # Pickle the preprocessed data dictionary
  557. SaveStr = QtWidgets.QFileDialog.getSaveFileName(self, "Save as", fdir, r"Processed data (*.yaml)")[0]
  558. spath,filen=os.path.split(str(SaveStr))
  559. f = open('.akvo.last.yaml.path', 'w')
  560. f.write( str(spath) ) # prompt last file
  561. INFO = {}
  562. INFO["headerstr"] = str(self.headerstr)
  563. INFO["pulseType"] = self.RAWDataProc.pulseType
  564. INFO["transFreq"] = self.RAWDataProc.transFreq.tolist()
  565. INFO["pulseLength"] = self.RAWDataProc.pulseLength.tolist()
  566. INFO["TuneCapacitance"] = self.RAWDataProc.TuneCapacitance.tolist()
  567. #INFO["samp"] = self.RAWDataProc.samp
  568. INFO["nPulseMoments"] = self.RAWDataProc.nPulseMoments
  569. #INFO["deadTime"] = self.RAWDataProc.deadTime
  570. INFO["processed"] = "Akvo v. 1.0, on " + time.strftime("%d/%m/%Y")
  571. # Pulse current info
  572. ip = 0
  573. INFO["Pulses"] = {}
  574. for pulse in self.RAWDataProc.DATADICT["PULSES"]:
  575. qq = []
  576. qv = []
  577. for ipm in range(self.RAWDataProc.DATADICT["nPulseMoments"]):
  578. #for istack in self.RAWDataProc.DATADICT["stacks"]:
  579. # print ("stack q", self.RAWDataProc.DATADICT[pulse]["Q"][ipm,istack-1])
  580. qq.append(np.mean( self.RAWDataProc.DATADICT[pulse]["Q"][ipm,:]) )
  581. qv.append(np.std( self.RAWDataProc.DATADICT[pulse]["Q"][ipm,:]/self.RAWDataProc.pulseLength[ip] ))
  582. qq = np.array(qq)
  583. qv = np.array(qv)
  584. iQ = np.argsort(np.array(qq))
  585. qq = np.array(qq)[iQ]
  586. print("qq", qq, iQ)
  587. qv = np.array(qv)[iQ]
  588. INFO["Pulses"][pulse] = {}
  589. INFO["Pulses"][pulse]["units"] = "A"
  590. INFO["Pulses"][pulse]["current"] = VectorXr(qq/self.RAWDataProc.pulseLength[ip])
  591. INFO["Pulses"][pulse]["variance"] = VectorXr(qv)
  592. ip += 1
  593. # Data
  594. if self.RAWDataProc.gated == True:
  595. INFO["Gated"] = {}
  596. INFO["Gated"]["abscissa units"] = "ms"
  597. INFO["Gated"]["data units"] = "nT"
  598. for pulse in self.RAWDataProc.DATADICT["PULSES"]:
  599. INFO["Gated"][pulse] = {}
  600. INFO["Gated"][pulse]["abscissa"] = VectorXr( self.RAWDataProc.GATEDABSCISSA )
  601. INFO["Gated"][pulse]["windows"] = VectorXr( self.RAWDataProc.GATEDWINDOW )
  602. for ichan in self.RAWDataProc.DATADICT[pulse]["chan"]:
  603. INFO["Gated"][pulse]["Chan. " + str(ichan)] = {}
  604. INFO["Gated"][pulse]["Chan. " + str(ichan)]["STD"] = VectorXr( np.std(self.RAWDataProc.GATED[ichan]["NR"], axis=0) )
  605. for ipm in range(self.RAWDataProc.DATADICT["nPulseMoments"]):
  606. INFO["Gated"][pulse]["Chan. " + str(ichan)]["Q-"+str(ipm) + " CA"] = VectorXr(self.RAWDataProc.GATED[ichan]["CA"][ipm])
  607. INFO["Gated"][pulse]["Chan. " + str(ichan)]["Q-"+str(ipm) + " RE"] = VectorXr(self.RAWDataProc.GATED[ichan]["RE"][ipm])
  608. INFO["Gated"][pulse]["Chan. " + str(ichan)]["Q-"+str(ipm) + " IM"] = VectorXr(self.RAWDataProc.GATED[ichan]["IM"][ipm])
  609. #INFO["Gated"][pulse]["Chan. " + str(ichan)]["Q-"+str(ipm) + " IP"] = VectorXr(self.RAWDataProc.GATED[ichan]["IP"][ipm])
  610. #INFO["Gated"][pulse]["Chan. " + str(ichan)]["Q-"+str(ipm) + " NR"] = VectorXr(self.RAWDataProc.GATED[ichan]["NR"][ipm])
  611. #INFO["Gated"][pulse]["Chan. " + str(ichan)]["Q-"+str(ipm) + " STD" ] = VectorXr(self.RAWDataProc.GATED[ichan]["SIGMA"][ipm])
  612. # we have gated data
  613. # Window edges
  614. # Window centres
  615. with open(SaveStr, 'w') as outfile:
  616. #for line in self.logText:
  617. # outfile.write(line+"\n")
  618. yaml.dump(self.YamlNode, outfile)
  619. yaml.dump(INFO, outfile) #, default_flow_style=False)
  620. def SavePreprocess(self):
  621. #if "Saved" not in self.YamlNode.Processing.keys():
  622. # self.YamlNode.Processing["Saved"] = []
  623. #self.YamlNode.Processing["Saved"].append(datetime.datetime.now().isoformat())
  624. #self.Log()
  625. import pickle, os
  626. try:
  627. with open('.akvo.last.path') as f:
  628. fpath = f.readline()
  629. pass
  630. except IOError as e:
  631. fpath = '.'
  632. fdir = os.path.dirname(fpath)
  633. # Pickle the preprocessed data dictionary
  634. SaveStr = QtWidgets.QFileDialog.getSaveFileName(self, "Save as", fdir, r"Pickle (*.dmp)")
  635. print(SaveStr)
  636. spath,filen=os.path.split(str(SaveStr[0]))
  637. f = open('.akvo.last.path', 'w')
  638. f.write( str(spath) ) # prompt last file
  639. save = open(SaveStr[0], 'wb')
  640. # Add some extra info
  641. INFO = {}
  642. INFO["pulseType"] = self.RAWDataProc.pulseType
  643. INFO["prePulseDelay"] = self.RAWDataProc.prePulseDelay
  644. INFO["interpulseDelay"] = self.RAWDataProc.interpulseDelay
  645. INFO["transFreq"] = self.RAWDataProc.transFreq
  646. INFO["pulseLength"] = self.RAWDataProc.pulseLength
  647. INFO["TuneCapacitance"] = self.RAWDataProc.TuneCapacitance
  648. INFO["samp"] = self.RAWDataProc.samp
  649. INFO["nPulseMoments"] = self.RAWDataProc.nPulseMoments
  650. INFO["deadTime"] = self.RAWDataProc.deadTime
  651. INFO["transFreq"] = self.RAWDataProc.transFreq
  652. INFO["headerstr"] = str(self.headerstr)
  653. INFO["nDAQVersion"] = self.RAWDataProc.nDAQVersion
  654. INFO["log"] = yaml.dump( self.YamlNode )
  655. TXRX = []
  656. for ir in range(0, self.ui.txRxTable.rowCount() ):
  657. txrx = []
  658. for ic in range(0, self.ui.txRxTable.columnCount() ):
  659. txrx.append( self.ui.txRxTable.item(ir, ic).text() )
  660. TXRX.append(txrx)
  661. INFO["TXRX"] = TXRX
  662. self.RAWDataProc.DATADICT["INFO"] = INFO
  663. print ("TXRX", TXRX)
  664. pickle.dump(self.RAWDataProc.DATADICT, save)
  665. save.close()
  666. # Export XML file suitable for USGS ScienceBase Data Release
  667. def ExportXML(self):
  668. """ This is a filler function for use by USGS collaborators
  669. """
  670. return 42
  671. def OpenPreprocess(self):
  672. import pickle
  673. try:
  674. with open('.akvo.last.path') as f:
  675. fpath = f.readline()
  676. pass
  677. except IOError as e:
  678. fpath = '.'
  679. #filename = QtWidgets.QFileDialog.getOpenFileName(self, 'Open File', '.')
  680. fpath = QtWidgets.QFileDialog.getOpenFileName(self, 'Open preprocessed file', fpath, r"Pickle Files (*.dmp)")[0]
  681. f = open('.akvo.last.path', 'w')
  682. f.write( str(fpath) ) # prompt last file
  683. self.ui.logTextBrowser.clear()
  684. self.logText = []
  685. if len(fpath) == 0:
  686. return
  687. pfile = open(fpath,'rb')
  688. unpickle = pickle.Unpickler(pfile)
  689. self.connectGMRDataProcessor()
  690. self.RAWDataProc.DATADICT = unpickle.load()
  691. # This line causes Akvo to crash, if the header file is no longer there. We don't need to load the
  692. # file. TODO, need to disable "Load Data" in Load command though, as that is no longer possible.
  693. #self.RAWDataProc.readHeaderFile(self.RAWDataProc.DATADICT["INFO"]["headerstr"])
  694. self.headerstr = self.RAWDataProc.DATADICT["INFO"]["headerstr"]
  695. self.RAWDataProc.pulseType = self.RAWDataProc.DATADICT["INFO"]["pulseType"]
  696. self.RAWDataProc.transFreq = self.RAWDataProc.DATADICT["INFO"]["transFreq"]
  697. self.RAWDataProc.pulseLength = self.RAWDataProc.DATADICT["INFO"]["pulseLength"]
  698. self.RAWDataProc.TuneCapacitance = self.RAWDataProc.DATADICT["INFO"]["TuneCapacitance"]
  699. self.RAWDataProc.samp = self.RAWDataProc.DATADICT["INFO"]["samp"]
  700. self.RAWDataProc.nPulseMoments = self.RAWDataProc.DATADICT["INFO"]["nPulseMoments"]
  701. self.RAWDataProc.deadTime = self.RAWDataProc.DATADICT["INFO"]["deadTime"]
  702. self.RAWDataProc.transFreq = self.RAWDataProc.DATADICT["INFO"]["transFreq"]
  703. self.RAWDataProc.nDAQVersion = self.RAWDataProc.DATADICT["INFO"]["nDAQVersion"]
  704. #self.RAWDataProc.prePulseDelay = self.RAWDataProc.DATADICT["INFO"]["prePulseDelay"]
  705. self.RAWDataProc.dt = 1./self.RAWDataProc.samp
  706. self.dataChan = self.RAWDataProc.DATADICT[ self.RAWDataProc.DATADICT["PULSES"][0] ]["chan"]
  707. # Keep backwards compatibility with prior saved pickles???
  708. #self.ui.logTextBrowser.clear()
  709. #self.ui.logTextBrowser.append( yaml.dump(self.YamlNode)) #, default_flow_style=False) )
  710. #for a in self.logText:
  711. # self.ui.logTextBrowser.append(str(a))
  712. #self.ui.logTextBrowser
  713. #self.ui.logTextBrowser.clear()
  714. #print ( self.RAWDataProc.DATADICT["INFO"]["log"] )
  715. if "TXRX" in self.RAWDataProc.DATADICT["INFO"].keys():
  716. TXRX = self.RAWDataProc.DATADICT["INFO"]["TXRX"]
  717. self.ui.txRxTable.setRowCount( len(TXRX))
  718. for irow, row in enumerate(TXRX):
  719. for icol, val in enumerate(row):
  720. pCell = QtWidgets.QTableWidgetItem()
  721. pCell.setText( val )
  722. pCell.setFlags( QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEnabled )
  723. self.ui.txRxTable.setItem(irow, icol, pCell)
  724. self.logText = self.RAWDataProc.DATADICT["INFO"]["log"] # YAML
  725. self.YamlNode = AkvoYamlNode( ) #self.logText )
  726. self.YamlNode.Akvo_VERSION = (yaml.load( self.logText, Loader=yaml.Loader )).Akvo_VERSION
  727. AKVO_VERSION = np.array(self.YamlNode.Akvo_VERSION.split("."), dtype=int)
  728. if AKVO_VERSION[0] >= 1 and AKVO_VERSION[1] >= 2 and AKVO_VERSION[2] >= 3:
  729. self.RAWDataProc.interpulseDelay = self.RAWDataProc.DATADICT["INFO"]["interpulseDelay"]
  730. self.YamlNode.Import = OrderedDict((yaml.load( self.logText, Loader=yaml.Loader )).Import)
  731. self.YamlNode.Processing = list((yaml.load( self.logText, Loader=yaml.Loader )).Processing)
  732. self.YamlNode.Stacking = OrderedDict((yaml.load( self.logText, Loader=yaml.Loader )).Stacking)
  733. self.YamlNode.META = OrderedDict((yaml.load( self.logText, Loader=yaml.Loader )).META)
  734. self.Log()
  735. #self.ui.logTextBrowser.append( yaml.dump(self.YamlNode)) #, default_flow_style=False) )
  736. #except KeyError:
  737. # pass
  738. # Remove "Saved" and "Loaded" from processing flow
  739. #if "Loaded" not in self.YamlNode.Processing.keys():
  740. # self.YamlNode.Processing["Loaded"] = []
  741. #self.YamlNode.Processing["Loaded"].append(datetime.datetime.now().isoformat())
  742. #self.Log()
  743. # If we got this far, enable all the widgets
  744. self.ui.lcdNumberTauPulse1.setEnabled(True)
  745. self.ui.lcdNumberNuTx.setEnabled(True)
  746. self.ui.lcdNumberTuneuF.setEnabled(True)
  747. self.ui.lcdNumberSampFreq.setEnabled(True)
  748. self.ui.lcdNumberNQ.setEnabled(True)
  749. self.ui.headerFileBox.setEnabled(True)
  750. self.ui.headerFileBox.setChecked( True )
  751. self.headerBoxShrink()
  752. #self.ui.headerBox2.setVisible(True)
  753. self.ui.inputRAWParametersBox.setEnabled(False)
  754. self.ui.loadDataPushButton.setEnabled(True)
  755. # make plots as you import the datasetmost
  756. self.ui.plotImportCheckBox.setEnabled(True)
  757. self.ui.plotImportCheckBox.setChecked(True)
  758. # enable the LCDs
  759. self.ui.lcdNumberFID1Length.setEnabled(1)
  760. self.ui.lcdNumberFID2Length.setEnabled(1)
  761. self.ui.lcdNumberResampFreq.setEnabled(1)
  762. self.ui.lcdTotalDeadTime.setEnabled(1)
  763. # enable META tab
  764. self.ui.METATab.setEnabled(1)
  765. self.ui.siteBox.setEnabled(1)
  766. #self.ui.lcdTotalDeadTime.display( 1e3*self.RAWDataProc.DATADICT["INFO"]["deadTime"] )
  767. self.ui.headerFileTextBrowser.clear( )
  768. self.ui.headerFileTextBrowser.append( self.RAWDataProc.DATADICT["INFO"]["headerstr"] )
  769. if u"Pulse 1" in self.RAWDataProc.DATADICT.keys():
  770. self.ui.lcdNumberFID1Length.display(self.RAWDataProc.DATADICT["Pulse 1"]["TIMES"][-1]- self.RAWDataProc.DATADICT["Pulse 1"]["TIMES"][0])
  771. self.ui.lcdTotalDeadTime.display( round(1e3*(self.RAWDataProc.DATADICT["Pulse 1"]["TIMES"][0]-self.RAWDataProc.DATADICT["Pulse 1"]["PULSE_TIMES"][-1]), 3) )
  772. print("CALC DEAD", (1e3*(self.RAWDataProc.prePulseDelay))) # - (self.RAWDataProc.DATADICT["Pulse 1"]["TIMES"][0]-self.RAWDataProc.DATADICT["Pulse 1"]["PULSE_TIMES"][-1])), 3) )
  773. if u"Pulse 2" in self.RAWDataProc.DATADICT.keys():
  774. self.ui.lcdNumberFID1Length.display(self.RAWDataProc.DATADICT["Pulse 2"]["TIMES"][-1]- self.RAWDataProc.DATADICT["Pulse 2"]["TIMES"][0])
  775. self.ui.lcdTotalDeadTime.display( 1e3 * (self.RAWDataProc.DATADICT["Pulse 2"]["TIMES"][0]-self.RAWDataProc.DATADICT["Pulse 2"]["PULSE_TIMES"][-1]) )
  776. # Update info from the header into the GUI
  777. self.ui.pulseTypeTextBrowser.clear()
  778. self.ui.pulseTypeTextBrowser.append(self.RAWDataProc.pulseType)
  779. self.ui.lcdNumberNuTx.display(self.RAWDataProc.transFreq)
  780. self.ui.lcdNumberTauPulse1.display(1e3*self.RAWDataProc.pulseLength[0])
  781. self.ui.lcdNumberTuneuF.display(self.RAWDataProc.TuneCapacitance)
  782. self.ui.lcdNumberResampFreq.display(self.RAWDataProc.samp)
  783. self.ui.lcdNumberSampFreq.display(50000) # TODO, if non GMR is supported, query
  784. self.ui.lcdNumberNQ.display(self.RAWDataProc.nPulseMoments)
  785. self.ui.DeadTimeSpinBox.setValue(1e3*self.RAWDataProc.deadTime)
  786. self.ui.CentralVSpinBox.setValue( self.RAWDataProc.transFreq )
  787. if self.RAWDataProc.pulseType != "FID":
  788. self.ui.lcdNumberTauPulse2.setEnabled(1)
  789. self.ui.lcdNumberTauPulse2.display(1e3*self.RAWDataProc.pulseLength[1])
  790. self.ui.lcdNumberTauDelay.setEnabled(1)
  791. self.ui.lcdNumberTauDelay.display(1e3*self.RAWDataProc.interpulseDelay)
  792. self.ui.FIDProcComboBox.clear()
  793. if self.RAWDataProc.pulseType == "4PhaseT1" or self.RAWDataProc.pulseType == "T1":
  794. self.ui.FIDProcComboBox.insertItem(0, "Pulse 1") #, const QVariant & userData = QVariant() )
  795. self.ui.FIDProcComboBox.insertItem(1, "Pulse 2") #, const QVariant & userData = QVariant() )
  796. self.ui.FIDProcComboBox.insertItem(2, "Both") #, const QVariant & userData = QVariant() )
  797. if len( self.RAWDataProc.DATADICT["PULSES"]) == 2:
  798. self.ui.FIDProcComboBox.setCurrentIndex (2)
  799. elif self.RAWDataProc.DATADICT["PULSES"][0] == "Pulse 1":
  800. self.ui.FIDProcComboBox.setCurrentIndex (0)
  801. else:
  802. self.ui.FIDProcComboBox.setCurrentIndex (1)
  803. elif self.RAWDataProc.pulseType == "FID":
  804. self.ui.FIDProcComboBox.insertItem(0, "Pulse 1") #, const QVariant & userData = QVariant() )
  805. self.ui.FIDProcComboBox.setCurrentIndex (0)
  806. # QtCore.QObject.connect(self.RAWDataProc, QtCore.SIGNAL("updateProgress(int)"), self.updateProgressBar)
  807. # QtCore.QObject.connect(self.RAWDataProc, QtCore.SIGNAL("enableDSP()"), self.enableDSP)
  808. # QtCore.QObject.connect(self.RAWDataProc, QtCore.SIGNAL("doneStatus()"), self.doneStatus)
  809. self.RAWDataProc.progressTrigger.connect(self.updateProgressBar)
  810. self.RAWDataProc.enableDSPTrigger.connect(self.enableDSP)
  811. self.RAWDataProc.doneTrigger.connect(self.doneStatus)
  812. self.enableAll()
  813. def loadRAW(self):
  814. #################################################
  815. # Check to make sure we are ready to process
  816. # Header
  817. if self.RAWDataProc == None:
  818. err_msg = "You need to load a header first."
  819. reply = QtGui.QMessageBox.critical(self, 'Error',
  820. err_msg) #, QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)
  821. return
  822. # Stacks
  823. try:
  824. self.procStacks = np.array(eval(str("np.r_["+self.ui.stacksLineEdit.text())+"]"))
  825. except:
  826. err_msg = "You need to set your stacks correctly.\n" + \
  827. "This should be a Python Numpy interpretable list\n" + \
  828. "of stack indices. For example 1:24 or 1:4,8:24"
  829. QtGui.QMessageBox.critical(self, 'Error', err_msg)
  830. return
  831. # Data Channels
  832. #Chan = np.arange(0,9,1)
  833. try:
  834. self.dataChan = np.array(eval(str("np.r_["+self.ui.dataChanLineEdit.text())+"]"))
  835. except:
  836. #QMessageBox messageBox;
  837. #messageBox.critical(0,"Error","An error has occured !");
  838. #messageBox.setFixedSize(500,200);
  839. #quit_msg = "Are you sure you want to exit the program?"
  840. #reply = QtGui.QMessageBox.question(self, 'Message',
  841. # quit_msg, QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)
  842. err_msg = "You need to set your data channels correctly.\n" + \
  843. "This should be a Python Numpy interpretable list\n" + \
  844. "of indices. For example 1 or 1:3 or 1:3 5\n\n" + \
  845. "valid GMR data channels fall between 1 and 8. Note that\n" +\
  846. "1:3 is not inclusive of 3 and is the same as 1,2 "
  847. reply = QtGui.QMessageBox.critical(self, 'Error',
  848. err_msg) #, QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)
  849. return
  850. #############################
  851. # Reference Channels
  852. # TODO make sure no overlap between data and ref channels
  853. self.refChan = np.array( () )
  854. if str(self.ui.refChanLineEdit.text()): # != "none":
  855. try:
  856. self.refChan = np.array(eval(str("np.r_["+self.ui.refChanLineEdit.text())+"]"))
  857. except:
  858. err_msg = "You need to set your reference channels correctly.\n" + \
  859. "This should be a Python Numpy interpretable list\n" + \
  860. "of indices. For example 1 or 1:3 or 1:3 5\n\n" + \
  861. "valid GMR data channels fall between 1 and 8. Note that\n" +\
  862. "1:3 is not inclusive of 3 and is the same as 1,2 "
  863. QtGui.QMessageBox.critical(self, 'Error', err_msg)
  864. return
  865. #####################################################
  866. # Load data
  867. self.lock("loading RAW GMR dataset")
  868. if self.RAWDataProc.pulseType == "FID":
  869. self.procThread = thread.start_new_thread(self.RAWDataProc.loadFIDData, \
  870. (str(self.headerstr), self.procStacks, self.dataChan, self.refChan, \
  871. str(self.ui.FIDProcComboBox.currentText()), self.ui.mplwidget, \
  872. 1e-3 * self.ui.DeadTimeSpinBox.value( ), self.ui.plotImportCheckBox.isChecked() )) #, self))
  873. elif self.RAWDataProc.pulseType == "4PhaseT1":
  874. self.procThread = thread.start_new_thread(self.RAWDataProc.load4PhaseT1Data, \
  875. (str(self.headerstr), self.procStacks, self.dataChan, self.refChan, \
  876. str(self.ui.FIDProcComboBox.currentText()), self.ui.mplwidget, \
  877. 1e-3 * self.ui.DeadTimeSpinBox.value( ), self.ui.plotImportCheckBox.isChecked() )) #, self))
  878. elif self.RAWDataProc.pulseType == "T1":
  879. self.procThread = thread.start_new_thread(self.RAWDataProc.loadT1Data, \
  880. (str(self.headerstr), self.procStacks, self.dataChan, self.refChan, \
  881. str(self.ui.FIDProcComboBox.currentText()), self.ui.mplwidget, \
  882. 1e-3 * self.ui.DeadTimeSpinBox.value( ), self.ui.plotImportCheckBox.isChecked() )) #, self))
  883. #self.procThread = thread.start_new_thread(self.RAWDataProc.load4PhaseT1Data, \
  884. # (str(self.headerstr), self.procStacks, self.dataChan, self.refChan, \
  885. # str(self.ui.FIDProcComboBox.currentText()), self.ui.mplwidget, \
  886. # 1e-3 * self.ui.DeadTimeSpinBox.value( ), self.ui.plotImportCheckBox.isChecked() )) #, self))
  887. self.YamlNode.Import["GMR Header"] = self.headerstr
  888. self.YamlNode.Import["opened"] = datetime.datetime.now().isoformat()
  889. self.YamlNode.Import["pulse Type"] = str(self.RAWDataProc.pulseType)
  890. self.YamlNode.Import["stacks"] = self.procStacks.tolist()
  891. self.YamlNode.Import["data channels"] = self.dataChan.tolist()
  892. self.YamlNode.Import["reference channels"] = self.refChan.tolist()
  893. self.YamlNode.Import["pulse records"] = str(self.ui.FIDProcComboBox.currentText())
  894. self.YamlNode.Import["instrument dead time"] = (1e-3 * self.ui.DeadTimeSpinBox.value( ))
  895. self.Log ( )
  896. # enable META tab
  897. self.ui.METATab.setEnabled(1)
  898. self.ui.siteBox.setEnabled(1)
  899. # should be already done
  900. # QtCore.QObject.connect(self.RAWDataProc, QtCore.SIGNAL("updateProgress(int)"), self.updateProgressBar)
  901. # QtCore.QObject.connect(self.RAWDataProc, QtCore.SIGNAL("enableDSP()"), self.enableDSP)
  902. # QtCore.QObject.connect(self.RAWDataProc, QtCore.SIGNAL("doneStatus()"), self.doneStatus)
  903. #self.ui.ProcessedBox.setEnabled(True)
  904. self.ui.lcdNumberFID1Length.setEnabled(1)
  905. self.ui.lcdNumberFID2Length.setEnabled(1)
  906. self.ui.lcdNumberResampFreq.setEnabled(1)
  907. self.ui.lcdTotalDeadTime.setEnabled(1)
  908. self.ui.lcdTotalDeadTime.display( self.ui.DeadTimeSpinBox.value( ) )
  909. #self.ui.lcdTotalDeadTime.display( round(1e3*(self.RAWDataProc.DATADICT["Pulse 1"]["TIMES"][0]-self.RAWDataProc.DATADICT["Pulse 1"]["PULSE_TIMES"][-1]), 3) )
  910. #self.ui.lcdNumberFID1Length.display(0)
  911. #self.ui.lcdNumberFID2Length.display(0)
  912. #self.ui.lcdNumberResampFreq.display( self.RAWDataProc.samp )
  913. self.mpl_toolbar = NavigationToolbar2QT(self.ui.mplwidget, self.ui.mplwidget)
  914. self.ui.mplwidget.draw()
  915. def Log(self):
  916. #for line in yaml.dump(self.YamlNode, default_flow_style=False):
  917. #for line in nlogText:
  918. # self.ui.logTextBrowser.append( line )
  919. # self.logText.append( line )
  920. self.ui.logTextBrowser.clear()
  921. self.ui.logTextBrowser.append( yaml.dump(self.YamlNode ))
  922. def disable(self):
  923. self.ui.inputRAWParametersBox.setEnabled(False)
  924. self.ui.BandPassBox.setEnabled(False)
  925. self.ui.downSampleGroupBox.setEnabled(False)
  926. self.ui.windowFilterGroupBox.setEnabled(False)
  927. self.ui.harmonicBox.setEnabled(False)
  928. # self.ui.despikeGroupBox.setEnabled(False)
  929. self.ui.adaptBox.setEnabled(False)
  930. self.ui.adaptFDBox.setEnabled(False)
  931. self.ui.qCalcGroupBox.setEnabled(False)
  932. self.ui.FDSmartStackGroupBox.setEnabled(False)
  933. self.ui.sumDataBox.setEnabled(False)
  934. self.ui.qdGroupBox.setEnabled(False)
  935. self.ui.gateBox.setEnabled(False)
  936. def enableAll(self):
  937. self.enableDSP()
  938. self.enableQC()
  939. def enableDSP(self):
  940. # Bandpass filter
  941. self.ui.BandPassBox.setEnabled(True)
  942. self.ui.BandPassBox.setChecked(True)
  943. self.ui.bandPassGO.setEnabled(False) # need to design first
  944. self.ui.plotBP.setEnabled(True)
  945. self.ui.plotBP.setChecked(True)
  946. # downsample
  947. self.ui.downSampleGroupBox.setEnabled(True)
  948. self.ui.downSampleGroupBox.setChecked(True)
  949. # window
  950. self.ui.windowFilterGroupBox.setEnabled(True)
  951. self.ui.windowFilterGroupBox.setChecked(True)
  952. # Despike
  953. # self.ui.despikeGroupBox.setEnabled(True)
  954. # self.ui.despikeGroupBox.setChecked(False)
  955. # Adaptive filtering
  956. self.ui.adaptBox.setEnabled(True)
  957. self.ui.adaptBox.setChecked(True)
  958. # FD Adaptive filtering
  959. self.ui.adaptFDBox.setEnabled(True)
  960. self.ui.adaptFDBox.setChecked(False)
  961. # Harmonic
  962. self.ui.harmonicBox.setEnabled(True)
  963. self.ui.harmonicBox.setChecked(True)
  964. self.LCDHarmonics()
  965. self.LCDHarmonics2()
  966. # sum group box
  967. try:
  968. if len(self.dataChan) > 1:
  969. self.ui.sumDataBox.setEnabled(True)
  970. self.ui.sumDataBox.setChecked(False)
  971. except:
  972. pass
  973. # Quadrature Detect
  974. self.ui.qdGroupBox.setEnabled(True)
  975. self.ui.qdGroupBox.setChecked(True)
  976. self.enableQC()
  977. def enableQC(self):
  978. # Q calc
  979. self.ui.qCalcGroupBox.setEnabled(True)
  980. self.ui.qCalcGroupBox.setChecked(True)
  981. # FD SmartStack
  982. self.ui.FDSmartStackGroupBox.setEnabled(True)
  983. self.ui.FDSmartStackGroupBox.setChecked(True)
  984. # Quadrature detect
  985. try:
  986. for pulse in self.RAWDataProc.DATADICT["PULSES"]:
  987. np.shape(self.RAWDataProc.DATADICT[pulse]["Q"])
  988. self.RAWDataProc.DATADICT["stack"]
  989. self.ui.qdGroupBox.setEnabled(True)
  990. self.ui.qdGroupBox.setChecked(True)
  991. except:
  992. self.ui.qdGroupBox.setEnabled(False)
  993. self.ui.qdGroupBox.setChecked(False)
  994. # Gating
  995. try:
  996. self.RAWDataProc.DATADICT["CA"]
  997. self.ui.gateBox.setEnabled(True)
  998. self.ui.gateBox.setChecked(True)
  999. except:
  1000. self.ui.gateBox.setEnabled(False)
  1001. self.ui.gateBox.setChecked(False)
  1002. def despikeFilter(self):
  1003. self.lock("despike filter")
  1004. thread.start_new_thread(self.RAWDataProc.despike, \
  1005. (self.ui.windowSpinBox.value(), \
  1006. self.ui.thresholdSpinBox.value(), \
  1007. str(self.ui.replComboBox.currentText()), \
  1008. self.ui.rollOnSpinBox.value(), \
  1009. self.ui.despikeInterpWinSpinBox.value(),
  1010. self.ui.mplwidget))
  1011. def calcQ(self):
  1012. if "Calc Q" not in self.YamlNode.Stacking.keys():
  1013. #print("In CalcQ", yaml.dump(self.YamlNode.Processing) )
  1014. self.YamlNode.Stacking["Calc Q"] = True
  1015. #print( yaml.dump(self.YamlNode.Processing) )
  1016. self.Log()
  1017. else:
  1018. err_msg = "Q values have already been calculated"
  1019. reply =QtWidgets.QMessageBox.critical(self, 'Error',
  1020. err_msg)
  1021. return
  1022. self.lock("pulse moment calculation")
  1023. thread.start_new_thread(self.RAWDataProc.effectivePulseMoment, \
  1024. (self.ui.CentralVSpinBox.value(), \
  1025. self.ui.mplwidget))
  1026. def harmonicModel(self):
  1027. self.lock("harmonic noise modelling")
  1028. Harm = OrderedDict()
  1029. Harm["STEP"] = "Harmonic modelling"
  1030. Harm["NF"] = str( self.ui.NHarmonicsFreqsSpin.value() )
  1031. Harm["Segments"] = str( self.ui.NSegments.value() )
  1032. Harm["Proc. ref."] = self.ui.harmRef.isChecked()
  1033. if self.ui.searchAll.currentText() == "All":
  1034. Harm["search"] = self.ui.searchAll.currentText()
  1035. Search = False
  1036. else:
  1037. #Harm["search"] = self.ui.searchAll.currentText()
  1038. Harm["search"] = str(self.ui.Nsearch.value())
  1039. Search = self.ui.Nsearch.value()
  1040. if self.ui.boundsCheck.isChecked():
  1041. Harm["Bounds"] = str(self.ui.bounds.value())
  1042. Bounds = self.ui.bounds.value()
  1043. else:
  1044. Harm["Bounds"] = self.ui.boundsCheck.isChecked()
  1045. Bounds = 0
  1046. Harm["f0K1"] = str( self.ui.f0K1Spin.value() )
  1047. Harm["f0KN"] = str( self.ui.f0KNSpin.value() )
  1048. Harm["f0Ks"] = str( self.ui.f0KsSpin.value() )
  1049. Harm["f0"] = str( self.ui.f0Spin.value() )
  1050. if self.ui.NHarmonicsFreqsSpin.value() > 1:
  1051. Harm["f1K1"] = str( self.ui.f1K1Spin.value() )
  1052. Harm["f1KN"] = str( self.ui.f1KNSpin.value() )
  1053. Harm["f1Ks"] = str( self.ui.f1KsSpin.value() )
  1054. Harm["f1"] = str( self.ui.f1Spin.value() )
  1055. self.YamlNode.Processing.append(Harm)
  1056. self.Log()
  1057. thread.start_new_thread(self.RAWDataProc.harmonicModel, \
  1058. ( \
  1059. self.ui.NHarmonicsFreqsSpin.value(), \
  1060. self.ui.f0Spin.value(), \
  1061. self.ui.f0K1Spin.value(), \
  1062. self.ui.f0KNSpin.value(), \
  1063. self.ui.f0KsSpin.value(), \
  1064. self.ui.NSegments.value(), \
  1065. self.ui.f1Spin.value(), \
  1066. self.ui.f1K1Spin.value(), \
  1067. self.ui.f1KNSpin.value(), \
  1068. self.ui.f1KsSpin.value(), \
  1069. Search, \
  1070. Bounds, \
  1071. self.ui.harmRef.isChecked(), \
  1072. self.ui.plotHarmonic.isChecked(), \
  1073. self.ui.mplwidget \
  1074. ) \
  1075. )
  1076. def FDSmartStack(self):
  1077. if "TD stack" not in self.YamlNode.Stacking.keys():
  1078. self.YamlNode.Stacking["TD stack"] = {}
  1079. self.YamlNode.Stacking["TD stack"]["outlier"] = str( self.ui.outlierTestCB.currentText() )
  1080. self.YamlNode.Stacking["TD stack"]["cutoff"] = str( self.ui.MADCutoff.value() )
  1081. self.Log()
  1082. else:
  1083. err_msg = "TD noise cancellation has already been applied!"
  1084. reply =QtWidgets.QMessageBox.critical(self, 'Error',
  1085. err_msg)
  1086. return
  1087. self.lock("time-domain smart stack")
  1088. thread.start_new_thread(self.RAWDataProc.TDSmartStack, \
  1089. (str(self.ui.outlierTestCB.currentText()), \
  1090. self.ui.MADCutoff.value(),
  1091. self.ui.mplwidget))
  1092. def adaptFilter(self):
  1093. self.lock("TD noise cancellation filter")
  1094. # Log processing
  1095. Adapt = OrderedDict()
  1096. Adapt["STEP"] = "TD noise cancellation"
  1097. #print(Adapt)
  1098. Adapt["n_Taps"] = str(self.ui.MTapsSpinBox.value())
  1099. Adapt["lambda"] = str(self.ui.adaptLambdaSpinBox.value())
  1100. Adapt["truncate"] = str(self.ui.adaptTruncateSpinBox.value())
  1101. Adapt["mu"] = str(self.ui.adaptMuSpinBox.value())
  1102. Adapt["PCA"] = str(self.ui.PCAComboBox.currentText())
  1103. #print(Adapt)
  1104. self.YamlNode.Processing.append(Adapt)
  1105. self.Log( )
  1106. thread.start_new_thread(self.RAWDataProc.adaptiveFilter, \
  1107. (self.ui.MTapsSpinBox.value(), \
  1108. self.ui.adaptLambdaSpinBox.value(), \
  1109. self.ui.adaptTruncateSpinBox.value(), \
  1110. self.ui.adaptMuSpinBox.value(), \
  1111. str(self.ui.PCAComboBox.currentText()), \
  1112. self.ui.mplwidget))
  1113. def sumDataChans(self):
  1114. self.lock("Summing data channels")
  1115. Sum = OrderedDict()
  1116. Sum["STEP"] = "Channel sum"
  1117. self.YamlNode.Processing.append(Sum)
  1118. self.Log( )
  1119. self.dataChan = [self.dataChan[0]]
  1120. self.ui.sumDataBox.setEnabled(False)
  1121. thread.start_new_thread( self.RAWDataProc.sumData, ( self.ui.mplwidget, 7 ) )
  1122. def adaptFilterFD(self):
  1123. self.lock("FD noise cancellation filter")
  1124. thread.start_new_thread(self.RAWDataProc.adaptiveFilterFD, \
  1125. (str(self.ui.windowTypeComboBox.currentText()), \
  1126. self.ui.windowBandwidthSpinBox.value(), \
  1127. self.ui.CentralVSpinBox.value(), \
  1128. self.ui.mplwidget))
  1129. def logSite(self):
  1130. self.YamlNode.META["Location"] = self.ui.locEdit.text()
  1131. self.YamlNode.META["Coordinates"] = OrderedDict()
  1132. self.YamlNode.META["Coordinates"]["UTM"] = self.ui.UTMzone.currentText()
  1133. self.YamlNode.META["Coordinates"]["LatBand"] = self.ui.latBand.currentText()
  1134. self.YamlNode.META["Coordinates"]["ellipsoid"] = self.ui.ellipsoid.currentText()
  1135. self.YamlNode.META["DateTime"] = self.ui.dateEdit.date().toString("yyyy-MM-dd") + "T" + str( self.ui.timeEdit.time().toString("hh:mm") )
  1136. self.YamlNode.META["Temp"] = self.ui.tempSpinBox.value()
  1137. self.YamlNode.META["B_0"] = OrderedDict()
  1138. self.YamlNode.META["B_0"]["inc"] = self.ui.incSpinBox.value()
  1139. self.YamlNode.META["B_0"]["dec"] = self.ui.decSpinBox.value()
  1140. self.YamlNode.META["B_0"]["intensity"] = self.ui.intensitySpinBox.value()
  1141. self.YamlNode.META["Field Notes"] = self.ui.txtComments.toPlainText()
  1142. self.YamlNode.META["Loops"] = OrderedDict()
  1143. for loop in self.loops:
  1144. print(self.loops[loop])
  1145. self.YamlNode.META["Loops"][loop] = loop + ".yml"
  1146. self.Log()
  1147. def bandPassFilter(self):
  1148. self.lock("bandpass filter")
  1149. # Log processing
  1150. Band = OrderedDict()
  1151. Band["STEP"] = "Bandpass filter"
  1152. Band["central_nu"] = str(self.ui.CentralVSpinBox.value())
  1153. Band["passband"] = str(self.ui.passBandSpinBox.value())
  1154. Band["stopband"] = str(self.ui.stopBandSpinBox.value())
  1155. Band["gpass"] = str(self.ui.gpassSpinBox.value())
  1156. Band["gstop"] = str(self.ui.gstopSpinBox.value())
  1157. Band["type"] = str(self.ui.fTypeComboBox.currentText())
  1158. self.YamlNode.Processing.append(Band)
  1159. self.Log( )
  1160. nv = self.ui.lcdTotalDeadTime.value( ) + self.ui.lcdNumberFTauDead.value()
  1161. self.ui.lcdTotalDeadTime.display( nv )
  1162. thread.start_new_thread(self.RAWDataProc.bandpassFilter, \
  1163. (self.ui.mplwidget, 0, self.ui.plotBP.isChecked() ))
  1164. def downsample(self):
  1165. self.lock("resampling")
  1166. # Log processing
  1167. Resample = OrderedDict()
  1168. Resample["STEP"] = "Resample"
  1169. Resample["downsample factor"] = str(self.ui.downSampleSpinBox.value())
  1170. Resample["truncate length"] = str(self.ui.truncateSpinBox.value())
  1171. self.YamlNode.Processing.append(Resample)
  1172. self.Log( )
  1173. thread.start_new_thread(self.RAWDataProc.downsample, \
  1174. (self.ui.truncateSpinBox.value(), \
  1175. self.ui.downSampleSpinBox.value(), \
  1176. self.ui.dsPlot.isChecked(), \
  1177. self.ui.mplwidget))
  1178. def quadDet(self):
  1179. method = ['trf','dogbox','lm'][int(self.ui.QDMethod.currentIndex())]
  1180. loss = ['linear','soft_l1','cauchy','huber'][int(self.ui.QDLoss.currentIndex())]
  1181. # allow overwrite of Quad Det.
  1182. self.YamlNode.Stacking["Quadrature detection"] = {}
  1183. self.YamlNode.Stacking["Quadrature detection"]["trim"] = str( self.ui.trimSpin.value() )
  1184. self.YamlNode.Stacking["Quadrature detection"]["method"] = method
  1185. self.YamlNode.Stacking["Quadrature detection"]["loss"] = loss
  1186. self.Log()
  1187. #if "Quadrature detection" not in self.YamlNode.Processing.keys():
  1188. # self.YamlNode.Processing["Quadrature detection"] = {}
  1189. # self.YamlNode.Processing["Quadrature detection"]["trim"] = str( self.ui.trimSpin.value() )
  1190. # self.Log()
  1191. #else:
  1192. # self.YamlNode.Processing["Quadrature detection"] = {}
  1193. # self.YamlNode.Processing["Quadrature detection"]["trim"] = str( self.ui.trimSpin.value() )
  1194. # self.Log()
  1195. #err_msg = "Quadrature detection has already been done!"
  1196. #reply =QtWidgets.QMessageBox.critical(self, 'Error',
  1197. # err_msg)
  1198. #return
  1199. self.lock("quadrature detection")
  1200. thread.start_new_thread(self.RAWDataProc.quadDet, \
  1201. (self.ui.trimSpin.value(), method, loss, self.ui.mplwidget))
  1202. self.ui.plotQD.setEnabled(True)
  1203. def plotQD(self):
  1204. self.lock("plot QD")
  1205. thread.start_new_thread(self.RAWDataProc.plotQuadDet, \
  1206. (self.ui.trimSpin.value(), int(self.ui.QDType.currentIndex()), self.ui.mplwidget))
  1207. def gateIntegrate(self):
  1208. if "Gate integrate" not in self.YamlNode.Stacking.keys():
  1209. self.YamlNode.Stacking["Gate integrate"] = {}
  1210. self.YamlNode.Stacking["Gate integrate"]["gpd"] = str(self.ui.GPDspinBox.value( ) )
  1211. self.Log()
  1212. self.lock("gate integration")
  1213. thread.start_new_thread(self.RAWDataProc.gateIntegrate, \
  1214. (self.ui.GPDspinBox.value(), self.ui.trimSpin.value(), self.ui.mplwidget))
  1215. self.ui.actionExport_Preprocessed_Dataset.setEnabled(True)
  1216. self.ui.plotGI.setEnabled(True)
  1217. def plotGI(self):
  1218. self.lock("plot gate integrate")
  1219. thread.start_new_thread(self.RAWDataProc.plotGateIntegrate, \
  1220. (self.ui.GPDspinBox.value(), self.ui.trimSpin.value(), \
  1221. self.ui.QDType_2.currentIndex(), self.ui.mplwidget))
  1222. def designFilter(self):
  1223. [bord, fe] = self.RAWDataProc.designFilter( \
  1224. self.ui.CentralVSpinBox.value(), \
  1225. self.ui.passBandSpinBox.value(), \
  1226. self.ui.stopBandSpinBox.value(), \
  1227. self.ui.gpassSpinBox.value(), \
  1228. self.ui.gstopSpinBox.value(), \
  1229. str(self.ui.fTypeComboBox.currentText()),
  1230. self.ui.mplwidget
  1231. )
  1232. self.ui.lcdNumberFilterOrder.display(bord)
  1233. self.ui.lcdNumberFTauDead.display(1e3*fe)
  1234. self.ui.bandPassGO.setEnabled(1)
  1235. ################################################################
  1236. # Hack for MacOS to force refresh of group box and plot
  1237. # this has an undesirable effect that it causes the groupbox to 'jump' up
  1238. # TODO come up with a better solution
  1239. self.ui.mplwidget.hide()
  1240. self.ui.mplwidget.show()
  1241. self.ui.BandPassBox.hide()
  1242. self.ui.BandPassBox.show()
  1243. def windowFilter(self):
  1244. self.lock("window filter")
  1245. # Log processing
  1246. Window = OrderedDict()
  1247. Window["STEP"] = "Window filter"
  1248. Window["type"] = str(self.ui.windowTypeComboBox.currentText())
  1249. Window["width"] = str(self.ui.windowBandwidthSpinBox.value())
  1250. Window["centre"] = str(self.ui.CentralVSpinBox.value() )
  1251. Window["trim"] = str(self.ui.windowTrim.isChecked())
  1252. self.YamlNode.Processing.append(Window)
  1253. self.Log( )
  1254. if self.ui.windowTrim.isChecked():
  1255. nv = self.ui.lcdTotalDeadTime.value( ) + self.ui.lcdWinDead.value()
  1256. self.ui.lcdTotalDeadTime.display( nv )
  1257. thread.start_new_thread(self.RAWDataProc.windowFilter, \
  1258. (str(self.ui.windowTypeComboBox.currentText()), \
  1259. self.ui.windowBandwidthSpinBox.value(), \
  1260. self.ui.CentralVSpinBox.value(), \
  1261. self.ui.windowTrim.isChecked(), \
  1262. self.ui.mplwidget))
  1263. def designFDFilter(self):
  1264. mPulse = "None"
  1265. if u"Pulse 1" in self.RAWDataProc.DATADICT.keys():
  1266. mPulse = u"Pulse 1"
  1267. elif u"Pulse 2" in self.RAWDataProc.DATADICT.keys():
  1268. mPulse = u"Pulse 2"
  1269. a,b,c,d,dead,ndead = self.RAWDataProc.computeWindow( \
  1270. mPulse,
  1271. self.ui.windowBandwidthSpinBox.value(), \
  1272. self.ui.CentralVSpinBox.value(), \
  1273. str(self.ui.windowTypeComboBox.currentText()), \
  1274. self.ui.mplwidget )
  1275. self.ui.lcdWinDead.display(dead)
  1276. ################################################################
  1277. # Hack for MacOS to force refresh of group box and plot
  1278. # this has an undesirable effect that it causes the groupbox to 'jump' up
  1279. # TODO come up with a better solution
  1280. self.ui.mplwidget.hide()
  1281. self.ui.mplwidget.show()
  1282. self.ui.windowFilterGroupBox.hide()
  1283. self.ui.windowFilterGroupBox.show()
  1284. def updateProgressBar(self, percent):
  1285. self.ui.barProgress.setValue(percent)
  1286. def updateProc(self):
  1287. if str(self.ui.FIDProcComboBox.currentText()) == "Pulse 1":
  1288. self.ui.lcdNumberFID1Length.display(self.RAWDataProc.DATADICT["Pulse 1"]["TIMES"][-1]- self.RAWDataProc.DATADICT["Pulse 1"]["TIMES"][0])
  1289. elif str(self.ui.FIDProcComboBox.currentText()) == "Pulse 2":
  1290. self.ui.lcdNumberFID2Length.display(self.RAWDataProc.DATADICT["Pulse 2"]["TIMES"][-1]- self.RAWDataProc.DATADICT["Pulse 2"]["TIMES"][0])
  1291. else:
  1292. self.ui.lcdNumberFID1Length.display(self.RAWDataProc.DATADICT["Pulse 1"]["TIMES"][-1]- self.RAWDataProc.DATADICT["Pulse 1"]["TIMES"][0])
  1293. self.ui.lcdNumberFID2Length.display(self.RAWDataProc.DATADICT["Pulse 2"]["TIMES"][-1]- self.RAWDataProc.DATADICT["Pulse 2"]["TIMES"][0])
  1294. self.ui.lcdNumberResampFreq.display( self.RAWDataProc.samp )
  1295. def doneStatus(self): # unlocks GUI
  1296. self.ui.statusbar.clearMessage ( )
  1297. self.ui.barProgress.hide()
  1298. self.updateProc()
  1299. self.enableAll()
  1300. def lock(self, string):
  1301. self.ui.statusbar.showMessage ( string )
  1302. self.ui.barProgress.show()
  1303. self.ui.barProgress.setValue(0)
  1304. self.disable()
  1305. def unlock(self):
  1306. self.ui.statusbar.clearMessage ( )
  1307. self.ui.barProgress.hide()
  1308. self.enableAll()
  1309. def done(self):
  1310. self.ui.statusbar.showMessage ( "" )
  1311. ################################################################
  1312. ################################################################
  1313. # Boiler plate main function
  1314. import pkg_resources
  1315. from pkg_resources import resource_string
  1316. import matplotlib.image as mpimg
  1317. import matplotlib.pyplot as plt
  1318. from akvo.gui.logo import plotLogo
  1319. def main():
  1320. # splash screen logo
  1321. logo = pkg_resources.resource_filename(__name__, 'akvo.png')
  1322. logo2 = pkg_resources.resource_filename(__name__, 'akvo2.png')
  1323. qApp = QtWidgets.QApplication(sys.argv)
  1324. ssplash = True
  1325. if ssplash:
  1326. pixmap = QtGui.QPixmap(logo)
  1327. splash = QtWidgets.QSplashScreen(pixmap, QtCore.Qt.WindowStaysOnTopHint)
  1328. splash.show()
  1329. aw = ApplicationWindow()
  1330. #img=mpimg.imread(logo)
  1331. for ax in [ aw.ui.mplwidget ]:
  1332. ax.fig.clear()
  1333. subplot = ax.fig.add_subplot(211)
  1334. # old logo plot
  1335. ax.fig.patch.set_facecolor( None )
  1336. ax.fig.patch.set_alpha( .0 )
  1337. #subplot.imshow(img)
  1338. #ax.fig.patch.set_visible(False)
  1339. subplot.axis('off')
  1340. plotLogo(subplot)
  1341. subplot.xaxis.set_major_locator(plt.NullLocator())
  1342. subplot.yaxis.set_major_locator(plt.NullLocator())
  1343. subplot2 = ax.fig.add_subplot(212)
  1344. subplot2.text(0.5, 1.,'surface NMR workbench',
  1345. horizontalalignment='center',
  1346. verticalalignment='center',
  1347. size=22,
  1348. transform = subplot2.transAxes)
  1349. subplot2.xaxis.set_major_locator(plt.NullLocator())
  1350. subplot2.yaxis.set_major_locator(plt.NullLocator())
  1351. subplot2.axis('off')
  1352. ax.draw()
  1353. if ssplash:
  1354. splash.showMessage("Loading modules")
  1355. splash.finish(aw)
  1356. #time.sleep(1)
  1357. aw.setWindowTitle("Akvo v"+str(VERSION))
  1358. aw.show()
  1359. qApp.setWindowIcon(QtGui.QIcon(logo2))
  1360. sys.exit(qApp.exec_())
  1361. if __name__ == "__main__":
  1362. main()