Merge branch 'develop' of ariadne.geophysik.ruhr-uni-bochum.de:/data/git/pylot into develop
Conflicts: pylot/core/util/utils.py
This commit is contained in:
commit
7921d12c80
@ -9,7 +9,7 @@ matplotlib.rcParams['backend.qt4']='PySide'
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from PySide import QtCore, QtGui
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from pylot.core.active import activeSeismoPick, surveyUtils, fmtomoUtils, seismicArrayPreparation
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from pylot.core.active.gui.asp3d_layout import *
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from pylot.core.active.gui.windows import Gen_SeisArray, Gen_Survey_from_SA, Gen_Survey_from_SR, Call_autopicker, Call_FMTOMO, Call_VTK_dialog
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from pylot.core.active.gui.windows import Gen_SeisArray, Gen_Survey_from_SA, Gen_Survey_from_SR, Call_autopicker, Call_FMTOMO, Call_VTK_dialog, Postprocessing
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from pylot.core.active.gui.windows import openFile, saveFile, browseDir, getMaxCPU
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from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
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@ -43,6 +43,7 @@ class gui_control(object):
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self.autopicker = None
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self.fmtomo = None
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self.vtktools = None
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self.postprocessing = None
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def setInitStates(self):
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self.setPickState(False)
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@ -362,8 +363,9 @@ class gui_control(object):
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if not self.checkSurveyState():
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self.printDialogMessage('No Survey defined.')
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return
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self.survey.plotAllPicks()
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self.refreshPickedWidgets() # wait until finished
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self.postprocessing = Postprocessing(self.mainwindow, self.survey)
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#self.survey.plotAllPicks()
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#self.refreshPickedWidgets() # wait until finished
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def load_survey(self):
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@ -1,6 +1,7 @@
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# -*- coding: utf-8 -*-
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import os
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import sys
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import math
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import numpy as np
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from pylot.core.active import seismicshot
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from pylot.core.active.surveyUtils import cleanUp
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@ -672,10 +673,29 @@ class Survey(object):
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'''
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import matplotlib.pyplot as plt
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import math
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plt.interactive(True)
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from pylot.core.active.surveyPlotTools import regions
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dist, pick, snrlog, pickerror, spe = self.preparePlotAllPicks(plotRemoved)
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color = {'log10SNR': snrlog,
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'pickerror': pickerror,
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'spe': spe}
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self.color = color
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if refreshPlot is False:
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ax, cbar, sc = self.createPlot(dist, pick, color[colorByVal],
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label='%s' % colorByVal)
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region = regions(ax, cbar, self)
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ax.legend()
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return (ax, region)
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if refreshPlot is True:
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ax, cbar, sc = self.createPlot(dist, pick, color[colorByVal],
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label='%s' % colorByVal, ax=ax,
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cbar=cbar)
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ax.legend()
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return ax
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def preparePlotAllPicks(self, plotRemoved = False):
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dist = []
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pick = []
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snrlog = []
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@ -693,29 +713,15 @@ class Survey(object):
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pickerror.append(shot.getPickError(traceID))
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spe.append(shot.getSymmetricPickError(traceID))
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color = {'log10SNR': snrlog,
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'pickerror': pickerror,
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'spe': spe}
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self.color = color
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if refreshPlot is False:
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ax, cbar = self.createPlot(dist, pick, color[colorByVal],
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label='%s' % colorByVal)
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region = regions(ax, cbar, self)
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ax.legend()
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return (ax, region)
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if refreshPlot is True:
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ax, cbar = self.createPlot(dist, pick, color[colorByVal],
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label='%s' % colorByVal, ax=ax,
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cbar=cbar)
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ax.legend()
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return ax
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return dist, pick, snrlog, pickerror, spe
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def createPlot(self, dist, pick, inkByVal, label, ax=None, cbar=None):
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'''
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Used by plotAllPicks.
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'''
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import matplotlib.pyplot as plt
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plt.interactive(True)
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#plt.interactive(True)
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cm = plt.cm.jet
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if ax is None:
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print('Generating new plot...')
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@ -723,7 +729,7 @@ class Survey(object):
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ax = fig.add_subplot(111)
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sc = ax.scatter(dist, pick, cmap=cm, c=inkByVal, s=5,
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edgecolors='none', label=label)
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cbar = plt.colorbar(sc, fraction=0.05)
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cbar = fig.colorbar(sc, fraction=0.05)
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cbar.set_label(label)
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ax.set_xlabel('Distance [m]')
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ax.set_ylabel('Time [s]')
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@ -732,14 +738,16 @@ class Survey(object):
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else:
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sc = ax.scatter(dist, pick, cmap=cm, c=inkByVal, s=5,
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edgecolors='none', label=label)
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cbar = plt.colorbar(sc, cax=cbar.ax)
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cbar.set_label(label)
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if cbar is not None:
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cbar.ax.clear()
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cbar = ax.figure.colorbar(sc, cax=cbar.ax)
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cbar.set_label(label)
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ax.set_xlabel('Distance [m]')
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ax.set_ylabel('Time [s]')
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ax.text(0.5, 0.95, 'Plot of all picks', transform=ax.transAxes,
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horizontalalignment='center')
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return (ax, cbar)
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return ax, cbar, sc
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def _update_progress(self, shotname, tend, progress):
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sys.stdout.write(
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'Working on shot %s. ETC is %02d:%02d:%02d [%2.2f %%]\r' % (
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@ -2,7 +2,7 @@
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# Form implementation generated from reading ui file 'asp3d_layout.ui'
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#
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# Created: Thu Aug 4 13:55:47 2016
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# Created: Wed Aug 10 14:11:07 2016
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# by: pyside-uic 0.2.15 running on PySide 1.2.2
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#
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# WARNING! All changes made in this file will be lost!
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@ -2,7 +2,7 @@
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# Form implementation generated from reading ui file 'fmtomo_parameters_layout.ui'
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#
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# Created: Thu Aug 4 13:55:47 2016
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# Created: Wed Aug 10 14:11:07 2016
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# by: pyside-uic 0.2.15 running on PySide 1.2.2
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#
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# WARNING! All changes made in this file will be lost!
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@ -2,7 +2,7 @@
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# Form implementation generated from reading ui file 'generate_seisarray_layout.ui'
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#
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# Created: Thu Aug 4 13:55:47 2016
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# Created: Wed Aug 10 14:11:07 2016
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# by: pyside-uic 0.2.15 running on PySide 1.2.2
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#
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# WARNING! All changes made in this file will be lost!
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@ -2,7 +2,7 @@
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# Form implementation generated from reading ui file 'generate_survey_layout.ui'
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#
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# Created: Thu Aug 4 13:55:47 2016
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# Created: Wed Aug 10 14:11:07 2016
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# by: pyside-uic 0.2.15 running on PySide 1.2.2
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#
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# WARNING! All changes made in this file will be lost!
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@ -2,7 +2,7 @@
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# Form implementation generated from reading ui file 'generate_survey_layout_minimal.ui'
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#
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# Created: Thu Aug 4 13:55:47 2016
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# Created: Wed Aug 10 14:11:07 2016
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# by: pyside-uic 0.2.15 running on PySide 1.2.2
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#
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# WARNING! All changes made in this file will be lost!
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@ -2,7 +2,7 @@
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# Form implementation generated from reading ui file 'picking_parameters_layout.ui'
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#
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# Created: Thu Aug 4 13:55:47 2016
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# Created: Wed Aug 10 14:11:07 2016
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# by: pyside-uic 0.2.15 running on PySide 1.2.2
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#
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# WARNING! All changes made in this file will be lost!
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@ -2,7 +2,7 @@
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# Form implementation generated from reading ui file 'postprocessing_layout.ui'
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#
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# Created: Tue Aug 9 10:36:58 2016
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# Created: Wed Aug 10 14:11:08 2016
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# by: pyside-uic 0.2.15 running on PySide 1.2.2
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#
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# WARNING! All changes made in this file will be lost!
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@ -12,34 +12,13 @@ from PySide import QtCore, QtGui
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class Ui_postprocessing(object):
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def setupUi(self, postprocessing):
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postprocessing.setObjectName("postprocessing")
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postprocessing.resize(640, 479)
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self.verticalLayout_2 = QtGui.QVBoxLayout(postprocessing)
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self.verticalLayout_2.setObjectName("verticalLayout_2")
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self.verticalLayout = QtGui.QVBoxLayout()
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postprocessing.resize(663, 617)
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self.verticalLayout = QtGui.QVBoxLayout(postprocessing)
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self.verticalLayout.setObjectName("verticalLayout")
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self.gridLayout = QtGui.QGridLayout()
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self.gridLayout.setObjectName("gridLayout")
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self.horizontalLayout = QtGui.QHBoxLayout()
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self.horizontalLayout.setObjectName("horizontalLayout")
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self.pushButton_rect = QtGui.QPushButton(postprocessing)
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sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Minimum)
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sizePolicy.setHorizontalStretch(0)
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sizePolicy.setVerticalStretch(0)
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sizePolicy.setHeightForWidth(self.pushButton_rect.sizePolicy().hasHeightForWidth())
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self.pushButton_rect.setSizePolicy(sizePolicy)
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self.pushButton_rect.setMaximumSize(QtCore.QSize(16777215, 30))
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self.pushButton_rect.setObjectName("pushButton_rect")
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self.horizontalLayout.addWidget(self.pushButton_rect)
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self.pushButton_poly = QtGui.QPushButton(postprocessing)
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sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Minimum)
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sizePolicy.setHorizontalStretch(0)
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sizePolicy.setVerticalStretch(0)
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sizePolicy.setHeightForWidth(self.pushButton_poly.sizePolicy().hasHeightForWidth())
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self.pushButton_poly.setSizePolicy(sizePolicy)
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self.pushButton_poly.setMaximumSize(QtCore.QSize(16777215, 30))
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self.pushButton_poly.setObjectName("pushButton_poly")
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self.horizontalLayout.addWidget(self.pushButton_poly)
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self.gridLayout.addLayout(self.horizontalLayout, 1, 0, 1, 1)
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self.horizontalLayout_2 = QtGui.QHBoxLayout()
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self.horizontalLayout_2.setObjectName("horizontalLayout_2")
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self.verticalLayout_3 = QtGui.QVBoxLayout()
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self.verticalLayout_3.setObjectName("verticalLayout_3")
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self.label = QtGui.QLabel(postprocessing)
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sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Minimum)
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sizePolicy.setHorizontalStretch(0)
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@ -49,7 +28,42 @@ class Ui_postprocessing(object):
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self.label.setMinimumSize(QtCore.QSize(0, 20))
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self.label.setMaximumSize(QtCore.QSize(16777215, 30))
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self.label.setObjectName("label")
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self.gridLayout.addWidget(self.label, 0, 0, 1, 1)
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self.verticalLayout_3.addWidget(self.label)
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self.horizontalLayout_4 = QtGui.QHBoxLayout()
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self.horizontalLayout_4.setObjectName("horizontalLayout_4")
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self.pushButton_rect = QtGui.QPushButton(postprocessing)
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sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Minimum)
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sizePolicy.setHorizontalStretch(0)
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sizePolicy.setVerticalStretch(0)
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sizePolicy.setHeightForWidth(self.pushButton_rect.sizePolicy().hasHeightForWidth())
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self.pushButton_rect.setSizePolicy(sizePolicy)
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self.pushButton_rect.setMaximumSize(QtCore.QSize(16777215, 30))
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self.pushButton_rect.setObjectName("pushButton_rect")
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self.horizontalLayout_4.addWidget(self.pushButton_rect)
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self.pushButton_poly = QtGui.QPushButton(postprocessing)
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sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Minimum)
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sizePolicy.setHorizontalStretch(0)
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sizePolicy.setVerticalStretch(0)
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sizePolicy.setHeightForWidth(self.pushButton_poly.sizePolicy().hasHeightForWidth())
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self.pushButton_poly.setSizePolicy(sizePolicy)
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self.pushButton_poly.setMaximumSize(QtCore.QSize(16777215, 30))
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self.pushButton_poly.setObjectName("pushButton_poly")
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self.horizontalLayout_4.addWidget(self.pushButton_poly)
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self.pushButton_plot = QtGui.QPushButton(postprocessing)
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self.pushButton_plot.setCheckable(False)
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self.pushButton_plot.setDefault(False)
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self.pushButton_plot.setFlat(False)
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self.pushButton_plot.setObjectName("pushButton_plot")
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self.horizontalLayout_4.addWidget(self.pushButton_plot)
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self.verticalLayout_3.addLayout(self.horizontalLayout_4)
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self.horizontalLayout_2.addLayout(self.verticalLayout_3)
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self.line = QtGui.QFrame(postprocessing)
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self.line.setFrameShape(QtGui.QFrame.VLine)
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self.line.setFrameShadow(QtGui.QFrame.Sunken)
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self.line.setObjectName("line")
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self.horizontalLayout_2.addWidget(self.line)
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self.verticalLayout_2 = QtGui.QVBoxLayout()
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self.verticalLayout_2.setObjectName("verticalLayout_2")
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self.label_2 = QtGui.QLabel(postprocessing)
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sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Minimum)
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sizePolicy.setHorizontalStretch(0)
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@ -59,9 +73,9 @@ class Ui_postprocessing(object):
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self.label_2.setMinimumSize(QtCore.QSize(0, 20))
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self.label_2.setMaximumSize(QtCore.QSize(16777215, 30))
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self.label_2.setObjectName("label_2")
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self.gridLayout.addWidget(self.label_2, 0, 1, 1, 1)
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self.horizontalLayout_3 = QtGui.QHBoxLayout()
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self.horizontalLayout_3.setObjectName("horizontalLayout_3")
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self.verticalLayout_2.addWidget(self.label_2)
|
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self.horizontalLayout_5 = QtGui.QHBoxLayout()
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self.horizontalLayout_5.setObjectName("horizontalLayout_5")
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self.pushButton_snr = QtGui.QPushButton(postprocessing)
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sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Minimum)
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sizePolicy.setHorizontalStretch(0)
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@ -70,7 +84,7 @@ class Ui_postprocessing(object):
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self.pushButton_snr.setSizePolicy(sizePolicy)
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self.pushButton_snr.setMaximumSize(QtCore.QSize(16777215, 30))
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self.pushButton_snr.setObjectName("pushButton_snr")
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self.horizontalLayout_3.addWidget(self.pushButton_snr)
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self.horizontalLayout_5.addWidget(self.pushButton_snr)
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self.pushButton_pe = QtGui.QPushButton(postprocessing)
|
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sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Minimum)
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sizePolicy.setHorizontalStretch(0)
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@ -79,7 +93,7 @@ class Ui_postprocessing(object):
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self.pushButton_pe.setSizePolicy(sizePolicy)
|
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self.pushButton_pe.setMaximumSize(QtCore.QSize(16777215, 30))
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self.pushButton_pe.setObjectName("pushButton_pe")
|
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self.horizontalLayout_3.addWidget(self.pushButton_pe)
|
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self.horizontalLayout_5.addWidget(self.pushButton_pe)
|
||||
self.pushButton_spe = QtGui.QPushButton(postprocessing)
|
||||
sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Minimum)
|
||||
sizePolicy.setHorizontalStretch(0)
|
||||
@ -88,29 +102,23 @@ class Ui_postprocessing(object):
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||||
self.pushButton_spe.setSizePolicy(sizePolicy)
|
||||
self.pushButton_spe.setMaximumSize(QtCore.QSize(16777215, 30))
|
||||
self.pushButton_spe.setObjectName("pushButton_spe")
|
||||
self.horizontalLayout_3.addWidget(self.pushButton_spe)
|
||||
self.gridLayout.addLayout(self.horizontalLayout_3, 1, 1, 1, 1)
|
||||
self.verticalLayout.addLayout(self.gridLayout)
|
||||
self.horizontalLayout_plot = QtGui.QHBoxLayout()
|
||||
self.horizontalLayout_plot.setObjectName("horizontalLayout_plot")
|
||||
self.verticalLayout.addLayout(self.horizontalLayout_plot)
|
||||
self.verticalLayout_2.addLayout(self.verticalLayout)
|
||||
self.buttonBox = QtGui.QDialogButtonBox(postprocessing)
|
||||
self.buttonBox.setOrientation(QtCore.Qt.Horizontal)
|
||||
self.buttonBox.setStandardButtons(QtGui.QDialogButtonBox.Ok)
|
||||
self.buttonBox.setObjectName("buttonBox")
|
||||
self.verticalLayout_2.addWidget(self.buttonBox)
|
||||
self.horizontalLayout_5.addWidget(self.pushButton_spe)
|
||||
self.verticalLayout_2.addLayout(self.horizontalLayout_5)
|
||||
self.horizontalLayout_2.addLayout(self.verticalLayout_2)
|
||||
self.verticalLayout.addLayout(self.horizontalLayout_2)
|
||||
self.verticalLayout_plot = QtGui.QVBoxLayout()
|
||||
self.verticalLayout_plot.setObjectName("verticalLayout_plot")
|
||||
self.verticalLayout.addLayout(self.verticalLayout_plot)
|
||||
|
||||
self.retranslateUi(postprocessing)
|
||||
QtCore.QObject.connect(self.buttonBox, QtCore.SIGNAL("accepted()"), postprocessing.accept)
|
||||
QtCore.QObject.connect(self.buttonBox, QtCore.SIGNAL("rejected()"), postprocessing.reject)
|
||||
QtCore.QMetaObject.connectSlotsByName(postprocessing)
|
||||
|
||||
def retranslateUi(self, postprocessing):
|
||||
postprocessing.setWindowTitle(QtGui.QApplication.translate("postprocessing", "Postprocessing", None, QtGui.QApplication.UnicodeUTF8))
|
||||
self.label.setText(QtGui.QApplication.translate("postprocessing", "Selection", None, QtGui.QApplication.UnicodeUTF8))
|
||||
self.pushButton_rect.setText(QtGui.QApplication.translate("postprocessing", "Rectangle", None, QtGui.QApplication.UnicodeUTF8))
|
||||
self.pushButton_poly.setText(QtGui.QApplication.translate("postprocessing", "Polygon", None, QtGui.QApplication.UnicodeUTF8))
|
||||
self.label.setText(QtGui.QApplication.translate("postprocessing", "Selection", None, QtGui.QApplication.UnicodeUTF8))
|
||||
self.pushButton_plot.setText(QtGui.QApplication.translate("postprocessing", "Plot", None, QtGui.QApplication.UnicodeUTF8))
|
||||
self.label_2.setText(QtGui.QApplication.translate("postprocessing", "Color by", None, QtGui.QApplication.UnicodeUTF8))
|
||||
self.pushButton_snr.setText(QtGui.QApplication.translate("postprocessing", "SNR", None, QtGui.QApplication.UnicodeUTF8))
|
||||
self.pushButton_pe.setText(QtGui.QApplication.translate("postprocessing", "PE", None, QtGui.QApplication.UnicodeUTF8))
|
||||
|
||||
@ -2,7 +2,7 @@
|
||||
|
||||
# Form implementation generated from reading ui file 'vtk_tools_layout.ui'
|
||||
#
|
||||
# Created: Thu Aug 4 13:55:47 2016
|
||||
# Created: Wed Aug 10 14:11:07 2016
|
||||
# by: pyside-uic 0.2.15 running on PySide 1.2.2
|
||||
#
|
||||
# WARNING! All changes made in this file will be lost!
|
||||
|
||||
@ -1,6 +1,9 @@
|
||||
#!/usr/bin/env python
|
||||
# -*- coding: utf-8 -*-
|
||||
import os
|
||||
import numpy as np
|
||||
import matplotlib
|
||||
import matplotlib.pyplot as plt
|
||||
from PySide import QtCore, QtGui
|
||||
from pylot.core.active import surveyUtils, activeSeismoPick, seismicArrayPreparation, fmtomoUtils
|
||||
from generate_survey_layout import Ui_generate_survey
|
||||
@ -8,11 +11,11 @@ from generate_survey_layout_minimal import Ui_generate_survey_minimal
|
||||
from generate_seisarray_layout import Ui_generate_seisarray
|
||||
from picking_parameters_layout import Ui_picking_parameters
|
||||
from fmtomo_parameters_layout import Ui_fmtomo_parameters
|
||||
from pylot.core.active.gui.vtk_tools_layout import Ui_vtk_tools
|
||||
from vtk_tools_layout import Ui_vtk_tools
|
||||
from postprocessing_layout import Ui_postprocessing
|
||||
|
||||
from pylot.core.active.surveyPlotTools import regions
|
||||
|
||||
import numpy as np
|
||||
import matplotlib
|
||||
matplotlib.use('Qt4Agg')
|
||||
matplotlib.rcParams['backend.qt4']='PySide'
|
||||
|
||||
@ -597,3 +600,88 @@ class Call_VTK_dialog(object):
|
||||
def newFileVTK(self):
|
||||
self.ui.lineEdit_vgout.setText(saveFile())
|
||||
|
||||
class Postprocessing(object):
|
||||
def __init__(self, mainwindow, survey):
|
||||
self.mainwindow = mainwindow
|
||||
self.survey = survey
|
||||
self.init_widget()
|
||||
self.start_widget()
|
||||
|
||||
def init_widget(self):
|
||||
qwidget = QtGui.QWidget()#
|
||||
ui = Ui_postprocessing()
|
||||
ui.setupUi(qwidget)
|
||||
self.ui = ui
|
||||
self.qwidget = qwidget
|
||||
self.initPlot()
|
||||
self.newPlot()
|
||||
self.connectButtons()
|
||||
self.region = regions(self.ax, self.cbar, self.survey, qt_interface = True)
|
||||
|
||||
def start_widget(self):
|
||||
self.qwidget.show()
|
||||
|
||||
def initPlot(self):
|
||||
self.figure = Figure()
|
||||
self.canvas = FigureCanvas(self.figure)
|
||||
self.ui.verticalLayout_plot.addWidget(self.canvas)
|
||||
self.toolbar = NavigationToolbar(self.canvas, self.mainwindow)
|
||||
self.ui.verticalLayout_plot.addWidget(self.toolbar)
|
||||
|
||||
def newPlot(self):
|
||||
ax = self.figure.add_subplot(111)
|
||||
dists, picks, snrlog, pe, spe = self.survey.preparePlotAllPicks(plotRemoved = False)
|
||||
self.dists = dists
|
||||
self.picks = picks
|
||||
self.inkDict = {'snrlog': snrlog,
|
||||
'pe': pe,
|
||||
'spe': spe}
|
||||
|
||||
ax, cbar, sc = self.survey.createPlot(dists, picks, snrlog, 'log10(SNR)', ax = ax, cbar = None)
|
||||
self.cbar = self.figure.colorbar(sc, ax = ax, fraction=0.05)
|
||||
self.ax = ax
|
||||
self.draw()
|
||||
|
||||
def refreshPlot(self, inkByVal = 'snrlog'):
|
||||
self.ax.clear()
|
||||
ax = self.ax
|
||||
ax, cbar, sc = self.survey.createPlot(self.dists, self.picks, self.inkDict[inkByVal],
|
||||
inkByVal, ax = ax, cbar = self.cbar)
|
||||
#self.cbar = self.figure.colorbar(sc, fraction=0.05)
|
||||
self.draw()
|
||||
|
||||
def update_survey(self, survey):
|
||||
self.survey = survey
|
||||
|
||||
def get_survey(self):
|
||||
return self.survey
|
||||
|
||||
def draw(self):
|
||||
self.canvas.draw()
|
||||
|
||||
def connectButtons(self):
|
||||
QtCore.QObject.connect(self.ui.pushButton_rect, QtCore.SIGNAL("clicked()"), self.chooseRect)
|
||||
QtCore.QObject.connect(self.ui.pushButton_poly, QtCore.SIGNAL("clicked()"), self.choosePoly)
|
||||
QtCore.QObject.connect(self.ui.pushButton_plot, QtCore.SIGNAL("clicked()"), self.plotPicks)
|
||||
QtCore.QObject.connect(self.ui.pushButton_snr, QtCore.SIGNAL("clicked()"), self.refrSNR)
|
||||
QtCore.QObject.connect(self.ui.pushButton_pe, QtCore.SIGNAL("clicked()"), self.refrPE)
|
||||
QtCore.QObject.connect(self.ui.pushButton_spe, QtCore.SIGNAL("clicked()"), self.refrSPE)
|
||||
|
||||
def chooseRect(self):
|
||||
self.region.chooseRectangles()
|
||||
|
||||
def choosePoly(self):
|
||||
self.region.choosePolygon()
|
||||
|
||||
def plotPicks(self):
|
||||
self.region.plotTracesInActiveRegions()
|
||||
|
||||
def refrSNR(self):
|
||||
self.refreshPlot('snrlog')
|
||||
|
||||
def refrPE(self):
|
||||
self.refreshPlot('pe')
|
||||
|
||||
def refrSPE(self):
|
||||
self.refreshPlot('spe')
|
||||
|
||||
|
||||
@ -29,7 +29,7 @@ class regions(object):
|
||||
|
||||
'''
|
||||
|
||||
def __init__(self, ax, cbar, survey):
|
||||
def __init__(self, ax, cbar, survey, qt_interface = False):
|
||||
self.ax = ax
|
||||
self.cbar = cbar
|
||||
self.cbv = 'log10SNR'
|
||||
@ -45,12 +45,13 @@ class regions(object):
|
||||
self._y1 = []
|
||||
self._polyx = []
|
||||
self._polyy = []
|
||||
self.buttons = {}
|
||||
self._allpicks = None
|
||||
self.shots_found = {}
|
||||
self.shots_for_deletion = {}
|
||||
self._generateList()
|
||||
self._addButtons()
|
||||
if not qt_interface:
|
||||
self.buttons = {}
|
||||
self._addButtons()
|
||||
self.addTextfield()
|
||||
self.drawFigure()
|
||||
|
||||
@ -525,4 +526,5 @@ class regions(object):
|
||||
if resetAxes == True:
|
||||
self.ax.set_xlim(self._xlim)
|
||||
self.ax.set_ylim(self._ylim)
|
||||
plt.draw()
|
||||
self.ax.figure.canvas.draw()
|
||||
|
||||
|
||||
@ -339,16 +339,30 @@ class PDFDictionary(object):
|
||||
|
||||
|
||||
class PDFstatistics(object):
|
||||
'''
|
||||
To do:
|
||||
plots for std, quantiles,
|
||||
'''
|
||||
"""
|
||||
This object can be used to get various statistic values from probabillity density functions.
|
||||
Takes a path as argument.
|
||||
"""
|
||||
|
||||
|
||||
def __init__(self, directory):
|
||||
"""Initiates some values needed when dealing with pdfs later"""
|
||||
self.directory = directory
|
||||
self.evtlist = list()
|
||||
self.return_phase = None
|
||||
|
||||
|
||||
def readTheta(self, arname, dir, fnpattern):
|
||||
"""
|
||||
Loads an array from file into object instance.
|
||||
:param arname: Name of Array beeing created.
|
||||
:type arname: string
|
||||
:param dir: Directory where file is to be found.
|
||||
:type dir: string
|
||||
:param fnpattern: file name pattern for reading multiple files into one array.
|
||||
:type fnpattern: string
|
||||
:return: a list with all args* from the files.
|
||||
"""
|
||||
exec('self.' + arname +' = []')
|
||||
filelist = glob.glob1(dir, fnpattern)
|
||||
for file in filelist:
|
||||
@ -359,8 +373,14 @@ class PDFstatistics(object):
|
||||
exec('self.' + arname + ' += list')
|
||||
fid.close()
|
||||
|
||||
|
||||
def makeFileList(self, fn_pattern='*.xml'):
|
||||
evtlist = list()
|
||||
"""
|
||||
Takes a file pattern and searches for that recursively in the set path for the object.
|
||||
:param fn_pattern: A pattern that can identify all datafiles. Default Value = '*.xml'
|
||||
:type fn_pattern: string
|
||||
:return: creates a list of events saved in the PDFstatistics object.
|
||||
"""
|
||||
evtlist = glob.glob1((os.path.join(self.directory)), fn_pattern)
|
||||
if not evtlist:
|
||||
for root, _, files in os.walk(self.directory):
|
||||
@ -369,7 +389,9 @@ class PDFstatistics(object):
|
||||
evtlist.append(os.path.join(root, file))
|
||||
self.evtlist = evtlist
|
||||
|
||||
|
||||
def __iter__(self):
|
||||
"""Iterating over the PDFstatistics object yields every single pdf from the list of events"""
|
||||
assert isinstance(self.return_phase, str), 'phase has to be set before being able to iterate over items...'
|
||||
for evt in self.evtlist:
|
||||
self.getPDFDict(self.directory, evt)
|
||||
@ -379,13 +401,30 @@ class PDFstatistics(object):
|
||||
except KeyError:
|
||||
continue
|
||||
|
||||
|
||||
def set_return_phase(self, type):
|
||||
"""
|
||||
Sets the phase typ of event data that is returned on iteration over the object.
|
||||
:param type: can be either p (p-phase) or s (s-phase).
|
||||
:type type: string
|
||||
:return: -
|
||||
"""
|
||||
if type.upper() not in 'PS':
|
||||
raise ValueError("phase type must be either 'P' or 'S'!")
|
||||
else:
|
||||
self.return_phase = type.upper()
|
||||
|
||||
|
||||
def getQD(self,value):
|
||||
"""
|
||||
Takes a probability value and and returns the distance
|
||||
between two complementary quantiles.
|
||||
For example: getQD(0.3) yields Quantile(1-0.3) - Quantile(0.3)
|
||||
:param value: 0 < value < 0.5
|
||||
:type value: float
|
||||
:return: returns a list of all quantile distances for all pdfs in
|
||||
the list of events.
|
||||
"""
|
||||
QDlist = []
|
||||
for pdf in self:
|
||||
QD = pdf.quantile_distance(value)
|
||||
@ -394,6 +433,16 @@ class PDFstatistics(object):
|
||||
|
||||
|
||||
def getQDQ(self,value):
|
||||
"""
|
||||
Takes a probability value and and returns the fraction of
|
||||
two quantile distances.
|
||||
For example:
|
||||
getQDQ(x) = getQD(0.5-x)/getQD(x)
|
||||
(Quantile(1-0.5-x) - Quantile(x)) / (Quantile(1-x) - Quantile(x))
|
||||
:param value: 0 < value < 0.25
|
||||
:return: returns a list of all quantile fractions for all pdfs in
|
||||
the list of events.
|
||||
"""
|
||||
QDQlist = []
|
||||
for pdf in self:
|
||||
QDQ = pdf.qtile_dist_quot(value)
|
||||
@ -402,6 +451,12 @@ class PDFstatistics(object):
|
||||
|
||||
|
||||
def getSTD(self):
|
||||
"""
|
||||
Iterates over PDFstatistics object and returns the standard
|
||||
deviation of all pdfs in the list of events.
|
||||
:return: saves an instance of self.p_stdarray or
|
||||
self.s_stdarray, depending on set phase.
|
||||
"""
|
||||
std = []
|
||||
for pdf in self:
|
||||
try:
|
||||
@ -413,6 +468,10 @@ class PDFstatistics(object):
|
||||
|
||||
|
||||
def set_stdarray(self, array):
|
||||
"""
|
||||
Helper function for self.getSTD(). This function
|
||||
should not be called directly.
|
||||
"""
|
||||
if self.return_phase == 'P':
|
||||
self.p_stdarray = array
|
||||
elif self.return_phase == 'S':
|
||||
@ -423,6 +482,22 @@ class PDFstatistics(object):
|
||||
|
||||
|
||||
def getBinList(self,l_boundary,u_boundary,nbins = 100):
|
||||
"""
|
||||
Helper function for self.histplot(). Takes in two boundaries and
|
||||
a number of bins and creates a list of bins which can be passed
|
||||
to self.histplot().
|
||||
:param l_boundary: Any number.
|
||||
:type l_boundary: float
|
||||
:param u_boundary: Any number that is greater than l_boundary.
|
||||
:type u_boundary: float
|
||||
:param nbins: Any positive integer.
|
||||
:type nbins: int
|
||||
:return: A list of equidistant bins.
|
||||
"""
|
||||
if u_boundary <= l_boundary:
|
||||
raise ValueError('Upper boundary must be greather than lower!')
|
||||
elif nbins <= 0:
|
||||
raise ValueError('Number of bins is not valid.')
|
||||
binlist = []
|
||||
for i in range(nbins):
|
||||
binlist.append(l_boundary + i*(u_boundary-l_boundary)/nbins)
|
||||
@ -430,24 +505,57 @@ class PDFstatistics(object):
|
||||
|
||||
|
||||
def histplot(self, array, binlist, xlab = 'Values',
|
||||
ylab = 'Frequency', title = None, label=None):
|
||||
ylab = 'Frequency', title = None, fnout = None):
|
||||
"""
|
||||
Method to quickly show some distribution of data. Takes array like data,
|
||||
and a list of bins. Editing detail and inserting a legend is not possible.
|
||||
:param array: List of values.
|
||||
:type array: Array like
|
||||
:param binlist: List of bins.
|
||||
:type binlist: list
|
||||
:param xlab: A label for the x-axes.
|
||||
:type xlab: str
|
||||
:param ylab: A label for the y-axes.
|
||||
:type ylab: str
|
||||
:param title: A title for the Plot.
|
||||
:type title: str
|
||||
:param fnout: A path to save the plot instead of showing.
|
||||
Has to contain filename and type. Like: 'path/to/file.png'
|
||||
:type fnout. str
|
||||
:return: -
|
||||
"""
|
||||
import matplotlib.pyplot as plt
|
||||
plt.hist(array,bins = binlist)
|
||||
plt.xlabel('Values')
|
||||
plt.ylabel('Frequency')
|
||||
plt.xlabel(xlab)
|
||||
plt.ylabel(ylab)
|
||||
if title:
|
||||
title_str = 'Quantile distance quotient distribution'
|
||||
if label:
|
||||
title_str += ' (' + label + ')'
|
||||
plt.title(title_str)
|
||||
plt.show()
|
||||
plt.title(title)
|
||||
if fnout:
|
||||
plt.savefig(fnout)
|
||||
else:
|
||||
plt.show()
|
||||
|
||||
|
||||
def getPDFDict(self, month, evt):
|
||||
"""
|
||||
Helper function for __iter__(). Should not be called directly.
|
||||
"""
|
||||
self.pdfdict = PDFDictionary.from_quakeml(os.path.join(self.directory,month,evt))
|
||||
|
||||
|
||||
def getStatistics(self):
|
||||
"""
|
||||
On call function will get mean, median and standard deviation values
|
||||
from self.p_stdarray and self.s_stdarray. Both must be
|
||||
instances before calling this function.
|
||||
:return: Creates instances of self.p_mean, self.p_std_std and self.p_median
|
||||
for both phases (simultaneously) for the PDFstatistics object.
|
||||
"""
|
||||
if not self.p_stdarray or not self.s_stdarray:
|
||||
raise NotImplementedError('Arrays are not properly set yet!')
|
||||
elif type(self.p_stdarray) != type(np.zeros(1)) or type(self.s_stdarray) != type(np.zeros(1)):
|
||||
raise TypeError('Array is not a proper numpy array.')
|
||||
|
||||
self.p_mean = self.p_stdarray.mean()
|
||||
self.p_std_std = self.p_stdarray.std()
|
||||
self.p_median = np.median(self.p_stdarray)
|
||||
@ -456,12 +564,22 @@ class PDFstatistics(object):
|
||||
self.s_median = np.median(self.s_stdarray)
|
||||
|
||||
|
||||
def writeThetaToFile(self,array,out_dir,filename = None):
|
||||
fid = open(os.path.join(out_dir,filename), 'w')
|
||||
def writeThetaToFile(self,array,out_dir):
|
||||
"""
|
||||
Method to write array like data to file. Useful since acquiring can take
|
||||
serious amount of time when dealing with large databases.
|
||||
:param array: List of values.
|
||||
:type array: list
|
||||
:param out_dir: Path to save file to including file name.
|
||||
:type out_dir: str
|
||||
:return: Saves a file at given output directory.
|
||||
"""
|
||||
fid = open(os.path.join(out_dir), 'w')
|
||||
for val in array:
|
||||
fid.write(str(val)+'\n')
|
||||
fid.close()
|
||||
|
||||
|
||||
def main():
|
||||
root_dir ='/home/sebastianp/Codetesting/xmls/'
|
||||
Insheim = PDFstatistics(root_dir)
|
||||
|
||||
@ -363,13 +363,15 @@ class ProbabilityDensityFunction(object):
|
||||
return m
|
||||
|
||||
def quantile_distance(self, prob_value):
|
||||
if 0 >= prob_value or prob_value >= 0.5:
|
||||
raise ValueError('Value out of range.')
|
||||
ql = self.quantile(prob_value)
|
||||
qu = self.quantile(1 - prob_value)
|
||||
return qu - ql
|
||||
|
||||
|
||||
def qtile_dist_quot(self,x):
|
||||
if x <= 0 or x >= 0.5:
|
||||
if x <= 0 or x >= 0.25:
|
||||
raise ValueError('Value out of range.')
|
||||
return self.quantile_distance(0.5-x)/self.quantile_distance(x)
|
||||
|
||||
|
||||
@ -82,8 +82,8 @@ def clims(lim1, lim2):
|
||||
|
||||
def demeanTrace(trace, window):
|
||||
"""
|
||||
returns the DATA where each trace is demean by the average value within
|
||||
WINDOW
|
||||
takes a trace object and returns the same trace object but with data
|
||||
demeaned within a certain time window
|
||||
:param trace: waveform trace object
|
||||
:type trace: `~obspy.core.stream.Trace`
|
||||
:param window:
|
||||
@ -100,9 +100,9 @@ def findComboBoxIndex(combo_box, val):
|
||||
Function findComboBoxIndex takes a QComboBox object and a string and
|
||||
returns either 0 or the index throughout all QComboBox items.
|
||||
:param combo_box: Combo box object.
|
||||
:type combo_box: QComboBox
|
||||
:type combo_box: `~QComboBox`
|
||||
:param val: Name of a combo box to search for.
|
||||
:type val:
|
||||
:type val: basestring
|
||||
:return: index value of item with name val or 0
|
||||
"""
|
||||
return combo_box.findText(val) if combo_box.findText(val) is not -1 else 0
|
||||
@ -110,21 +110,35 @@ def findComboBoxIndex(combo_box, val):
|
||||
|
||||
def find_nearest(array, value):
|
||||
'''
|
||||
Function find_nearest takes an array and a value and returns the
|
||||
index of the nearest value found in the array.
|
||||
:param array:
|
||||
:param value:
|
||||
:return:
|
||||
function find_nearest takes an array and a value and returns the
|
||||
index of the nearest value found in the array
|
||||
:param array: array containing values
|
||||
:type array: `~numpy.ndarray`
|
||||
:param value: number searched for
|
||||
:return: index of the array item being nearest to the value
|
||||
|
||||
>>> a = np.array([ 1.80339578, -0.72546654, 0.95769195, -0.98320759, 0.85922623])
|
||||
>>> find_nearest(a, 1.3)
|
||||
2
|
||||
>>> find_nearest(a, 0)
|
||||
1
|
||||
>>> find_nearest(a, 2)
|
||||
0
|
||||
>>> find_nearest(a, -1)
|
||||
3
|
||||
>>> a = np.array([ 1.1, -0.7, 0.9, -0.9, 0.8])
|
||||
>>> find_nearest(a, 0.849)
|
||||
4
|
||||
'''
|
||||
return (np.abs(array - value)).argmin()
|
||||
|
||||
|
||||
def fnConstructor(s):
|
||||
'''
|
||||
|
||||
:param s:
|
||||
:type s:
|
||||
:return:
|
||||
takes a string and returns a valid filename (especially on windows machines)
|
||||
:param s: desired filename
|
||||
:type s: str
|
||||
:return: valid filename
|
||||
'''
|
||||
if type(s) is str:
|
||||
s = s.split(':')[-1]
|
||||
@ -142,7 +156,21 @@ def fnConstructor(s):
|
||||
|
||||
|
||||
def four_digits(year):
|
||||
if year + 2000 < UTCDateTime.utcnow().year:
|
||||
"""
|
||||
takes a two digit year integer and returns the correct four digit equivalent
|
||||
from the last 100 years
|
||||
:param year: two digit year
|
||||
:type year: int
|
||||
:return: four digit year correspondant
|
||||
|
||||
>>> four_digits(20)
|
||||
1920
|
||||
>>> four_digits(16)
|
||||
2016
|
||||
>>> four_digits(00)
|
||||
2000
|
||||
"""
|
||||
if year + 2000 <= UTCDateTime.utcnow().year:
|
||||
year += 2000
|
||||
else:
|
||||
year += 1900
|
||||
@ -151,10 +179,11 @@ def four_digits(year):
|
||||
|
||||
def getGlobalTimes(stream):
|
||||
'''
|
||||
|
||||
:param stream:
|
||||
:type stream
|
||||
:return:
|
||||
takes a stream object and returns the latest end and the earliest start
|
||||
time of all contained trace objects
|
||||
:param stream: seismological data stream
|
||||
:type stream: `~obspy.core.stream.Stream`
|
||||
:return: minimum start time and maximum end time
|
||||
'''
|
||||
min_start = UTCDateTime()
|
||||
max_end = None
|
||||
@ -168,6 +197,8 @@ def getGlobalTimes(stream):
|
||||
|
||||
def getHash(time):
|
||||
'''
|
||||
takes a time object and returns the corresponding SHA1 hash of the
|
||||
formatted date string
|
||||
:param time: time object for which a hash should be calculated
|
||||
:type time: :class: `~obspy.core.utcdatetime.UTCDateTime` object
|
||||
:return: str
|
||||
@ -179,27 +210,27 @@ def getHash(time):
|
||||
|
||||
def getLogin():
|
||||
'''
|
||||
returns the actual user's login id
|
||||
:return: User ID
|
||||
returns the actual user's login ID
|
||||
:return: login ID
|
||||
'''
|
||||
return pwd.getpwuid(os.getuid())[0]
|
||||
|
||||
|
||||
def getOwner(fn):
|
||||
'''
|
||||
takes filename and returns the User ID of the owner of the file
|
||||
:param fn: filename
|
||||
takes a filename and return the login ID of the actual owner of the file
|
||||
:param fn: filename of the file tested
|
||||
:type fn: str
|
||||
:return: User ID
|
||||
:return: login ID of the file's owner
|
||||
'''
|
||||
return pwd.getpwuid(os.stat(fn).st_uid).pw_name
|
||||
|
||||
|
||||
def getPatternLine(fn, pattern):
|
||||
"""
|
||||
Takes a file name and a pattern string to search for in the file and
|
||||
returns the first line which contains the pattern string otherwise None.
|
||||
:param fn: filename
|
||||
takes a file name and a pattern string to search for in the file and
|
||||
returns the first line which contains the pattern string otherwise 'None'
|
||||
:param fn: file name
|
||||
:type fn: str
|
||||
:param pattern: pattern string to search for
|
||||
:type pattern: str
|
||||
@ -221,22 +252,52 @@ def getPatternLine(fn, pattern):
|
||||
|
||||
def isSorted(iterable):
|
||||
'''
|
||||
takes a python variable and returns True if the iterable is sorted and False otherwise
|
||||
:param iterable: a python variable
|
||||
takes an iterable and returns 'True' if the items are in order otherwise
|
||||
'False'
|
||||
:param iterable: an iterable object
|
||||
:type iterable:
|
||||
:return:
|
||||
:return: Boolean
|
||||
|
||||
>>> isSorted(1)
|
||||
Traceback (most recent call last):
|
||||
...
|
||||
AssertionError: object is not iterable; object: 1
|
||||
>>> isSorted([1,2,3,4])
|
||||
True
|
||||
>>> isSorted('abcd')
|
||||
True
|
||||
>>> isSorted('bcad')
|
||||
False
|
||||
>>> isSorted([2,3,1,4])
|
||||
False
|
||||
'''
|
||||
assert isIterable(iterable), 'object is not iterable; object: {' \
|
||||
'0}'.format(iterable)
|
||||
if type(iterable) is str:
|
||||
iterable = [s for s in iterable]
|
||||
return sorted(iterable) == iterable
|
||||
|
||||
|
||||
def isIterable(obj):
|
||||
"""
|
||||
takes a python object and returns 'True' is the object is iterable and
|
||||
'False' otherwise
|
||||
:param obj: a python object
|
||||
:return: True of False
|
||||
"""
|
||||
try:
|
||||
iterator = iter(obj)
|
||||
except TypeError as te:
|
||||
return False
|
||||
return True
|
||||
|
||||
def prepTimeAxis(stime, trace):
|
||||
'''
|
||||
takes a starttime 'stime' and a trace object 'trace' and return a vector containing as much time stamps as data values in the trace object are available
|
||||
:param stime:
|
||||
:type stime:
|
||||
:param trace:
|
||||
:type trace:
|
||||
:return: time axis
|
||||
takes a starttime and a trace object and returns a valid time axis for
|
||||
plotting
|
||||
:param stime: start time of the actual seismogram as UTCDateTime
|
||||
:param trace: seismic trace object
|
||||
:return: valid numpy array with time stamps for plotting
|
||||
'''
|
||||
nsamp = trace.stats.npts
|
||||
srate = trace.stats.sampling_rate
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user