From 8ee075c2b13bb28f2d54b889e4cc3e5ce85eb59f Mon Sep 17 00:00:00 2001
From: Marcel Paffrath <marcel.paffrath@rub.de>
Date: Thu, 14 Jul 2016 13:59:52 +0200
Subject: [PATCH 1/9] added SNR modification/plot

---
 pylot/core/active/ActiveSeismoPick3D_GUI.py   | 58 ++++++++++++-
 pylot/core/active/asp3d_layout.py             |  2 +-
 pylot/core/active/fmtomo_parameters_layout.py |  2 +-
 .../core/active/generate_seisarray_layout.py  |  2 +-
 pylot/core/active/generate_survey_layout.py   |  9 +-
 .../active/generate_survey_layout_minimal.py  |  2 +-
 .../core/active/picking_parameters_layout.py  | 86 ++++++++++++++++---
 pylot/core/active/surveyUtils.py              | 13 +--
 pylot/core/active/vtk_tools_layout.py         |  2 +-
 9 files changed, 148 insertions(+), 28 deletions(-)

diff --git a/pylot/core/active/ActiveSeismoPick3D_GUI.py b/pylot/core/active/ActiveSeismoPick3D_GUI.py
index 01449aec..f68360a6 100755
--- a/pylot/core/active/ActiveSeismoPick3D_GUI.py
+++ b/pylot/core/active/ActiveSeismoPick3D_GUI.py
@@ -110,8 +110,7 @@ class gui_control(object):
             self.initNewSurvey()
 
     def initNewSurvey(self):
-        self.survey.setArtificialPick(0, 0) # artificial pick at source origin                                         
-        surveyUtils.setDynamicFittedSNR(self.survey.getShotDict())
+        self.survey.setArtificialPick(0, 0) # artificial pick at source origin
         self.setSurveyState(True)
         self.setPickState(False)
 
@@ -147,7 +146,9 @@ class gui_control(object):
             self.survey = activeSeismoPick.Survey(obsdir, srcfile, recfile,
                                                   useDefaultParas = True,
                                                   fstart = fstart, fend = fend)
-            self.setConnected2SurveyState(False)
+            self.setConnected2SurveyState(True)
+            self.seisarray = self.survey.seisarray
+            self.setSeisArrayState(True)
             return True
 
     def addArrayPlot(self):
@@ -313,11 +314,15 @@ class gui_control(object):
         self.printSeisArrayTextbox(init = False)
         
     def getPickParameters(self, ui, Picking_parameters):
+        self.initDynSNRplot()
+        self.plotDynSNR()
+
         if Picking_parameters.exec_():
             ncores = int(ui.ncores.value())
             vmin = float(ui.lineEdit_vmin.text())
             vmax = float(ui.lineEdit_vmax.text())
             folm = float(ui.slider_folm.value())/100.
+            print('folm =', folm)
             AIC = ui.checkBox_AIC.isChecked()
             aicwindow = (int(ui.lineEdit_aicleft.text()), int(ui.lineEdit_aicright.text()))
             return ncores, vmin, vmax, folm, AIC, aicwindow
@@ -358,6 +363,10 @@ class gui_control(object):
         ui.ncores.setMaximum(self.getMaxCPU())
         self.picker_ui = ui
         QtCore.QObject.connect(self.picker_ui.slider_folm, QtCore.SIGNAL("valueChanged(int)"), self.refreshFolm)
+        QtCore.QObject.connect(self.picker_ui.shift_snr, QtCore.SIGNAL("valueChanged(int)"), self.plotDynSNR)
+        QtCore.QObject.connect(self.picker_ui.shift_dist, QtCore.SIGNAL("valueChanged(int)"), self.plotDynSNR)
+        QtCore.QObject.connect(self.picker_ui.p1, QtCore.SIGNAL("valueChanged(double)"), self.plotDynSNR)
+        QtCore.QObject.connect(self.picker_ui.p2, QtCore.SIGNAL("valueChanged(double)"), self.plotDynSNR)
         try:
             ncores, vmin, vmax, folm, AIC, aicwindow = self.getPickParameters(ui, Picking_parameters)
         except TypeError:
@@ -368,12 +377,55 @@ class gui_control(object):
         else:
             HosAic = 'hos'
 
+        shiftSNR = float(self.picker_ui.shift_snr.value())
+        shiftDist = float(self.picker_ui.shift_dist.value())
+        p1 = float(self.picker_ui.p1.value())
+        p2 = float(self.picker_ui.p2.value())
+
+        surveyUtils.setDynamicFittedSNR(self.survey.getShotDict(), shiftdist = shiftDist,
+                                        shiftSNR = shiftSNR, p1 = p1, p2 = p2)
+
         self.survey.pickAllShots(vmin = vmin, vmax = vmax,
                                  folm = folm, HosAic = HosAic,
                                  aicwindow = aicwindow, cores = ncores)
+        QtGui.qApp.processEvents() # test
         self.setPickState(True)
         self.printSurveyTextbox(init = False)
 
+    def plotDynSNR(self):
+        fig = self.snrFig
+        fig.clear()
+        ax = fig.add_subplot(111)
+        snrthresholds = []
+        dists_p = []; snr_p = []
+        shiftSNR = float(self.picker_ui.shift_snr.value())
+        shiftDist = float(self.picker_ui.shift_dist.value())
+        p1 = float(self.picker_ui.p1.value())
+        p2 = float(self.picker_ui.p2.value())
+        dists = range(200)
+        if self.checkPickState():
+            for shot in self.survey.data.values():
+                for traceID in shot.getTraceIDlist():
+                    dists_p.append(shot.getDistance(traceID))
+                    snr_p.append(shot.getSNR(traceID)[0])
+
+            ax.scatter(dists_p, snr_p, s = 0.5, c='k')
+            
+        for dist in dists:
+            dist += shiftDist
+            snrthresholds.append(surveyUtils.snr_fit_func(surveyUtils.get_fit_fn(p1, p2), dist, shiftSNR))
+        ax.plot(dists, snrthresholds)
+        ax.set_xlabel('Distance [m]')
+        ax.set_ylabel('SNR')
+        self.snrCanvas.draw()
+
+    def initDynSNRplot(self):
+        self.snrFig = Figure()
+        self.snrCanvas = FigureCanvas(self.snrFig)
+        self.picker_ui.vlayout_plot.addWidget(self.snrCanvas)
+        self.snrToolbar = NavigationToolbar(self.snrCanvas, self.mainwindow)
+        self.picker_ui.vlayout_plot.addWidget(self.snrToolbar)
+
     def startFMTOMO(self):
         if not self.checkSurveyState():
             self.printDialogMessage('No Survey defined.')
diff --git a/pylot/core/active/asp3d_layout.py b/pylot/core/active/asp3d_layout.py
index 3392a068..8854e998 100644
--- a/pylot/core/active/asp3d_layout.py
+++ b/pylot/core/active/asp3d_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'asp3d_layout.ui'
 #
-# Created: Tue Jul 12 21:41:12 2016
+# Created: Thu Jul 14 13:36:37 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
diff --git a/pylot/core/active/fmtomo_parameters_layout.py b/pylot/core/active/fmtomo_parameters_layout.py
index 04f4ad60..285bac94 100644
--- a/pylot/core/active/fmtomo_parameters_layout.py
+++ b/pylot/core/active/fmtomo_parameters_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'fmtomo_parameters_layout.ui'
 #
-# Created: Tue Jul 12 21:41:12 2016
+# Created: Thu Jul 14 13:36:37 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
diff --git a/pylot/core/active/generate_seisarray_layout.py b/pylot/core/active/generate_seisarray_layout.py
index 98320874..10c297d1 100644
--- a/pylot/core/active/generate_seisarray_layout.py
+++ b/pylot/core/active/generate_seisarray_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'generate_seisarray_layout.ui'
 #
-# Created: Tue Jul 12 21:41:13 2016
+# Created: Thu Jul 14 13:36:38 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
diff --git a/pylot/core/active/generate_survey_layout.py b/pylot/core/active/generate_survey_layout.py
index f33fe9d7..69591b1e 100644
--- a/pylot/core/active/generate_survey_layout.py
+++ b/pylot/core/active/generate_survey_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'generate_survey_layout.ui'
 #
-# Created: Tue Jul 12 21:41:13 2016
+# Created: Thu Jul 14 13:36:38 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
@@ -12,7 +12,7 @@ from PySide import QtCore, QtGui
 class Ui_generate_survey(object):
     def setupUi(self, generate_survey):
         generate_survey.setObjectName("generate_survey")
-        generate_survey.resize(382, 211)
+        generate_survey.resize(382, 220)
         icon = QtGui.QIcon()
         icon.addPixmap(QtGui.QPixmap("../asp3d_icon.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off)
         generate_survey.setWindowIcon(icon)
@@ -50,6 +50,11 @@ class Ui_generate_survey(object):
         self.verticalLayout_2.addLayout(self.gridLayout)
         self.verticalLayout = QtGui.QVBoxLayout()
         self.verticalLayout.setObjectName("verticalLayout")
+        self.line_2 = QtGui.QFrame(generate_survey)
+        self.line_2.setFrameShape(QtGui.QFrame.HLine)
+        self.line_2.setFrameShadow(QtGui.QFrame.Sunken)
+        self.line_2.setObjectName("line_2")
+        self.verticalLayout.addWidget(self.line_2)
         self.label = QtGui.QLabel(generate_survey)
         self.label.setObjectName("label")
         self.verticalLayout.addWidget(self.label)
diff --git a/pylot/core/active/generate_survey_layout_minimal.py b/pylot/core/active/generate_survey_layout_minimal.py
index 1c87cfa8..90956e2a 100644
--- a/pylot/core/active/generate_survey_layout_minimal.py
+++ b/pylot/core/active/generate_survey_layout_minimal.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'generate_survey_layout_minimal.ui'
 #
-# Created: Tue Jul 12 21:41:13 2016
+# Created: Thu Jul 14 13:36:38 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
diff --git a/pylot/core/active/picking_parameters_layout.py b/pylot/core/active/picking_parameters_layout.py
index 12a41274..7bedfa94 100644
--- a/pylot/core/active/picking_parameters_layout.py
+++ b/pylot/core/active/picking_parameters_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'picking_parameters_layout.ui'
 #
-# Created: Tue Jul 12 21:41:13 2016
+# Created: Thu Jul 14 13:36:38 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
@@ -12,10 +12,10 @@ from PySide import QtCore, QtGui
 class Ui_picking_parameters(object):
     def setupUi(self, picking_parameters):
         picking_parameters.setObjectName("picking_parameters")
-        picking_parameters.resize(321, 254)
-        picking_parameters.setMinimumSize(QtCore.QSize(0, 0))
-        self.verticalLayout_3 = QtGui.QVBoxLayout(picking_parameters)
-        self.verticalLayout_3.setObjectName("verticalLayout_3")
+        picking_parameters.resize(400, 550)
+        picking_parameters.setMinimumSize(QtCore.QSize(0, 550))
+        self.verticalLayout_4 = QtGui.QVBoxLayout(picking_parameters)
+        self.verticalLayout_4.setObjectName("verticalLayout_4")
         self.label_7 = QtGui.QLabel(picking_parameters)
         sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Fixed)
         sizePolicy.setHorizontalStretch(0)
@@ -28,7 +28,7 @@ class Ui_picking_parameters(object):
         font.setBold(True)
         self.label_7.setFont(font)
         self.label_7.setObjectName("label_7")
-        self.verticalLayout_3.addWidget(self.label_7)
+        self.verticalLayout_4.addWidget(self.label_7)
         self.horizontalLayout = QtGui.QHBoxLayout()
         self.horizontalLayout.setObjectName("horizontalLayout")
         self.label = QtGui.QLabel(picking_parameters)
@@ -45,7 +45,7 @@ class Ui_picking_parameters(object):
         self.ncores.setMaximum(10000)
         self.ncores.setObjectName("ncores")
         self.horizontalLayout.addWidget(self.ncores)
-        self.verticalLayout_3.addLayout(self.horizontalLayout)
+        self.verticalLayout_4.addLayout(self.horizontalLayout)
         self.horizontalLayout_3 = QtGui.QHBoxLayout()
         self.horizontalLayout_3.setObjectName("horizontalLayout_3")
         self.verticalLayout_2 = QtGui.QVBoxLayout()
@@ -78,7 +78,7 @@ class Ui_picking_parameters(object):
         self.lineEdit_vmax.setObjectName("lineEdit_vmax")
         self.verticalLayout.addWidget(self.lineEdit_vmax)
         self.horizontalLayout_3.addLayout(self.verticalLayout)
-        self.verticalLayout_3.addLayout(self.horizontalLayout_3)
+        self.verticalLayout_4.addLayout(self.horizontalLayout_3)
         self.horizontalLayout_4 = QtGui.QHBoxLayout()
         self.horizontalLayout_4.setObjectName("horizontalLayout_4")
         self.label_4 = QtGui.QLabel(picking_parameters)
@@ -110,7 +110,7 @@ class Ui_picking_parameters(object):
         self.label_folm.setObjectName("label_folm")
         self.horizontalLayout_2.addWidget(self.label_folm)
         self.horizontalLayout_4.addLayout(self.horizontalLayout_2)
-        self.verticalLayout_3.addLayout(self.horizontalLayout_4)
+        self.verticalLayout_4.addLayout(self.horizontalLayout_4)
         self.horizontalLayout_5 = QtGui.QHBoxLayout()
         self.horizontalLayout_5.setObjectName("horizontalLayout_5")
         self.label_5 = QtGui.QLabel(picking_parameters)
@@ -126,7 +126,7 @@ class Ui_picking_parameters(object):
         self.checkBox_AIC.setChecked(True)
         self.checkBox_AIC.setObjectName("checkBox_AIC")
         self.horizontalLayout_5.addWidget(self.checkBox_AIC)
-        self.verticalLayout_3.addLayout(self.horizontalLayout_5)
+        self.verticalLayout_4.addLayout(self.horizontalLayout_5)
         self.horizontalLayout_6 = QtGui.QHBoxLayout()
         self.horizontalLayout_6.setObjectName("horizontalLayout_6")
         self.label_6 = QtGui.QLabel(picking_parameters)
@@ -148,12 +148,67 @@ class Ui_picking_parameters(object):
         self.lineEdit_aicright.setObjectName("lineEdit_aicright")
         self.horizontalLayout_7.addWidget(self.lineEdit_aicright)
         self.horizontalLayout_6.addLayout(self.horizontalLayout_7)
-        self.verticalLayout_3.addLayout(self.horizontalLayout_6)
+        self.verticalLayout_4.addLayout(self.horizontalLayout_6)
+        self.verticalLayout_snr = QtGui.QVBoxLayout()
+        self.verticalLayout_snr.setObjectName("verticalLayout_snr")
+        self.line = QtGui.QFrame(picking_parameters)
+        self.line.setFrameShape(QtGui.QFrame.HLine)
+        self.line.setFrameShadow(QtGui.QFrame.Sunken)
+        self.line.setObjectName("line")
+        self.verticalLayout_snr.addWidget(self.line)
+        self.label_8 = QtGui.QLabel(picking_parameters)
+        self.label_8.setObjectName("label_8")
+        self.verticalLayout_snr.addWidget(self.label_8)
+        self.gridLayout_2 = QtGui.QGridLayout()
+        self.gridLayout_2.setObjectName("gridLayout_2")
+        self.label_9 = QtGui.QLabel(picking_parameters)
+        self.label_9.setObjectName("label_9")
+        self.gridLayout_2.addWidget(self.label_9, 1, 0, 1, 1)
+        self.label_10 = QtGui.QLabel(picking_parameters)
+        self.label_10.setObjectName("label_10")
+        self.gridLayout_2.addWidget(self.label_10, 2, 0, 1, 1)
+        self.p1 = QtGui.QDoubleSpinBox(picking_parameters)
+        self.p1.setDecimals(6)
+        self.p1.setMinimum(-100.0)
+        self.p1.setMaximum(100.0)
+        self.p1.setSingleStep(0.0001)
+        self.p1.setProperty("value", 0.004)
+        self.p1.setObjectName("p1")
+        self.gridLayout_2.addWidget(self.p1, 2, 1, 1, 1)
+        self.label_11 = QtGui.QLabel(picking_parameters)
+        self.label_11.setObjectName("label_11")
+        self.gridLayout_2.addWidget(self.label_11, 1, 2, 1, 1)
+        self.label_12 = QtGui.QLabel(picking_parameters)
+        self.label_12.setObjectName("label_12")
+        self.gridLayout_2.addWidget(self.label_12, 2, 2, 1, 1)
+        self.p2 = QtGui.QDoubleSpinBox(picking_parameters)
+        self.p2.setDecimals(6)
+        self.p2.setMinimum(-100.0)
+        self.p2.setMaximum(100.0)
+        self.p2.setSingleStep(0.0001)
+        self.p2.setProperty("value", -0.0007)
+        self.p2.setObjectName("p2")
+        self.gridLayout_2.addWidget(self.p2, 2, 3, 1, 1)
+        self.shift_dist = QtGui.QSpinBox(picking_parameters)
+        self.shift_dist.setMaximum(10000)
+        self.shift_dist.setProperty("value", 30)
+        self.shift_dist.setObjectName("shift_dist")
+        self.gridLayout_2.addWidget(self.shift_dist, 1, 1, 1, 1)
+        self.shift_snr = QtGui.QSpinBox(picking_parameters)
+        self.shift_snr.setMaximum(10000)
+        self.shift_snr.setProperty("value", 100)
+        self.shift_snr.setObjectName("shift_snr")
+        self.gridLayout_2.addWidget(self.shift_snr, 1, 3, 1, 1)
+        self.verticalLayout_snr.addLayout(self.gridLayout_2)
+        self.verticalLayout_4.addLayout(self.verticalLayout_snr)
+        self.vlayout_plot = QtGui.QVBoxLayout()
+        self.vlayout_plot.setObjectName("vlayout_plot")
+        self.verticalLayout_4.addLayout(self.vlayout_plot)
         self.buttonBox = QtGui.QDialogButtonBox(picking_parameters)
         self.buttonBox.setOrientation(QtCore.Qt.Horizontal)
         self.buttonBox.setStandardButtons(QtGui.QDialogButtonBox.Cancel|QtGui.QDialogButtonBox.Ok)
         self.buttonBox.setObjectName("buttonBox")
-        self.verticalLayout_3.addWidget(self.buttonBox)
+        self.verticalLayout_4.addWidget(self.buttonBox)
 
         self.retranslateUi(picking_parameters)
         QtCore.QObject.connect(self.buttonBox, QtCore.SIGNAL("accepted()"), picking_parameters.accept)
@@ -167,7 +222,7 @@ class Ui_picking_parameters(object):
         self.label.setText(QtGui.QApplication.translate("picking_parameters", "nproc [?]", None, QtGui.QApplication.UnicodeUTF8))
         self.label_2.setToolTip(QtGui.QApplication.translate("picking_parameters", "Minimum permitted direct velocity (apparent velocity!).", None, QtGui.QApplication.UnicodeUTF8))
         self.label_2.setText(QtGui.QApplication.translate("picking_parameters", "vmin [m/s] [?]", None, QtGui.QApplication.UnicodeUTF8))
-        self.lineEdit_vmin.setText(QtGui.QApplication.translate("picking_parameters", "333", None, QtGui.QApplication.UnicodeUTF8))
+        self.lineEdit_vmin.setText(QtGui.QApplication.translate("picking_parameters", "100", None, QtGui.QApplication.UnicodeUTF8))
         self.label_3.setToolTip(QtGui.QApplication.translate("picking_parameters", "Maximum permitted direct velocity (apparent velocity!).", None, QtGui.QApplication.UnicodeUTF8))
         self.label_3.setText(QtGui.QApplication.translate("picking_parameters", "vmax [m/s] [?]", None, QtGui.QApplication.UnicodeUTF8))
         self.lineEdit_vmax.setText(QtGui.QApplication.translate("picking_parameters", "5000", None, QtGui.QApplication.UnicodeUTF8))
@@ -181,4 +236,9 @@ class Ui_picking_parameters(object):
 "(only if AIC checked)", None, QtGui.QApplication.UnicodeUTF8))
         self.lineEdit_aicleft.setText(QtGui.QApplication.translate("picking_parameters", "15", None, QtGui.QApplication.UnicodeUTF8))
         self.lineEdit_aicright.setText(QtGui.QApplication.translate("picking_parameters", "0", None, QtGui.QApplication.UnicodeUTF8))
+        self.label_8.setText(QtGui.QApplication.translate("picking_parameters", "SNR threshold (advanced)", None, QtGui.QApplication.UnicodeUTF8))
+        self.label_9.setText(QtGui.QApplication.translate("picking_parameters", "Shift distance", None, QtGui.QApplication.UnicodeUTF8))
+        self.label_10.setText(QtGui.QApplication.translate("picking_parameters", "p1", None, QtGui.QApplication.UnicodeUTF8))
+        self.label_11.setText(QtGui.QApplication.translate("picking_parameters", "Shift SNR", None, QtGui.QApplication.UnicodeUTF8))
+        self.label_12.setText(QtGui.QApplication.translate("picking_parameters", "p2", None, QtGui.QApplication.UnicodeUTF8))
 
diff --git a/pylot/core/active/surveyUtils.py b/pylot/core/active/surveyUtils.py
index 0cc22b1b..27cb6e01 100644
--- a/pylot/core/active/surveyUtils.py
+++ b/pylot/core/active/surveyUtils.py
@@ -1,5 +1,5 @@
 from __future__ import print_function
-
+import numpy as np
 
 def readParameters(parfile, parameter):
     """
@@ -90,10 +90,9 @@ def setDynamicFittedSNR(shot_dict, shiftdist=30, shiftSNR=100, p1=0.004, p2=-0.0
     :type p2: float
     :return:
     """
-    import numpy as np
     minSNR = 2.5
     # fit_fn = fitSNR4dist(shot_dict)
-    fit_fn = np.poly1d([p1, p2])
+    fit_fn = get_fit_fn(p1, p2)
     for shot in shot_dict.values():
         for traceID in shot.getTraceIDlist():  ### IMPROVE
             dist = shot.getDistance(traceID) + shiftdist
@@ -104,13 +103,17 @@ def setDynamicFittedSNR(shot_dict, shiftdist=30, shiftSNR=100, p1=0.004, p2=-0.0
                 shot.setSNRthreshold(traceID, minSNR)
             else:
                 shot.setSNRthreshold(traceID, snrthreshold)
-    print("setDynamicFittedSNR: Finished setting of fitted SNR-threshold")
+    print("setDynamicFittedSNR: Finished setting of fitted SNR-threshold.\n"
+          "Parameters: ShiftDist = %s, ShiftSNR = %s, p1 = %s, p2 = %s"
+          %(shiftdist, shiftSNR, p1, p2))
 
 def snr_fit_func(fit_fn, dist, shiftSNR):
-    import numpy as np
     snrthreshold = (1 / (fit_fn(dist) ** 2)) - shiftSNR * np.exp(-0.05 * dist)
     return snrthreshold
 
+def get_fit_fn(p1, p2):
+    return np.poly1d([p1, p2])
+
 def setConstantSNR(shot_dict, snrthreshold=2.5):
     """
     Set a constant SNR value to all Seismicshots in a dictionary (e.g. survey.getShotDict()).
diff --git a/pylot/core/active/vtk_tools_layout.py b/pylot/core/active/vtk_tools_layout.py
index 49ae3cd0..b7bcf57c 100644
--- a/pylot/core/active/vtk_tools_layout.py
+++ b/pylot/core/active/vtk_tools_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'vtk_tools_layout.ui'
 #
-# Created: Tue Jul 12 21:41:13 2016
+# Created: Thu Jul 14 13:36:38 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!

From c7f7d9785b4dd5ddf62063a38203cb1a6b9164a6 Mon Sep 17 00:00:00 2001
From: Marcel Paffrath <marcel.paffrath@rub.de>
Date: Mon, 18 Jul 2016 11:54:29 +0200
Subject: [PATCH 2/9] Rearranged Main Layout (buttons to top menu), several
 tweaks for plotDynSNR

---
 pylot/core/active/ActiveSeismoPick3D_GUI.py   |  45 ++--
 pylot/core/active/asp3d_layout.py             | 206 +++++++-----------
 pylot/core/active/fmtomo_parameters_layout.py |   2 +-
 .../core/active/generate_seisarray_layout.py  |   4 +-
 pylot/core/active/generate_survey_layout.py   |   2 +-
 .../active/generate_survey_layout_minimal.py  |   2 +-
 .../core/active/picking_parameters_layout.py  |   2 +-
 pylot/core/active/vtk_tools_layout.py         |   2 +-
 8 files changed, 120 insertions(+), 145 deletions(-)

diff --git a/pylot/core/active/ActiveSeismoPick3D_GUI.py b/pylot/core/active/ActiveSeismoPick3D_GUI.py
index f68360a6..16e8fa66 100755
--- a/pylot/core/active/ActiveSeismoPick3D_GUI.py
+++ b/pylot/core/active/ActiveSeismoPick3D_GUI.py
@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 import os
+import sys
 import matplotlib
 matplotlib.use('Qt4Agg')
 matplotlib.rcParams['backend.qt4']='PySide'
@@ -45,22 +46,23 @@ class gui_control(object):
         self.setConnected2SurveyState(False)
 
     def connectButtons(self):
-        QtCore.QObject.connect(self.mainUI.gen_new_seisarray, QtCore.SIGNAL("clicked()"), self.gen_seisarray)
-        QtCore.QObject.connect(self.mainUI.load_seisarray, QtCore.SIGNAL("clicked()"), self.load_seisarray)
-        QtCore.QObject.connect(self.mainUI.save_seisarray, QtCore.SIGNAL("clicked()"), self.save_seisarray)
-        QtCore.QObject.connect(self.mainUI.connect_to_survey, QtCore.SIGNAL("clicked()"), self.connect2Survey)
-        QtCore.QObject.connect(self.mainUI.interpolate_receivers, QtCore.SIGNAL("clicked()"), self.interpolate_receivers)
-        QtCore.QObject.connect(self.mainUI.gen_new_survey, QtCore.SIGNAL("clicked()"), self.gen_survey)
-        QtCore.QObject.connect(self.mainUI.load_survey, QtCore.SIGNAL("clicked()"), self.load_survey)
-        QtCore.QObject.connect(self.mainUI.save_survey, QtCore.SIGNAL("clicked()"), self.save_survey)
-        QtCore.QObject.connect(self.mainUI.picker, QtCore.SIGNAL("clicked()"), self.callPicker)
-        QtCore.QObject.connect(self.mainUI.postprocessing, QtCore.SIGNAL("clicked()"), self.postprocessing)
-        QtCore.QObject.connect(self.mainUI.fmtomo, QtCore.SIGNAL("clicked()"), self.startFMTOMO)
-        QtCore.QObject.connect(self.mainUI.vtk_tools, QtCore.SIGNAL("clicked()"), self.startVTKtools)
+        QtCore.QObject.connect(self.mainUI.actionGenerate_new_Seismic_Array, QtCore.SIGNAL("triggered()"), self.gen_seisarray)
+        QtCore.QObject.connect(self.mainUI.actionLoad_Seismic_Array, QtCore.SIGNAL("triggered()"), self.load_seisarray)
+        QtCore.QObject.connect(self.mainUI.actionSave_Seismic_Array, QtCore.SIGNAL("triggered()"), self.save_seisarray)
+        QtCore.QObject.connect(self.mainUI.actionLoad_Survey, QtCore.SIGNAL("triggered()"), self.load_survey)
+        QtCore.QObject.connect(self.mainUI.actionSave_Survey, QtCore.SIGNAL("triggered()"), self.save_survey)
+        QtCore.QObject.connect(self.mainUI.actionConnect_to_Survey, QtCore.SIGNAL("triggered()"), self.connect2Survey)
+        QtCore.QObject.connect(self.mainUI.actionInterpolate_Receivers, QtCore.SIGNAL("triggered()"), self.interpolate_receivers)
+        QtCore.QObject.connect(self.mainUI.actionGenerate_new_Survey, QtCore.SIGNAL("triggered()"), self.gen_survey)
+        QtCore.QObject.connect(self.mainUI.actionAutomatic_Picking, QtCore.SIGNAL("triggered()"), self.callPicker)
+        QtCore.QObject.connect(self.mainUI.actionPostprocessing, QtCore.SIGNAL("triggered()"), self.postprocessing)
+        QtCore.QObject.connect(self.mainUI.actionStart_FMTOMO_Simulation, QtCore.SIGNAL("triggered()"), self.startFMTOMO)
+        QtCore.QObject.connect(self.mainUI.actionVTK_Visualization, QtCore.SIGNAL("triggered()"), self.startVTKtools)
+        QtCore.QObject.connect(self.mainUI.actionExit, QtCore.SIGNAL("triggered()"), self.exitApp)
         QtCore.QObject.connect(self.mainUI.comboBox_stats, QtCore.SIGNAL("activated(int)"), self.refreshPickedWidgets)
         QtCore.QObject.connect(self.mainUI.shot_left, QtCore.SIGNAL("clicked()"), self.decreaseShotnumber)
         QtCore.QObject.connect(self.mainUI.shot_right, QtCore.SIGNAL("clicked()"), self.increaseShotnumber)
-        QtCore.QObject.connect(self.mainUI.plot_shot, QtCore.SIGNAL("clicked()"), self.plotShot)
+
 
     def gen_seisarray(self):
         disconnect = False
@@ -394,8 +396,15 @@ class gui_control(object):
 
     def plotDynSNR(self):
         fig = self.snrFig
-        fig.clear()
-        ax = fig.add_subplot(111)
+        if fig.axes == []:
+            ax = fig.add_subplot(111)
+            xlim = None
+            ylim = None
+        else:
+            ax = fig.axes[0]
+            xlim = ax.get_xlim()
+            ylim = ax.get_ylim()
+        ax.clear()
         snrthresholds = []
         dists_p = []; snr_p = []
         shiftSNR = float(self.picker_ui.shift_snr.value())
@@ -417,6 +426,8 @@ class gui_control(object):
         ax.plot(dists, snrthresholds)
         ax.set_xlabel('Distance [m]')
         ax.set_ylabel('SNR')
+        ax.set_xlim(xlim)
+        ax.set_ylim(ylim)
         self.snrCanvas.draw()
 
     def initDynSNRplot(self):
@@ -825,8 +836,10 @@ class gui_control(object):
         if len(directory) > 0:
             return directory
 
+    def exitApp(self):
+        QtCore.QCoreApplication.instance().quit()
+
 if __name__ == "__main__":
-    import sys
     app = QtGui.QApplication(sys.argv)
     MainWindow = QtGui.QMainWindow()
     ui = Ui_MainWindow()
diff --git a/pylot/core/active/asp3d_layout.py b/pylot/core/active/asp3d_layout.py
index 8854e998..b74ac231 100644
--- a/pylot/core/active/asp3d_layout.py
+++ b/pylot/core/active/asp3d_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'asp3d_layout.ui'
 #
-# Created: Thu Jul 14 13:36:37 2016
+# Created: Mon Jul 18 11:26:32 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
@@ -53,22 +53,6 @@ class Ui_MainWindow(object):
         self.label_2.setAlignment(QtCore.Qt.AlignCenter)
         self.label_2.setObjectName("label_2")
         self.verticalLayout.addWidget(self.label_2)
-        self.gen_new_seisarray = QtGui.QPushButton(self.centralwidget)
-        self.gen_new_seisarray.setEnabled(True)
-        self.gen_new_seisarray.setObjectName("gen_new_seisarray")
-        self.verticalLayout.addWidget(self.gen_new_seisarray)
-        self.load_seisarray = QtGui.QPushButton(self.centralwidget)
-        self.load_seisarray.setObjectName("load_seisarray")
-        self.verticalLayout.addWidget(self.load_seisarray)
-        self.save_seisarray = QtGui.QPushButton(self.centralwidget)
-        self.save_seisarray.setObjectName("save_seisarray")
-        self.verticalLayout.addWidget(self.save_seisarray)
-        self.interpolate_receivers = QtGui.QPushButton(self.centralwidget)
-        self.interpolate_receivers.setObjectName("interpolate_receivers")
-        self.verticalLayout.addWidget(self.interpolate_receivers)
-        self.connect_to_survey = QtGui.QPushButton(self.centralwidget)
-        self.connect_to_survey.setObjectName("connect_to_survey")
-        self.verticalLayout.addWidget(self.connect_to_survey)
         self.horizontalLayout_2 = QtGui.QHBoxLayout()
         self.horizontalLayout_2.setObjectName("horizontalLayout_2")
         self.seisarray_active = QtGui.QLabel(self.centralwidget)
@@ -142,15 +126,6 @@ class Ui_MainWindow(object):
         self.label_3.setAlignment(QtCore.Qt.AlignCenter)
         self.label_3.setObjectName("label_3")
         self.verticalLayout_2.addWidget(self.label_3)
-        self.gen_new_survey = QtGui.QPushButton(self.centralwidget)
-        self.gen_new_survey.setObjectName("gen_new_survey")
-        self.verticalLayout_2.addWidget(self.gen_new_survey)
-        self.load_survey = QtGui.QPushButton(self.centralwidget)
-        self.load_survey.setObjectName("load_survey")
-        self.verticalLayout_2.addWidget(self.load_survey)
-        self.save_survey = QtGui.QPushButton(self.centralwidget)
-        self.save_survey.setObjectName("save_survey")
-        self.verticalLayout_2.addWidget(self.save_survey)
         self.horizontalLayout = QtGui.QHBoxLayout()
         self.horizontalLayout.setObjectName("horizontalLayout")
         self.survey_active = QtGui.QLabel(self.centralwidget)
@@ -202,79 +177,10 @@ class Ui_MainWindow(object):
         self.textBox_survey.setObjectName("textBox_survey")
         self.verticalLayout_2.addWidget(self.textBox_survey)
         self.verticalLayout_5.addLayout(self.verticalLayout_2)
-        self.line_3 = QtGui.QFrame(self.centralwidget)
-        self.line_3.setMinimumSize(QtCore.QSize(0, 5))
-        self.line_3.setFrameShape(QtGui.QFrame.HLine)
-        self.line_3.setFrameShadow(QtGui.QFrame.Sunken)
-        self.line_3.setObjectName("line_3")
-        self.verticalLayout_5.addWidget(self.line_3)
         self.verticalLayout_3 = QtGui.QVBoxLayout()
         self.verticalLayout_3.setObjectName("verticalLayout_3")
-        self.label_7 = QtGui.QLabel(self.centralwidget)
-        sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Fixed)
-        sizePolicy.setHorizontalStretch(0)
-        sizePolicy.setVerticalStretch(0)
-        sizePolicy.setHeightForWidth(self.label_7.sizePolicy().hasHeightForWidth())
-        self.label_7.setSizePolicy(sizePolicy)
-        font = QtGui.QFont()
-        font.setFamily("Sans Serif")
-        font.setPointSize(10)
-        font.setWeight(75)
-        font.setBold(True)
-        self.label_7.setFont(font)
-        self.label_7.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_7.setObjectName("label_7")
-        self.verticalLayout_3.addWidget(self.label_7)
-        self.picker = QtGui.QPushButton(self.centralwidget)
-        self.picker.setObjectName("picker")
-        self.verticalLayout_3.addWidget(self.picker)
-        self.postprocessing = QtGui.QPushButton(self.centralwidget)
-        self.postprocessing.setObjectName("postprocessing")
-        self.verticalLayout_3.addWidget(self.postprocessing)
-        self.line_2 = QtGui.QFrame(self.centralwidget)
-        self.line_2.setMinimumSize(QtCore.QSize(0, 5))
-        self.line_2.setFrameShape(QtGui.QFrame.HLine)
-        self.line_2.setFrameShadow(QtGui.QFrame.Sunken)
-        self.line_2.setObjectName("line_2")
-        self.verticalLayout_3.addWidget(self.line_2)
         self.verticalLayout_4 = QtGui.QVBoxLayout()
         self.verticalLayout_4.setObjectName("verticalLayout_4")
-        self.label_8 = QtGui.QLabel(self.centralwidget)
-        sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Fixed)
-        sizePolicy.setHorizontalStretch(0)
-        sizePolicy.setVerticalStretch(0)
-        sizePolicy.setHeightForWidth(self.label_8.sizePolicy().hasHeightForWidth())
-        self.label_8.setSizePolicy(sizePolicy)
-        font = QtGui.QFont()
-        font.setFamily("Sans Serif")
-        font.setPointSize(10)
-        font.setWeight(75)
-        font.setBold(True)
-        self.label_8.setFont(font)
-        self.label_8.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_8.setObjectName("label_8")
-        self.verticalLayout_4.addWidget(self.label_8)
-        self.fmtomo = QtGui.QPushButton(self.centralwidget)
-        self.fmtomo.setObjectName("fmtomo")
-        self.verticalLayout_4.addWidget(self.fmtomo)
-        self.label_9 = QtGui.QLabel(self.centralwidget)
-        sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Fixed)
-        sizePolicy.setHorizontalStretch(0)
-        sizePolicy.setVerticalStretch(0)
-        sizePolicy.setHeightForWidth(self.label_9.sizePolicy().hasHeightForWidth())
-        self.label_9.setSizePolicy(sizePolicy)
-        font = QtGui.QFont()
-        font.setFamily("Sans Serif")
-        font.setPointSize(10)
-        font.setWeight(75)
-        font.setBold(True)
-        self.label_9.setFont(font)
-        self.label_9.setAlignment(QtCore.Qt.AlignCenter)
-        self.label_9.setObjectName("label_9")
-        self.verticalLayout_4.addWidget(self.label_9)
-        self.vtk_tools = QtGui.QPushButton(self.centralwidget)
-        self.vtk_tools.setObjectName("vtk_tools")
-        self.verticalLayout_4.addWidget(self.vtk_tools)
         self.progressBar = QtGui.QProgressBar(self.centralwidget)
         self.progressBar.setEnabled(True)
         self.progressBar.setProperty("value", 0)
@@ -369,10 +275,73 @@ class Ui_MainWindow(object):
         self.menubar = QtGui.QMenuBar(MainWindow)
         self.menubar.setGeometry(QtCore.QRect(0, 0, 1029, 23))
         self.menubar.setObjectName("menubar")
+        self.menuFile = QtGui.QMenu(self.menubar)
+        self.menuFile.setObjectName("menuFile")
+        self.menuSeismic_Array = QtGui.QMenu(self.menubar)
+        self.menuSeismic_Array.setObjectName("menuSeismic_Array")
+        self.menuSurvey = QtGui.QMenu(self.menubar)
+        self.menuSurvey.setObjectName("menuSurvey")
+        self.menuPicking = QtGui.QMenu(self.menubar)
+        self.menuPicking.setObjectName("menuPicking")
+        self.menuSimulation = QtGui.QMenu(self.menubar)
+        self.menuSimulation.setObjectName("menuSimulation")
+        self.menuTools = QtGui.QMenu(self.menubar)
+        self.menuTools.setObjectName("menuTools")
         MainWindow.setMenuBar(self.menubar)
         self.statusbar = QtGui.QStatusBar(MainWindow)
         self.statusbar.setObjectName("statusbar")
         MainWindow.setStatusBar(self.statusbar)
+        self.actionLoad_Seismic_Array = QtGui.QAction(MainWindow)
+        self.actionLoad_Seismic_Array.setCheckable(False)
+        self.actionLoad_Seismic_Array.setObjectName("actionLoad_Seismic_Array")
+        self.actionSave_Seismic_Array = QtGui.QAction(MainWindow)
+        self.actionSave_Seismic_Array.setObjectName("actionSave_Seismic_Array")
+        self.actionLoad_Survey = QtGui.QAction(MainWindow)
+        self.actionLoad_Survey.setObjectName("actionLoad_Survey")
+        self.actionSave_Survey = QtGui.QAction(MainWindow)
+        self.actionSave_Survey.setObjectName("actionSave_Survey")
+        self.actionExit = QtGui.QAction(MainWindow)
+        self.actionExit.setObjectName("actionExit")
+        self.actionGenerate_new_Seismic_Array = QtGui.QAction(MainWindow)
+        self.actionGenerate_new_Seismic_Array.setObjectName("actionGenerate_new_Seismic_Array")
+        self.actionInterpolate_Receivers = QtGui.QAction(MainWindow)
+        self.actionInterpolate_Receivers.setObjectName("actionInterpolate_Receivers")
+        self.actionConnect_to_Survey = QtGui.QAction(MainWindow)
+        self.actionConnect_to_Survey.setObjectName("actionConnect_to_Survey")
+        self.actionGenerate_new_Survey = QtGui.QAction(MainWindow)
+        self.actionGenerate_new_Survey.setObjectName("actionGenerate_new_Survey")
+        self.actionAutomatic_Picking = QtGui.QAction(MainWindow)
+        self.actionAutomatic_Picking.setObjectName("actionAutomatic_Picking")
+        self.actionPostprocessing = QtGui.QAction(MainWindow)
+        self.actionPostprocessing.setObjectName("actionPostprocessing")
+        self.actionStart_FMTOMO_Simulation = QtGui.QAction(MainWindow)
+        self.actionStart_FMTOMO_Simulation.setObjectName("actionStart_FMTOMO_Simulation")
+        self.actionVTK_Visualization = QtGui.QAction(MainWindow)
+        self.actionVTK_Visualization.setObjectName("actionVTK_Visualization")
+        self.actionSeismic_Array = QtGui.QAction(MainWindow)
+        self.actionSeismic_Array.setEnabled(False)
+        self.actionSeismic_Array.setObjectName("actionSeismic_Array")
+        self.menuFile.addSeparator()
+        self.menuFile.addAction(self.actionExit)
+        self.menuSeismic_Array.addAction(self.actionGenerate_new_Seismic_Array)
+        self.menuSeismic_Array.addAction(self.actionLoad_Seismic_Array)
+        self.menuSeismic_Array.addAction(self.actionSave_Seismic_Array)
+        self.menuSeismic_Array.addSeparator()
+        self.menuSeismic_Array.addAction(self.actionInterpolate_Receivers)
+        self.menuSeismic_Array.addAction(self.actionConnect_to_Survey)
+        self.menuSurvey.addAction(self.actionGenerate_new_Survey)
+        self.menuSurvey.addAction(self.actionLoad_Survey)
+        self.menuSurvey.addAction(self.actionSave_Survey)
+        self.menuPicking.addAction(self.actionAutomatic_Picking)
+        self.menuPicking.addAction(self.actionPostprocessing)
+        self.menuSimulation.addAction(self.actionStart_FMTOMO_Simulation)
+        self.menuTools.addAction(self.actionVTK_Visualization)
+        self.menubar.addAction(self.menuFile.menuAction())
+        self.menubar.addAction(self.menuSurvey.menuAction())
+        self.menubar.addAction(self.menuSeismic_Array.menuAction())
+        self.menubar.addAction(self.menuPicking.menuAction())
+        self.menubar.addAction(self.menuSimulation.menuAction())
+        self.menubar.addAction(self.menuTools.menuAction())
 
         self.retranslateUi(MainWindow)
         QtCore.QMetaObject.connectSlotsByName(MainWindow)
@@ -380,41 +349,34 @@ class Ui_MainWindow(object):
     def retranslateUi(self, MainWindow):
         MainWindow.setWindowTitle(QtGui.QApplication.translate("MainWindow", "ActiveSeismoPick 3D", None, QtGui.QApplication.UnicodeUTF8))
         self.label_2.setText(QtGui.QApplication.translate("MainWindow", "Seismic Array", None, QtGui.QApplication.UnicodeUTF8))
-        self.gen_new_seisarray.setToolTip(QtGui.QApplication.translate("MainWindow", "Generate a new Seismic Array object.", None, QtGui.QApplication.UnicodeUTF8))
-        self.gen_new_seisarray.setText(QtGui.QApplication.translate("MainWindow", "Create new Seismic Array", None, QtGui.QApplication.UnicodeUTF8))
-        self.load_seisarray.setToolTip(QtGui.QApplication.translate("MainWindow", "Load an existing Seismic Array object saved as \'.pickle\' file.", None, QtGui.QApplication.UnicodeUTF8))
-        self.load_seisarray.setText(QtGui.QApplication.translate("MainWindow", "Load Seismic Array", None, QtGui.QApplication.UnicodeUTF8))
-        self.save_seisarray.setToolTip(QtGui.QApplication.translate("MainWindow", "Save current Seismic Array object to \'.pickle\' file.", None, QtGui.QApplication.UnicodeUTF8))
-        self.save_seisarray.setText(QtGui.QApplication.translate("MainWindow", "Save Seismic Array", None, QtGui.QApplication.UnicodeUTF8))
-        self.interpolate_receivers.setToolTip(QtGui.QApplication.translate("MainWindow", "Interpolate positions of receivers in between that were not manually measured.", None, QtGui.QApplication.UnicodeUTF8))
-        self.interpolate_receivers.setText(QtGui.QApplication.translate("MainWindow", "Interpolate Receivers", None, QtGui.QApplication.UnicodeUTF8))
-        self.connect_to_survey.setToolTip(QtGui.QApplication.translate("MainWindow", "Save the current Seismic Array to the current Survey object.", None, QtGui.QApplication.UnicodeUTF8))
-        self.connect_to_survey.setText(QtGui.QApplication.translate("MainWindow", "Connect to Survey", None, QtGui.QApplication.UnicodeUTF8))
         self.label_5.setText(QtGui.QApplication.translate("MainWindow", "active", None, QtGui.QApplication.UnicodeUTF8))
         self.label_6.setText(QtGui.QApplication.translate("MainWindow", "connected to Survey", None, QtGui.QApplication.UnicodeUTF8))
         self.label_3.setText(QtGui.QApplication.translate("MainWindow", "Survey", None, QtGui.QApplication.UnicodeUTF8))
-        self.gen_new_survey.setToolTip(QtGui.QApplication.translate("MainWindow", "Generate a new Survey object.", None, QtGui.QApplication.UnicodeUTF8))
-        self.gen_new_survey.setText(QtGui.QApplication.translate("MainWindow", "Generate new Survey", None, QtGui.QApplication.UnicodeUTF8))
-        self.load_survey.setToolTip(QtGui.QApplication.translate("MainWindow", "Load an existing Survey object from a \'.pickle\' file.", None, QtGui.QApplication.UnicodeUTF8))
-        self.load_survey.setText(QtGui.QApplication.translate("MainWindow", "Load Survey", None, QtGui.QApplication.UnicodeUTF8))
-        self.save_survey.setToolTip(QtGui.QApplication.translate("MainWindow", "Save current Survey object to \'.pickle\' file.", None, QtGui.QApplication.UnicodeUTF8))
-        self.save_survey.setText(QtGui.QApplication.translate("MainWindow", "Save Survey", None, QtGui.QApplication.UnicodeUTF8))
         self.label_4.setText(QtGui.QApplication.translate("MainWindow", "active", None, QtGui.QApplication.UnicodeUTF8))
         self.label.setText(QtGui.QApplication.translate("MainWindow", "picked", None, QtGui.QApplication.UnicodeUTF8))
-        self.label_7.setText(QtGui.QApplication.translate("MainWindow", "Picking", None, QtGui.QApplication.UnicodeUTF8))
-        self.picker.setToolTip(QtGui.QApplication.translate("MainWindow", "Choose parameters and call automatic picking routines.", None, QtGui.QApplication.UnicodeUTF8))
-        self.picker.setText(QtGui.QApplication.translate("MainWindow", "Automatic Picking", None, QtGui.QApplication.UnicodeUTF8))
-        self.postprocessing.setToolTip(QtGui.QApplication.translate("MainWindow", "Manual control and postprocessing of a picked Survey.", None, QtGui.QApplication.UnicodeUTF8))
-        self.postprocessing.setText(QtGui.QApplication.translate("MainWindow", "Postprocessing", None, QtGui.QApplication.UnicodeUTF8))
-        self.label_8.setText(QtGui.QApplication.translate("MainWindow", "Simulation", None, QtGui.QApplication.UnicodeUTF8))
-        self.fmtomo.setToolTip(QtGui.QApplication.translate("MainWindow", "Set parameters and call Fast Marching Tomography algorithm.", None, QtGui.QApplication.UnicodeUTF8))
-        self.fmtomo.setText(QtGui.QApplication.translate("MainWindow", "FMTOMO Simulation", None, QtGui.QApplication.UnicodeUTF8))
-        self.label_9.setText(QtGui.QApplication.translate("MainWindow", "Visualization", None, QtGui.QApplication.UnicodeUTF8))
-        self.vtk_tools.setToolTip(QtGui.QApplication.translate("MainWindow", "Set parameters and call Fast Marching Tomography algorithm.", None, QtGui.QApplication.UnicodeUTF8))
-        self.vtk_tools.setText(QtGui.QApplication.translate("MainWindow", "VTK tools", None, QtGui.QApplication.UnicodeUTF8))
         self.label_11.setText(QtGui.QApplication.translate("MainWindow", "Plot Receiver and Shots of the Array colord by:", None, QtGui.QApplication.UnicodeUTF8))
         self.label_10.setText(QtGui.QApplication.translate("MainWindow", "Plot a single Shot:", None, QtGui.QApplication.UnicodeUTF8))
         self.shot_left.setText(QtGui.QApplication.translate("MainWindow", "<", None, QtGui.QApplication.UnicodeUTF8))
         self.shot_right.setText(QtGui.QApplication.translate("MainWindow", ">", None, QtGui.QApplication.UnicodeUTF8))
         self.plot_shot.setText(QtGui.QApplication.translate("MainWindow", "Plot", None, QtGui.QApplication.UnicodeUTF8))
+        self.menuFile.setTitle(QtGui.QApplication.translate("MainWindow", "File", None, QtGui.QApplication.UnicodeUTF8))
+        self.menuSeismic_Array.setTitle(QtGui.QApplication.translate("MainWindow", "Seismic Array", None, QtGui.QApplication.UnicodeUTF8))
+        self.menuSurvey.setTitle(QtGui.QApplication.translate("MainWindow", "Survey", None, QtGui.QApplication.UnicodeUTF8))
+        self.menuPicking.setTitle(QtGui.QApplication.translate("MainWindow", "Picking", None, QtGui.QApplication.UnicodeUTF8))
+        self.menuSimulation.setTitle(QtGui.QApplication.translate("MainWindow", "Simulation", None, QtGui.QApplication.UnicodeUTF8))
+        self.menuTools.setTitle(QtGui.QApplication.translate("MainWindow", "Tools", None, QtGui.QApplication.UnicodeUTF8))
+        self.actionLoad_Seismic_Array.setText(QtGui.QApplication.translate("MainWindow", "Load Seismic Array", None, QtGui.QApplication.UnicodeUTF8))
+        self.actionSave_Seismic_Array.setText(QtGui.QApplication.translate("MainWindow", "Save Seismic Array", None, QtGui.QApplication.UnicodeUTF8))
+        self.actionLoad_Survey.setText(QtGui.QApplication.translate("MainWindow", "Load Survey", None, QtGui.QApplication.UnicodeUTF8))
+        self.actionSave_Survey.setText(QtGui.QApplication.translate("MainWindow", "Save Survey", None, QtGui.QApplication.UnicodeUTF8))
+        self.actionExit.setText(QtGui.QApplication.translate("MainWindow", "Exit", None, QtGui.QApplication.UnicodeUTF8))
+        self.actionGenerate_new_Seismic_Array.setText(QtGui.QApplication.translate("MainWindow", "Generate new Seismic Array", None, QtGui.QApplication.UnicodeUTF8))
+        self.actionInterpolate_Receivers.setText(QtGui.QApplication.translate("MainWindow", "Interpolate Receivers", None, QtGui.QApplication.UnicodeUTF8))
+        self.actionConnect_to_Survey.setText(QtGui.QApplication.translate("MainWindow", "Connect to Survey", None, QtGui.QApplication.UnicodeUTF8))
+        self.actionGenerate_new_Survey.setText(QtGui.QApplication.translate("MainWindow", "Generate new Survey", None, QtGui.QApplication.UnicodeUTF8))
+        self.actionAutomatic_Picking.setText(QtGui.QApplication.translate("MainWindow", "Automatic Picking", None, QtGui.QApplication.UnicodeUTF8))
+        self.actionPostprocessing.setText(QtGui.QApplication.translate("MainWindow", "Postprocessing", None, QtGui.QApplication.UnicodeUTF8))
+        self.actionStart_FMTOMO_Simulation.setText(QtGui.QApplication.translate("MainWindow", "Start FMTOMO Simulation", None, QtGui.QApplication.UnicodeUTF8))
+        self.actionVTK_Visualization.setText(QtGui.QApplication.translate("MainWindow", "VTK Visualization", None, QtGui.QApplication.UnicodeUTF8))
+        self.actionSeismic_Array.setText(QtGui.QApplication.translate("MainWindow", "Seismic Array", None, QtGui.QApplication.UnicodeUTF8))
 
diff --git a/pylot/core/active/fmtomo_parameters_layout.py b/pylot/core/active/fmtomo_parameters_layout.py
index 285bac94..9151d4ad 100644
--- a/pylot/core/active/fmtomo_parameters_layout.py
+++ b/pylot/core/active/fmtomo_parameters_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'fmtomo_parameters_layout.ui'
 #
-# Created: Thu Jul 14 13:36:37 2016
+# Created: Mon Jul 18 11:26:32 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
diff --git a/pylot/core/active/generate_seisarray_layout.py b/pylot/core/active/generate_seisarray_layout.py
index 10c297d1..79a614aa 100644
--- a/pylot/core/active/generate_seisarray_layout.py
+++ b/pylot/core/active/generate_seisarray_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'generate_seisarray_layout.ui'
 #
-# Created: Thu Jul 14 13:36:38 2016
+# Created: Mon Jul 18 11:26:32 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
@@ -138,7 +138,7 @@ class Ui_generate_seisarray(object):
 "<p style=\" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;\">Third geophone on the second receiver line with the trace ID 50 and the coordinates (10.5 [m], 20.4 [m], 30.3 [m]).</p>\n"
 "<p style=\"-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;\"></p>\n"
 "<p style=\" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;\">50  2  3  10.5  20.4  30.3</p></body></html>", None, QtGui.QApplication.UnicodeUTF8))
-        self.radioButton_interpolatable.setText(QtGui.QApplication.translate("generate_seisarray", "interpolatable [?]", None, QtGui.QApplication.UnicodeUTF8))
+        self.radioButton_interpolatable.setText(QtGui.QApplication.translate("generate_seisarray", "interpolation [?]", None, QtGui.QApplication.UnicodeUTF8))
         self.pushButton_rec.setText(QtGui.QApplication.translate("generate_seisarray", "Browse", None, QtGui.QApplication.UnicodeUTF8))
         self.label_src.setToolTip(QtGui.QApplication.translate("generate_seisarray", "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0//EN\" \"http://www.w3.org/TR/REC-html40/strict.dtd\">\n"
 "<html><head><meta name=\"qrichtext\" content=\"1\" /><style type=\"text/css\">\n"
diff --git a/pylot/core/active/generate_survey_layout.py b/pylot/core/active/generate_survey_layout.py
index 69591b1e..a4f1312f 100644
--- a/pylot/core/active/generate_survey_layout.py
+++ b/pylot/core/active/generate_survey_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'generate_survey_layout.ui'
 #
-# Created: Thu Jul 14 13:36:38 2016
+# Created: Mon Jul 18 11:26:32 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
diff --git a/pylot/core/active/generate_survey_layout_minimal.py b/pylot/core/active/generate_survey_layout_minimal.py
index 90956e2a..97d8d3d7 100644
--- a/pylot/core/active/generate_survey_layout_minimal.py
+++ b/pylot/core/active/generate_survey_layout_minimal.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'generate_survey_layout_minimal.ui'
 #
-# Created: Thu Jul 14 13:36:38 2016
+# Created: Mon Jul 18 11:26:33 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
diff --git a/pylot/core/active/picking_parameters_layout.py b/pylot/core/active/picking_parameters_layout.py
index 7bedfa94..43405994 100644
--- a/pylot/core/active/picking_parameters_layout.py
+++ b/pylot/core/active/picking_parameters_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'picking_parameters_layout.ui'
 #
-# Created: Thu Jul 14 13:36:38 2016
+# Created: Mon Jul 18 11:26:33 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
diff --git a/pylot/core/active/vtk_tools_layout.py b/pylot/core/active/vtk_tools_layout.py
index b7bcf57c..fb90795f 100644
--- a/pylot/core/active/vtk_tools_layout.py
+++ b/pylot/core/active/vtk_tools_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'vtk_tools_layout.ui'
 #
-# Created: Thu Jul 14 13:36:38 2016
+# Created: Mon Jul 18 11:26:33 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!

From 05cc8e52b9889ac84e94945a1ba2a6365c00f0af Mon Sep 17 00:00:00 2001
From: Marcel Paffrath <marcel.paffrath@rub.de>
Date: Tue, 19 Jul 2016 12:16:37 +0200
Subject: [PATCH 3/9] last commit before structural changes (classes for each
 window)

---
 pylot/core/active/ActiveSeismoPick3D_GUI.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pylot/core/active/ActiveSeismoPick3D_GUI.py b/pylot/core/active/ActiveSeismoPick3D_GUI.py
index 16e8fa66..71966d9b 100755
--- a/pylot/core/active/ActiveSeismoPick3D_GUI.py
+++ b/pylot/core/active/ActiveSeismoPick3D_GUI.py
@@ -62,7 +62,7 @@ class gui_control(object):
         QtCore.QObject.connect(self.mainUI.comboBox_stats, QtCore.SIGNAL("activated(int)"), self.refreshPickedWidgets)
         QtCore.QObject.connect(self.mainUI.shot_left, QtCore.SIGNAL("clicked()"), self.decreaseShotnumber)
         QtCore.QObject.connect(self.mainUI.shot_right, QtCore.SIGNAL("clicked()"), self.increaseShotnumber)
-
+        QtCore.QObject.connect(self.mainUI.plot_shot, QtCore.SIGNAL("clicked()"), self.plotShot)
 
     def gen_seisarray(self):
         disconnect = False

From 3273709b54ac28fd49b2b8b608ff213fcd52eed8 Mon Sep 17 00:00:00 2001
From: Marcel Paffrath <marcel.paffrath@rub.de>
Date: Tue, 19 Jul 2016 15:19:03 +0200
Subject: [PATCH 4/9] code for first three windows changed to class structure

---
 pylot/core/active/ActiveSeismoPick3D_GUI.py | 463 ++++++++++++++------
 1 file changed, 328 insertions(+), 135 deletions(-)

diff --git a/pylot/core/active/ActiveSeismoPick3D_GUI.py b/pylot/core/active/ActiveSeismoPick3D_GUI.py
index 71966d9b..2e43bcf3 100755
--- a/pylot/core/active/ActiveSeismoPick3D_GUI.py
+++ b/pylot/core/active/ActiveSeismoPick3D_GUI.py
@@ -21,6 +21,27 @@ from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as Navigatio
 import matplotlib.pyplot as plt
 from matplotlib.figure import Figure
 
+def openFile(name = 'Open'):
+    dialog = QtGui.QFileDialog()
+    dialog.setWindowTitle(name)                #not working yet
+    filename = dialog.getOpenFileName()
+    if len(filename[0]) > 0:
+        return filename[0]
+
+def saveFile(name = 'Save'):
+    dialog = QtGui.QFileDialog()
+    dialog.setWindowTitle(name)
+    filename = dialog.getSaveFileName()
+    if len(filename[0]) > 0:
+        return filename[0]
+
+def browseDir(name = 'Open Directory'):
+    dialog = QtGui.QFileDialog()
+    dialog.setWindowTitle(name)
+    directory = dialog.getExistingDirectory()
+    if len(directory) > 0:
+        return directory
+
 class gui_control(object):
     def __init__(self):
         self.mainwindow = MainWindow
@@ -38,6 +59,9 @@ class gui_control(object):
         self.mainUI.progressBar.setVisible(False)
         self.printSurveyTextbox()
         self.printSeisArrayTextbox()
+        self.gsa = None
+        self.gssa = None
+        self.gssr = None
 
     def setInitStates(self):
         self.setPickState(False)
@@ -64,6 +88,186 @@ class gui_control(object):
         QtCore.QObject.connect(self.mainUI.shot_right, QtCore.SIGNAL("clicked()"), self.increaseShotnumber)
         QtCore.QObject.connect(self.mainUI.plot_shot, QtCore.SIGNAL("clicked()"), self.plotShot)
 
+    class Gen_SeisArray(object):
+        def __init__(self, mainwindow):
+            self.mainwindow = mainwindow
+            self.seisarray = None
+            self.srcfile = None
+            self.recfile = None
+            self.ptsfile = None
+            self.init_dialog()
+            self.start_dialog()
+
+        def init_dialog(self):
+            qdialog = QtGui.QDialog(self.mainwindow)
+            ui = Ui_generate_seisarray()
+            ui.setupUi(qdialog)
+            self.ui = ui
+            self.qdialog = qdialog
+            self.connectButtons()
+            
+        def start_dialog(self):
+            self.init_last_selection()
+            if self.qdialog.exec_():
+                self.refresh_filenames()
+                if self.ui.radioButton_interpolatable.isChecked():
+                    self.seisarray = seismicArrayPreparation.SeisArray(self.recfile, True)
+                elif self.ui.radioButton_normal.isChecked():
+                    self.seisarray = seismicArrayPreparation.SeisArray(self.recfile, False)
+                if len(self.srcfile) > 0:
+                    self.seisarray.addSourceLocations(self.srcfile)
+                if len(self.ptsfile) > 0:
+                    self.seisarray.addMeasuredTopographyPoints(self.ptsfile)
+                self.executed = True
+            else:
+                self.refresh_filenames()
+                self.executed = False
+
+        def refresh_filenames(self):
+            self.srcfile = self.ui.lineEdit_src.text()
+            self.recfile = self.ui.lineEdit_rec.text()
+            self.ptsfile = self.ui.lineEdit_pts.text()
+
+        def init_last_selection(self):
+            self.ui.lineEdit_src.setText(self.srcfile)
+            self.ui.lineEdit_rec.setText(self.recfile)
+            self.ui.lineEdit_pts.setText(self.ptsfile)
+
+        def get_seisarray(self):
+            if self.seisarray is not None:
+                return self.seisarray
+
+        def connectButtons(self):
+            QtCore.QObject.connect(self.ui.pushButton_rec, QtCore.SIGNAL("clicked()"), self.chooseMeasuredRec)
+            QtCore.QObject.connect(self.ui.pushButton_src, QtCore.SIGNAL("clicked()"), self.chooseMeasuredSrc)
+            QtCore.QObject.connect(self.ui.pushButton_obs, QtCore.SIGNAL("clicked()"), self.chooseMeasuredPts)
+
+        def chooseMeasuredSrc(self):
+            self.ui.lineEdit_src.setText(openFile('Open measured sources file.'))
+
+        def chooseMeasuredRec(self):
+            self.ui.lineEdit_rec.setText(openFile('Open measured receivers file.'))
+
+        def chooseMeasuredPts(self):
+            self.ui.lineEdit_pts.setText(openFile('Open measured points file.'))
+
+
+
+    class Gen_Survey_from_SA(object):
+        def __init__(self, mainwindow, seisarray):
+            self.mainwindow = mainwindow
+            self.seisarray = seisarray
+            self.survey = None
+            self.obsdir = None
+            self.fstart = 'shot'
+            self.fend = '.dat'
+            self.init_dialog()
+            self.start_dialog()
+
+        def init_dialog(self):
+            qdialog = QtGui.QDialog(self.mainwindow)
+            ui = Ui_generate_survey_minimal()
+            ui.setupUi(qdialog)
+            self.ui = ui
+            self.qdialog = qdialog
+            self.connectButtons()
+            
+        def start_dialog(self):
+            self.init_last_selection()
+            if self.qdialog.exec_():
+                self.refresh_filenames()
+                self.survey = activeSeismoPick.Survey(self.obsdir, seisArray = self.seisarray,
+                                                      useDefaultParas = True, fstart = self.fstart,
+                                                      fend = self.fend)
+                self.executed = True
+            else:
+                self.refresh_filenames()
+                self.executed = False
+        
+        def refresh_filenames(self):
+            self.obsdir = self.ui.lineEdit_obs.text()
+            self.fstart = self.ui.fstart.text()
+            self.fend = self.ui.fend.text()
+
+        def init_last_selection(self):
+            self.ui.lineEdit_obs.setText(self.obsdir)
+            self.ui.fstart.setText(self.fstart)
+            self.ui.fend.setText(self.fend)
+        
+        def get_survey(self):
+            return self.survey
+
+        def connectButtons(self):
+            QtCore.QObject.connect(self.ui.pushButton_obs, QtCore.SIGNAL("clicked()"), self.chooseObsdir)
+
+        def chooseObsdir(self):
+            self.ui.lineEdit_obs.setText(browseDir('Choose observation directory.'))
+
+
+    class Gen_Survey_from_SR(object):
+        def __init__(self, mainwindow):
+            self.mainwindow = mainwindow
+            self.survey = None
+            self.obsdir = None
+            self.srcfile = None
+            self.recfile = None
+            self.fstart = 'shot'
+            self.fend = '.dat'
+            self.init_dialog()
+            self.start_dialog()
+
+        def init_dialog(self):
+            qdialog = QtGui.QDialog(self.mainwindow)
+            ui = Ui_generate_survey()
+            ui.setupUi(qdialog)
+            self.ui = ui
+            self.qdialog = qdialog
+            self.connectButtons()
+            
+        def start_dialog(self):
+            self.init_last_selection()
+            if self.qdialog.exec_():
+                self.refresh_filenames()
+                self.survey = activeSeismoPick.Survey(self.obsdir, self.srcfile, self.recfile,
+                                                      useDefaultParas = True,
+                                                      fstart = self.fstart, fend = self.fend)
+                self.executed = True
+            else:
+                self.refresh_filenames()
+                self.executed = False
+        
+        def refresh_filenames(self):
+            self.obsdir = self.ui.lineEdit_obs.text()
+            self.srcfile = self.ui.lineEdit_src.text()
+            self.recfile = self.ui.lineEdit_rec.text()
+            self.fstart = self.ui.fstart.text()
+            self.fend = self.ui.fend.text()
+
+        def init_last_selection(self):
+            self.ui.lineEdit_obs.setText(self.obsdir)
+            self.ui.lineEdit_src.setText(self.srcfile)
+            self.ui.lineEdit_rec.setText(self.recfile)
+            self.ui.fstart.setText(self.fstart)
+            self.ui.fend.setText(self.fend)
+        
+        def get_survey(self):
+            return self.survey
+
+        def connectButtons(self):
+            QtCore.QObject.connect(self.ui.pushButton_obs, QtCore.SIGNAL("clicked()"), self.chooseObsdir)
+            QtCore.QObject.connect(self.ui.pushButton_src, QtCore.SIGNAL("clicked()"), self.chooseSourcefile)
+            QtCore.QObject.connect(self.ui.pushButton_rec, QtCore.SIGNAL("clicked()"), self.chooseRecfile)
+
+        def chooseObsdir(self):
+            self.ui.lineEdit_obs.setText(browseDir('Choose observation directory.'))
+
+        def chooseSourcefile(self):
+            self.ui.lineEdit_src.setText(openFile('Open sourcefile.'))
+
+        def chooseRecfile(self):
+            self.ui.lineEdit_rec.setText(openFile('Open receiverfile.'))
+
+
     def gen_seisarray(self):
         disconnect = False
         if self.checkSeisArrayState():
@@ -76,82 +280,58 @@ class gui_control(object):
             else:
                 self.survey.seisarray = None
                 disconnect = True
-        qdialog = QtGui.QDialog(self.mainwindow)
-        ui = Ui_generate_seisarray()
-        ui.setupUi(qdialog)
-        self.gen_new_seisarray = ui
-        self.connectButtons_gen_seisarray()
-        if qdialog.exec_():
-            srcfile = self.gen_new_seisarray.lineEdit_src.text()
-            recfile = self.gen_new_seisarray.lineEdit_rec.text()
-            ptsfile = self.gen_new_seisarray.lineEdit_pts.text()
-            if self.gen_new_seisarray.radioButton_interpolatable.isChecked():
-                self.seisarray = seismicArrayPreparation.SeisArray(recfile, True)
-            elif self.gen_new_seisarray.radioButton_normal.isChecked():
-                self.seisarray = seismicArrayPreparation.SeisArray(recfile, False)
-            if len(srcfile) > 0:
-                self.seisarray.addSourceLocations(srcfile)
-            if len(ptsfile) > 0:
-                self.seisarray.addMeasuredTopographyPoints(ptsfile)
+        
+        if self.gsa is None:
+            self.gsa = self.Gen_SeisArray(self.mainwindow)
+        else:
+            self.gsa.start_dialog()
+
+        if self.gsa.executed:
+            self.seisarray = self.gsa.get_seisarray()
             if disconnect:
                 self.setConnected2SurveyState(False)
             self.setSeisArrayState(True)
 
+
     def gen_survey(self):
         if self.checkSurveyState():
             if not self.continueDialogExists('Survey'):
                 return
         if self.checkSeisArrayState():
-            if self.continueDialogMessage('Use geometry information of active Seismic Array?'):
-               if self.gen_survey_fromSeisArray():
-                   self.initNewSurvey()
-                   return
-               else:
-                   return
-        if self.gen_survey_fromSRfiles():
+            if len(self.seisarray.getSourceCoordinates()) > 0:
+                if self.continueDialogMessage('Use geometry information of active Seismic Array?'):
+                    if self.gssa is None:
+                        self.gssa = self.Gen_Survey_from_SA(self.mainwindow, self.seisarray)
+                    else:
+                        self.gssa.start_dialog()
+                    if self.gssa.executed:
+                        self.survey = self.gssa.get_survey()
+                        self.initNewSurvey()
+                        self.setConnected2SurveyState(True)
+                        self.setPickState(False)
+                    return
+            else:
+                if not self.continueDialogMessage('Can not use current Seismic Array,'
+                                                  ' because there are no sources given.'):
+                    return
+        if self.gssr is None:
+            self.gssr = self.Gen_Survey_from_SR(self.mainwindow)
+        else:
+            self.gssr.start_dialog()
+        if self.gssr.executed:
+            self.survey = self.gssr.get_survey()
+            self.seisarray = self.survey.seisarray
             self.initNewSurvey()
+            self.setConnected2SurveyState(True)
+            self.setPickState(False)
+
+
 
     def initNewSurvey(self):
         self.survey.setArtificialPick(0, 0) # artificial pick at source origin
         self.setSurveyState(True)
         self.setPickState(False)
 
-    def gen_survey_fromSeisArray(self):
-        qdialog = QtGui.QDialog(self.mainwindow)
-        ui = Ui_generate_survey_minimal()
-        ui.setupUi(qdialog)
-        self.gen_new_survey_min = ui
-        self.connectButtons_gen_survey_min()
-        if qdialog.exec_():
-            obsdir = self.gen_new_survey_min.lineEdit_obs.text()
-            fstart = self.gen_new_survey_min.fstart.text()
-            fend = self.gen_new_survey_min.fend.text()
-            self.survey = activeSeismoPick.Survey(obsdir, seisArray = self.seisarray,
-                                                  useDefaultParas = True, fstart = fstart,
-                                                  fend = fend)
-            self.setConnected2SurveyState(True)
-            self.setPickState(False)
-            return True
-
-    def gen_survey_fromSRfiles(self):
-        qdialog = QtGui.QDialog(self.mainwindow)
-        ui = Ui_generate_survey()
-        ui.setupUi(qdialog)
-        self.gen_new_survey = ui
-        self.connectButtons_gen_survey()
-        if qdialog.exec_():
-            srcfile = self.gen_new_survey.lineEdit_src.text()
-            recfile = self.gen_new_survey.lineEdit_rec.text()
-            obsdir = self.gen_new_survey.lineEdit_obs.text()
-            fstart = self.gen_new_survey.fstart.text()
-            fend = self.gen_new_survey.fend.text()
-            self.survey = activeSeismoPick.Survey(obsdir, srcfile, recfile,
-                                                  useDefaultParas = True,
-                                                  fstart = fstart, fend = fend)
-            self.setConnected2SurveyState(True)
-            self.seisarray = self.survey.seisarray
-            self.setSeisArrayState(True)
-            return True
 
     def addArrayPlot(self):
         self.seisArrayFigure = Figure()
@@ -160,11 +340,13 @@ class gui_control(object):
         self.seisArrayToolbar = NavigationToolbar(self.seisArrayCanvas, self.mainwindow)
         self.mainUI.verticalLayout_tr1.addWidget(self.seisArrayToolbar)
 
+
     def addSurfacePlot(self):
         self.surfaceFigure = Figure()
         self.surfaceCanvas = FigureCanvas(self.surfaceFigure)
         self.mainUI.horizontalLayout_tr.addWidget(self.surfaceCanvas)
 
+
     def addStatPlots(self):
         self.statFigure_left = Figure()
         self.statCanvas_left = FigureCanvas(self.statFigure_left)
@@ -181,6 +363,7 @@ class gui_control(object):
 
         self.addItems2StatsComboBox()
 
+
     def addItems2StatsComboBox(self):
         self.mainUI.comboBox_stats.insertItem(0, 'picked traces')
         self.mainUI.comboBox_stats.insertItem(1, 'mean SNR')
@@ -189,6 +372,7 @@ class gui_control(object):
         self.mainUI.comboBox_stats.insertItem(4, 'median SPE')
         self.enablePickedTools(False)
 
+
     def addItems2ShotsComboBox(self):
         shotnumbers = self.survey.data.keys()
         shotnumbers.sort()
@@ -196,6 +380,7 @@ class gui_control(object):
             self.mainUI.comboBox_shots.insertItem(index, 'Shot: %s'%shotnumber)
         self.mainUI.comboBox_shots.setMaxCount(len(shotnumbers))
 
+
     def increaseShotnumber(self):
         currentIndex = self.mainUI.comboBox_shots.currentIndex()
         maxindex = self.mainUI.comboBox_shots.maxCount() - 1
@@ -204,6 +389,7 @@ class gui_control(object):
         else:
             self.mainUI.comboBox_shots.setCurrentIndex(currentIndex + 1)
 
+
     def decreaseShotnumber(self):
         currentIndex = self.mainUI.comboBox_shots.currentIndex()
         maxindex = self.mainUI.comboBox_shots.maxCount() - 1
@@ -211,21 +397,26 @@ class gui_control(object):
             self.mainUI.comboBox_shots.setCurrentIndex(maxindex)
         else:
             self.mainUI.comboBox_shots.setCurrentIndex(currentIndex - 1)
+
         
     def plotShot(self):
         shotnumber = int(self.mainUI.comboBox_shots.currentText().split()[1])
         self.survey.data[shotnumber].matshow()
 
+
     def addArrayAxes(self):
         self.seisArrayAx = self.seisArrayFigure.add_subplot(111)
 
+
     def addSurfaceAxes(self):
         self.surfaceAx = self.surfaceFigure.add_subplot(111, projection = '3d')
 
+
     def addStatAxes(self):
         self.statAx_left = self.statFigure_left.add_subplot(111)
         self.statAx_right = self.statFigure_right.add_subplot(111)
 
+
     def enablePickedTools(self, bool, twoDim = False):
         self.mainUI.comboBox_stats.setEnabled(bool)
         self.statToolbar_left.setEnabled(bool)
@@ -238,26 +429,40 @@ class gui_control(object):
         if bool == False:
             self.mainUI.comboBox_shots.clear()
 
+
     def replotArray(self):
         self.seisArrayFigure.clf()
         self.addArrayAxes()
         self.plotArray()
         self.seisArrayCanvas.draw()
 
+
     def replotSurface(self):
         self.surfaceFigure.clf()
         self.addSurfaceAxes()
         self.plotSurface()
         self.surfaceCanvas.draw()
 
+
     def plotArray(self):
         self.seisarray.plotArray2D(self.seisArrayAx, highlight_measured = True, plot_topo = True, twoDim = self.seisarray.twoDim)
 
+
     def plotSurface(self):
         if not self.seisarray.twoDim:
             self.seisarray.plotSurface3D(ax = self.surfaceAx, exag = True)
         self.seisarray.plotArray3D(ax = self.surfaceAx, legend = False, markersize = 3)
 
+
+    def InitPickedWidgets(self):
+        if self.checkPickState():
+            surveyUtils.plotScatterStats4Receivers(self.survey, self.mainUI.comboBox_stats.currentText(),
+                                                   self.statAx_left, twoDim = self.survey.twoDim)
+            surveyUtils.plotScatterStats4Shots(self.survey, self.mainUI.comboBox_stats.currentText(),
+                                               self.statAx_right, twoDim = self.survey.twoDim)
+            self.addItems2ShotsComboBox()
+
+
     def refreshPickedWidgets(self):
         self.statFigure_left.clf()
         self.statFigure_right.clf()
@@ -266,13 +471,6 @@ class gui_control(object):
         self.statCanvas_left.draw()
         self.statCanvas_right.draw()
 
-    def InitPickedWidgets(self):
-        if self.checkPickState():
-            surveyUtils.plotScatterStats4Receivers(self.survey, self.mainUI.comboBox_stats.currentText(),
-                                                   self.statAx_left, twoDim = self.survey.twoDim)
-            surveyUtils.plotScatterStats4Shots(self.survey, self.mainUI.comboBox_stats.currentText(),
-                                               self.statAx_right, twoDim = self.survey.twoDim)
-            self.addItems2ShotsComboBox()
 
     def printSurveyTextbox(self, init = True):
         if init == True:
@@ -289,6 +487,7 @@ class gui_control(object):
         string = surveyTitle + surveyText
         self.mainUI.textBox_survey.setText(string)
 
+
     def printSeisArrayTextbox(self, init = True):
         if init == True:
             seistup = (0, 0, 0)
@@ -303,6 +502,7 @@ class gui_control(object):
         string = seisArrayTitle + seisArrayText
         self.mainUI.textBox_seisarray.setText(string)
 
+
     def interpolate_receivers(self):
         if not self.checkSeisArrayState():
             self.printDialogMessage('No Seismic Array defined.')
@@ -310,10 +510,12 @@ class gui_control(object):
         self.seisarray.interpolateAll()
         self.refreshSeisArrayWidgets()
 
+
     def refreshSeisArrayWidgets(self):
         self.replotArray()
         self.replotSurface()
         self.printSeisArrayTextbox(init = False)
+
         
     def getPickParameters(self, ui, Picking_parameters):
         self.initDynSNRplot()
@@ -329,6 +531,7 @@ class gui_control(object):
             aicwindow = (int(ui.lineEdit_aicleft.text()), int(ui.lineEdit_aicright.text()))
             return ncores, vmin, vmax, folm, AIC, aicwindow
 
+
     def connect2Survey(self):
         if not self.checkSurveyState():
             self.printDialogMessage('No Survey defined.')
@@ -345,13 +548,16 @@ class gui_control(object):
         self.printSurveyTextbox(init = False)
         print('Connected Seismic Array to active Survey object.')
 
+
     def getMaxCPU(self):
         import multiprocessing
         return multiprocessing.cpu_count()
 
+
     def refreshFolm(self):
         self.picker_ui.label_folm.setText('%s %%'%self.picker_ui.slider_folm.value())
 
+
     def callPicker(self):
         if not self.checkSurveyState():
             self.printDialogMessage('No Survey defined.')
@@ -394,6 +600,7 @@ class gui_control(object):
         self.setPickState(True)
         self.printSurveyTextbox(init = False)
 
+
     def plotDynSNR(self):
         fig = self.snrFig
         if fig.axes == []:
@@ -411,7 +618,7 @@ class gui_control(object):
         shiftDist = float(self.picker_ui.shift_dist.value())
         p1 = float(self.picker_ui.p1.value())
         p2 = float(self.picker_ui.p2.value())
-        dists = range(200)
+        dists = range(200) # CHANGE
         if self.checkPickState():
             for shot in self.survey.data.values():
                 for traceID in shot.getTraceIDlist():
@@ -430,6 +637,7 @@ class gui_control(object):
         ax.set_ylim(ylim)
         self.snrCanvas.draw()
 
+
     def initDynSNRplot(self):
         self.snrFig = Figure()
         self.snrCanvas = FigureCanvas(self.snrFig)
@@ -437,6 +645,7 @@ class gui_control(object):
         self.snrToolbar = NavigationToolbar(self.snrCanvas, self.mainwindow)
         self.picker_ui.vlayout_plot.addWidget(self.snrToolbar)
 
+
     def startFMTOMO(self):
         if not self.checkSurveyState():
             self.printDialogMessage('No Survey defined.')
@@ -453,6 +662,7 @@ class gui_control(object):
         self.connectButtons_startFMTOMO()
         self.getFMTOMOparameters(ui, fmtomo_parameters)
 
+
     def startVTKtools(self):
         vtk_tools = QtGui.QDialog(self.mainwindow)
         ui = Ui_vtk_tools()
@@ -462,9 +672,11 @@ class gui_control(object):
         self.connectButtons_vtk_tools()
         self.openVTKdialog(ui, vtk_tools)
 
+
     def openVTKdialog(self, ui, vtk_tools):
         vtk_tools.exec_()
 
+
     def getFMTOMOparameters(self, ui, fmtomo_parameters):
         if fmtomo_parameters.exec_():
             fmtomo_dir = ui.fmtomo_dir.text()
@@ -496,12 +708,14 @@ class gui_control(object):
 
             tomo = fmtomoUtils.Tomo3d(fmtomo_dir, simuldir)
             tomo.runTOMO3D(nproc, nIter)
+
                             
     def connectButtons_startFMTOMO(self):
         QtCore.QObject.connect(self.fmtomo_parameters_ui.browse_tomodir, QtCore.SIGNAL("clicked()"), self.chooseFMTOMOdir)
         QtCore.QObject.connect(self.fmtomo_parameters_ui.browse_customgrid, QtCore.SIGNAL("clicked()"), self.chooseCustomgrid)
         QtCore.QObject.connect(self.fmtomo_parameters_ui.browse_simuldir, QtCore.SIGNAL("clicked()"), self.chooseSimuldir)
 
+
     def connectButtons_vtk_tools(self):
         QtCore.QObject.connect(self.vtk_tools_ui.pushButton_vg, QtCore.SIGNAL("clicked()"), self.chooseVgrid)
         QtCore.QObject.connect(self.vtk_tools_ui.pushButton_vgref, QtCore.SIGNAL("clicked()"), self.chooseVgridref)
@@ -514,17 +728,21 @@ class gui_control(object):
         QtCore.QObject.connect(self.vtk_tools_ui.radioButton_rel, QtCore.SIGNAL("clicked()"), self.activateVgref)
         QtCore.QObject.connect(self.vtk_tools_ui.radioButton_abs, QtCore.SIGNAL("clicked()"), self.deactivateVgref)
 
+
     def openFileParaview(self):
         os.system('paraview %s &'%self.vtk_tools_ui.lineEdit_vgout.text())
 
+
     def activateVgref(self):
         self.vtk_tools_ui.lineEdit_vgref.setEnabled(True)
         self.vtk_tools_ui.pushButton_vgref.setEnabled(True)
 
+
     def deactivateVgref(self):
         self.vtk_tools_ui.lineEdit_vgref.setEnabled(False)
         self.vtk_tools_ui.pushButton_vgref.setEnabled(False)
 
+
     def checkVgStartButton(self):
         ui = self.vtk_tools_ui
         if ui.radioButton_rel.isChecked():
@@ -538,6 +756,7 @@ class gui_control(object):
             else:
                 ui.start_vg.setEnabled(False)                
 
+
     def checkRaysStartButton(self):
         ui = self.vtk_tools_ui
         if ui.lineEdit_rays.text() != '' and ui.lineEdit_raysout.text() != '':
@@ -545,22 +764,27 @@ class gui_control(object):
         else:
             ui.start_rays.setEnabled(False)
 
+
     def chooseVgrid(self):
-        self.vtk_tools_ui.lineEdit_vg.setText(self.openFile())
+        self.vtk_tools_ui.lineEdit_vg.setText(openFile())
         self.checkVgStartButton()
 
+
     def chooseVgridref(self):
-        self.vtk_tools_ui.lineEdit_vgref.setText(self.openFile())
+        self.vtk_tools_ui.lineEdit_vgref.setText(openFile())
         self.checkVgStartButton()
 
+
     def chooseRaysIn(self):
-        self.vtk_tools_ui.lineEdit_rays.setText(self.openFile())
+        self.vtk_tools_ui.lineEdit_rays.setText(openFile())
         self.checkRaysStartButton()
 
+
     def chooseRaysOutDir(self):
-        self.vtk_tools_ui.lineEdit_raysout.setText(self.browseDir())
+        self.vtk_tools_ui.lineEdit_raysout.setText(browseDir())
         self.checkRaysStartButton()
 
+
     def startvgvtk(self):
         ui = self.vtk_tools_ui
         if ui.lineEdit_vgout.text() == '':
@@ -576,24 +800,31 @@ class gui_control(object):
                                    absOrRel='rel',
                                    inputfileref = ui.lineEdit_vgref.text())
 
+
     def startraysvtk(self):
         ui = self.vtk_tools_ui
         fmtomoUtils.rays2VTK(ui.lineEdit_rays.text(), ui.lineEdit_raysout.text())
 
+
     def newFileVTK(self):
-        self.vtk_tools_ui.lineEdit_vgout.setText(self.saveFile())
+        self.vtk_tools_ui.lineEdit_vgout.setText(saveFile())
+
 
     def chooseFMTOMOdir(self):
-        self.fmtomo_parameters_ui.fmtomo_dir.setText(self.browseDir())
+        self.fmtomo_parameters_ui.fmtomo_dir.setText(browseDir())
+
 
     def chooseCustomgrid(self):
-        self.fmtomo_parameters_ui.customgrid.setText(self.openFile())
+        self.fmtomo_parameters_ui.customgrid.setText(openFile())
+
 
     def chooseSimuldir(self):
-        self.fmtomo_parameters_ui.simuldir.setText(self.browseDir())
+        self.fmtomo_parameters_ui.simuldir.setText(browseDir())
+
 
     def chooseSeisarray(self):
-        self.fmtomo_parameters_ui.seisarray.setText(self.openFile())
+        self.fmtomo_parameters_ui.seisarray.setText(openFile())
+
 
     def postprocessing(self):
         if not self.checkSurveyState():
@@ -601,12 +832,13 @@ class gui_control(object):
             return
         self.survey.plotAllPicks()
         self.refreshPickedWidgets() # wait until finished
+
         
     def load_survey(self):
         if self.checkSurveyState():
             if not self.continueDialogExists('Survey'):
                 return
-        filename = self.openFile()
+        filename = openFile()
         if filename is None:
             return
         try:
@@ -638,6 +870,7 @@ class gui_control(object):
             self.setSeisArrayState(False)
             self.printDialogMessage('Loaded Survey.')
 
+
     def load_seisarray(self):
         disconnect = False
         if self.checkSeisArrayState():
@@ -651,7 +884,7 @@ class gui_control(object):
                 self.survey.seisarray = None
                 disconnect = True
 
-        filename = self.openFile()
+        filename = openFile()
         if filename is None:
             return
         try:
@@ -668,24 +901,27 @@ class gui_control(object):
         self.seisarray = seisarray
         self.setSeisArrayState(True)
 
+
     def save_seisarray(self):
         if not self.checkSeisArrayState():
             self.printDialogMessage('No Seismic Array defined.')
             return
-        filename = self.saveFile()
+        filename = saveFile()
         if filename is None:
             return
         self.seisarray.saveSeisArray(filename)
 
+
     def save_survey(self):
         if not self.checkSurveyState():
             self.printDialogMessage('No Survey defined.')
             return
-        filename = self.saveFile()
+        filename = saveFile()
         if filename is None:
             return
         self.survey.saveSurvey(filename)
 
+
     def setSurveyState(self, state):
         if state == True:
             self.mainUI.survey_active.setPixmap(self.applypixmap)
@@ -693,18 +929,21 @@ class gui_control(object):
         elif state == False:
             self.mainUI.survey_active.setPixmap(self.cancelpixmap)
 
+
     def checkSurveyState(self):
         if self.survey == None:
             return False
         else:
             return True
 
+
     def checkSeisArrayState(self):
         if self.seisarray == None:
             return False
         else:
             return True
 
+
     def setPickState(self, state):
         if state == True and self.checkSurveyState():
             self.mainUI.picked_active.setPixmap(self.applypixmap)
@@ -722,6 +961,7 @@ class gui_control(object):
                 self.enablePickedTools(False)
                 self.survey.picked = False
 
+
     def setSeisArrayState(self, state):
         if state == True:
             self.mainUI.seisarray_active.setPixmap(self.applypixmap)
@@ -733,12 +973,14 @@ class gui_control(object):
             if self.seisArrayFigure is not None:
                 self.seisArrayFigure.clf()
 
+
     def setConnected2SurveyState(self, state):
         if state == True:
             self.mainUI.seisarray_on_survey_active.setPixmap(self.applypixmap)
         elif state == False:
             self.mainUI.seisarray_on_survey_active.setPixmap(self.cancelpixmap)
 
+
     def checkConnected2SurveyState(self):
         if self.checkSurveyState():
             if self.survey.seisarray != None:
@@ -746,12 +988,14 @@ class gui_control(object):
         else:
             return False
 
+
     def checkPickState(self):
         if not self.survey:
             self.printDialogMessage('No Survey defined.')
             return
         return self.survey.picked
 
+
     def printDialogMessage(self, message):
         qmb = QtGui.QMessageBox()
         qmb.setText(message)
@@ -759,6 +1003,7 @@ class gui_control(object):
         qmb.setIcon(QtGui.QMessageBox.Warning)
         qmb.exec_()
 
+
     def continueDialogExists(self, name):
         qmb = QtGui.QMessageBox()
         qmb.setText('%s object already exists. Overwrite?'%name)
@@ -770,6 +1015,7 @@ class gui_control(object):
         else:
             return False
 
+
     def continueDialogMessage(self, message):
         qmb = QtGui.QMessageBox()
         qmb.setText(message)
@@ -781,64 +1027,11 @@ class gui_control(object):
         else:
             return False
 
-    def connectButtons_gen_survey(self):
-        QtCore.QObject.connect(self.gen_new_survey.pushButton_rec, QtCore.SIGNAL("clicked()"), self.chooseReceiverfile)
-        QtCore.QObject.connect(self.gen_new_survey.pushButton_src, QtCore.SIGNAL("clicked()"), self.chooseSourcefile)
-        QtCore.QObject.connect(self.gen_new_survey.pushButton_obs, QtCore.SIGNAL("clicked()"), self.chooseObsdir)
-
-    def connectButtons_gen_survey_min(self):
-        QtCore.QObject.connect(self.gen_new_survey_min.pushButton_obs, QtCore.SIGNAL("clicked()"), self.chooseObsdir_min)
-
-    def connectButtons_gen_seisarray(self):
-        QtCore.QObject.connect(self.gen_new_seisarray.pushButton_rec, QtCore.SIGNAL("clicked()"), self.chooseMeasuredRec)
-        QtCore.QObject.connect(self.gen_new_seisarray.pushButton_src, QtCore.SIGNAL("clicked()"), self.chooseMeasuredSrc)
-        QtCore.QObject.connect(self.gen_new_seisarray.pushButton_obs, QtCore.SIGNAL("clicked()"), self.chooseMeasuredPts)
-
-    def chooseMeasuredSrc(self):
-        self.gen_new_seisarray.lineEdit_src.setText(self.openFile('Open measured sources file.'))
-
-    def chooseMeasuredRec(self):
-        self.gen_new_seisarray.lineEdit_rec.setText(self.openFile('Open measured receivers file.'))
-
-    def chooseMeasuredPts(self):
-        self.gen_new_seisarray.lineEdit_pts.setText(self.openFile('Open measured points file.'))
-
-    def chooseSourcefile(self):
-        self.gen_new_survey.lineEdit_src.setText(self.openFile('Open sourcefile.'))
-
-    def chooseReceiverfile(self):
-        self.gen_new_survey.lineEdit_rec.setText(self.openFile('Open receiverfile.'))
-
-    def chooseObsdir(self):
-        self.gen_new_survey.lineEdit_obs.setText(self.browseDir('Choose observation directory.'))
-
-    def chooseObsdir_min(self):
-        self.gen_new_survey_min.lineEdit_obs.setText(self.browseDir('Choose observation directory.'))
-
-    def openFile(self, name = 'Open'):
-        dialog = QtGui.QFileDialog()
-        dialog.setWindowTitle(name)                #not working yet
-        filename = dialog.getOpenFileName()
-        if len(filename[0]) > 0:
-            return filename[0]
-
-    def saveFile(self, name = 'Save'):
-        dialog = QtGui.QFileDialog()
-        dialog.setWindowTitle(name)
-        filename = dialog.getSaveFileName()
-        if len(filename[0]) > 0:
-            return filename[0]
-
-    def browseDir(self, name = 'Open Directory'):
-        dialog = QtGui.QFileDialog()
-        dialog.setWindowTitle(name)
-        directory = dialog.getExistingDirectory()
-        if len(directory) > 0:
-            return directory
 
     def exitApp(self):
         QtCore.QCoreApplication.instance().quit()
 
+
 if __name__ == "__main__":
     app = QtGui.QApplication(sys.argv)
     MainWindow = QtGui.QMainWindow()

From 48c0dbacfb076e9447a3220673dd1dc508f9ee85 Mon Sep 17 00:00:00 2001
From: Marcel Paffrath <marcel.paffrath@rub.de>
Date: Tue, 26 Jul 2016 14:48:08 +0200
Subject: [PATCH 5/9] changed structure of active GUI code, autopicker window
 changed to class

---
 pylot/core/active/ActiveSeismoPick3D_GUI.py   | 309 +---------------
 pylot/core/active/__init__.py                 |   2 +-
 pylot/core/active/asp3d_test.py               | 264 -------------
 pylot/core/active/gui/__init__.py             |   2 +
 pylot/core/active/{ => gui}/asp3d_layout.py   |   0
 .../{ => gui}/fmtomo_parameters_layout.py     |   0
 .../{ => gui}/generate_seisarray_layout.py    |   0
 .../{ => gui}/generate_survey_layout.py       |   0
 .../generate_survey_layout_minimal.py         |   0
 .../{ => gui}/picking_parameters_layout.py    |   0
 .../core/active/{ => gui}/vtk_tools_layout.py |   0
 pylot/core/active/gui/windows.py              | 347 ++++++++++++++++++
 pylot/core/active/seismicArrayPreparation.py  |   2 +-
 13 files changed, 370 insertions(+), 556 deletions(-)
 delete mode 100644 pylot/core/active/asp3d_test.py
 create mode 100644 pylot/core/active/gui/__init__.py
 rename pylot/core/active/{ => gui}/asp3d_layout.py (100%)
 rename pylot/core/active/{ => gui}/fmtomo_parameters_layout.py (100%)
 rename pylot/core/active/{ => gui}/generate_seisarray_layout.py (100%)
 rename pylot/core/active/{ => gui}/generate_survey_layout.py (100%)
 rename pylot/core/active/{ => gui}/generate_survey_layout_minimal.py (100%)
 rename pylot/core/active/{ => gui}/picking_parameters_layout.py (100%)
 rename pylot/core/active/{ => gui}/vtk_tools_layout.py (100%)
 create mode 100644 pylot/core/active/gui/windows.py

diff --git a/pylot/core/active/ActiveSeismoPick3D_GUI.py b/pylot/core/active/ActiveSeismoPick3D_GUI.py
index 2e43bcf3..5074f479 100755
--- a/pylot/core/active/ActiveSeismoPick3D_GUI.py
+++ b/pylot/core/active/ActiveSeismoPick3D_GUI.py
@@ -6,14 +6,11 @@ import matplotlib
 matplotlib.use('Qt4Agg')
 matplotlib.rcParams['backend.qt4']='PySide'
 
-from PySide import QtCore, QtGui, QtCore
-from asp3d_layout import *
-from fmtomo_parameters_layout import *
-from generate_survey_layout import *
-from generate_survey_layout_minimal import *
-from generate_seisarray_layout import *
-from picking_parameters_layout import *
-from vtk_tools_layout import *
+from PySide import QtCore, QtGui
+from pylot.core.active.gui.asp3d_layout import *
+from pylot.core.active.gui.fmtomo_parameters_layout import *
+from pylot.core.active.gui.vtk_tools_layout import *
+from pylot.core.active.gui.windows import Gen_SeisArray, Gen_Survey_from_SA, Gen_Survey_from_SR, Call_autopicker
 from pylot.core.active import activeSeismoPick, surveyUtils, fmtomoUtils, seismicArrayPreparation
 
 from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
@@ -62,6 +59,7 @@ class gui_control(object):
         self.gsa = None
         self.gssa = None
         self.gssr = None
+        self.autopicker = None
 
     def setInitStates(self):
         self.setPickState(False)
@@ -88,186 +86,6 @@ class gui_control(object):
         QtCore.QObject.connect(self.mainUI.shot_right, QtCore.SIGNAL("clicked()"), self.increaseShotnumber)
         QtCore.QObject.connect(self.mainUI.plot_shot, QtCore.SIGNAL("clicked()"), self.plotShot)
 
-    class Gen_SeisArray(object):
-        def __init__(self, mainwindow):
-            self.mainwindow = mainwindow
-            self.seisarray = None
-            self.srcfile = None
-            self.recfile = None
-            self.ptsfile = None
-            self.init_dialog()
-            self.start_dialog()
-
-        def init_dialog(self):
-            qdialog = QtGui.QDialog(self.mainwindow)
-            ui = Ui_generate_seisarray()
-            ui.setupUi(qdialog)
-            self.ui = ui
-            self.qdialog = qdialog
-            self.connectButtons()
-            
-        def start_dialog(self):
-            self.init_last_selection()
-            if self.qdialog.exec_():
-                self.refresh_filenames()
-                if self.ui.radioButton_interpolatable.isChecked():
-                    self.seisarray = seismicArrayPreparation.SeisArray(self.recfile, True)
-                elif self.ui.radioButton_normal.isChecked():
-                    self.seisarray = seismicArrayPreparation.SeisArray(self.recfile, False)
-                if len(self.srcfile) > 0:
-                    self.seisarray.addSourceLocations(self.srcfile)
-                if len(self.ptsfile) > 0:
-                    self.seisarray.addMeasuredTopographyPoints(self.ptsfile)
-                self.executed = True
-            else:
-                self.refresh_filenames()
-                self.executed = False
-
-        def refresh_filenames(self):
-            self.srcfile = self.ui.lineEdit_src.text()
-            self.recfile = self.ui.lineEdit_rec.text()
-            self.ptsfile = self.ui.lineEdit_pts.text()
-
-        def init_last_selection(self):
-            self.ui.lineEdit_src.setText(self.srcfile)
-            self.ui.lineEdit_rec.setText(self.recfile)
-            self.ui.lineEdit_pts.setText(self.ptsfile)
-
-        def get_seisarray(self):
-            if self.seisarray is not None:
-                return self.seisarray
-
-        def connectButtons(self):
-            QtCore.QObject.connect(self.ui.pushButton_rec, QtCore.SIGNAL("clicked()"), self.chooseMeasuredRec)
-            QtCore.QObject.connect(self.ui.pushButton_src, QtCore.SIGNAL("clicked()"), self.chooseMeasuredSrc)
-            QtCore.QObject.connect(self.ui.pushButton_obs, QtCore.SIGNAL("clicked()"), self.chooseMeasuredPts)
-
-        def chooseMeasuredSrc(self):
-            self.ui.lineEdit_src.setText(openFile('Open measured sources file.'))
-
-        def chooseMeasuredRec(self):
-            self.ui.lineEdit_rec.setText(openFile('Open measured receivers file.'))
-
-        def chooseMeasuredPts(self):
-            self.ui.lineEdit_pts.setText(openFile('Open measured points file.'))
-
-
-
-    class Gen_Survey_from_SA(object):
-        def __init__(self, mainwindow, seisarray):
-            self.mainwindow = mainwindow
-            self.seisarray = seisarray
-            self.survey = None
-            self.obsdir = None
-            self.fstart = 'shot'
-            self.fend = '.dat'
-            self.init_dialog()
-            self.start_dialog()
-
-        def init_dialog(self):
-            qdialog = QtGui.QDialog(self.mainwindow)
-            ui = Ui_generate_survey_minimal()
-            ui.setupUi(qdialog)
-            self.ui = ui
-            self.qdialog = qdialog
-            self.connectButtons()
-            
-        def start_dialog(self):
-            self.init_last_selection()
-            if self.qdialog.exec_():
-                self.refresh_filenames()
-                self.survey = activeSeismoPick.Survey(self.obsdir, seisArray = self.seisarray,
-                                                      useDefaultParas = True, fstart = self.fstart,
-                                                      fend = self.fend)
-                self.executed = True
-            else:
-                self.refresh_filenames()
-                self.executed = False
-        
-        def refresh_filenames(self):
-            self.obsdir = self.ui.lineEdit_obs.text()
-            self.fstart = self.ui.fstart.text()
-            self.fend = self.ui.fend.text()
-
-        def init_last_selection(self):
-            self.ui.lineEdit_obs.setText(self.obsdir)
-            self.ui.fstart.setText(self.fstart)
-            self.ui.fend.setText(self.fend)
-        
-        def get_survey(self):
-            return self.survey
-
-        def connectButtons(self):
-            QtCore.QObject.connect(self.ui.pushButton_obs, QtCore.SIGNAL("clicked()"), self.chooseObsdir)
-
-        def chooseObsdir(self):
-            self.ui.lineEdit_obs.setText(browseDir('Choose observation directory.'))
-
-
-    class Gen_Survey_from_SR(object):
-        def __init__(self, mainwindow):
-            self.mainwindow = mainwindow
-            self.survey = None
-            self.obsdir = None
-            self.srcfile = None
-            self.recfile = None
-            self.fstart = 'shot'
-            self.fend = '.dat'
-            self.init_dialog()
-            self.start_dialog()
-
-        def init_dialog(self):
-            qdialog = QtGui.QDialog(self.mainwindow)
-            ui = Ui_generate_survey()
-            ui.setupUi(qdialog)
-            self.ui = ui
-            self.qdialog = qdialog
-            self.connectButtons()
-            
-        def start_dialog(self):
-            self.init_last_selection()
-            if self.qdialog.exec_():
-                self.refresh_filenames()
-                self.survey = activeSeismoPick.Survey(self.obsdir, self.srcfile, self.recfile,
-                                                      useDefaultParas = True,
-                                                      fstart = self.fstart, fend = self.fend)
-                self.executed = True
-            else:
-                self.refresh_filenames()
-                self.executed = False
-        
-        def refresh_filenames(self):
-            self.obsdir = self.ui.lineEdit_obs.text()
-            self.srcfile = self.ui.lineEdit_src.text()
-            self.recfile = self.ui.lineEdit_rec.text()
-            self.fstart = self.ui.fstart.text()
-            self.fend = self.ui.fend.text()
-
-        def init_last_selection(self):
-            self.ui.lineEdit_obs.setText(self.obsdir)
-            self.ui.lineEdit_src.setText(self.srcfile)
-            self.ui.lineEdit_rec.setText(self.recfile)
-            self.ui.fstart.setText(self.fstart)
-            self.ui.fend.setText(self.fend)
-        
-        def get_survey(self):
-            return self.survey
-
-        def connectButtons(self):
-            QtCore.QObject.connect(self.ui.pushButton_obs, QtCore.SIGNAL("clicked()"), self.chooseObsdir)
-            QtCore.QObject.connect(self.ui.pushButton_src, QtCore.SIGNAL("clicked()"), self.chooseSourcefile)
-            QtCore.QObject.connect(self.ui.pushButton_rec, QtCore.SIGNAL("clicked()"), self.chooseRecfile)
-
-        def chooseObsdir(self):
-            self.ui.lineEdit_obs.setText(browseDir('Choose observation directory.'))
-
-        def chooseSourcefile(self):
-            self.ui.lineEdit_src.setText(openFile('Open sourcefile.'))
-
-        def chooseRecfile(self):
-            self.ui.lineEdit_rec.setText(openFile('Open receiverfile.'))
-
-
     def gen_seisarray(self):
         disconnect = False
         if self.checkSeisArrayState():
@@ -282,7 +100,7 @@ class gui_control(object):
                 disconnect = True
         
         if self.gsa is None:
-            self.gsa = self.Gen_SeisArray(self.mainwindow)
+            self.gsa = Gen_SeisArray(self.mainwindow)
         else:
             self.gsa.start_dialog()
 
@@ -301,7 +119,7 @@ class gui_control(object):
             if len(self.seisarray.getSourceCoordinates()) > 0:
                 if self.continueDialogMessage('Use geometry information of active Seismic Array?'):
                     if self.gssa is None:
-                        self.gssa = self.Gen_Survey_from_SA(self.mainwindow, self.seisarray)
+                        self.gssa = Gen_Survey_from_SA(self.mainwindow, self.seisarray)
                     else:
                         self.gssa.start_dialog()
                     if self.gssa.executed:
@@ -315,7 +133,7 @@ class gui_control(object):
                                                   ' because there are no sources given.'):
                     return
         if self.gssr is None:
-            self.gssr = self.Gen_Survey_from_SR(self.mainwindow)
+            self.gssr = Gen_Survey_from_SR(self.mainwindow)
         else:
             self.gssr.start_dialog()
         if self.gssr.executed:
@@ -517,21 +335,6 @@ class gui_control(object):
         self.printSeisArrayTextbox(init = False)
 
         
-    def getPickParameters(self, ui, Picking_parameters):
-        self.initDynSNRplot()
-        self.plotDynSNR()
-
-        if Picking_parameters.exec_():
-            ncores = int(ui.ncores.value())
-            vmin = float(ui.lineEdit_vmin.text())
-            vmax = float(ui.lineEdit_vmax.text())
-            folm = float(ui.slider_folm.value())/100.
-            print('folm =', folm)
-            AIC = ui.checkBox_AIC.isChecked()
-            aicwindow = (int(ui.lineEdit_aicleft.text()), int(ui.lineEdit_aicright.text()))
-            return ncores, vmin, vmax, folm, AIC, aicwindow
-
-
     def connect2Survey(self):
         if not self.checkSurveyState():
             self.printDialogMessage('No Survey defined.')
@@ -549,15 +352,11 @@ class gui_control(object):
         print('Connected Seismic Array to active Survey object.')
 
 
-    def getMaxCPU(self):
+    def getMaxCPU(self): ### OLD
         import multiprocessing
         return multiprocessing.cpu_count()
 
 
-    def refreshFolm(self):
-        self.picker_ui.label_folm.setText('%s %%'%self.picker_ui.slider_folm.value())
-
-
     def callPicker(self):
         if not self.checkSurveyState():
             self.printDialogMessage('No Survey defined.')
@@ -565,85 +364,15 @@ class gui_control(object):
         if self.checkPickState():
             if not self.continueDialogMessage('Survey already picked. Continue?'):
                 return
-        Picking_parameters = QtGui.QDialog(self.mainwindow)
-        ui = Ui_picking_parameters()
-        ui.setupUi(Picking_parameters)
-        ui.ncores.setMaximum(self.getMaxCPU())
-        self.picker_ui = ui
-        QtCore.QObject.connect(self.picker_ui.slider_folm, QtCore.SIGNAL("valueChanged(int)"), self.refreshFolm)
-        QtCore.QObject.connect(self.picker_ui.shift_snr, QtCore.SIGNAL("valueChanged(int)"), self.plotDynSNR)
-        QtCore.QObject.connect(self.picker_ui.shift_dist, QtCore.SIGNAL("valueChanged(int)"), self.plotDynSNR)
-        QtCore.QObject.connect(self.picker_ui.p1, QtCore.SIGNAL("valueChanged(double)"), self.plotDynSNR)
-        QtCore.QObject.connect(self.picker_ui.p2, QtCore.SIGNAL("valueChanged(double)"), self.plotDynSNR)
-        try:
-            ncores, vmin, vmax, folm, AIC, aicwindow = self.getPickParameters(ui, Picking_parameters)
-        except TypeError:
-            return
+
+        if self.autopicker is None:
+            self.autopicker = Call_autopicker(self.mainwindow, self.survey)
+        else:
+            self.autopicker.start_dialog()
         
-        if AIC == True:
-            HosAic = 'aic'
-        else:
-            HosAic = 'hos'
-
-        shiftSNR = float(self.picker_ui.shift_snr.value())
-        shiftDist = float(self.picker_ui.shift_dist.value())
-        p1 = float(self.picker_ui.p1.value())
-        p2 = float(self.picker_ui.p2.value())
-
-        surveyUtils.setDynamicFittedSNR(self.survey.getShotDict(), shiftdist = shiftDist,
-                                        shiftSNR = shiftSNR, p1 = p1, p2 = p2)
-
-        self.survey.pickAllShots(vmin = vmin, vmax = vmax,
-                                 folm = folm, HosAic = HosAic,
-                                 aicwindow = aicwindow, cores = ncores)
-        QtGui.qApp.processEvents() # test
-        self.setPickState(True)
-        self.printSurveyTextbox(init = False)
-
-
-    def plotDynSNR(self):
-        fig = self.snrFig
-        if fig.axes == []:
-            ax = fig.add_subplot(111)
-            xlim = None
-            ylim = None
-        else:
-            ax = fig.axes[0]
-            xlim = ax.get_xlim()
-            ylim = ax.get_ylim()
-        ax.clear()
-        snrthresholds = []
-        dists_p = []; snr_p = []
-        shiftSNR = float(self.picker_ui.shift_snr.value())
-        shiftDist = float(self.picker_ui.shift_dist.value())
-        p1 = float(self.picker_ui.p1.value())
-        p2 = float(self.picker_ui.p2.value())
-        dists = range(200) # CHANGE
-        if self.checkPickState():
-            for shot in self.survey.data.values():
-                for traceID in shot.getTraceIDlist():
-                    dists_p.append(shot.getDistance(traceID))
-                    snr_p.append(shot.getSNR(traceID)[0])
-
-            ax.scatter(dists_p, snr_p, s = 0.5, c='k')
-            
-        for dist in dists:
-            dist += shiftDist
-            snrthresholds.append(surveyUtils.snr_fit_func(surveyUtils.get_fit_fn(p1, p2), dist, shiftSNR))
-        ax.plot(dists, snrthresholds)
-        ax.set_xlabel('Distance [m]')
-        ax.set_ylabel('SNR')
-        ax.set_xlim(xlim)
-        ax.set_ylim(ylim)
-        self.snrCanvas.draw()
-
-
-    def initDynSNRplot(self):
-        self.snrFig = Figure()
-        self.snrCanvas = FigureCanvas(self.snrFig)
-        self.picker_ui.vlayout_plot.addWidget(self.snrCanvas)
-        self.snrToolbar = NavigationToolbar(self.snrCanvas, self.mainwindow)
-        self.picker_ui.vlayout_plot.addWidget(self.snrToolbar)
+        if self.autopicker.executed:
+            self.setPickState(True)
+            self.printSurveyTextbox(init = False)
 
 
     def startFMTOMO(self):
@@ -703,7 +432,7 @@ class gui_control(object):
                 interpolationMethod = 'nearest'
             self.survey.seisarray.generateFMTOMOinputFromArray(propgrid, vgrid, (bbot, btop), cushionfactor,
                                                           interpolationMethod, customgrid = customgrid,
-                                                          writeVTK = False)
+                                                          writeVTK = True)
             os.chdir(cwd)
 
             tomo = fmtomoUtils.Tomo3d(fmtomo_dir, simuldir)
diff --git a/pylot/core/active/__init__.py b/pylot/core/active/__init__.py
index 9ef8ae9f..aafb279b 100644
--- a/pylot/core/active/__init__.py
+++ b/pylot/core/active/__init__.py
@@ -1,2 +1,2 @@
 # -*- coding: utf-8 -*-
-__author__ = 'sebastianw'
+__author__ = 'marcel'
diff --git a/pylot/core/active/asp3d_test.py b/pylot/core/active/asp3d_test.py
deleted file mode 100644
index 1ef23d06..00000000
--- a/pylot/core/active/asp3d_test.py
+++ /dev/null
@@ -1,264 +0,0 @@
-# -*- coding: utf-8 -*-
-
-import sys
-from PySide import QtCore, QtGui
-from pylot.core.active import activeSeismoPick
-
-class Ui_ActiveSeismoPick3D(object):
-    def __init__(self):
-        self.survey = None
-        
-    def setupUi(self, MainWindow):
-        MainWindow.setObjectName("MainWindow")
-        MainWindow.resize(550, 350)
-        
-        self.centralwidget = QtGui.QWidget(MainWindow)
-        self.centralwidget.setObjectName("centralwidget")
-        self.addBrowseButtons()
-        self.addButtons()
-        self.addLineEdits()
-        self.addLabels()
-        
-        MainWindow.setCentralWidget(self.centralwidget)
-
-        self.setMenubar(MainWindow)
-        
-        self.menuPreferences = QtGui.QMenu(self.menubar)
-        self.menuPreferences.setObjectName("menuPreferences")
-        MainWindow.setMenuBar(self.menubar)
-
-        self.statusbar = QtGui.QStatusBar(MainWindow)
-        self.statusbar.setObjectName("statusbar")
-        MainWindow.setStatusBar(self.statusbar)
-        self.menubar.addAction(self.menuPreferences.menuAction())
-
-        self.retranslateUi(MainWindow)
-        self.connectButtons()
-
-    def setMenubar(self, window):
-        self.menubar = QtGui.QMenuBar(window)
-        self.menubar.setGeometry(QtCore.QRect(0, 0, 603, 21))
-        self.menubar.setObjectName("menubar")
-        
-    def connectButtons(self):
-        QtCore.QObject.connect(self.browseButton_rec, QtCore.SIGNAL("clicked()"), self.chooseReceiverfile)
-        QtCore.QObject.connect(self.browseButton_src, QtCore.SIGNAL("clicked()"), self.chooseSourcefile)
-        QtCore.QObject.connect(self.browseButton_obsdir, QtCore.SIGNAL("clicked()"), self.chooseObsdir)
-        QtCore.QObject.connect(self.start_picking, QtCore.SIGNAL("clicked()"), self.callPicker)
-        QtCore.QObject.connect(self.gen_survey, QtCore.SIGNAL("clicked()"), self.generateSurvey)
-        QtCore.QMetaObject.connectSlotsByName(MainWindow)
-        
-    def addLabels(self):
-        self.label = QtGui.QLabel(self.centralwidget)
-        self.label.setGeometry(QtCore.QRect(40, 70, 131, 20))
-        self.label.setObjectName("label")
-        
-        self.label_2 = QtGui.QLabel(self.centralwidget)
-        self.label_2.setGeometry(QtCore.QRect(40, 110, 131, 20))
-        self.label_2.setObjectName("label_2")
-        
-        self.label_3 = QtGui.QLabel(self.centralwidget)
-        self.label_3.setGeometry(QtCore.QRect(40, 150, 131, 20))
-        self.label_3.setObjectName("label_3")
-
-    def addLineEdits(self):
-        self.receiverfile_lineEdit = QtGui.QLineEdit(self.centralwidget)
-        self.receiverfile_lineEdit.setGeometry(QtCore.QRect(192, 70, 231, 20))
-        self.receiverfile_lineEdit.setObjectName("receiverfile_lineEdit")
-
-        self.sourcefile_lineEdit = QtGui.QLineEdit(self.centralwidget)
-        self.sourcefile_lineEdit.setGeometry(QtCore.QRect(192, 110, 231, 20))
-        self.sourcefile_lineEdit.setObjectName("sourcefile_lineEdit")
-
-        self.obsdir_lineEdit = QtGui.QLineEdit(self.centralwidget)
-        self.obsdir_lineEdit.setGeometry(QtCore.QRect(192, 150, 231, 20))
-        self.obsdir_lineEdit.setText("")
-        self.obsdir_lineEdit.setObjectName("obsdir_lineEdit")
-
-    def addBrowseButtons(self):
-        self.browseButton_rec = QtGui.QPushButton(self.centralwidget)
-        self.browseButton_rec.setGeometry(QtCore.QRect(440, 70, 75, 23))
-        self.browseButton_rec.setObjectName("browseButton_rec")
-        
-        self.browseButton_src = QtGui.QPushButton(self.centralwidget)
-        self.browseButton_src.setGeometry(QtCore.QRect(440, 110, 75, 23))
-        self.browseButton_src.setObjectName("browseButton_src")
-
-        self.browseButton_obsdir = QtGui.QPushButton(self.centralwidget)
-        self.browseButton_obsdir.setGeometry(QtCore.QRect(440, 150, 75, 23))
-        self.browseButton_obsdir.setObjectName("browseButton_obsdir")
-
-    def addButtons(self):
-        self.gen_survey = QtGui.QPushButton(self.centralwidget)
-        self.gen_survey.setGeometry(QtCore.QRect(80, 230, 61, 61))
-        self.gen_survey.setObjectName("gen_survey")
-
-        self.start_picking = QtGui.QPushButton(self.centralwidget)
-        self.start_picking.setGeometry(QtCore.QRect(160, 230, 61, 61))
-        self.start_picking.setObjectName("start_picking")
-
-    def addProgressBar(self):
-        self.progressBar = QtGui.QProgressBar(self.centralwidget)
-        self.progressBar.setGeometry(QtCore.QRect(470, 280, 118, 23))
-        self.progressBar.setObjectName("progressBar")
-
-    def updateProgressBar(self):
-        self.progressBar.setProperty("value", 24)
-
-    def browseFile(self):
-        dialog = QtGui.QFileDialog()
-        filename = dialog.getOpenFileName()
-        return filename[0]
-
-    def browseDir(self):
-        dialog = QtGui.QFileDialog()
-        directory = dialog.getExistingDirectory()
-        return directory
-
-    def chooseSourcefile(self):
-        self.sourcefile_lineEdit.setText(self.browseFile())
-
-    def chooseReceiverfile(self):
-        self.receiverfile_lineEdit.setText(self.browseFile())
-
-    def chooseObsdir(self):
-        self.obsdir_lineEdit.setText(self.browseDir())
-    
-    def getSourcefile(self):
-        return self.sourcefile_lineEdit.text()
-
-    def getReceiverfile(self):
-        return self.receiverfile_lineEdit.text()
-
-    def getObsdir(self):
-        return self.obsdir_lineEdit.text()
-    
-    def retranslateUi(self, MainWindow):
-        MainWindow.setWindowTitle(QtGui.QApplication.translate("MainWindow", "ActiveSeismoPick3D", None, QtGui.QApplication.UnicodeUTF8))
-        self.browseButton_rec.setText(QtGui.QApplication.translate("MainWindow", "Browse", None, QtGui.QApplication.UnicodeUTF8))
-        self.browseButton_src.setText(QtGui.QApplication.translate("MainWindow", "Browse", None, QtGui.QApplication.UnicodeUTF8))
-        self.label.setText(QtGui.QApplication.translate("MainWindow", "Receiver File", None, QtGui.QApplication.UnicodeUTF8))
-        self.label_2.setText(QtGui.QApplication.translate("MainWindow", "Source File", None, QtGui.QApplication.UnicodeUTF8))
-        self.start_picking.setText(QtGui.QApplication.translate("MainWindow", "Start\n"
-"Picking", None, QtGui.QApplication.UnicodeUTF8))
-        self.browseButton_obsdir.setText(QtGui.QApplication.translate("MainWindow", "Browse", None, QtGui.QApplication.UnicodeUTF8))
-        self.gen_survey.setText(QtGui.QApplication.translate("MainWindow", "Gemerate\nSurvey", None, QtGui.QApplication.UnicodeUTF8))
-        self.label_3.setText(QtGui.QApplication.translate("MainWindow", "Seismogram Directory", None, QtGui.QApplication.UnicodeUTF8))
-        self.menuPreferences.setTitle(QtGui.QApplication.translate("MainWindow", "Preferences", None, QtGui.QApplication.UnicodeUTF8))
-
-    def generateSurvey(self):
-        obsdir = self.getObsdir()
-        self.survey = activeSeismoPick.Survey(self.getObsdir(), self.getSourcefile(), self.getReceiverfile(),
-                                         useDefaultParas = True)
-                                         
-        
-    def callPicker(self):
-        Picking_parameters = QtGui.QDialog(self.centralwidget)
-        ui = Ui_Picking_parameters()
-        ui.setupUi(Picking_parameters)
-        ncores, vmin, vmax, folm, AIC, aicwindow = ui.getParameters(Picking_parameters)
-        if AIC == True:
-            HosAic = 'aic'
-        else:
-            HosAic = 'hos'
-        if self.survey is None:
-            print('Survey not defined.')
-            return
-                
-        self.survey.pickAllShots(vmin = vmin, vmax = vmax,
-                                 folm = folm, HosAic = HosAic,
-                                 aicwindow = aicwindow, cores = ncores)
-        
-    
-class Ui_Picking_parameters(object):
-    def setupUi(self, Picking_parameters):
-        Picking_parameters.setObjectName("Picking_parameters")
-        Picking_parameters.resize(300, 300)
-        self.gridLayoutWidget = QtGui.QWidget(Picking_parameters)
-        self.gridLayoutWidget.setGeometry(QtCore.QRect(20, 20, 250, 211))
-        self.gridLayoutWidget.setObjectName("gridLayoutWidget")
-        self.gridLayout = QtGui.QGridLayout(self.gridLayoutWidget)
-        self.gridLayout.setContentsMargins(0, 0, 0, 0)
-        self.gridLayout.setObjectName("gridLayout")
-        self.label_cores = QtGui.QLabel(self.gridLayoutWidget)
-        self.label_cores.setObjectName("label_cores")
-        self.gridLayout.addWidget(self.label_cores, 0, 0, 1, 1)
-        self.label_vmax = QtGui.QLabel(self.gridLayoutWidget)
-        self.label_vmax.setObjectName("label_vmax")
-        self.gridLayout.addWidget(self.label_vmax, 2, 0, 1, 1)
-        self.label_vmin = QtGui.QLabel(self.gridLayoutWidget)
-        self.label_vmin.setObjectName("label_vmin")
-        self.gridLayout.addWidget(self.label_vmin, 1, 0, 1, 1)
-        self.lineEdit_ncores = QtGui.QLineEdit(self.gridLayoutWidget)
-        self.lineEdit_ncores.setObjectName("lineEdit_ncores")
-        self.gridLayout.addWidget(self.lineEdit_ncores, 0, 1, 1, 1)
-        self.lineEdit_vmin = QtGui.QLineEdit(self.gridLayoutWidget)
-        self.lineEdit_vmin.setObjectName("lineEdit_vmin")
-        self.gridLayout.addWidget(self.lineEdit_vmin, 1, 1, 1, 1)
-        self.lineEdit_vmax = QtGui.QLineEdit(self.gridLayoutWidget)
-        self.lineEdit_vmax.setObjectName("lineEdit_vmax")
-        self.gridLayout.addWidget(self.lineEdit_vmax, 2, 1, 1, 1)
-        self.checkBox = QtGui.QCheckBox(self.gridLayoutWidget)
-        self.checkBox.setObjectName("checkBox")
-        self.gridLayout.addWidget(self.checkBox, 4, 1, 1, 1)
-        self.label_folm = QtGui.QLabel(self.gridLayoutWidget)
-        self.label_folm.setObjectName("label_folm")
-        self.gridLayout.addWidget(self.label_folm, 3, 0, 1, 1)
-        self.label_aic = QtGui.QLabel(self.gridLayoutWidget)
-        self.label_aic.setObjectName("label_aic")
-        self.gridLayout.addWidget(self.label_aic, 4, 0, 1, 1)
-        self.lineEdit_folm = QtGui.QLineEdit(self.gridLayoutWidget)
-        self.lineEdit_folm.setObjectName("lineEdit_folm")
-        self.gridLayout.addWidget(self.lineEdit_folm, 3, 1, 1, 1)
-        self.label_aicwindow = QtGui.QLabel(self.gridLayoutWidget)
-        self.label_aicwindow.setObjectName("label_aicwindow")
-        self.gridLayout.addWidget(self.label_aicwindow, 5, 0, 1, 1)
-        self.lineEdit_aicwindow = QtGui.QLineEdit(self.gridLayoutWidget)
-        self.lineEdit_aicwindow.setObjectName("lineEdit_aicwindow")
-        self.gridLayout.addWidget(self.lineEdit_aicwindow, 5, 1, 1, 1)
-        self.buttonBox = QtGui.QDialogButtonBox(Picking_parameters)
-        self.buttonBox.setOrientation(QtCore.Qt.Horizontal)
-        self.buttonBox.setStandardButtons(QtGui.QDialogButtonBox.Cancel|QtGui.QDialogButtonBox.Ok)
-        self.buttonBox.setObjectName("buttonBox")
-        self.buttonBox.setGeometry(QtCore.QRect(10, 240, 250, 32))
-
-        QtCore.QObject.connect(self.buttonBox, QtCore.SIGNAL("accepted()"), Picking_parameters.accept)
-        QtCore.QObject.connect(self.buttonBox, QtCore.SIGNAL("rejected()"), Picking_parameters.reject)
-        self.retranslateUi(Picking_parameters)
-        QtCore.QMetaObject.connectSlotsByName(Picking_parameters)
-
-    def getParameters(self, Picking_parameters):
-        if Picking_parameters.exec_():
-            ncores = int(self.lineEdit_ncores.text())
-            vmin = float(self.lineEdit_vmin.text())
-            vmax = float(self.lineEdit_vmax.text())
-            folm = float(self.lineEdit_folm.text())
-            AIC = self.checkBox.isChecked()
-            aicwindow = [float(val) for val in self.lineEdit_aicwindow.text().split(',')]
-            
-            return ncores, vmin, vmax, folm, AIC, tuple(aicwindow)
-            
-    def retranslateUi(self, Picking_parameters):
-        Picking_parameters.setWindowTitle(QtGui.QApplication.translate("Picking_parameters", "Picking_parameters", None, QtGui.QApplication.UnicodeUTF8))
-        self.label_cores.setText(QtGui.QApplication.translate("Picking_parameters", "Number of cores", None, QtGui.QApplication.UnicodeUTF8))
-        self.label_vmax.setText(QtGui.QApplication.translate("Picking_parameters", "Vmax (default = 5000m/s)", None, QtGui.QApplication.UnicodeUTF8))
-        self.label_vmin.setText(QtGui.QApplication.translate("Picking_parameters", "Vmin (default = 333 m/s)", None, QtGui.QApplication.UnicodeUTF8))
-        self.lineEdit_ncores.setText(QtGui.QApplication.translate("Picking_parameters", "1", None, QtGui.QApplication.UnicodeUTF8))
-        self.lineEdit_vmin.setText(QtGui.QApplication.translate("Picking_parameters", "333", None, QtGui.QApplication.UnicodeUTF8))
-        self.lineEdit_vmax.setText(QtGui.QApplication.translate("Picking_parameters", "5000", None, QtGui.QApplication.UnicodeUTF8))
-        self.label_folm.setText(QtGui.QApplication.translate("Picking_parameters", "Fraction of local maximum\n"
-"(default = 0.6)", None, QtGui.QApplication.UnicodeUTF8))
-        self.label_aic.setText(QtGui.QApplication.translate("Picking_parameters", "AIC", None, QtGui.QApplication.UnicodeUTF8))
-        self.lineEdit_folm.setText(QtGui.QApplication.translate("Picking_parameters", "0.6", None, QtGui.QApplication.UnicodeUTF8))
-        self.label_aicwindow.setText(QtGui.QApplication.translate("Picking_parameters", "AIC window (only if AIC\n"
-" is checked)", None, QtGui.QApplication.UnicodeUTF8))
-        self.lineEdit_aicwindow.setText(QtGui.QApplication.translate("Picking_parameters", "15, 0", None, QtGui.QApplication.UnicodeUTF8))
-
-if __name__ == "__main__":
-    app = QtGui.QApplication(sys.argv)
-    MainWindow = QtGui.QMainWindow()
-    ui = Ui_ActiveSeismoPick3D()
-    ui.setupUi(MainWindow)
-    MainWindow.show()
-    sys.exit(app.exec_())
-
diff --git a/pylot/core/active/gui/__init__.py b/pylot/core/active/gui/__init__.py
new file mode 100644
index 00000000..aafb279b
--- /dev/null
+++ b/pylot/core/active/gui/__init__.py
@@ -0,0 +1,2 @@
+# -*- coding: utf-8 -*-
+__author__ = 'marcel'
diff --git a/pylot/core/active/asp3d_layout.py b/pylot/core/active/gui/asp3d_layout.py
similarity index 100%
rename from pylot/core/active/asp3d_layout.py
rename to pylot/core/active/gui/asp3d_layout.py
diff --git a/pylot/core/active/fmtomo_parameters_layout.py b/pylot/core/active/gui/fmtomo_parameters_layout.py
similarity index 100%
rename from pylot/core/active/fmtomo_parameters_layout.py
rename to pylot/core/active/gui/fmtomo_parameters_layout.py
diff --git a/pylot/core/active/generate_seisarray_layout.py b/pylot/core/active/gui/generate_seisarray_layout.py
similarity index 100%
rename from pylot/core/active/generate_seisarray_layout.py
rename to pylot/core/active/gui/generate_seisarray_layout.py
diff --git a/pylot/core/active/generate_survey_layout.py b/pylot/core/active/gui/generate_survey_layout.py
similarity index 100%
rename from pylot/core/active/generate_survey_layout.py
rename to pylot/core/active/gui/generate_survey_layout.py
diff --git a/pylot/core/active/generate_survey_layout_minimal.py b/pylot/core/active/gui/generate_survey_layout_minimal.py
similarity index 100%
rename from pylot/core/active/generate_survey_layout_minimal.py
rename to pylot/core/active/gui/generate_survey_layout_minimal.py
diff --git a/pylot/core/active/picking_parameters_layout.py b/pylot/core/active/gui/picking_parameters_layout.py
similarity index 100%
rename from pylot/core/active/picking_parameters_layout.py
rename to pylot/core/active/gui/picking_parameters_layout.py
diff --git a/pylot/core/active/vtk_tools_layout.py b/pylot/core/active/gui/vtk_tools_layout.py
similarity index 100%
rename from pylot/core/active/vtk_tools_layout.py
rename to pylot/core/active/gui/vtk_tools_layout.py
diff --git a/pylot/core/active/gui/windows.py b/pylot/core/active/gui/windows.py
new file mode 100644
index 00000000..207e2deb
--- /dev/null
+++ b/pylot/core/active/gui/windows.py
@@ -0,0 +1,347 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+from PySide import QtCore, QtGui
+from generate_survey_layout import *
+from generate_survey_layout_minimal import *
+from generate_seisarray_layout import *
+from pylot.core.active.gui.picking_parameters_layout import *
+from pylot.core.active import surveyUtils
+
+import numpy as np
+import matplotlib
+matplotlib.use('Qt4Agg')
+matplotlib.rcParams['backend.qt4']='PySide'
+
+from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
+from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
+from matplotlib.figure import Figure
+
+def getMaxCPU():
+    import multiprocessing
+    return multiprocessing.cpu_count()
+
+class Gen_SeisArray(object):
+    def __init__(self, mainwindow):
+        self.mainwindow = mainwindow
+        self.seisarray = None
+        self.srcfile = None
+        self.recfile = None
+        self.ptsfile = None
+        self.init_dialog()
+        self.start_dialog()
+
+    def init_dialog(self):
+        qdialog = QtGui.QDialog(self.mainwindow)
+        ui = Ui_generate_seisarray()
+        ui.setupUi(qdialog)
+        self.ui = ui
+        self.qdialog = qdialog
+        self.connectButtons()
+
+    def start_dialog(self):
+        self.init_last_selection()
+        if self.qdialog.exec_():
+            self.refresh_filenames()
+            if self.ui.radioButton_interpolatable.isChecked():
+                self.seisarray = seismicArrayPreparation.SeisArray(self.recfile, True)
+            elif self.ui.radioButton_normal.isChecked():
+                self.seisarray = seismicArrayPreparation.SeisArray(self.recfile, False)
+            if len(self.srcfile) > 0:
+                self.seisarray.addSourceLocations(self.srcfile)
+            if len(self.ptsfile) > 0:
+                self.seisarray.addMeasuredTopographyPoints(self.ptsfile)
+            self.executed = True
+        else:
+            self.refresh_filenames()
+            self.executed = False
+
+    def refresh_filenames(self):
+        self.srcfile = self.ui.lineEdit_src.text()
+        self.recfile = self.ui.lineEdit_rec.text()
+        self.ptsfile = self.ui.lineEdit_pts.text()
+
+    def init_last_selection(self):
+        self.ui.lineEdit_src.setText(self.srcfile)
+        self.ui.lineEdit_rec.setText(self.recfile)
+        self.ui.lineEdit_pts.setText(self.ptsfile)
+
+    def get_seisarray(self):
+        if self.seisarray is not None:
+            return self.seisarray
+
+    def connectButtons(self):
+        QtCore.QObject.connect(self.ui.pushButton_rec, QtCore.SIGNAL("clicked()"), self.chooseMeasuredRec)
+        QtCore.QObject.connect(self.ui.pushButton_src, QtCore.SIGNAL("clicked()"), self.chooseMeasuredSrc)
+        QtCore.QObject.connect(self.ui.pushButton_obs, QtCore.SIGNAL("clicked()"), self.chooseMeasuredPts)
+
+    def chooseMeasuredSrc(self):
+        self.ui.lineEdit_src.setText(openFile('Open measured sources file.'))
+
+    def chooseMeasuredRec(self):
+        self.ui.lineEdit_rec.setText(openFile('Open measured receivers file.'))
+
+    def chooseMeasuredPts(self):
+        self.ui.lineEdit_pts.setText(openFile('Open measured points file.'))
+
+
+
+class Gen_Survey_from_SA(object):
+    def __init__(self, mainwindow, seisarray):
+        self.mainwindow = mainwindow
+        self.seisarray = seisarray
+        self.survey = None
+        self.obsdir = None
+        self.fstart = 'shot'
+        self.fend = '.dat'
+        self.init_dialog()
+        self.start_dialog()
+
+    def init_dialog(self):
+        qdialog = QtGui.QDialog(self.mainwindow)
+        ui = Ui_generate_survey_minimal()
+        ui.setupUi(qdialog)
+        self.ui = ui
+        self.qdialog = qdialog
+        self.connectButtons()
+
+    def start_dialog(self):
+        self.init_last_selection()
+        if self.qdialog.exec_():
+            self.refresh_filenames()
+            self.survey = activeSeismoPick.Survey(self.obsdir, seisArray = self.seisarray,
+                                                  useDefaultParas = True, fstart = self.fstart,
+                                                  fend = self.fend)
+            self.executed = True
+        else:
+            self.refresh_filenames()
+            self.executed = False
+
+    def refresh_filenames(self):
+        self.obsdir = self.ui.lineEdit_obs.text()
+        self.fstart = self.ui.fstart.text()
+        self.fend = self.ui.fend.text()
+
+    def init_last_selection(self):
+        self.ui.lineEdit_obs.setText(self.obsdir)
+        self.ui.fstart.setText(self.fstart)
+        self.ui.fend.setText(self.fend)
+
+    def get_survey(self):
+        return self.survey
+
+    def connectButtons(self):
+        QtCore.QObject.connect(self.ui.pushButton_obs, QtCore.SIGNAL("clicked()"), self.chooseObsdir)
+
+    def chooseObsdir(self):
+        self.ui.lineEdit_obs.setText(browseDir('Choose observation directory.'))
+
+
+class Gen_Survey_from_SR(object):
+    def __init__(self, mainwindow):
+        self.mainwindow = mainwindow
+        self.survey = None
+        self.obsdir = None
+        self.srcfile = None
+        self.recfile = None
+        self.fstart = 'shot'
+        self.fend = '.dat'
+        self.init_dialog()
+        self.start_dialog()
+
+    def init_dialog(self):
+        qdialog = QtGui.QDialog(self.mainwindow)
+        ui = Ui_generate_survey()
+        ui.setupUi(qdialog)
+        self.ui = ui
+        self.qdialog = qdialog
+        self.connectButtons()
+
+    def start_dialog(self):
+        self.init_last_selection()
+        if self.qdialog.exec_():
+            self.refresh_filenames()
+            self.survey = activeSeismoPick.Survey(self.obsdir, self.srcfile, self.recfile,
+                                                  useDefaultParas = True,
+                                                  fstart = self.fstart, fend = self.fend)
+            self.executed = True
+        else:
+            self.refresh_filenames()
+            self.executed = False
+
+    def refresh_filenames(self):
+        self.obsdir = self.ui.lineEdit_obs.text()
+        self.srcfile = self.ui.lineEdit_src.text()
+        self.recfile = self.ui.lineEdit_rec.text()
+        self.fstart = self.ui.fstart.text()
+        self.fend = self.ui.fend.text()
+
+    def init_last_selection(self):
+        self.ui.lineEdit_obs.setText(self.obsdir)
+        self.ui.lineEdit_src.setText(self.srcfile)
+        self.ui.lineEdit_rec.setText(self.recfile)
+        self.ui.fstart.setText(self.fstart)
+        self.ui.fend.setText(self.fend)
+
+    def get_survey(self):
+        return self.survey
+
+    def connectButtons(self):
+        QtCore.QObject.connect(self.ui.pushButton_obs, QtCore.SIGNAL("clicked()"), self.chooseObsdir)
+        QtCore.QObject.connect(self.ui.pushButton_src, QtCore.SIGNAL("clicked()"), self.chooseSourcefile)
+        QtCore.QObject.connect(self.ui.pushButton_rec, QtCore.SIGNAL("clicked()"), self.chooseRecfile)
+
+    def chooseObsdir(self):
+        self.ui.lineEdit_obs.setText(browseDir('Choose observation directory.'))
+
+    def chooseSourcefile(self):
+        self.ui.lineEdit_src.setText(openFile('Open sourcefile.'))
+
+    def chooseRecfile(self):
+        self.ui.lineEdit_rec.setText(openFile('Open receiverfile.'))
+
+
+
+class Call_autopicker(object):
+    def __init__(self, mainwindow, survey):
+        self.mainwindow = mainwindow
+        self.survey = survey
+        self.maxSRdist = None
+        self.init_dialog()
+        self.refresh_selection()                                        
+        self.start_dialog()
+        
+    def init_dialog(self):
+        qdialog = QtGui.QDialog(self.mainwindow)
+        ui = Ui_picking_parameters()
+        ui.setupUi(qdialog)
+        ui.ncores.setMaximum(getMaxCPU())
+        self.ui = ui
+        self.qdialog = qdialog
+        self.initDynSNRplot()
+        self.connectButtons()
+
+    def getMaxSRdist(self):
+        if self.maxSRdist is not None:
+            return self.maxSRdist
+        else:
+            SRdists = []
+            for shot in self.survey.data.values():
+                for traceID in shot.getTraceIDlist():
+                    SRdists.append(shot.getDistance(traceID))
+            self.maxSRdist = max(SRdists)
+            return self.maxSRdist
+        
+    def initDynSNRplot(self):
+        self.snrFig = Figure()
+        self.snrCanvas = FigureCanvas(self.snrFig)
+        self.ui.vlayout_plot.addWidget(self.snrCanvas)
+        self.snrToolbar = NavigationToolbar(self.snrCanvas, self.mainwindow)
+        self.ui.vlayout_plot.addWidget(self.snrToolbar)
+
+    def plotDynSNR(self):
+        fig = self.snrFig
+        if fig.axes == []:
+            ax = fig.add_subplot(111)
+            xlim = None
+            ylim = None
+        else:
+            ax = fig.axes[0]
+            xlim = ax.get_xlim()
+            ylim = ax.get_ylim()
+        ax.clear()
+        snrthresholds = []
+        dists_p = []; snr_p = []
+        shiftSNR = float(self.ui.shift_snr.value())
+        shiftDist = float(self.ui.shift_dist.value())
+        p1 = float(self.ui.p1.value())
+        p2 = float(self.ui.p2.value())
+        dists = np.arange(0, self.getMaxSRdist() + 1, 1)
+        if self.survey.picked:
+            for shot in self.survey.data.values():
+                for traceID in shot.getTraceIDlist():
+                    dists_p.append(shot.getDistance(traceID))
+                    snr_p.append(shot.getSNR(traceID)[0])
+
+            ax.scatter(dists_p, snr_p, s = 0.5, c='k')
+            
+        for dist in dists:
+            dist += shiftDist
+            snrthresholds.append(surveyUtils.snr_fit_func(surveyUtils.get_fit_fn(p1, p2), dist, shiftSNR))
+        ax.plot(dists, snrthresholds)
+        ax.set_xlabel('Distance [m]')
+        ax.set_ylabel('SNR')
+        ax.set_xlim(xlim)
+        ax.set_ylim(ylim)
+        self.snrCanvas.draw()
+
+    def start_dialog(self):
+        self.init_last_selection()
+        self.plotDynSNR()
+        if self.qdialog.exec_():
+            self.refresh_selection()
+
+            if self.AIC == True:
+                HosAic = 'aic'
+            else:
+                HosAic = 'hos'
+
+            surveyUtils.setDynamicFittedSNR(self.survey.getShotDict(), shiftdist = self.shiftDist,
+                                            shiftSNR = self.shiftSNR, p1 = self.p1, p2 = self.p2)
+
+            self.survey.pickAllShots(vmin = self.vmin, vmax = self.vmax,
+                                     folm = self.folm/100., HosAic = HosAic,
+                                     aicwindow = self.aicwindow, cores = self.ncores)
+            
+            #QtGui.qApp.processEvents() # test
+            self.executed = True
+        else:
+            self.refresh_selection()
+            self.executed = False
+
+    def refreshFolm(self):
+        self.ui.label_folm.setText('%s %%'%self.ui.slider_folm.value())
+
+    def refresh_selection(self):
+        self.ncores = int(self.ui.ncores.value())
+        self.vmin = float(self.ui.lineEdit_vmin.text())
+        self.vmax = float(self.ui.lineEdit_vmax.text())
+        self.folm = float(self.ui.slider_folm.value())
+        self.AIC = self.ui.checkBox_AIC.isChecked()
+        self.aicwindow = (int(self.ui.lineEdit_aicleft.text()), int(self.ui.lineEdit_aicright.text()))
+        self.shiftSNR = float(self.ui.shift_snr.value())
+        self.shiftDist = float(self.ui.shift_dist.value())
+        self.p1 = float(self.ui.p1.value())
+        self.p2 = float(self.ui.p2.value())
+
+    def init_last_selection(self):
+        self.ui.ncores.setValue(self.ncores)
+        self.ui.lineEdit_vmin.setText(str(self.vmin))
+        self.ui.lineEdit_vmax.setText(str(self.vmax))
+        self.ui.slider_folm.setValue(self.folm)
+        self.ui.checkBox_AIC.setChecked(self.AIC)
+        self.ui.lineEdit_aicleft.setText(str(self.aicwindow[0]))
+        self.ui.lineEdit_aicright.setText(str(self.aicwindow[1]))
+        self.ui.shift_snr.setValue(self.shiftSNR)
+        self.ui.shift_snr.setValue(self.shiftDist)
+        self.ui.p1.setValue(self.p1)
+        self.ui.p2.setValue(self.p2)
+
+    def get_survey(self):
+        return self.survey
+
+    def connectButtons(self):
+        QtCore.QObject.connect(self.ui.slider_folm, QtCore.SIGNAL("valueChanged(int)"), self.refreshFolm)
+        QtCore.QObject.connect(self.ui.shift_snr, QtCore.SIGNAL("valueChanged(int)"), self.plotDynSNR)
+        QtCore.QObject.connect(self.ui.shift_dist, QtCore.SIGNAL("valueChanged(int)"), self.plotDynSNR)
+        QtCore.QObject.connect(self.ui.p1, QtCore.SIGNAL("valueChanged(double)"), self.plotDynSNR)
+        QtCore.QObject.connect(self.ui.p2, QtCore.SIGNAL("valueChanged(double)"), self.plotDynSNR)
+
+    def chooseObsdir(self):
+        self.ui.lineEdit_obs.setText(browseDir('Choose observation directory.'))
+
+    def chooseSourcefile(self):
+        self.ui.lineEdit_src.setText(openFile('Open sourcefile.'))
+
+    def chooseRecfile(self):
+        self.ui.lineEdit_rec.setText(openFile('Open receiverfile.'))
+
diff --git a/pylot/core/active/seismicArrayPreparation.py b/pylot/core/active/seismicArrayPreparation.py
index 40b6a174..976c37f3 100644
--- a/pylot/core/active/seismicArrayPreparation.py
+++ b/pylot/core/active/seismicArrayPreparation.py
@@ -507,7 +507,7 @@ class SeisArray(object):
             self.surface2VTK(interf2, filename='interface2.vtk')
             self.receivers2VTK()
             self.sources2VTK()
-            fmtomoUtils.vgrids2VTK()
+            #fmtomoUtils.vgrids2VTK()
 
     def generateReceiversIn(self, outfilename='receivers.in'):
         outfile = open(outfilename, 'w')

From 987ee597fd4d7e50c7514bd327fdad80d279f2d7 Mon Sep 17 00:00:00 2001
From: Marcel Paffrath <marcel.paffrath@rub.de>
Date: Wed, 27 Jul 2016 11:12:27 +0200
Subject: [PATCH 6/9] Release version modified!?!?

---
 pylot/RELEASE-VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pylot/RELEASE-VERSION b/pylot/RELEASE-VERSION
index e760bf7c..30ada269 100644
--- a/pylot/RELEASE-VERSION
+++ b/pylot/RELEASE-VERSION
@@ -1 +1 @@
-8714-dirty
+55a58-dirty

From 8bd9f7debc564dd021b657adb0eb377866b22122 Mon Sep 17 00:00:00 2001
From: Marcel Paffrath <marcel.paffrath@rub.de>
Date: Wed, 27 Jul 2016 11:13:20 +0200
Subject: [PATCH 7/9] rename

---
 pylot/core/active/{control_script.py => run_asp3d.py} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename pylot/core/active/{control_script.py => run_asp3d.py} (100%)

diff --git a/pylot/core/active/control_script.py b/pylot/core/active/run_asp3d.py
similarity index 100%
rename from pylot/core/active/control_script.py
rename to pylot/core/active/run_asp3d.py

From adfe9cc02747803c516cfc9abf88abd07abb1cd5 Mon Sep 17 00:00:00 2001
From: Marcel Paffrath <marcel.paffrath@rub.de>
Date: Wed, 27 Jul 2016 13:46:42 +0200
Subject: [PATCH 8/9] bugfixes

---
 pylot/core/active/ActiveSeismoPick3D_GUI.py   | 34 +++----------------
 pylot/core/active/gui/asp3d_layout.py         |  6 ++--
 .../active/gui/fmtomo_parameters_layout.py    |  4 +--
 .../active/gui/generate_seisarray_layout.py   |  2 +-
 .../core/active/gui/generate_survey_layout.py |  2 +-
 .../gui/generate_survey_layout_minimal.py     |  2 +-
 .../active/gui/picking_parameters_layout.py   |  6 ++--
 pylot/core/active/gui/vtk_tools_layout.py     |  2 +-
 pylot/core/active/gui/windows.py              | 25 ++++++++++++--
 9 files changed, 39 insertions(+), 44 deletions(-)

diff --git a/pylot/core/active/ActiveSeismoPick3D_GUI.py b/pylot/core/active/ActiveSeismoPick3D_GUI.py
index 5074f479..49aa6ed4 100755
--- a/pylot/core/active/ActiveSeismoPick3D_GUI.py
+++ b/pylot/core/active/ActiveSeismoPick3D_GUI.py
@@ -7,38 +7,18 @@ matplotlib.use('Qt4Agg')
 matplotlib.rcParams['backend.qt4']='PySide'
 
 from PySide import QtCore, QtGui
+from pylot.core.active import activeSeismoPick, surveyUtils, fmtomoUtils, seismicArrayPreparation
 from pylot.core.active.gui.asp3d_layout import *
 from pylot.core.active.gui.fmtomo_parameters_layout import *
 from pylot.core.active.gui.vtk_tools_layout import *
 from pylot.core.active.gui.windows import Gen_SeisArray, Gen_Survey_from_SA, Gen_Survey_from_SR, Call_autopicker
-from pylot.core.active import activeSeismoPick, surveyUtils, fmtomoUtils, seismicArrayPreparation
+from pylot.core.active.gui.windows import openFile, saveFile, browseDir, getMaxCPU
 
 from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
 from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
 import matplotlib.pyplot as plt
 from matplotlib.figure import Figure
 
-def openFile(name = 'Open'):
-    dialog = QtGui.QFileDialog()
-    dialog.setWindowTitle(name)                #not working yet
-    filename = dialog.getOpenFileName()
-    if len(filename[0]) > 0:
-        return filename[0]
-
-def saveFile(name = 'Save'):
-    dialog = QtGui.QFileDialog()
-    dialog.setWindowTitle(name)
-    filename = dialog.getSaveFileName()
-    if len(filename[0]) > 0:
-        return filename[0]
-
-def browseDir(name = 'Open Directory'):
-    dialog = QtGui.QFileDialog()
-    dialog.setWindowTitle(name)
-    directory = dialog.getExistingDirectory()
-    if len(directory) > 0:
-        return directory
-
 class gui_control(object):
     def __init__(self):
         self.mainwindow = MainWindow
@@ -140,9 +120,8 @@ class gui_control(object):
             self.survey = self.gssr.get_survey()
             self.seisarray = self.survey.seisarray
             self.initNewSurvey()
+            self.setSeisArrayState(True)
             self.setConnected2SurveyState(True)
-            self.setPickState(False)
-
 
 
     def initNewSurvey(self):
@@ -352,11 +331,6 @@ class gui_control(object):
         print('Connected Seismic Array to active Survey object.')
 
 
-    def getMaxCPU(self): ### OLD
-        import multiprocessing
-        return multiprocessing.cpu_count()
-
-
     def callPicker(self):
         if not self.checkSurveyState():
             self.printDialogMessage('No Survey defined.')
@@ -385,7 +359,7 @@ class gui_control(object):
         fmtomo_parameters = QtGui.QDialog(self.mainwindow)
         ui = Ui_fmtomo_parameters()
         ui.setupUi(fmtomo_parameters)                
-        ui.nproc.setMaximum(self.getMaxCPU())
+        ui.nproc.setMaximum(getMaxCPU())
 
         self.fmtomo_parameters_ui = ui
         self.connectButtons_startFMTOMO()
diff --git a/pylot/core/active/gui/asp3d_layout.py b/pylot/core/active/gui/asp3d_layout.py
index b74ac231..f958fdee 100644
--- a/pylot/core/active/gui/asp3d_layout.py
+++ b/pylot/core/active/gui/asp3d_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'asp3d_layout.ui'
 #
-# Created: Mon Jul 18 11:26:32 2016
+# Created: Wed Jul 27 11:15:05 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
@@ -354,7 +354,7 @@ class Ui_MainWindow(object):
         self.label_3.setText(QtGui.QApplication.translate("MainWindow", "Survey", None, QtGui.QApplication.UnicodeUTF8))
         self.label_4.setText(QtGui.QApplication.translate("MainWindow", "active", None, QtGui.QApplication.UnicodeUTF8))
         self.label.setText(QtGui.QApplication.translate("MainWindow", "picked", None, QtGui.QApplication.UnicodeUTF8))
-        self.label_11.setText(QtGui.QApplication.translate("MainWindow", "Plot Receiver and Shots of the Array colord by:", None, QtGui.QApplication.UnicodeUTF8))
+        self.label_11.setText(QtGui.QApplication.translate("MainWindow", "Plot Receiver and Shots of the Array colored by:", None, QtGui.QApplication.UnicodeUTF8))
         self.label_10.setText(QtGui.QApplication.translate("MainWindow", "Plot a single Shot:", None, QtGui.QApplication.UnicodeUTF8))
         self.shot_left.setText(QtGui.QApplication.translate("MainWindow", "<", None, QtGui.QApplication.UnicodeUTF8))
         self.shot_right.setText(QtGui.QApplication.translate("MainWindow", ">", None, QtGui.QApplication.UnicodeUTF8))
@@ -363,7 +363,7 @@ class Ui_MainWindow(object):
         self.menuSeismic_Array.setTitle(QtGui.QApplication.translate("MainWindow", "Seismic Array", None, QtGui.QApplication.UnicodeUTF8))
         self.menuSurvey.setTitle(QtGui.QApplication.translate("MainWindow", "Survey", None, QtGui.QApplication.UnicodeUTF8))
         self.menuPicking.setTitle(QtGui.QApplication.translate("MainWindow", "Picking", None, QtGui.QApplication.UnicodeUTF8))
-        self.menuSimulation.setTitle(QtGui.QApplication.translate("MainWindow", "Simulation", None, QtGui.QApplication.UnicodeUTF8))
+        self.menuSimulation.setTitle(QtGui.QApplication.translate("MainWindow", "Inversion", None, QtGui.QApplication.UnicodeUTF8))
         self.menuTools.setTitle(QtGui.QApplication.translate("MainWindow", "Tools", None, QtGui.QApplication.UnicodeUTF8))
         self.actionLoad_Seismic_Array.setText(QtGui.QApplication.translate("MainWindow", "Load Seismic Array", None, QtGui.QApplication.UnicodeUTF8))
         self.actionSave_Seismic_Array.setText(QtGui.QApplication.translate("MainWindow", "Save Seismic Array", None, QtGui.QApplication.UnicodeUTF8))
diff --git a/pylot/core/active/gui/fmtomo_parameters_layout.py b/pylot/core/active/gui/fmtomo_parameters_layout.py
index 9151d4ad..59db2dc4 100644
--- a/pylot/core/active/gui/fmtomo_parameters_layout.py
+++ b/pylot/core/active/gui/fmtomo_parameters_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'fmtomo_parameters_layout.ui'
 #
-# Created: Mon Jul 18 11:26:32 2016
+# Created: Wed Jul 27 11:15:05 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
@@ -270,7 +270,7 @@ class Ui_fmtomo_parameters(object):
 "Too low values will cause error.", None, QtGui.QApplication.UnicodeUTF8))
         self.label_13.setText(QtGui.QApplication.translate("fmtomo_parameters", "Cushion factor [?]", None, QtGui.QApplication.UnicodeUTF8))
         self.label_12.setText(QtGui.QApplication.translate("fmtomo_parameters", "%", None, QtGui.QApplication.UnicodeUTF8))
-        self.label_4.setText(QtGui.QApplication.translate("fmtomo_parameters", "Number of Ponts", None, QtGui.QApplication.UnicodeUTF8))
+        self.label_4.setText(QtGui.QApplication.translate("fmtomo_parameters", "Number of Points", None, QtGui.QApplication.UnicodeUTF8))
         self.label_5.setText(QtGui.QApplication.translate("fmtomo_parameters", "X", None, QtGui.QApplication.UnicodeUTF8))
         self.label_6.setText(QtGui.QApplication.translate("fmtomo_parameters", "Y", None, QtGui.QApplication.UnicodeUTF8))
         self.label_7.setText(QtGui.QApplication.translate("fmtomo_parameters", "Z", None, QtGui.QApplication.UnicodeUTF8))
diff --git a/pylot/core/active/gui/generate_seisarray_layout.py b/pylot/core/active/gui/generate_seisarray_layout.py
index 79a614aa..3116febb 100644
--- a/pylot/core/active/gui/generate_seisarray_layout.py
+++ b/pylot/core/active/gui/generate_seisarray_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'generate_seisarray_layout.ui'
 #
-# Created: Mon Jul 18 11:26:32 2016
+# Created: Wed Jul 27 11:15:06 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
diff --git a/pylot/core/active/gui/generate_survey_layout.py b/pylot/core/active/gui/generate_survey_layout.py
index a4f1312f..cdfbb769 100644
--- a/pylot/core/active/gui/generate_survey_layout.py
+++ b/pylot/core/active/gui/generate_survey_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'generate_survey_layout.ui'
 #
-# Created: Mon Jul 18 11:26:32 2016
+# Created: Wed Jul 27 11:15:06 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
diff --git a/pylot/core/active/gui/generate_survey_layout_minimal.py b/pylot/core/active/gui/generate_survey_layout_minimal.py
index 97d8d3d7..34939458 100644
--- a/pylot/core/active/gui/generate_survey_layout_minimal.py
+++ b/pylot/core/active/gui/generate_survey_layout_minimal.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'generate_survey_layout_minimal.ui'
 #
-# Created: Mon Jul 18 11:26:33 2016
+# Created: Wed Jul 27 11:15:06 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
diff --git a/pylot/core/active/gui/picking_parameters_layout.py b/pylot/core/active/gui/picking_parameters_layout.py
index 43405994..272dd630 100644
--- a/pylot/core/active/gui/picking_parameters_layout.py
+++ b/pylot/core/active/gui/picking_parameters_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'picking_parameters_layout.ui'
 #
-# Created: Mon Jul 18 11:26:33 2016
+# Created: Wed Jul 27 11:15:06 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
@@ -12,8 +12,8 @@ from PySide import QtCore, QtGui
 class Ui_picking_parameters(object):
     def setupUi(self, picking_parameters):
         picking_parameters.setObjectName("picking_parameters")
-        picking_parameters.resize(400, 550)
-        picking_parameters.setMinimumSize(QtCore.QSize(0, 550))
+        picking_parameters.resize(400, 700)
+        picking_parameters.setMinimumSize(QtCore.QSize(0, 700))
         self.verticalLayout_4 = QtGui.QVBoxLayout(picking_parameters)
         self.verticalLayout_4.setObjectName("verticalLayout_4")
         self.label_7 = QtGui.QLabel(picking_parameters)
diff --git a/pylot/core/active/gui/vtk_tools_layout.py b/pylot/core/active/gui/vtk_tools_layout.py
index fb90795f..3bef8448 100644
--- a/pylot/core/active/gui/vtk_tools_layout.py
+++ b/pylot/core/active/gui/vtk_tools_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'vtk_tools_layout.ui'
 #
-# Created: Mon Jul 18 11:26:33 2016
+# Created: Wed Jul 27 11:15:06 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
diff --git a/pylot/core/active/gui/windows.py b/pylot/core/active/gui/windows.py
index 207e2deb..ffba7efd 100644
--- a/pylot/core/active/gui/windows.py
+++ b/pylot/core/active/gui/windows.py
@@ -1,11 +1,11 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 from PySide import QtCore, QtGui
+from pylot.core.active import surveyUtils, activeSeismoPick, seismicArrayPreparation
 from generate_survey_layout import *
 from generate_survey_layout_minimal import *
 from generate_seisarray_layout import *
-from pylot.core.active.gui.picking_parameters_layout import *
-from pylot.core.active import surveyUtils
+from picking_parameters_layout import *
 
 import numpy as np
 import matplotlib
@@ -16,6 +16,27 @@ from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
 from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
 from matplotlib.figure import Figure
 
+def openFile(name = 'Open'):
+    dialog = QtGui.QFileDialog()
+    dialog.setWindowTitle(name)                #not working yet
+    filename = dialog.getOpenFileName()
+    if len(filename[0]) > 0:
+        return filename[0]
+
+def saveFile(name = 'Save'):
+    dialog = QtGui.QFileDialog()
+    dialog.setWindowTitle(name)
+    filename = dialog.getSaveFileName()
+    if len(filename[0]) > 0:
+        return filename[0]
+
+def browseDir(name = 'Open Directory'):
+    dialog = QtGui.QFileDialog()
+    dialog.setWindowTitle(name)
+    directory = dialog.getExistingDirectory()
+    if len(directory) > 0:
+        return directory
+
 def getMaxCPU():
     import multiprocessing
     return multiprocessing.cpu_count()

From 638f552d6dbb91c0168eb249c3c1292048ebdf9b Mon Sep 17 00:00:00 2001
From: Marcel Paffrath <marcel.paffrath@rub.de>
Date: Wed, 27 Jul 2016 14:42:11 +0200
Subject: [PATCH 9/9] changed structure of callFMTOMO to class

---
 pylot/core/active/ActiveSeismoPick3D_GUI.py |  79 ++----------
 pylot/core/active/gui/windows.py            | 126 +++++++++++++++++---
 2 files changed, 122 insertions(+), 83 deletions(-)

diff --git a/pylot/core/active/ActiveSeismoPick3D_GUI.py b/pylot/core/active/ActiveSeismoPick3D_GUI.py
index 49aa6ed4..558fddc8 100755
--- a/pylot/core/active/ActiveSeismoPick3D_GUI.py
+++ b/pylot/core/active/ActiveSeismoPick3D_GUI.py
@@ -9,9 +9,8 @@ matplotlib.rcParams['backend.qt4']='PySide'
 from PySide import QtCore, QtGui
 from pylot.core.active import activeSeismoPick, surveyUtils, fmtomoUtils, seismicArrayPreparation
 from pylot.core.active.gui.asp3d_layout import *
-from pylot.core.active.gui.fmtomo_parameters_layout import *
 from pylot.core.active.gui.vtk_tools_layout import *
-from pylot.core.active.gui.windows import Gen_SeisArray, Gen_Survey_from_SA, Gen_Survey_from_SR, Call_autopicker
+from pylot.core.active.gui.windows import Gen_SeisArray, Gen_Survey_from_SA, Gen_Survey_from_SR, Call_autopicker, Call_FMTOMO
 from pylot.core.active.gui.windows import openFile, saveFile, browseDir, getMaxCPU
 
 from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
@@ -36,10 +35,14 @@ class gui_control(object):
         self.mainUI.progressBar.setVisible(False)
         self.printSurveyTextbox()
         self.printSeisArrayTextbox()
+        self.initWindowObjects()
+
+    def initWindowObjects(self):
         self.gsa = None
         self.gssa = None
         self.gssr = None
         self.autopicker = None
+        self.fmtomo = None
 
     def setInitStates(self):
         self.setPickState(False)
@@ -56,7 +59,7 @@ class gui_control(object):
         QtCore.QObject.connect(self.mainUI.actionConnect_to_Survey, QtCore.SIGNAL("triggered()"), self.connect2Survey)
         QtCore.QObject.connect(self.mainUI.actionInterpolate_Receivers, QtCore.SIGNAL("triggered()"), self.interpolate_receivers)
         QtCore.QObject.connect(self.mainUI.actionGenerate_new_Survey, QtCore.SIGNAL("triggered()"), self.gen_survey)
-        QtCore.QObject.connect(self.mainUI.actionAutomatic_Picking, QtCore.SIGNAL("triggered()"), self.callPicker)
+        QtCore.QObject.connect(self.mainUI.actionAutomatic_Picking, QtCore.SIGNAL("triggered()"), self.startPicker)
         QtCore.QObject.connect(self.mainUI.actionPostprocessing, QtCore.SIGNAL("triggered()"), self.postprocessing)
         QtCore.QObject.connect(self.mainUI.actionStart_FMTOMO_Simulation, QtCore.SIGNAL("triggered()"), self.startFMTOMO)
         QtCore.QObject.connect(self.mainUI.actionVTK_Visualization, QtCore.SIGNAL("triggered()"), self.startVTKtools)
@@ -331,7 +334,7 @@ class gui_control(object):
         print('Connected Seismic Array to active Survey object.')
 
 
-    def callPicker(self):
+    def startPicker(self):
         if not self.checkSurveyState():
             self.printDialogMessage('No Survey defined.')
             return
@@ -356,15 +359,14 @@ class gui_control(object):
         if not self.checkPickState():
             self.printDialogMessage('Survey not picked.')
             return
-        fmtomo_parameters = QtGui.QDialog(self.mainwindow)
-        ui = Ui_fmtomo_parameters()
-        ui.setupUi(fmtomo_parameters)                
-        ui.nproc.setMaximum(getMaxCPU())
 
-        self.fmtomo_parameters_ui = ui
-        self.connectButtons_startFMTOMO()
-        self.getFMTOMOparameters(ui, fmtomo_parameters)
+        if self.fmtomo is None:
+            self.fmtomo = Call_FMTOMO(self.mainwindow, self.survey)
+        else:
+            self.fmtomo.start_dialog()
 
+        #if self.fmtomo.executed:
+        
 
     def startVTKtools(self):
         vtk_tools = QtGui.QDialog(self.mainwindow)
@@ -380,45 +382,6 @@ class gui_control(object):
         vtk_tools.exec_()
 
 
-    def getFMTOMOparameters(self, ui, fmtomo_parameters):
-        if fmtomo_parameters.exec_():
-            fmtomo_dir = ui.fmtomo_dir.text()
-            nIter = int(ui.nIter.value())
-            nproc = int(ui.nproc.value())
-            btop = float(ui.btop.text())
-            bbot = float(ui.bbot.text())
-            propgrid = (int(ui.pgrid_x.text()), int(ui.pgrid_y.text()), int(ui.pgrid_z.text()))
-            vgrid = (int(ui.invgrid_x.text()), int(ui.invgrid_y.text()), int(ui.invgrid_z.text()))
-            cushionfactor = float(ui.cushion.text())/100.
-            customgrid = ui.customgrid.text()
-            simuldir = ui.simuldir.text()
-            picks_dir = os.path.join(simuldir, 'picks')
-
-            if not os.path.isdir(picks_dir):
-                err = os.mkdir(picks_dir)
-
-            self.survey.exportFMTOMO(picks_dir)
-
-            cwd = os.getcwd()
-            interpolationMethod = 'linear'
-            os.chdir(simuldir)
-            if self.seisarray.twoDim:
-                interpolationMethod = 'nearest'
-            self.survey.seisarray.generateFMTOMOinputFromArray(propgrid, vgrid, (bbot, btop), cushionfactor,
-                                                          interpolationMethod, customgrid = customgrid,
-                                                          writeVTK = True)
-            os.chdir(cwd)
-
-            tomo = fmtomoUtils.Tomo3d(fmtomo_dir, simuldir)
-            tomo.runTOMO3D(nproc, nIter)
-
-                            
-    def connectButtons_startFMTOMO(self):
-        QtCore.QObject.connect(self.fmtomo_parameters_ui.browse_tomodir, QtCore.SIGNAL("clicked()"), self.chooseFMTOMOdir)
-        QtCore.QObject.connect(self.fmtomo_parameters_ui.browse_customgrid, QtCore.SIGNAL("clicked()"), self.chooseCustomgrid)
-        QtCore.QObject.connect(self.fmtomo_parameters_ui.browse_simuldir, QtCore.SIGNAL("clicked()"), self.chooseSimuldir)
-
-
     def connectButtons_vtk_tools(self):
         QtCore.QObject.connect(self.vtk_tools_ui.pushButton_vg, QtCore.SIGNAL("clicked()"), self.chooseVgrid)
         QtCore.QObject.connect(self.vtk_tools_ui.pushButton_vgref, QtCore.SIGNAL("clicked()"), self.chooseVgridref)
@@ -513,22 +476,6 @@ class gui_control(object):
         self.vtk_tools_ui.lineEdit_vgout.setText(saveFile())
 
 
-    def chooseFMTOMOdir(self):
-        self.fmtomo_parameters_ui.fmtomo_dir.setText(browseDir())
-
-
-    def chooseCustomgrid(self):
-        self.fmtomo_parameters_ui.customgrid.setText(openFile())
-
-
-    def chooseSimuldir(self):
-        self.fmtomo_parameters_ui.simuldir.setText(browseDir())
-
-
-    def chooseSeisarray(self):
-        self.fmtomo_parameters_ui.seisarray.setText(openFile())
-
-
     def postprocessing(self):
         if not self.checkSurveyState():
             self.printDialogMessage('No Survey defined.')
diff --git a/pylot/core/active/gui/windows.py b/pylot/core/active/gui/windows.py
index ffba7efd..8756fafe 100644
--- a/pylot/core/active/gui/windows.py
+++ b/pylot/core/active/gui/windows.py
@@ -1,11 +1,13 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+import os
 from PySide import QtCore, QtGui
-from pylot.core.active import surveyUtils, activeSeismoPick, seismicArrayPreparation
-from generate_survey_layout import *
-from generate_survey_layout_minimal import *
-from generate_seisarray_layout import *
-from picking_parameters_layout import *
+from pylot.core.active import surveyUtils, activeSeismoPick, seismicArrayPreparation, fmtomoUtils
+from generate_survey_layout import Ui_generate_survey
+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
 
 import numpy as np
 import matplotlib
@@ -62,7 +64,7 @@ class Gen_SeisArray(object):
     def start_dialog(self):
         self.init_last_selection()
         if self.qdialog.exec_():
-            self.refresh_filenames()
+            self.refresh_selection()
             if self.ui.radioButton_interpolatable.isChecked():
                 self.seisarray = seismicArrayPreparation.SeisArray(self.recfile, True)
             elif self.ui.radioButton_normal.isChecked():
@@ -73,10 +75,10 @@ class Gen_SeisArray(object):
                 self.seisarray.addMeasuredTopographyPoints(self.ptsfile)
             self.executed = True
         else:
-            self.refresh_filenames()
+            self.refresh_selection()
             self.executed = False
 
-    def refresh_filenames(self):
+    def refresh_selection(self):
         self.srcfile = self.ui.lineEdit_src.text()
         self.recfile = self.ui.lineEdit_rec.text()
         self.ptsfile = self.ui.lineEdit_pts.text()
@@ -128,16 +130,16 @@ class Gen_Survey_from_SA(object):
     def start_dialog(self):
         self.init_last_selection()
         if self.qdialog.exec_():
-            self.refresh_filenames()
+            self.refresh_selection()
             self.survey = activeSeismoPick.Survey(self.obsdir, seisArray = self.seisarray,
                                                   useDefaultParas = True, fstart = self.fstart,
                                                   fend = self.fend)
             self.executed = True
         else:
-            self.refresh_filenames()
+            self.refresh_selection()
             self.executed = False
 
-    def refresh_filenames(self):
+    def refresh_selection(self):
         self.obsdir = self.ui.lineEdit_obs.text()
         self.fstart = self.ui.fstart.text()
         self.fend = self.ui.fend.text()
@@ -180,16 +182,16 @@ class Gen_Survey_from_SR(object):
     def start_dialog(self):
         self.init_last_selection()
         if self.qdialog.exec_():
-            self.refresh_filenames()
+            self.refresh_selection()
             self.survey = activeSeismoPick.Survey(self.obsdir, self.srcfile, self.recfile,
                                                   useDefaultParas = True,
                                                   fstart = self.fstart, fend = self.fend)
             self.executed = True
         else:
-            self.refresh_filenames()
+            self.refresh_selection()
             self.executed = False
 
-    def refresh_filenames(self):
+    def refresh_selection(self):
         self.obsdir = self.ui.lineEdit_obs.text()
         self.srcfile = self.ui.lineEdit_src.text()
         self.recfile = self.ui.lineEdit_rec.text()
@@ -347,9 +349,6 @@ class Call_autopicker(object):
         self.ui.p1.setValue(self.p1)
         self.ui.p2.setValue(self.p2)
 
-    def get_survey(self):
-        return self.survey
-
     def connectButtons(self):
         QtCore.QObject.connect(self.ui.slider_folm, QtCore.SIGNAL("valueChanged(int)"), self.refreshFolm)
         QtCore.QObject.connect(self.ui.shift_snr, QtCore.SIGNAL("valueChanged(int)"), self.plotDynSNR)
@@ -366,3 +365,96 @@ class Call_autopicker(object):
     def chooseRecfile(self):
         self.ui.lineEdit_rec.setText(openFile('Open receiverfile.'))
 
+
+
+class Call_FMTOMO(object):
+    def __init__(self, mainwindow, survey):
+        self.mainwindow = mainwindow
+        self.survey = survey
+        self.init_dialog()
+        self.refresh_selection()                                        
+        self.start_dialog()
+
+    def init_dialog(self):
+        qdialog = QtGui.QDialog(self.mainwindow)
+        ui = Ui_fmtomo_parameters()
+        ui.setupUi(qdialog)
+        ui.nproc.setMaximum(getMaxCPU())
+        self.ui = ui
+        self.qdialog = qdialog
+        self.connectButtons()
+        
+    def start_dialog(self):
+        self.init_last_selection()
+        if self.qdialog.exec_():
+            self.refresh_selection()
+
+            if not os.path.isdir(self.picks_dir):
+                err = os.mkdir(self.picks_dir) # error not handled yet
+
+            self.survey.exportFMTOMO(self.picks_dir)
+
+            cwd = os.getcwd()
+            interpolationMethod = 'linear'
+            os.chdir(self.simuldir)
+            if self.survey.seisarray.twoDim:
+                interpolationMethod = 'nearest'
+            self.survey.seisarray.generateFMTOMOinputFromArray(self.propgrid, self.vgrid, (self.bbot, self.btop),
+                                                               self.cushionfactor/100., interpolationMethod,
+                                                               customgrid = self.customgrid, writeVTK = True)
+            os.chdir(cwd)
+
+            tomo = fmtomoUtils.Tomo3d(self.fmtomo_dir, self.simuldir)
+            tomo.runTOMO3D(self.nproc, self.nIter)
+
+            self.executed = True
+        else:
+            self.refresh_selection()
+            self.executed = False
+
+    def refresh_selection(self):
+        self.fmtomo_dir = self.ui.fmtomo_dir.text()
+        self.nIter = int(self.ui.nIter.value())
+        self.nproc = int(self.ui.nproc.value())
+        self.btop = float(self.ui.btop.text())
+        self.bbot = float(self.ui.bbot.text())
+        self.propgrid = (int(self.ui.pgrid_x.value()), int(self.ui.pgrid_y.value()), int(self.ui.pgrid_z.value()))
+        self.vgrid = (int(self.ui.invgrid_x.value()), int(self.ui.invgrid_y.value()), int(self.ui.invgrid_z.value()))
+        self.cushionfactor = float(self.ui.cushion.value())
+        self.customgrid = self.ui.customgrid.text()
+        self.simuldir = self.ui.simuldir.text()
+        self.picks_dir = os.path.join(self.simuldir, 'picks')
+        
+    def init_last_selection(self):
+        self.ui.fmtomo_dir.setText(self.fmtomo_dir)
+        self.ui.nIter.setValue(self.nIter)
+        self.ui.nproc.setValue(self.nproc)
+        self.ui.btop.setText(str(self.btop))
+        self.ui.bbot.setText(str(self.bbot))
+        self.ui.pgrid_x.setValue(self.propgrid[0])
+        self.ui.pgrid_y.setValue(self.propgrid[1])
+        self.ui.pgrid_z.setValue(self.propgrid[2])
+        self.ui.invgrid_x.setValue(self.vgrid[0])
+        self.ui.invgrid_y.setValue(self.vgrid[1])
+        self.ui.invgrid_z.setValue(self.vgrid[2])
+        self.ui.cushion.setValue(self.cushionfactor)
+        self.ui.customgrid.setText(self.customgrid)
+        self.ui.simuldir.setText(self.simuldir)
+
+    def connectButtons(self):
+        QtCore.QObject.connect(self.ui.browse_tomodir, QtCore.SIGNAL("clicked()"), self.chooseFMTOMOdir)
+        QtCore.QObject.connect(self.ui.browse_customgrid, QtCore.SIGNAL("clicked()"), self.chooseCustomgrid)
+        QtCore.QObject.connect(self.ui.browse_simuldir, QtCore.SIGNAL("clicked()"), self.chooseSimuldir)
+
+    def chooseFMTOMOdir(self):
+        self.ui.fmtomo_dir.setText(browseDir())
+
+    def chooseCustomgrid(self):
+        self.ui.customgrid.setText(openFile())
+
+    def chooseSimuldir(self):
+        self.ui.simuldir.setText(browseDir())
+
+
+
+