Merge remote-tracking branch 'origin/develop' into develop

pylot/core/active/activeSeismoPick.py

@@ -74,7 +74,7 @@ class Survey(object):
             self._coordsFromSeisArray()
         else:
             self._coordsFromFiles()
-            self.loadArray(self._obsdir, self._recile, self._sourcefile)
+            self.loadArray(self._obsdir, self._recfile, self._sourcefile)
         for shotnumber in self.data.keys():
             shot = self.data[shotnumber]
             shot.setShotnumber(shotnumber)
@@ -91,7 +91,7 @@ class Survey(object):
             #fileending = '.sg2'
             if fend == None:
                 fend = '_pickle.dat'
-            obsfile = fstart + os.path.join(self._obsdir, str(shotnumber)) + fend
+            obsfile = os.path.join(self._obsdir, fstart + str(shotnumber)) + fend
             if obsfile not in shot_dict.keys():
                 shot_dict[shotnumber] = []
             shot_dict[shotnumber] = seismicshot.SeismicShot(obsfile)

pylot/core/active/asp3d_layout.py

@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'asp3d_layout.ui'
 #
-# Created: Tue Jul 12 14:03:29 2016
+# Created: Tue Jul 12 21:41:12 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!

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 14:03:29 2016
+# Created: Tue Jul 12 21:41:12 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
@@ -105,8 +105,10 @@ class Ui_fmtomo_parameters(object):
         self.label_13 = QtGui.QLabel(fmtomo_parameters)
         self.label_13.setObjectName("label_13")
         self.horizontalLayout.addWidget(self.label_13)
-        self.cushion = QtGui.QLineEdit(fmtomo_parameters)
+        self.cushion = QtGui.QSpinBox(fmtomo_parameters)
-        self.cushion.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
+        self.cushion.setMinimum(2)
+        self.cushion.setMaximum(100)
+        self.cushion.setProperty("value", 10)
         self.cushion.setObjectName("cushion")
         self.horizontalLayout.addWidget(self.cushion)
         self.label_12 = QtGui.QLabel(fmtomo_parameters)
@@ -159,34 +161,46 @@ class Ui_fmtomo_parameters(object):
         self.label_7.setAlignment(QtCore.Qt.AlignCenter)
         self.label_7.setObjectName("label_7")
         self.gridLayout.addWidget(self.label_7, 0, 3, 1, 1)
-        self.label_8 = QtGui.QLabel(fmtomo_parameters)
-        self.label_8.setObjectName("label_8")
-        self.gridLayout.addWidget(self.label_8, 1, 0, 1, 1)
-        self.pgrid_x = QtGui.QLineEdit(fmtomo_parameters)
-        self.pgrid_x.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
-        self.pgrid_x.setObjectName("pgrid_x")
-        self.gridLayout.addWidget(self.pgrid_x, 1, 1, 1, 1)
-        self.pgrid_y = QtGui.QLineEdit(fmtomo_parameters)
-        self.pgrid_y.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
-        self.pgrid_y.setObjectName("pgrid_y")
-        self.gridLayout.addWidget(self.pgrid_y, 1, 2, 1, 1)
-        self.pgrid_z = QtGui.QLineEdit(fmtomo_parameters)
-        self.pgrid_z.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
-        self.pgrid_z.setObjectName("pgrid_z")
-        self.gridLayout.addWidget(self.pgrid_z, 1, 3, 1, 1)
         self.label_9 = QtGui.QLabel(fmtomo_parameters)
         self.label_9.setObjectName("label_9")
         self.gridLayout.addWidget(self.label_9, 2, 0, 1, 1)
-        self.invgrid_x = QtGui.QLineEdit(fmtomo_parameters)
+        self.pgrid_x = QtGui.QSpinBox(fmtomo_parameters)
-        self.invgrid_x.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
+        self.pgrid_x.setMinimum(2)
+        self.pgrid_x.setMaximum(10000)
+        self.pgrid_x.setProperty("value", 100)
+        self.pgrid_x.setObjectName("pgrid_x")
+        self.gridLayout.addWidget(self.pgrid_x, 1, 1, 1, 1)
+        self.pgrid_y = QtGui.QSpinBox(fmtomo_parameters)
+        self.pgrid_y.setMinimum(2)
+        self.pgrid_y.setMaximum(10000)
+        self.pgrid_y.setProperty("value", 100)
+        self.pgrid_y.setObjectName("pgrid_y")
+        self.gridLayout.addWidget(self.pgrid_y, 1, 2, 1, 1)
+        self.pgrid_z = QtGui.QSpinBox(fmtomo_parameters)
+        self.pgrid_z.setMinimum(2)
+        self.pgrid_z.setMaximum(10000)
+        self.pgrid_z.setProperty("value", 120)
+        self.pgrid_z.setObjectName("pgrid_z")
+        self.gridLayout.addWidget(self.pgrid_z, 1, 3, 1, 1)
+        self.label_8 = QtGui.QLabel(fmtomo_parameters)
+        self.label_8.setObjectName("label_8")
+        self.gridLayout.addWidget(self.label_8, 1, 0, 1, 1)
+        self.invgrid_x = QtGui.QSpinBox(fmtomo_parameters)
+        self.invgrid_x.setMinimum(2)
+        self.invgrid_x.setMaximum(10000)
+        self.invgrid_x.setProperty("value", 60)
         self.invgrid_x.setObjectName("invgrid_x")
         self.gridLayout.addWidget(self.invgrid_x, 2, 1, 1, 1)
-        self.invgrid_y = QtGui.QLineEdit(fmtomo_parameters)
+        self.invgrid_y = QtGui.QSpinBox(fmtomo_parameters)
-        self.invgrid_y.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
+        self.invgrid_y.setMinimum(2)
+        self.invgrid_y.setMaximum(10000)
+        self.invgrid_y.setProperty("value", 60)
         self.invgrid_y.setObjectName("invgrid_y")
         self.gridLayout.addWidget(self.invgrid_y, 2, 2, 1, 1)
-        self.invgrid_z = QtGui.QLineEdit(fmtomo_parameters)
+        self.invgrid_z = QtGui.QSpinBox(fmtomo_parameters)
-        self.invgrid_z.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
+        self.invgrid_z.setMinimum(2)
+        self.invgrid_z.setMaximum(10000)
+        self.invgrid_z.setProperty("value", 80)
         self.invgrid_z.setObjectName("invgrid_z")
         self.gridLayout.addWidget(self.invgrid_z, 2, 3, 1, 1)
         self.verticalLayout.addLayout(self.gridLayout)
@@ -255,24 +269,17 @@ class Ui_fmtomo_parameters(object):
         self.label_13.setToolTip(QtGui.QApplication.translate("fmtomo_parameters", "Extension of the model around the maximum values of the receiver grid (X and Y).\n"
 "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.cushion.setText(QtGui.QApplication.translate("fmtomo_parameters", "10", 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_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))
-        self.label_8.setToolTip(QtGui.QApplication.translate("fmtomo_parameters", "Number of points for forward simulation in X, Y, Z.\n"
-"Must be higher than number of inversion grid points.", None, QtGui.QApplication.UnicodeUTF8))
-        self.label_8.setText(QtGui.QApplication.translate("fmtomo_parameters", "Propagation Grid [?]", None, QtGui.QApplication.UnicodeUTF8))
-        self.pgrid_x.setText(QtGui.QApplication.translate("fmtomo_parameters", "100", None, QtGui.QApplication.UnicodeUTF8))
-        self.pgrid_y.setText(QtGui.QApplication.translate("fmtomo_parameters", "100", None, QtGui.QApplication.UnicodeUTF8))
-        self.pgrid_z.setText(QtGui.QApplication.translate("fmtomo_parameters", "100", None, QtGui.QApplication.UnicodeUTF8))
         self.label_9.setToolTip(QtGui.QApplication.translate("fmtomo_parameters", "Number of inversion grid (velocity grid) points in X, Y, Z.\n"
 "Must be lower than for propagation grid.", None, QtGui.QApplication.UnicodeUTF8))
         self.label_9.setText(QtGui.QApplication.translate("fmtomo_parameters", "Inversion Grid [?]", None, QtGui.QApplication.UnicodeUTF8))
-        self.invgrid_x.setText(QtGui.QApplication.translate("fmtomo_parameters", "50", None, QtGui.QApplication.UnicodeUTF8))
+        self.label_8.setToolTip(QtGui.QApplication.translate("fmtomo_parameters", "Number of points for forward simulation in X, Y, Z.\n"
-        self.invgrid_y.setText(QtGui.QApplication.translate("fmtomo_parameters", "50", None, QtGui.QApplication.UnicodeUTF8))
+"Must be higher than number of inversion grid points.", None, QtGui.QApplication.UnicodeUTF8))
-        self.invgrid_z.setText(QtGui.QApplication.translate("fmtomo_parameters", "50", None, QtGui.QApplication.UnicodeUTF8))
+        self.label_8.setText(QtGui.QApplication.translate("fmtomo_parameters", "Propagation Grid [?]", None, QtGui.QApplication.UnicodeUTF8))
         self.label_15.setToolTip(QtGui.QApplication.translate("fmtomo_parameters", "<!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"
 "p, li { white-space: pre-wrap; }\n"

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 14:03:29 2016
+# Created: Tue Jul 12 21:41:13 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!

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 14:03:29 2016
+# Created: Tue Jul 12 21:41:13 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!

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 14:03:29 2016
+# Created: Tue Jul 12 21:41:13 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!

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 14:03:30 2016
+# Created: Tue Jul 12 21:41:13 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
@@ -171,7 +171,7 @@ class Ui_picking_parameters(object):
         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))
-        self.label_4.setToolTip(QtGui.QApplication.translate("picking_parameters", "Value between 0 and 1 for threshold picking algorithm (Default = 60%).", None, QtGui.QApplication.UnicodeUTF8))
+        self.label_4.setToolTip(QtGui.QApplication.translate("picking_parameters", "Value between 1 and 100 % for threshold picking algorithm (Default = 60%).", None, QtGui.QApplication.UnicodeUTF8))
         self.label_4.setText(QtGui.QApplication.translate("picking_parameters", "Fraction of local maximum [?]", None, QtGui.QApplication.UnicodeUTF8))
         self.label_folm.setText(QtGui.QApplication.translate("picking_parameters", "60 %", None, QtGui.QApplication.UnicodeUTF8))
         self.label_5.setToolTip(QtGui.QApplication.translate("picking_parameters", "Use additional Akaike Information Criterion for picking.", None, QtGui.QApplication.UnicodeUTF8))

pylot/core/active/seismicArrayPreparation.py

@@ -604,9 +604,9 @@ class SeisArray(object):
         cushionTheta = abs(theta_max - theta_min) * cushionfactor
         # 2D Case only:
         if cushionPhi == 0.:
-            cushionPhi = 0.05
+            cushionPhi = 0.1
         if cushionTheta == 0.:
-            cushionTheta = 0.05
+            cushionTheta = 0.1
         phiWE = (phi_min - cushionPhi, phi_max + cushionPhi)
         thetaSN = (theta_min - cushionTheta, theta_max + cushionTheta)
         return thetaSN, phiWE
@@ -649,6 +649,11 @@ class SeisArray(object):
 
         thetaSN, phiWE = self.getThetaPhiFromArray(cushionfactor)
 
+        # +2 cushion nodes
+        nTheta += 2
+        nPhi += 2
+        nR += 2
+
         thetaS = thetaSN[0] + cushionpropgrid
         thetaN = thetaSN[1] - cushionpropgrid
         phiW = phiWE[0] + cushionpropgrid

pylot/core/active/surveyUtils.py

@@ -97,7 +97,7 @@ def setDynamicFittedSNR(shot_dict, shiftdist=30, shiftSNR=100, p1=0.004, p2=-0.0
     for shot in shot_dict.values():
         for traceID in shot.getTraceIDlist():  ### IMPROVE
             dist = shot.getDistance(traceID) + shiftdist
-            snrthreshold = (1 / (fit_fn(dist) ** 2)) - shiftSNR * np.exp(-0.05 * dist)
+            snrthreshold = snr_fit_func(fit_fn, dist, shiftSNR)
             if snrthreshold < minSNR:
                 print('WARNING: SNR threshold %s lower %s. Set SNR threshold to %s.'
                       % (snrthreshold, minSNR, minSNR))
@@ -106,6 +106,10 @@ def setDynamicFittedSNR(shot_dict, shiftdist=30, shiftSNR=100, p1=0.004, p2=-0.0
                 shot.setSNRthreshold(traceID, snrthreshold)
     print("setDynamicFittedSNR: Finished setting of fitted SNR-threshold")
 
+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 setConstantSNR(shot_dict, snrthreshold=2.5):
     """

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 14:03:30 2016
+# Created: Tue Jul 12 21:41:13 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!