From 28d2464aeeabc4745954fb47c96903d512c47ed7 Mon Sep 17 00:00:00 2001
From: Marcel Paffrath <marcel.paffrath@rub.de>
Date: Tue, 9 Aug 2016 11:48:37 +0200
Subject: [PATCH 1/5] got working window layout for postprocessing (no
 functions yet)

---
 pylot/core/active/ActiveSeismoPick3D_GUI.py   |  8 ++-
 pylot/core/active/activeSeismoPick.py         | 49 ++++++++------
 pylot/core/active/gui/asp3d_layout.py         |  2 +-
 .../active/gui/fmtomo_parameters_layout.py    |  2 +-
 .../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   |  2 +-
 .../core/active/gui/postprocessing_layout.py  | 18 ++---
 pylot/core/active/gui/vtk_tools_layout.py     |  2 +-
 pylot/core/active/gui/windows.py              | 66 +++++++++++++++++--
 11 files changed, 109 insertions(+), 46 deletions(-)

diff --git a/pylot/core/active/ActiveSeismoPick3D_GUI.py b/pylot/core/active/ActiveSeismoPick3D_GUI.py
index eec13af5..839fc80f 100755
--- a/pylot/core/active/ActiveSeismoPick3D_GUI.py
+++ b/pylot/core/active/ActiveSeismoPick3D_GUI.py
@@ -9,7 +9,7 @@ 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.windows import Gen_SeisArray, Gen_Survey_from_SA, Gen_Survey_from_SR, Call_autopicker, Call_FMTOMO, Call_VTK_dialog
+from pylot.core.active.gui.windows import Gen_SeisArray, Gen_Survey_from_SA, Gen_Survey_from_SR, Call_autopicker, Call_FMTOMO, Call_VTK_dialog, Postprocessing
 from pylot.core.active.gui.windows import openFile, saveFile, browseDir, getMaxCPU
 
 from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
@@ -43,6 +43,7 @@ class gui_control(object):
         self.autopicker = None
         self.fmtomo = None
         self.vtktools = None
+        self.postprocessing = None
 
     def setInitStates(self):
         self.setPickState(False)
@@ -362,8 +363,9 @@ class gui_control(object):
         if not self.checkSurveyState():
             self.printDialogMessage('No Survey defined.')
             return
-        self.survey.plotAllPicks()
-        self.refreshPickedWidgets() # wait until finished
+        self.postprocessing = Postprocessing(self.mainwindow, self.survey)
+        #self.survey.plotAllPicks()
+        #self.refreshPickedWidgets() # wait until finished
 
         
     def load_survey(self):
diff --git a/pylot/core/active/activeSeismoPick.py b/pylot/core/active/activeSeismoPick.py
index 98d8569b..4a52fde2 100644
--- a/pylot/core/active/activeSeismoPick.py
+++ b/pylot/core/active/activeSeismoPick.py
@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 import os
 import sys
+import math
 import numpy as np
 from pylot.core.active import seismicshot
 from pylot.core.active.surveyUtils import cleanUp
@@ -672,10 +673,29 @@ class Survey(object):
         '''
 
         import matplotlib.pyplot as plt
-        import math
         plt.interactive(True)
         from pylot.core.active.surveyPlotTools import regions
 
+        dist, pick, snrlog, pickerror, spe = self.preparePlotAllPicks(plotRemoved)
+        
+        color = {'log10SNR': snrlog,
+                 'pickerror': pickerror,
+                 'spe': spe}
+        self.color = color
+        if refreshPlot is False:
+            ax, cbar, sc = self.createPlot(dist, pick, color[colorByVal],
+                                       label='%s' % colorByVal)
+            region = regions(ax, cbar, self)
+            ax.legend()
+            return (ax, region)
+        if refreshPlot is True:
+            ax, cbar, sc = self.createPlot(dist, pick, color[colorByVal],
+                                       label='%s' % colorByVal, ax=ax,
+                                       cbar=cbar)
+            ax.legend()
+            return ax
+
+    def preparePlotAllPicks(self, plotRemoved = False):
         dist = []
         pick = []
         snrlog = []
@@ -693,23 +713,9 @@ class Survey(object):
                         pickerror.append(shot.getPickError(traceID))
                         spe.append(shot.getSymmetricPickError(traceID))
 
-        color = {'log10SNR': snrlog,
-                 'pickerror': pickerror,
-                 'spe': spe}
-        self.color = color
-        if refreshPlot is False:
-            ax, cbar = self.createPlot(dist, pick, color[colorByVal],
-                                       label='%s' % colorByVal)
-            region = regions(ax, cbar, self)
-            ax.legend()
-            return (ax, region)
-        if refreshPlot is True:
-            ax, cbar = self.createPlot(dist, pick, color[colorByVal],
-                                       label='%s' % colorByVal, ax=ax,
-                                       cbar=cbar)
-            ax.legend()
-            return ax
+        return dist, pick, snrlog, pickerror, spe
 
+                            
     def createPlot(self, dist, pick, inkByVal, label, ax=None, cbar=None):
         '''
         Used by plotAllPicks.
@@ -732,14 +738,15 @@ class Survey(object):
         else:
             sc = ax.scatter(dist, pick, cmap=cm, c=inkByVal, s=5,
                             edgecolors='none', label=label)
-            cbar = plt.colorbar(sc, cax=cbar.ax)
-            cbar.set_label(label)
+            if cbar is not None:
+                cbar = plt.colorbar(sc, cax=cbar.ax)
+                cbar.set_label(label)
             ax.set_xlabel('Distance [m]')
             ax.set_ylabel('Time [s]')
             ax.text(0.5, 0.95, 'Plot of all picks', transform=ax.transAxes,
                     horizontalalignment='center')
-        return (ax, cbar)
-
+        return ax, cbar, sc
+    
     def _update_progress(self, shotname, tend, progress):
         sys.stdout.write(
             'Working on shot %s. ETC is %02d:%02d:%02d [%2.2f %%]\r' % (
diff --git a/pylot/core/active/gui/asp3d_layout.py b/pylot/core/active/gui/asp3d_layout.py
index 0d5553c6..e7ee467f 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: Thu Aug  4 13:55:47 2016
+# Created: Tue Aug  9 11:40:26 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/fmtomo_parameters_layout.py b/pylot/core/active/gui/fmtomo_parameters_layout.py
index ab987e0b..20a3c46f 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: Thu Aug  4 13:55:47 2016
+# Created: Tue Aug  9 11:40:26 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_seisarray_layout.py b/pylot/core/active/gui/generate_seisarray_layout.py
index 94a35c79..9c96ff87 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: Thu Aug  4 13:55:47 2016
+# Created: Tue Aug  9 11:40:26 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 87e435c3..864d0247 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: Thu Aug  4 13:55:47 2016
+# Created: Tue Aug  9 11:40:26 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 17d6352b..be8034ad 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: Thu Aug  4 13:55:47 2016
+# Created: Tue Aug  9 11:40:27 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 db9ccc8c..17548ceb 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: Thu Aug  4 13:55:47 2016
+# Created: Tue Aug  9 11:40:27 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/postprocessing_layout.py b/pylot/core/active/gui/postprocessing_layout.py
index 43507ed6..8337f053 100644
--- a/pylot/core/active/gui/postprocessing_layout.py
+++ b/pylot/core/active/gui/postprocessing_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'postprocessing_layout.ui'
 #
-# Created: Tue Aug  9 10:36:58 2016
+# Created: Tue Aug  9 11:40:27 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_postprocessing(object):
     def setupUi(self, postprocessing):
         postprocessing.setObjectName("postprocessing")
-        postprocessing.resize(640, 479)
+        postprocessing.resize(640, 480)
         self.verticalLayout_2 = QtGui.QVBoxLayout(postprocessing)
         self.verticalLayout_2.setObjectName("verticalLayout_2")
         self.verticalLayout = QtGui.QVBoxLayout()
@@ -91,19 +91,15 @@ class Ui_postprocessing(object):
         self.horizontalLayout_3.addWidget(self.pushButton_spe)
         self.gridLayout.addLayout(self.horizontalLayout_3, 1, 1, 1, 1)
         self.verticalLayout.addLayout(self.gridLayout)
+        self.verticalLayout_2.addLayout(self.verticalLayout)
+        self.verticalLayout_plot = QtGui.QVBoxLayout()
+        self.verticalLayout_plot.setObjectName("verticalLayout_plot")
         self.horizontalLayout_plot = QtGui.QHBoxLayout()
         self.horizontalLayout_plot.setObjectName("horizontalLayout_plot")
-        self.verticalLayout.addLayout(self.horizontalLayout_plot)
-        self.verticalLayout_2.addLayout(self.verticalLayout)
-        self.buttonBox = QtGui.QDialogButtonBox(postprocessing)
-        self.buttonBox.setOrientation(QtCore.Qt.Horizontal)
-        self.buttonBox.setStandardButtons(QtGui.QDialogButtonBox.Ok)
-        self.buttonBox.setObjectName("buttonBox")
-        self.verticalLayout_2.addWidget(self.buttonBox)
+        self.verticalLayout_plot.addLayout(self.horizontalLayout_plot)
+        self.verticalLayout_2.addLayout(self.verticalLayout_plot)
 
         self.retranslateUi(postprocessing)
-        QtCore.QObject.connect(self.buttonBox, QtCore.SIGNAL("accepted()"), postprocessing.accept)
-        QtCore.QObject.connect(self.buttonBox, QtCore.SIGNAL("rejected()"), postprocessing.reject)
         QtCore.QMetaObject.connectSlotsByName(postprocessing)
 
     def retranslateUi(self, postprocessing):
diff --git a/pylot/core/active/gui/vtk_tools_layout.py b/pylot/core/active/gui/vtk_tools_layout.py
index de492841..da475fc4 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: Thu Aug  4 13:55:47 2016
+# Created: Tue Aug  9 11:40:27 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 1b7c61e4..84d63790 100644
--- a/pylot/core/active/gui/windows.py
+++ b/pylot/core/active/gui/windows.py
@@ -1,6 +1,9 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 import os
+import numpy as np
+import matplotlib
+import matplotlib.pyplot as plt
 from PySide import QtCore, QtGui
 from pylot.core.active import surveyUtils, activeSeismoPick, seismicArrayPreparation, fmtomoUtils
 from generate_survey_layout import Ui_generate_survey
@@ -8,11 +11,9 @@ from generate_survey_layout_minimal import Ui_generate_survey_minimal
 from generate_seisarray_layout import Ui_generate_seisarray
 from picking_parameters_layout import Ui_picking_parameters
 from fmtomo_parameters_layout import Ui_fmtomo_parameters
-from pylot.core.active.gui.vtk_tools_layout import Ui_vtk_tools
+from vtk_tools_layout import Ui_vtk_tools
+from postprocessing_layout import Ui_postprocessing
 
-
-import numpy as np
-import matplotlib
 matplotlib.use('Qt4Agg')
 matplotlib.rcParams['backend.qt4']='PySide'
 
@@ -597,3 +598,60 @@ class Call_VTK_dialog(object):
     def newFileVTK(self):
         self.ui.lineEdit_vgout.setText(saveFile())
 
+class Postprocessing(object):
+    def __init__(self, mainwindow, survey):
+        self.mainwindow = mainwindow
+        self.survey = survey
+        self.init_dialog()
+        self.start_dialog()
+
+    def init_dialog(self):
+        qwidget = QtGui.QWidget()#
+        ui = Ui_postprocessing()
+        ui.setupUi(qwidget)
+        self.ui = ui
+        self.qwidget = qwidget
+        self.initPlot()
+        self.plot()
+        #self.connectButtons()
+
+    def start_dialog(self):
+        self.qwidget.show()
+        # if self.qwidget.exec_():
+        #     #self.refresh_selection()
+        #     self.executed = True
+        # else:
+        #     self.refresh_selection()
+        #     self.executed = False
+
+    def initPlot(self):
+        self.figure = Figure()
+        self.canvas = FigureCanvas(self.figure)
+        self.ui.verticalLayout_plot.addWidget(self.canvas)
+        self.toolbar = NavigationToolbar(self.canvas, self.mainwindow)
+        self.ui.verticalLayout_plot.addWidget(self.toolbar)
+        
+    def plot(self):
+        survey = self.survey
+        ax = self.figure.add_subplot(111)
+        dist, pick, snrlog, pickerror, spe = survey.preparePlotAllPicks(plotRemoved = False)
+        ax, cbar, sc = survey.createPlot(dist, pick, snrlog, '123', ax = ax, cbar = None)
+        self.cbar = self.figure.colorbar(sc, fraction=0.05)
+        self.ax = ax
+        
+    # def refresh_selection(self):
+    #     self.obsdir = self.ui.lineEdit_obs.text()
+    #     self.fstart = self.ui.fstart.text()
+    #     self.fend = self.ui.fend.text()
+
+    def update_survey(self, survey):
+        self.survey = survey
+        
+    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.'))

From 14c22d73b7b4db931de9dc4f9e107b0515dbe938 Mon Sep 17 00:00:00 2001
From: sebastianp <sebastian.priebe@rub.de>
Date: Wed, 10 Aug 2016 10:06:34 +0200
Subject: [PATCH 2/5] [enhancement] adding a save option for plotting

---
 pylot/core/pick/compare.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/pylot/core/pick/compare.py b/pylot/core/pick/compare.py
index 3116f137..4fc8ee19 100644
--- a/pylot/core/pick/compare.py
+++ b/pylot/core/pick/compare.py
@@ -424,7 +424,8 @@ class PDFstatistics(object):
 
 
     def histplot(self, array, binlist, xlab = 'Values',
-                 ylab = 'Frequency', title = None, label=None):
+                 ylab = 'Frequency', title = None, label=None,
+                 fnout = None):
         import matplotlib.pyplot as plt
         plt.hist(array,bins = binlist)
         plt.xlabel('Values')
@@ -434,7 +435,10 @@ class PDFstatistics(object):
             if label:
                 title_str += ' (' + label + ')'
             plt.title(title_str)
-        plt.show()
+        if fnout:
+            plt.savefig(fnout+'histplot.png')
+        else:
+            plt.show()
 
 
     def getPDFDict(self, month, evt):

From 7b9d1f172aef9456a9d91037cfe7490294b65d66 Mon Sep 17 00:00:00 2001
From: Marcel Paffrath <marcel.paffrath@rub.de>
Date: Wed, 10 Aug 2016 14:24:07 +0200
Subject: [PATCH 3/5] semi working QT interface for postprocessing

---
 pylot/core/active/activeSeismoPick.py         |  7 +-
 pylot/core/active/gui/asp3d_layout.py         |  2 +-
 .../active/gui/fmtomo_parameters_layout.py    |  2 +-
 .../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   |  2 +-
 .../core/active/gui/postprocessing_layout.py  | 98 +++++++++++--------
 pylot/core/active/gui/vtk_tools_layout.py     |  2 +-
 pylot/core/active/gui/windows.py              | 86 ++++++++++------
 pylot/core/active/surveyPlotTools.py          | 10 +-
 11 files changed, 130 insertions(+), 85 deletions(-)

diff --git a/pylot/core/active/activeSeismoPick.py b/pylot/core/active/activeSeismoPick.py
index 4a52fde2..02bda997 100644
--- a/pylot/core/active/activeSeismoPick.py
+++ b/pylot/core/active/activeSeismoPick.py
@@ -721,7 +721,7 @@ class Survey(object):
         Used by plotAllPicks.
         '''
         import matplotlib.pyplot as plt
-        plt.interactive(True)
+        #plt.interactive(True)
         cm = plt.cm.jet
         if ax is None:
             print('Generating new plot...')
@@ -729,7 +729,7 @@ class Survey(object):
             ax = fig.add_subplot(111)
             sc = ax.scatter(dist, pick, cmap=cm, c=inkByVal, s=5,
                             edgecolors='none', label=label)
-            cbar = plt.colorbar(sc, fraction=0.05)
+            cbar = fig.colorbar(sc, fraction=0.05)
             cbar.set_label(label)
             ax.set_xlabel('Distance [m]')
             ax.set_ylabel('Time [s]')
@@ -739,7 +739,8 @@ class Survey(object):
             sc = ax.scatter(dist, pick, cmap=cm, c=inkByVal, s=5,
                             edgecolors='none', label=label)
             if cbar is not None:
-                cbar = plt.colorbar(sc, cax=cbar.ax)
+                cbar.ax.clear()
+                cbar = ax.figure.colorbar(sc, cax=cbar.ax)
                 cbar.set_label(label)
             ax.set_xlabel('Distance [m]')
             ax.set_ylabel('Time [s]')
diff --git a/pylot/core/active/gui/asp3d_layout.py b/pylot/core/active/gui/asp3d_layout.py
index e7ee467f..359d41d0 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: Tue Aug  9 11:40:26 2016
+# Created: Wed Aug 10 14:11:07 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
diff --git a/pylot/core/active/gui/fmtomo_parameters_layout.py b/pylot/core/active/gui/fmtomo_parameters_layout.py
index 20a3c46f..c63c98c6 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: Tue Aug  9 11:40:26 2016
+# Created: Wed Aug 10 14:11:07 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
diff --git a/pylot/core/active/gui/generate_seisarray_layout.py b/pylot/core/active/gui/generate_seisarray_layout.py
index 9c96ff87..010ed513 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: Tue Aug  9 11:40:26 2016
+# Created: Wed Aug 10 14:11:07 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
diff --git a/pylot/core/active/gui/generate_survey_layout.py b/pylot/core/active/gui/generate_survey_layout.py
index 864d0247..05492585 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: Tue Aug  9 11:40:26 2016
+# Created: Wed Aug 10 14:11:07 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
diff --git a/pylot/core/active/gui/generate_survey_layout_minimal.py b/pylot/core/active/gui/generate_survey_layout_minimal.py
index be8034ad..423c3c95 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: Tue Aug  9 11:40:27 2016
+# Created: Wed Aug 10 14:11:07 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
diff --git a/pylot/core/active/gui/picking_parameters_layout.py b/pylot/core/active/gui/picking_parameters_layout.py
index 17548ceb..129c1fa1 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: Tue Aug  9 11:40:27 2016
+# Created: Wed Aug 10 14:11:07 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
diff --git a/pylot/core/active/gui/postprocessing_layout.py b/pylot/core/active/gui/postprocessing_layout.py
index 8337f053..15fe772b 100644
--- a/pylot/core/active/gui/postprocessing_layout.py
+++ b/pylot/core/active/gui/postprocessing_layout.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'postprocessing_layout.ui'
 #
-# Created: Tue Aug  9 11:40:27 2016
+# Created: Wed Aug 10 14:11:08 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
@@ -12,34 +12,13 @@ from PySide import QtCore, QtGui
 class Ui_postprocessing(object):
     def setupUi(self, postprocessing):
         postprocessing.setObjectName("postprocessing")
-        postprocessing.resize(640, 480)
-        self.verticalLayout_2 = QtGui.QVBoxLayout(postprocessing)
-        self.verticalLayout_2.setObjectName("verticalLayout_2")
-        self.verticalLayout = QtGui.QVBoxLayout()
+        postprocessing.resize(663, 617)
+        self.verticalLayout = QtGui.QVBoxLayout(postprocessing)
         self.verticalLayout.setObjectName("verticalLayout")
-        self.gridLayout = QtGui.QGridLayout()
-        self.gridLayout.setObjectName("gridLayout")
-        self.horizontalLayout = QtGui.QHBoxLayout()
-        self.horizontalLayout.setObjectName("horizontalLayout")
-        self.pushButton_rect = QtGui.QPushButton(postprocessing)
-        sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Minimum)
-        sizePolicy.setHorizontalStretch(0)
-        sizePolicy.setVerticalStretch(0)
-        sizePolicy.setHeightForWidth(self.pushButton_rect.sizePolicy().hasHeightForWidth())
-        self.pushButton_rect.setSizePolicy(sizePolicy)
-        self.pushButton_rect.setMaximumSize(QtCore.QSize(16777215, 30))
-        self.pushButton_rect.setObjectName("pushButton_rect")
-        self.horizontalLayout.addWidget(self.pushButton_rect)
-        self.pushButton_poly = QtGui.QPushButton(postprocessing)
-        sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Minimum)
-        sizePolicy.setHorizontalStretch(0)
-        sizePolicy.setVerticalStretch(0)
-        sizePolicy.setHeightForWidth(self.pushButton_poly.sizePolicy().hasHeightForWidth())
-        self.pushButton_poly.setSizePolicy(sizePolicy)
-        self.pushButton_poly.setMaximumSize(QtCore.QSize(16777215, 30))
-        self.pushButton_poly.setObjectName("pushButton_poly")
-        self.horizontalLayout.addWidget(self.pushButton_poly)
-        self.gridLayout.addLayout(self.horizontalLayout, 1, 0, 1, 1)
+        self.horizontalLayout_2 = QtGui.QHBoxLayout()
+        self.horizontalLayout_2.setObjectName("horizontalLayout_2")
+        self.verticalLayout_3 = QtGui.QVBoxLayout()
+        self.verticalLayout_3.setObjectName("verticalLayout_3")
         self.label = QtGui.QLabel(postprocessing)
         sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Minimum)
         sizePolicy.setHorizontalStretch(0)
@@ -49,7 +28,42 @@ class Ui_postprocessing(object):
         self.label.setMinimumSize(QtCore.QSize(0, 20))
         self.label.setMaximumSize(QtCore.QSize(16777215, 30))
         self.label.setObjectName("label")
-        self.gridLayout.addWidget(self.label, 0, 0, 1, 1)
+        self.verticalLayout_3.addWidget(self.label)
+        self.horizontalLayout_4 = QtGui.QHBoxLayout()
+        self.horizontalLayout_4.setObjectName("horizontalLayout_4")
+        self.pushButton_rect = QtGui.QPushButton(postprocessing)
+        sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Minimum)
+        sizePolicy.setHorizontalStretch(0)
+        sizePolicy.setVerticalStretch(0)
+        sizePolicy.setHeightForWidth(self.pushButton_rect.sizePolicy().hasHeightForWidth())
+        self.pushButton_rect.setSizePolicy(sizePolicy)
+        self.pushButton_rect.setMaximumSize(QtCore.QSize(16777215, 30))
+        self.pushButton_rect.setObjectName("pushButton_rect")
+        self.horizontalLayout_4.addWidget(self.pushButton_rect)
+        self.pushButton_poly = QtGui.QPushButton(postprocessing)
+        sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Minimum)
+        sizePolicy.setHorizontalStretch(0)
+        sizePolicy.setVerticalStretch(0)
+        sizePolicy.setHeightForWidth(self.pushButton_poly.sizePolicy().hasHeightForWidth())
+        self.pushButton_poly.setSizePolicy(sizePolicy)
+        self.pushButton_poly.setMaximumSize(QtCore.QSize(16777215, 30))
+        self.pushButton_poly.setObjectName("pushButton_poly")
+        self.horizontalLayout_4.addWidget(self.pushButton_poly)
+        self.pushButton_plot = QtGui.QPushButton(postprocessing)
+        self.pushButton_plot.setCheckable(False)
+        self.pushButton_plot.setDefault(False)
+        self.pushButton_plot.setFlat(False)
+        self.pushButton_plot.setObjectName("pushButton_plot")
+        self.horizontalLayout_4.addWidget(self.pushButton_plot)
+        self.verticalLayout_3.addLayout(self.horizontalLayout_4)
+        self.horizontalLayout_2.addLayout(self.verticalLayout_3)
+        self.line = QtGui.QFrame(postprocessing)
+        self.line.setFrameShape(QtGui.QFrame.VLine)
+        self.line.setFrameShadow(QtGui.QFrame.Sunken)
+        self.line.setObjectName("line")
+        self.horizontalLayout_2.addWidget(self.line)
+        self.verticalLayout_2 = QtGui.QVBoxLayout()
+        self.verticalLayout_2.setObjectName("verticalLayout_2")
         self.label_2 = QtGui.QLabel(postprocessing)
         sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Minimum)
         sizePolicy.setHorizontalStretch(0)
@@ -59,9 +73,9 @@ class Ui_postprocessing(object):
         self.label_2.setMinimumSize(QtCore.QSize(0, 20))
         self.label_2.setMaximumSize(QtCore.QSize(16777215, 30))
         self.label_2.setObjectName("label_2")
-        self.gridLayout.addWidget(self.label_2, 0, 1, 1, 1)
-        self.horizontalLayout_3 = QtGui.QHBoxLayout()
-        self.horizontalLayout_3.setObjectName("horizontalLayout_3")
+        self.verticalLayout_2.addWidget(self.label_2)
+        self.horizontalLayout_5 = QtGui.QHBoxLayout()
+        self.horizontalLayout_5.setObjectName("horizontalLayout_5")
         self.pushButton_snr = QtGui.QPushButton(postprocessing)
         sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Minimum)
         sizePolicy.setHorizontalStretch(0)
@@ -70,7 +84,7 @@ class Ui_postprocessing(object):
         self.pushButton_snr.setSizePolicy(sizePolicy)
         self.pushButton_snr.setMaximumSize(QtCore.QSize(16777215, 30))
         self.pushButton_snr.setObjectName("pushButton_snr")
-        self.horizontalLayout_3.addWidget(self.pushButton_snr)
+        self.horizontalLayout_5.addWidget(self.pushButton_snr)
         self.pushButton_pe = QtGui.QPushButton(postprocessing)
         sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Minimum)
         sizePolicy.setHorizontalStretch(0)
@@ -79,7 +93,7 @@ class Ui_postprocessing(object):
         self.pushButton_pe.setSizePolicy(sizePolicy)
         self.pushButton_pe.setMaximumSize(QtCore.QSize(16777215, 30))
         self.pushButton_pe.setObjectName("pushButton_pe")
-        self.horizontalLayout_3.addWidget(self.pushButton_pe)
+        self.horizontalLayout_5.addWidget(self.pushButton_pe)
         self.pushButton_spe = QtGui.QPushButton(postprocessing)
         sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Minimum)
         sizePolicy.setHorizontalStretch(0)
@@ -88,25 +102,23 @@ class Ui_postprocessing(object):
         self.pushButton_spe.setSizePolicy(sizePolicy)
         self.pushButton_spe.setMaximumSize(QtCore.QSize(16777215, 30))
         self.pushButton_spe.setObjectName("pushButton_spe")
-        self.horizontalLayout_3.addWidget(self.pushButton_spe)
-        self.gridLayout.addLayout(self.horizontalLayout_3, 1, 1, 1, 1)
-        self.verticalLayout.addLayout(self.gridLayout)
-        self.verticalLayout_2.addLayout(self.verticalLayout)
+        self.horizontalLayout_5.addWidget(self.pushButton_spe)
+        self.verticalLayout_2.addLayout(self.horizontalLayout_5)
+        self.horizontalLayout_2.addLayout(self.verticalLayout_2)
+        self.verticalLayout.addLayout(self.horizontalLayout_2)
         self.verticalLayout_plot = QtGui.QVBoxLayout()
         self.verticalLayout_plot.setObjectName("verticalLayout_plot")
-        self.horizontalLayout_plot = QtGui.QHBoxLayout()
-        self.horizontalLayout_plot.setObjectName("horizontalLayout_plot")
-        self.verticalLayout_plot.addLayout(self.horizontalLayout_plot)
-        self.verticalLayout_2.addLayout(self.verticalLayout_plot)
+        self.verticalLayout.addLayout(self.verticalLayout_plot)
 
         self.retranslateUi(postprocessing)
         QtCore.QMetaObject.connectSlotsByName(postprocessing)
 
     def retranslateUi(self, postprocessing):
         postprocessing.setWindowTitle(QtGui.QApplication.translate("postprocessing", "Postprocessing", None, QtGui.QApplication.UnicodeUTF8))
+        self.label.setText(QtGui.QApplication.translate("postprocessing", "Selection", None, QtGui.QApplication.UnicodeUTF8))
         self.pushButton_rect.setText(QtGui.QApplication.translate("postprocessing", "Rectangle", None, QtGui.QApplication.UnicodeUTF8))
         self.pushButton_poly.setText(QtGui.QApplication.translate("postprocessing", "Polygon", None, QtGui.QApplication.UnicodeUTF8))
-        self.label.setText(QtGui.QApplication.translate("postprocessing", "Selection", None, QtGui.QApplication.UnicodeUTF8))
+        self.pushButton_plot.setText(QtGui.QApplication.translate("postprocessing", "Plot", None, QtGui.QApplication.UnicodeUTF8))
         self.label_2.setText(QtGui.QApplication.translate("postprocessing", "Color by", None, QtGui.QApplication.UnicodeUTF8))
         self.pushButton_snr.setText(QtGui.QApplication.translate("postprocessing", "SNR", None, QtGui.QApplication.UnicodeUTF8))
         self.pushButton_pe.setText(QtGui.QApplication.translate("postprocessing", "PE", None, QtGui.QApplication.UnicodeUTF8))
diff --git a/pylot/core/active/gui/vtk_tools_layout.py b/pylot/core/active/gui/vtk_tools_layout.py
index da475fc4..0782de77 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: Tue Aug  9 11:40:27 2016
+# Created: Wed Aug 10 14:11:07 2016
 #      by: pyside-uic 0.2.15 running on PySide 1.2.2
 #
 # WARNING! All changes made in this file will be lost!
diff --git a/pylot/core/active/gui/windows.py b/pylot/core/active/gui/windows.py
index 84d63790..50d15b0f 100644
--- a/pylot/core/active/gui/windows.py
+++ b/pylot/core/active/gui/windows.py
@@ -14,6 +14,8 @@ from fmtomo_parameters_layout import Ui_fmtomo_parameters
 from vtk_tools_layout import Ui_vtk_tools
 from postprocessing_layout import Ui_postprocessing
 
+from pylot.core.active.surveyPlotTools import regions
+
 matplotlib.use('Qt4Agg')
 matplotlib.rcParams['backend.qt4']='PySide'
 
@@ -602,27 +604,22 @@ class Postprocessing(object):
     def __init__(self, mainwindow, survey):
         self.mainwindow = mainwindow
         self.survey = survey
-        self.init_dialog()
-        self.start_dialog()
-
-    def init_dialog(self):
+        self.init_widget()
+        self.start_widget()
+        
+    def init_widget(self):
         qwidget = QtGui.QWidget()#
         ui = Ui_postprocessing()
         ui.setupUi(qwidget)
         self.ui = ui
         self.qwidget = qwidget
         self.initPlot()
-        self.plot()
-        #self.connectButtons()
-
-    def start_dialog(self):
+        self.newPlot()
+        self.connectButtons()
+        self.region = regions(self.ax, self.cbar, self.survey, qt_interface = True)
+        
+    def start_widget(self):
         self.qwidget.show()
-        # if self.qwidget.exec_():
-        #     #self.refresh_selection()
-        #     self.executed = True
-        # else:
-        #     self.refresh_selection()
-        #     self.executed = False
 
     def initPlot(self):
         self.figure = Figure()
@@ -631,27 +628,60 @@ class Postprocessing(object):
         self.toolbar = NavigationToolbar(self.canvas, self.mainwindow)
         self.ui.verticalLayout_plot.addWidget(self.toolbar)
         
-    def plot(self):
-        survey = self.survey
+    def newPlot(self):
         ax = self.figure.add_subplot(111)
-        dist, pick, snrlog, pickerror, spe = survey.preparePlotAllPicks(plotRemoved = False)
-        ax, cbar, sc = survey.createPlot(dist, pick, snrlog, '123', ax = ax, cbar = None)
-        self.cbar = self.figure.colorbar(sc, fraction=0.05)
+        dists, picks, snrlog, pe, spe = self.survey.preparePlotAllPicks(plotRemoved = False)
+        self.dists = dists
+        self.picks = picks
+        self.inkDict = {'snrlog': snrlog,
+                        'pe': pe,
+                        'spe': spe}
+                   
+        ax, cbar, sc = self.survey.createPlot(dists, picks, snrlog, 'log10(SNR)', ax = ax, cbar = None)
+        self.cbar = self.figure.colorbar(sc, ax = ax, fraction=0.05)
         self.ax = ax
-        
-    # def refresh_selection(self):
-    #     self.obsdir = self.ui.lineEdit_obs.text()
-    #     self.fstart = self.ui.fstart.text()
-    #     self.fend = self.ui.fend.text()
+        self.draw()
 
+    def refreshPlot(self, inkByVal = 'snrlog'):
+        self.ax.clear()
+        ax = self.ax
+        ax, cbar, sc = self.survey.createPlot(self.dists, self.picks, self.inkDict[inkByVal],
+                                              inkByVal, ax = ax, cbar = self.cbar)
+        #self.cbar = self.figure.colorbar(sc, fraction=0.05)
+        self.draw()
+        
     def update_survey(self, survey):
         self.survey = survey
         
     def get_survey(self):
         return self.survey
 
-    # def connectButtons(self):
-    #     QtCore.QObject.connect(self.ui.pushButton_obs, QtCore.SIGNAL("clicked()"), self.chooseObsdir)
+    def draw(self):
+        self.canvas.draw()
+        
+    def connectButtons(self):
+        QtCore.QObject.connect(self.ui.pushButton_rect, QtCore.SIGNAL("clicked()"), self.chooseRect)
+        QtCore.QObject.connect(self.ui.pushButton_poly, QtCore.SIGNAL("clicked()"), self.choosePoly)
+        QtCore.QObject.connect(self.ui.pushButton_plot, QtCore.SIGNAL("clicked()"), self.plotPicks)
+        QtCore.QObject.connect(self.ui.pushButton_snr, QtCore.SIGNAL("clicked()"), self.refrSNR)
+        QtCore.QObject.connect(self.ui.pushButton_pe, QtCore.SIGNAL("clicked()"), self.refrPE)
+        QtCore.QObject.connect(self.ui.pushButton_spe, QtCore.SIGNAL("clicked()"), self.refrSPE)
+
+    def chooseRect(self):
+        self.region.chooseRectangles()
+
+    def choosePoly(self):
+        self.region.choosePolygon()
+
+    def plotPicks(self):
+        self.region.plotTracesInActiveRegions()
+
+    def refrSNR(self):
+        self.refreshPlot('snrlog')
+
+    def refrPE(self):
+        self.refreshPlot('pe')
+
+    def refrSPE(self):
+        self.refreshPlot('spe')
 
-    # def chooseObsdir(self):
-    #     self.ui.lineEdit_obs.setText(browseDir('Choose observation directory.'))
diff --git a/pylot/core/active/surveyPlotTools.py b/pylot/core/active/surveyPlotTools.py
index 5dd34d81..c196fc51 100644
--- a/pylot/core/active/surveyPlotTools.py
+++ b/pylot/core/active/surveyPlotTools.py
@@ -29,7 +29,7 @@ class regions(object):
 
     '''
 
-    def __init__(self, ax, cbar, survey):
+    def __init__(self, ax, cbar, survey, qt_interface = False):
         self.ax = ax
         self.cbar = cbar
         self.cbv = 'log10SNR'
@@ -45,12 +45,13 @@ class regions(object):
         self._y1 = []
         self._polyx = []
         self._polyy = []
-        self.buttons = {}
         self._allpicks = None
         self.shots_found = {}
         self.shots_for_deletion = {}
         self._generateList()
-        self._addButtons()
+        if not qt_interface:
+            self.buttons = {}
+            self._addButtons()
         self.addTextfield()
         self.drawFigure()
 
@@ -525,4 +526,5 @@ class regions(object):
         if resetAxes == True:
             self.ax.set_xlim(self._xlim)
             self.ax.set_ylim(self._ylim)
-        plt.draw()
+        self.ax.figure.canvas.draw()
+        

From 36e7bc1bb287a9376107943cfb8f8ae6ccc80591 Mon Sep 17 00:00:00 2001
From: sebastianp <sebastian.priebe@rub.de>
Date: Thu, 11 Aug 2016 16:13:53 +0200
Subject: [PATCH 4/5] [documentation] adding docstring to all the methods.

---
 pylot/core/pick/compare.py | 146 +++++++++++++++++++++++++++++++++----
 pylot/core/util/pdf.py     |   4 +-
 pylot/core/util/utils.py   |   8 +-
 3 files changed, 137 insertions(+), 21 deletions(-)

diff --git a/pylot/core/pick/compare.py b/pylot/core/pick/compare.py
index 2cb128b7..a56e58e8 100644
--- a/pylot/core/pick/compare.py
+++ b/pylot/core/pick/compare.py
@@ -339,16 +339,30 @@ class PDFDictionary(object):
 
 
 class PDFstatistics(object):
-    '''
-    To do:
-    plots for std, quantiles,
-    '''
+    """
+    This object can be used to get various statistic values from probabillity density functions.
+    Takes a path as argument.
+    """
+
+
     def __init__(self, directory):
+        """Initiates some values needed when dealing with pdfs later"""
         self.directory = directory
         self.evtlist = list()
         self.return_phase = None
 
+
     def readTheta(self, arname, dir, fnpattern):
+        """
+        Loads an array from file into object instance.
+        :param arname: Name of Array beeing created.
+        :type  arname: string
+        :param dir: Directory where file is to be found.
+        :type  dir: string
+        :param fnpattern: file name pattern for reading multiple files into one array.
+        :type  fnpattern: string
+        :return: a list with all args* from the files.
+        """
         exec('self.' + arname +' = []')
         filelist = glob.glob1(dir, fnpattern)
         for file in filelist:
@@ -359,8 +373,14 @@ class PDFstatistics(object):
             exec('self.' + arname + ' += list')
             fid.close()
 
+
     def makeFileList(self, fn_pattern='*.xml'):
-        evtlist = list()
+        """
+        Takes a file pattern and searches for that recursively in the set path for the object.
+        :param fn_pattern: A pattern that can identify all datafiles. Default Value = '*.xml'
+        :type  fn_pattern: string
+        :return: creates a list of events saved in the PDFstatistics object.
+        """
         evtlist = glob.glob1((os.path.join(self.directory)), fn_pattern)
         if not evtlist:
              for root, _, files in os.walk(self.directory):
@@ -369,7 +389,9 @@ class PDFstatistics(object):
                          evtlist.append(os.path.join(root, file))
         self.evtlist = evtlist
 
+
     def __iter__(self):
+        """Iterating over the PDFstatistics object yields every single pdf from the list of events"""
         assert isinstance(self.return_phase, str), 'phase has to be set before being able to iterate over items...'
         for evt in self.evtlist:
             self.getPDFDict(self.directory, evt)
@@ -379,13 +401,30 @@ class PDFstatistics(object):
                 except KeyError:
                     continue
 
+
     def set_return_phase(self, type):
+        """
+        Sets the phase typ of event data that is returned on iteration over the object.
+        :param type: can be either p (p-phase) or s (s-phase).
+        :type  type: string
+        :return: -
+        """
         if type.upper() not in 'PS':
             raise ValueError("phase type must be either 'P' or 'S'!")
         else:
             self.return_phase = type.upper()
 
+
     def getQD(self,value):
+        """
+        Takes a probability value and and returns the distance
+        between two complementary quantiles.
+        For example: getQD(0.3) yields Quantile(1-0.3) - Quantile(0.3)
+        :param value: 0 < value < 0.5
+        :type  value: float
+        :return: returns a list of all quantile distances for all pdfs in
+                 the list of events.
+        """
         QDlist = []
         for pdf in self:
             QD = pdf.quantile_distance(value)
@@ -394,6 +433,16 @@ class PDFstatistics(object):
 
 
     def getQDQ(self,value):
+        """
+        Takes a probability value and and returns the fraction of
+        two quantile distances.
+        For example:
+        getQDQ(x) = getQD(0.5-x)/getQD(x)
+        (Quantile(1-0.5-x) - Quantile(x)) / (Quantile(1-x) - Quantile(x))
+        :param value: 0 < value < 0.25
+        :return: returns a list of all quantile fractions for all pdfs in
+                 the list of events.
+        """
         QDQlist = []
         for pdf in self:
             QDQ = pdf.qtile_dist_quot(value)
@@ -402,6 +451,12 @@ class PDFstatistics(object):
 
 
     def getSTD(self):
+        """
+        Iterates over PDFstatistics object and returns the standard
+        deviation of all pdfs in the list of events.
+        :return: saves an instance of self.p_stdarray or
+                 self.s_stdarray, depending on set phase.
+        """
         std = []
         for pdf in self:
             try:
@@ -413,6 +468,10 @@ class PDFstatistics(object):
 
 
     def set_stdarray(self, array):
+        """
+        Helper function for self.getSTD(). This function
+        should not be called directly.
+        """
         if self.return_phase == 'P':
             self.p_stdarray = array
         elif self.return_phase == 'S':
@@ -423,6 +482,22 @@ class PDFstatistics(object):
 
 
     def getBinList(self,l_boundary,u_boundary,nbins = 100):
+        """
+        Helper function for self.histplot(). Takes in two boundaries and
+        a number of bins and creates a list of bins which can be passed
+        to self.histplot().
+        :param l_boundary: Any number.
+        :type  l_boundary: float
+        :param u_boundary: Any number that is greater than l_boundary.
+        :type  u_boundary: float
+        :param nbins: Any positive integer.
+        :type  nbins: int
+        :return: A list of equidistant bins.
+        """
+        if u_boundary <= l_boundary:
+            raise ValueError('Upper boundary must be greather than lower!')
+        elif nbins <= 0:
+            raise ValueError('Number of bins is not valid.')
         binlist = []
         for i in range(nbins):
             binlist.append(l_boundary + i*(u_boundary-l_boundary)/nbins)
@@ -430,28 +505,57 @@ class PDFstatistics(object):
 
 
     def histplot(self, array, binlist, xlab = 'Values',
-                 ylab = 'Frequency', title = None, label=None,
-                 fnout = None):
+                 ylab = 'Frequency', title = None, fnout = None):
+        """
+        Method to quickly show some distribution of data. Takes array like data,
+        and a list of bins. Editing detail and inserting a legend is not possible.
+        :param array: List of values.
+        :type  array: Array like
+        :param binlist: List of bins.
+        :type  binlist: list
+        :param xlab: A label for the x-axes.
+        :type  xlab: str
+        :param ylab: A label for the y-axes.
+        :type  ylab: str
+        :param title: A title for the Plot.
+        :type  title: str
+        :param fnout: A path to save the plot instead of showing.
+                      Has to contain filename and type. Like: 'path/to/file.png'
+        :type  fnout. str
+        :return: -
+        """
         import matplotlib.pyplot as plt
         plt.hist(array,bins = binlist)
-        plt.xlabel('Values')
-        plt.ylabel('Frequency')
+        plt.xlabel(xlab)
+        plt.ylabel(ylab)
         if title:
-            title_str = 'Quantile distance quotient distribution'
-            if label:
-                title_str += ' (' + label + ')'
-            plt.title(title_str)
+            plt.title(title)
         if fnout:
-            plt.savefig(fnout+'histplot.png')
+            plt.savefig(fnout)
         else:
             plt.show()
 
 
     def getPDFDict(self, month, evt):
+        """
+        Helper function for __iter__(). Should not be called directly.
+        """
         self.pdfdict = PDFDictionary.from_quakeml(os.path.join(self.directory,month,evt))
 
 
     def getStatistics(self):
+        """
+        On call function will get mean, median and standard deviation values
+        from self.p_stdarray and self.s_stdarray. Both must be
+        instances before calling this function.
+        :return: Creates instances of self.p_mean, self.p_std_std and self.p_median
+                 for both phases (simultaneously) for the PDFstatistics object.
+        """
+        if not self.p_stdarray or not self.s_stdarray:
+            raise NotImplementedError('Arrays are not properly set yet!')
+        elif type(self.p_stdarray) != type(np.zeros(1)) or type(self.s_stdarray) != type(np.zeros(1)):
+            raise TypeError('Array is not a proper numpy array.')
+
         self.p_mean = self.p_stdarray.mean()
         self.p_std_std = self.p_stdarray.std()
         self.p_median = np.median(self.p_stdarray)
@@ -460,12 +564,22 @@ class PDFstatistics(object):
         self.s_median = np.median(self.s_stdarray)
 
 
-    def writeThetaToFile(self,array,out_dir,filename = None):
-        fid = open(os.path.join(out_dir,filename), 'w')
+    def writeThetaToFile(self,array,out_dir):
+        """
+        Method to write array like data to file. Useful since acquiring can take
+        serious amount of time when dealing with large databases.
+        :param array: List of values.
+        :type  array: list
+        :param out_dir: Path to save file to including file name.
+        :type  out_dir: str
+        :return: Saves a file at given output directory.
+        """
+        fid = open(os.path.join(out_dir), 'w')
         for val in array:
             fid.write(str(val)+'\n')
         fid.close()
 
+
 def main():
     root_dir ='/home/sebastianp/Codetesting/xmls/'
     Insheim = PDFstatistics(root_dir)
diff --git a/pylot/core/util/pdf.py b/pylot/core/util/pdf.py
index 94c847ce..814b7112 100644
--- a/pylot/core/util/pdf.py
+++ b/pylot/core/util/pdf.py
@@ -363,13 +363,15 @@ class ProbabilityDensityFunction(object):
         return m
 
     def quantile_distance(self, prob_value):
+        if 0 >= prob_value or prob_value >= 0.5:
+            raise ValueError('Value out of range.')
         ql = self.quantile(prob_value)
         qu = self.quantile(1 - prob_value)
         return qu - ql
 
 
     def qtile_dist_quot(self,x):
-        if x <= 0 or x >= 0.5:
+        if x <= 0 or x >= 0.25:
             raise ValueError('Value out of range.')
         return self.quantile_distance(0.5-x)/self.quantile_distance(x)
 
diff --git a/pylot/core/util/utils.py b/pylot/core/util/utils.py
index b24efb4d..1149ae4f 100644
--- a/pylot/core/util/utils.py
+++ b/pylot/core/util/utils.py
@@ -223,10 +223,10 @@ def getPatternLine(fn, pattern):
 
 def isSorted(iterable):
     '''
-
-    :param iterable:
-    :type iterable:
-    :return:
+    Takes an iterable and checks if args* are in order.
+    :param iterable: any with defined __ls__() and __gs__()
+    :type iterable: list
+    :return: Boolean
     '''
     return sorted(iterable) == iterable
 

From 49727b25df5e33d108aa75bcef1cfd4684ca3600 Mon Sep 17 00:00:00 2001
From: Sebastianw Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Fri, 12 Aug 2016 09:50:36 +0200
Subject: [PATCH 5/5] [change] improved docstrings and testing of utils.py

---
 pylot/core/util/utils.py | 132 ++++++++++++++++++++++++++++-----------
 1 file changed, 96 insertions(+), 36 deletions(-)

diff --git a/pylot/core/util/utils.py b/pylot/core/util/utils.py
index 1149ae4f..f49dd67d 100644
--- a/pylot/core/util/utils.py
+++ b/pylot/core/util/utils.py
@@ -83,8 +83,8 @@ def clims(lim1, lim2):
 
 def demeanTrace(trace, window):
     """
-    returns the DATA where each trace is demean by the average value within
-    WINDOW
+    takes a trace object and returns the same trace object but with data
+    demeaned within a certain time window
     :param trace: waveform trace object
     :type trace: `~obspy.core.stream.Trace`
     :param window:
@@ -101,9 +101,9 @@ def findComboBoxIndex(combo_box, val):
     Function findComboBoxIndex takes a QComboBox object and a string and
     returns either 0 or the index throughout all QComboBox items.
     :param combo_box: Combo box object.
-    :type combo_box: QComboBox
+    :type combo_box: `~QComboBox`
     :param val: Name of a combo box to search for.
-    :type val:
+    :type val: basestring
     :return: index value of item with name val or 0
     """
     return combo_box.findText(val) if combo_box.findText(val) is not -1 else 0
@@ -111,21 +111,35 @@ def findComboBoxIndex(combo_box, val):
 
 def find_nearest(array, value):
     '''
-    Function find_nearest takes an array and a value and returns the
-    index of the nearest value found in the array.
-    :param array:
-    :param value:
-    :return:
+    function find_nearest takes an array and a value and returns the
+    index of the nearest value found in the array
+    :param array: array containing values
+    :type array: `~numpy.ndarray`
+    :param value: number searched for
+    :return: index of the array item being nearest to the value
+
+    >>> a = np.array([ 1.80339578, -0.72546654,  0.95769195, -0.98320759, 0.85922623])
+    >>> find_nearest(a, 1.3)
+    2
+    >>> find_nearest(a, 0)
+    1
+    >>> find_nearest(a, 2)
+    0
+    >>> find_nearest(a, -1)
+    3
+    >>> a = np.array([ 1.1, -0.7,  0.9, -0.9, 0.8])
+    >>> find_nearest(a, 0.849)
+    4
     '''
     return (np.abs(array - value)).argmin()
 
 
 def fnConstructor(s):
     '''
-
-    :param s:
-    :type s:
-    :return:
+    takes a string and returns a valid filename (especially on windows machines)
+    :param s: desired filename
+    :type s: str
+    :return: valid filename
     '''
     if type(s) is str:
         s = s.split(':')[-1]
@@ -143,7 +157,21 @@ def fnConstructor(s):
 
 
 def four_digits(year):
-    if year + 2000 < UTCDateTime.utcnow().year:
+    """
+    takes a two digit year integer and returns the correct four digit equivalent
+    from the last 100 years
+    :param year: two digit year
+    :type year: int
+    :return: four digit year correspondant
+
+    >>> four_digits(20)
+    1920
+    >>> four_digits(16)
+    2016
+    >>> four_digits(00)
+    2000
+    """
+    if year + 2000 <= UTCDateTime.utcnow().year:
         year += 2000
     else:
         year += 1900
@@ -152,10 +180,11 @@ def four_digits(year):
 
 def getGlobalTimes(stream):
     '''
-
-    :param stream:
-    :type stream
-    :return:
+    takes a stream object and returns the latest end and the earliest start
+    time of all contained trace objects
+    :param stream: seismological data stream
+    :type stream: `~obspy.core.stream.Stream`
+    :return: minimum start time and maximum end time
     '''
     min_start = UTCDateTime()
     max_end = None
@@ -169,6 +198,8 @@ def getGlobalTimes(stream):
 
 def getHash(time):
     '''
+    takes a time object and returns the corresponding SHA1 hash of the
+    formatted date string
     :param time: time object for which a hash should be calculated
     :type time: :class: `~obspy.core.utcdatetime.UTCDateTime` object
     :return: str
@@ -180,27 +211,26 @@ def getHash(time):
 
 def getLogin():
     '''
-
-    :return:
+    returns the actual user's login ID
+    :return: login ID
     '''
     return pwd.getpwuid(os.getuid())[0]
 
 
 def getOwner(fn):
     '''
-
-    :param fn:
-    :type fn:
-    :return:
+    takes a filename and return the login ID of the actual owner of the file
+    :param fn: filename of the file tested
+    :type fn: str
+    :return: login ID of the file's owner
     '''
     return pwd.getpwuid(os.stat(fn).st_uid).pw_name
 
 
 def getPatternLine(fn, pattern):
     """
-    Takes a file name and a pattern string to search for in the file and
-    returns the first line which contains the pattern string otherwise None.
-
+    takes a file name and a pattern string to search for in the file and
+    returns the first line which contains the pattern string otherwise 'None'
     :param fn: file name
     :type fn: str
     :param pattern: pattern string to search for
@@ -223,22 +253,52 @@ def getPatternLine(fn, pattern):
 
 def isSorted(iterable):
     '''
-    Takes an iterable and checks if args* are in order.
-    :param iterable: any with defined __ls__() and __gs__()
-    :type iterable: list
+    takes an iterable and returns 'True' if the items are in order otherwise
+    'False'
+    :param iterable: an iterable object
+    :type iterable:
     :return: Boolean
+
+    >>> isSorted(1)
+    Traceback (most recent call last):
+    ...
+    AssertionError: object is not iterable; object: 1
+    >>> isSorted([1,2,3,4])
+    True
+    >>> isSorted('abcd')
+    True
+    >>> isSorted('bcad')
+    False
+    >>> isSorted([2,3,1,4])
+    False
     '''
+    assert isIterable(iterable), 'object is not iterable; object: {' \
+                                 '0}'.format(iterable)
+    if type(iterable) is str:
+        iterable = [s for s in iterable]
     return sorted(iterable) == iterable
 
 
+def isIterable(obj):
+    """
+    takes a python object and returns 'True' is the object is iterable and
+    'False' otherwise
+    :param obj: a python object
+    :return: True of False
+    """
+    try:
+        iterator = iter(obj)
+    except TypeError as te:
+        return False
+    return True
+
 def prepTimeAxis(stime, trace):
     '''
-
-    :param stime:
-    :type stime:
-    :param trace:
-     :type trace:
-    :return:
+    takes a starttime and a trace object and returns a valid time axis for
+    plotting
+    :param stime: start time of the actual seismogram as UTCDateTime
+    :param trace: seismic trace object
+    :return: valid numpy array with time stamps for plotting
     '''
     nsamp = trace.stats.npts
     srate = trace.stats.sampling_rate