Implemented merge suggestions #11

PyLoT.py

@@ -36,10 +36,6 @@ import traceback
 import json
 from datetime import datetime
 
-# set environment variables to use Qt5 and don't convert to Qt4 syntax
-# os.environ['PYQTGRAPH_QT_LIB'] = 'PyQt5'
-# os.environ["QT_API"] = "pyqt5"
-
 matplotlib.use('Qt5Agg')
 
 from PySide2 import QtGui, QtCore, QtWidgets
@@ -3249,8 +3245,6 @@ class MainWindow(QMainWindow):
                         'auto': event.pylot_autopicks}
             ma_count = {'manual': 0,
                         'auto': 0}
-            #ma_count_total = {'manual': 0,
-            #                  'auto': 0}
 
             for ma in ma_props.keys():
                 if ma_props[ma]:
@@ -3260,7 +3254,6 @@ class MainWindow(QMainWindow):
                                 continue
                             if pick.get('spe'):
                                 ma_count[ma] += 1
-                            #ma_count_total[ma] += 1
 
             # init table items for current row
             item_delete = QTableWidgetItem()

pylot.yml

@@ -115,4 +115,4 @@ dependencies:
   - zipp=3.4.1=pyhd8ed1ab_0
   - zlib=1.2.11=h516909a_1010
   - zstd=1.4.9=ha95c52a_0
-prefix: /home/kaan/.conda/envs/pylot_py35
+prefix:

pylot/core/io/data.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env pyth n
+#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
 import copy
@@ -21,10 +21,6 @@ from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT
 from pylot.core.util.utils import fnConstructor, full_range, check4rotated, \
     check4gapsAndMerge, trim_station_components
 
-try:
-    str_TypeLst = [str, unicode]  # if python 2.X
-except NameError:
-    str_TypeLst = [str]  # if python 3.*
 
 class Data(object):
     """
@@ -52,7 +48,7 @@ class Data(object):
         elif isinstance(evtdata, dict):
             evt = readPILOTEvent(**evtdata)
             evtdata = evt
-        elif type(evtdata) in str_TypeLst:
+        elif isinstance(evtdata, str):
             try:
                 cat = read_events(evtdata)
                 if len(cat) != 1:

pylot/core/util/array_map.py

@@ -8,16 +8,12 @@ import matplotlib
 from PySide2 import QtCore, QtGui, QtWidgets
 from PySide2.QtCore import Qt
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
-from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
-from matplotlib.figure import Figure
 import matplotlib.patheffects as PathEffects
 
 import cartopy.crs as ccrs
 import matplotlib.pyplot as plt
 import cartopy.feature as cf
-import cartopy.io.shapereader as shpr
-from cartopy.feature import ShapelyFeature
-from cartopy.mpl.gridliner import LONGITUDE_FORMATTER, LATITUDE_FORMATTER
+from cartopy.mpl.gridliner import LongitudeFormatter, LatitudeFormatter
 
 import traceback
 import obspy
@@ -30,7 +26,6 @@ from pylot.core.pick.utils import get_quality_class
 matplotlib.use('Qt5Agg')
 
 
-
 class MplCanvas(FigureCanvas):
 
     def __init__(self, parent=None, extern_axes=None, width=5, height=4, dpi=100):
@@ -47,7 +42,6 @@ class MplCanvas(FigureCanvas):
 class Array_map(QtWidgets.QWidget):
     def __init__(self, parent, metadata, parameter=None, axes=None, annotate=True, pointsize=25.,
                  linewidth=1.5, width=5e6, height=2e6):
-        # super(Array_map, self).__init__(parent)
         QtWidgets.QWidget.__init__(self)
 
         assert (parameter is not None or parent is not None), 'either parent or parameter has to be set'
@@ -95,7 +89,7 @@ class Array_map(QtWidgets.QWidget):
 
     def init_graphics(self):
         """
-        Initializes all GUI components and figure elements to be populeted by other functions
+        Initializes all GUI components and figure elements to be populated by other functions
         """
         # initialize figure elements
 
@@ -104,8 +98,6 @@ class Array_map(QtWidgets.QWidget):
             self.plotWidget = FigureCanvas(self.canvas.fig)
         else:
             self.canvas = MplCanvas(self, extern_axes=self.extern_plot_axes)
-            #self.canvas.axes = self.extern_plot_axes
-            #self.canvas.fig = self.extern_plot_axes.figure
             self.plotWidget = FigureCanvas(self.canvas.fig)
 
         # initialize GUI elements
@@ -113,7 +105,6 @@ class Array_map(QtWidgets.QWidget):
         self.map_reset_button = QtWidgets.QPushButton('Reset Map View')
         self.save_map_button = QtWidgets.QPushButton('Save Map')
         self.go2eq_button = QtWidgets.QPushButton('Go to Event Location')
-        # self.map_reset_button.resize(150, 50)
 
         self.main_box = QtWidgets.QVBoxLayout()
         self.setLayout(self.main_box)
@@ -153,9 +144,6 @@ class Array_map(QtWidgets.QWidget):
         self.top_row.addWidget(self.refresh_button)
 
         self.main_box.addWidget(self.plotWidget, 1)
-        # self.main_box.addWidget(self.map_reset_button, 0)
-        # self.main_box.addWidget(NavigationToolbar(self.plotWidget, self), 0)
-        # self.main_box.addWidget(self.status_label, 0)
 
         self.bot_row = QtWidgets.QHBoxLayout()
         self.main_box.addLayout(self.bot_row, 0.3)
@@ -163,7 +151,6 @@ class Array_map(QtWidgets.QWidget):
         self.bot_row.addWidget(self.go2eq_button)
         self.bot_row.addWidget(self.save_map_button)
         self.bot_row.addWidget(self.status_label)
-        # self.connectSignals()
 
     def init_colormap(self):
         self.init_lat_lon_dimensions()
@@ -182,21 +169,17 @@ class Array_map(QtWidgets.QWidget):
         # parallels and meridians
         self.add_merid_paral()
 
-        # self.canvas.axes.set_global()
         self.canvas.fig.tight_layout()
-        # self.plotWidget.draw_idle()
 
     def add_merid_paral(self):
-        self.gridlines = self.canvas.axes.gridlines(draw_labels=False, alpha=0.8, color='dimgray', linewidth=self.linewidth, zorder=7)
-        # current cartopy version does not support label removal. Devs are working on it.
-        # Should be fixed with next cartopy version
+        self.gridlines = self.canvas.axes.gridlines(draw_labels=False, alpha=0.8, color='gray', linewidth=self.linewidth/2, zorder=7)
+        # TODO: current cartopy version does not support label removal. Devs are working on it.
+        #  Should be fixed with next cartopy version
         # self.gridlines.xformatter = LONGITUDE_FORMATTER
         # self.gridlines.yformatter = LATITUDE_FORMATTER
 
     def remove_merid_paral(self):
         if len(self.gridlines.xline_artists):
-            # for i in self.gridlines.xline_artists:
-            #    i.remove()
             self.gridlines.xline_artists[0].remove()
             self.gridlines.yline_artists[0].remove()
 
@@ -482,8 +465,6 @@ class Array_map(QtWidgets.QWidget):
                                                                   facecolors='none', zorder=12,
                                                                   transform=ccrs.PlateCarree(), label='deleted'))
 
-        # self.canvas.idle_draw()
-
     def openPickDlg(self, ind):
         data = self._parent.get_data().getWFData()
         for index in ind:
@@ -526,22 +507,18 @@ class Array_map(QtWidgets.QWidget):
                 print(message, e)
                 print(traceback.format_exc())
 
-    def draw_contour_filled(self, nlevel=100):
-        # self.test_gradient()
-
+    def draw_contour_filled(self, nlevel=50):
         levels = np.linspace(self.get_min_from_picks(), self.get_max_from_picks(), nlevel)
 
         self.contourf = self.canvas.axes.contourf(self.longrid, self.latgrid, self.picksgrid_active, levels,
-                                                  linewidths=self.linewidth, transform=ccrs.PlateCarree(),
-                                                  alpha=0.7, zorder=8, cmap=self.get_colormap())
+                                                  linewidths=self.linewidth*4, transform=ccrs.PlateCarree(),
+                                                  alpha=0.4, zorder=8, cmap=self.get_colormap())
 
     def get_colormap(self):
         return plt.get_cmap(self.cmaps_box.currentText())
 
     def scatter_all_stations(self):
         stations, lats, lons = self.get_st_lat_lon_for_plot()
-        # self.sc = self.basemap.scatter(lons, lats, s=self.pointsize, facecolor='none', latlon=True, marker='.',
-        #                               zorder=10, picker=True, edgecolor='0.5', label='Not Picked')
 
         self.sc = self.canvas.axes.scatter(lons, lats, s=self.pointsize * 3, facecolor='none', marker='.',
                                            zorder=10, picker=True, edgecolor='0.5', label='Not Picked',
@@ -593,6 +570,7 @@ class Array_map(QtWidgets.QWidget):
                                               linewidth=self.pointsize / 15., foreground='k')]))
 
         self.legend = self.canvas.axes.legend(loc=1, framealpha=1)
+        self.legend.set_zorder(100)
         self.legend.get_frame().set_facecolor((1, 1, 1, 0.95))
 
     def add_cbar(self, label):

pylot/core/util/generate_array_maps.py

@@ -79,11 +79,9 @@ if __name__ == '__main__':
     cl = argparse.ArgumentParser()
     cl.add_argument('--dataroot', help='Directory containing the PyLoT .plp file', type=str)
     cl.add_argument('--infiles', help='.plp files to use', nargs='+')
+    cl.add_argument('--ncores', hepl='Specify number of parallel processes', type=int, default=1)
     args = cl.parse_args()
-    #dataroot = '/home/kaan/master_thesis/waveformData/dmt_dir_proj'
-    #infiles = ['mag_8_sym_proj.plp']
 
     for infile in args.infiles:
-        main(os.path.join(args.dataroot, infile), f_ext='_correlated_0.03-0.1', ncores=1)
-    # main('E:\Shared\AlpArray\\test_aa.plp', f_ext='_correlated_0.5Hz', ncores=1)
-    # main('/home/marcel/alparray_m6.5-6.9_mantle_correlated_v3.plp', f_ext='_correlated_0.5Hz')
+        main(os.path.join(args.dataroot, infile), f_ext='_correlated_0.03-0.1', ncores=args.ncores)
+

pylot/core/util/widgets.py

@@ -53,13 +53,12 @@ from pylot.core.util.utils import prepTimeAxis, full_range, demeanTrace, isSorte
     pick_linestyle_plt, pick_color_plt, \
     check4rotated, check4doubled, merge_stream, identifyPhase, \
     loopIdentifyPhase, trim_station_components, transformFilteroptions2String, \
-    identifyPhaseID, get_Bool, get_None, pick_color, getAutoFilteroptions, SetChannelComponents,\
+    identifyPhaseID, get_Bool, get_None, pick_color, getAutoFilteroptions, SetChannelComponents, \
     station_id_remove_channel
 from autoPyLoT import autoPyLoT
 from pylot.core.util.thread import Thread
 from pylot.core.util.dataprocessing import Metadata
 
-
 if sys.version_info.major == 3:
     import icons_rc_3 as icons_rc
 elif sys.version_info.major == 2:
@@ -67,6 +66,7 @@ elif sys.version_info.major == 2:
 else:
     raise ImportError('Could not determine python version.')
 
+
 # workaround to prevent PyCharm from deleting icons_rc import when optimizing imports
 # icons_rc = icons_rc
 
@@ -302,7 +302,7 @@ class AddMetadataWidget(QWidget):
         item = QtGui.QStandardItem(inventory_path)
         item.setEditable(False)
         self.inventories_add.append(inventory_path)
-        self.list_model.appendRow(item)             # adds path to visible list
+        self.list_model.appendRow(item)  # adds path to visible list
         self.selection_box.setText("")
 
     def remove_item(self):
@@ -313,8 +313,8 @@ class AddMetadataWidget(QWidget):
         """
         for index in reversed(sorted(self.list_view.selectionModel().selectedIndexes())):
             item = self.list_model.itemData(index)
-            inventory_path = item[0]                        # marked path
-            self.list_model.removeRow(index.row())          # aus der Anzeige-Liste gelöscht
+            inventory_path = item[0]  # marked path
+            self.list_model.removeRow(index.row())  # aus der Anzeige-Liste gelöscht
             if inventory_path in self.inventories_add:
                 self.inventories_add.remove(inventory_path)
             else:
@@ -876,7 +876,8 @@ class WaveformWidgetPG(QtWidgets.QWidget):
                 times = np.array([time for index, time in enumerate(time_ax) if not index % nth_sample])
                 times_syn = np.array(
                     [time for index, time in enumerate(time_ax_syn) if not index % nth_sample] if st_syn else [])
-                trace.data = np.array([datum * gain + n for index, datum in enumerate(trace.data) if not index % nth_sample])
+                trace.data = np.array(
+                    [datum * gain + n for index, datum in enumerate(trace.data) if not index % nth_sample])
                 trace_syn.data = np.array([datum + n for index, datum in enumerate(trace_syn.data)
                                            if not index % nth_sample] if st_syn else [])
                 plots.append((times, trace.data,
@@ -1518,8 +1519,6 @@ class SingleTextLineDialog(QtWidgets.QDialog):
         self._buttonbox.rejected.connect(self.reject)
 
 
-
-
 class PhaseDefaults(QtWidgets.QDialog):
     def __init__(self, parent=None, nrow=10,
                  phase_defaults=['P', 'S'],
@@ -1988,6 +1987,7 @@ class PickDlg(QDialog):
         settings = QtCore.QSettings()
         p_phases = settings.value('p_phases')
         s_phases = settings.value('s_phases')
+        phases = ''
         if not p_phases and not s_phases:
             print('No phases for TauPy selected in Preferences.')
         if p_phases and s_phases:
@@ -2235,7 +2235,6 @@ class PickDlg(QDialog):
             self.draw()
         else:
             self.draw()
-        # self.pick_block = self.togglePickBlocker()
         self.disconnect_pick_delete()
 
     def deactivatePicking(self):
@@ -2446,7 +2445,7 @@ class PickDlg(QDialog):
         data.normalize()
         if not data:
             QtWidgets.QMessageBox.warning(self, 'No channel to plot',
-                                      'No channel to plot for phase: {}.'.format(phase))
+                                          'No channel to plot for phase: {}.'.format(phase))
             self.leave_picking_mode()
             return
 
@@ -2460,7 +2459,8 @@ class PickDlg(QDialog):
                 # wfdata.filter(**filteroptions)# MP MP removed filtering of original data
             except ValueError as e:
                 self.qmb = QtWidgets.QMessageBox(QtWidgets.QMessageBox.Icon.Information,
-                                             'Denied', 'setIniPick{}: Could not filter waveform: {}'.format(phase, e))
+                                                 'Denied',
+                                                 'setIniPick{}: Could not filter waveform: {}'.format(phase, e))
                 self.qmb.show()
 
         snr = []
@@ -2545,7 +2545,7 @@ class PickDlg(QDialog):
                 wfdata.filter(**filteroptions)
             except ValueError as e:
                 self.qmb = QtWidgets.QMessageBox(QtWidgets.QMessageBox.Icon.Information,
-                                             'Denied', 'setPick: Could not filter waveform: {}'.format(e))
+                                                 'Denied', 'setPick: Could not filter waveform: {}'.format(e))
                 self.qmb.show()
 
         # get earliest and latest possible pick and symmetric pick error
@@ -2585,9 +2585,8 @@ class PickDlg(QDialog):
             minFMSNR = parameter.get('minFMSNR')
             quality = get_quality_class(spe, parameter.get('timeerrorsP'))
             if quality <= minFMweight and snr >= minFMSNR:
-                FM = fmpicker(self.getWFData().select(channel=channel), wfdata, parameter.get('fmpickwin'), 
-                               pick -stime_diff)
-
+                FM = fmpicker(self.getWFData().select(channel=channel), wfdata, parameter.get('fmpickwin'),
+                              pick - stime_diff)
 
         # save pick times for actual phase
         phasepicks = dict(epp=epp, lpp=lpp, mpp=mpp, spe=spe, fm=FM,
@@ -2602,8 +2601,6 @@ class PickDlg(QDialog):
         self.disconnectPressEvent()
         self.enable_ar_buttons()
         self.zoomAction.setEnabled(True)
-        # self.pick_block = self.togglPickBlocker()
-        # self.resetZoom()
 
         self.leave_picking_mode()
 
@@ -2617,7 +2614,7 @@ class PickDlg(QDialog):
 
     def warn_unknown_phase(self, phase=None):
         QtWidgets.QMessageBox.warning(self, 'Unknown phase ID',
-                                  'Could not identify phase ID: {}.'.format(phase))
+                                      'Could not identify phase ID: {}.'.format(phase))
 
     def disconnectPressEvent(self):
         self.multicompfig.mpl_disconnect(self.cidpress)
@@ -2798,7 +2795,7 @@ class PickDlg(QDialog):
                 self.renamePhaseInDict(picks, phase, new_phase)
             except KeyError as e:
                 QtWidgets.QMessageBox.warning(self, 'Could not rename phase',
-                                          'Could not rename phase {} to {}: {}'.format(phase, new_phase, e))
+                                              'Could not rename phase {} to {}: {}'.format(phase, new_phase, e))
         self.leave_rename_phase()
         self.refreshPlot()
 
@@ -2905,11 +2902,6 @@ class PickDlg(QDialog):
             if phase:
                 filtoptions = self.getFilterOptions(self.getPhaseID(phase), gui_filter=True).parseFilterOptions()
 
-            # if self.filterActionP.isChecked() or self.filterActionS.isChecked():
-            #     if not phase:
-            #         filtoptions = FilterOptionsDialog.getFilterObject()
-            #         filtoptions = filtoptions.parseFilterOptions()
-
             if filtoptions is not None:
                 data.detrend('linear')
                 data.taper(0.02, type='cosine')
@@ -3028,8 +3020,6 @@ class PickDlg(QDialog):
 
         # set channel labels
         self.multicompfig.setYTickLabels(pos, labels)
-        # self.multicompfig.setXLims(ax, self.getXLims())
-        # self.multicompfig.setYLims(ax, self.getYLims())
 
     def zoom(self):
         if self.zoomAction.isChecked() and self.pick_block:
@@ -3064,7 +3054,7 @@ class PickDlg(QDialog):
         else:
             self.refreshPlot()
             self.qmb = QtWidgets.QMessageBox(QtWidgets.QMessageBox.Icon.Information,
-                                         'Denied', 'New picks rejected!')
+                                             'Denied', 'New picks rejected!')
             self.qmb.show()
 
     def accept(self):
@@ -3073,7 +3063,7 @@ class PickDlg(QDialog):
             QDialog.accept(self)
         else:
             self.qmb = QtWidgets.QMessageBox(QtWidgets.QMessageBox.Icon.Information,
-                                         'Accepted', 'New picks applied!')
+                                             'Accepted', 'New picks applied!')
             self.qmb.show()
 
 
@@ -3091,7 +3081,7 @@ class CanvasWidget(QWidget):
     '''
 
     def __init__(self, parent, canvas):
-        QtWidgets.QWidget.__init__(self, parent)#, 1)
+        QtWidgets.QWidget.__init__(self, parent)  # , 1)
         canvas = canvas
         self.main_layout = QtWidgets.QVBoxLayout()
         self.setLayout(self.main_layout)
@@ -3811,7 +3801,7 @@ class TuneAutopicker(QWidget):
                 'savexml': False,
                 'obspyDMT_wfpath': wfpath}
         event = self.get_current_event()
-        #self.parent().saveData(event, event.path, '.xml') MP MP uncommented because overwriting pick files in tune mode
+        # self.parent().saveData(event, event.path, '.xml') MP MP uncommented because overwriting pick files in tune mode
         for key in self.fig_dict.keys():
             if not key == 'plot_style':
                 self.fig_dict[key].clear()
@@ -3887,7 +3877,7 @@ class TuneAutopicker(QWidget):
 
     def _warn(self, message, info=None):
         self.qmb = QtWidgets.QMessageBox(QtWidgets.QMessageBox.Icon.Warning,
-                                     'Warning', message)
+                                         'Warning', message)
         self.qmb.setDetailedText(str(info))
         self.qmb.show()
 
@@ -4130,7 +4120,7 @@ class PylotParaBox(QtWidgets.QWidget):
         layout = QtWidgets.QVBoxLayout()
         dialog.setLayout(layout)
         buttonbox = QtWidgets.QDialogButtonBox(QDialogButtonBox.Ok |
-                                           QDialogButtonBox.Cancel)
+                                               QDialogButtonBox.Cancel)
         buttonbox.accepted.connect(dialog.accept)
         buttonbox.accepted.connect(self.refresh)
         buttonbox.accepted.connect(self.params_from_gui)
@@ -4314,7 +4304,7 @@ class PylotParaBox(QtWidgets.QWidget):
 
     def _warn(self, message):
         self.qmb = QtWidgets.QMessageBox(QtWidgets.QMessageBox.Icon.Warning,
-                                     'Warning', message)
+                                         'Warning', message)
         self.qmb.show()
 
 
@@ -4684,7 +4674,7 @@ class InputsTab(PropTab):
                   "data/Structure": self.structureSelect.setCurrentIndex(index),
                   "tstart": self.tstartBox.setValue(0),
                   "tstop": self.tstopBox.setValue(1e6),
-                  "autosaveXML": self.autosaveXML_checkbox.setChecked(True),}
+                  "autosaveXML": self.autosaveXML_checkbox.setChecked(True), }
         return values