[update] added possibility to remove the mean from picks (WIP for residual plotting)

# Conflicts:
#	pylot/core/util/widgets.py

PyLoT.py

@@ -686,10 +686,9 @@ class MainWindow(QMainWindow):
         # add scroll area used in case number of traces gets too high
         self.wf_scroll_area = QtWidgets.QScrollArea(self)
         self.wf_scroll_area.setVisible(False)
-        self.no_data_label = QLabel('No Data')
+        self.no_data_label = QLabel('No Data. If data were already loaded, try to select the event again in the eventbox.')
         self.no_data_label.setStyleSheet('color: red')
         self.no_data_label.setAlignment(Qt.AlignCenter)
-
         # create central matplotlib figure canvas widget
         self.init_wfWidget()
 
@@ -1032,6 +1031,21 @@ class MainWindow(QMainWindow):
                 fname = self.filename_from_action(action)
                 if not fname:
                     return
+
+        qmb = QMessageBox(self, icon=QMessageBox.Question,
+                          text='Do you want to overwrite this data?',)
+        overwrite_button = qmb.addButton('Overwrite', QMessageBox.YesRole)
+        merge_button = qmb.addButton('Merge', QMessageBox.NoRole)
+
+        qmb.exec_()
+
+        if qmb.clickedButton() == overwrite_button:
+            merge_strategy = 'Overwrite'
+        elif qmb.clickedButton() == merge_button:
+            merge_strategy = 'Merge'
+        else:
+            return
+
         if not event:
             event = self.get_current_event()
         data = Data(self, event)

README.md

@@ -11,7 +11,7 @@ PILOT has originally been developed in Mathworks' MatLab. In order to distribute
 problems, it has been decided to redevelop the software package in Python. The great work of the ObsPy group allows easy
 handling of a bunch of seismic data and PyLoT will benefit a lot compared to the former MatLab version.
 
-The development of PyLoT is part of the joint research project MAGS2 and AlpArray.
+The development of PyLoT is part of the joint research project MAGS2, AlpArray and AdriaArray.
 
 ## Installation
 
@@ -27,28 +27,30 @@ Afterwards run (from the PyLoT main directory where the files *requirements.txt*
     conda env create -f pylot.yml
 or
     
-    conda create --name pylot_38 --file requirements.txt
+    conda create -c conda-forge --name pylot_311 python=3.11 --file requirements.txt
 
-to create a new Anaconda environment called "pylot_38".
+to create a new Anaconda environment called *pylot_311*.
 
 Afterwards activate the environment by typing
 
-    conda activate pylot_38
+    conda activate pylot_311
 
 #### Prerequisites:
 
 In order to run PyLoT you need to install:
 
 - Python 3
-- obspy
-- pyside2
-- pyqtgraph
 - cartopy
+- joblib
+- obspy
+- pyaml
+- pyqtgraph
+- pyside2
 
 (the following are already dependencies of the above packages):
 - scipy
 - numpy
-- matplotlib <= 3.3.x
+- matplotlib
 
 #### Some handwork:
 
@@ -108,4 +110,4 @@ Others: A. Bruestle, T. Meier, W. Friederich
 
 [ObsPy]: http://github.com/obspy/obspy/wiki
 
-April 2022
+August 2024

pylot.yml

@@ -1,14 +1,12 @@
-name: pylot_38
+name: pylot_311
 channels:
   - conda-forge
   - defaults
 dependencies:
-  - cartopy=0.20.2
+  - cartopy=0.23.0=py311hcf9f919_1
-  - matplotlib-base=3.3.4
+  - joblib=1.4.2=pyhd8ed1ab_0
-  - numpy=1.22.3
+  - obspy=1.4.1=py311he736701_3
-  - obspy=1.3.0
+  - pyaml=24.7.0=pyhd8ed1ab_0
-  - pyqtgraph=0.12.4
+  - pyqtgraph=0.13.7=pyhd8ed1ab_0
-  - pyside2>=5.13.2
+  - pyside2=5.15.8=py311h3d699ce_4
-  - python=3.8.12
+  - pytest=8.3.2=pyhd8ed1ab_0
-  - qt>=5.12.9
-  - scipy=1.8.0

pylot/core/util/array_map.py

@@ -5,12 +5,13 @@ import traceback
 
 import cartopy.crs as ccrs
 import cartopy.feature as cf
+from cartopy.mpl.ticker import LongitudeFormatter, LatitudeFormatter
 import matplotlib
 import matplotlib.patheffects as PathEffects
 import matplotlib.pyplot as plt
 import numpy as np
 import obspy
-from PySide2 import QtWidgets
+from PySide2 import QtWidgets, QtGui
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes
 from pylot.core.util.utils import identifyPhaseID
@@ -24,10 +25,10 @@ matplotlib.use('Qt5Agg')
 
 class MplCanvas(FigureCanvas):
 
-    def __init__(self, parent=None, extern_axes=None, width=5, height=4, dpi=100):
+    def __init__(self, extern_axes=None, projection=None, width=15, height=5, dpi=100):
         if extern_axes is None:
             self.fig = plt.figure(figsize=(width, height), dpi=dpi)
-            self.axes = self.fig.add_subplot(111)
+            self.axes = self.fig.add_subplot(111, projection=projection)
         else:
             self.fig = extern_axes.figure
             self.axes = extern_axes
@@ -63,20 +64,25 @@ class Array_map(QtWidgets.QWidget):
         self.highlighted_stations = []
 
         # call functions to draw everything
+        self.projection = ccrs.PlateCarree()
         self.init_graphics()
+        self.ax = self.canvas.axes
+        self.ax.set_adjustable('datalim')
+
         self.init_stations()
         self.init_crtpyMap()
         self.init_map()
+
         # set original map limits to fall back on when home button is pressed
-        self.org_xlim = self.canvas.axes.get_xlim()
+        self.org_xlim = self.ax.get_xlim()
-        self.org_ylim = self.canvas.axes.get_ylim()
+        self.org_ylim = self.ax.get_ylim()
+
         # initial map without event
-        self.canvas.axes.set_xlim(self.org_xlim[0], self.org_xlim[1])
+        self.ax.set_xlim(self.org_xlim[0], self.org_xlim[1])
-        self.canvas.axes.set_ylim(self.org_ylim[0], self.org_ylim[1])
+        self.ax.set_ylim(self.org_ylim[0], self.org_ylim[1])
 
         self._style = None if not hasattr(parent, '_style') else parent._style
 
-
     def init_map(self):
         self.init_colormap()
         self.connectSignals()
@@ -89,11 +95,11 @@ class Array_map(QtWidgets.QWidget):
         # initialize figure elements
 
         if self.extern_plot_axes is None:
-            self.canvas = MplCanvas(self)
+            self.canvas = MplCanvas(projection=self.projection)
-            self.plotWidget = FigureCanvas(self.canvas.fig)
         else:
-            self.canvas = MplCanvas(self, extern_axes=self.extern_plot_axes)
+            self.canvas = MplCanvas(extern_axes=self.extern_plot_axes)
-            self.plotWidget = FigureCanvas(self.canvas.fig)
+
+        self.plotWidget = self.canvas
 
         # initialize GUI elements
         self.status_label = QtWidgets.QLabel()
@@ -105,7 +111,7 @@ class Array_map(QtWidgets.QWidget):
         self.setLayout(self.main_box)
 
         self.top_row = QtWidgets.QHBoxLayout()
-        self.main_box.addLayout(self.top_row, 1)
+        self.main_box.addLayout(self.top_row, 0)
 
         self.comboBox_phase = QtWidgets.QComboBox()
         self.comboBox_phase.insertItem(0, 'P')
@@ -138,10 +144,10 @@ class Array_map(QtWidgets.QWidget):
         self.top_row.addWidget(self.auto_refresh_box)
         self.top_row.addWidget(self.refresh_button)
 
-        self.main_box.addWidget(self.plotWidget, 1)
+        self.main_box.addWidget(self.plotWidget, 10)
 
         self.bot_row = QtWidgets.QHBoxLayout()
-        self.main_box.addLayout(self.bot_row, 0.3)
+        self.main_box.addLayout(self.bot_row, 0)
         self.bot_row.addWidget(QtWidgets.QLabel(''), 5)
         self.bot_row.addWidget(self.map_reset_button, 2)
         self.bot_row.addWidget(self.go2eq_button, 2)
@@ -153,14 +159,12 @@ class Array_map(QtWidgets.QWidget):
         self.init_lat_lon_grid()
 
     def init_crtpyMap(self):
-        self.canvas.axes.cla()
+        self.ax.add_feature(cf.LAND)
-        self.canvas.axes = plt.axes(projection=ccrs.PlateCarree())
+        self.ax.add_feature(cf.OCEAN)
-        self.canvas.axes.add_feature(cf.LAND)
+        self.ax.add_feature(cf.COASTLINE, linewidth=1, edgecolor='gray')
-        self.canvas.axes.add_feature(cf.OCEAN)
+        self.ax.add_feature(cf.BORDERS, alpha=0.7)
-        self.canvas.axes.add_feature(cf.COASTLINE, linewidth=1, edgecolor='gray')
+        self.ax.add_feature(cf.LAKES, alpha=0.7)
-        self.canvas.axes.add_feature(cf.BORDERS, alpha=0.7)
+        self.ax.add_feature(cf.RIVERS, linewidth=1)
-        self.canvas.axes.add_feature(cf.LAKES, alpha=0.7)
-        self.canvas.axes.add_feature(cf.RIVERS, linewidth=1)
 
         # parallels and meridians
         self.add_merid_paral()
@@ -168,12 +172,8 @@ class Array_map(QtWidgets.QWidget):
         self.canvas.fig.tight_layout()
 
     def add_merid_paral(self):
-        self.gridlines = self.canvas.axes.gridlines(draw_labels=False, alpha=0.6, color='gray',
+        self.gridlines = self.ax.gridlines(draw_labels=False, alpha=0.6, color='gray',
-                                                    linewidth=self.linewidth / 2, zorder=7)
+                                           linewidth=self.linewidth / 2, zorder=7, crs=ccrs.PlateCarree())
-        # TODO: current cartopy version does not support label removal. Devs are working on it.
-        #  Should be fixed in coming cartopy versions
-        # self.gridlines.xformatter = LONGITUDE_FORMATTER
-        # self.gridlines.yformatter = LATITUDE_FORMATTER
 
     def remove_merid_paral(self):
         if len(self.gridlines.xline_artists):
@@ -181,24 +181,24 @@ class Array_map(QtWidgets.QWidget):
             self.gridlines.yline_artists[0].remove()
 
     def org_map_view(self):
-        self.canvas.axes.set_xlim(self.org_xlim[0], self.org_xlim[1])
+        self.ax.set_xlim(self.org_xlim[0], self.org_xlim[1])
-        self.canvas.axes.set_ylim(self.org_ylim[0], self.org_ylim[1])
+        self.ax.set_ylim(self.org_ylim[0], self.org_ylim[1])
         # parallels and meridians
-        self.remove_merid_paral()
+        #self.remove_merid_paral()
-        self.add_merid_paral()
+        #self.add_merid_paral()
 
-        self.canvas.axes.figure.canvas.draw_idle()
+        self.canvas.draw_idle()
 
     def go2eq(self):
         if self.eventLoc:
             lats, lons = self.eventLoc
-            self.canvas.axes.set_xlim(lons - 10, lons + 10)
+            self.ax.set_xlim(lons - 10, lons + 10)
-            self.canvas.axes.set_ylim(lats - 5, lats + 5)
+            self.ax.set_ylim(lats - 5, lats + 5)
             # parallels and meridians
-            self.remove_merid_paral()
+            #self.remove_merid_paral()
-            self.add_merid_paral()
+            #self.add_merid_paral()
 
-            self.canvas.axes.figure.canvas.draw_idle()
+            self.canvas.draw_idle()
 
         else:
             self.status_label.setText('No event information available')
@@ -220,21 +220,32 @@ class Array_map(QtWidgets.QWidget):
 
     # set mouse events -----------------------------------------------------
     def mouse_moved(self, event):
-        if not event.inaxes == self.canvas.axes:
+        if not event.inaxes == self.ax:
             return
+        else:
+            cont, inds = self.sc.contains(event)
         lat = event.ydata
         lon = event.xdata
-        self.status_label.setText('Latitude: {:3.5f}, Longitude: {:3.5f}'.format(lat, lon))
+        text = f'Longitude: {lon:3.3f}, Latitude: {lat:3.3f}'
+
+        if cont:
+            indices = inds['ind']
+            text += ' | Station: ' if len(indices) == 1 else ' | Stations: '
+            text += ' - '.join([self._station_onpick_ids[index] for index in indices[:5]])
+            if len(indices) > 5:
+                text += '...'
+
+        self.status_label.setText(text)
 
     def mouse_scroll(self, event):
-        if not event.inaxes == self.canvas.axes:
+        if not event.inaxes == self.ax:
             return
 
         zoom = {'up': 1. / 2., 'down': 2.}
 
         if event.button in zoom:
-            xlim = self.canvas.axes.get_xlim()
+            xlim = self.ax.get_xlim()
-            ylim = self.canvas.axes.get_ylim()
+            ylim = self.ax.get_ylim()
 
             x, y = event.xdata, event.ydata
 
@@ -246,24 +257,24 @@ class Array_map(QtWidgets.QWidget):
             yb = y - 0.5 * ydiff
             yt = y + 0.5 * ydiff
 
-            self.canvas.axes.set_xlim(xl, xr)
+            self.ax.set_xlim(xl, xr)
-            self.canvas.axes.set_ylim(yb, yt)
+            self.ax.set_ylim(yb, yt)
             # parallels and meridians
-            self.remove_merid_paral()
+            #self.remove_merid_paral()
-            self.add_merid_paral()
+            #self.add_merid_paral()
 
-            self.canvas.axes.figure.canvas.draw_idle()
+            self.ax.figure.canvas.draw_idle()
 
     def mouseLeftPress(self, event):
-        if not event.inaxes == self.canvas.axes:
+        if not event.inaxes == self.ax:
             return
         self.map_x = event.xdata
         self.map_y = event.ydata
-        self.map_xlim = self.canvas.axes.get_xlim()
+        self.map_xlim = self.ax.get_xlim()
-        self.map_ylim = self.canvas.axes.get_ylim()
+        self.map_ylim = self.ax.get_ylim()
 
     def mouseLeftRelease(self, event):
-        if not event.inaxes == self.canvas.axes:
+        if not event.inaxes == self.ax:
             return
         new_x = event.xdata
         new_y = event.ydata
@@ -271,13 +282,13 @@ class Array_map(QtWidgets.QWidget):
         dx = new_x - self.map_x
         dy = new_y - self.map_y
 
-        self.canvas.axes.set_xlim((self.map_xlim[0] - dx, self.map_xlim[1] - dx))
+        self.ax.set_xlim((self.map_xlim[0] - dx, self.map_xlim[1] - dx))
-        self.canvas.axes.set_ylim(self.map_ylim[0] - dy, self.map_ylim[1] - dy)
+        self.ax.set_ylim(self.map_ylim[0] - dy, self.map_ylim[1] - dy)
         # parallels and meridians
-        self.remove_merid_paral()
+        #self.remove_merid_paral()
-        self.add_merid_paral()
+        #self.add_merid_paral()
 
-        self.canvas.axes.figure.canvas.draw_idle()
+        self.ax.figure.canvas.draw_idle()
 
     def onpick(self, event):
         btn_msg = {1: ' in selection. Aborted', 2: ' to delete a pick on. Aborted', 3: ' to display info.'}
@@ -421,6 +432,9 @@ class Array_map(QtWidgets.QWidget):
                     picks_rel[st_id] = pick
             return picks_rel
 
+        def get_picks_rel_mean_corr(picks):
+            return get_picks_rel(picks, func=np.nanmean)
+
         self.picks, self.uncertainties = get_picks(self.stations_dict)
         self.picks_rel = get_picks_rel(self.picks)
 
@@ -469,13 +483,20 @@ class Array_map(QtWidgets.QWidget):
         stat_dict = self.stations_dict['{}.{}'.format(network, station)]
         lat = stat_dict['latitude']
         lon = stat_dict['longitude']
-        self.highlighted_stations.append(self.canvas.axes.scatter(lon, lat, s=self.pointsize, edgecolors=color,
+        self.highlighted_stations.append(self.ax.scatter(lon, lat, s=self.pointsize, edgecolors=color,
                                                          facecolors='none', zorder=12,
                                                          transform=ccrs.PlateCarree(), label='deleted'))
 
     def openPickDlg(self, ind):
+        try:
             wfdata = self._parent.get_data().getWFData()
-        wfdata_comp = self._parent.get_data().getWFDataComp()
+        except AttributeError:
+            QtWidgets.QMessageBox.warning(
+                self, "PyLoT Warning",
+                "No waveform data found. Check if they were already loaded in Waveform plot tab."
+            )
+            return
+        wfdata_comp = self._parent.get_data().getAltWFdata()
         for index in ind:
             network, station = self._station_onpick_ids[index].split('.')[:2]
             pyl_mw = self._parent
@@ -521,7 +542,7 @@ class Array_map(QtWidgets.QWidget):
     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,
+        self.contourf = self.ax.contourf(self.longrid, self.latgrid, self.picksgrid_active, levels,
                                          linewidths=self.linewidth * 5, transform=ccrs.PlateCarree(),
                                          alpha=0.4, zorder=8, cmap=self.get_colormap())
 
@@ -531,7 +552,7 @@ class Array_map(QtWidgets.QWidget):
     def scatter_all_stations(self):
         stations, lats, lons = self.get_st_lat_lon_for_plot()
 
-        self.sc = self.canvas.axes.scatter(lons, lats, s=self.pointsize * 3, facecolor='none', marker='.',
+        self.sc = self.ax.scatter(lons, lats, s=self.pointsize * 3, facecolor='none', marker='.',
                                   zorder=10, picker=True, edgecolor='0.5', label='Not Picked',
                                   transform=ccrs.PlateCarree())
 
@@ -539,7 +560,7 @@ class Array_map(QtWidgets.QWidget):
         self._station_onpick_ids = stations
         if self.eventLoc:
             lats, lons = self.eventLoc
-            self.sc_event = self.canvas.axes.scatter(lons, lats, s=5 * self.pointsize, facecolor='red', zorder=11,
+            self.sc_event = self.ax.scatter(lons, lats, s=5 * self.pointsize, facecolor='red', zorder=11,
                                             label='Event (might be outside map region)', marker='*',
                                             edgecolors='black',
                                             transform=ccrs.PlateCarree())
@@ -555,7 +576,7 @@ class Array_map(QtWidgets.QWidget):
                           for uncertainty in uncertainties])
 
         cmap = self.get_colormap()
-        self.sc_picked = self.canvas.axes.scatter(lons, lats, s=sizes, edgecolors='white', cmap=cmap,
+        self.sc_picked = self.ax.scatter(lons, lats, s=sizes, edgecolors='white', cmap=cmap,
                                          c=picks, zorder=11, label='Picked', transform=ccrs.PlateCarree())
 
     def annotate_ax(self):
@@ -574,20 +595,20 @@ class Array_map(QtWidgets.QWidget):
             if st in self.marked_stations:
                 color = 'red'
             self.annotations.append(
-                self.canvas.axes.annotate(' %s' % st, xy=(x + 0.003, y + 0.003), fontsize=self.pointsize / 4.,
+                self.ax.annotate(f'{st}', xy=(x + 0.003, y + 0.003), fontsize=self.pointsize / 4.,
                                  fontweight='semibold', color=color, alpha=0.8,
                                  transform=ccrs.PlateCarree(), zorder=14,
                                  path_effects=[PathEffects.withStroke(
                                      linewidth=self.pointsize / 15., foreground='k')]))
 
-        self.legend = self.canvas.axes.legend(loc=1, framealpha=1)
+        self.legend = self.ax.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):
-        self.cbax_bg = inset_axes(self.canvas.axes, width="6%", height="75%", loc=5)
+        self.cbax_bg = inset_axes(self.ax, width="6%", height="75%", loc=5)
-        cbax = inset_axes(self.canvas.axes, width='2%', height='70%', loc=5)
+        cbax = inset_axes(self.ax, width='2%', height='70%', loc=5)
-        cbar = self.canvas.axes.figure.colorbar(self.sc_picked, cax=cbax)
+        cbar = self.ax.figure.colorbar(self.sc_picked, cax=cbax)
         cbar.set_label(label)
         cbax.yaxis.tick_left()
         cbax.yaxis.set_label_position('left')

pylot/core/util/utils.py

@@ -1084,8 +1084,9 @@ def check4rotated(data, metadata=None, verbosity=1):
                 azimuths.append(metadata.get_coordinates(tr_id, t_start)['azimuth'])
                 dips.append(metadata.get_coordinates(tr_id, t_start)['dip'])
         except (KeyError, TypeError) as err:
-            logging.error(f"{type(err)=} occurred: {err=} Rotating not possible, not all azimuth and dip information "
+            logging.warning(f"Rotating not possible, not all azimuth and dip information "
                             f"available in metadata. Stream remains unchanged.")
+            logging.debug(f"Rotating not possible, {err=}, {type(err)=}")
             return wfs_in
         except Exception as err:
             print(f"Unexpected {err=}, {type(err)=}")

requirements.txt

@@ -1,12 +1,7 @@
-# This file may be used to create an environment using:
+Cartopy==0.23.0
-# $ conda create --name <env> --file <this file>
+joblib==1.4.2
-# platform: win-64
+obspy==1.4.1
-cartopy=0.20.2
+pyaml==24.7.0
-matplotlib-base=3.3.4
+pyqtgraph==0.13.7
-numpy=1.22.3
+PySide2==5.15.8
-obspy=1.3.0
+pytest==8.3.2
-pyqtgraph=0.12.4
-pyside2=5.13.2
-python=3.8.12
-qt=5.12.9
-scipy=1.8.0