Enabled plotting of figures when called from terminal.

autoPyLoT.py

@@ -450,16 +450,13 @@ if __name__ == "__main__":
                        autoregressive prediction and AIC followed by locating the seismic events using 
                        NLLoc''')
 
-    # parser.add_argument('-d', '-D', '--input_dict', type=str,
-    #                    action='store',
-    #                    help='''optional, dictionary containing processing parameters''')
-    # parser.add_argument('-p', '-P', '--parameter', type=str,
-    #                    action='store',
-    #                    help='''parameter file, default=None''')
     parser.add_argument('-i', '-I', '--inputfile', type=str,
                         action='store',
                         help='''full path to the file containing the input
                         parameters for autoPyLoT''')
+    parser.add_argument('-p', '-P', '--iplot', type=int, 
+                        action='store',
+                        help='''Boolean flag for plotting: 0=none, 1=partial, 2=all''') 
     parser.add_argument('-f', '-F', '--fnames', type=str,
                         action='store',
                         help='''optional, list of data file names''')
@@ -472,12 +469,9 @@ if __name__ == "__main__":
     parser.add_argument('-c', '-C', '--ncores', type=int,
                         action='store', default=0,
                         help='''optional, number of CPU cores used for parallel processing (default: all available)''')
-    # parser.add_argument('-v', '-V', '--version', action='version',
-    #                    version='autoPyLoT ' + __version__,
-    #                    help='show version information and exit')
 
     cla = parser.parse_args()
 
     picks = autoPyLoT(inputfile=str(cla.inputfile), fnames=str(cla.fnames),
                       eventid=str(cla.eventid), savepath=str(cla.spath),
-                      ncores=cla.ncores)
+                      ncores=cla.ncores, iplot=str(cla.iplot))

pylot/core/pick/autopick.py

@@ -44,27 +44,27 @@ def autopickevent(data, param, iplot=0, fig_dict=None, ncores=0, metadata=None,
     for station in stations:
         topick = data.select(station=station)
 
-        if not iplot:
+        #if not iplot:
-            input_tuples.append((topick, param, apverbose, metadata, origin))
+        #    input_tuples.append((topick, param, apverbose, metadata, origin))
-        if iplot > 0:
+        #if iplot > 0:
         all_onsets[station] = autopickstation(topick, param, verbose=apverbose,
                                               iplot=iplot, fig_dict=fig_dict,
                                               metadata=metadata, origin=origin)
 
-    if iplot > 0:
+    #if iplot > 0:
-        print('iPlot Flag active: NO MULTIPROCESSING possible.')
+    #    print('iPlot Flag active: NO MULTIPROCESSING possible.')
-        return all_onsets
+    #    return all_onsets
 
-    pool = gen_Pool(ncores)
+    #pool = gen_Pool(ncores)
-    result = pool.map(call_autopickstation, input_tuples)
+    #result = pool.map(call_autopickstation, input_tuples)
-    pool.close()
+    #pool.close()
 
-    for pick in result:
+    #for pick in result:
-        station = pick['station']
+    #    station = pick['station']
-        pick.pop('station')
+    #    pick.pop('station')
-        all_onsets[station] = pick
+    #    all_onsets[station] = pick
 
-    return all_onsets
+    #return all_onsets
 
     # quality control
     # median check and jackknife on P-onset times
@@ -95,10 +95,9 @@ def autopickstation(wfstream, pickparam, verbose=False,
 
     # declaring pickparam variables (only for convenience)
     # read your autoPyLoT.in for details!
+    plt_flag = 0
 
     # special parameters for P picking
-    iplot = iplot
-
     algoP = pickparam.get('algoP')
     pstart = pickparam.get('pstart')
     pstop = pickparam.get('pstop')
@@ -761,6 +760,7 @@ def autopickstation(wfstream, pickparam, verbose=False,
         # plot vertical trace
         if not fig_dict:
             fig = plt.figure()
+            plt_flag = 1
         else:
             fig = fig_dict['mainFig']
         ax1 = fig.add_subplot(311)
@@ -905,6 +905,10 @@ def autopickstation(wfstream, pickparam, verbose=False,
             ax3.set_xlabel('Time [s] after %s' % tr_filt.stats.starttime)
             ax3.set_ylabel('Normalized Counts')
             ax3.set_title(trH2_filt.stats.channel)
+            if plt_flag == 1:
+                fig.show()
+                raw_input()
+                plt.close(fig)
     ##########################################################################
     # calculate "real" onset times
     if lpickP is not None and lpickP == mpickP:

pylot/core/pick/picker.py

@@ -154,6 +154,7 @@ class AICPicker(AutoPicker):
         self.Pick = None
         self.slope = None
         self.SNR = None
+        plt_flag = 0
         # find NaN's
         nn = np.isnan(self.cf)
         if len(nn) > 1:
@@ -244,6 +245,7 @@ class AICPicker(AutoPicker):
                     if self.iplot > 1:
                         if not self.fig:
                             fig = plt.figure()  # self.iplot) ### WHY? MP MP
+                            plt_flag = 1
                         else:
                             fig = self.fig
                         ax = fig.add_subplot(111)
@@ -254,6 +256,10 @@ class AICPicker(AutoPicker):
                         ax.set_xlabel('Time [s] since %s' % self.Data[0].stats.starttime)
                         ax.set_yticks([])
                         ax.set_title(self.Data[0].stats.station)
+                        if plt_flag == 1:
+                            fig.show()
+                            raw_input()
+                            plt.close(fig)
                     return
                 iislope = islope[0][0:imax]
             dataslope = self.Data[0].data[iislope]
@@ -273,6 +279,7 @@ class AICPicker(AutoPicker):
         if self.iplot > 1:
             if not self.fig:
                 fig = plt.figure()  # self.iplot)
+                plt_flag = 1
             else:
                 fig = self.fig
             ax1 = fig.add_subplot(211)
@@ -307,8 +314,16 @@ class AICPicker(AutoPicker):
                 ax2.set_ylabel('Counts')
                 ax2.set_yticks([])
                 ax2.legend()
+                if plt_flag == 1:
+                    fig.show()
+                    raw_input()
+                    plt.close(fig)
             else:
                 ax1.set_title(self.Data[0].stats.station)
+                if plt_flag == 1:
+                    fig.show()
+                    raw_input()
+                    plt.close(fig)
 
         if self.Pick == None:
             print('AICPicker: Could not find minimum, picking window too short?')
@@ -330,6 +345,7 @@ class PragPicker(AutoPicker):
             self.SNR = None
             self.slope = None
             pickflag = 0
+            plt_flag = 0
             # smooth CF
             ismooth = int(round(self.Tsmooth / self.dt))
             cfsmooth = np.zeros(len(self.cf))
@@ -408,6 +424,7 @@ class PragPicker(AutoPicker):
             if self.getiplot() > 1:
                 if not self.fig:
                     fig = plt.figure()  # self.getiplot())
+                    plt_flag = 1
                 else:
                     fig = self.fig
                 ax = fig.add_subplot(111)
@@ -419,6 +436,10 @@ class PragPicker(AutoPicker):
                 ax.set_yticks([])
                 ax.set_title(self.Data[0].stats.station)
                 ax.legend()
+                if plt_flag == 1:
+                    fig.show()
+                    raw_input()
+                    plt.close(fig)
                 return
 
         else:

pylot/core/pick/utils.py

@@ -50,6 +50,7 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None):
     LPick = None
     EPick = None
     PickError = None
+    plt_flag = 0
     if verbosity:
         print('earllatepicker: Get earliest and latest possible pick'
               ' relative to most likely pick ...')
@@ -120,6 +121,7 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None):
     if iplot > 1:
         if not fig:
             fig = plt.figure()  # iplot)
+            plt_flag = 1
         ax = fig.add_subplot(111)
         ax.plot(t, x, 'k', label='Data')
         ax.axvspan(t[inoise[0]], t[inoise[-1]], color='y', alpha=0.2, lw=0, label='Noise Window')
@@ -141,6 +143,10 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None):
             'Earliest-/Latest Possible/Most Likely Pick & Symmetric Pick Error, %s' %
             X[0].stats.station)
         ax.legend()
+        if plt_flag == 1:
+            fig.show()
+            raw_input()
+            plt.close(fig)
 
     return EPick, LPick, PickError
 
@@ -167,6 +173,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None):
     :type: int
     '''
 
+    plt_flag = 0
     warnings.simplefilter('ignore', np.RankWarning)
 
     assert isinstance(Xraw, Stream), "%s is not a stream object" % str(Xraw)
@@ -292,6 +299,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None):
     if iplot > 1:
         if not fig:
             fig = plt.figure()  # iplot)
+            plt_flag = 1
         ax1 = fig.add_subplot(211)
         ax1.plot(t, xraw, 'k')
         ax1.plot([Pick, Pick], [max(xraw), -max(xraw)], 'b', linewidth=2, label='Pick')
@@ -317,6 +325,10 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None):
             ax2.text(Pick + 0.02, max(xraw) / 2, '%s' % FM, fontsize=14)
         ax2.set_xlabel('Time [s] since %s' % Xraw[0].stats.starttime)
         ax2.set_yticks([])
+        if plt_flag == 1:
+            fig.show()
+            raw_input()
+            plt.close(fig)
 
     return FM
 
@@ -685,6 +697,7 @@ def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot=0, fi
     : type:  int
     '''
 
+    plt_flag = 0
     assert isinstance(X, Stream), "%s is not a stream object" % str(X)
 
     print("Checking signal length ...")
@@ -729,6 +742,7 @@ def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot=0, fi
     if iplot == 2:
         if not fig:
             fig = plt.figure()  # iplot)
+            plt_flag = 1
         ax = fig.add_subplot(111)
         ax.plot(t, rms, 'k', label='RMS Data')
         ax.axvspan(t[inoise[0]], t[inoise[-1]], color='y', alpha=0.2, lw=0, label='Noise Window')
@@ -741,6 +755,10 @@ def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot=0, fi
         ax.set_ylabel('Counts')
         ax.set_title('Check for Signal Length, Station %s' % X[0].stats.station)
         ax.set_yticks([])
+        if plt_flag == 1:
+            fig.show()
+            raw_input()
+            plt.close(fig)
 
     return returnflag