Spectrum() class redesign

Class is redesigned so that it does not inherit anymore from ObsPy's
Trace class. This allows to have a more flexible class that can be
expanded in the future.

Also add a SpectrumStream class to handle a collection of
Spectrum objects.

sourcespec/source_model.py

@@ -89,10 +89,10 @@ def main():
     }
     config = configure(
         options, progname='source_model', config_overrides=conf_overrides)
+    from sourcespec.spectrum import SpectrumStream
     from sourcespec.ssp_read_traces import read_traces
     from sourcespec.ssp_process_traces import process_traces
     from sourcespec.ssp_build_spectra import build_spectra
-    from obspy.core import Stream
 
     # We don't use weighting in source_model
     config.weighting = 'no_weight'
@@ -105,16 +105,16 @@ def main():
         if len(spec_st) == 0:
             ssp_exit()
         # We keep just horizontal component:
-        spec_st = Stream([x for x in spec_st.traces
-                          if x.stats.channel[-1] == 'H'])
+        spec_st = SpectrumStream(
+            [x for x in spec_st if x.stats.channel[-1] == 'H'])
 
         for trace_spec in spec_st:
             orientation = trace_spec.stats.channel[-1]
             if orientation != 'H':
                 continue
             make_synth(config, spec_st, trace_spec)
     else:
-        spec_st = Stream()
+        spec_st = SpectrumStream()
         make_synth(config, spec_st)
 
     from sourcespec.ssp_plot_spectra import plot_spectra

sourcespec/source_residuals.py

@@ -7,7 +7,7 @@
     2013-2014 Claudio Satriano <satriano@ipgp.fr>,
               Agnes Chounet <chounet@ipgp.fr>
 
-    2015-2023 Claudio Satriano <satriano@ipgp.fr>
+    2015-2024 Claudio Satriano <satriano@ipgp.fr>
 :license:
     CeCILL Free Software License Agreement v2.1
     (http://www.cecill.info/licences.en.html)
@@ -17,11 +17,10 @@
 from collections import defaultdict
 import pickle
 from argparse import ArgumentParser
-from obspy.core import Stream
 import matplotlib
 import matplotlib.pyplot as plt
 from sourcespec.ssp_util import moment_to_mag, mag_to_moment
-from sourcespec.spectrum import Spectrum
+from sourcespec.spectrum import Spectrum, SpectrumStream
 matplotlib.use('Agg')  # NOQA
 
 
@@ -77,7 +76,7 @@ def read_residuals(resfiles_dir):
         )
     if not resfiles:
         sys.exit(f'No residual file found in directory: {resfiles_dir}')
-    residual_dict = defaultdict(Stream)
+    residual_dict = defaultdict(SpectrumStream)
     for resfile in resfiles:
         print(f'Found residual file: {resfile}')
         with open(resfile, 'rb') as fp:
@@ -100,10 +99,10 @@ def compute_mean_residuals(residual_dict, min_spectra=20):
 
     Returns
     -------
-    residual_mean : Stream
+    residual_mean : SpectrumStream
         Stream containing mean residuals for each station.
     """
-    residual_mean = Stream()
+    residual_mean = SpectrumStream()
     for stat_id in sorted(residual_dict.keys()):
         if len(residual_dict[stat_id]) < min_spectra:
             continue
@@ -118,15 +117,14 @@ def compute_mean_residuals(residual_dict, min_spectra=20):
 
         spec_mean = Spectrum()
         spec_mean.id = stat_id
-        spec_mean.stats.begin = freq_min
+        spec_mean.stats.startfreq = freq_min
         spec_mean.stats.delta = res[0].stats.delta
-        spec_mean.data_mag = None
         for spec in res:
             spec_slice = spec.slice(freq_min, freq_max, pad=True,
                                     fill_value=mag_to_moment(0))
             spec_slice.data_mag = moment_to_mag(spec_slice.data)
             norm = (spec_slice.data_mag != 0).astype(int)
-            if spec_mean.data_mag is None:
+            if len(spec_mean.data_mag) == 0:
                 spec_mean.data_mag = spec_slice.data_mag
                 norm_mean = norm
             else:
@@ -150,8 +148,8 @@ def plot_residuals(residual_dict, residual_mean, outdir):
     ----------
     residual_dict : dict
         Dictionary containing residuals for each station.
-    residual_mean : Stream
-        Stream containing mean residuals for each station.
+    residual_mean : SpectrumStream
+        SpectrumStream containing mean residuals for each station.
     outdir : str
         Output directory.
     """