Merge pull request #233 from rmodrak/master

Consistent units in archived waveform data, other miscellaneous fixes
uafgeotools · Oct 30, 2023 · 0641750 · 0641750
2 parents f698c11 + cf746bd
commit 0641750
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Showing 26 changed files with 67 additions and 39 deletions.
diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml
@@ -40,6 +40,7 @@ jobs:
          python tests/benchmark_cap_vs_mtuq.py --no_figures
          python tests/test_grid_search_mt.py --no_figures
          python tests/test_grid_search_mt_depth.py --no_figures
+         python tests/test_greens_SPECFEM3D_SAC.py --no_figures
 
     # unfortunately, these Conda installation tests exceed the resource limits
     # for GitHub workflows

diff --git a/data/examples/20090407201255351.tgz b/data/examples/20090407201255351.tgz
diff --git a/data/examples/SPECFEM3D_SGT.tgz b/data/examples/SPECFEM3D_SGT.tgz
diff --git a/docs/README b/docs/README
@@ -19,10 +19,12 @@ HOW TO UPDATE DOCS
    Modify the sphinx autosummary source code by adding  'jinja2.ext.do' to the jinja
    Environment() extensions list
 
-   See for example this line of the source code:
+   See in particular this line of the autosummary source code:
+
    https://github.com/sphinx-doc/sphinx/blob/a6032e852a650c070aed66f0790e612905159f15/sphinx/ext/autosummary/generate.py#L111
 
    See also:
+
    https://stackoverflow.com/questions/39858191/do-statement-not-working-in-jinja
 
 

diff --git a/docs/install/index.rst b/docs/install/index.rst
@@ -39,7 +39,7 @@ Finally, install PyGMT:
 
 .. code::
 
-    conda install 'pygmt>=0.9'
+    conda install 'pygmt=0.9'
 
 .. note::
 

diff --git a/examples/DetailedAnalysis.py b/examples/DetailedAnalysis.py
@@ -161,7 +161,7 @@
         data = read(path_data, format='sac', 
             event_id=event_id,
             station_id_list=station_id_list,
-            tags=['units:cm', 'type:velocity']) 
+            tags=['units:m', 'type:velocity']) 
 
 
         data.sort_by_distance()

diff --git a/examples/GridSearch.DoubleCouple+Magnitude+Depth.py b/examples/GridSearch.DoubleCouple+Magnitude+Depth.py
@@ -147,7 +147,7 @@
         data = read(path_data, format='sac', 
             event_id=event_id,
             station_id_list=station_id_list,
-            tags=['units:cm', 'type:velocity']) 
+            tags=['units:m', 'type:velocity']) 
 
 
         data.sort_by_distance()

diff --git a/examples/GridSearch.DoubleCouple+Magnitude+Hypocenter.py b/examples/GridSearch.DoubleCouple+Magnitude+Hypocenter.py
@@ -166,7 +166,7 @@
         data = read(path_data, format='sac', 
             event_id=event_id,
             station_id_list=station_id_list,
-            tags=['units:cm', 'type:velocity']) 
+            tags=['units:m', 'type:velocity']) 
 
 
         data.sort_by_distance()

diff --git a/examples/GridSearch.DoubleCouple.py b/examples/GridSearch.DoubleCouple.py
@@ -134,7 +134,7 @@
         data = read(path_data, format='sac', 
             event_id=event_id,
             station_id_list=station_id_list,
-            tags=['units:cm', 'type:velocity']) 
+            tags=['units:m', 'type:velocity']) 
 
 
         data.sort_by_distance()

diff --git a/examples/GridSearch.FullMomentTensor.py b/examples/GridSearch.FullMomentTensor.py
@@ -126,7 +126,7 @@
         data = read(path_data, format='sac', 
             event_id=event_id,
             station_id_list=station_id_list,
-            tags=['units:cm', 'type:velocity']) 
+            tags=['units:m', 'type:velocity']) 
 
 
         data.sort_by_distance()

diff --git a/examples/SerialGridSearch.DoubleCouple.py b/examples/SerialGridSearch.DoubleCouple.py
@@ -129,7 +129,7 @@
     data = read(path_data, format='sac',
         event_id=event_id,
         station_id_list=station_id_list,
-        tags=['units:cm', 'type:velocity']) 
+        tags=['units:m', 'type:velocity']) 
 
 
     data.sort_by_distance()

diff --git a/examples/Waveforms+Polarities.py b/examples/Waveforms+Polarities.py
@@ -141,7 +141,7 @@
         data = read(path_data, format='sac', 
             event_id=event_id,
             station_id_list=station_id_list,
-            tags=['units:cm', 'type:velocity']) 
+            tags=['units:m', 'type:velocity']) 
 
 
         data.sort_by_distance()

diff --git a/mtuq/__init__.py b/mtuq/__init__.py
@@ -8,7 +8,16 @@
 # of numpy, it will be understood as (type, (1,)) / '(1,)type'.
 
 import warnings
-warnings.simplefilter(action='ignore', category=FutureWarning)
+warnings.simplefilter(action='ignore',
+    category=FutureWarning)
+
+
+# Suppress Instaseis warning that gets raised unnecessarily during git+https
+# installation
+
+warnings.filterwarnings(action='ignore',
+     message='.*'+'Use the proper pypi release or install from git.'+'.*')
+
 
 
 #

diff --git a/mtuq/graphics/waveforms.py b/mtuq/graphics/waveforms.py
@@ -100,7 +100,7 @@ def plot_waveforms1(filename,
                 continue
 
             _plot_ZRT(axes[ir], 1, dat, syn, component, 
-                normalize, trace_labels, max_amplitude, total_misfit)
+                normalize, trace_label_writer, max_amplitude, total_misfit)
 
         ir += 1
 

diff --git a/mtuq/greens_tensor/SPECFEM3D.py b/mtuq/greens_tensor/SPECFEM3D.py
@@ -14,16 +14,16 @@ class GreensTensor(GreensTensorBase):
 
       SPECFEM3D Green's functions describe the impulse response of a general
       inhomogeneous medium.  Time series represent vertical, radial, and 
-      transverse velocity in units of m*(N-m)^-1 s^-1
+      transverse displacement in units of m*(N-m)^-1
     """
     def __init__(self, *args, **kwargs):
         super(GreensTensor, self).__init__(*args, **kwargs)
 
         if 'type:greens' not in self.tags:
             self.tags += ['type:greens']
 
-        if 'type:velocity' not in self.tags:
-            self.tags += ['type:velocity']
+        if 'type:velocity' not in self.tags or 'type:displacement' not in self.tags:
+            self.tags += ['type:displacement']
 
         if 'units:m' not in self.tags:
             self.tags += ['units:m']

diff --git a/mtuq/util/gallery.py b/mtuq/util/gallery.py
@@ -104,7 +104,7 @@
     data = read(path_data, format='sac',
         event_id=event_id,
         station_id_list=station_id_list,
-        tags=['units:cm', 'type:velocity']) 
+        tags=['units:m', 'type:velocity']) 
 
 
     data.sort_by_distance()

diff --git a/setup/code_generator.py b/setup/code_generator.py
@@ -175,9 +175,14 @@
     #
     # Grid search integration test
     #
-    # This script is similar to examples/SerialGridSearch.DoubleCouple.py,
-    # except here we included mangitude and depth and use a coarser grid
+    # For speed, the script tests the iterative machinery for depth
+    # searches in a somewhat degenerate case, using only a length one 
+    # container
+    #
+    # For a depth search in the more usual sense, see
+    # examples/GridSearch.DoubleCouple+Magnitude+Depth.py
     #
+
 """
 
 
@@ -748,7 +753,7 @@
         data = read(path_data, format='sac', 
             event_id=event_id,
             station_id_list=station_id_list,
-            tags=['units:cm', 'type:velocity']) 
+            tags=['units:m', 'type:velocity']) 
 
 
         data.sort_by_distance()
@@ -812,7 +817,7 @@
     data = read(path_data, format='sac',
         event_id=event_id,
         station_id_list=station_id_list,
-        tags=['units:cm', 'type:velocity']) 
+        tags=['units:m', 'type:velocity']) 
 
 
     data.sort_by_distance()
@@ -859,7 +864,7 @@
     data = read(path_data, format='sac', 
         event_id=event_id,
         station_id_list=station_id_list,
-        tags=['units:cm', 'type:velocity']) 
+        tags=['units:m', 'type:velocity']) 
 
     data.sort_by_distance()
     stations = data.get_stations()
@@ -905,7 +910,7 @@
     data = read(path_data, format='sac',
         event_id=event_id,
         station_id_list=station_id_list,
-        tags=['units:cm', 'type:velocity'])
+        tags=['units:m', 'type:velocity'])
 
 
     data.sort_by_distance()
@@ -1631,7 +1636,7 @@ def isclose(a, b, atol=1.e6, rtol=1.e-6):
     print('Reading data...\\n')
     data = read(path_data, format='sac', 
         event_id=event_id,
-        tags=['units:cm', 'type:velocity']) 
+        tags=['units:m', 'type:velocity']) 
 
     data.sort_by_distance()
 
@@ -1671,7 +1676,7 @@ def isclose(a, b, atol=1.e6, rtol=1.e-6):
         if run_figures:
             plot_waveforms2('cap_vs_mtuq_'+str(_i)+'.png',
                 cap_bw, cap_sw, mtuq_bw, mtuq_sw, 
-                stations, origin, trace_labels=False)
+                stations, origin, trace_label_writer=None)
 
         if run_checks:
             compare_cap_mtuq(
@@ -1687,7 +1692,7 @@ def isclose(a, b, atol=1.e6, rtol=1.e-6):
 
         plot_waveforms2('cap_vs_mtuq_data.png',
             cap_bw, cap_sw, mtuq_bw, mtuq_sw, 
-            stations, origin, trace_labels=False, normalize=False)
+            stations, origin, trace_label_writer=None, normalize=False)
 
     print('\\nSUCCESS\\n')
 

diff --git a/tests/benchmark_cap_vs_mtuq.py b/tests/benchmark_cap_vs_mtuq.py
@@ -173,7 +173,7 @@
     print('Reading data...\n')
     data = read(path_data, format='sac', 
         event_id=event_id,
-        tags=['units:cm', 'type:velocity']) 
+        tags=['units:m', 'type:velocity']) 
 
     data.sort_by_distance()
 
@@ -213,7 +213,7 @@
         if run_figures:
             plot_waveforms2('cap_vs_mtuq_'+str(_i)+'.png',
                 cap_bw, cap_sw, mtuq_bw, mtuq_sw, 
-                stations, origin, trace_labels=False)
+                stations, origin, trace_label_writer=None)
 
         if run_checks:
             compare_cap_mtuq(
@@ -229,7 +229,7 @@
 
         plot_waveforms2('cap_vs_mtuq_data.png',
             cap_bw, cap_sw, mtuq_bw, mtuq_sw, 
-            stations, origin, trace_labels=False, normalize=False)
+            stations, origin, trace_label_writer=None, normalize=False)
 
     print('\nSUCCESS\n')
 
diff --git a/tests/test_HMC_DoubleCouple.py b/tests/test_HMC_DoubleCouple.py
@@ -18,11 +18,14 @@
 
 
 if __name__=='__main__':
+
+    print('WARNING: need to update Greens functions from velocity to displacement?')
+
     #
     # Carries out Hamiltonian Monte Carlo (HMC) sampling over double couple moment tensors
     #
     # USAGE
-    #   mpirun -n <NPROC> python HMC.DoubleCouple.py
+    #   mpirun -n <NPROC> python test_HMC_DoubleCouple.py
     #
     #
 
@@ -128,7 +131,7 @@
         data = read(path_data, format='sac',
             event_id=event_id,
             station_id_list=station_id_list,
-            tags=['units:cm', 'type:velocity'])
+            tags=['units:m', 'type:velocity'])
 
 
         data.sort_by_distance()

diff --git a/tests/test_HMC_FullMomentTensor.py b/tests/test_HMC_FullMomentTensor.py
@@ -17,11 +17,14 @@
 
 
 if __name__=='__main__':
+
+    print('WARNING: need to update Greens functions from velocity to displacement?')
+
     #
     # Carries out Hamiltonian Monte Carlo (HMC) sampling over full moment tensors
     #
     # USAGE
-    #   mpirun -n <NPROC> python HMC.FullMomentTensor.py
+    #   mpirun -n <NPROC> python test_HMC_FullMomentTensor.py
     #
     #
 
@@ -129,7 +132,7 @@
         data = read(path_data, format='sac',
             event_id=event_id,
             station_id_list=station_id_list,
-            tags=['units:cm', 'type:velocity'])
+            tags=['units:m', 'type:velocity'])
 
 
         data.sort_by_distance()

diff --git a/tests/test_graphics.py b/tests/test_graphics.py
@@ -83,7 +83,7 @@
     data = read(path_data, format='sac',
         event_id=event_id,
         station_id_list=station_id_list,
-        tags=['units:cm', 'type:velocity'])
+        tags=['units:m', 'type:velocity'])
 
 
     data.sort_by_distance()

diff --git a/tests/test_greens_SPECFEM3D_SAC.py b/tests/test_greens_SPECFEM3D_SAC.py
@@ -106,7 +106,7 @@
     data = read(path_data, format='sac',
         event_id=event_id,
         station_id_list=station_id_list,
-        tags=['units:cm', 'type:velocity']) 
+        tags=['units:m', 'type:velocity']) 
 
 
     data.sort_by_distance()

diff --git a/tests/test_greens_SPECFEM3D_SGT.py b/tests/test_greens_SPECFEM3D_SGT.py
@@ -108,7 +108,7 @@
     data = read(path_data, format='sac',
         event_id=event_id,
         station_id_list=station_id_list,
-        tags=['units:cm', 'type:velocity']) 
+        tags=['units:m', 'type:velocity']) 
 
 
     data.sort_by_distance()

diff --git a/tests/test_grid_search_mt.py b/tests/test_grid_search_mt.py
@@ -117,7 +117,7 @@
     data = read(path_data, format='sac',
         event_id=event_id,
         station_id_list=station_id_list,
-        tags=['units:cm', 'type:velocity']) 
+        tags=['units:m', 'type:velocity']) 
 
 
     data.sort_by_distance()

diff --git a/tests/test_grid_search_mt_depth.py b/tests/test_grid_search_mt_depth.py
@@ -18,9 +18,14 @@
     #
     # Grid search integration test
     #
-    # This script is similar to examples/SerialGridSearch.DoubleCouple.py,
-    # except here we included mangitude and depth and use a coarser grid
+    # For speed, the script tests the iterative machinery for depth
+    # searches in a somewhat degenerate case, using only a length one 
+    # container
     #
+    # For a depth search in the more usual sense, see
+    # examples/GridSearch.DoubleCouple+Magnitude+Depth.py
+    #
+
 
     # by default, the script runs with figure generation and error checking
     # turned on
@@ -118,7 +123,7 @@
     data = read(path_data, format='sac', 
         event_id=event_id,
         station_id_list=station_id_list,
-        tags=['units:cm', 'type:velocity']) 
+        tags=['units:m', 'type:velocity']) 
 
     data.sort_by_distance()
     stations = data.get_stations()

diff --git a/tests/test_misfit.py b/tests/test_misfit.py
@@ -123,7 +123,7 @@
     data = read(path_data, format='sac',
         event_id=event_id,
         station_id_list=station_id_list,
-        tags=['units:cm', 'type:velocity']) 
+        tags=['units:m', 'type:velocity']) 
 
 
     data.sort_by_distance()