Merge 73b5959 into 777e86a

README.rst

@@ -59,6 +59,24 @@ is in your ``PYTHONPATH`` environment variable.  E.g. in bash shell, if ``~/dev/
 - ``export PYTHONPATH=~/dev/hiperseis:$PYTHONPATH``
 
 
+Third Party Library Dependencies
+================================
+
+Certain modules require specific third party (non-Python) libraries to be installed
+on the host system. For example, scripts that convert to sc3ml format also require Seiscomp3 to be
+installed and to be visible in the PATH. In most cases, Python libraries that depend on third party
+libraries will indicate their dependencies either during attempted installation, or when used at
+runtime. Note that the following list includes indirect dependencies, i.e. dependencies that come
+from Python libraries used by HiPerSeis.
+
+Current third party dependencies (actual requirements may vary by platform or Python distribution):
+
+- `HDF5 <http://hdfgroup.org/>`_
+- MPI, for example `Open MPI <https://www.open-mpi.org/>`_
+- `PROJ <https://proj.org/>`_
+- `GEOS <https://trac.osgeo.org/geos>`_
+
+
 License
 ===============
 

docs/seismic.rst

@@ -53,3 +53,57 @@ HiPerSeis Package: Seismic
 
 .. automodule:: seismic.gps_corrections.relative_tt_residuals_plotter
 	:members:
+
+**Receiver Functions**
+======================
+
+.. automodule:: seismic.receiver_fn.bulk_rf_report
+	:members:
+
+.. automodule:: seismic.receiver_fn.extract_event_traces
+	:members:
+
+.. automodule:: seismic.receiver_fn.generate_rf
+	:members:
+
+.. automodule:: seismic.receiver_fn.plot_ccp
+	:members:
+
+.. automodule:: seismic.receiver_fn.rf_3dmigrate
+	:members:
+
+.. automodule:: seismic.receiver_fn.rf_deconvolution
+	:members:
+
+.. automodule:: seismic.receiver_fn.rf_h5_file_event_iterator
+	:members:
+
+.. automodule:: seismic.receiver_fn.rf_h5_file_station_iterator
+	:members:
+
+.. automodule:: seismic.receiver_fn.rf_inversion_export
+	:members:
+
+.. automodule:: seismic.receiver_fn.rf_network_dict
+	:members:
+
+.. automodule:: seismic.receiver_fn.rf_plot_utils
+	:members:
+
+.. automodule:: seismic.receiver_fn.rf_plot_vespagram
+	:members:
+
+.. automodule:: seismic.receiver_fn.rf_process_io
+	:members:
+
+.. automodule:: seismic.receiver_fn.rf_quality_filter
+	:members:
+
+.. automodule:: seismic.receiver_fn.rf_stacking
+	:members:
+
+.. automodule:: seismic.receiver_fn.rf_synthetic
+	:members:
+
+.. automodule:: seismic.receiver_fn.rf_util
+	:members:

seismic/gps_corrections/picks_reader_utils.py

@@ -50,6 +50,7 @@ def read_picks_ensemble(csv_file):
     """
     df_raw_picks = pd.read_csv(csv_file, r'\s+', header=0, dtype=PICKS_TABLE_SCHEMA)
     return df_raw_picks
+# end func
 
 
 def get_network_stations(df, netcode):
@@ -64,6 +65,7 @@ def get_network_stations(df, netcode):
     :rtype: list(str)
     """
     return sorted(df[df['net'] == netcode]['sta'].unique().tolist())
+# end func
 
 
 def get_network_location_mean(df, netcode):
@@ -94,6 +96,7 @@ def get_network_location_mean(df, netcode):
         return (mean_lat, mean_lon)
     else:
         return (np.nan, np.nan)
+# end func
 
 
 def get_network_date_range(df, netcode):
@@ -115,6 +118,7 @@ def get_network_date_range(df, netcode):
         return (obspy.UTCDateTime(min_date), obspy.UTCDateTime(max_date))
     else:
         return (None, None)
+# end func
 
 
 def get_station_date_range(df, netcode, statcode):
@@ -140,6 +144,7 @@ def get_station_date_range(df, netcode, statcode):
         return (obspy.UTCDateTime(min_date), obspy.UTCDateTime(max_date))
     else:
         return (None, None)
+# end func
 
 
 def compute_matching_network_mask(df, net_dict):
@@ -165,6 +170,7 @@ def compute_matching_network_mask(df, net_dict):
     for n, s in zip(net_dict['net'], net_dict['sta']):
         mask = (mask | ((_df['net'] == n) & (_df['sta'] == s)))
     return mask
+# end func
 
 
 def get_overlapping_date_range(df, network_1, network_2):
@@ -217,6 +223,7 @@ def get_overlapping_date_range(df, network_1, network_2):
                 obspy.UTCDateTime(df_masked['originTimestamp'].max()))
 
     return (None, None)
+# end func
 
 
 def generate_large_events_catalog(df_picks, min_magnitude=8.0, min_record_count=400, label_historical_events=True):
@@ -266,3 +273,4 @@ def generate_large_events_catalog(df_picks, min_magnitude=8.0, min_record_count=
         significant_events.loc['2016-08-24', 'name'] = '2016 Myanmar earthquake'
 
     return significant_events
+# end func

seismic/inventory/README.md

@@ -11,24 +11,15 @@ The purpose of this package is to provide tools and workflow for
 ## Requirements
 
 The Python library requirements for using the tools and workflow of this package
-are listed in `requirements_common.txt` for all platforms, plus additional platform
-specific requirements listed in `requirements_linux.txt` for Linux and
-`requirements_win32.txt` for Windows. The package is written for Python version 2.7
+are listed in `requirements.txt`. The package is written for Python version 2.7
 or >=3.5. To install the library requirements, run
 
-    `pip install -r requirements_common.txt`
+    `pip install -r requirements.txt`
 
-followed by platform-specific requirements:
+Scripts that convert inventory files to sc3ml format also require Seiscomp3 to be installed on the
+host system and to be visible in the PATH. The installation of Seiscomp3 generally requires admin
+privileges and configuration by a knowledgable user.
 
-    `pip install -r requirements_linux.txt`  (for Linux)
-
-OR
-
-    `pip install -r requirements_win32.txt`  (for Windows)
-
-Scripts that convert to sc3ml format also require Seiscomp3 to be installed on the host
-system and to be visible in the PATH. The installation of Seiscomp3 requires
-admin privileges and configuration by a knowledgable user.
 
 ### Performance note
 
@@ -142,7 +133,7 @@ to force a regeneration of the `.pkl` file.
 ## Future development roadmap <a name="future"></a>
 
 Agenda for future development:
-* Factor our the STN file readers into a separate module so that any reader can be
+* Factor out the STN file readers into a separate module so that any reader can be
   substituted, as long as it generates Pandas DataFrame output, to support arbitrary
   input file formats.
 * Performance improvements reading files in function `engd2stxml.read_isc()`. E.g. change
@@ -159,111 +150,6 @@ Python 3.6.7 (default, Dec  5 2018, 15:02:05)
 [GCC 4.8.5 20150623 (Red Hat 4.8.5-36)]
 ```
 
-Obspy (standard release):
-```
-'1.1.0'
-```
-
-Obspy (custom):
-```
-'1.1.1rc1.post0+552.g8478dae0aa.obspy.master'
-```
-
-Python libraries (via `pip freeze`):
-```
-arrow==0.13.0
-astroid==2.1.0
-backcall==0.1.0
-basemap==1.2.0
-bleach==3.1.0
-certifi==2018.11.29
-chardet==3.0.4
-ciso8601==2.1.1
-Click==7.0
-cycler==0.10.0
-dask==1.1.0
-decorator==4.3.2
-defusedxml==0.5.0
-dill==0.2.9
-entrypoints==0.3
-future==0.17.1
-graphviz==0.10.1
-h5py==2.9.0
-idna==2.8
-ipykernel==5.1.0
-ipython==7.2.0
-ipython-genutils==0.2.0
-ipywidgets==7.4.2
-isort==4.3.4
-jedi==0.13.2
-Jinja2==2.10
-jsonschema==2.6.0
-jupyter==1.0.0
-jupyter-client==5.2.4
-jupyter-console==6.0.0
-jupyter-core==4.4.0
-kiwisolver==1.0.1
-lazy-object-proxy==1.3.1
-line-profiler==2.1.2
-llvmlite==0.27.0
-lxml==4.3.0
-MarkupSafe==1.1.0
-matplotlib==3.0.2
-mccabe==0.6.1
-mistune==0.8.4
-nbconvert==5.4.0
-nbformat==4.4.0
-notebook==5.7.4
-numba==0.42.0
-numexpr==2.6.9
-numpy==1.16.1
--e git+https://github.com/obspy/obspy.git@8478dae0aac6d647171ab3092c48384ac666d5be#egg=obspy
-pandas==0.24.1
-pandoc==1.0.2
-pandocfilters==1.4.2
-parso==0.3.2
-pexpect==4.6.0
-pickleshare==0.7.5
-ply==3.11
-proj==0.1.0
-prometheus-client==0.5.0
-prompt-toolkit==2.0.8
-ptyprocess==0.6.0
-Pygments==2.3.1
-pyimgur==0.6.0
-pylint==2.2.2
-pyparsing==2.3.1
-pyproj==1.9.6
-pyshp==2.0.1
-python-dateutil==2.7.5
-pytz==2018.9
-pyzmq==17.1.2
-qtconsole==4.4.3
-requests==2.21.0
-rope==0.11.0
-Rtree==0.8.3
-scikit-learn==0.20.2
-scipy==1.2.0
-seaborn==0.9.0
-Send2Trash==1.5.0
-six==1.12.0
-SQLAlchemy==1.2.17
-tables==3.4.4
-terminado==0.8.1
-testpath==0.4.2
-tornado==5.1.1
-tqdm==4.30.0
-traitlets==4.3.2
-typed-ast==1.2.0
-urllib3==1.24.1
-versioneer==0.18
-wcwidth==0.1.7
-webencodings==0.5.1
-widgetsnbextension==3.4.2
-wrapt==1.11.1
-xlrd==1.2.0
-```
-
 Seiscomp3 fdsnxml2inv converter:
 ```
 fdsnxml2inv: Jakarta 2017.124

seismic/inventory/generate_network_plots.py

@@ -11,36 +11,58 @@
 """
 
 import os
-import sys
+import click
+
 import pandas as pd
 
 from seismic.inventory.plotting import save_network_local_plots, save_station_local_plots
 
 try:
     import tqdm
     show_progress = True
-except:
+except ImportError:
     show_progress = False
     print("Run 'pip install tqdm' to see progress bar.")
+# end try
+
+@click.command()
+@click.option('--plot-type', type=click.Option(['network', 'station']), default='network',
+              help='Whether to plot on map per network or one map per station')
+@click.argument('inventory-h5-file', type=click.Path(exists=True, dir_okay=False), required=True)
+def main(inventory_h5_file, plot_type):
+    """Generate map plots of station locations for an inventory of stations.
+
+    Arguments:
+    :param inventory_h5_file: Name of input HDF5 file containing a station inventory
+    :type inventory_h5_file: str or Path
+    :param plot_type: Type of plots to make - per network or per station
+    :type plot_type: str
+    """
+    # Set up file names
+    print("Loading file {0}".format(inventory_h5_file))
+    basename, _ = os.path.splitext(inventory_h5_file)
+    _, basename = os.path.split(basename)
+    folder_name = "plots." + basename
+    print("Saving plots to {0}".format(folder_name))
+
+    # Read inventory from hdf5 file
+    db = pd.read_hdf(inventory_h5_file, mode='r', key='inventory')
+
+    if show_progress:
+        pbar = tqdm.tqdm(total=len(db), ascii=True)
+        progressor = pbar.update
+    else:
+        progressor = None
+    # end if
+
+    # Save network plots to files
+    plot_functor = {'network': save_network_local_plots, 'station': save_station_local_plots}
+    plot_functor[plot_type](db, folder_name, progressor=progressor)
+    if show_progress:
+        pbar.close()
+    # end if
+# end main
 
-# Set up file names
-infile_name = sys.argv[1]
-print("Loading file {0}".format(infile_name))
-basename, _ = os.path.splitext(infile_name)
-_, basename = os.path.split(basename)
-folder_name = "plots." + basename
-print("Saving plots to {0}".format(folder_name))
-
-# Read inventory from hdf5 file
-db = pd.read_hdf(infile_name, mode='r', key='inventory')
-
-if show_progress:
-    pbar = tqdm.tqdm(total=len(db), ascii=True)
-    progressor = pbar.update
-else:
-    progressor = None
-
-# Save network plots to files
-save_network_local_plots(db, folder_name, progressor=progressor)
-if show_progress:
-    pbar.close()
+if __name__ == "__main__":
+    main()  # pylint: disable=no-value-for-parameter
+# end if