Fixed a small plotting bug and updated instructions

seismic/README.md

@@ -1,6 +1,6 @@
 # Dependencies
 The workflow requires MPI (mpi4py) and parallel HDF5 (h5py) capabilities on the NCI.
-Installation instructions for NCI (Gadi ) are as follows:
+Installation instructions for the NCI (Gadi), to be executed from a login node, are as follows:
 
 ### Load system modules:
   1. `module purge`
@@ -119,6 +119,7 @@ mpirun -np 48 python extract_event_traces.py --waveform-database asdf_files.txt
 --event-catalog-file OA_events.xml --event-trace-datafile OA_waveforms.h5 
 --network-list "OA" --p-data --s-data --sw-data > out.txt 2>&1
 ```
+See [extract_waveforms.pbs](pbs/extract_waveforms.pbs) for a concrete example.
 ## Orientation Analysis
 
 Station-orientation reports are generated by an MPI-parallel driving script: 
@@ -128,3 +129,5 @@ based on (i) Receiver Functions and (ii) Surface-wave Polarization.
 ### Typical usage:
 `mpirun -np 48 python bulk_station_orientations.py 
 OA_waveforms_X-Y.h5 'OA' --output-basename OA_orientations`
+
+See [bulk_orientations.pbs](pbs/bulk_orientations.pbs) for a concrete example.

seismic/pbs/bulk_orientations.pbs

@@ -0,0 +1,26 @@
+#!/bin/bash
+#PBS -P vy72
+#PBS -N bulk_orientations
+#PBS -q express
+#PBS -l walltime=24:00:00,mem=192GB,ncpus=48,jobfs=50GB
+#PBS -l storage=scratch/rxh562+gdata/ha3
+#PBS -l wd
+#PBS -j oe
+#PBS -M rakib.hassan@ga.gov.au
+#PBS -m bae
+
+module purge
+module load pbs
+module load python3-as-python
+module load openmpi/3.1.4
+module load hdf5/1.10.5p
+module load geos
+
+export PATH=$HOME/.local/bin:$PATH
+export PYTHONPATH=/g/data/ha3/rakib/seismic/pst/hiperseis/:$PYTHONPATH
+export LC_ALL=en_AU.UTF-8
+export LANG=en_AU.UTF-8
+
+mpirun -np 48 python /g/data/ha3/rakib/seismic/pst/hiperseis/seismic/bulk_station_orientations.py /g/data/ha3/Passive/SHARED_DATA/DataQuality/Orientation/OA/OA_waveforms_20170911T000036-20210401T053646.h5 'OA' --output-basename /g/data/ha3/Passive/SHARED_DATA/DataQuality/Orientation/OA/OA_orientations
+
+

seismic/pbs/extract_waveforms.pbs

@@ -0,0 +1,26 @@
+#!/bin/bash
+#PBS -P vy72
+#PBS -N extract_waveforms
+#PBS -q express
+#PBS -l walltime=24:00:00,mem=192GB,ncpus=48,jobfs=50GB
+#PBS -l storage=scratch/rxh562+gdata/ha3
+#PBS -l wd
+#PBS -j oe
+#PBS -M rakib.hassan@ga.gov.au
+#PBS -m bae
+
+module purge
+module load pbs
+module load python3-as-python
+module load openmpi/3.1.4
+module load hdf5/1.10.5p
+module load geos
+
+export PATH=$HOME/.local/bin:$PATH
+export PYTHONPATH=/g/data/ha3/rakib/seismic/pst/hiperseis/:$PYTHONPATH
+export LC_ALL=en_AU.UTF-8
+export LANG=en_AU.UTF-8
+
+mpirun -np 48 python /g/data/ha3/rakib/seismic/pst/hiperseis/seismic/extract_event_traces.py --waveform-database /g/data/ha3/Passive/SHARED_DATA/Index/asdf_files.txt --event-catalog-file /g/data/ha3/rakib/seismic/pst/orientation/OA_events_20170911T000036-20210401T053646.xml --event-trace-datafile /g/data/ha3/Passive/SHARED_DATA/DataQuality/Orientation/OA/OA_waveforms.h5 --network-list "OA" --p-data --s-data --sw-data > /g/data/ha3/rakib/seismic/pst/orientation/out.txt 2>&1
+
+

seismic/swp_station_orientations.py

@@ -695,9 +695,9 @@ def analyze_station_orientations(ned, grv_dict, save_plots_path=None, ax=None):
         plt.subplot(1, 1, 1)
         plt.title('DLOPy results: ' + full_code, fontsize=16)
         plt.plot([0, 1], [corr, corr], '-', linewidth=4, color=(0.8, 0.8, 0.8), zorder=5)
-        sc = plt.scatter(r1cc, centerat(r1phi, m=CEN), c=c, marker='o', cmap=cm.viridis, alpha=0.5, zorder=1,
+        sc = plt.scatter(r1cc, centerat(-r1phi, m=CEN), c=c, marker='o', cmap=cm.viridis, alpha=0.5, zorder=1,
                          label='R1')
-        plt.scatter(r2cc, centerat(r2phi, m=CEN), c=c, marker='^', cmap=cm.viridis, alpha=0.5, zorder=1,
+        plt.scatter(r2cc, centerat(-r2phi, m=CEN), c=c, marker='^', cmap=cm.viridis, alpha=0.5, zorder=1,
                     label='R2')
         plt.text(0.5, corr, 'Mean: {0:.3f} deg'.format(corr), fontsize=14, zorder=10)
         cbar = plt.colorbar(sc)
@@ -720,9 +720,9 @@ def analyze_station_orientations(ned, grv_dict, save_plots_path=None, ax=None):
     elif(ax is not None):
         fig = ax.get_figure()
         ax.plot([0, 1], [corr, corr], '-', linewidth=4, color=(0.8, 0.8, 0.8), zorder=5)
-        sc = ax.scatter(r1cc, centerat(r1phi, m=CEN), c=c, marker='o', cmap=cm.viridis, alpha=0.5, zorder=1,
+        sc = ax.scatter(r1cc, centerat(-r1phi, m=CEN), c=c, marker='o', cmap=cm.viridis, alpha=0.5, zorder=1,
                          label='R1')
-        ax.scatter(r2cc, centerat(r2phi, m=CEN), c=c, marker='^', cmap=cm.viridis, alpha=0.5, zorder=1,
+        ax.scatter(r2cc, centerat(-r2phi, m=CEN), c=c, marker='^', cmap=cm.viridis, alpha=0.5, zorder=1,
                     label='R2')
         ax.text(0.5, corr, 'Mean: {0:.3f} deg'.format(corr), fontsize=14, zorder=10)