add adjoint station convert script

Author: wjlei1990

scripts/convert_adjoint_stations/.nfs0000000006ea19ee0000123c

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+#!/bin/bash
+
+#PBS -A GEO111
+#PBS -N weighting
+#PBS -j oe
+#PBS -l walltime=6:00:00
+#PBS -l nodes=1
+
+#cd $PBS_O_WORKDIR
+echo "pwd: `pwd`"
+echo "start at `date`"
+
+eventfile="../eventlist.wenjie"
+
+idx=0
+for event in `cat $eventfile`
+do
+  idx=$(( $idx + 1 ))
+  echo "========================"
+  echo "[$idx]$event"
+  path=paths/$event.adjoint_stations.path.json
+  if [ ! -f $path ]; then
+    echo "Path not exists: $path"
+    exit
+  fi
+  pypaw-generate_adjoint_stations -f $path
+  echo "Time: `date`"
+
+done
+
+echo
+echo "job done at `date`"

scripts/convert_adjoint_stations/README.md

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+### Introduction
+
+This is the script used to generate the STATIONS_ADJOINT for adjoint simulation in specfem3d_Globe.
+
+There are two things it needs:
+  1. the measurements files generated by pyadjoint, including multiple period bands, which includes those stations with measurements for one event.
+  2. the stations.json file which contains stations location information.
+
+If you have multiple period bands, be sure to include all the measurement files inside the path json file.
+
+#### Usage
+1. Generate the path json file by running:
+  ```
+  python generate_path_adjoint_stations.py
+  ```
+  Be sure to modify the path information and eventlist in the script.
+
+2. Run the converting using:
+  ```
+  pypaw-generate_adjoint_stations -f event1.path.json
+  ```

scripts/convert_adjoint_stations/generate_path_adjoint_stations.py

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+import os
+import json
+
+
+def load_txt(fn):
+    with open(fn) as fh:
+        return [line.rstrip() for line in fh]
+
+
+def dump_json(content, fn):
+    with open(fn, 'w') as fh:
+        json.dump(content, fh, indent=2, sort_keys=True)
+
+
+def file_exists(fn):
+    if not os.path.exists(fn):
+        raise ValueError("File not exists: %s" % fn)
+
+
+def generate_adjoint_station_paths(
+        eventname, period_bands, basedir, path_dir):
+    measure_dir = os.path.join(basedir, "measure")
+    station_dir = os.path.join(basedir, "stations")
+    output_dir = os.path.join(basedir, "stations_adjoint")
+
+    measure_files = {}
+    for pb in period_bands:
+        fn = os.path.join(
+            measure_dir, "%s.%s.measure_adj.json" % (eventname, pb))
+        file_exists(fn)
+        measure_files[pb] = fn
+
+    station_file = os.path.join(station_dir, "%s.stations.json" % eventname)
+    output_file = os.path.join(output_dir, "STATIONS_ADJOINT.%s" % eventname)
+
+    content = {"measure_files": measure_files, "station_file": station_file,
+               "output_file": output_file}
+
+    path_json = os.path.join(path_dir, "%s.adjoint_stations.path.json" %
+                             eventname)
+    dump_json(content, path_json)
+
+
+def main():
+    period_bands = ["17_40", "40_100", "90_250"]
+    basedir = "/lustre/atlas/proj-shared/geo111/Wenjie/DATA_M16"
+    pathdir = "paths"
+
+    print("Output path dir: %s" % pathdir)
+    if not os.path.exists(pathdir):
+        os.makedirs(pathdir)
+
+    eventlist = load_txt("../eventlist.wenjie")
+    print("Number of events: %d" % len(eventlist))
+    for event in eventlist:
+        generate_adjoint_station_paths(event, period_bands, basedir, pathdir)
+
+
+
+if __name__ == "__main__":
+    main()

scripts/convert_adjoint_stations/paths/C201411021717A.adjoint_stations.path.json

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+{
+  "measure_files": {
+    "17_40": "/lustre/atlas/proj-shared/geo111/Wenjie/DATA_M16/measure/C201411021717A.17_40.measure_adj.json", 
+    "40_100": "/lustre/atlas/proj-shared/geo111/Wenjie/DATA_M16/measure/C201411021717A.40_100.measure_adj.json", 
+    "90_250": "/lustre/atlas/proj-shared/geo111/Wenjie/DATA_M16/measure/C201411021717A.90_250.measure_adj.json"
+  }, 
+  "output_file": "/lustre/atlas/proj-shared/geo111/Wenjie/DATA_M16/stations_adjoint/STATIONS_ADJOINT.C201411021717A", 
+  "station_file": "/lustre/atlas/proj-shared/geo111/Wenjie/DATA_M16/stations/C201411021717A.stations.json"
+}

scripts/convert_adjoint_stations/run_convert.bash

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+#!/bin/bash
+
+#PBS -A GEO111
+#PBS -N convert_adjoint_sta
+#PBS -j oe
+#PBS -l walltime=1:00:00
+#PBS -l nodes=1
+
+cd $PBS_O_WORKDIR
+echo "pwd: `pwd`"
+echo "start at `date`"
+
+eventfile="../eventlist.wenjie"
+
+idx=0
+for event in `cat $eventfile`
+do
+  idx=$(( $idx + 1 ))
+  echo "======================================"
+  echo "[$idx]$event"
+  path=paths/$event.adjoint_stations.path.json
+  if [ ! -f $path ]; then
+    echo "Path not exists: $path"
+    exit
+  fi
+  pypaw-generate_adjoint_stations -f $path
+  echo "Time: `date`"
+
+done
+
+echo
+echo "job done at `date`"