allow multiple depths in single run, read depths from quakeml file ar…

…g if given. Remove duplicate Locations from stationxml. JSON has sourceDepths as list and each Arrival includes the source depth calculated from. Other refactor of JSON output code.
crotwell · Sep 6, 2024 · 1f0f9f1 · 1f0f9f1
1 parent 1464a61
commit 1f0f9f1
Show file tree

Hide file tree

Showing 62 changed files with 905 additions and 575 deletions.
diff --git a/docs/manual/taup_curve.html b/docs/manual/taup_curve.html
@@ -3051,10 +3051,11 @@ <h3 id="searchlabel">Quick search</h3>
                   [--mapwidth=&lt;mapwidth&gt;] [--mapwidthunit=&lt;mapWidthUnit&gt;]
                   [--mw=&lt;mw&gt;] [-o=&lt;outFile&gt;] [--prop=&lt;toolPropsFilename&gt;]
                   [--reddeg=deg/s] [--redkm=km/s] [--rel=phase] [-x=type]
-                  [-y=type] [--xminmax=x x]... [--yminmax=y y]... [[-h=depth]
-                  [--mod=&lt;modelname&gt;] [--stadepth=depth] [--scat=s s]...]
-                  [[-p=phase[,phase...]]... [--phasefile=&lt;phaseFiles&gt;]...]
-                  [--gmt | --json | --svg | --text]
+                  [-y=type] [--xminmax=x x]... [--yminmax=y y]...
+                  [[--mod=&lt;modelname&gt;] [--stadepth=depth] [-h=depth[,
+                  depth...]]... [--scat=s s]...] [[-p=phase[,phase...]]...
+                  [--phasefile=&lt;phaseFiles&gt;]...] [--gmt | --json | --svg |
+                  --text]
 Plot travel time vs. distance and other curves for seismic phases.
 
 Options:
@@ -3100,7 +3101,7 @@ <h3 id="searchlabel">Quick search</h3>
       --ylog               Y axis is log
       --yminmax=y y        min and max y axis for plotting
 Model Args
-  -h, --evdepth, --sourcedepth=depth
+  -h, --evdepth, --sourcedepth=depth[,depth...]
                            source depth in km
       --mod, --model=&lt;modelname&gt;
                            use velocity model &quot;modelname&quot; for calculations.

diff --git a/docs/manual/taup_find.html b/docs/manual/taup_find.html
@@ -182,8 +182,8 @@ <h3 id="searchlabel">Quick search</h3>
                  --max=&lt;maxActions&gt; [--mw=&lt;mw&gt;] [-o=&lt;outFile&gt;]
                  [--prop=&lt;toolPropsFilename&gt;] [--deg=d[,d...]]...
                  [--rayparamdeg=s/deg [s/deg]]... [--rayparamkm=s/km [s/km]]...
-                 [--time=t [t]]... [--exclude=depth...]... [[-h=depth]
-                 [--mod=&lt;modelname&gt;] [--stadepth=depth] [--scat=s s]...]
+                 [--time=t [t]]... [--exclude=depth...]... [[--mod=&lt;modelname&gt;]
+                 [--stadepth=depth] [-h=depth[,depth...]]... [--scat=s s]...]
                  [[-p=phase[,phase...]]... [--phasefile=&lt;phaseFiles&gt;]...]
                  [--json | --text]
 Find seismic phases in an earth model.
@@ -219,7 +219,7 @@ <h3 id="searchlabel">Quick search</h3>
       --time=t [t]         find arrivals within the given range
       --verbose            enable verbose output
 Model Args
-  -h, --evdepth, --sourcedepth=depth
+  -h, --evdepth, --sourcedepth=depth[,depth...]
                            source depth in km
       --mod, --model=&lt;modelname&gt;
                            use velocity model &quot;modelname&quot; for calculations.

diff --git a/docs/manual/taup_path.html b/docs/manual/taup_path.html
@@ -2217,17 +2217,18 @@ <h3 id="searchlabel">Quick search</h3>
                  [--color=&lt;coloring&gt;] [--ellipflattening=f]
                  [--mapwidth=&lt;mapwidth&gt;] [--mapwidthunit=&lt;mapWidthUnit&gt;]
                  [--maxpathinc=&lt;maxPathInc&gt;] [-o=&lt;outFile&gt;]
-                 [--prop=&lt;toolPropsFilename&gt;] [--xaxis=type] [--yaxis=type]
+                 [--prop=&lt;toolPropsFilename&gt;] [--qml=&lt;quakemlFilename&gt;]
+                 [--staxml=&lt;stationxmlFilename&gt;] [--xaxis=type] [--yaxis=type]
                  [--degminmax=deg deg]... [--depthminmax=km km]... [--evt=l
-                 l]... [--evt=l l]... [--sta=l l]... [--sta=l l]... [[-h=depth]
-                 [--mod=&lt;modelname&gt;] [--stadepth=depth] [--scat=s s]...]
-                 [[-p=phase[,phase...]]... [--phasefile=&lt;phaseFiles&gt;]...]
-                 [[--deg=d[,d...]]... [--exactdegree=d[,d...]]...
-                 [--exactkilometer=km[,km...]]... [--km=km[,km...]]...
-                 [--rayparamdeg=s/deg[,s/deg...]]... [--rayparamidx=i[,
-                 i...]]... [--rayparamkm=s/km[,s/km...]]... [--rayparamrad=s/rad
-                 [,s/rad...]]... [--takeoff=deg[,deg...]]...]... [--gmt |
-                 --json | --svg | --text]
+                 l]... [--evt=l l]... [--sta=l l]... [--sta=l l]...
+                 [[--mod=&lt;modelname&gt;] [--stadepth=depth] [-h=depth[,
+                 depth...]]... [--scat=s s]...] [[-p=phase[,phase...]]...
+                 [--phasefile=&lt;phaseFiles&gt;]...] [[--deg=d[,d...]]...
+                 [--exactdegree=d[,d...]]... [--exactkilometer=km[,km...]]...
+                 [--km=km[,km...]]... [--rayparamdeg=s/deg[,s/deg...]]...
+                 [--rayparamidx=i[,i...]]... [--rayparamkm=s/km[,s/km...]]...
+                 [--rayparamrad=s/rad[,s/rad...]]... [--takeoff=deg[,
+                 deg...]]...]... [--gmt | --json | --svg | --text]
 Plot ray paths, distance vs. depth, through the earth.
 
 Options:
@@ -2257,6 +2258,11 @@ <h3 id="searchlabel">Quick search</h3>
                                discontinuities like moho, cmb, iocb
       --prop=&lt;toolPropsFilename&gt;
                              load defaults from properties file
+      --qml, --quakeml=&lt;quakemlFilename&gt;
+                             QuakeML file to load for earthquake origins to use
+      --staxml=&lt;stationxmlFilename&gt;
+                             StationXML file to extract station latitudes and
+                               longitudes from
       --verbose              enable verbose output
       --withtime             include time for each path point, no effect for
                                SVG.
@@ -2267,7 +2273,7 @@ <h3 id="searchlabel">Quick search</h3>
                                radius
                              No effect for SVG output.
 Model Args
-  -h, --evdepth, --sourcedepth=depth
+  -h, --evdepth, --sourcedepth=depth[,depth...]
                              source depth in km
       --mod, --model=&lt;modelname&gt;
                              use velocity model &quot;modelname&quot; for calculations.

diff --git a/docs/manual/taup_phase.html b/docs/manual/taup_phase.html
@@ -147,9 +147,10 @@ <h3 id="searchlabel">Quick search</h3>
 </div>
 <p>The usage is:</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>Usage: taup phase [--debug] [--help] [--verbose] [-o=&lt;outFile&gt;]
-                  [--prop=&lt;toolPropsFilename&gt;] [[-h=depth] [--mod=&lt;modelname&gt;]
-                  [--stadepth=depth] [--scat=s s]...] [[-p=phase[,phase...]]...
-                  [--phasefile=&lt;phaseFiles&gt;]...] [--json | --text]
+                  [--prop=&lt;toolPropsFilename&gt;] [[--mod=&lt;modelname&gt;]
+                  [--stadepth=depth] [-h=depth[,depth...]]... [--scat=s s]...]
+                  [[-p=phase[,phase...]]... [--phasefile=&lt;phaseFiles&gt;]...]
+                  [--json | --text]
 Describe a seismic phase in the current model.
 
 Options:
@@ -161,7 +162,7 @@ <h3 id="searchlabel">Quick search</h3>
                            load defaults from properties file
       --verbose            enable verbose output
 Model Args
-  -h, --evdepth, --sourcedepth=depth
+  -h, --evdepth, --sourcedepth=depth[,depth...]
                            source depth in km
       --mod, --model=&lt;modelname&gt;
                            use velocity model &quot;modelname&quot; for calculations.

diff --git a/docs/manual/taup_pierce.html b/docs/manual/taup_pierce.html
@@ -205,15 +205,16 @@ <h3 id="searchlabel">Quick search</h3>
                    [--verbose] [--az=&lt;azimuth&gt;] [--az=&lt;azimuth&gt;]
                    [--baz=&lt;backAzimuth&gt;] [--baz=&lt;backAzimuth&gt;]
                    [--ellipflattening=f] [--mw=&lt;mw&gt;] [-o=&lt;outFile&gt;]
-                   [--prop=&lt;toolPropsFilename&gt;] [--pierce=depth[,depth...]]...
-                   [--rel=phase[,phase...]]... [--evt=l l]... [--evt=l l]...
-                   [--sta=l l]... [--sta=l l]... [[-h=depth]
-                   [--mod=&lt;modelname&gt;] [--stadepth=depth] [--scat=s s]...]
-                   [[-p=phase[,phase...]]... [--phasefile=&lt;phaseFiles&gt;]...]
-                   [[--deg=d[,d...]]... [--exactdegree=d[,d...]]...
-                   [--exactkilometer=km[,km...]]... [--km=km[,km...]]...
-                   [--rayparamdeg=s/deg[,s/deg...]]... [--rayparamidx=i[,
-                   i...]]... [--rayparamkm=s/km[,s/km...]]...
+                   [--prop=&lt;toolPropsFilename&gt;] [--qml=&lt;quakemlFilename&gt;]
+                   [--staxml=&lt;stationxmlFilename&gt;] [--pierce=depth[,
+                   depth...]]... [--rel=phase[,phase...]]... [--evt=l l]...
+                   [--evt=l l]... [--sta=l l]... [--sta=l l]...
+                   [[--mod=&lt;modelname&gt;] [--stadepth=depth] [-h=depth[,
+                   depth...]]... [--scat=s s]...] [[-p=phase[,phase...]]...
+                   [--phasefile=&lt;phaseFiles&gt;]...] [[--deg=d[,d...]]...
+                   [--exactdegree=d[,d...]]... [--exactkilometer=km[,km...]]...
+                   [--km=km[,km...]]... [--rayparamdeg=s/deg[,s/deg...]]...
+                   [--rayparamidx=i[,i...]]... [--rayparamkm=s/km[,s/km...]]...
                    [--rayparamrad=s/rad[,s/rad...]]... [--takeoff=deg[,
                    deg...]]...]... [--json | --text]
 Calculate pierce points for phases at discontinuities in the model.
@@ -241,16 +242,21 @@ <h3 id="searchlabel">Quick search</h3>
                              additional depth for calculating pierce points
       --prop=&lt;toolPropsFilename&gt;
                              load defaults from properties file
+      --qml, --quakeml=&lt;quakemlFilename&gt;
+                             QuakeML file to load for earthquake origins to use
       --rayp, --onlyrayp     only output the ray parameter
       --rel=phase[,phase...] times relative to the first of the given phases
       --rev                  only prints underside and bottom turn points, e.g.
                                ^ and v
+      --staxml=&lt;stationxmlFilename&gt;
+                             StationXML file to extract station latitudes and
+                               longitudes from
       --time, --onlytime     only output travel time
       --turn                 only prints bottom turning points, e.g. v
       --under                only prints underside reflection points, e.g. ^
       --verbose              enable verbose output
 Model Args
-  -h, --evdepth, --sourcedepth=depth
+  -h, --evdepth, --sourcedepth=depth[,depth...]
                              source depth in km
       --mod, --model=&lt;modelname&gt;
                              use velocity model &quot;modelname&quot; for calculations.

diff --git a/docs/manual/taup_refltrans.html b/docs/manual/taup_refltrans.html
@@ -3311,8 +3311,9 @@ <h3 id="searchlabel">Quick search</h3>
                       [-o=&lt;outFile&gt;] [--prop=&lt;toolPropsFilename&gt;]
                       [--rpstep=s/km] [-x=type] [--xminmax=x x]... [--yminmax=y
                       y]... [--layer=v v v v v v]... [-y=type...]... [--gmt |
-                      --json | --svg | --text] [[-h=depth] [--mod=&lt;modelname&gt;]
-                      [--stadepth=depth] [--scat=s s]...]
+                      --json | --svg | --text] [[--mod=&lt;modelname&gt;]
+                      [--stadepth=depth] [-h=depth[,depth...]]... [--scat=s
+                      s]...]
 Plot reflection and transmission coefficients for a discontinuity.
 
 Options:
@@ -3360,7 +3361,7 @@ <h3 id="searchlabel">Quick search</h3>
       --svg                 outputs as SVG
       --text                outputs as Text
 Model Args
-  -h, --evdepth, --sourcedepth=depth
+  -h, --evdepth, --sourcedepth=depth[,depth...]
                             source depth in km
       --mod, --model=&lt;modelname&gt;
                             use velocity model &quot;modelname&quot; for calculations.

diff --git a/docs/manual/taup_setms3.html b/docs/manual/taup_setms3.html
@@ -140,13 +140,13 @@ <h3 id="searchlabel">Quick search</h3>
 </pre></div>
 </div>
 <p>The usage is:</p>
-<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>Usage: taup setms3 [--debug] [--geodetic] [--help] [--verbose] [--eh=&lt;ehKey&gt;]
+<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>Usage: taup setms3 [--debug] [--geodetic] [--help] [--verbose]
                    [--ellipflattening=f] [--prop=&lt;toolPropsFilename&gt;]
                    [--qml=&lt;quakemlFilename&gt;] [--qmltol=&lt;quakeOTimeTol&gt;]
-                   [--staxml=&lt;stationxmlFilename&gt;] [[-h=depth]
-                   [--mod=&lt;modelname&gt;] [--stadepth=depth] [--scat=s s]...]
-                   [[-p=phase[,phase...]]... [--phasefile=&lt;phaseFiles&gt;]...]
-                   [mseed3file...]
+                   [--staxml=&lt;stationxmlFilename&gt;] [--taupeh=&lt;ehKey&gt;]
+                   [[--mod=&lt;modelname&gt;] [--stadepth=depth] [-h=depth[,
+                   depth...]]... [--scat=s s]...] [[-p=phase[,phase...]]...
+                   [--phasefile=&lt;phaseFiles&gt;]...] [mseed3file...]
 Save travel times in the extra header of miniseed3 files.
     https://crotwell.github.io/ms3eh/
 has details on the JSON structure.
@@ -156,9 +156,6 @@ <h3 id="searchlabel">Quick search</h3>
 Options:
 
       --debug               enable debugging output
-      --eh=&lt;ehKey&gt;          key to store full TauP JSON output within extra
-                              headers within, otherwise use abbreviated &#39;bag&#39;
-                              markers
       --ellipflattening=f   Elliptical flattening for distance calculations
                               when --geodetic, defaults to WGS84 ~ 1/298.257
       --geodetic            use geodetic latitude for distance calculations,
@@ -170,16 +167,19 @@ <h3 id="searchlabel">Quick search</h3>
       --prop=&lt;toolPropsFilename&gt;
                             load defaults from properties file
       --qml, --quakeml=&lt;quakemlFilename&gt;
-                            QuakeML file to load to search for origins that
-                              match this waveform
+                            QuakeML file to load for earthquake origins to use
       --qmltol=&lt;quakeOTimeTol&gt;
                             time window to search for origins in a QuakeML file
                               as an ISO8601 string, default value is PT1H.
       --staxml=&lt;stationxmlFilename&gt;
-                            StationXML file to extract station lat/lon from
+                            StationXML file to extract station latitudes and
+                              longitudes from
+      --taupeh=&lt;ehKey&gt;      key to store full TauP JSON output within extra
+                              headers within, otherwise use abbreviated &#39;bag&#39;
+                              style markers.
       --verbose             enable verbose output
 Model Args
-  -h, --evdepth, --sourcedepth=depth
+  -h, --evdepth, --sourcedepth=depth[,depth...]
                             source depth in km
       --mod, --model=&lt;modelname&gt;
                             use velocity model &quot;modelname&quot; for calculations.

diff --git a/docs/manual/taup_setsac.html b/docs/manual/taup_setsac.html
@@ -178,8 +178,8 @@ <h3 id="searchlabel">Quick search</h3>
 <p>The usage is:</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>Usage: taup setsac [--debug] [--evdpkm] [--geodetic] [--help] [--verbose]
                    [--ellipflattening=f] [--prop=&lt;toolPropsFilename&gt;]
-                   [[-h=depth] [--mod=&lt;modelname&gt;] [--stadepth=depth] [--scat=s
-                   s]...] [[-p=phase[,phase...]]...
+                   [[--mod=&lt;modelname&gt;] [--stadepth=depth] [-h=depth[,
+                   depth...]]... [--scat=s s]...] [[-p=phase[,phase...]]...
                    [--phasefile=&lt;phaseFiles&gt;]...] [sacfile...]
 Set headers to travel times of phases using depth and distance from SAC files.
       [sacfile...]          SAC files to process
@@ -200,7 +200,7 @@ <h3 id="searchlabel">Quick search</h3>
                             load defaults from properties file
       --verbose             enable verbose output
 Model Args
-  -h, --evdepth, --sourcedepth=depth
+  -h, --evdepth, --sourcedepth=depth[,depth...]
                             source depth in km
       --mod, --model=&lt;modelname&gt;
                             use velocity model &quot;modelname&quot; for calculations.

diff --git a/docs/manual/taup_spikes.html b/docs/manual/taup_spikes.html
@@ -130,10 +130,11 @@ <h3 id="searchlabel">Quick search</h3>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>Usage: taup spikes [--debug] [--geodetic] [--help] [--verbose] [--az=&lt;azimuth&gt;]
                    [--az=&lt;azimuth&gt;] [--baz=&lt;backAzimuth&gt;] [--baz=&lt;backAzimuth&gt;]
                    [--ellipflattening=f] [--mw=&lt;mw&gt;] [-o=&lt;outFile&gt;]
-                   [--otime=&lt;origintime&gt;] [--prop=&lt;toolPropsFilename&gt;] [--evt=l
-                   l]... [--evt=l l]... [--sta=l l]... [--sta=l l]...
-                   [[-h=depth] [--mod=&lt;modelname&gt;] [--stadepth=depth] [--scat=s
-                   s]...] [[-p=phase[,phase...]]...
+                   [--otime=&lt;origintime&gt;] [--prop=&lt;toolPropsFilename&gt;]
+                   [--qml=&lt;quakemlFilename&gt;] [--staxml=&lt;stationxmlFilename&gt;]
+                   [--evt=l l]... [--evt=l l]... [--sta=l l]... [--sta=l l]...
+                   [[--mod=&lt;modelname&gt;] [--stadepth=depth] [-h=depth[,
+                   depth...]]... [--scat=s s]...] [[-p=phase[,phase...]]...
                    [--phasefile=&lt;phaseFiles&gt;]...] [[--deg=d[,d...]]...
                    [--exactdegree=d[,d...]]... [--exactkilometer=km[,km...]]...
                    [--km=km[,km...]]... [--rayparamdeg=s/deg[,s/deg...]]...
@@ -159,9 +160,14 @@ <h3 id="searchlabel">Quick search</h3>
       --otime=&lt;origintime&gt;   event origin time, as ISO8601
       --prop=&lt;toolPropsFilename&gt;
                              load defaults from properties file
+      --qml, --quakeml=&lt;quakemlFilename&gt;
+                             QuakeML file to load for earthquake origins to use
+      --staxml=&lt;stationxmlFilename&gt;
+                             StationXML file to extract station latitudes and
+                               longitudes from
       --verbose              enable verbose output
 Model Args
-  -h, --evdepth, --sourcedepth=depth
+  -h, --evdepth, --sourcedepth=depth[,depth...]
                              source depth in km
       --mod, --model=&lt;modelname&gt;
                              use velocity model &quot;modelname&quot; for calculations.

diff --git a/docs/manual/taup_table.html b/docs/manual/taup_table.html
@@ -147,10 +147,11 @@ <h3 id="searchlabel">Quick search</h3>
 locsat style travel time files.</p>
 <p>The usage is:</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>Usage: taup table [--debug] [--help] [--verbose] [--header=&lt;headerFile&gt;]
-                  [-o=&lt;outFile&gt;] [--prop=&lt;toolPropsFilename&gt;] [[-h=depth]
-                  [--mod=&lt;modelname&gt;] [--stadepth=depth] [--scat=s s]...]
-                  [[-p=phase[,phase...]]... [--phasefile=&lt;phaseFiles&gt;]...]
-                  [--csv | --json | --locsat | --text]
+                  [-o=&lt;outFile&gt;] [--prop=&lt;toolPropsFilename&gt;]
+                  [[--mod=&lt;modelname&gt;] [--stadepth=depth] [-h=depth[,
+                  depth...]]... [--scat=s s]...] [[-p=phase[,phase...]]...
+                  [--phasefile=&lt;phaseFiles&gt;]...] [--csv | --json | --locsat |
+                  --text]
 Create a table of travel times for a range of depths and distances.
 
 Options:
@@ -165,7 +166,7 @@ <h3 id="searchlabel">Quick search</h3>
                            load defaults from properties file
       --verbose            enable verbose output
 Model Args
-  -h, --evdepth, --sourcedepth=depth
+  -h, --evdepth, --sourcedepth=depth[,depth...]
                            source depth in km
       --mod, --model=&lt;modelname&gt;
                            use velocity model &quot;modelname&quot; for calculations.