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Fixing broken links in readme file
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geojunky committed Jun 30, 2022
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Expand Up @@ -23,7 +23,7 @@ developed by Tom Eulenfeld](https://doi.org/10.21105/joss.01808).

## [1. Event Trace Extraction](../README.md#event-trace-extraction)

## 2. Receiver Function Calculation / Correction
## 2. Receiver Function Calculation and Correction

The `generate_rf.py` script reads the event traces produced by `extract_event_traces.py`
and generates receiver functions. The script parallelizes RF computation over stations
Expand Down Expand Up @@ -163,10 +163,10 @@ config_rfs.json:
A small percentage of stations in some networks (e.g. OA) suffer from channel orientation
problems. Those stations can be corrected through a combination of channel rotation, negation
or swapping (N/E). Typically, one would generate the RFs and visualize them as described in
[Visualization of RFs](#visualization-of-rfs) -- note that the
[Visualization of RFs](#4-analyses-and-visualization-of-rfs) -- note that the
[RF Quality Filtering](#rf-quality-filtering) step can be skipped for the corrections and
completed afterwards. A pdf report generated as described in
[Visualization of RFs](#visualization-of-rfs) helps identify stations with orientation problems.
[Visualization of RFs](#4-analyses-and-visualization-of-rfs) helps identify stations with orientation problems.
Once a list of problematic stations is compiled, users need to run `generate_rf.py` with the same
input/output parameters, but with a `correction` block added to the json configuration file, as
follows:
Expand Down Expand Up @@ -256,13 +256,13 @@ To use script `rf_quality_filter.py`, the following parameters should be provide
For additional options, see `rf_quality_filter.py --help`.


## 4. Analyses/Visualization of RFs
## 4. Analyses and Visualization of RFs

Automatic report generation on a full set of RF results is performed using the MPI-parallelized
`bulk_rf_report.py` script.
This script needs to be provided with an input H5 file containing RFs generated in
[Receiver Function Calculation](#receiver-function-calculation) or that in
[RF Quality Filtering](#rf-quality-filtering) and an output file name -- it then generates
[Receiver Function Calculation](#2-receiver-function-calculation-and-correction) or that in
[RF Quality Filtering](#3-rf-quality-filtering) and an output file name -- it then generates
a PDF report containing a standard set of visualisations of the RFs:

* Pinwheel diagram showing RFs source directions around the full azimuthal range
Expand All @@ -275,9 +275,9 @@ Quality filters can be used to filter out spurious RFs, as described in usage de
`bulk_rf_report.py --help`.

Note that, if `bulk_rf_report.py` is run on RFs produced in
[Receiver Function Calculation](#receiver-function-calculation), `--min-slope-ratio` is
[Receiver Function Calculation](#2-receiver-function-calculation-and-correction), `--min-slope-ratio` is
the only quality-filter available. Otherwise, if run on the output generated in
[RF Quality Filtering](#rf-quality-filtering), all quality-filters described above
[RF Quality Filtering](#3-rf-quality-filtering), all quality-filters described above
are available for use. Use of at least one of these options is highly recommended to
remove spurious RFs.

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