initial readme

readme.md

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+# Signal injection and testing for GREENBURST
+
+These scripts are developed to:
+1) Create and inject bursts of varying DM and width to existing FILTERBANK files (signalgen.py), and
+2) Analyze the results of running the resulting files through the GREENBURST pipeline (testanalysis.py).
+
+## Environment
+
+The inject_env.yml file contains the enviroment declaration necessary to run these scripts. On the GREENBURST machine, this enviroment is accessed via `conda activate inject`.
+
+## Running
+
+### Signal Generation
+
+Signalgen has 2 modes - generation and plotting. Generation is the default, while plotting is accessed via the `-p` flag.
+
+Files may be provided in three ways:
+- Directly and one at a time, via `-f`
+- Through a file containing a list of file paths, via `-l`
+- Contained in a directory via `-D`, where Signalgen will act on all `.fil` files in the directory.
+
+The injected signals can be of a specified DM (`-d`) and/or width (`-w`), and the number of samples taken by the `will` package can be adjusted as well (`-n`). 
+
+For bulk processing, the `-r` flag should be used to randomize the pulse parameters and output the injected pulse infomation to a timestamped file.
+
+By default, the resulting files will be output to `./out/`, but a different directory may be specified with `-o`. Note that `-p` will always output the plots into the same directory as the source `.fil` file.
+
+### Test Analysis
+
+After running the GREENBURST pipeline using the `-t` flag with stage 3, a `plotOut.txt` file will be output (by default, to `/ldata/dev_tests/repro/`). Provide the timestamped file from Signalgen and this `plotOut.txt` file to Testanalysis by editing the paths at the top of the script, and run the file. Information will be output to the log, and plots will be output to `./out/`.