initial readme

inject_env.yml

@@ -0,0 +1,122 @@
+name: inject
+channels:
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=main
+  - _openmp_mutex=5.1=1_gnu
+  - aom=3.6.0=h6a678d5_0
+  - blas=1.0=mkl
+  - brotli-python=1.0.9=py313h6a678d5_9
+  - bzip2=1.0.8=h5eee18b_6
+  - c-ares=1.19.1=h5eee18b_0
+  - ca-certificates=2025.2.25=h06a4308_0
+  - cairo=1.16.0=he5ede1b_6
+  - contourpy=1.3.1=py313hdb19cb5_0
+  - cycler=0.11.0=pyhd3eb1b0_0
+  - cyrus-sasl=2.1.28=h1110e0f_3
+  - dav1d=1.2.1=h5eee18b_0
+  - expat=2.7.1=h6a678d5_0
+  - fontconfig=2.14.1=h55d465d_3
+  - fonttools=4.55.3=py313h5eee18b_0
+  - freetype=2.13.3=h4a9f257_0
+  - fribidi=1.0.10=h7b6447c_0
+  - graphite2=1.3.14=h295c915_1
+  - harfbuzz=10.2.0=hdfddeaa_1
+  - icu=73.1=h6a678d5_0
+  - intel-openmp=2023.1.0=hdb19cb5_46306
+  - jpeg=9e=h5eee18b_3
+  - kiwisolver=1.4.8=py313h6a678d5_0
+  - krb5=1.20.1=h143b758_1
+  - lcms2=2.16=h92b89f2_1
+  - ld_impl_linux-64=2.40=h12ee557_0
+  - lerc=4.0.0=h6a678d5_0
+  - libabseil=20250127.0=cxx17_h6a678d5_0
+  - libavif=1.1.1=h5eee18b_0
+  - libcups=2.4.2=h252cb56_2
+  - libcurl=8.14.1=hc1efc7f_1
+  - libdeflate=1.22=h5eee18b_0
+  - libedit=3.1.20230828=h5eee18b_0
+  - libev=4.33=h7f8727e_1
+  - libffi=3.4.4=h6a678d5_1
+  - libgcc-ng=11.2.0=h1234567_1
+  - libgfortran-ng=11.2.0=h00389a5_1
+  - libgfortran5=11.2.0=h1234567_1
+  - libgl=1.7.0=h5eee18b_2
+  - libglib=2.84.2=h37c7471_0
+  - libglvnd=1.7.0=h5eee18b_2
+  - libglx=1.7.0=h5eee18b_2
+  - libgomp=11.2.0=h1234567_1
+  - libiconv=1.16=h5eee18b_3
+  - libkrb5=1.21.3=h520c7b4_3
+  - libmpdec=4.0.0=h5eee18b_0
+  - libnghttp2=1.57.0=h2d74bed_0
+  - libpng=1.6.39=h5eee18b_0
+  - libpq=17.4=h02b6914_2
+  - libprotobuf=5.29.3=h3cdef7c_1
+  - libssh2=1.11.1=h251f7ec_0
+  - libstdcxx-ng=11.2.0=h1234567_1
+  - libtiff=4.7.0=hde9077f_0
+  - libuuid=1.41.5=h5eee18b_0
+  - libwebp-base=1.3.2=h5eee18b_1
+  - libxcb=1.17.0=h9b100fa_0
+  - libxkbcommon=1.9.1=h69220b7_0
+  - libxml2=2.13.8=hfdd30dd_0
+  - lmdb=0.9.29=h2531618_0
+  - lz4-c=1.9.4=h6a678d5_1
+  - matplotlib=3.10.0=py313h06a4308_1
+  - matplotlib-base=3.10.0=py313h68cf311_1
+  - mkl=2023.1.0=h213fc3f_46344
+  - mkl-service=2.4.0=py313h5eee18b_2
+  - mkl_fft=1.3.11=py313h5eee18b_0
+  - mkl_random=1.2.8=py313h06d7b56_0
+  - mysql=8.4.0=h721767e_2
+  - ncurses=6.5=h7934f7d_0
+  - numpy=2.3.1=py313h8d96ed3_0
+  - numpy-base=2.3.1=py313h8e760e0_0
+  - openjpeg=2.5.2=h0d4d230_1
+  - openldap=2.6.4=h42fbc30_0
+  - openssl=3.0.17=h5eee18b_0
+  - packaging=25.0=py313h06a4308_0
+  - pcre2=10.42=hebb0a14_1
+  - pillow=11.3.0=py313hb1c3d2d_0
+  - pip=25.1=pyhc872135_2
+  - pixman=0.40.0=h7f8727e_1
+  - pthread-stubs=0.3=h0ce48e5_1
+  - pyparsing=3.2.0=py313h06a4308_0
+  - pyqt=6.7.1=py313h8dad735_2
+  - pyqt6-sip=13.9.1=py313h6ce4db3_2
+  - python=3.13.5=h4612cfd_100_cp313
+  - python-dateutil=2.9.0post0=py313h06a4308_2
+  - python_abi=3.13=0_cp313
+  - qtbase=6.7.3=hdaa5aa8_0
+  - qtdeclarative=6.7.3=h7934f7d_1
+  - qtsvg=6.7.3=he4bddd1_1
+  - qttools=6.7.3=h5a8de97_1
+  - qtwebchannel=6.7.3=h7934f7d_1
+  - qtwebsockets=6.7.3=h7934f7d_1
+  - readline=8.2=h5eee18b_0
+  - scipy=1.16.0=py313h0cc6016_0
+  - setuptools=72.1.0=py313h06a4308_0
+  - sip=6.10.0=py313h6a678d5_0
+  - six=1.17.0=py313h06a4308_0
+  - sqlite=3.50.2=hb25bd0a_1
+  - tbb=2021.8.0=hdb19cb5_0
+  - tk=8.6.14=h993c535_1
+  - tornado=6.5.1=py313h5eee18b_0
+  - tzdata=2025b=h04d1e81_0
+  - wheel=0.45.1=py313h06a4308_0
+  - xcb-util=0.4.1=h5eee18b_2
+  - xcb-util-cursor=0.1.5=h5eee18b_0
+  - xcb-util-image=0.4.0=h5eee18b_2
+  - xcb-util-renderutil=0.3.10=h5eee18b_0
+  - xkeyboard-config=2.44=h5eee18b_0
+  - xorg-libx11=1.8.12=h9b100fa_1
+  - xorg-libxau=1.0.12=h9b100fa_0
+  - xorg-libxdmcp=1.1.5=h9b100fa_0
+  - xorg-libxext=1.3.6=h9b100fa_0
+  - xorg-libxrender=0.9.12=h9b100fa_0
+  - xorg-xorgproto=2024.1=h5eee18b_1
+  - xz=5.6.4=h5eee18b_1
+  - zlib=1.2.13=h5eee18b_1
+  - zstd=1.5.6=hc292b87_0
+prefix: /home/dagarwal/miniconda3/envs/inject

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/`.

testanalysis.py

@@ -11,6 +11,9 @@ import pandas as pd
 logger = logging.getLogger(__name__)
 logging.basicConfig(level=logging.INFO) #change for debug prints
 
+INJECTION_FILE = os.path.join(".","out","2025-07-31T17-25-54.txt")
+DETECTION_FILE = os.path.join(".","out","plotOut.txt")
+
 def linesplit(line):
     """
     Splits line of file into useful components.
@@ -49,14 +52,14 @@ detectedDic = {
 }
 
 #load injected data into dataframe
-with open(os.path.join(".","out","2025-07-31T17-25-54.txt"), "r") as file:
+with open(INJECTION_FILE, "r") as file:
     lines = file.readlines()
     updateDic(lines, injectedDic)
 
 injections = pd.DataFrame(data=injectedDic) #this is our main object for injection data
 
 #load detection data into dataframe
-with open(os.path.join(".","out","plotOut.txt"), "r") as file:
+with open(DETECTION_FILE, "r") as file:
     lines = file.readlines()
     updateDic(lines, detectedDic)
 

testfiles.txt

@@ -1,6 +0,0 @@
-/minish/keh00032/gb/2025/data_2025-05-05_07-08-36/
-/minish/keh00032/gb/2025/data_2025-05-05_07-16-59/
-/minish/keh00032/gb/2025/data_2025-05-05_07-25-22/
-/minish/keh00032/gb/2025/data_2025-05-05_07-33-46/
-/minish/keh00032/gb/2025/data_2025-05-05_07-42-09/
-/minish/keh00032/gb/2025/data_2025-05-05_07-50-32/