Merge pull request #246 from vijayvarma392/posterior

add submodule for postprocessing

Author: vijayvarma392

README.md

@@ -16,7 +16,7 @@
 # About
 
 **gw_eccentricity** provides methods to measure eccentricity and mean anomaly
-from gravitational waveforms.
+from gravitational waveforms of binaries on generic bound orbits.
 
 These methods are described in the following paper: <br/>
 - [1] Md Arif Shaikh, Vijay Varma, Harald Pfeiffer, Antoni Ramos-Buades and
@@ -44,12 +44,22 @@ the main branch at the top of this page.
 ```shell
 pip install gw_eccentricity
 ```
+or
+```shell
+pip install "gw_eccentricity[postprocess]"
+```
+to additionally install the functionality for postprocessing posterior samples from
+parameter estimation pipelines.
 
 ## Conda
 **gw_eccentricity** can be installed using `conda` also:
 ```shell
 conda install -c conda-forge gw_eccentricity
 ```
+or
+```shell
+conda install -c conda-forge gw_eccentricity gw_eccentricity-postprocess
+```
 
 ## From source
 
@@ -58,6 +68,10 @@ git clone git@github.com:vijayvarma392/gw_eccentricity.git
 cd gw_eccentricity
 pip install .
 ```
+or
+```
+pip install .["postprocess"]
+```
 
 If you do not have root permissions, replace the last step with
 `pip install --user .`
@@ -77,7 +91,13 @@ See example notebooks:
 * [gw_eccentricity demo](https://github.com/vijayvarma392/gw_eccentricity/blob/main/examples/gw_eccentricity_demo.ipynb) for how to use the package, along with diagnostic plots.
 * [Load waveforms demo](https://github.com/vijayvarma392/gw_eccentricity/blob/main/examples/load_waveform_demo.ipynb) for loading waveform data into a dictionary format suitable for gw_eccentricity, including for LAL, SXS, and LVCNR waveforms.
   - [TEOBResumS-Dali demo](https://github.com/vijayvarma392/gw_eccentricity/blob/main/examples/egw_from_TEOBResumS-DALI_demo.ipynb) for the same for `TEOBResumS-Dali`.
-  - [SEOBNRv5EHM demo](https://github.com/vijayvarma392/gw_eccentricity/blob/main/examples/egw_from_SEOBNRv5EHM_demo.ipynb) for the same for `SEOBNRv5EHM`.
+  - [SEOBNRv5EHM
+    demo](https://github.com/vijayvarma392/gw_eccentricity/blob/main/examples/egw_from_SEOBNRv5EHM_demo.ipynb)
+    for the same for `SEOBNRv5EHM`.
+## Postprocessing posterior samples
+See the example notebooks and scripts
+[here](https://github.com/vijayvarma392/gw_eccentricity/blob/main/examples/postprocessing)
+for postprocessing posterior from parameter estimation pipelines.
 
 # Making contributions
 See this

examples/postprocessing/postprocess.condor.sub

@@ -0,0 +1,30 @@
+# HTCondor submit file for running postprocess.sh
+#
+# Usage:
+#   cd gw_eccentricity/postprocess/examples
+#   chmod +x postprocess.sh
+#   condor_submit postprocess.condor.sub
+#
+# Adjust NPROCS/request_cpus as needed. postprocess.sh will run with MPI
+# only when NPROCS > 1.
+
+universe = vanilla
+executable = postprocess.sh
+
+# Set process count consumed by postprocess.sh (NPROCS env var).
+environment = "NPROCS=4"
+
+# Resource requests (edit for your cluster).
+request_cpus = 4
+request_memory = 8 GB
+request_disk = 4 GB
+
+# Logs
+log = postprocess.$(Cluster).log
+output = postprocess.$(Cluster).$(Process).out
+error = postprocess.$(Cluster).$(Process).err
+
+# Keep files on shared filesystem; set to YES and configure transfer_* if needed.
+should_transfer_files = NO
+
+queue 1

examples/postprocessing/postprocess.sh

@@ -0,0 +1,32 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Initialize conda
+source ~/anaconda3/etc/profile.d/conda.sh
+
+# Activate your env
+conda activate gw_eccentricity_postprocess
+
+NPROCS=${NPROCS:-1}
+
+CMD=(
+	gw-eccentricity-postprocess
+	--posterior-path "/Users/arif/Desktop/TEOB_chi0_9_ecc0_3_samples.hdf5"
+	--parameter-columns "mass_1,mass_2,spin_1z,spin_2z,luminosity_distance,minimum_frequency,eccentricity,mean_per_ano"
+	--output-dir "/Users/arif/Desktop/"
+	--output-format csv
+	--save-every none
+	--samples 0:1000
+	--fref 10
+	--tref none
+	--method Amplitude
+	--data-dict-generator "/Users/arif/gw_eccentricity/examples/postprocessing/teobresums_dali.py:teob_data_dict_generator"
+	--data-dict-generator-extra-kwargs '{"backwards":"yes","ode_tmax":1}'
+	--gw-eccentricity-kwargs '{"extra_kwargs":{"omega_gw_extrema_interpolation_method":"spline"}}'
+)
+
+if [ "$NPROCS" -gt 1 ]; then
+	mpirun -n "$NPROCS" "${CMD[@]}"
+else
+	"${CMD[@]}"
+fi