PycWB 0.23.1__tar.gz → 0.24.0__tar.gz

{pycwb-0.23.1 → pycwb-0.24.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PycWB
-Version: 0.23.1
+Version: 0.24.0
 Summary: A Python package for coherent gravitational wave burst analysis
 Home-page: https://git.ligo.org/yumeng.xu/pycwb
 Author-email: The PycWB team <yumeng.xu@ligo.org>
@@ -34,14 +34,14 @@ Requires-Dist: htcondor
 
 # PycWB
 
-[![Documentations](https://readthedocs.org/projects/pycwb/badge/?version=latest)](https://pycwb.readthedocs.io/en/latest/)
+[![Documentations](https://readthedocs.org/projects/pycwb/badge/?version=latest)](https://pycwb.readthedocs.io)
 [![Build Status](https://git.ligo.org/yumeng.xu/pycwb/badges/main/pipeline.svg)](https://git.ligo.org/yumeng.xu/pycwb/-/pipelines)
 [![Releases](https://git.ligo.org/yumeng.xu/pycwb/-/badges/release.svg)](https://git.ligo.org/yumeng.xu/pycwb/-/releases)
 [![PyPI version](https://badge.fury.io/py/pycWB.svg)](https://badge.fury.io/py/pycWB)
 [![License](https://img.shields.io/badge/license-GPLv3-blue)](https://git.ligo.org/yumeng.xu/pycwb/-/blob/main/LICENSE)
 
 PycWB is a modularized Python package for gravitational wave burst search based on the core function of cWB.
-The documentation can be found at [pycwb.readthedocs.io](https://pycwb.readthedocs.io/en/latest/).
+The documentation can be found at [pycwb.readthedocs.io](https://pycwb.readthedocs.io).
 
 ## Installation
 
@@ -62,10 +62,13 @@ Currently, pycWB is only available for x64 architecture.
 For Apple Silicon users, you can install the dependencies with the following commands:
 
 ```bash
-conda create -n pycwb "python>=3.9,<3.11"
+# make sure rosetta is installed
+softwareupdate --install-rosetta --agree-to-license
+# Optional: export CONDA_BUILD=1
+conda create -n pycwb
 conda activate pycwb
 conda config --env --set subdir osx-64
-conda install -c conda-forge root=6.26.10 healpix_cxx=3.81 nds2-client python-nds2-client lalsuite setuptools_scm cmake pkg-config htcondor
+conda install -c conda-forge "python>=3.9,<3.11" root=6.26.10 healpix_cxx=3.81 nds2-client python-nds2-client lalsuite setuptools_scm cmake pkg-config ruamel.yaml htcondor
 ```
 
 ### Install pycWB from source

{pycwb-0.23.1 → pycwb-0.24.0}/PycWB.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PycWB
-Version: 0.23.1
+Version: 0.24.0
 Summary: A Python package for coherent gravitational wave burst analysis
 Home-page: https://git.ligo.org/yumeng.xu/pycwb
 Author-email: The PycWB team <yumeng.xu@ligo.org>
@@ -34,14 +34,14 @@ Requires-Dist: htcondor
 
 # PycWB
 
-[![Documentations](https://readthedocs.org/projects/pycwb/badge/?version=latest)](https://pycwb.readthedocs.io/en/latest/)
+[![Documentations](https://readthedocs.org/projects/pycwb/badge/?version=latest)](https://pycwb.readthedocs.io)
 [![Build Status](https://git.ligo.org/yumeng.xu/pycwb/badges/main/pipeline.svg)](https://git.ligo.org/yumeng.xu/pycwb/-/pipelines)
 [![Releases](https://git.ligo.org/yumeng.xu/pycwb/-/badges/release.svg)](https://git.ligo.org/yumeng.xu/pycwb/-/releases)
 [![PyPI version](https://badge.fury.io/py/pycWB.svg)](https://badge.fury.io/py/pycWB)
 [![License](https://img.shields.io/badge/license-GPLv3-blue)](https://git.ligo.org/yumeng.xu/pycwb/-/blob/main/LICENSE)
 
 PycWB is a modularized Python package for gravitational wave burst search based on the core function of cWB.
-The documentation can be found at [pycwb.readthedocs.io](https://pycwb.readthedocs.io/en/latest/).
+The documentation can be found at [pycwb.readthedocs.io](https://pycwb.readthedocs.io).
 
 ## Installation
 
@@ -62,10 +62,13 @@ Currently, pycWB is only available for x64 architecture.
 For Apple Silicon users, you can install the dependencies with the following commands:
 
 ```bash
-conda create -n pycwb "python>=3.9,<3.11"
+# make sure rosetta is installed
+softwareupdate --install-rosetta --agree-to-license
+# Optional: export CONDA_BUILD=1
+conda create -n pycwb
 conda activate pycwb
 conda config --env --set subdir osx-64
-conda install -c conda-forge root=6.26.10 healpix_cxx=3.81 nds2-client python-nds2-client lalsuite setuptools_scm cmake pkg-config htcondor
+conda install -c conda-forge "python>=3.9,<3.11" root=6.26.10 healpix_cxx=3.81 nds2-client python-nds2-client lalsuite setuptools_scm cmake pkg-config ruamel.yaml htcondor
 ```
 
 ### Install pycWB from source

{pycwb-0.23.1 → pycwb-0.24.0}/PycWB.egg-info/SOURCES.txt

@@ -177,6 +177,7 @@ examples/benchmark/input/OPBM_L1.frames
 examples/colab/pycWB_GW150914.ipynb
 examples/injection/pycwb_injection.ipynb
 examples/injection/user_parameters_injection.yaml
+examples/injection/wdmXTalk/OverlapCatalog16-1024.bin
 examples/lvk_sep_2023/demo.ipynb
 examples/lvk_sep_2023/user_parameters.yaml
 examples/multiple_injection/pycwb_injection.py
@@ -273,6 +274,10 @@ pycwb/modules/data_conditioning/regression.py
 pycwb/modules/data_conditioning/whitening.py
 pycwb/modules/energy_threshold/__init__.py
 pycwb/modules/energy_threshold/threshold.py
+pycwb/modules/gracedb/__init__.py
+pycwb/modules/gracedb/gracedb.py
+pycwb/modules/gracedb/module.yaml
+pycwb/modules/gracedb/test_gracedb.py
 pycwb/modules/job_segment/__init__.py
 pycwb/modules/job_segment/dq_segment.py
 pycwb/modules/job_segment/frame.py
@@ -280,6 +285,7 @@ pycwb/modules/job_segment/job_segment.py
 pycwb/modules/job_segment/module.yaml
 pycwb/modules/job_segment/plots.py
 pycwb/modules/job_segment/super_lag.py
+pycwb/modules/job_segment/test_job_segment.py
 pycwb/modules/likelihood/__init__.py
 pycwb/modules/likelihood/likelihood.py
 pycwb/modules/likelihood/module.yaml

{pycwb-0.23.1 → pycwb-0.24.0}/README.md

@@ -1,13 +1,13 @@
 # PycWB
 
-[![Documentations](https://readthedocs.org/projects/pycwb/badge/?version=latest)](https://pycwb.readthedocs.io/en/latest/)
+[![Documentations](https://readthedocs.org/projects/pycwb/badge/?version=latest)](https://pycwb.readthedocs.io)
 [![Build Status](https://git.ligo.org/yumeng.xu/pycwb/badges/main/pipeline.svg)](https://git.ligo.org/yumeng.xu/pycwb/-/pipelines)
 [![Releases](https://git.ligo.org/yumeng.xu/pycwb/-/badges/release.svg)](https://git.ligo.org/yumeng.xu/pycwb/-/releases)
 [![PyPI version](https://badge.fury.io/py/pycWB.svg)](https://badge.fury.io/py/pycWB)
 [![License](https://img.shields.io/badge/license-GPLv3-blue)](https://git.ligo.org/yumeng.xu/pycwb/-/blob/main/LICENSE)
 
 PycWB is a modularized Python package for gravitational wave burst search based on the core function of cWB.
-The documentation can be found at [pycwb.readthedocs.io](https://pycwb.readthedocs.io/en/latest/).
+The documentation can be found at [pycwb.readthedocs.io](https://pycwb.readthedocs.io).
 
 ## Installation
 
@@ -28,10 +28,13 @@ Currently, pycWB is only available for x64 architecture.
 For Apple Silicon users, you can install the dependencies with the following commands:
 
 ```bash
-conda create -n pycwb "python>=3.9,<3.11"
+# make sure rosetta is installed
+softwareupdate --install-rosetta --agree-to-license
+# Optional: export CONDA_BUILD=1
+conda create -n pycwb
 conda activate pycwb
 conda config --env --set subdir osx-64
-conda install -c conda-forge root=6.26.10 healpix_cxx=3.81 nds2-client python-nds2-client lalsuite setuptools_scm cmake pkg-config htcondor
+conda install -c conda-forge "python>=3.9,<3.11" root=6.26.10 healpix_cxx=3.81 nds2-client python-nds2-client lalsuite setuptools_scm cmake pkg-config ruamel.yaml htcondor
 ```
 
 ### Install pycWB from source

{pycwb-0.23.1 → pycwb-0.24.0}/cwb-core/CMakeLists.txt

@@ -50,7 +50,8 @@ if(NOT DEFINED XIFO)
    set(XIFO 4)
 endif()
 
-set(CWB_OPTS "XIFO=${XIFO}" "_USE_CPP")
+# Fix the macso cross-compilation issue, see git.ligo.org issue#4
+set(CWB_OPTS "XIFO=${XIFO}" "_USE_CPP" "_Float16=short")
 
 
 #Find ROOT

{pycwb-0.23.1 → pycwb-0.24.0}/docs/source/tutorial_injection.rst

@@ -25,10 +25,6 @@ Next, load the environment and the configuration file:
     from pycwb.config import Config
     from pycwb.modules.logger import logger_init
 
-    if not os.environ.get('HOME_WAT_FILTERS'):
-        pyburst_path = os.path.dirname(os.path.abspath(pycwb.__file__))
-        os.environ['HOME_WAT_FILTERS'] = f"{os.path.abspath(pyburst_path)}/vendor"
-
     logger_init()
 
     config = Config('./user_parameters_injection.yaml')
@@ -39,12 +35,13 @@ Now, create an injection job using the parameters specified in the configuration
 
 .. code-block:: python
 
-    from pycwb.modules.read_data import generate_injection
+    from pycwb.modules.read_data import generate_injection, generate_noise_for_job_seg
     from pycwb.modules.job_segment import create_job_segment_from_injection
 
     job_segments = create_job_segment_from_injection(config.ifo, config.simulation, config.injection)
 
-    data = generate_injection(config, job_segments[0])
+    data = generate_noise_for_job_seg(job_segments[0], config.inRate)
+    data = generate_injection(config, job_segments[0], data)
 
 A pyCBC time series is generated for each detector defined in the configuration file.
 
@@ -85,7 +82,7 @@ Finally, calculate the likelihood for each supercluster:
 
     from pycwb.modules.likelihood import likelihood
 
-    events, clusters = likelihood(config, network, pwc_list)
+    events, clusters, skymap_statistics = likelihood(config, network, pwc_list)
 
 You can use the following code to plot the events on the spectrogram:
 

{pycwb-0.23.1 → pycwb-0.24.0}/docs/source/tutorial_search.rst

@@ -22,16 +22,6 @@ Initialize logger with log_file and log_level, if log_file is None, log will be
    from pycwb.modules.logger import logger_init
    logger_init(log_file, log_level)
 
-set env HOME_WAT_FILTERS to the path of xdmXTalk. pycWB stops including xdmXTalk file in the package.
-The xdmXTalk file can be downloaded from https://github.com/PycWB/xtalk-data.
-You can also use your own xdmXTalk file.
-
-.. code-block:: python
-
-   import os, pycwb
-
-   pycwb_path = os.path.dirname(os.path.abspath(pycwb.__file__))
-   os.environ['HOME_WAT_FILTERS'] = <You path to the folder containing xdmXTalk files>
 
 read user parameters from user_parameters.yaml to a :py:class:`.Config` object.
 

{pycwb-0.23.1 → pycwb-0.24.0}/examples/injection/pycwb_injection.ipynb

@@ -2,11 +2,9 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
    "metadata": {
     "collapsed": true
    },
-   "outputs": [],
    "source": [
     "import os\n",
     "\n",
@@ -14,15 +12,13 @@
     "from pycwb.config import Config\n",
     "from pycwb.modules.logger import logger_init\n",
     "\n",
-    "if not os.environ.get('HOME_WAT_FILTERS'):\n",
-    "    pyburst_path = os.path.dirname(os.path.abspath(pycwb.__file__))\n",
-    "    os.environ['HOME_WAT_FILTERS'] = f\"{os.path.abspath(pyburst_path)}/vendor\"\n",
-    "\n",
     "logger_init()\n",
     "\n",
     "config = Config('./user_parameters_injection.yaml')\n",
     "config.ifo, config.injection"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
@@ -35,33 +31,34 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [],
    "source": [
-    "from pycwb.modules.read_data import generate_injection\n",
+    "from pycwb.modules.read_data import generate_injection, generate_noise_for_job_seg\n",
     "from pycwb.modules.job_segment import create_job_segment_from_injection\n",
     "\n",
     "job_segments = create_job_segment_from_injection(config.ifo, config.simulation, config.injection)\n",
     "\n",
-    "data = generate_injection(config, job_segments[0])\n",
+    "data = generate_noise_for_job_seg(job_segments[0], config.inRate)\n",
+    "data = generate_injection(config, job_segments[0], data)\n",
     "data"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [],
    "source": [
     "%matplotlib inline\n",
     "# plot the pycbc time series for L1\n",
     "data[0].plot()"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
@@ -74,11 +71,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [],
    "source": [
     "from pycwb.modules.data_conditioning import data_conditioning\n",
     "from pycwb.modules.plot import plot_spectrogram\n",
@@ -91,7 +86,9 @@
     "ax.set_ylim(15,1024)\n",
     "\n",
     "strains, nRMS"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
@@ -104,17 +101,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [],
    "source": [
     "from pycwb.modules.coherence import coherence\n",
     "\n",
     "# calculate coherence\n",
     "fragment_clusters = coherence(config, strains, nRMS)\n"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
@@ -127,11 +124,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [],
    "source": [
     "from pycwb.modules.super_cluster import supercluster\n",
     "from pycwb.types.network import Network\n",
@@ -139,7 +134,9 @@
     "network = Network(config, strains, nRMS)\n",
     "\n",
     "pwc_list = supercluster(config, network, fragment_clusters, strains)"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
@@ -152,24 +149,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [],
    "source": [
     "from pycwb.modules.likelihood import likelihood\n",
     "\n",
-    "events, clusters = likelihood(config, network, pwc_list)"
-   ]
+    "events, clusters, skymap_statistics = likelihood(config, network, pwc_list)"
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [],
    "source": [
     "%matplotlib inline\n",
     "from pycwb.modules.plot import plot_event_on_spectrogram\n",
@@ -177,7 +172,9 @@
     "for i, tf_map in enumerate(strains):\n",
     "    plt = plot_event_on_spectrogram(tf_map, events)\n",
     "    plt.show()"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "attachments": {},
@@ -189,11 +186,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [],
    "source": [
     "%matplotlib inline\n",
     "from gwpy.spectrogram import Spectrogram\n",
@@ -203,13 +198,13 @@
     "\n",
     "    plt = Spectrogram(merged_map, t0=start, dt=dt, f0=0, df=df).plot()\n",
     "    plt.colorbar()"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "metadata": {},
-   "outputs": [],
    "source": [
     "%matplotlib inline\n",
     "from gwpy.spectrogram import Spectrogram\n",
@@ -219,7 +214,16 @@
     "\n",
     "    plt = Spectrogram(merged_map, t0=start, dt=dt, f0=0, df=df).plot()\n",
     "    plt.colorbar()"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": "",
+   "outputs": [],
+   "execution_count": null
   }
  ],
  "metadata": {

{pycwb-0.23.1 → pycwb-0.24.0}/examples/injection/user_parameters_injection.yaml

@@ -2,6 +2,14 @@
 
 outputDir: "output"
 nproc: 6
+plot_trigger: True
+plot_waveform: True
+plot_injection: True
+plot_sky_map: True
+save_sky_map: True
+save_injection: True
+save_waveform: True
+
 ###### search ######
 
 #calibVer: "C01"

{pycwb-0.23.1 → pycwb-0.24.0}/pycwb/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.23.1'
-__version_tuple__ = version_tuple = (0, 23, 1)
+__version__ = version = '0.24.0'
+__version_tuple__ = version_tuple = (0, 24, 0)

{pycwb-0.23.1 → pycwb-0.24.0}/pycwb/constants/user_parameters_schema.py

@@ -99,6 +99,46 @@ schema = {
             "default": {},
             "cwb": False
         },
+        "gps_start": {
+            "type": "number",
+            "description": "start gps time, used together with gps_end for generating job segments",
+            "cwb": False
+        },
+        "gps_end": {
+            "type": "number",
+            "description": "end gps time, used together with gps_start for generating job segments",
+            "cwb": False
+        },
+        "gps_center": {
+            "type": "number",
+            "description": "center gps time, used together with time_left and time_right for generating job segments",
+            "cwb": False
+        },
+        "time_left": {
+            "type": "number",
+            "description": "left time offset from gps_center, used together with gps_center and time_right for generating job segments",
+            "cwb": False
+        },
+        "time_right": {
+            "type": "number",
+            "description": "right time offset from gps_center, used together with gps_center and time_left for generating job segments",
+            "cwb": False
+        },
+        "superevent": {
+            "type": "string",
+            "description": "superevent name, used together with time_left and time_right for generating job segments",
+            "cwb": False
+        },
+        "gwdatafind": {
+            "type": "object",
+            "description": "If the gwdatafind is set, the framefiles can be pulled from the LIGO data server, "
+                           "the support keys are: site, frametype, host. Example: ",
+                           "     site: ['L','H']"
+                           "     frametype: ['L1_HOFT_C00','H1_HOFT_C00']"
+                           "     host: 'datafind.ldas.cit:80'"
+            "default": {},
+            "cwb": False
+        },
         "WDM_beta_order": {
             "type": "integer",
             "description": "WDM default parameters: beta function order for Meyer",

pycwb-0.24.0/pycwb/modules/gracedb/__init__.py

@@ -0,0 +1 @@
+from .gracedb import *

pycwb-0.24.0/pycwb/modules/gracedb/gracedb.py

@@ -0,0 +1,40 @@
+from ligo.gracedb.rest import GraceDb
+from ligo.gracedb.exceptions import HTTPError
+
+
+def get_superevent(event_name):
+    """
+    Get the super event for a given event name.
+
+    :param event_name: The name of the event.
+    :type event_name: str
+    :return: The super event.
+    :rtype: dict
+    """
+    client = GraceDb()
+    try:
+        response = client.superevent(event_name).json()
+    except HTTPError as e:
+        if e.response.status_code == 404:
+            print('No super event found for event {}'.format(event_name))
+            return None
+        else:
+            raise
+
+    return response
+
+
+def get_superevent_t0(event_name):
+    """
+    Get the GPS time of the super event for a given event name.
+
+    :param event_name: The name of the event.
+    :type event_name: str
+    :return: The GPS time of the super event.
+    :rtype: float
+    """
+    super_event = get_superevent(event_name)
+    if super_event is None:
+        return None
+
+    return super_event['t_0']

pycwb-0.24.0/pycwb/modules/gracedb/module.yaml

@@ -0,0 +1,4 @@
+name: gracedb
+author: pycWB
+description: A interface for the LIGO/Virgo GraceDB database
+dependencies: ["ligo-proxy-utils", "ligo-gracedb"]

pycwb-0.24.0/pycwb/modules/gracedb/test_gracedb.py

@@ -0,0 +1,27 @@
+import unittest
+from .gracedb import get_superevent_t0, get_superevent
+
+class TestGraceDB(unittest.TestCase):
+
+    def test_get_superevent_t0(self):
+        event_name = 'S241011k'
+        t0 = get_superevent_t0(event_name)
+        self.assertAlmostEqual(t0, 1412725132.96, places=1)
+
+    def test_get_superevent_t0_no_event(self):
+        event_name = 'S000000a'
+        t0 = get_superevent_t0(event_name)
+        self.assertIsNone(t0)
+
+    def test_get_superevent(self):
+        event_name = 'S241011k'
+        super_event = get_superevent(event_name)
+        self.assertEqual(super_event['superevent_id'], event_name)
+
+    def test_get_superevent_no_event(self):
+        event_name = 'S000000a'
+        super_event = get_superevent(event_name)
+        self.assertIsNone(super_event)
+
+if __name__ == '__main__':
+    unittest.main()