daxa 0.0.2__tar.gz

daxa-0.0.2/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2022, David J Turner
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

daxa-0.0.2/MANIFEST.in

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+# include versioneer.py
+# include daxa/_version.py
+recursive-include daxa/files *

daxa-0.0.2/PKG-INFO

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+Metadata-Version: 2.1
+Name: daxa
+Version: 0.0.2
+Summary: Democratising Astronomy X-ray Archives (DAXA) is an easy-to-use Python module which enables the simple processing and reduction of archives of X-ray telescope observations.
+Home-page: https://github.com/DavidT3/DAXA
+Author: David J Turner
+Author-email: turne540@msu.edu
+License: BSD 3
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy==1.23.4
+Requires-Dist: astroquery==0.4.6
+Requires-Dist: pandas==1.5.1
+Requires-Dist: astropy==5.1.1
+Requires-Dist: packaging==21.3
+Requires-Dist: tqdm==4.64.1
+Requires-Dist: exceptiongroup==1.0.4
+Requires-Dist: scipy==1.1.0
+Requires-Dist: tabulate==0.9.0
+Requires-Dist: unlzw3==0.2.2
+
+<p align="center">
+    <img src="https://raw.githubusercontent.com/DavidT3/DAXA/master/daxa/files/daxa-high-resolution-logo-black-on-white-background.png" width="500">
+</p>
+
+[![Documentation Status](https://readthedocs.org/projects/daxa/badge/?version=latest)](https://daxa.readthedocs.io/en/latest/?badge=latest)
+
+# What is Democratising Archival X-ray Astronomy (DAXA)?
+
+DAXA is a Python module designed to make the acquisition and processing of archives of X-ray astronomy data as
+painless as possible. It provides a consistent interface to the downloading and cleaning processes of each telescope, 
+allowing the user to easily create multi-mission X-ray archives, allowing for the community to make better use of
+archival X-ray data. This process can be as simple or as in-depth as the user requires; if the default settings are 
+used then data can be acquired and processed into an archive in only a few lines of code.
+
+As the missions (i.e. telescopes) that should be included in the archive are defined, the user can filter the desired
+observations based on a unique identifier (i.e. observation ID), on whether observations are near to a coordinate (or 
+set of coordinates), and the time frame in which the observations were taken. As such it is possible to very quickly
+identify what archival data might be available for a set of objects you wish to study. It is also possible to place
+no filters on the desired observations, and as such process every observation available for a set of missions. 
+
+Documentation is available on ReadTheDocs, and [can be found here](https://daxa.readthedocs.io), or
+accessed by clicking on the documentation build status at the top of the README. The source for the documentation can
+be found in the 'docs' directory in this repository.
+
+# Which missions are supported?
+
+**_DAXA is still in an early stage of development, and as such the list of supported telescopes is currently
+limited. Support for more telescopes is either currently under development or being actively planned._** 
+
+* XMM-Newton Pointed
+* eROSITA Commissioning
+* eROSITA All-Sky Survey DR1 (German Half)
+* **_[Under Development - data acquisition implemented]_** NuSTAR
+* **_[Under Development - data acquisition implemented]_** Chandra
+* **_[Under Development - RASS/pointed data acquisition implemented]_** ROSAT
+* **_[Under Development - XRT/BAT/UVOT data acquisition implemented]_** Swift
+* **_[Under Development - data acquisition implemented]_** Suzaku
+* **_[Under Development - data acquisition implemented]_** ASCA
+* **_[Under Development - data acquisition implemented]_** INTEGRAL
+
+_If you would like to help with any of the telescopes above, or adding another X-ray telescope, please get in contact!_
+
+# Required telescope-specific software
+
+DAXA makes significant use of existing processing software released by the telescope teams, and as such there are some
+specific non-Python dependencies that need to be installed if that mission is to be included in a DAXA generated archive.
+
+## An alternative to installing the dependencies yourself
+
+**_[Under Development]_** - A docker image containing relevant telescope-specific software is being created. The 
+built image will be released on DockerHub (or some other convenient platform), and the actual dockerfile used for
+building the image will also be released for anyone to use/modify. The dockerfile is heavily inspired by/based off of 
+the HEASoft docker image.
+
+## XMM-Newton
+Science Analysis System (SAS) - v14 or higher
+
+## 
+
+# Analysing the processed archives
+Once an archive of cleaned X-ray data has been created, it can be analysed in all the standard ways, however you may
+also wish to consider [X-ray: Generate and Analyse (XGA)](https://github.com/DavidT3/XGA), a companion module to DAXA.
+
+XGA is also completely open source, and is a generalised tool for the analysis of X-ray emission from astrophysical 
+sources. The software operates on a 'source based' paradigm, where the user declares sources or samples of objects
+which are analogous to astrophysical sources in the sky, with XGA determining which data (if any) are relevant to a 
+particular source, and providing a powerful (but easy to use) interface for the generation and analysis of data 
+products. The module is fully documented, with tutorials and API documentation available (**support for telescopes 
+other than XMM is still under development**).
+
+# Problems and Questions
+If you encounter a bug, or would like to make a feature request, please use the GitHub
+[issues](https://github.com/DavidT3/DAXA/issues) page, it really helps to keep track of everything.
+
+However, if you have further questions, or just want to make doubly sure I notice the issue, feel free to send
+me an email at turne540@msu.edu
+
+
+
+
+

daxa-0.0.2/README.md

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+<p align="center">
+    <img src="https://raw.githubusercontent.com/DavidT3/DAXA/master/daxa/files/daxa-high-resolution-logo-black-on-white-background.png" width="500">
+</p>
+
+[![Documentation Status](https://readthedocs.org/projects/daxa/badge/?version=latest)](https://daxa.readthedocs.io/en/latest/?badge=latest)
+
+# What is Democratising Archival X-ray Astronomy (DAXA)?
+
+DAXA is a Python module designed to make the acquisition and processing of archives of X-ray astronomy data as
+painless as possible. It provides a consistent interface to the downloading and cleaning processes of each telescope, 
+allowing the user to easily create multi-mission X-ray archives, allowing for the community to make better use of
+archival X-ray data. This process can be as simple or as in-depth as the user requires; if the default settings are 
+used then data can be acquired and processed into an archive in only a few lines of code.
+
+As the missions (i.e. telescopes) that should be included in the archive are defined, the user can filter the desired
+observations based on a unique identifier (i.e. observation ID), on whether observations are near to a coordinate (or 
+set of coordinates), and the time frame in which the observations were taken. As such it is possible to very quickly
+identify what archival data might be available for a set of objects you wish to study. It is also possible to place
+no filters on the desired observations, and as such process every observation available for a set of missions. 
+
+Documentation is available on ReadTheDocs, and [can be found here](https://daxa.readthedocs.io), or
+accessed by clicking on the documentation build status at the top of the README. The source for the documentation can
+be found in the 'docs' directory in this repository.
+
+# Which missions are supported?
+
+**_DAXA is still in an early stage of development, and as such the list of supported telescopes is currently
+limited. Support for more telescopes is either currently under development or being actively planned._** 
+
+* XMM-Newton Pointed
+* eROSITA Commissioning
+* eROSITA All-Sky Survey DR1 (German Half)
+* **_[Under Development - data acquisition implemented]_** NuSTAR
+* **_[Under Development - data acquisition implemented]_** Chandra
+* **_[Under Development - RASS/pointed data acquisition implemented]_** ROSAT
+* **_[Under Development - XRT/BAT/UVOT data acquisition implemented]_** Swift
+* **_[Under Development - data acquisition implemented]_** Suzaku
+* **_[Under Development - data acquisition implemented]_** ASCA
+* **_[Under Development - data acquisition implemented]_** INTEGRAL
+
+_If you would like to help with any of the telescopes above, or adding another X-ray telescope, please get in contact!_
+
+# Required telescope-specific software
+
+DAXA makes significant use of existing processing software released by the telescope teams, and as such there are some
+specific non-Python dependencies that need to be installed if that mission is to be included in a DAXA generated archive.
+
+## An alternative to installing the dependencies yourself
+
+**_[Under Development]_** - A docker image containing relevant telescope-specific software is being created. The 
+built image will be released on DockerHub (or some other convenient platform), and the actual dockerfile used for
+building the image will also be released for anyone to use/modify. The dockerfile is heavily inspired by/based off of 
+the HEASoft docker image.
+
+## XMM-Newton
+Science Analysis System (SAS) - v14 or higher
+
+## 
+
+# Analysing the processed archives
+Once an archive of cleaned X-ray data has been created, it can be analysed in all the standard ways, however you may
+also wish to consider [X-ray: Generate and Analyse (XGA)](https://github.com/DavidT3/XGA), a companion module to DAXA.
+
+XGA is also completely open source, and is a generalised tool for the analysis of X-ray emission from astrophysical 
+sources. The software operates on a 'source based' paradigm, where the user declares sources or samples of objects
+which are analogous to astrophysical sources in the sky, with XGA determining which data (if any) are relevant to a 
+particular source, and providing a powerful (but easy to use) interface for the generation and analysis of data 
+products. The module is fully documented, with tutorials and API documentation available (**support for telescopes 
+other than XMM is still under development**).
+
+# Problems and Questions
+If you encounter a bug, or would like to make a feature request, please use the GitHub
+[issues](https://github.com/DavidT3/DAXA/issues) page, it really helps to keep track of everything.
+
+However, if you have further questions, or just want to make doubly sure I notice the issue, feel free to send
+me an email at turne540@msu.edu
+
+
+
+
+

daxa-0.0.2/daxa/__init__.py

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+#  This code is a part of the Democratising Archival X-ray Astronomy (DAXA) module.
+#  Last modified by David J Turner (turne540@msu.edu) 15/04/2024, 14:49. Copyright (c) The Contributors
+
+from .config import daxa_conf, OUTPUT, NUM_CORES, sb_rate
+from .mission.xmm import *

daxa-0.0.2/daxa/config.py

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+#  This code is a part of the Democratising Archival X-ray Astronomy (DAXA) module.
+#  Last modified by David J Turner (turne540@msu.edu) 15/04/2024, 14:49. Copyright (c) The Contributors
+
+import os
+from configparser import ConfigParser
+from warnings import warn
+
+import pandas as pd
+import pkg_resources
+from astropy.units import def_unit, ct, deg, s
+from numpy import floor
+
+from .exceptions import DAXAConfigError
+
+# If XDG_CONFIG_HOME is set, then use that, otherwise use this default config path
+CONFIG_PATH = os.environ.get('XDG_CONFIG_HOME', os.path.join(os.path.expanduser('~'), '.config', 'daxa'))
+# DAXA config file path
+CONFIG_FILE = os.path.join(CONFIG_PATH, 'daxa.cfg')
+# Section of the config file for setting up the DAXA module
+DAXA_CONFIG = {"daxa_save_path": "daxa_output/",
+               "num_cores": -1}
+
+if not os.path.exists(CONFIG_PATH):
+    os.makedirs(CONFIG_PATH)
+
+# If first DAXA run, creates default config file
+if not os.path.exists(CONFIG_FILE):
+    daxa_default = ConfigParser()
+    daxa_default.add_section("DAXA_SETUP")
+    daxa_default["DAXA_SETUP"] = DAXA_CONFIG
+    with open(CONFIG_FILE, 'w') as new_cfg:
+        daxa_default.write(new_cfg)
+
+    # First time run triggers this message
+    warn("A configuration file has been created ({}); you can use it to control where DAXA "
+         "stores data by default.".format(CONFIG_FILE), stacklevel=2)
+
+daxa_conf = ConfigParser()
+# It would be nice to do configparser interpolation, but it wouldn't handle the lists of energy values
+daxa_conf.read(CONFIG_FILE)
+
+try:
+    cfg_cores = daxa_conf['DAXA_SETUP'].getint('num_cores')
+except ValueError:
+    raise DAXAConfigError("The 'num_cores' configuration parameter must be an integer, with -1 corresponding "
+                          "to a null value and meaning that DAXA will determine the number of cores to use itself.")
+
+# As it turns out, the ConfigParser class is a pain to work with, so we're converting to a dict here
+# Addressing works just the same
+daxa_conf = {str(sect): dict(daxa_conf[str(sect)]) for sect in daxa_conf}
+
+if cfg_cores != -1 and cfg_cores <= os.cpu_count():
+    # If the user has set a number of cores in the config file then we'll use that.
+    NUM_CORES = int(daxa_conf["DAXA_SETUP"]["num_cores"])
+elif cfg_cores != -1:
+    raise DAXAConfigError("You have set a num_cores values that is greater than the number of cores available in"
+                          " the current system ({}).".format(os.cpu_count()))
+else:
+    # Going to allow multi-core processing to use 90% of available cores by default, but
+    # this can be over-ridden in individual SAS calls.
+    NUM_CORES = max(int(floor(os.cpu_count() * 0.9)), 1)  # Makes sure that at least one core is used
+
+
+# This is the default output directory for archives setup by DAXA, though it can be overridden on
+#  a mission level
+OUTPUT = os.path.abspath(daxa_conf["DAXA_SETUP"]["daxa_save_path"]) + "/"
+
+# Here we read in files that list the errors and warnings in SAS
+errors = pd.read_csv(pkg_resources.resource_filename(__name__, "files/sas_errors.csv"), header="infer")
+warnings = pd.read_csv(pkg_resources.resource_filename(__name__, "files/sas_warnings.csv"), header="infer")
+# Just the names of the errors in two handy constants
+SASERROR_LIST = errors["ErrName"].values
+SASWARNING_LIST = warnings["WarnName"].values
+
+# Reading in the file with information on the eROSITA observations that were made available in the
+#  eROSITA CalPV release
+EROSITA_CALPV_INFO = pd.read_csv(pkg_resources.resource_filename(__name__, "files/erosita_calpv_info.csv"),
+                                 header="infer", dtype={'ObsID': str})
+# TODO This may end up changing when we get access to the DR1 release - it could be in a format that makes this
+#  a bad way of doing it
+# Then doing the same thing, but for the German eRASS:1 release
+ERASS_DE_DR1_INFO = pd.read_csv(pkg_resources.resource_filename(__name__, "files/erass_de_dr1_info.csv"),
+                                header="infer", dtype={'ObsID': str, 'FIELD1': str, 'FIELD2': str, 'FIELD3': str,
+                                                       'FIELD4': str, 'FIELD5': str, 'FIELD6': str, 'FIELD7': str,
+                                                       'FIELD8': str, 'FIELD9': str})
+
+# We define a surface brightness rate astropy unit for use in flaregti to measure thresholds in
+sb_rate = def_unit('sb_rate', ct / (deg**2 * s))