Update tool Meerkat Galaxy clusters to 0.0.1+galaxy0

tools/meerkat-galaxy-clusters/.shed.yml

@@ -0,0 +1,9 @@
+categories:
+- Astronomy
+description: Meerkat Galaxy clusters
+homepage_url: null
+long_description: Meerkat Galaxy clusters
+name: meerkat_galaxy_clusters_astro_tool
+owner: astroteam
+remote_repository_url: https://github.com/esg-epfl-apc/tools-astro/tree/main/tools
+type: unrestricted

tools/meerkat-galaxy-clusters/meerkat_galaxy_clusters_astro_tool.xml

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+<tool id="meerkat_galaxy_clusters_astro_tool" name="Meerkat Galaxy clusters" version="0.0.1+galaxy0" profile="23.0">
+  <requirements>
+    <requirement type="package" version="8.31.0">ipython</requirement>
+    <requirement type="package" version="2.2.3">pandas</requirement>
+    <requirement type="package" version="3.10.0">matplotlib</requirement>
+    <requirement type="package" version="7.0.0">astropy</requirement>
+    <requirement type="package" version="2.2.1">numpy</requirement>
+    <requirement type="package" version="1.2.27">oda-api</requirement>
+    <requirement type="package" version="2.0.2">photutils</requirement>
+    <requirement type="package" version="1.35.88">boto3</requirement>
+    <requirement type="package" version="7.16.4">nbconvert</requirement>
+    <!--Requirements string 'nb2workflow[cwl,service,rdf,mmoda]
+' can't be converted automatically. Please add the galaxy/conda requirement manually or modify the requirements file!-->
+  </requirements>
+  <command detect_errors="exit_code">python '$__tool_directory__/ps_around_source.py'</command>
+  <configfiles>
+    <inputs name="inputs" filename="inputs.json" data_style="paths" />
+  </configfiles>
+  <inputs>
+    <param name="ra" type="float" value="260" label="ra (unit: deg)" />
+    <param name="dec" type="float" value="-82" label="dec (unit: deg)" />
+    <param name="thresh_arcmin" type="integer" value="20" label="thresh_arcmin (unit: arcmin)" />
+    <param name="clust_name" type="text" value="test_if_in_clusters(ra, dec)" label="clust_name" />
+  </inputs>
+  <outputs />
+  <tests>
+    <test expect_num_outputs="0">
+      <param name="ra" value="260" />
+      <param name="dec" value="-82" />
+      <param name="thresh_arcmin" value="20" />
+      <param name="clust_name" value="test_if_in_clusters(ra, dec)" />
+      <assert_stdout>
+        <has_text text="*** Job finished successfully ***" />
+      </assert_stdout>
+    </test>
+  </tests>
+  <environment_variables>
+    <environment_variable name="BASEDIR">$__tool_directory__</environment_variable>
+    <environment_variable name="GALAXY_TOOL_DIR">$__tool_directory__</environment_variable>
+  </environment_variables>
+</tool>

tools/meerkat-galaxy-clusters/ps_around_source.py

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+#!/usr/bin/env python
+# coding: utf-8
+
+# flake8: noqa
+
+import json
+import os
+import warnings
+
+warnings.filterwarnings("ignore")
+
+from catalogs_methods import *
+from data_treatment import *
+from parameters import *
+from plots import *
+
+# ------------------------------------------------------------------------------------
+# ra/dec coordinates of target point of the sky, and the aperture to find sources in
+# ------------------------------------------------------------------------------------
+ra = 260  # http://odahub.io/ontology#AngleDegrees
+dec = -82  # http://odahub.io/ontology#AngleDegrees
+thresh_arcmin = 20  # http://odahub.io/ontology#arcmin
+
+# -----------------------------------------------------
+# Handling errors and exceptions
+# -----------------------------------------------------
+if ra < 0 or ra > 360:
+    raise ValueError(
+        "Wrong value: the right ascension (ra) must be between 0 and 360 degrees!"
+    )
+if dec < -90 or dec > 90:
+    raise ValueError(
+        "Wrong value: the declination (dec) must be between -90 and 90 degrees!"
+    )
+
+# Test if the ra/dec coordinates lie in a MGCLS field (cluster)
+# -----------------------------------------------------------------------------
+clust_name = test_if_in_clusters(ra, dec)
+
+if clust_name == 0:
+
+    raise Exception(
+        "Error: the entered coordinates do not lie within any MGCLS field (cluster)"
+    )
+
+_galaxy_wd = os.getcwd()
+
+with open("inputs.json", "r") as fd:
+    inp_dic = json.load(fd)
+if "_data_product" in inp_dic.keys():
+    inp_pdic = inp_dic["_data_product"]
+else:
+    inp_pdic = inp_dic
+
+for _vn in ["ra", "dec", "thresh_arcmin", "clust_name"]:
+    globals()[_vn] = type(globals()[_vn])(inp_pdic[_vn])
+
+# ----------------------------------------------------------------------------------
+# Determination of the sources found (or not) in the given aperture
+# ----------------------------------------------------------------------------------
+sources = find_sources_around_coordinates(ra, dec, thresh_arcmin)
+msg_out = sources["out_msg"]  # http://odahub.io/ontology#String
+print(msg_out)
+
+# ----------------------------------------------------------------------------------
+# Computation of the power spectrum of the sources within the aperture
+# ----------------------------------------------------------------------------------
+plot_power_spectrum(ra, dec, thresh_arcmin)
+
+# # ----------------------------------------------------------------------------------
+# # Plotting of the enhanced image, the target location and the corresponding sources
+# # ----------------------------------------------------------------------------------
+# freq_index = 0
+# plot_enhanced_image(clust_name, freq_index)
+# plt.show()
+
+# # ----------------------------------------------------------------------------------
+# # Plotting of the enhanced image, the target location and the corresponding sources
+# # ----------------------------------------------------------------------------------
+# freq_index = 0
+# plot_enhanced_image(clust_name, freq_index)
+# plt.show()
+
+# output gathering
+_galaxy_meta_data = {}
+
+with open(os.path.join(_galaxy_wd, "galaxy.json"), "w") as fd:
+    json.dump(_galaxy_meta_data, fd)
+print("*** Job finished successfully ***")