Update tool MWA to 0.0.1+galaxy0

tools/mwa/.shed.yml

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

tools/mwa/Image.py

@@ -0,0 +1,91 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+# flake8: noqa
+
+import json
+import os
+import shutil
+
+import astropy.units as u
+import matplotlib.pyplot as plt
+from astropy.wcs import WCS
+from astroquery.skyview import SkyView
+from oda_api.data_products import ImageDataProduct, PictureProduct
+from oda_api.json import CustomJSONEncoder
+
+src_name = "1ES 0229+200"  # http://odahub.io/ontology#AstrophysicalObject
+RA = 38.202562  # http://odahub.io/ontology#PointOfInterestRA
+DEC = 20.288191  # http://odahub.io/ontology#PointOfInterestDEC
+T1 = "2000-10-09T13:16:00.0"  # http://odahub.io/ontology#StartTime
+T2 = "2022-10-10T13:16:00.0"  # http://odahub.io/ontology#EndTime
+Radius = 1.0  # http://odahub.io/ontology#AngleDegrees
+pixsize = 0.01  # http://odahub.io/ontology#AngleDegrees
+Frequency = "GLEAM 170-231 MHz"  # http://odahub.io/ontology#String ; oda:allowed_value "GLEAM 72-103 MHz","GLEAM 103-134 MHz","GLEAM 139-170 MHz","GLEAM 170-231 MHz"
+
+_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, vv in inp_pdic.items():
+    if vn != "_selector":
+        globals()[vn] = type(globals()[vn])(vv)
+
+pixels = int(2 * Radius / pixsize) + 1
+Radius *= u.deg
+pos = str(RA) + ", " + str(DEC)
+pixels
+
+hdul = SkyView.get_images(
+    position=pos, survey=[Frequency], pixels=pixels, radius=Radius
+)
+
+hdu = hdul[0]
+hdu[0].header
+wcs = WCS(hdu[0].header)
+
+image = hdu[0].data
+
+ax = plt.subplot(projection=wcs)
+im = ax.imshow(image, origin="lower")
+ax.coords.grid(True, color="white", ls="solid")
+plt.colorbar(im, label="Jy/beam")
+plt.savefig("Image.png", format="png", bbox_inches="tight")
+
+hdu.writeto("Image.fits", overwrite=True)
+bin_image = PictureProduct.from_file("Image.png")
+fits_image = ImageDataProduct.from_fits_file("Image.fits")
+
+picture = bin_image  # http://odahub.io/ontology#ODAPictureProduct
+image = fits_image  # http://odahub.io/ontology#Image
+
+# output gathering
+_galaxy_meta_data = {}
+_oda_outs = []
+_oda_outs.append(("out_Image_picture", "picture_galaxy.output", picture))
+_oda_outs.append(("out_Image_image", "image_galaxy.output", image))
+
+for _outn, _outfn, _outv in _oda_outs:
+    _galaxy_outfile_name = os.path.join(_galaxy_wd, _outfn)
+    if isinstance(_outv, str) and os.path.isfile(_outv):
+        shutil.move(_outv, _galaxy_outfile_name)
+        _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
+    elif getattr(_outv, "write_fits_file", None):
+        _outv.write_fits_file(_galaxy_outfile_name)
+        _galaxy_meta_data[_outn] = {"ext": "fits"}
+    elif getattr(_outv, "write_file", None):
+        _outv.write_file(_galaxy_outfile_name)
+        _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
+    else:
+        with open(_galaxy_outfile_name, "w") as fd:
+            json.dump(_outv, fd, cls=CustomJSONEncoder)
+        _galaxy_meta_data[_outn] = {"ext": "json"}
+
+with open(os.path.join(_galaxy_wd, "galaxy.json"), "w") as fd:
+    json.dump(_galaxy_meta_data, fd)
+print("*** Job finished successfully ***")

tools/mwa/Spectrum.py

@@ -0,0 +1,117 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+# flake8: noqa
+
+import json
+import os
+import shutil
+
+import astropy.units as u
+import matplotlib.pyplot as plt
+import numpy as np
+from astropy.constants import h
+from oda_api.data_products import ODAAstropyTable, PictureProduct
+from oda_api.json import CustomJSONEncoder
+from pyvo import registry  # version >=1.4.1
+
+src_name = "1ES 0229+200"  # http://odahub.io/ontology#AstrophysicalObject
+RA = 38.202562  # http://odahub.io/ontology#PointOfInterestRA
+DEC = 20.288191  # http://odahub.io/ontology#PointOfInterestDEC
+T1 = "2000-10-09T13:16:00.0"  # http://odahub.io/ontology#StartTime
+T2 = "2022-10-10T13:16:00.0"  # http://odahub.io/ontology#EndTime
+Radius = 0.05  # http://odahub.io/ontology#AngleDegrees
+
+_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, vv in inp_pdic.items():
+    if vn != "_selector":
+        globals()[vn] = type(globals()[vn])(vv)
+
+conesearch_radius = Radius  # in degrees
+conesearch_center = (RA, DEC)
+
+# the catalogue name in VizieR
+CATALOGUE = "VIII/100"
+# each resource in the VO has an identifier, called ivoid. For vizier catalogs,
+# the VO ids can be constructed like this:
+catalogue_ivoid = f"ivo://CDS.VizieR/{CATALOGUE}"
+# the actual query to the registry
+voresource = registry.search(ivoid=catalogue_ivoid)[0]
+
+conesearch_records = voresource.get_service("conesearch").search(
+    pos=conesearch_center,
+    sr=conesearch_radius,
+)
+conesearch_records
+
+h_p = (h / u.s).to(u.eV).value  # Planck constant in eV*s
+
+conesearch_records.fieldnames
+nu = []
+F = []
+F_err = []
+for f in conesearch_records.fieldnames:
+    if (f[:4] == "Fint") and (f[4] != "w") and (f[4] != "f"):
+        nu.append(int(f[-3:]) * 1e6)  # in Hz
+        F.append(conesearch_records[f][0] * nu[-1] * 1e-23)
+        F_err.append(conesearch_records["e_" + f][0] * nu[-1] * 1e-23)
+
+E = h_p * np.array(nu)
+plt.errorbar(E, F, F_err)
+plt.xscale("log")
+plt.yscale("log")
+plt.xlabel("$E$, eV")
+plt.ylabel("$E F_E$, erg/cm$^2$s")
+plt.savefig("Spectrum.png", format="png", bbox_inches="tight")
+
+bin_image = PictureProduct.from_file("Spectrum.png")
+from astropy.table import Table
+
+data = [E, F, F_err]
+names = ("E[eV]", "Flux[erg/cm2s]", "Flux_error[erg/cm2s]")
+spec = ODAAstropyTable(Table(data, names=names))
+
+picture_png = bin_image  # http://odahub.io/ontology#ODAPictureProduct
+spectrum_astropy_table = spec  # http://odahub.io/ontology#ODAAstropyTable
+
+# output gathering
+_galaxy_meta_data = {}
+_oda_outs = []
+_oda_outs.append(
+    ("out_Spectrum_picture_png", "picture_png_galaxy.output", picture_png)
+)
+_oda_outs.append(
+    (
+        "out_Spectrum_spectrum_astropy_table",
+        "spectrum_astropy_table_galaxy.output",
+        spectrum_astropy_table,
+    )
+)
+
+for _outn, _outfn, _outv in _oda_outs:
+    _galaxy_outfile_name = os.path.join(_galaxy_wd, _outfn)
+    if isinstance(_outv, str) and os.path.isfile(_outv):
+        shutil.move(_outv, _galaxy_outfile_name)
+        _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
+    elif getattr(_outv, "write_fits_file", None):
+        _outv.write_fits_file(_galaxy_outfile_name)
+        _galaxy_meta_data[_outn] = {"ext": "fits"}
+    elif getattr(_outv, "write_file", None):
+        _outv.write_file(_galaxy_outfile_name)
+        _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
+    else:
+        with open(_galaxy_outfile_name, "w") as fd:
+            json.dump(_outv, fd, cls=CustomJSONEncoder)
+        _galaxy_meta_data[_outn] = {"ext": "json"}
+
+with open(os.path.join(_galaxy_wd, "galaxy.json"), "w") as fd:
+    json.dump(_galaxy_meta_data, fd)
+print("*** Job finished successfully ***")

tools/mwa/mwa_astro_tool.xml

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+<tool id="mwa_astro_tool" name="MWA" version="0.0.1+galaxy0" profile="23.0">
+  <requirements>
+    <requirement type="package" version="8.28.0">ipython</requirement>
+    <requirement type="package" version="5.3.4">astropy</requirement>
+    <requirement type="package" version="1.2">gammapy</requirement>
+    <requirement type="package" version="3.9.2">matplotlib</requirement>
+    <requirement type="package" version="0.4.7">astroquery</requirement>
+    <requirement type="package" version="1.14.1">scipy</requirement>
+    <requirement type="package" version="1.2.28">oda-api</requirement>
+    <requirement type="package" version="7.16.4">nbconvert</requirement>
+    <requirement type="package" version="1.21.4">wget</requirement>
+    <requirement type="package" version="2.2.3">pandas</requirement>
+    <!--Requirements string 'nb2workflow[cwl,service,rdf,mmoda]>=1.3.30 
+' can't be converted automatically. Please add the galaxy/conda requirement manually or modify the requirements file!-->
+  </requirements>
+  <command detect_errors="exit_code">python '$__tool_directory__/${_data_product._selector}.py'</command>
+  <configfiles>
+    <inputs name="inputs" filename="inputs.json" data_style="paths" />
+  </configfiles>
+  <inputs>
+    <conditional name="_data_product">
+      <param name="_selector" type="select" label="Data Product">
+        <option value="Image" selected="true">Image</option>
+        <option value="Spectrum" selected="false">Spectrum</option>
+      </param>
+      <when value="Image">
+        <param name="src_name" type="text" value="1ES 0229+200" label="src_name" />
+        <param name="RA" type="float" value="38.202562" label="RA (unit: deg)" />
+        <param name="DEC" type="float" value="20.288191" label="DEC (unit: deg)" />
+        <param name="T1" type="text" value="2000-10-09T13:16:00.0" label="T1" />
+        <param name="T2" type="text" value="2022-10-10T13:16:00.0" label="T2" />
+        <param name="Radius" type="float" value="1.0" label="Radius (unit: deg)" />
+        <param name="pixsize" type="float" value="0.01" label="pixsize (unit: deg)" />
+        <param name="Frequency" type="select" label="Frequency">
+          <option value="GLEAM 103-134 MHz">GLEAM 103-134 MHz</option>
+          <option value="GLEAM 139-170 MHz">GLEAM 139-170 MHz</option>
+          <option value="GLEAM 170-231 MHz" selected="true">GLEAM 170-231 MHz</option>
+          <option value="GLEAM 72-103 MHz">GLEAM 72-103 MHz</option>
+        </param>
+      </when>
+      <when value="Spectrum">
+        <param name="src_name" type="text" value="1ES 0229+200" label="src_name" />
+        <param name="RA" type="float" value="38.202562" label="RA (unit: deg)" />
+        <param name="DEC" type="float" value="20.288191" label="DEC (unit: deg)" />
+        <param name="T1" type="text" value="2000-10-09T13:16:00.0" label="T1" />
+        <param name="T2" type="text" value="2022-10-10T13:16:00.0" label="T2" />
+        <param name="Radius" type="float" value="0.05" label="Radius (unit: deg)" />
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data label="${tool.name} -&gt; Image picture" name="out_Image_picture" format="auto" from_work_dir="picture_galaxy.output">
+      <filter>_data_product['_selector'] == 'Image'</filter>
+    </data>
+    <data label="${tool.name} -&gt; Image image" name="out_Image_image" format="auto" from_work_dir="image_galaxy.output">
+      <filter>_data_product['_selector'] == 'Image'</filter>
+    </data>
+    <data label="${tool.name} -&gt; Spectrum picture_png" name="out_Spectrum_picture_png" format="auto" from_work_dir="picture_png_galaxy.output">
+      <filter>_data_product['_selector'] == 'Spectrum'</filter>
+    </data>
+    <data label="${tool.name} -&gt; Spectrum spectrum_astropy_table" name="out_Spectrum_spectrum_astropy_table" format="auto" from_work_dir="spectrum_astropy_table_galaxy.output">
+      <filter>_data_product['_selector'] == 'Spectrum'</filter>
+    </data>
+  </outputs>
+  <tests>
+    <test expect_num_outputs="2">
+      <conditional name="_data_product">
+        <param name="_selector" value="Image" />
+        <param name="src_name" value="1ES 0229+200" />
+        <param name="RA" value="38.202562" />
+        <param name="DEC" value="20.288191" />
+        <param name="T1" value="2000-10-09T13:16:00.0" />
+        <param name="T2" value="2022-10-10T13:16:00.0" />
+        <param name="Radius" value="1.0" />
+        <param name="pixsize" value="0.01" />
+        <param name="Frequency" value="GLEAM 170-231 MHz" />
+      </conditional>
+      <assert_stdout>
+        <has_text text="*** Job finished successfully ***" />
+      </assert_stdout>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="_data_product">
+        <param name="_selector" value="Spectrum" />
+        <param name="src_name" value="1ES 0229+200" />
+        <param name="RA" value="38.202562" />
+        <param name="DEC" value="20.288191" />
+        <param name="T1" value="2000-10-09T13:16:00.0" />
+        <param name="T2" value="2022-10-10T13:16:00.0" />
+        <param name="Radius" value="0.05" />
+      </conditional>
+      <assert_stdout>
+        <has_text text="*** Job finished successfully ***" />
+      </assert_stdout>
+    </test>
+  </tests>
+  <help>This is help for MWA
+</help>
+  <citations>
+    <citation type="doi">10.1093/mnras/stw2337</citation>
+  </citations>
+</tool>