Update tool MWA to 0.0.4+galaxy0

tools/mwa/Image.py

@@ -0,0 +1,168 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+# In[ ]:
+
+
+import json
+import os
+import shutil
+import sys
+
+try:
+    import numpy as np
+    _numpy_available = True
+except ImportError:
+    _numpy_available = False
+
+try:
+    from oda_api.json import CustomJSONEncoder
+except ImportError:
+    from json import JSONEncoder as CustomJSONEncoder
+
+_galaxy_wd = os.getcwd()
+
+
+# In[1]:
+
+
+from astropy.io import fits
+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 PictureProduct
+from oda_api.data_products import ImageDataProduct
+
+
+# In[2]:
+
+
+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.  #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"
+
+
+# In[ ]:
+
+
+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)
+
+
+# In[3]:
+
+
+pixels=int(2*Radius/pixsize)+1
+Radius*=u.deg
+pos=str(RA)+', '+str(DEC)
+pixels
+
+
+# In[4]:
+
+
+hdul=SkyView.get_images(position=pos,
+                       survey=[Frequency],pixels=pixels,radius=Radius)  
+
+
+# In[5]:
+
+
+hdu=hdul[0]
+hdu[0].header
+wcs = WCS(hdu[0].header)
+
+
+# In[6]:
+
+
+image=hdu[0].data
+
+
+# In[7]:
+
+
+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')
+
+
+# In[8]:
+
+
+hdu.writeto('Image.fits',overwrite=True)
+bin_image = PictureProduct.from_file('Image.png')
+fits_image=ImageDataProduct.from_fits_file('Image.fits')
+
+
+# In[9]:
+
+
+picture = bin_image # http://odahub.io/ontology#ODAPictureProduct
+image = fits_image # http://odahub.io/ontology#Image
+
+
+# In[ ]:
+
+
+
+
+
+# In[ ]:
+
+
+_simple_outs, _oda_outs = [], []
+_galaxy_meta_data = {}
+_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'}
+
+for _outn, _outfn, _outv in _simple_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 _numpy_available and isinstance(_outv, np.ndarray):
+        with open(_galaxy_outfile_name, 'wb') as fd:
+            np.savez(fd, _outv)
+        _galaxy_meta_data[_outn] = {'ext': 'npz'}
+    else:
+        with open(_galaxy_outfile_name, 'w') as fd:
+            json.dump(_outv, fd)
+        _galaxy_meta_data[_outn] = {'ext': 'expression.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 +1,188 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+# In[ ]:
+
+
+import json
+import os
+import shutil
+import sys
+
+try:
+    import numpy as np
+    _numpy_available = True
+except ImportError:
+    _numpy_available = False
+
+try:
+    from oda_api.json import CustomJSONEncoder
+except ImportError:
+    from json import JSONEncoder as CustomJSONEncoder
+
+_galaxy_wd = os.getcwd()
+
+
+# In[1]:
+
+
+from pyvo import registry  # version >=1.4.1 
+import matplotlib.pyplot as plt
+from numpy import pi
+import astropy.units as u
+from astropy.constants import h
+import numpy as np
+
+from oda_api.data_products import PictureProduct
+from oda_api.data_products import ODAAstropyTable
+
+
+# In[2]:
+
+
+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
+
+
+# In[ ]:
+
+
+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)
+
+
+# In[3]:
+
+
+conesearch_radius = Radius  # in degrees
+conesearch_center = (RA, DEC)
+
+
+
+# In[4]:
+
+
+# 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]
+
+
+# In[5]:
+
+
+conesearch_records = voresource.get_service("conesearch").search(
+    pos=conesearch_center,
+    sr=conesearch_radius,
+)
+conesearch_records
+
+
+# In[6]:
+
+
+h_p=(h/u.s).to(u.eV).value # Planck constant in eV*s
+
+
+# In[7]:
+
+
+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')
+
+
+# In[8]:
+
+
+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))
+
+
+# In[9]:
+
+
+picture_png = bin_image # http://odahub.io/ontology#ODAPictureProduct
+spectrum_astropy_table = spec # http://odahub.io/ontology#ODAAstropyTable
+
+
+# In[ ]:
+
+
+
+
+
+# In[ ]:
+
+
+_simple_outs, _oda_outs = [], []
+_galaxy_meta_data = {}
+_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'}
+
+for _outn, _outfn, _outv in _simple_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 _numpy_available and isinstance(_outv, np.ndarray):
+        with open(_galaxy_outfile_name, 'wb') as fd:
+            np.savez(fd, _outv)
+        _galaxy_meta_data[_outn] = {'ext': 'npz'}
+    else:
+        with open(_galaxy_outfile_name, 'w') as fd:
+            json.dump(_outv, fd)
+        _galaxy_meta_data[_outn] = {'ext': 'expression.json'}
+
+with open(os.path.join(_galaxy_wd, 'galaxy.json'), 'w') as fd:
+    json.dump(_galaxy_meta_data, fd)
+print("*** Job finished successfully ***")
+