Mercurial > repos > astroteam > plot_tools_astro_tool

comparison sky_plot.py @ 0:2b1759ccaa8b draft default tip

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planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
author astroteam
date Fri, 25 Apr 2025 21:48:27 +0000
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-1:000000000000 0:2b1759ccaa8b
1 #!/usr/bin/env python
2 # coding: utf-8
3
4 #!/usr/bin/env python
5
6 # This script is generated with nb2galaxy
7
8 # flake8: noqa
9
10 import json
11 import os
12 import shutil
13
14 from oda_api.json import CustomJSONEncoder
15
16 fn = "data.tsv" # oda:POSIXPath
17 skiprows = 0 # http://odahub.io/ontology#Integer
18 sep = "whitespace" # http://odahub.io/ontology#String ; oda:allowed_value "auto", "comma", "tab", "whitespace", "semicolon"
19
20 ra_col = "c3" # http://odahub.io/ontology#String
21 dec_col = "c4" # http://odahub.io/ontology#String
22 weight_col = "" # http://odahub.io/ontology#String
23 binsz = 0.02 # http://odahub.io/ontology#Float
24 window_size_RA = 2.0 # http://odahub.io/ontology#Degree
25 window_size_DEC = 2.0 # http://odahub.io/ontology#Degree
26
27 _galaxy_wd = os.getcwd()
28
29 with open("inputs.json", "r") as fd:
30 inp_dic = json.load(fd)
31 if "C_data_product_" in inp_dic.keys():
32 inp_pdic = inp_dic["C_data_product_"]
33 else:
34 inp_pdic = inp_dic
35 fn = str(inp_pdic["fn"])
36 skiprows = int(inp_pdic["skiprows"])
37 sep = str(inp_pdic["sep"])
38 ra_col = str(inp_pdic["ra_col"])
39 dec_col = str(inp_pdic["dec_col"])
40 weight_col = str(inp_pdic["weight_col"])
41 binsz = float(inp_pdic["binsz"])
42 window_size_RA = float(inp_pdic["window_size_RA"])
43 window_size_DEC = float(inp_pdic["window_size_DEC"])
44
45 import astropy.units as u
46 import matplotlib.pyplot as plt
47 import numpy as np
48 import pandas as pd
49 from astropy.coordinates import SkyCoord
50 from gammapy.maps import Map
51 from oda_api.data_products import ImageDataProduct, PictureProduct
52
53 separators = {
54 "tab": "\t",
55 "comma": ",",
56 "semicolon": ";",
57 "whitespace": "\s+",
58 "space": " ",
59 }
60
61 df = None
62
63 if sep == "auto":
64 for name, s in separators.items():
65 try:
66 df = pd.read_csv(fn, sep=s, index_col=False, skiprows=skiprows)
67 if len(df.columns) > 2:
68 sep = s
69 print("Detected separator: ", name)
70 break
71 except Exception as e:
72 print("Separator ", s, " failed", e)
73 assert sep != "auto", "Failed to find valid separator"
74
75 if df is None:
76 df = pd.read_csv(fn, sep=separators[sep], index_col=False)
77
78 df.columns
79
80 def read_data(df, colname, optional=False):
81 for i, c in enumerate(df.columns):
82 if colname == f"c{i+1}":
83 print(colname, c)
84 return df[c].values
85 elif colname == c:
86 print(colname, c)
87 return df[c].values
88
89 assert optional, colname + " column not found"
90 return None
91
92 ra = read_data(df, ra_col)
93 dec = read_data(df, dec_col)
94 w = read_data(df, weight_col, optional=True)
95 if w is None:
96 w = np.ones_like(ra)
97
98 source = SkyCoord(ra=np.mean(ra) * u.deg, dec=np.mean(dec) * u.deg)
99
100 map = Map.create(
101 binsz=binsz,
102 width=(window_size_RA * u.deg, window_size_DEC * u.deg),
103 frame="icrs",
104 axes=[],
105 skydir=SkyCoord(source),
106 )
107
108 map.fill_by_coord({"lat": dec * u.deg, "lon": ra * u.deg}, weights=w)
109
110 map.plot()
111 plt.savefig("map.png")
112
113 map.write("map.fits", overwrite=True)
114 fits_image = ImageDataProduct.from_fits_file("map.fits")
115
116 plot = PictureProduct.from_file("map.png")
117
118 plot = plot # http://odahub.io/ontology#ODAPictureProduct
119 fits_image = fits_image # http://odahub.io/ontology#Image
120
121 # output gathering
122 _galaxy_meta_data = {}
123 _oda_outs = []
124 _oda_outs.append(("out_sky_plot_plot", "plot_galaxy.output", plot))
125 _oda_outs.append(
126 ("out_sky_plot_fits_image", "fits_image_galaxy.output", fits_image)
127 )
128
129 for _outn, _outfn, _outv in _oda_outs:
130 _galaxy_outfile_name = os.path.join(_galaxy_wd, _outfn)
131 if isinstance(_outv, str) and os.path.isfile(_outv):
132 shutil.move(_outv, _galaxy_outfile_name)
133 _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
134 elif getattr(_outv, "write_fits_file", None):
135 _outv.write_fits_file(_galaxy_outfile_name)
136 _galaxy_meta_data[_outn] = {"ext": "fits"}
137 elif getattr(_outv, "write_file", None):
138 _outv.write_file(_galaxy_outfile_name)
139 _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
140 else:
141 with open(_galaxy_outfile_name, "w") as fd:
142 json.dump(_outv, fd, cls=CustomJSONEncoder)
143 _galaxy_meta_data[_outn] = {"ext": "json"}
144
145 with open(os.path.join(_galaxy_wd, "galaxy.json"), "w") as fd:
146 json.dump(_galaxy_meta_data, fd)
147 print("*** Job finished successfully ***")