Update tool lightcurve-analysis to 0.0.1+galaxy0

tools/lightcurve-analysis/.shed.yml

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

tools/lightcurve-analysis/correlate.py

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+#!/usr/bin/env python
+# coding: utf-8
+
+# flake8: noqa
+
+import json
+import os
+import shutil
+
+from oda_api.json import CustomJSONEncoder
+
+light_curve_1 = "spiacs_lc_query.fits"  # http://odahub.io/ontology#POSIXPath
+light_curve_2 = "spiacs_lc_query.fits"  # http://odahub.io/ontology#POSIXPath
+mode = (
+    "Background"  # oda:String; oda:allowed_value 'Background','Peak','Focus'.
+)
+
+_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)
+
+from astropy.io import fits
+from astropy.time import Time
+from matplotlib import pylab as plt
+from oda_api.data_products import LightCurveDataProduct, PictureProduct
+
+lc1 = fits.open(light_curve_1)[1].data
+lc2 = fits.open(light_curve_2)[1].data
+
+plt.figure()
+
+plt.plot(lc1["TIME"], lc1["RATE"])
+plt.plot(lc2["TIME"], lc2["RATE"])
+
+plt.savefig("lc.png")
+
+outlcpng = PictureProduct.from_file("lc.png")
+outlc = LightCurveDataProduct.from_arrays(
+    times=Time(lc2["TIME"], format="mjd"),
+    rates=lc2["RATE"],
+    errors=lc2["ERROR"],
+)
+
+detection_image = outlcpng  # oda:ODAPictureProduct
+processed_lc = outlc  # oda:LightCurve
+
+# output gathering
+_galaxy_meta_data = {}
+_oda_outs = []
+_oda_outs.append(
+    (
+        "out_correlate_detection_image",
+        "detection_image_galaxy.output",
+        detection_image,
+    )
+)
+_oda_outs.append(
+    ("out_correlate_processed_lc", "processed_lc_galaxy.output", processed_lc)
+)
+
+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/lightcurve-analysis/detect_impulsive.py

@@ -0,0 +1,118 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+# flake8: noqa
+
+import json
+import os
+import shutil
+
+from oda_api.json import CustomJSONEncoder
+
+light_curve = "spiacs_lc_query.fits"  # http://odahub.io/ontology#POSIXPath
+time_column = "TIME"
+rate_column = "FLUX"
+rate_err_column = "FLUX_ERR"
+mode = "Background"  # oda:String; oda:allowed_value 'Background','Peak','Focus', 'Standartize'.
+
+_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)
+
+import numpy as np
+from astropy.io import fits
+from oda_api.data_products import LightCurveDataProduct, PictureProduct
+
+lc = fits.open(light_curve)[1].data
+
+lc
+
+lc.columns.names
+
+def get_one_of_names(d, names):
+    for n in names:
+        if n in lc.columns.names:
+            return lc[n]
+
+t = get_one_of_names(lc, ["TIME", "Tmean[MJD]", time_column])
+rate = get_one_of_names(lc, ["RATE", "FLUX", "Flux[counts/cm2s]", rate_column])
+rate_err = get_one_of_names(
+    lc, ["ERROR", "Flux_error[counts/cm2s]", rate_err_column]
+)
+
+bkg = np.mean(rate)
+
+peak_i = rate.argmax()
+
+if mode == "Background":
+    rate -= bkg
+
+from matplotlib import pylab as plt
+
+plt.figure()
+
+plt.errorbar(t, rate, rate_err)
+
+plt.axvline(t[peak_i], c="r")
+
+plt.xlabel("seconds since T$_0$")
+plt.ylabel("counts/s")
+
+plt.savefig("lc.png")
+
+from astropy.time import Time
+
+outlcpng = PictureProduct.from_file("lc.png")
+outlc = LightCurveDataProduct.from_arrays(
+    times=Time(t, format="mjd"), rates=rate, errors=rate_err
+)
+
+detection_image = outlcpng  # oda:ODAPictureProduct
+processed_lc = outlc  # oda:LightCurve
+
+# output gathering
+_galaxy_meta_data = {}
+_oda_outs = []
+_oda_outs.append(
+    (
+        "out_detect_impulsive_detection_image",
+        "detection_image_galaxy.output",
+        detection_image,
+    )
+)
+_oda_outs.append(
+    (
+        "out_detect_impulsive_processed_lc",
+        "processed_lc_galaxy.output",
+        processed_lc,
+    )
+)
+
+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/lightcurve-analysis/lightcurve_analysis_astro_tool.xml

@@ -0,0 +1,91 @@
+<tool id="lightcurve_analysis_astro_tool" name="lightcurve-analysis" version="0.0.1+galaxy0" profile="23.0">
+  <requirements>
+    <requirement type="package" version="2.2.2">pandas</requirement>
+    <requirement type="package" version="1.2.20">oda-api</requirement>
+    <requirement type="package" version="3.9.0">matplotlib</requirement>
+    <requirement type="package" version="2.32.3">requests</requirement>
+    <requirement type="package" version="0.4.7">astroquery</requirement>
+    <requirement type="package" version="7.0.0">rdflib</requirement>
+    <requirement type="package" version="4.12.3">beautifulsoup4</requirement>
+    <requirement type="package" version="2.0.0">sparqlwrapper</requirement>
+    <requirement type="package" version="3.3">networkx</requirement>
+    <requirement type="package" version="1.14.0">scipy</requirement>
+    <requirement type="package" version="8.26.0">ipython</requirement>
+    <requirement type="package" version="6.1.1">astropy</requirement>
+    <requirement type="package" version="2.0.0">numpy</requirement>
+    <!--Requirements string 'nb2workflow' 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="correlate" selected="true">correlate</option>
+        <option value="detect_impulsive" selected="false">detect_impulsive</option>
+      </param>
+      <when value="correlate">
+        <param name="light_curve_1" type="data" label="light_curve_1" format="data" />
+        <param name="light_curve_2" type="data" label="light_curve_2" format="data" />
+        <param name="mode" type="select" label="mode">
+          <option value="Background" selected="true">Background</option>
+          <option value="Focus">Focus</option>
+          <option value="Peak">Peak</option>
+        </param>
+      </when>
+      <when value="detect_impulsive">
+        <param name="light_curve" type="data" label="light_curve" format="data" />
+        <param name="time_column" type="text" value="TIME" label="time_column" />
+        <param name="rate_column" type="text" value="FLUX" label="rate_column" />
+        <param name="rate_err_column" type="text" value="FLUX_ERR" label="rate_err_column" />
+        <param name="mode" type="select" label="mode">
+          <option value="Background" selected="true">Background</option>
+          <option value="Focus">Focus</option>
+          <option value="Peak">Peak</option>
+          <option value="Standartize">Standartize</option>
+        </param>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data label="${tool.name} -&gt; correlate detection_image" name="out_correlate_detection_image" format="auto" from_work_dir="detection_image_galaxy.output">
+      <filter>_data_product['_selector'] == 'correlate'</filter>
+    </data>
+    <data label="${tool.name} -&gt; correlate processed_lc" name="out_correlate_processed_lc" format="auto" from_work_dir="processed_lc_galaxy.output">
+      <filter>_data_product['_selector'] == 'correlate'</filter>
+    </data>
+    <data label="${tool.name} -&gt; detect_impulsive detection_image" name="out_detect_impulsive_detection_image" format="auto" from_work_dir="detection_image_galaxy.output">
+      <filter>_data_product['_selector'] == 'detect_impulsive'</filter>
+    </data>
+    <data label="${tool.name} -&gt; detect_impulsive processed_lc" name="out_detect_impulsive_processed_lc" format="auto" from_work_dir="processed_lc_galaxy.output">
+      <filter>_data_product['_selector'] == 'detect_impulsive'</filter>
+    </data>
+  </outputs>
+  <tests>
+    <test expect_num_outputs="2">
+      <conditional name="_data_product">
+        <param name="_selector" value="correlate" />
+        <param name="light_curve_1" location="https://gitlab.renkulab.io/astronomy/mmoda/lightcurve-analysis/-/raw/fdeef1d7e716c836601f41dc961ebfb288fa456f/spiacs_lc_query.fits" />
+        <param name="light_curve_2" location="https://gitlab.renkulab.io/astronomy/mmoda/lightcurve-analysis/-/raw/fdeef1d7e716c836601f41dc961ebfb288fa456f/spiacs_lc_query.fits" />
+        <param name="mode" value="Background" />
+      </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="detect_impulsive" />
+        <param name="light_curve" location="https://gitlab.renkulab.io/astronomy/mmoda/lightcurve-analysis/-/raw/fdeef1d7e716c836601f41dc961ebfb288fa456f/spiacs_lc_query.fits" />
+        <param name="time_column" value="TIME" />
+        <param name="rate_column" value="FLUX" />
+        <param name="rate_err_column" value="FLUX_ERR" />
+        <param name="mode" value="Background" />
+      </conditional>
+      <assert_stdout>
+        <has_text text="*** Job finished successfully ***" />
+      </assert_stdout>
+    </test>
+  </tests>
+</tool>