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osa_lightcurve_query.py
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osa_lightcurve_query.py
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"""
Overview
--------
general info about this module
Classes and Inheritance Structure
----------------------------------------------
.. inheritance-diagram::
Summary
---------
.. autosummary::
list of the module you want
Module API
----------
"""
from __future__ import absolute_import, division, print_function
from builtins import (bytes, str, open, super, range,
zip, round, input, int, pow, object, map, zip)
__author__ = "Andrea Tramacere"
# Standard library
# eg copy
# absolute import rg:from copy import deepcopy
import os
# Dependencies
# eg numpy
# absolute import eg: import numpy as np
# Project
# relative import eg: from .mod import f
import ddaclient as dc
# Project
# relative import eg: from .mod import f
import numpy as np
from numpy.lib.recfunctions import append_fields
from pathlib import Path
from astropy.io import fits as pf
from cdci_data_analysis.analysis.io_helper import FitsFile
from cdci_data_analysis.analysis.queries import LightCurveQuery,ProductQuery
from cdci_data_analysis.analysis.products import LightCurveProduct,QueryProductList,QueryOutput
from cdci_data_analysis.analysis.io_helper import FilePath
from cdci_data_analysis.analysis.parameters import TimeDelta
from cdci_data_analysis.analysis.plot_tools import ScatterPlot
from oda_api.data_products import NumpyDataProduct
from .osa_dataserve_dispatcher import OsaDispatcher
from .osa_common_pars import DummyOsaRes
class OsaLigthtCurve(LightCurveProduct):
def __init__(self,
name='osa_lc',
file_name=None,
data=None,
file_dir=None,
prod_prefix=None,
src_name='',
meta_data={}):
if meta_data == {} or meta_data is None:
self.meta_data = {'product': 'osa_lc', 'instrument': 'integral', 'src_name': src_name}
else:
self.meta_data = meta_data
self.meta_data['time']='TIME'
self.meta_data['rate'] ='RATE'
self.meta_data['rate_err'] = 'ERROR'
data.name=name
super(OsaLigthtCurve, self).__init__(name=name,
data=data,
name_prefix=prod_prefix,
file_dir=file_dir,
file_name=file_name,
meta_data=meta_data)
#@staticmethod
#def make_ogip_compliant(du):
# timedel = du.header['TIMEDEL']
# timepix = du.header['TIMEPIXR']
# t_lc = du.data['TIME'] + (0.5 - timepix) * timedel
# dt_lc = (timedel / 2) * np.ones(t_lc.shape)
#
# for i in range(len(t_lc) - 1):
# dt_lc[i + 1] = min(timedel / 2, t_lc[i + 1] - t_lc[i] - dt_lc[i])
#
# _d = np.array(du.data)
# _o = append_fields(_d, 'TIMEDEL', dt_lc*2)
# du.data = _o.data
@classmethod
def build_isgri_lc_from_ddosa_res(cls,
res,
src_name='',
prod_prefix='',
file_dir=None,
api=False):
lc_list = []
if file_dir is None:
file_dir = './'
if prod_prefix is None:
prod_prefix=''
for source_name, lightcurve_attr in res.extracted_sources:
meta_data = {}
input_lc_paht = getattr(res, lightcurve_attr)
npd = NumpyDataProduct.from_fits_file(input_lc_paht, meta_data=meta_data)
du = npd.get_data_unit_by_name('ISGR-SRC.-LCR')
if du is not None:
src_name = du.header['NAME']
meta_data['src_name'] = src_name
meta_data['time_bin'] = du.header['TIMEDEL']
out_file_name = Path(input_lc_paht).resolve().stem
#OsaLigthtCurve.make_ogip_compliant(du)
lc = cls(name='isgri_lc', data=npd, file_name=out_file_name, file_dir=file_dir, prod_prefix=prod_prefix,
src_name=src_name,meta_data=meta_data)
lc_list.append(lc)
return lc_list
@classmethod
def build_jemx_lc_from_ddosa_res(cls,
res,
src_name='',
prod_prefix='',
file_dir=None,
api=False):
lc_list=[]
lc_path_list = [getattr(res,attr) for attr in dir(res) if attr.startswith("lc_")]
src_name_list = [attr for attr in dir(res) if attr.startswith("lc_")]
src_name_list = [n.replace('lc_','') for n in src_name_list]
src_name_list = [n.replace('_', ' ') for n in src_name_list]
print ('->',lc_path_list,src_name_list)
if file_dir is None:
file_dir = './'
if prod_prefix is None:
prod_prefix = ''
for source_name, input_lc_paht in zip(src_name_list,lc_path_list):
meta_data = {}
npd = NumpyDataProduct.from_fits_file(input_lc_paht, meta_data=meta_data)
du = npd.get_data_unit_by_name('JMX2-SRC.-LCR')
if du is None:
du = npd.get_data_unit_by_name('JMX1-SRC.-LCR')
if du is None:
# warning, this one is empty (add to warning list)
continue
# raise RuntimeError('Missing data unit with light curve in the fits file')
if du is not None:
meta_data['src_name'] = source_name
meta_data['time_bin'] = du.header['TIMEDEL']
out_file_name = Path(input_lc_paht).resolve().stem
#OsaLigthtCurve.make_ogip_compliant(du)
lc = cls(name='jemx_lc', data=npd, file_name=out_file_name, file_dir=file_dir, prod_prefix=prod_prefix,
src_name=src_name, meta_data=meta_data)
lc_list.append(lc)
return lc_list
def get_html_draw(self, plot=False):
#
npd = NumpyDataProduct.from_fits_file(self.file_path.path)
du = npd.get_data_unit_by_name('ISGR-SRC.-LCR')
if du is None:
du = npd.get_data_unit_by_name('JMX2-SRC.-LCR')
if du is None:
du = npd.get_data_unit_by_name('JMX1-SRC.-LCR')
if du is None:
raise RuntimeError('du with lc not found in fits file')
data = du.data
header = du.header
#filtering zero flux values
msk_non_zero = np.count_nonzero([data['RATE'], data['ERROR']], axis=0) > 0
data=data[msk_non_zero]
x = data['TIME']
dx= data['TIMEDEL']*0.5
y = data['RATE']
dy = data['ERROR']
try:
mjdref = header['mjdref'] + np.int(x.min())
except:
mjdref = header['MJDREF'] + np.int(x.min())
x = x - np.int(x.min())
sp=ScatterPlot(w=600,h=600,x_label='MJD-%d (days)' % mjdref,y_label='Rate (cts/s)')
sp.add_errorbar(x,y,yerr=dy,xerr=dx)
footer_str=None
if self.name == 'jemx_lc':
exposure = np.sum(data['FRACEXP']) * du.header['TIMEDEL']
exposure *= 86400.
elif self.name == 'isgri_lc':
exposure = np.sum(data['FRACEXP'] * du.header['XAX_E']) * 2
exposure *= 86400.
else:
# TODO update this option
footer_str ='Exposure non evaluated for product %s'%self.name
if footer_str!=None:
footer_str = 'Exposure %5.5f (s) \n' % exposure
try:
slope = None
normalized_slope = None
chisq_red = None
poly_deg = 0
p, chisq, chisq_red, dof,xf,yf = self.do_linear_fit(x, y, dy, poly_deg, 'constant fit')
sp.add_line(xf,yf,'constant fit',color='green')
if p is not None:
footer_str += '\n'
footer_str += 'Constant fit\n'
footer_str += 'flux level %5.5f (cts/s)\n' % p[0]
footer_str += 'dof ' + '%d' % dof + '\n'
footer_str += 'Chi-squared red. %5.5f\n' % chisq_red
except:
pass
try:
poly_deg = 1
p, chisq, chisq_red, dof,xf,yf = self.do_linear_fit(x, y, dy, poly_deg, 'linear fit')
if p is not None:
footer_str += '\n'
footer_str += 'Linear fit\n'
footer_str += 'slope %5.5f\n' % p[0]
footer_str += 'dof ' + '%d' % dof + '\n'
footer_str += 'Chi-squared red. %5.5f\n' % chisq_red
sp.add_line(xf, yf, 'linear fit',color='orange')
except:
pass
html_dict= sp.get_html_draw()
res_dict = {}
res_dict['image'] =html_dict
res_dict['header_text'] = ''
res_dict['table_text'] = ''
res_dict['footer_text'] = footer_str
return res_dict
def do_linear_fit(self, x, y, dy, poly_deg, label):
p = None
chisq = None
chisq_red = None
dof = None
x_grid = None
y_grid=None
if y.size > poly_deg + 1:
p = np.polyfit(x, y, poly_deg)
x_grid = np.linspace(x.min(), x.max(), 100)
lin_fit = np.poly1d(p)
chisq = (lin_fit(x) - y) ** 2 / dy ** 2
dof = y.size - (poly_deg + 1)
chisq_red = chisq.sum() / float(dof)
y_grid=lin_fit(x_grid)
return p, chisq, chisq_red, dof,x_grid, y_grid
class OSATimebin(TimeDelta):
def __init__(self,
value=None,
delta_T_format_name=None,
name=None):
self.t_bin_max_seconds = 4000.
super(OSATimebin, self).__init__(value=value,
delta_T_format_name=delta_T_format_name,
name=name)
@property
def value(self):
return self._astropy_time_delta.value
@value.setter
def value(self, v):
units = self.units
self._set_time(v, format=units)
print('setting time bine to',v)
if self._astropy_time_delta.sec>self.t_bin_max_seconds:
raise RuntimeError('Time bin max value exceeded =%f'%self.t_bin_max_seconds)
class OsaLightCurveQuery(ProductQuery):
def __init__(self, name):
#super(OsaLightCurveQuery, self).__init__(name)
# TODO define TimeDelta parameter with max value = 3ks
# TODO done, verify
osa_time_bin = OSATimebin(value=1000., name='time_bin', delta_T_format_name='time_bin_format')
parameters_list = [osa_time_bin]
super(OsaLightCurveQuery, self).__init__(name, parameters_list)
def get_data_server_query(self, instrument,
config=None):
scwlist_assumption, cat, extramodules, inject=OsaDispatcher.get_osa_query_base(instrument)
E1=instrument.get_par_by_name('E1_keV').value
E2=instrument.get_par_by_name('E2_keV').value
src_name = instrument.get_par_by_name('src_name').value
delta_t = instrument.get_par_by_name('time_bin')._astropy_time_delta.sec
osa_version = instrument.get_par_by_name('osa_version').value
if (isinstance(self,JemxLightCurveQuery)):
jemx_num = instrument.get_par_by_name('jemx_num').value
target, modules, assume=self.set_instr_dictionaries(extramodules, scwlist_assumption, E1, E2, src_name,
delta_t, osa_version=osa_version,jemx_num=jemx_num)
else:
target, modules, assume = self.set_instr_dictionaries(extramodules, scwlist_assumption, E1, E2, src_name,
delta_t, osa_version=osa_version)
q = OsaDispatcher(config=config,instrument=instrument, target=target, modules=modules, assume=assume, inject=inject)
return q
def set_instr_dictionaries(self, extramodules,scwlist_assumption,E1,E2,src_name,delta_t):
raise RuntimeError('Must be specified for each instrument')
def process_product_method(self, instrument, prod_list,api=False, **kw):
_names = []
_lc_path = []
_html_fig = []
_data_list=[]
for query_lc in prod_list.prod_list:
#print('--> lc name',query_lc.name)
#print('-->file name', query_lc.file_path.path)
query_lc.add_url_to_fits_file(instrument._current_par_dic, url=instrument.disp_conf.products_url)
query_lc.write()
if api==False:
_names.append(query_lc.meta_data['src_name'])
_lc_path.append(str(query_lc.file_path.name))
_html_fig.append(query_lc.get_html_draw())
if api==True:
_data_list.append(query_lc.data)
query_out = QueryOutput()
if api == True:
query_out.prod_dictionary['numpy_data_product_list'] = _data_list
else:
query_out.prod_dictionary['name'] = _names
query_out.prod_dictionary['file_name'] = _lc_path
query_out.prod_dictionary['image'] =_html_fig
query_out.prod_dictionary['download_file_name'] = 'light_curve.fits.gz'
query_out.prod_dictionary['prod_process_message'] = ''
return query_out
class IsgriLightCurveQuery(OsaLightCurveQuery):
def __init__(self,name ):
super(IsgriLightCurveQuery, self).__init__(name)
def build_product_list(self,instrument,res,out_dir,prod_prefix=None,api=False):
meta_data = {'product': 'light_curve', 'instrument': 'isgri', 'src_name': ''}
meta_data['query_parameters'] = self.get_parameters_list_as_json()
prod_list = OsaLigthtCurve.build_isgri_lc_from_ddosa_res(res,
prod_prefix=prod_prefix,
file_dir=out_dir,
api=api)
return prod_list
def get_dummy_products(self, instrument, config, out_dir='./',prod_prefix=None,api=False):
meta_data = {'product': 'light_curve', 'instrument': 'isgri', 'src_name': ''}
meta_data['query_parameters'] = self.get_parameters_list_as_json()
dummy_cache = config.dummy_cache
res =DummyOsaRes()
res.__setattr__('dummy_src','dummy_src')
res.__setattr__('dummy_lc','%s/isgri_query_lc.fits' % dummy_cache)
res.__setattr__('extracted_sources',[('dummy_src','dummy_lc')])
prod_list = OsaLigthtCurve.build_isgri_lc_from_ddosa_res(res,
prod_prefix=prod_prefix,
file_dir=out_dir,
api=api)
prod_list = QueryProductList(prod_list=prod_list)
return prod_list
def set_instr_dictionaries(self, extramodules, scwlist_assumption, E1, E2, src_name, delta_t, osa_version="OSA10.2"):
#print('-->lc standard mode from scw_list', scwlist_assumption)
#print('-->src_name', src_name)
target = "ISGRILCSum"
if extramodules is None:
extramodules = []
if osa_version == "OSA10.2":
modules = ["git://ddosa/staging-1-3",'git://process_isgri_lc'] + extramodules + ['git://ddosa_delegate/staging-1-3']
elif osa_version == "OSA11.0":
modules = ["git://ddosa/staging-1-3", "git://findic/icversionpy37","git://ddosa11/icversion",'git://process_isgri_lc'] + extramodules + ['git://ddosa_delegate/staging-1-3']
else:
raise Exception("unknown osa version: "+osa_version)
assume = ['process_isgri_lc.ScWLCList(input_scwlist=%s)' % scwlist_assumption[0],
scwlist_assumption[1],
'ddosa.ImageBins(use_ebins=[(%(E1)s,%(E2)s)],use_version="onebin_%(E1)s_%(E2)s")' % dict(E1=E1,
E2=E2),
'ddosa.LCEnergyBins(use_ebins=[(%(E1)s,%(E2)s)],use_version="onebin_%(E1)s_%(E2)s")' % dict(E1=E1,
E2=E2),
'ddosa.ImagingConfig(use_SouFit=0,use_version="soufit0_p2",use_DoPart2=1)',
'ddosa.CatForLC(use_minsig=3)',
'ddosa.LCTimeBin(use_time_bin_seconds=%f)' % delta_t]
return target, modules, assume
class JemxLightCurveQuery(OsaLightCurveQuery):
def __init__(self, name):
super(JemxLightCurveQuery, self).__init__(name)
def build_product_list(self, instrument, res, out_dir, prod_prefix=None, api=False):
meta_data = {'product': 'light_curve', 'instrument': 'jemx', 'src_name': ''}
meta_data['query_parameters'] = self.get_parameters_list_as_json()
prod_list = OsaLigthtCurve.build_jemx_lc_from_ddosa_res(res,
prod_prefix=prod_prefix,
file_dir=out_dir,
api=api)
return prod_list
def get_dummy_products(self, instrument, config, out_dir='./', prod_prefix=None, api=False):
meta_data = {'product': 'light_curve', 'instrument': 'jemx', 'src_name': ''}
meta_data['query_parameters'] = self.get_parameters_list_as_json()
dummy_cache = config.dummy_cache
res = DummyOsaRes()
res.__setattr__('lc_crab', '%s/jemx_query_lc.fits.gz' % dummy_cache)
#res.__setattr__('extracted_sources', [('dummy_src', 'dummy_lc')])
prod_list = OsaLigthtCurve.build_jemx_lc_from_ddosa_res(res,
prod_prefix=prod_prefix,
file_dir=out_dir,
api=api)
prod_list = QueryProductList(prod_list=prod_list)
return prod_list
def set_instr_dictionaries(self, extramodules, scwlist_assumption, E1, E2, src_name, delta_t,jemx_num,
osa_version="OSA10.2"):
target = "lc_pick"
if extramodules is None:
extramodules = []
if osa_version == "OSA10.2":
modules = ["git://ddosa/staging-1-3","git://ddjemx"] + extramodules +['git://ddosa_delegate/staging-1-3']
elif osa_version == "OSA11.0":
modules = ["git://ddosa/staging-1-3","git://ddjemx", "git://findic/icversionpy37", "git://ddosa11/icversion"] \
+ extramodules + ['git://ddosa_delegate/staging-1-3']
else:
raise Exception("unknown osa version: " + osa_version)
assume = ['ddjemx.JMXLCGroups(input_scwlist=%s)' % scwlist_assumption[0],
scwlist_assumption[1],
'ddjemx.JEnergyBinsLC (use_bins=[(%(E1)s,%(E2)s)])' % dict(E1=E1, E2=E2),
'ddjemx.LCTimeBin(use_time_bin_seconds=%f)' % delta_t,
'ddjemx.JEMX(use_num=%d)' % jemx_num]
return target, modules, assume