Load your data in jaxspec¶

Most of the data you will use when manipulating X-ray spectra will be in the form of a PHA file. This file contains the measured spectra, the background spectra, and also links to the response matrix file and the ancillary response file.

Loading an instrumental setup¶

jaxspec provides a simple way to load this data using the Observation.from_pha_file function. If you only want to load the instrument related data (i.e. the response matrix and the ancillary response file), you can use the Instrument.from_ogip_file function.

In [1]:

from jaxspec.data import Instrument

instrument = Instrument.from_ogip_file("data/PN.rmf", arf_path="data/PN.arf")

from jaxspec.data import Instrument instrument = Instrument.from_ogip_file("data/PN.rmf", arf_path="data/PN.arf")

Instrument and observation objects are subclasses of xarray's datasets, which mean they can be interactively explored when using jupyter notebooks.

In [2]:

instrument

instrument

Out[2]:

<xarray.Instrument> Size: 19MB
Dimensions:         (instrument_channel: 4096, unfolded_channel: 2067)
Coordinates:
    e_min_unfolded  (unfolded_channel) float64 17kB 0.05 0.051 ... 15.98 15.99
    e_max_unfolded  (unfolded_channel) float64 17kB 0.051 0.052 ... 15.99 16.0
    e_min_channel   (instrument_channel) float64 33kB 0.0 0.00537 ... 20.48
    e_max_channel   (instrument_channel) float64 33kB 0.00537 0.01074 ... 20.48
Dimensions without coordinates: instrument_channel, unfolded_channel
Data variables:
    redistribution  (instrument_channel, unfolded_channel) float32 19MB <COO: nnz=929478, fill_value=0.0>
    area            (unfolded_channel) float64 17kB 1.239 4.504 ... 1.693 1.671
Attributes:
    description:  X-ray instrument response dataset

xarray.Instrument

• Dimensions:
  • instrument_channel: 4096
  • unfolded_channel: 2067
• Coordinates: (4)
  • e_min_unfolded
    (unfolded_channel)
    float64
    0.05 0.051 0.052 ... 15.98 15.99

    description :

    Low bin energy for ingoing channels

    units :

    keV

    array([ 0.05      ,  0.051     ,  0.052     , ..., 15.96000004,
           15.97500038, 15.98999977])

  • e_max_unfolded
    (unfolded_channel)
    float64
    0.051 0.052 0.053 ... 15.99 16.0

    description :

    High bin energy for ingoing channels

    units :

    keV

    array([ 0.051     ,  0.052     ,  0.053     , ..., 15.97500038,
           15.98999977, 16.00499916])

  • e_min_channel
    (instrument_channel)
    float64
    0.0 0.00537 0.01074 ... 20.47 20.48

    description :

    Low bin energy for outgoing channels

    units :

    keV

    array([0.00000000e+00, 5.36998967e-03, 1.07398992e-02, ...,
           2.04650002e+01, 2.04699993e+01, 2.04750004e+01])

  • e_max_channel
    (instrument_channel)
    float64
    0.00537 0.01074 ... 20.48 20.48

    description :

    High bin energy for outgoing channels

    units :

    keV

    array([5.36998967e-03, 1.07398992e-02, 1.61096994e-02, ...,
           2.04699993e+01, 2.04750004e+01, 2.04799995e+01])

• Data variables: (2)
  • redistribution
    (instrument_channel, unfolded_channel)
    float32
    <COO: nnz=929478, fill_value=0.0>

    description :

    Redistribution matrix

    Format	coo
    Data Type	float32
    Shape	(4096, 2067)
    nnz	929478
    Density	0.10978390897133526
    Read-only	True
    Size	17.7M
    Storage ratio	0.55

  • area
    (unfolded_channel)
    float64
    1.239 4.504 9.953 ... 1.693 1.671

    description :

    Effective area

    units :

    cm^2

    array([1.23948348, 4.50446463, 9.95264435, ..., 1.71521497, 1.69298089,
           1.67072606])

• Indexes: (0)
• Attributes: (1)

  description :

  X-ray instrument response dataset

You can display insights about your instrumental setup with the following commands

In [3]:

import matplotlib.pyplot as plt
instrument.plot_redistribution()
plt.show()

import matplotlib.pyplot as plt instrument.plot_redistribution() plt.show()

In [4]:

import matplotlib.pyplot as plt
instrument.plot_area()
plt.show()

import matplotlib.pyplot as plt instrument.plot_area() plt.show()

Loading a given observation¶

In [5]:

from jaxspec.data import Observation

observation = Observation.from_pha_file("data/PN_spectrum_grp20.fits")
observation

from jaxspec.data import Observation observation = Observation.from_pha_file("data/PN_spectrum_grp20.fits") observation

Out[5]:

<xarray.Observation> Size: 273kB
Dimensions:            (instrument_channel: 4096, folded_channel: 1230)
Coordinates:
    channel            (instrument_channel) int64 33kB 0 1 2 ... 4093 4094 4095
    grouped_channel    (folded_channel) int64 10kB 0 1 2 3 ... 1227 1228 1229
Dimensions without coordinates: instrument_channel, folded_channel
Data variables:
    counts             (instrument_channel) int64 33kB 0 0 0 0 0 0 ... 0 0 0 0 0
    folded_counts      (folded_channel) int64 10kB 0 0 0 0 0 0 0 ... 0 0 0 0 0 0
    grouping           (folded_channel, instrument_channel) bool 70kB <COO: nnz=4096, fill_value=False>
    quality            (instrument_channel) int64 33kB 0 0 0 0 0 0 ... 0 0 0 0 0
    exposure           float64 8B 2.027e+04
    backratio          (instrument_channel) float64 33kB 0.2928 ... 0.2928
    folded_backratio   (folded_channel) float64 10kB 0.2928 0.2928 ... 0.2928
    background         (instrument_channel) int64 33kB 0 0 0 0 0 0 ... 0 0 0 0 0
    folded_background  (folded_channel) int64 10kB 0 0 0 0 0 0 0 ... 0 0 0 0 0 0
Attributes:
    observation_file:         data/PN_spectrum_grp20.fits
    background_file:          data/PNbackground_spectrum.fits
    response_matrix_file:     data/PN.rmf
    ancillary_response_file:  data/PN.arf
    description:              X-ray observation dataset

xarray.Observation

• Dimensions:
  • instrument_channel: 4096
  • folded_channel: 1230
• Coordinates: (2)
  • channel
    (instrument_channel)
    int64
    0 1 2 3 4 ... 4092 4093 4094 4095

    description :

    Channel number

    array([   0,    1,    2, ..., 4093, 4094, 4095])

  • grouped_channel
    (folded_channel)
    int64
    0 1 2 3 4 ... 1226 1227 1228 1229

    description :

    Channel number

    array([   0,    1,    2, ..., 1227, 1228, 1229])

• Data variables: (9)
  • counts
    (instrument_channel)
    int64
    0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0

    description :

    Counts

    unit :

    photons

    array([0, 0, 0, ..., 0, 0, 0])

  • folded_counts
    (folded_channel)
    int64
    0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0

    description :

    Folded counts, after grouping

    unit :

    photons

    array([0, 0, 0, ..., 0, 0, 0])

  • grouping
    (folded_channel, instrument_channel)
    bool
    <COO: nnz=4096, fill_value=False>

    description :

    Grouping matrix.

    Format	coo
    Data Type	bool
    Shape	(1230, 4096)
    nnz	4096
    Density	0.0008130081300813008
    Read-only	True
    Size	68.0K
    Storage ratio	0.01

  • quality
    (instrument_channel)
    int64
    0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0

    description :

    Quality flag.

    array([0, 0, 0, ..., 0, 0, 0])

  • exposure
    ()
    float64
    2.027e+04

    description :

    Total exposure

    unit :

    s

    array(20265.98058616)

  • backratio
    (instrument_channel)
    float64
    0.2928 0.2928 ... 0.2928 0.2928

    description :

    Background scaling (SRC_BACKSCAL/BKG_BACKSCAL)

    array([0.29275291, 0.29275291, 0.29275291, ..., 0.29275291, 0.29275291,
           0.29275291])

  • folded_backratio
    (folded_channel)
    float64
    0.2928 0.2928 ... 0.2928 0.2928

    description :

    Background scaling after grouping

    array([0.29275291, 0.29275291, 0.29275291, ..., 0.29275291, 0.29275291,
           0.29275291])

  • background
    (instrument_channel)
    int64
    0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0

    description :

    Background counts

    unit :

    photons

    array([0, 0, 0, ..., 0, 0, 0])

  • folded_background
    (folded_channel)
    int64
    0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0

    description :

    Background counts

    unit :

    photons

    array([0, 0, 0, ..., 0, 0, 0])

• Indexes: (0)
• Attributes: (5)

  observation_file :

  data/PN_spectrum_grp20.fits

  background_file :

  data/PNbackground_spectrum.fits

  response_matrix_file :

  data/PN.rmf

  ancillary_response_file :

  data/PN.arf

  description :

  X-ray observation dataset

You can highlight the grouping bound to your observation, and understand how you photon are packed into new bins.

In [6]:

observation.plot_grouping()
plt.show()

observation.plot_grouping() plt.show()

Define an Observational Setup¶

The ObsConfiguration is the key component of a jaxspec inference problem. It will define a transfer matrix which carries the information about how your spectrum is folded through your instrument and binned with your observation. To build a folding matrix, you usually require an instrument and an observation, and add the energy band you consider.

In [7]:

from jaxspec.data import ObsConfiguration

folding_model = ObsConfiguration.from_instrument(instrument, observation, low_energy=0.5, high_energy=8)

from jaxspec.data import ObsConfiguration folding_model = ObsConfiguration.from_instrument(instrument, observation, low_energy=0.5, high_energy=8)

You can also directly load it from a .pha file

In [8]:

folding_model = ObsConfiguration.from_pha_file('data/PN_spectrum_grp20.fits', low_energy=0.5, high_energy=8)
folding_model

folding_model = ObsConfiguration.from_pha_file('data/PN_spectrum_grp20.fits', low_energy=0.5, high_energy=8) folding_model

Out[8]:

<xarray.ObsConfiguration> Size: 854kB
Dimensions:            (folded_channel: 102, unfolded_channel: 2067)
Coordinates:
    e_min_folded       (folded_channel) float64 816B 0.5215 0.5572 ... 7.365
    e_max_folded       (folded_channel) float64 816B 0.5572 0.5926 ... 7.795
    e_min_unfolded     (unfolded_channel) float64 17kB 0.05 0.051 ... 15.99
    e_max_unfolded     (unfolded_channel) float64 17kB 0.051 0.052 ... 16.0
Dimensions without coordinates: folded_channel, unfolded_channel
Data variables:
    transfer_matrix    (folded_channel, unfolded_channel) float64 800kB <COO: nnz=50028, fill_value=0.0>
    area               (unfolded_channel) float64 17kB 1.239 4.504 ... 1.671
    exposure           float64 8B 2.027e+04
    folded_counts      (folded_channel) int64 816B 265 227 196 209 ... 20 20 20
    folded_backratio   (folded_channel) float64 816B 2.049 2.049 ... 17.57 25.18
    folded_background  (folded_channel) int64 816B 23 27 22 18 ... 12 10 13 21
Attributes:
    observation_file:         data/PN_spectrum_grp20.fits
    background_file:          data/PNbackground_spectrum.fits
    response_matrix_file:     data/PN.rmf
    ancillary_response_file:  data/PN.arf
    description:              X-ray instrument response dataset

xarray.ObsConfiguration

• Dimensions:
  • folded_channel: 102
  • unfolded_channel: 2067
• Coordinates: (4)
  • e_min_folded
    (folded_channel)
    float64
    0.5215 0.5572 ... 7.065 7.365

    description :

    Low energy of folded channel

    array([0.52154797, 0.55716199, 0.59259301, 0.62784696, 0.66293401,
           0.69786102, 0.73264098, 0.76728302, 0.801799  , 0.83620203,
           0.87050498, 0.904719  , 0.93885702, 0.97293198, 1.01180995,
           1.05063999, 1.08943999, 1.12820995, 1.16698003, 1.20576   ,
           1.24456   , 1.28338003, 1.32224   , 1.36115003, 1.40011001,
           1.44400001, 1.48307991, 1.52711999, 1.57123995, 1.61543   ,
           1.65478003, 1.69418991, 1.73364997, 1.77316999, 1.81273997,
           1.85236001, 1.90193999, 1.95158994, 2.00129008, 2.05602002,
           2.11080003, 2.16064   , 2.20551991, 2.25540996, 2.30032015,
           2.35524988, 2.40518999, 2.46513987, 2.51011014, 2.55508018,
           2.6050601 , 2.66504002, 2.72502995, 2.7950201 , 2.85501003,
           2.90500998, 2.95500994, 3.00501013, 3.05500007, 3.1099999 ,
           3.17000008, 3.22000003, 3.2750001 , 3.33999991, 3.41499996,
           3.47000003, 3.53500009, 3.58999991, 3.64499998, 3.71000004,
           3.79500008, 3.88499999, 3.95000005, 4.0250001 , 4.11000013,
           4.21500015, 4.2750001 , 4.33500004, 4.40500021, 4.5250001 ,
           4.59000015, 4.65500021, 4.73000002, 4.79500008, 4.875     ,
           4.96999979, 5.05999994, 5.13999987, 5.23500013, 5.32000017,
           5.42999983, 5.55999994, 5.67500019, 5.79500008, 5.9749999 ,
           6.07999992, 6.26999998, 6.44500017, 6.63500023, 6.86499977,
           7.06500006, 7.36499977])

  • e_max_folded
    (folded_channel)
    float64
    0.5572 0.5926 ... 7.365 7.795

    description :

    High energy of folded channel

    array([0.55716199, 0.59259301, 0.62784696, 0.66293401, 0.69786102,
           0.73264098, 0.76728302, 0.801799  , 0.83620203, 0.87050498,
           0.904719  , 0.93885702, 0.97293198, 1.01180995, 1.05063999,
           1.08943999, 1.12820995, 1.16698003, 1.20576   , 1.24456   ,
           1.28338003, 1.32224   , 1.36115003, 1.40011001, 1.44400001,
           1.48307991, 1.52711999, 1.57123995, 1.61543   , 1.65478003,
           1.69418991, 1.73364997, 1.77316999, 1.81273997, 1.85236001,
           1.90193999, 1.95158994, 2.00129008, 2.05602002, 2.11080003,
           2.16064   , 2.20551991, 2.25540996, 2.30032015, 2.35524988,
           2.40518999, 2.46513987, 2.51011014, 2.55508018, 2.6050601 ,
           2.66504002, 2.72502995, 2.7950201 , 2.85501003, 2.90500998,
           2.95500994, 3.00501013, 3.05500007, 3.1099999 , 3.17000008,
           3.22000003, 3.2750001 , 3.33999991, 3.41499996, 3.47000003,
           3.53500009, 3.58999991, 3.64499998, 3.71000004, 3.79500008,
           3.88499999, 3.95000005, 4.0250001 , 4.11000013, 4.21500015,
           4.2750001 , 4.33500004, 4.40500021, 4.5250001 , 4.59000015,
           4.65500021, 4.73000002, 4.79500008, 4.875     , 4.96999979,
           5.05999994, 5.13999987, 5.23500013, 5.32000017, 5.42999983,
           5.55999994, 5.67500019, 5.79500008, 5.9749999 , 6.07999992,
           6.26999998, 6.44500017, 6.63500023, 6.86499977, 7.06500006,
           7.36499977, 7.79500008])

  • e_min_unfolded
    (unfolded_channel)
    float64
    0.05 0.051 0.052 ... 15.98 15.99

    description :

    Low energy of unfolded channel

    array([ 0.05      ,  0.051     ,  0.052     , ..., 15.96000004,
           15.97500038, 15.98999977])

  • e_max_unfolded
    (unfolded_channel)
    float64
    0.051 0.052 0.053 ... 15.99 16.0

    description :

    High energy of unfolded channel

    array([ 0.051     ,  0.052     ,  0.053     , ..., 15.97500038,
           15.98999977, 16.00499916])

• Data variables: (6)
  • transfer_matrix
    (folded_channel, unfolded_channel)
    float64
    <COO: nnz=50028, fill_value=0.0>

    description :

    Transfer matrix to use to fold the incoming spectrum. It is built and restricted using the grouping, redistribution matrix, effective area, quality flags and energy bands defined by the user.

    Format	coo
    Data Type	float64
    Shape	(102, 2067)
    nnz	50028
    Density	0.23728620620962462
    Read-only	True
    Size	781.7K
    Storage ratio	0.47

  • area
    (unfolded_channel)
    float64
    1.239 4.504 9.953 ... 1.693 1.671

    description :

    Effective area with the same restrictions as the transfer matrix.

    units :

    cm^2

    array([1.23948348, 4.50446463, 9.95264435, ..., 1.71521497, 1.69298089,
           1.67072606])

  • exposure
    ()
    float64
    2.027e+04

    description :

    Total exposure

    unit :

    s

    array(20265.98058616)

  • folded_counts
    (folded_channel)
    int64
    265 227 196 209 231 ... 20 20 20 20

    description :

    Folded counts after grouping, with the same restrictions as the transfer matrix.

    unit :

    photons

    array([265, 227, 196, 209, 231, 253, 219, 199, 218, 222, 216, 221, 208,
           247, 254, 229, 216, 203, 214, 194, 212, 196, 190, 190, 221, 163,
           184, 159, 163, 136, 117, 139, 154, 110, 131, 145, 126, 123, 145,
           130,  95,  78,  94,  78,  72,  65,  75,  48,  43,  63,  65,  66,
            69,  68,  47,  43,  44,  42,  43,  62,  44,  46,  43,  74,  40,
            42,  43,  45,  42,  44,  44,  43,  44,  44,  41,  20,  20,  21,
            42,  21,  21,  22,  20,  20,  20,  22,  22,  20,  20,  21,  21,
            20,  21,  21,  21,  20,  21,  20,  20,  20,  20,  20])

  • folded_backratio
    (folded_channel)
    float64
    2.049 2.049 2.049 ... 17.57 25.18

    description :

    Background scaling after grouping, with the same restrictions as the transfer matrix.

    array([ 2.04927034,  2.04927034,  2.04927034,  2.04927034,  2.04927034,
            2.04927034,  2.04927034,  2.04927034,  2.04927034,  2.04927034,
            2.04927034,  2.04927034,  2.04927034,  2.34202324,  2.34202324,
            2.34202324,  2.34202324,  2.34202324,  2.34202324,  2.34202324,
            2.34202324,  2.34202324,  2.34202324,  2.34202324,  2.63477615,
            2.34202324,  2.63477615,  2.63477615,  2.63477615,  2.34202324,
            2.34202324,  2.34202324,  2.34202324,  2.34202324,  2.34202324,
            2.92752906,  2.92752906,  2.92752906,  3.22028196,  3.22028196,
            2.92752906,  2.63477615,  2.92752906,  2.63477615,  3.22028196,
            2.92752906,  3.51303487,  2.63477615,  2.63477615,  2.92752906,
            3.51303487,  3.51303487,  4.09854068,  3.51303487,  2.92752906,
            2.92752906,  2.92752906,  2.92752906,  3.22028196,  3.51303487,
            2.92752906,  3.22028196,  3.80578777,  4.39129358,  3.22028196,
            3.80578777,  3.22028196,  3.22028196,  3.80578777,  4.97679939,
            5.2695523 ,  3.80578777,  4.39129358,  4.97679939,  6.14781102,
            3.51303487,  3.51303487,  4.09854068,  7.02606973,  3.80578777,
            3.80578777,  4.39129358,  3.80578777,  4.68404649,  5.56230521,
            5.2695523 ,  4.68404649,  5.56230521,  4.97679939,  6.44056392,
            7.61157554,  6.73331683,  7.02606973, 10.5391046 ,  6.14781102,
           11.12461041, 10.24635169, 11.12461041, 13.46663365, 11.71011622,
           17.56517433, 25.17674988])

  • folded_background
    (folded_channel)
    int64
    23 27 22 18 13 7 ... 5 12 10 13 21

    description :

    Folded background counts after grouping, with the same restrictions as the transfer matrix.

    unit :

    photons

    array([23, 27, 22, 18, 13,  7,  8, 12,  7, 10, 10,  9,  8,  5, 11,  5,  7,
            2,  8, 10,  6,  6,  4,  5,  8, 18, 17, 13,  5,  8,  7,  5,  3,  9,
            4,  4,  5,  6,  4,  6,  6,  6,  7,  2,  3,  3,  6,  3,  4,  3, 11,
            4,  3,  5,  6,  2,  7,  5,  2,  5,  4,  6,  5,  8,  5,  3,  3,  3,
            1,  5,  6,  3,  2,  2,  9,  4,  2,  4,  9,  6,  3,  6,  1, 10,  7,
            8,  3,  4,  0,  9, 10,  7,  2,  9,  3, 11,  7,  5, 12, 10, 13, 21])

• Indexes: (0)
• Attributes: (5)

  observation_file :

  data/PN_spectrum_grp20.fits

  background_file :

  data/PNbackground_spectrum.fits

  response_matrix_file :

  data/PN.rmf

  ancillary_response_file :

  data/PN.arf

  description :

  X-ray instrument response dataset