jaxspec 0.0.2__py3-none-any.whl → 0.0.4__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- jaxspec/analysis/results.py +1 -1
- jaxspec/data/__init__.py +3 -0
- jaxspec/data/example_data/fakeit.pha +335 -1
- jaxspec/data/instrument.py +14 -9
- jaxspec/data/obsconf.py +109 -51
- jaxspec/data/observation.py +45 -18
- jaxspec/data/ogip.py +100 -40
- jaxspec/data/util.py +51 -47
- jaxspec/fit.py +19 -9
- jaxspec/model/abc.py +29 -6
- jaxspec/model/additive.py +87 -22
- jaxspec/model/background.py +5 -5
- jaxspec/model/multiplicative.py +56 -15
- {jaxspec-0.0.2.dist-info → jaxspec-0.0.4.dist-info}/METADATA +8 -4
- {jaxspec-0.0.2.dist-info → jaxspec-0.0.4.dist-info}/RECORD +17 -16
- {jaxspec-0.0.2.dist-info → jaxspec-0.0.4.dist-info}/LICENSE.md +0 -0
- {jaxspec-0.0.2.dist-info → jaxspec-0.0.4.dist-info}/WHEEL +0 -0
jaxspec/analysis/results.py
CHANGED
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@@ -343,7 +343,7 @@ class ChainResult:
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folding_model.out_energies,
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y_observed=folding_model.folded_background.data,
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y_samples=bkg_count,
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denominator=denominator
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denominator=denominator * folding_model.folded_backratio.data,
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color=(0.26787604, 0.60085972, 0.63302651),
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percentile=percentile,
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)
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jaxspec/data/__init__.py
CHANGED
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@@ -5,3 +5,6 @@ from .observation import Observation # noqa: F401
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import astropy.units as u
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u.add_enabled_aliases({"counts": u.count})
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u.add_enabled_aliases({"channel": u.dimensionless_unscaled})
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# Arbitrary units are found in .rsp files , let's hope it is compatible with what we would expect as the rmf x arf
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# u.add_enabled_aliases({"au": u.dimensionless_unscaled})
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SIMPLE = T / file does conform to FITS standard BITPIX = 8 / number of bits per data pixel NAXIS = 0 / number of data axes EXTEND = T / FITS dataset may contain extensions COMMENT FITS (Flexible Image Transport System) format is defined in 'AstronomyCOMMENT and Astrophysics', volume 376, page 359; bibcode: 2001A&A...376..359H END XTENSION= 'BINTABLE' / binary table extension BITPIX = 8 / 8-bit bytes NAXIS = 2 / 2-dimensional binary table NAXIS1 = 12 / width of table in bytes NAXIS2 = 4096 / number of rows in table PCOUNT = 0 / size of special data area GCOUNT = 1 / one data group (required keyword) TFIELDS = 4 / number of fields in each row TTYPE1 = 'CHANNEL ' / label for field 1 TFORM1 = 'J ' / data format of field: 4-byte INTEGER TTYPE2 = 'COUNTS ' / label for field 2 TFORM2 = 'J ' / data format of field: 4-byte INTEGER TTYPE3 = 'QUALITY ' / label for field 3 TFORM3 = 'I ' / data format of field: 2-byte INTEGER TTYPE4 = 'GROUPING' / label for field 4 TFORM4 = 'I ' / data format of field: 2-byte INTEGER EXTNAME = 'SPECTRUM' / name of this binary table extension HDUCLASS= 'OGIP ' / format conforms to OGIP standard HDUCLAS1= 'SPECTRUM' / PHA dataset (OGIP memo OGIP-92-007) HDUVERS = '1.2.1 ' / Version of format (OGIP memo OGIP-92-007a) TELESCOP= 'XMM ' / mission/satellite name INSTRUME= 'EPN ' / instrument name DETNAM = 'UNKNOWN ' / detector name FILTER = 'Medium ' / filter name STOKESPR= 'UNKNOWN ' / Stokes parameter(s) STOKESWT= 'UNKNOWN ' / Stokes weighting CHANTYPE= 'PI ' / channel type (PHA, PI etc) DATE = '2024-03-20T11:51:55' / file creation date (YYYY-MM-DDThh:mm:ss UT) HISTORY Fake data file created by XSPEC version: 12.13.1 "fakeit" command FKSRC001= 'cutoffpl' FKRSP001= 'PN.rmf ' FKARF001= 'PN.arf ' RESPFILE= 'PN.rmf ' / associated redistrib matrix filename ANCRFILE= 'PN.arf ' / associated ancillary response filename CORRFILE= ' ' / associated correction filename CORRSCAL= 1. / correction file scaling factor BACKFILE= ' ' / associated background filename EXPOSURE= 10000. / exposure (in seconds) TLMIN1 = 0 / Lowest legal channel number TLMAX1 = 4095 / Highest legal channel number DETCHANS= 4096 / total number possible channels POISSERR= T / Pois. err assumed ? AREASCAL= 1. / area scaling factor BACKSCAL= 1. / background file scaling factor END �!�x��� ��a��$8 0�
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E F G H
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+
I J K L M N O P Q R
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S T U V W X Y
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+
Z [ \ ] ^ _ ` a b c d e f g h i j k l m n o p q r s t u
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+
v w x y z { | } ~ � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �
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jaxspec/data/instrument.py
CHANGED
|
@@ -1,6 +1,7 @@
|
|
|
1
1
|
import os
|
|
2
2
|
import numpy as np
|
|
3
3
|
import xarray as xr
|
|
4
|
+
from matplotlib import colors
|
|
4
5
|
from .ogip import DataARF, DataRMF
|
|
5
6
|
|
|
6
7
|
|
|
@@ -64,21 +65,26 @@ class Instrument(xr.Dataset):
|
|
|
64
65
|
)
|
|
65
66
|
|
|
66
67
|
@classmethod
|
|
67
|
-
def from_ogip_file(cls,
|
|
68
|
+
def from_ogip_file(cls, rmf_path: str | os.PathLike, arf_path: str | os.PathLike = None):
|
|
68
69
|
"""
|
|
69
70
|
Load the data from OGIP files.
|
|
70
71
|
|
|
71
72
|
Parameters:
|
|
72
|
-
|
|
73
|
-
|
|
73
|
+
rmf_path: The RMF file path.
|
|
74
|
+
arf_path: The ARF file path.
|
|
74
75
|
exposure: The exposure time in second.
|
|
75
76
|
grouping: The grouping matrix.
|
|
76
77
|
"""
|
|
77
78
|
|
|
78
|
-
|
|
79
|
-
rmf = DataRMF.from_file(rmf_file)
|
|
79
|
+
rmf = DataRMF.from_file(rmf_path)
|
|
80
80
|
|
|
81
|
-
|
|
81
|
+
if arf_path is not None:
|
|
82
|
+
specresp = DataARF.from_file(arf_path).specresp
|
|
83
|
+
|
|
84
|
+
else:
|
|
85
|
+
specresp = np.ones(rmf.energ_lo.shape)
|
|
86
|
+
|
|
87
|
+
return cls.from_matrix(rmf.sparse_matrix, specresp, rmf.energ_lo, rmf.energ_hi, rmf.e_min, rmf.e_max)
|
|
82
88
|
|
|
83
89
|
def plot_redistribution(self, **kwargs):
|
|
84
90
|
"""
|
|
@@ -95,9 +101,8 @@ class Instrument(xr.Dataset):
|
|
|
95
101
|
y="e_max_channel",
|
|
96
102
|
xscale="log",
|
|
97
103
|
yscale="log",
|
|
98
|
-
cmap=cmr.
|
|
99
|
-
vmin=
|
|
100
|
-
vmax=0.075,
|
|
104
|
+
cmap=cmr.ember_r,
|
|
105
|
+
norm=colors.LogNorm(vmin=1e-6, vmax=1),
|
|
101
106
|
add_labels=True,
|
|
102
107
|
**kwargs,
|
|
103
108
|
)
|
jaxspec/data/obsconf.py
CHANGED
|
@@ -1,5 +1,7 @@
|
|
|
1
1
|
import numpy as np
|
|
2
2
|
import xarray as xr
|
|
3
|
+
import sparse
|
|
4
|
+
import scipy
|
|
3
5
|
from .instrument import Instrument
|
|
4
6
|
from .observation import Observation
|
|
5
7
|
|
|
@@ -51,31 +53,27 @@ class ObsConfiguration(xr.Dataset):
|
|
|
51
53
|
|
|
52
54
|
out_energies = np.stack(
|
|
53
55
|
(
|
|
54
|
-
np.asarray(self.coords["e_min_folded"], dtype=np.float64),
|
|
55
|
-
np.asarray(self.coords["e_max_folded"], dtype=np.float64),
|
|
56
|
+
np.asarray(self.coords["e_min_folded"].data, dtype=np.float64),
|
|
57
|
+
np.asarray(self.coords["e_max_folded"].data, dtype=np.float64),
|
|
56
58
|
)
|
|
57
59
|
)
|
|
58
60
|
|
|
59
61
|
return out_energies
|
|
60
62
|
|
|
61
63
|
@classmethod
|
|
62
|
-
def from_pha_file(
|
|
63
|
-
|
|
64
|
-
|
|
65
|
-
|
|
66
|
-
|
|
67
|
-
|
|
68
|
-
|
|
69
|
-
|
|
70
|
-
|
|
71
|
-
|
|
72
|
-
|
|
73
|
-
|
|
74
|
-
|
|
75
|
-
background=bkg.counts if bkg is not None else None,
|
|
76
|
-
backratio=pha.backscal / bkg.backscal if bkg is not None else 1.0,
|
|
77
|
-
attributes=metadata,
|
|
78
|
-
)
|
|
64
|
+
def from_pha_file(
|
|
65
|
+
cls, pha_path, rmf_path=None, arf_path=None, bkg_path=None, low_energy: float = 1e-20, high_energy: float = 1e20
|
|
66
|
+
):
|
|
67
|
+
from .util import data_path_finder
|
|
68
|
+
|
|
69
|
+
arf_path_default, rmf_path_default, bkg_path_default = data_path_finder(pha_path)
|
|
70
|
+
|
|
71
|
+
arf_path = arf_path_default if arf_path is None else arf_path
|
|
72
|
+
rmf_path = rmf_path_default if rmf_path is None else rmf_path
|
|
73
|
+
bkg_path = bkg_path_default if bkg_path is None else bkg_path
|
|
74
|
+
|
|
75
|
+
instrument = Instrument.from_ogip_file(rmf_path, arf_path=arf_path)
|
|
76
|
+
observation = Observation.from_pha_file(pha_path, bkg_path=bkg_path)
|
|
79
77
|
|
|
80
78
|
return cls.from_instrument(instrument, observation, low_energy=low_energy, high_energy=high_energy)
|
|
81
79
|
|
|
@@ -83,48 +81,108 @@ class ObsConfiguration(xr.Dataset):
|
|
|
83
81
|
def from_instrument(
|
|
84
82
|
cls, instrument: Instrument, observation: Observation, low_energy: float = 1e-20, high_energy: float = 1e20
|
|
85
83
|
):
|
|
86
|
-
|
|
84
|
+
# First we unpack all the xarray data to classical np array for efficiency
|
|
85
|
+
# We also exclude the bins that are flagged with bad quality on the instrument
|
|
86
|
+
quality_filter = observation.quality.data == 0
|
|
87
|
+
grouping = scipy.sparse.csr_array(observation.grouping.data.to_scipy_sparse()) * quality_filter
|
|
88
|
+
e_min_channel = instrument.coords["e_min_channel"].data
|
|
89
|
+
e_max_channel = instrument.coords["e_max_channel"].data
|
|
90
|
+
e_min_unfolded = instrument.coords["e_min_unfolded"].data
|
|
91
|
+
e_max_unfolded = instrument.coords["e_max_unfolded"].data
|
|
92
|
+
redistribution = scipy.sparse.csr_array(instrument.redistribution.data.to_scipy_sparse())
|
|
93
|
+
area = instrument.area.data
|
|
94
|
+
exposure = observation.exposure.data
|
|
87
95
|
|
|
88
96
|
# Computing the lower and upper energies of the bins after grouping
|
|
89
97
|
# This is just a trick to compute it without 10 lines of code
|
|
90
|
-
|
|
91
|
-
|
|
92
|
-
)
|
|
93
|
-
e_max =
|
|
94
|
-
skipna=True, dim="instrument_channel"
|
|
95
|
-
)
|
|
98
|
+
grouping_nan = observation.grouping.data * quality_filter
|
|
99
|
+
grouping_nan.fill_value = np.nan
|
|
100
|
+
e_min = sparse.nanmin(grouping_nan * e_min_channel, axis=1).todense()
|
|
101
|
+
e_max = sparse.nanmax(grouping_nan * e_max_channel, axis=1).todense()
|
|
96
102
|
|
|
97
|
-
|
|
98
|
-
transfer_matrix =
|
|
103
|
+
# Compute the transfer matrix
|
|
104
|
+
transfer_matrix = grouping @ (redistribution * area * exposure)
|
|
99
105
|
|
|
100
|
-
# Exclude the bins
|
|
101
|
-
quality_filter = observation.quality == 0
|
|
102
|
-
grouping[:, ~quality_filter] = 0
|
|
106
|
+
# Exclude bins out of the considered energy range, and bins without contribution from the RMF
|
|
103
107
|
|
|
104
|
-
row_idx =
|
|
105
|
-
|
|
106
|
-
row_idx *= grouping.sum(dim="instrument_channel") > 0 # Exclude channels with no contribution
|
|
108
|
+
row_idx = (e_min > low_energy) & (e_max < high_energy) & (grouping.sum(axis=1) > 0)
|
|
109
|
+
col_idx = (e_min_unfolded > 0) & (redistribution.sum(axis=0) > 0)
|
|
107
110
|
|
|
108
|
-
|
|
109
|
-
|
|
110
|
-
|
|
111
|
-
|
|
112
|
-
|
|
113
|
-
|
|
111
|
+
# Apply this reduction to all the relevant arrays
|
|
112
|
+
transfer_matrix = sparse.COO.from_scipy_sparse(transfer_matrix[row_idx][:, col_idx])
|
|
113
|
+
folded_counts = observation.folded_counts.data[row_idx]
|
|
114
|
+
folded_backratio = observation.folded_backratio.data[row_idx]
|
|
115
|
+
area = instrument.area.data[col_idx]
|
|
116
|
+
e_min_folded = e_min[row_idx]
|
|
117
|
+
e_max_folded = e_max[row_idx]
|
|
118
|
+
e_min_unfolded = e_min_unfolded[col_idx]
|
|
119
|
+
e_max_unfolded = e_max_unfolded[col_idx]
|
|
114
120
|
|
|
115
121
|
if observation.folded_background is not None:
|
|
116
|
-
folded_background = observation.folded_background.
|
|
117
|
-
|
|
122
|
+
folded_background = observation.folded_background.data[row_idx]
|
|
118
123
|
else:
|
|
119
|
-
folded_background =
|
|
124
|
+
folded_background = np.zeros_like(folded_counts)
|
|
125
|
+
|
|
126
|
+
data_dict = {
|
|
127
|
+
"transfer_matrix": (
|
|
128
|
+
["folded_channel", "unfolded_channel"],
|
|
129
|
+
transfer_matrix,
|
|
130
|
+
{
|
|
131
|
+
"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."
|
|
132
|
+
},
|
|
133
|
+
),
|
|
134
|
+
"area": (
|
|
135
|
+
["unfolded_channel"],
|
|
136
|
+
area,
|
|
137
|
+
{"description": "Effective area with the same restrictions as the transfer matrix.", "units": "cm^2"},
|
|
138
|
+
),
|
|
139
|
+
"exposure": ([], exposure, {"description": "Total exposure", "unit": "s"}),
|
|
140
|
+
"folded_counts": (
|
|
141
|
+
["folded_channel"],
|
|
142
|
+
folded_counts,
|
|
143
|
+
{
|
|
144
|
+
"description": "Folded counts after grouping, with the same restrictions as the transfer matrix.",
|
|
145
|
+
"unit": "photons",
|
|
146
|
+
},
|
|
147
|
+
),
|
|
148
|
+
"folded_backratio": (
|
|
149
|
+
["folded_channel"],
|
|
150
|
+
folded_backratio,
|
|
151
|
+
{"description": "Background scaling after grouping, with the same restrictions as the transfer matrix."},
|
|
152
|
+
),
|
|
153
|
+
"folded_background": (
|
|
154
|
+
["folded_channel"],
|
|
155
|
+
folded_background,
|
|
156
|
+
{
|
|
157
|
+
"description": "Folded background counts after grouping, with the same restrictions as the transfer matrix.",
|
|
158
|
+
"unit": "photons",
|
|
159
|
+
},
|
|
160
|
+
),
|
|
161
|
+
}
|
|
120
162
|
|
|
121
163
|
return cls(
|
|
122
|
-
|
|
123
|
-
|
|
124
|
-
"
|
|
125
|
-
|
|
126
|
-
|
|
127
|
-
|
|
128
|
-
|
|
129
|
-
|
|
164
|
+
data_dict,
|
|
165
|
+
coords={
|
|
166
|
+
"e_min_folded": (
|
|
167
|
+
["folded_channel"],
|
|
168
|
+
e_min_folded,
|
|
169
|
+
{"description": "Low energy of folded channel"},
|
|
170
|
+
),
|
|
171
|
+
"e_max_folded": (
|
|
172
|
+
["folded_channel"],
|
|
173
|
+
e_max_folded,
|
|
174
|
+
{"description": "High energy of folded channel"},
|
|
175
|
+
),
|
|
176
|
+
"e_min_unfolded": (
|
|
177
|
+
["unfolded_channel"],
|
|
178
|
+
e_min_unfolded,
|
|
179
|
+
{"description": "Low energy of unfolded channel"},
|
|
180
|
+
),
|
|
181
|
+
"e_max_unfolded": (
|
|
182
|
+
["unfolded_channel"],
|
|
183
|
+
e_max_unfolded,
|
|
184
|
+
{"description": "High energy of unfolded channel"},
|
|
185
|
+
),
|
|
186
|
+
},
|
|
187
|
+
attrs=observation.attrs | instrument.attrs,
|
|
130
188
|
)
|