.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/Tutorial_notebook.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title .. _sphx_glr_auto_examples_Tutorial_notebook.py: Basic pulsar analysis using Fermi-LAT data ========================================== .. GENERATED FROM PYTHON SOURCE LINES 6-14 .. code-block:: Python :lineno-start: 7 from ptiming_ana.phaseogram import PulsarAnalysis from astropy.io import fits import numpy as np import matplotlib.pyplot as plt # sphinx_gallery_multi_image = "single" .. GENERATED FROM PYTHON SOURCE LINES 15-17 Create the PulsarAnalysis object and settings --------------------------------------------- .. GENERATED FROM PYTHON SOURCE LINES 17-21 .. code-block:: Python :lineno-start: 18 h = PulsarAnalysis() h.set_config('./example_data/config_tutorial.yaml') .. GENERATED FROM PYTHON SOURCE LINES 22-24 Alternatively we can set the parameters directly ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. GENERATED FROM PYTHON SOURCE LINES 24-42 .. code-block:: Python :lineno-start: 25 h = PulsarAnalysis() h.setBackgroundLimits([0.52,0.87]) h.setPeaklimits( P1_limits=[0,0.026, 0.983, 1], P2_limits=[0.377, 0.422], P3_limits=None ) h.setBinning(50, xmin=0, xmax=1) h.setTimeInterval(tint=3600*24) h.setFittingParams(model='dgaussian', binned=True) h.setEnergybinning( np.geomspace(0.1/1e3, 1/1e3, 3), do_diff=True, do_integral=False ) # in TeV .. GENERATED FROM PYTHON SOURCE LINES 43-47 Extracting phases, times and energies from file and give them to the object --------------------------------------------------------------------------- For Fermi data there is a class to read these lists and use them in the main object. .. GENERATED FROM PYTHON SOURCE LINES 47-51 .. code-block:: Python :lineno-start: 48 h.setFermiInputFile('./example_data/merged2_pulsar.fits') .. GENERATED FROM PYTHON SOURCE LINES 52-54 But in general we can read our file (FITS, DL2, DL3…) and extract phases, times and energies as lists and read them as follows: .. GENERATED FROM PYTHON SOURCE LINES 54-67 .. code-block:: Python :lineno-start: 55 f=fits.open('./example_data/merged2_pulsar.fits') fits_table=f[1].data times=np.sort(fits_table['BARYCENTRIC_TIME'].byteswap().newbyteorder()) phases=fits_table['PULSE_PHASE'].byteswap().newbyteorder() energies=fits_table['ENERGY'].byteswap().newbyteorder() h.setListsInput(phases, times, energies/1e6, tel='fermi', energy_units='TeV') h.get_results = False .. GENERATED FROM PYTHON SOURCE LINES 68-70 Run the code ------------ .. GENERATED FROM PYTHON SOURCE LINES 70-74 .. code-block:: Python :lineno-start: 71 h.run() .. rst-class:: sphx-glr-script-out .. code-block:: none /home/runner/work/PulsarTimingAnalysis/PulsarTimingAnalysis/src/ptiming_ana/phaseogram/phase_regions.py:226: RuntimeWarning: divide by zero encountered in scalar divide self.sign_ratio = self.sign / np.sqrt(tobs) .. GENERATED FROM PYTHON SOURCE LINES 75-80 Show the results ---------------- Overall results ^^^^^^^^^^^^^^^ .. GENERATED FROM PYTHON SOURCE LINES 80-87 .. code-block:: Python :lineno-start: 81 phaseogram=h.draw_phaseogram( phase_limits=[0, 2], colorhist='xkcd:baby blue' ) plt.tight_layout() .. image-sg:: /auto_examples/images/sphx_glr_Tutorial_notebook_001.png :alt: Tutorial notebook :srcset: /auto_examples/images/sphx_glr_Tutorial_notebook_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 88-92 .. code-block:: Python :lineno-start: 89 results=h.show_Presults() .. rst-class:: sphx-glr-script-out .. code-block:: none RESULTS FOR THE PEAK STATISTICS: P1 P2 P1+P2 Significance 108.591359 58.006568 110.165719 Nex 5959.237143 2677.271429 8636.508571 Nex_error 84.220286 62.208240 105.936656 Number 6969.000000 3734.000000 10703.000000 noff 1009.762857 1056.728571 2066.491429 sign_t_ratio 451.841088 241.361292 458.391889 s/n ratio 187.534413 82.358927 189.985915 P1/P2 ratio=2.23+/-0.06 RESULTS FOR THE PERIODICITY SEARCH: Chi_square_test Zn_test H_test Statistic 2.697743e+04 2.599217e+04 2.810141e+04 p-value 0.000000e+00 0.000000e+00 0.000000e+00 Number of $\sigma$ inf inf inf .. GENERATED FROM PYTHON SOURCE LINES 93-95 Result of the fitting ^^^^^^^^^^^^^^^^^^^^^ .. GENERATED FROM PYTHON SOURCE LINES 97-99 .. code-block:: Python :lineno-start: 97 h.fit_model .. rst-class:: sphx-glr-script-out .. code-block:: none 'dgaussian' .. GENERATED FROM PYTHON SOURCE LINES 100-102 .. code-block:: Python :lineno-start: 100 fit_result = h.show_fit_results() .. rst-class:: sphx-glr-script-out .. code-block:: none Name Value Error 0 mu 0.992423 0.001566 1 sigma 0.026305 0.001470 2 mu_2 1.376341 0.004402 3 sigma_2 0.050986 0.004192 4 A 466.437500 0.000000 5 B 200.237289 10.903034 6 C 145.133366 11.041673 .. GENERATED FROM PYTHON SOURCE LINES 103-111 .. code-block:: Python :lineno-start: 103 phaseogram = h.draw_phaseogram( phase_limits=[0, 2], colorhist='xkcd:baby blue', fit=True ) plt.tight_layout() .. image-sg:: /auto_examples/images/sphx_glr_Tutorial_notebook_002.png :alt: Tutorial notebook :srcset: /auto_examples/images/sphx_glr_Tutorial_notebook_002.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 112-114 Results vs Time ^^^^^^^^^^^^^^^ .. GENERATED FROM PYTHON SOURCE LINES 114-118 .. code-block:: Python :lineno-start: 115 TimeEv = h.show_timeEvolution() .. rst-class:: sphx-glr-horizontal * .. image-sg:: /auto_examples/images/sphx_glr_Tutorial_notebook_003.png :alt: P1, P2, P1+P2 :srcset: /auto_examples/images/sphx_glr_Tutorial_notebook_003.png :class: sphx-glr-single-img * .. image-sg:: /auto_examples/images/sphx_glr_Tutorial_notebook_004.png :alt: P1, P2, P1+P2 :srcset: /auto_examples/images/sphx_glr_Tutorial_notebook_004.png :class: sphx-glr-single-img * .. image-sg:: /auto_examples/images/sphx_glr_Tutorial_notebook_005.png :alt: H test, Z test, Chi square test :srcset: /auto_examples/images/sphx_glr_Tutorial_notebook_005.png :class: sphx-glr-single-img * .. image-sg:: /auto_examples/images/sphx_glr_Tutorial_notebook_006.png :alt: Tutorial notebook :srcset: /auto_examples/images/sphx_glr_Tutorial_notebook_006.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 119-121 The periodicity tests are not available since the signal is too strong (p_value too low to extrapolate a significance). .. GENERATED FROM PYTHON SOURCE LINES 124-126 Results vs Energy ^^^^^^^^^^^^^^^^^ .. GENERATED FROM PYTHON SOURCE LINES 126-129 .. code-block:: Python :lineno-start: 127 h.show_lcVsEnergy() .. rst-class:: sphx-glr-horizontal * .. image-sg:: /auto_examples/images/sphx_glr_Tutorial_notebook_007.png :alt: Tutorial notebook :srcset: /auto_examples/images/sphx_glr_Tutorial_notebook_007.png :class: sphx-glr-single-img * .. image-sg:: /auto_examples/images/sphx_glr_Tutorial_notebook_008.png :alt: Tutorial notebook :srcset: /auto_examples/images/sphx_glr_Tutorial_notebook_008.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none [
,
] .. GENERATED FROM PYTHON SOURCE LINES 130-132 .. code-block:: Python :lineno-start: 130 energy_lc=h.show_all_lc(ylimits=None) .. image-sg:: /auto_examples/images/sphx_glr_Tutorial_notebook_009.png :alt: Tutorial notebook :srcset: /auto_examples/images/sphx_glr_Tutorial_notebook_009.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 133-135 .. code-block:: Python :lineno-start: 133 energy_results=h.show_EnergyPresults() .. rst-class:: sphx-glr-script-out .. code-block:: none Energies(GeV):0-0 RESULTS FOR THE PEAK STATISTICS: P1 P2 P1+P2 Significance 64.283110 32.326941 64.254439 Nex 2329.814286 994.642857 3324.457143 Nex_error 53.751332 39.787330 67.825823 Number 2828.000000 1516.000000 4344.000000 noff 498.185714 521.357143 1019.542857 sign_t_ratio 621.192620 312.387765 620.915556 s/n ratio 104.382013 43.561167 104.116125 P1/P2 ratio=2.34+/-0.11 RESULTS FOR THE PERIODICITY SEARCH: Chi_square_test Zn_test H_test Statistic 9894.812087 9539.380325 1.016913e+04 p-value 0.000000 0.000000 0.000000e+00 Number of $\sigma$ inf inf inf ------------------------------------------------------------------- Energies(GeV):0-1 RESULTS FOR THE PEAK STATISTICS: P1 P2 P1+P2 Significance 72.157101 39.603539 73.624074 Nex 2428.965714 1109.057143 3538.022857 Nex_error 53.037924 38.897574 66.437898 Number 2771.000000 1467.000000 4238.000000 noff 342.034286 357.942857 699.977143 sign_t_ratio 753.379730 413.493661 768.696142 s/n ratio 131.336840 58.620170 133.726878 P1/P2 ratio=2.19+/-0.09 RESULTS FOR THE PERIODICITY SEARCH: Chi_square_test Zn_test H_test Statistic 1.236040e+04 1.193614e+04 1.290660e+04 p-value 0.000000e+00 0.000000e+00 0.000000e+00 Number of $\sigma$ inf inf inf ------------------------------------------------------------------- .. GENERATED FROM PYTHON SOURCE LINES 136-139 .. code-block:: Python :lineno-start: 136 energy_plots=h.show_EnergyAna() .. image-sg:: /auto_examples/images/sphx_glr_Tutorial_notebook_010.png :alt: P1/P2 vs Energy :srcset: /auto_examples/images/sphx_glr_Tutorial_notebook_010.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 140-142 Fit vs Energy ^^^^^^^^^^^^^ .. GENERATED FROM PYTHON SOURCE LINES 142-146 .. code-block:: Python :lineno-start: 143 mean_energy_plot=h.show_meanVsEnergy() h.show_EnergyFitresults() .. image-sg:: /auto_examples/images/sphx_glr_Tutorial_notebook_011.png :alt: P1 mean phase, P2 mean phase :srcset: /auto_examples/images/sphx_glr_Tutorial_notebook_011.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none Energies(GeV):0.10-0.32 Name Value Error 0 mu 0.990064 0.001285 1 sigma 0.025658 0.001199 2 mu_2 1.384944 0.003914 3 sigma_2 0.048394 0.003781 4 A 231.375000 0.000000 5 B 80.804887 3.667207 6 C 51.361385 3.643919 ------------------------------------------------------------------- Energies(GeV):0.32-1.00 Name Value Error 0 mu 0.991737 0.001711 1 sigma 0.026729 0.001598 2 mu_2 1.376496 0.004604 3 sigma_2 0.050032 0.004348 4 A 156.375000 0.000000 5 B 83.366327 4.920670 6 C 58.966419 4.808841 ------------------------------------------------------------------- [ Name Value Error 0 mu 0.990064 0.001285 1 sigma 0.025658 0.001199 2 mu_2 1.384944 0.003914 3 sigma_2 0.048394 0.003781 4 A 231.375000 0.000000 5 B 80.804887 3.667207 6 C 51.361385 3.643919, Name Value Error 0 mu 0.991737 0.001711 1 sigma 0.026729 0.001598 2 mu_2 1.376496 0.004604 3 sigma_2 0.050032 0.004348 4 A 156.375000 0.000000 5 B 83.366327 4.920670 6 C 58.966419 4.808841] .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 18.994 seconds) .. _sphx_glr_download_auto_examples_Tutorial_notebook.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: Tutorial_notebook.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: Tutorial_notebook.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: Tutorial_notebook.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_