diff --git a/anesthetic/read/chain.py b/anesthetic/read/chain.py index 5dc55b5f..e5530012 100644 --- a/anesthetic/read/chain.py +++ b/anesthetic/read/chain.py @@ -5,6 +5,7 @@ from anesthetic.read.multinest import read_multinest from anesthetic.read.ultranest import read_ultranest from anesthetic.read.nestedfit import read_nestedfit +from anesthetic.read.dnest4 import read_dnest4 from anesthetic.read.csv import read_csv @@ -19,6 +20,7 @@ def read_chains(root, *args, **kwargs): * `Nested_fit `_, * `CosmoMC `_, * `Cobaya `_, + * `DNest4 `_, * anything `GetDist `_ compatible, * files produced using ``DataFrame.to_csv()`` from anesthetic. @@ -53,7 +55,7 @@ def read_chains(root, *args, **kwargs): ) errors = [] readers = [ - read_polychord, read_multinest, read_cobaya, read_ultranest, + read_polychord, read_multinest, read_cobaya, read_ultranest, read_dnest4, read_nestedfit, read_getdist, read_csv ] for read in readers: diff --git a/anesthetic/read/dnest4.py b/anesthetic/read/dnest4.py new file mode 100644 index 00000000..79c24eb2 --- /dev/null +++ b/anesthetic/read/dnest4.py @@ -0,0 +1,45 @@ +"""Read NestedSamples from dnest4 output files""" +import os +import numpy as np +from anesthetic.samples import MCMCSamples + + +def heuristically_determine_columns(n_params): + """ + heuristically determines column names. If none are given, parameters are named x_i + """ + return [f'x{i}' for i in range(n_params)] + + +def read_dnest4(root, + *args, + **kwargs): + """Read dnest4 output files. + + Parameters + ---------- + levels_file default output name from dnest4 + sample_file default output name from dnest4 + sample_info_file default output name from dnest4 + root : str + root specify the directory only, no specific roots, + The files read files are levels_file, sample_file and sample_info. + """ + levels_file = 'levels.txt' + sample_file = 'sample.txt' + sample_info_file = 'sample_info.txt' + weights_file = 'weights.txt' + + levels = np.loadtxt(os.path.join(root, levels_file), dtype=float, delimiter=' ', comments='#') + samples = np.genfromtxt(os.path.join(root, sample_file), dtype=float, delimiter=' ', comments='#', skip_header=1) + sample_info = np.loadtxt(os.path.join(root, sample_info_file), dtype=float, delimiter=' ', comments='#') + weights = np.loadtxt(os.path.join(root, weights_file), dtype=float, delimiter=' ', comments='#') + n_params = samples.shape[1] + columns = heuristically_determine_columns(n_params) + + return MCMCSamples(data=samples, + columns=columns, + weights=weights, + logL=sample_info[:, 1], + labels=columns, *args, + **kwargs) diff --git a/docs/source/anesthetic.read.rst b/docs/source/anesthetic.read.rst index 518686da..3624f7b2 100644 --- a/docs/source/anesthetic.read.rst +++ b/docs/source/anesthetic.read.rst @@ -24,6 +24,15 @@ anesthetic.read.cobaya module :undoc-members: :show-inheritance: +anesthetic.read.dnest4 module +----------------------------- + +.. automodule:: anesthetic.read.dnest4 + :members: + :undoc-members: + :show-inheritance: + + anesthetic.read.getdist module ------------------------------ diff --git a/tests/example_data/dnest4/README.md b/tests/example_data/dnest4/README.md new file mode 100644 index 00000000..98e16ca9 --- /dev/null +++ b/tests/example_data/dnest4/README.md @@ -0,0 +1,2 @@ +these results are generated with https://github.com/eggplantbren/DNest4/tree/master/code/Examples/Rosenbrock +after hard-coding the number of dimensions to 3 and then postprocessing with showresults.p \ No newline at end of file diff --git a/tests/example_data/dnest4/levels.txt b/tests/example_data/dnest4/levels.txt new file mode 100644 index 00000000..4866c179 --- /dev/null +++ b/tests/example_data/dnest4/levels.txt @@ -0,0 +1,28 @@ +# log_X, log_likelihood, tiebreaker, accepts, tries, exceeds, visits +0 -1.79769313486e+308 0 34004 34004 11180 29004 +-0.969533002366 -354500.27465 0.184673637139 23998 31610 14123 39627 +-1.992093494 -51190.6265937 0.102641250532 19348 31083 15920 42045 +-2.97105585853 -11243.6222298 0.10325874618 16150 32920 16626 45679 +-3.97897207133 -3228.1447332 0.0925587904123 13328 34880 17901 48344 +-4.97405916511 -1131.35058306 0.852351592573 11151 35275 18846 50013 +-5.95575811056 -427.258976564 0.701862363078 10072 37653 19414 53338 +-6.96396646863 -162.646813112 0.68451125986 9137 39867 21029 56120 +-7.94957402697 -64.8403524809 0.613021892441 8647 43702 20432 61568 +-9.03067901421 -26.3056692322 0.547511916734 7828 44506 24788 61778 +-9.96095625455 -13.8309395233 0.334151142837 8156 49730 25984 71356 +-10.9692987447 -7.50274694105 0.126042530841 7817 52371 33317 75193 +-11.8132222594 -4.65369550562 0.853768724211 8272 60078 29479 90233 +-12.9133196991 -2.48807948192 0.61849557121 7804 61733 25002 88050 +-14.128256649 -1.16046735761 0.99591232612 7330 60886 26282 82727 +-15.2498883059 -0.562856436041 0.130358708691 7127 64485 34548 87606 +-16.1907059421 -0.325470154533 0.755185646839 7784 74101 16481 105486 +-17.8844715844 -0.13177445907 0.64628464408 5675 57277 8900 70597 +-19.6545796919 -0.0423777562198 0.393064674565 3095 33798 8676 39537 +-20.9945860552 -0.0201426854991 0.336737451471 2296 26703 9618 32218 +-22.1297830757 -0.0109547712599 0.186364854844 2101 23981 9711 30437 +-23.2211859552 -0.00633328574242 0.761743194641 1908 22712 7536 29262 +-24.4377625857 -0.00321219414708 0.379439831193 1392 17613 6798 21988 +-25.5351949699 -0.00173432053459 0.0956554015875 1166 15570 3206 19207 +-26.8913310896 -0.000907997439061 0.454404674518 667 8955 1351 9000 +-28.133055436 -0.000638533356738 0.942850144857 290 3915 142 2105 +-29.2339238102 -0.000420761812001 0.219330831487 37 592 0 0 diff --git a/tests/example_data/dnest4/log_prior_weights.txt b/tests/example_data/dnest4/log_prior_weights.txt new file mode 100644 index 00000000..45284a84 --- /dev/null +++ b/tests/example_data/dnest4/log_prior_weights.txt @@ -0,0 +1,1000 @@ +-6.008277038498961886e+00 +-3.616436140836704727e+00 +-4.810835391228776459e+00 +-3.616436140836706059e+00 +-3.616436140836702062e+00 +-4.810835391228773794e+00 +-4.810835391228773794e+00 +-4.810835391228776459e+00 +-4.810835391228777347e+00 +-4.810835391228772018e+00 +-3.616436140836704283e+00 +-6.787889186521522511e+00 +-6.787889186521517182e+00 +-6.008277038498962774e+00 +-3.616436140836703839e+00 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pytables_mark_xfail, h5py_mark_xfail, getdist_mark_skip @@ -331,3 +332,20 @@ def test_read_csv(tmp_path, root): samples_ = read_chains(filename) samples_.root = samples.root assert_frame_equal(samples, samples_) + + +def test_read_dnest(): + np.random.seed(3) + ns = read_dnest4('./tests/example_data/dnest4') + params = ['x0', 'x1', 'x2', 'logL'] + assert_array_equal(ns.drop_labels().columns, params) + labels = ['x0', + 'x1', + 'x2', + r'$\ln\mathcal{L}$' + ] + assert_array_equal(ns.get_labels(), labels) + + assert isinstance(ns, MCMCSamples) + ns.plot_2d(['x0', 'x1', 'x2']) + ns.plot_1d(['x0', 'x1', 'x2'])