Merge branch 'maite.mateu-lucena/bilby_pipe-imrphenomx-nestcheck' into 'master'

Add waveform-arguments-dict and numerical-relativity file

See merge request lscsoft/bilby_pipe!361

bilby_pipe/data_analysis.py

@@ -82,6 +82,8 @@ class DataAnalysisInput(Input):
         self.pn_phase_order = args.pn_phase_order
         self.pn_amplitude_order = args.pn_amplitude_order
         self.mode_array = args.mode_array
+        self.waveform_arguments_dict = args.waveform_arguments_dict
+        self.numerical_relativity_file = args.numerical_relativity_file
         self.frequency_domain_source_model = args.frequency_domain_source_model
         self.likelihood_type = args.likelihood_type
         self.reference_frame = args.reference_frame

bilby_pipe/data_generation.py

@@ -134,6 +134,8 @@ class DataGenerationInput(Input):
         self.pn_phase_order = args.pn_phase_order
         self.pn_amplitude_order = args.pn_amplitude_order
         self.mode_array = args.mode_array
+        self.waveform_arguments_dict = args.waveform_arguments_dict
+        self.numerical_relativity_file = args.numerical_relativity_file
         self.injection_waveform_approximant = args.injection_waveform_approximant
         self.frequency_domain_source_model = args.frequency_domain_source_model
         self.likelihood_type = args.likelihood_type

bilby_pipe/input.py

@@ -24,6 +24,7 @@ from .utils import (
     get_colored_string,
     get_time_prior,
     logger,
+    pretty_print_dictionary,
 )
 
 
@@ -350,7 +351,7 @@ class Input(object):
             raise BilbyPipeError(f"mode_array {self._mode_array} is invalid")
 
     def get_default_waveform_arguments(self):
-        return dict(
+        wfa = dict(
             reference_frequency=self.reference_frequency,
             waveform_approximant=self.waveform_approximant,
             minimum_frequency=self.minimum_frequency,
@@ -363,6 +364,12 @@ class Input(object):
             mode_array=self.mode_array,
         )
 
+        if self.waveform_arguments_dict is not None:
+            wfa.update(convert_string_to_dict(self.waveform_arguments_dict))
+
+        logger.debug(f"Default waveform_arguments: {pretty_print_dictionary(wfa)}")
+        return wfa
+
     def get_injection_waveform_arguments(self):
         """Get the dict of the waveform arguments needed for creating injections.
 
@@ -374,6 +381,7 @@ class Input(object):
             self.injection_waveform_approximant = self.waveform_approximant
         waveform_arguments = self.get_default_waveform_arguments()
         waveform_arguments["waveform_approximant"] = self.injection_waveform_approximant
+        waveform_arguments["numerical_relativity_file"] = self.numerical_relativity_file
         return waveform_arguments
 
     @property
@@ -1299,6 +1307,5 @@ class Input(object):
             raise BilbyPipeError(
                 get_colored_string(f"Unable to parse prior, exception raised {e}")
             )
-        prior_as_str = {key: str(val) for key, val in prior.items()}
-        pp = json.dumps(prior_as_str, indent=2)
+        pp = pretty_print_dictionary(prior)
         logger.info(f"Input prior = {pp}")

bilby_pipe/parser.py

@@ -853,7 +853,24 @@ def create_parser(top_level=True):
         help="Post-Newtonian order to use for the amplitude. Also "
         "used to determine the waveform starting frequency.",
     )
-
+    waveform_parser.add(
+        "--numerical-relativity-file",
+        default=None,
+        type=nonestr,
+        help=(
+            "Path to a h5 numerical relativity file to inject, see"
+            "https://git.ligo.org/waveforms/lvcnr-lfs for examples"
+        ),
+    )
+    waveform_parser.add(
+        "--waveform-arguments-dict",
+        default=None,
+        type=nonestr,
+        help=(
+            "A dictionary of arbitrary additional waveform-arguments to pass"
+            "  to the bilby waveform generator's `waveform_arguments`"
+        ),
+    )
     waveform_parser.add(
         "--mode-array",
         default=None,
@@ -862,7 +879,6 @@ def create_parser(top_level=True):
         help="Array of modes to use for the waveform. Should be "
         "a list of lists, eg. [[2,2], [2,-2]]",
     )
-
     waveform_parser.add(
         "--frequency-domain-source-model",
         default="lal_binary_black_hole",

bilby_pipe/utils.py

@@ -2,6 +2,7 @@
 A set of generic utilities used in bilby_pipe
 """
 import ast
+import json
 import logging
 import math
 import os
@@ -300,7 +301,7 @@ def setup_logger(outdir=None, label=None, log_level="INFO"):
         in https://docs.python.org/2/library/logging.html#logging-levels
     """
 
-    if "-v" in sys.argv:
+    if "-v" in sys.argv or "--verbose" in sys.argv:
         log_level = "DEBUG"
 
     if isinstance(log_level, str):
@@ -709,5 +710,23 @@ def check_if_represents_int(s):
         return False
 
 
+def pretty_print_dictionary(dictionary):
+    """Convert an input dictionary to a pretty-printed string
+
+    Parameters
+    ----------
+    dictionary: dict
+        Input dictionary
+
+    Returns
+    -------
+    pp: str
+        The dictionary pretty-printed as a string
+
+    """
+    dict_as_str = {key: str(val) for key, val in dictionary.items()}
+    return json.dumps(dict_as_str, indent=2)
+
+
 setup_logger()
 logger = logging.getLogger("bilby_pipe")

tests/input_test.py

@@ -235,6 +235,7 @@ class TestInput(unittest.TestCase):
         inputs.pn_phase_order = -1
         inputs.pn_amplitude_order = 0
         inputs.mode_array = None
+        inputs.waveform_arguments_dict = None
         inputs.catch_waveform_errors = False
         wfa = inputs.get_default_waveform_arguments()
         self.assertEqual(wfa["reference_frequency"], 20)
@@ -249,6 +250,39 @@ class TestInput(unittest.TestCase):
         self.assertFalse(wfa["catch_waveform_errors"])
         self.assertEqual(len(wfa), 10)
 
+    def test_added_waveform_arguments(self):
+        inputs = bilby_pipe.main.Input()
+        inputs.detectors = ["H1"]
+        inputs.reference_frequency = 20
+        inputs.minimum_frequency = 20
+        inputs.maximum_frequency = 1024
+        inputs.waveform_approximant = "IMRPhenomPv2"
+        inputs.pn_spin_order = -1
+        inputs.pn_tidal_order = -1
+        inputs.pn_phase_order = -1
+        inputs.pn_amplitude_order = 0
+        inputs.mode_array = None
+        inputs.waveform_arguments_dict = "{a: 10, b=test, c=[1, 2]}"
+        inputs.catch_waveform_errors = False
+        wfa = inputs.get_default_waveform_arguments()
+        self.assertEqual(wfa["reference_frequency"], 20)
+        self.assertEqual(wfa["minimum_frequency"], 20)
+        self.assertEqual(wfa["maximum_frequency"], 1024)
+        self.assertEqual(wfa["waveform_approximant"], "IMRPhenomPv2")
+        self.assertEqual(wfa["pn_spin_order"], -1)
+        self.assertEqual(wfa["pn_tidal_order"], -1)
+        self.assertEqual(wfa["pn_phase_order"], -1)
+        self.assertEqual(wfa["pn_amplitude_order"], 0)
+        self.assertIsNone(wfa["mode_array"])
+        self.assertFalse(wfa["catch_waveform_errors"])
+
+        # Check of added arguments
+        self.assertEqual(wfa["a"], 10)
+        self.assertEqual(wfa["b"], "test")
+        self.assertEqual(wfa["c"], ["1", "2"])
+
+        self.assertEqual(len(wfa), 13)
+
     def test_mode_array(self):
         inputs = bilby_pipe.main.Input()
         inputs.detectors = ["H1"]
@@ -261,6 +295,14 @@ class TestInput(unittest.TestCase):
         inputs.pn_tidal_order = -1
         inputs.pn_phase_order = -1
         inputs.pn_amplitude_order = 0
+        inputs.phenomXPHMTwistPhenomHM = None
+        inputs.phenomXPFinalSpinMod = None
+        inputs.phenomXPConvention = None
+        inputs.phenomXPrecVersion = None
+        inputs.phenomXPHMMband = None
+        inputs.phenomXHMMband = None
+        inputs.numerical_relativity_file = None
+        inputs.waveform_arguments_dict = None
 
         inputs.mode_array = "[[2, 2], [2, -2]]"
         wfa = inputs.get_default_waveform_arguments()
@@ -287,8 +329,10 @@ class TestInput(unittest.TestCase):
         inputs.pn_tidal_order = -1
         inputs.pn_phase_order = -1
         inputs.pn_amplitude_order = 0
+        inputs.numerical_relativity_file = None
         inputs.catch_waveform_errors = False
         inputs.mode_array = None
+        inputs.waveform_arguments_dict = None
 
         # injection-waveform-approx not provided
         inputs.waveform_approximant = "IMRPhenomPv2"
@@ -303,7 +347,8 @@ class TestInput(unittest.TestCase):
         self.assertEqual(wfa["pn_phase_order"], -1)
         self.assertEqual(wfa["pn_amplitude_order"], 0)
         self.assertIsNone(wfa["mode_array"])
-        self.assertEqual(len(wfa), 10)
+        self.assertIsNone(wfa["numerical_relativity_file"])
+        self.assertEqual(len(wfa), 11)
 
         # injection-waveform-approx provided
         inputs.waveform_approximant = "IMRPhenomPv2"
@@ -312,7 +357,35 @@ class TestInput(unittest.TestCase):
         self.assertEqual(wfa["reference_frequency"], 20)
         self.assertEqual(wfa["minimum_frequency"], 20)
         self.assertEqual(wfa["waveform_approximant"], "SEOBNRv4")
-        self.assertEqual(len(wfa), 10)
+        self.assertEqual(len(wfa), 11)
+
+    def test_numerical_relativity_file(self):
+        inputs = bilby_pipe.main.Input()
+        inputs.detectors = ["H1"]
+        inputs.reference_frequency = 20
+        inputs.minimum_frequency = 20
+        inputs.maximum_frequency = 1024
+        inputs.pn_spin_order = -1
+        inputs.pn_tidal_order = -1
+        inputs.pn_phase_order = -1
+        inputs.pn_amplitude_order = 0
+        inputs.phenomXPHMTwistPhenomHM = None
+        inputs.phenomXPFinalSpinMod = None
+        inputs.phenomXPConvention = None
+        inputs.phenomXPrecVersion = None
+        inputs.phenomXPHMMband = None
+        inputs.phenomXHMMband = None
+        inputs.catch_waveform_errors = False
+        inputs.mode_array = None
+        inputs.waveform_approximant = "IMRPhenomPv2"
+        inputs.injection_waveform_approximant = None
+        inputs.waveform_arguments_dict = None
+
+        # numerical-relativity-file given
+        filename = "somedir/file.h5"
+        inputs.numerical_relativity_file = filename
+        wfa = inputs.get_injection_waveform_arguments()
+        self.assertEqual(wfa["numerical_relativity_file"], filename)
 
     def test_injection_number(self):
         inputs = bilby_pipe.main.Input()