Add calibration uncertainty model (#54)

* add base Recalibrate class and CubicSpline * Adding calibration preamble * fix extraction of frequencies from strain object * add call to super.__init__ * add parameter prefix as argument * add documentation * add reading from config * fix bug in prefix removal * Typos * remove model name from options * make loading from config more generic * update loading of calibration * force inputs to have the correct type * force inputs to have the correct type * Adding warning for too few spline points * make recalibration objects know the ifo name * add base Recalibrate class and CubicSpline * Adding calibration preamble * fix extraction of frequencies from strain object * add call to super.__init__ * add parameter prefix as argument * add documentation * add reading from config * fix bug in prefix removal * Typos * remove model name from options * make loading from config more generic * update loading of calibration * force inputs to have the correct type * force inputs to have the correct type * Adding warning for too few spline points * make recalibration objects know the ifo name * add calibration ini file for cubic spline * add calibration ini to docs * Commenting config file * make lines < 80 characters * use var not stdev * allow multiple config files in workflow * typo fix * standardise ini file name, allow for multiple ini files * update workflow docs for using multiple calibration files * add tests for calibration * remove unused import * style fix * fix style * make cubic spline raise error if too few points are provided * add test of too few spline points * placate codeclimate * use correct frequency array * address comments to pull request * remove useless statement
gwastro · Jul 20, 2018 · 91214d7 · 91214d7
1 parent 5be86c7
commit 91214d7
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diff --git a/bin/gwin b/bin/gwin
@@ -34,6 +34,7 @@ import gwin
 from gwin import (__version__, burn_in, option_utils)
 from gwin.io.hdf import InferenceFile
 from gwin.option_utils import validate_checkpoint_files
+from gwin.calibration import Recalibrate
 
 # command line usage
 parser = argparse.ArgumentParser(usage=__file__ + " [--options]",
@@ -198,9 +199,9 @@ with ctx:
     # get ifo-specific instances of calibration model
     if cp.has_section('calibration'):
         logging.info("Initializing calibration model")
-        recalib = {ifo : strain.read_model_from_config(cp, ifo) for
-                   ifo in opts.instruments}
-        model_args['recalib'] = recalib
+        recalibration = {ifo: Recalibrate.from_config(cp, ifo, section='calibration') for
+                         ifo in opts.instruments}
+        model_args['recalibration'] = recalibration
 
     # get gates for templates
     gates = strain.gates_from_cli(opts)

diff --git a/bin/gwin_make_workflow b/bin/gwin_make_workflow
@@ -94,9 +94,9 @@ parser.add_argument("--gps-end-time", type=float, nargs="+", default=None,
                          "this option is ignored.")
 
 # input configuration file options
-parser.add_argument("--inference-config-file", type=str, required=True,
+parser.add_argument("--inference-config-file", type=str, nargs='+', required=True,
                     help="workflow.WorkflowConfigParser parsable file with "
-                         "proir information.")
+                         "prior information.")
 parser.add_argument("--prior-section", type=str, default="prior",
                     help="Name of the section in inference configuration file "
                          "that contains priors.")
@@ -154,9 +154,6 @@ workflow_options = opts.bank_file != None \
 if not workflow_options and not (opts.gps_end_time != None):
     raise ValueError("Must use either workflow options or --gps-end-time")
 
-# typecast str from command line to File instances
-config_file = to_file(opts.inference_config_file)
-
 # sections for output HTML pages
 rdir = layout.SectionNumber("results",
                             ["detector_sensitivity", "priors", "posteriors",
@@ -194,9 +191,6 @@ workflow_options = opts.bank_file != None \
 if not workflow_options and not (opts.gps_end_time != None):
     raise ValueError("Must use either workflow options or --gps-end-time")
 
-# typecast str from command line to File instances
-config_file = to_file(opts.inference_config_file)
-
 # if using workflow files to find analysis times
 if workflow_options:
 
@@ -239,7 +233,11 @@ inference_exe = wf.Executable(workflow.cp, "inference", ifos=workflow.ifos,
                               out_dir=opts.output_dir)
 
 # read inference configuration file
-cp = WorkflowConfigParser([opts.inference_config_file])
+# typecast str from command line to File instances
+cp = WorkflowConfigParser(opts.inference_config_file)
+with open('inference.ini', 'w') as ff:
+    cp.write(ff)
+config_file = to_file('inference.ini')
 
 # get channel names
 channel_names = {}

diff --git a/docs/command-line/gwin_make_workflow.rst b/docs/command-line/gwin_make_workflow.rst
@@ -78,11 +78,19 @@ A simple configuration file for parameter estimation on the ringdown is::
 
 If you want to use another variable parameter in the inference sampler then add its name to ``[variable_params]`` and add a prior section like shown above.
 
+When working on real data, it is necessary to marginalise over calibration uncertainty.
+The model and parameters describing the calibration uncertainty can be passed in another ini file, e.g.:
+
+.. literalinclude:: ../../examples/workflow/GW150914_example/calibration.ini
+:language: ini
+
 =====================
 Generate the workflow
 =====================
 
-To generate a workflow you will need your configuration files. We set the following enviroment variables for this example::
+To generate a workflow you will need your configuration files.
+The workflow creates a single config file ``inference.ini`` from all the files specified in ``INFERENCE_CONFIG_PATH``.
+We set the following enviroment variables for this example::
 
     # name of the workflow
     WORKFLOW_NAME="r1"
@@ -92,7 +100,7 @@ To generate a workflow you will need your configuration files. We set the follow
 
     # input configuration files
     CONFIG_PATH=workflow.ini
-    INFERENCE_CONFIG_PATH=gwin.ini
+    INFERENCE_CONFIG_PATH="gwin.ini calibration.ini"
 
 Specify a directory to save the HTML pages::
 

diff --git a/examples/workflow/GW150914_example/calibration.ini b/examples/workflow/GW150914_example/calibration.ini
@@ -0,0 +1,132 @@
+# Details of set up as given in the O1 Binary Black Hole Paper https://arxiv.org/abs/1606.04856
+[calibration]
+h1_model = cubic_spline
+h1_minimum_frequency = 10
+h1_maximum_frequency = 1024
+h1_n_points = 5
+l1_model = cubic_spline
+l1_minimum_frequency = 10
+l1_maximum_frequency = 1024
+l1_n_points = 5
+
+[variable_params]
+recalib_amplitude_h1_0 =
+recalib_amplitude_h1_1 =
+recalib_amplitude_h1_2 =
+recalib_amplitude_h1_3 =
+recalib_amplitude_h1_4 =
+recalib_phase_h1_0 =
+recalib_phase_h1_1 =
+recalib_phase_h1_2 =
+recalib_phase_h1_3 =
+recalib_phase_h1_4 =
+recalib_amplitude_l1_0 =
+recalib_amplitude_l1_1 =
+recalib_amplitude_l1_2 =
+recalib_amplitude_l1_3 =
+recalib_amplitude_l1_4 =
+recalib_phase_l1_0 =
+recalib_phase_l1_1 =
+recalib_phase_l1_2 =
+recalib_phase_l1_3 =
+recalib_phase_l1_4 =
+
+[prior-recalib_amplitude_h1_0]
+name = gaussian
+recalib_amplitude_h1_0_mean = 0
+recalib_amplitude_h1_0_var = 0.0023
+
+[prior-recalib_amplitude_h1_1]
+name = gaussian
+recalib_amplitude_h1_1_mean = 0
+recalib_amplitude_h1_1_var = 0.0023
+
+[prior-recalib_amplitude_h1_2]
+name = gaussian
+recalib_amplitude_h1_2_mean = 0
+recalib_amplitude_h1_2_var = 0.0023
+
+[prior-recalib_amplitude_h1_3]
+name = gaussian
+recalib_amplitude_h1_3_mean = 0
+recalib_amplitude_h1_3_var = 0.0023
+
+[prior-recalib_amplitude_h1_4]
+name = gaussian
+recalib_amplitude_h1_4_mean = 0
+recalib_amplitude_h1_4_var = 0.0023
+
+[prior-recalib_amplitude_l1_0]
+name = gaussian
+recalib_amplitude_l1_0_mean = 0
+recalib_amplitude_l1_0_var = 0.0068
+
+[prior-recalib_amplitude_l1_1]
+name = gaussian
+recalib_amplitude_l1_1_mean = 0
+recalib_amplitude_l1_1_var = 0.0068
+
+[prior-recalib_amplitude_l1_2]
+name = gaussian
+recalib_amplitude_l1_2_mean = 0
+recalib_amplitude_l1_2_var = 0.0068
+
+[prior-recalib_amplitude_l1_3]
+name = gaussian
+recalib_amplitude_l1_3_mean = 0
+recalib_amplitude_l1_3_var = 0.0068
+
+[prior-recalib_amplitude_l1_4]
+name = gaussian
+recalib_amplitude_l1_4_mean = 0
+recalib_amplitude_l1_4_var = 0.0068
+
+[prior-recalib_phase_h1_0]
+name = gaussian
+recalib_phase_h1_0_mean = 0
+recalib_phase_h1_0_var = 0.0030
+
+[prior-recalib_phase_h1_1]
+name = gaussian
+recalib_phase_h1_1_mean = 0
+recalib_phase_h1_1_var = 0.0030
+
+[prior-recalib_phase_h1_2]
+name = gaussian
+recalib_phase_h1_2_mean = 0
+recalib_phase_h1_2_var = 0.0030
+
+[prior-recalib_phase_h1_3]
+name = gaussian
+recalib_phase_h1_3_mean = 0
+recalib_phase_h1_3_var = 0.0030
+
+[prior-recalib_phase_h1_4]
+name = gaussian
+recalib_phase_h1_4_mean = 0
+recalib_phase_h1_4_var = 0.0030
+
+[prior-recalib_phase_l1_0]
+name = gaussian
+recalib_phase_l1_0_mean = 0
+recalib_phase_l1_0_var = 0.0054
+
+[prior-recalib_phase_l1_1]
+name = gaussian
+recalib_phase_l1_1_mean = 0
+recalib_phase_l1_1_var = 0.0054
+
+[prior-recalib_phase_l1_2]
+name = gaussian
+recalib_phase_l1_2_mean = 0
+recalib_phase_l1_2_var = 0.0054
+
+[prior-recalib_phase_l1_3]
+name = gaussian
+recalib_phase_l1_3_mean = 0
+recalib_phase_l1_3_var = 0.0054
+
+[prior-recalib_phase_l1_4]
+name = gaussian
+recalib_phase_l1_4_mean = 0
+recalib_phase_l1_4_var = 0.0054