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henry-wallace-physhenry-wallace-phys
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Feature plotting utils (#9)
* adds scalar, makes demo config config more helpful * more config updates * Adds basic version of diagnostics package from T2K MaCh3, will not work just yet... * update gitignore * Implements plotting lib * Small patches' * More small fixes to naming * EVEN MORE REQUIREMENTS * Switch off deprecation warning * Oops summary diags
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-55
lines changed

‎.gitignore

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*env*
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*__pycache__*
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*pdf
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*.pkl
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*.pkl
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*.keras

‎MaCh3PythonUtils/config_reader.py

Lines changed: 189 additions & 27 deletions
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@@ -3,71 +3,233 @@
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from file_handling.chain_handler import ChainHandler
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from machine_learning.ml_factory import MLFactory
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from machine_learning.fml_interface import FmlInterface
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from diagnostics.interface.plotting_interface import PlottingInterface
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import diagnostics.mcmc_plots.posteriors as m3post
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import diagnostics.mcmc_plots.diagnostics as m3diag
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from pydantic.v1.utils import deep_update
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class ConfigReader:
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# Strictly unecessary but nice conceptually
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_file_handler = None
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_interface = None
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_plot_interface = None
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__default_settings = {
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# Settings for file and I/O
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"FileSettings" : {
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# Name of input file
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"FileName": "",
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# Name of chain in file
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"ChainName": "",
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# More printouts
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"Verbose": False,
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# Make posteriors from chain?
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"MakePosteriors": False,
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# Run Diagnostics code?
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"MakeDiagnostics": False,
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# Make an ML model to replicate the chain likelihood model
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"MakeMLModel": False
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},
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"ParameterSettings":{
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"CircularParameters" : [],
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# List of parameter names
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"ParameterNames":[],
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# List of cuts
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"ParameterCuts":[],
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# Name of label branch, used in ML
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"LabelName": "",
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# Any parameters we want to ignore
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"IgnoredParameters":[]
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},
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# Settings for plotting tools
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"PlottingSettings":{
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# Specific Settings for posterior plots
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"PosteriorSettings": {
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# Make 2D Posterior Plots?
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"Make2DPosteriors": False,
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# Make a triangle plot
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"MakeTrianglePlot": False,
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# Variables in the triangle plot
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"TrianglePlot": [],
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# 1D credible intervals
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"MakeCredibleIntervals": False,
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# Output file
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"PosteriorOutputFile": "posteriors.pdf"
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},
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# Specific Settings for diagnostic plots
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"DiagnosticsSettings": {
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# Make violin plot?
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"MakeViolin": False,
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# Make trace + AC plot?
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"MakeTraceAC": False,
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# Make effective sample size plot?
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"MakeESS": False,
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# Make MCSE plot?
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"MakeMCSE": False,
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# Make suboptimality plot
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"MakeSuboptimality": False,
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# Step for calculation
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"SuboptimalitySteps": 0,
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# Output file
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"DiagnosticsOutputFile": "diagnostics.pdf",
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# Print summary statistic
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"PrintSummary": False
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}
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},
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# Specific Settings for ML Applications
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"MLSettings": {
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# Fitter package either SciKit or TensorFlow
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"FitterPackage": "",
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# Fitter Model
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"FitterName": "",
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# Keyword arguments for fitter
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"FitterKwargs" : {},
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#Use an external model that's already been trained?
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"AddFromExternalModel": False,
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# Proportion of input data set used for testing (range of 0-1 )
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"TestSize": 0.0,
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# Name to save ML model in
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"MLOutputFile": "mlmodel"
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}
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}
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14103
def __init__(self, config: str):
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with open(config, 'r') as c:
16105
self._yaml_config = yaml.safe_load(c)
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# Update default settings
108+
self.__chain_settings = deep_update(self.__default_settings, self._yaml_config)
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18-
19-
def setup_file_handler(self)->None:
110+
def make_file_handler(self)->None:
20111
# Process MCMC chain
21-
self._file_handler = ChainHandler(self._yaml_config["FileSettings"]["FileName"],
22-
self._yaml_config["FileSettings"]["ChainName"],
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self._yaml_config["FileSettings"]["Verbose"])
112+
self._file_handler = ChainHandler(self.__chain_settings["FileSettings"]["FileName"],
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self.__chain_settings["FileSettings"]["ChainName"],
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self.__chain_settings["FileSettings"]["Verbose"])
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25-
self._file_handler.ignore_plots(self._yaml_config["FileSettings"]["IgnoredParameters"])
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self._file_handler.add_additional_plots(self._yaml_config["FileSettings"]["ParameterNames"])
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self._file_handler.add_additional_plots(self._yaml_config["FileSettings"]["LabelName"], True)
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self._file_handler.ignore_plots(self.__chain_settings["ParameterSettings"]["IgnoredParameters"])
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self._file_handler.add_additional_plots(self.__chain_settings["ParameterSettings"]["ParameterNames"])
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self._file_handler.add_additional_plots(self.__chain_settings["ParameterSettings"]["LabelName"], True)
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29-
self._file_handler.add_new_cuts(self._yaml_config["FileSettings"]["ParameterCuts"])
121+
self._file_handler.add_new_cuts(self.__chain_settings["ParameterSettings"]["ParameterCuts"])
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31123
self._file_handler.convert_ttree_to_array()
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33125

34-
def setup_ml_interface(self)->None:
126+
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def make_posterior_plots(self):
128+
if self._plot_interface is None:
129+
self._plot_interface = PlottingInterface(self._file_handler)
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131+
posterior_labels = []
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133+
if self.__chain_settings['PlottingSettings']['PosteriorSettings']['Make2DPosteriors']:
134+
self._plot_interface.initialise_new_plotter(m3post.PosteriorPlotter2D(self._file_handler), 'posterior_2d')
135+
posterior_labels.append('posterior_2d')
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137+
if self.__chain_settings['PlottingSettings']['PosteriorSettings']['MakeTrianglePlot']:
138+
self._plot_interface.initialise_new_plotter(m3post.TrianglePlotter(self._file_handler), 'posterior_triangle')
139+
posterior_labels.append('posterior_triangle')
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# Which variables do we actually want 2D plots for?
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self._plot_interface.set_variables_to_plot(self.__chain_settings['PlottingSettings']['PosteriorSettings']['TrianglePlot'], posterior_labels)
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if self.__chain_settings['PlottingSettings']['PosteriorSettings']['Make1DPosteriors']:
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self._plot_interface.initialise_new_plotter(m3post.PosteriorPlotter1D(self._file_handler), 'posterior_1d')
146+
posterior_labels.append('posterior_1d')
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self._plot_interface.set_credible_intervals(self.__chain_settings['PlottingSettings']['PosteriorSettings']['CredibleIntervals'])
150+
self._plot_interface.set_is_circular(self.__chain_settings['ParameterSettings']['CircularParameters'])
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self._plot_interface.make_plots(self.__chain_settings['PlottingSettings']['PosteriorSettings']['PosteriorOutputFile'], posterior_labels)
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154+
def make_diagnostics_plots(self):
155+
if self._plot_interface is None:
156+
self._plot_interface = PlottingInterface(self._file_handler)
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158+
diagnostic_labels = []
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160+
if self.__chain_settings['PlottingSettings']['DiagnosticsSettings']['MakeViolin']:
161+
self._plot_interface.initialise_new_plotter(m3diag.ViolinPlotter(self._file_handler), 'violin_plotter')
162+
diagnostic_labels.append('violin_plotter')
163+
if self.__chain_settings['PlottingSettings']['DiagnosticsSettings']['MakeTraceAC']:
164+
self._plot_interface.initialise_new_plotter(m3diag.AutocorrelationTracePlotter(self._file_handler), 'trace_autocorr')
165+
diagnostic_labels.append('trace_autocorr')
166+
if self.__chain_settings['PlottingSettings']['DiagnosticsSettings']['MakeESS']:
167+
self._plot_interface.initialise_new_plotter(m3diag.EffectiveSampleSizePlotter(self._file_handler), 'ess_plot')
168+
diagnostic_labels.append('ess_plot')
169+
if self.__chain_settings['PlottingSettings']['DiagnosticsSettings']['MakeMCSE']:
170+
self._plot_interface.initialise_new_plotter(m3diag.MarkovChainStandardError(self._file_handler), 'msce_plot')
171+
diagnostic_labels.append('msce_plot')
172+
173+
self._plot_interface.make_plots(self.__chain_settings['PlottingSettings']['DiagnosticsSettings']['DiagnosticsOutputFile'], diagnostic_labels)
174+
175+
# Final one, covariance plotter
176+
if self.__chain_settings['PlottingSettings']['DiagnosticsSettings']['MakeSuboptimality']:
177+
suboptimality_obj = m3diag.CovarianceMatrixUtils(self._file_handler)
178+
suboptimality_obj.calculate_suboptimality(self.__chain_settings['PlottingSettings']['DiagnosticsSettings']['SuboptimalitySteps'], self.__chain_settings['PlottingSettings']['DiagnosticsSettings']['SubOptimalityMin'])
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suboptimality_obj.plot_suboptimality(f"suboptimality_{self.__chain_settings['PlottingSettings']['DiagnosticsSettings']['DiagnosticsOutputFile']}")
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# Finally let's make a quick simmary
182+
if self.__chain_settings['PlottingSettings']['DiagnosticsSettings']['PrintSummary']:
183+
self._plot_interface.print_summary(f"summary_{self.__chain_settings['PlottingSettings']['DiagnosticsSettings']['DiagnosticsOutputFile']}.txt")
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185+
def make_ml_interface(self)->None:
35186
if self._file_handler is None:
36187
raise Exception("Cannot initialise ML interface without first setting up file handler!")
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38189

39-
factory = MLFactory(self._file_handler, self._yaml_config["FileSettings"]["LabelName"])
40-
if self._yaml_config["FitterSettings"]["FitterPackage"].lower() == "scikit":
41-
self._interface = factory.setup_scikit_model(self._yaml_config["FitterSettings"]["FitterName"],
42-
**self._yaml_config["FitterSettings"]["FitterKwargs"])
190+
factory = MLFactory(self._file_handler, self.__chain_settings["ParameterSettings"]["LabelName"])
191+
if self.__chain_settings["MLSettings"]["FitterPackage"].lower() == "scikit":
192+
self._interface = factory.make_scikit_model(self.__chain_settings["MLSettings"]["FitterName"],
193+
**self.__chain_settings["MLSettings"]["FitterKwargs"])
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44-
elif self._yaml_config["FitterSettings"]["FitterPackage"].lower() == "tensorflow":
45-
self._interface = factory.setup_tensorflow_model(self._yaml_config["FitterSettings"]["FitterName"],
46-
**self._yaml_config["FitterSettings"]["FitterKwargs"])
195+
elif self.__chain_settings["MLSettings"]["FitterPackage"].lower() == "tensorflow":
196+
self._interface = factory.make_tensorflow_model(self.__chain_settings["MLSettings"]["FitterName"],
197+
**self.__chain_settings["MLSettings"]["FitterKwargs"])
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48199
else:
49200
raise ValueError("Input not recognised!")
50201

51-
if self._yaml_config["FitterSettings"].get("AddFromExternalModel"):
52-
external_model = self._yaml_config["FitterSettings"]["ExternalModel"]
202+
if self.__chain_settings["MLSettings"].get("AddFromExternalModel"):
203+
external_model = self.__chain_settings["MLSettings"]["ExternalModel"]
53204
self._interface.load_model(external_model)
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55206
else:
56-
self._interface.set_training_test_set(self._yaml_config["FitterSettings"]["TestSize"])
207+
self._interface.set_training_test_set(self.__chain_settings["MLSettings"]["TestSize"])
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58209
self._interface.train_model()
59210
self._interface.test_model()
60-
self._interface.save_model(self._yaml_config["FileSettings"]["ModelOutputName"])
61-
62-
def __call__(self) -> None:
63-
self.setup_file_handler()
64-
self.setup_ml_interface()
211+
self._interface.save_model(self.__chain_settings["MLSettings"]["MLOutputFile"])
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213+
214+
215+
def __call__(self) -> None:
216+
217+
self.make_file_handler()
218+
if self.__chain_settings["FileSettings"]["MakePosteriors"]:
219+
self.make_posterior_plots()
66220

221+
if self.__chain_settings["FileSettings"]["MakeDiagnostics"]:
222+
self.make_diagnostics_plots()
223+
224+
if self.__chain_settings["FileSettings"]["MakeMLModel"]:
225+
self.make_ml_interface()
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67228
@property
68229
def chain_handler(self)->ChainHandler | None:
69230
return self._file_handler
70231

71232
@property
72233
def ml_interface(self)->FmlInterface | None:
73-
return self._interface
234+
return self._interface
235+

‎MaCh3PythonUtils/diagnostics/__init__.py

Whitespace-only changes.

‎MaCh3PythonUtils/diagnostics/interface/__init__.py

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from .plotting_interface import PlottingInterface

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