From 9da557dab7fe8982b7a3b5469d5f2fbc52ad9675 Mon Sep 17 00:00:00 2001
From: David Hendriks <davidhendriks93@gmail.com>
Date: Sat, 28 Mar 2020 14:40:27 +0000
Subject: [PATCH] adding plot_system routine to easily plot some of the
standard things of the binary evolution
---
binarycpython/utils/functions.py | 42 +++---
binarycpython/utils/grid.py | 9 +-
binarycpython/utils/plot_functions.py | 162 ++++++++++++++++++++++
binarycpython/utils/run_system_wrapper.py | 2 -
requirements.txt | 83 ++++++-----
5 files changed, 234 insertions(+), 64 deletions(-)
create mode 100644 binarycpython/utils/plot_functions.py
diff --git a/binarycpython/utils/functions.py b/binarycpython/utils/functions.py
index b15dcc5d9..5e401986f 100644
--- a/binarycpython/utils/functions.py
+++ b/binarycpython/utils/functions.py
@@ -363,6 +363,22 @@ def get_help_all(print_help=True, return_dict=False):
else:
return None
+def filter_arg_dict(arg_dict):
+ """
+ Function to filter out keys that contain values included in ['NULL', 'Function', '']
+ """
+
+ old_dict = arg_dict.copy()
+ new_dict = {}
+
+ for key in old_dict.keys():
+ if not old_dict[key] in ["NULL", "Function"]:
+ if not old_dict[key] == "":
+ new_dict[key] = old_dict[key]
+
+ return new_dict
+
+
def create_arg_string(arg_dict, sort=False, filter_values=False):
"""
@@ -375,18 +391,12 @@ def create_arg_string(arg_dict, sort=False, filter_values=False):
"""
arg_string = ""
- #
- keys = sorted(arg_dict.keys()) if sort else arg_dict.keys()
+ if filter_values:
+ arg_dict = filter_values(arg_dict)
- #
+ keys = sorted(arg_dict.keys()) if sort else arg_dict.keys()
for key in keys:
- # Filter out NULLS (not compiled anyway)
- if filter_values:
- if not arg_dict[key] in ["NULL", "Function"]:
- if not arg_dict[key] == "":
- arg_string += "{key} {value} ".format(key=key, value=arg_dict[key])
- else:
- arg_string += "{key} {value} ".format(key=key, value=arg_dict[key])
+ arg_string += "{key} {value} ".format(key=key, value=arg_dict[key])
arg_string = arg_string.strip()
return arg_string
@@ -405,16 +415,10 @@ def get_defaults(filter_values=False):
for default in default_output.split("\n"):
if not default in ["__ARG_BEGIN", "__ARG_END", ""]:
key, value = default.split(" = ")
+ default_dict[key] = value
- # Filter out NULLS (not compiled anyway)
- if filter_values:
- if not value in ["NULL", "Function"]:
- if not value == "":
- default_dict[key] = value
-
- # On default, just show everything
- else:
- default_dict[key] = value
+ if filter_values:
+ default_dict = filter_arg_dict(default_dict)
return default_dict
diff --git a/binarycpython/utils/grid.py b/binarycpython/utils/grid.py
index 41e77311d..5a3953a22 100644
--- a/binarycpython/utils/grid.py
+++ b/binarycpython/utils/grid.py
@@ -27,6 +27,7 @@ from binarycpython.utils.functions import (
parse_binary_c_version_info,
output_lines,
remove_file,
+ filter_arg_dict,
)
@@ -1258,14 +1259,12 @@ class Population(object):
- "NULL"
- ""
- "Function"
-
+
+ Uses the function from utils.functions
"""
- cleaned_dict = {}
binary_c_defaults = self.return_binary_c_defaults().copy()
- for key in binary_c_defaults:
- if not binary_c_defaults[key] in ["NULL", "", "Function"]:
- cleaned_dict[key] = binary_c_defaults[key]
+ cleaned_dict = filter_arg_dict(binary_c_defaults)
return cleaned_dict
diff --git a/binarycpython/utils/plot_functions.py b/binarycpython/utils/plot_functions.py
new file mode 100644
index 000000000..052970293
--- /dev/null
+++ b/binarycpython/utils/plot_functions.py
@@ -0,0 +1,162 @@
+"""
+Module that contains plotting routines for single systems.
+
+The idea to do this is to provide the user with some quick
+commands to plot the evolution of a system
+
+There is no preloaded matplotlib rc, you should do that yourself
+"""
+
+import pandas as pd
+import numpy as np
+
+import matplotlib.pyplot as plt
+from david_phd_functions.plotting.plot_functions import plot_orbit, plot_masses, plot_HR_diagram
+
+from binarycpython.utils.functions import get_arg_keys, output_lines
+from binarycpython.utils.run_system_wrapper import run_system
+from binarycpython.utils.custom_logging_functions import binary_c_log_code
+
+# Define the custom_logging_strings. These are kept to the minimum necessary for each plotting routine.
+
+custom_logging_string_masses = ""
+custom_logging_string_orbit = ""
+
+custom_logging_string_HR_diagram = """
+Printf("HR_PLOTTING %30.12e %d %d %g %g %g %g %g %g\\n",
+ //
+ stardata->model.time, // 1
+
+ // stellar types
+ stardata->star[0].stellar_type, //2
+ stardata->star[1].stellar_type, //3
+
+ // luminosity and radii
+ stardata->star[0].luminosity, // 4
+ stardata->star[1].luminosity, // 5
+ stardata->star[0].radius, // 6
+ stardata->star[1].radius, // 7
+
+ // masses
+ stardata->star[0].pms_mass, // 8
+ stardata->star[1].pms_mass // 9
+ );
+"""
+
+
+
+
+
+
+
+
+# Define the parse functions for the plotting routines
+def dummy():
+ pass
+
+
+
+def parse_function_hr_diagram(output):
+ """
+ Parsing function for the HR plotting routine
+ """
+
+ # extract info from the single evolution
+
+ values_list = []
+
+ parameters = ['time',
+ 'stellar_type_1', 'stellar_type_2',
+ 'luminosity_1', 'luminosity_2',
+ 'radius_1', 'radius_2', 'pms_mass_1', 'pms_mass_2']
+
+ # Go over the output.
+ for el in output_lines(output):
+ headerline = el.split()[0]
+
+ # Check the header and act accordingly
+ if (headerline=='HR_PLOTTING'):
+ values = el.split()[1:]
+ values_list.append(values)
+
+ df = pd.DataFrame(values_list)
+ df.columns = parameters
+
+
+ df = df.astype(np.float64)
+ df['stellar_type_1'] = df['stellar_type_1'].astype(np.int64)
+ df['stellar_type_2'] = df['stellar_type_2'].astype(np.int64)
+
+ return df
+
+def plot_system(plot_type, **kwargs):
+ """
+ TODO: Complex Function!
+ TODO: make sure this way of passing args works correctly.
+ TODO: make the plotting specific keywords available via the inspect stuff
+ Function to plot the evolution of the system.
+
+ This goes (in general) via the following steps:
+ - a preset custom logging for a specific plotting routine is loaded.
+ - This is used for the run_system call
+ - The output of this run_system is loaded into a dataframe by parsing it with a corresponding parsing function
+ - The dataframe is passed to the plotting routine
+ - plot is shown or returned.
+
+ There are several pre-set plots to choose from
+
+ All keywords are considered kwargs, except for plot_type
+ input:
+ plot_type: string input should be one of the following types: ['mass_evolution', 'orbit_evolution', 'hr_diagram'].
+ Input will be matched against this, and then go through a dictionary to pick the correct plotting function.
+ return_fig: boolean whether to return the fig object instead of plotting the plot (makes so that you can customize it)
+ show_stellar_types: whether to plot the stellar type evolution on a second pane. This is not included in all the plotting routines.
+ Other input: other kwargs that are passed to run_system (inspect the docstring of run_system for more info)
+ """
+
+ # set defaults and options
+ return_fig = False
+ show_stellar_types = False
+
+ plot_types_dict = {
+ 'mass_evolution': {'plot_function': plot_masses, 'custom_logging_string': custom_logging_string_masses, 'parse_function': dummy},
+ 'orbit_evolution': {'plot_function': plot_orbit, 'custom_logging_string': custom_logging_string_orbit, 'parse_function': dummy},
+ 'hr_diagram': {'plot_function': plot_HR_diagram, 'custom_logging_string': custom_logging_string_HR_diagram, 'parse_function': parse_function_hr_diagram},
+ }
+ plot_system_specific_keywords = ['plot_type', 'show_plot', 'show_stellar_types']
+
+ # First check on the plot_type input
+ if not plot_type in plot_types_dict.keys():
+ print("Warning, the provided plot type is not known. Please choose one from the following:\n\t{}".format(plot_types_dict.keys()))
+ raise ValueError
+
+ # First: check all the arguments. Chosen to not check all the keywords for run_system and binary_c specifically, but just to pick out the ones needed for this routine. run_system will handle the rest
+ run_system_arg_dict = {}
+
+ for key in kwargs.keys():
+ if key == 'show_plot':
+ show_plot = kwargs[key]
+ elif key == 'show_stellar_types':
+ show_stellar_types = kwargs[key]
+
+ # The rest will be passed to run_system
+ else:
+ run_system_arg_dict[key] = kwargs[key]
+
+ # TODO: When a list of plot_types is passed, make it so that the strings are chained, and that the output of the binary_c call is handled by multiple parsers
+ custom_logging_code = binary_c_log_code(plot_types_dict[plot_type]['custom_logging_string'])
+ run_system_arg_dict['custom_logging_code'] = custom_logging_code
+
+ run_system_arg_dict['parse_function'] = plot_types_dict[plot_type]['parse_function']
+
+ # Run and get the output of the parse function
+ binary_c_output_df = run_system(**run_system_arg_dict)
+
+
+ fig = plot_types_dict[plot_type]['plot_function'](binary_c_output_df, show_plot=show_plot, show_stellar_types=show_stellar_types)
+
+ if not show_plot:
+ return fig
+
+
+plot_system(plot_type='hr_diagram', M_1=10, M_2=5, orbital_period=100000, max_evolution_time=15000, show_plot=True)
\ No newline at end of file
diff --git a/binarycpython/utils/run_system_wrapper.py b/binarycpython/utils/run_system_wrapper.py
index 7166b0318..0a247f1f0 100644
--- a/binarycpython/utils/run_system_wrapper.py
+++ b/binarycpython/utils/run_system_wrapper.py
@@ -40,8 +40,6 @@ def run_system(**kwargs):
other_keywords = ['custom_logging_code', 'log_filename', 'parse_function']
-
-
# Set default values
func_memaddr = -1
write_logfile = 0
diff --git a/requirements.txt b/requirements.txt
index 6329c5c64..1c79312a3 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,57 +1,64 @@
-astropy==3.2.1
-attrs==19.1.0
+alabaster==0.7.12
+astropy==4.0.1
+Babel==2.7.0
backcall==0.1.0
-bleach==3.1.0
+binarycpython==0.1
+certifi==2019.9.11
+chardet==3.0.4
+clang==6.0.0.2
cycler==0.10.0
-decorator==4.4.0
-defusedxml==0.6.0
+decorator==4.4.1
dill==0.3.1.1
-entrypoints==0.3
+docutils==0.15.2
h5py==2.10.0
-ipykernel==5.1.2
-ipython==7.7.0
+hawkmoth==0.4
+idna==2.8
+imagesize==1.1.0
+ipython==7.9.0
ipython-genutils==0.2.0
-ipywidgets==7.5.1
-ivs-sse==0.0
jedi==0.15.1
-Jinja2==2.10.1
-jsonschema==3.0.2
-jupyter==1.0.0
-jupyter-client==5.3.1
-jupyter-console==6.0.0
-jupyter-core==4.5.0
+Jinja2==2.10.3
kiwisolver==1.1.0
+lxml==4.5.0
+m2r==0.2.1
MarkupSafe==1.1.1
+matplotlib==3.1.2
mistune==0.8.4
multiprocess==0.70.9
-nbconvert==5.6.0
-nbformat==4.4.0
-notebook==6.0.0
-numpy==1.17.0
-#pandas==0.25.0
-pandocfilters==1.4.2
+mypy==0.770
+mypy-extensions==0.4.3
+numpy==1.17.4
+packaging==19.2
+pandas==0.25.3
parso==0.5.1
pathos==0.2.5
pexpect==4.7.0
pickleshare==0.7.5
pox==0.2.7
ppft==1.6.6.1
-prometheus-client==0.7.1
-prompt-toolkit==2.0.9
+prompt-toolkit==2.0.10
+psutil==5.6.7
ptyprocess==0.6.0
Pygments==2.4.2
-pyparsing==2.4.2
-pyrsistent==0.15.4
-python-dateutil==2.8.0
-pytz==2019.2
-pyzmq==18.1.0
-qtconsole==4.5.2
-Send2Trash==1.5.0
-six==1.12.0
-terminado==0.8.2
-testpath==0.4.2
-tornado==6.0.3
-traitlets==4.3.2
+pyparsing==2.4.5
+python-dateutil==2.8.1
+pytz==2019.3
+requests==2.22.0
+scipy==1.4.1
+seaborn==0.10.0
+setproctitle==1.1.10
+six==1.13.0
+snowballstemmer==2.0.0
+Sphinx==2.2.1
+sphinx-rtd-theme==0.4.3
+sphinxcontrib-applehelp==1.0.1
+sphinxcontrib-devhelp==1.0.1
+sphinxcontrib-htmlhelp==1.0.2
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.2
+sphinxcontrib-serializinghtml==1.1.3
+traitlets==4.3.3
+typed-ast==1.4.1
+typing-extensions==3.7.4.1
+urllib3==1.25.7
wcwidth==0.1.7
-webencodings==0.5.1
-widgetsnbextension==3.5.1
--
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