added notebook and pdf

*.nfs*

*.swp

.python-version

.ipynb_checkpoints/

#!/usr/bin/python3

import binary_c_python_api

############################################################

# Test script to run a binary using the binary_c Python

# module.

############################################################

def run_test_binary():

    m1 = 15.0  # Msun

    m2 = 14.0  # Msun

    separation = 0  # 0 = ignored, use period

    orbital_period = 4530.0  # days

    eccentricity = 0.0

    metallicity = 0.02

    max_evolution_time = 15000

    buffer = ""

    argstring = "binary_c M_1 {0:g} M_2 {1:g} separation {2:g} orbital_period {3:g} eccentricity {4:g} metallicity {5:g} max_evolution_time {6:g}  ".format(

        m1,

        m2,

        separation,

        orbital_period,

        eccentricity,

        metallicity,

        max_evolution_time,

    )

    output = binary_c_python_api.run_binary(argstring)

    print("\n\nBinary_c output:\n\n")

    print(output)

# binary_star = binary_c_python_api.new_system()

# print(binary_star)

run_test_binary()

 No newline at end of file

If you want to be able to import the binary_c module correctly for child directories (or anywhere for that matter), execute or put the following code in your .bashrc/.zshrc: 

```

export LD_LIBRARY_PATH=<full path to directory containing libbinary_c_api.so>:$LD_LIBRARY_PATH

export PYTHONPATH=<full path to directory containing libbinary_c_api.so>:$PYTHONPATH

export LD_LIBRARY_PATH=<full path to root dir of repo>:$LD_LIBRARY_PATH

export PYTHONPATH=<full path to root dir of repo>:$PYTHONPATH

```

Usage notes

import os

import textwrap

import subprocess

import socket

import tempfile

import ctypes

def autogen_C_logging_code(logging_dict):

    """

    Function that autogenerates PRINTF statements for binaryc. intput is a dictionary where the key is the header of that logging line and items which are lists of parameters\

    that will be put in that logging line

    Example::

        {'MY_STELLAR_DATA': 

            [

                'model.time',

                'star[0].mass',

                'model.probability',

                'model.dt'

            ]

        }

    """

    # Check if the input is of the correct form

    if not type(logging_dict) == dict:

        print("Error: please use a dictionary as input")

        return None

    code = ""

    # Loop over dict keys

    for key in logging_dict:

        logging_dict_entry = logging_dict[key]

        # Check if item is of correct type:

        if type(logging_dict_entry) == list:

            # Construct print statement

            code += 'Printf("{}'.format(key)

            code += " {}".format("%g " * len(logging_dict_entry))

            code = code.strip()

            code += '\\n"'

            # Add format keys

            for param in logging_dict_entry:

                code += ",((double)stardata->{})".format(param)

            code += ");\n"

        else:

            print(

                "Error: please use a list for the list of parameters that you want to have logged"

            )

    code = code.strip()

    # print("MADE AUTO CODE\n\n{}\n\n{}\n\n{}\n".format('*'*60, repr(code), '*'*60))

    return code

####################################################################################

def binary_c_log_code(code):

    """

    Function to construct the code to construct the custom logging function

    """

    custom_logging_function_string = """\

#pragma push_macro(\"MAX\")

#pragma push_macro(\"MIN\")

#undef MAX

#undef MIN

#include \"binary_c.h\"

// add visibility __attribute__ ((visibility ("default"))) to it 

void binary_c_API_function custom_output_function(struct stardata_t * stardata);

void binary_c_API_function custom_output_function(struct stardata_t * stardata)

{{

    // struct stardata_t * stardata = (struct stardata_t *)x;

    {};

}}

#undef MAX 

#undef MIN

#pragma pop_macro(\"MIN\")

#pragma pop_macro(\"MAX\")\

    """.format(

        code

    )

    # print(repr(textwrap.dedent(custom_logging_function_string)))

    return textwrap.dedent(custom_logging_function_string)

def binary_c_write_log_code(code, filename):

    """

    Function to write the generated logging code to a file

    """

    cwd = os.getcwd()

    filePath = os.path.join(cwd, filename)

    if os.path.exists(filePath):

        try:

            os.remove(filePath)

        except:

            print("Error while deleting file {}".format(filePath))

    with open(filePath, "w") as f:

        f.write(code)

def from_binary_c_config(config_file, flag):

    """

    Function to run the binaryc_config command with flags

    """

    res = subprocess.check_output(

        "{config_file} {flag}".format(config_file=config_file, flag=flag),

        shell=True,

        stderr=subprocess.STDOUT,

    )

    # convert and chop off newline

    res = res.decode("utf").rstrip()

    return res

def return_compilation_dict(verbose=False):

    """

    Function to build the compile command for the shared library

    inspired by binary_c_inline_config command in perl

    TODO: this function still has some cleaning up to do wrt default values for the compile command

    # https://developers.redhat.com/blog/2018/03/21/compiler-and-linker-flags-gcc/

    returns:

     - string containing the command to build the shared library

    """

    # use binary_c-config to get necessary flags

    BINARY_C_DIR = os.getenv("BINARY_C")

    if BINARY_C_DIR:

        BINARY_C_CONFIG = os.path.join(BINARY_C_DIR, "binary_c-config")

        BINARY_C_SRC_DIR = os.path.join(BINARY_C_DIR, "src")

        # TODO: build in check to see whether the file exists

    else:

        raise NameError("Envvar BINARY_C doesnt exist")

        return None

    # TODO: make more options for the compiling

    cc = from_binary_c_config(BINARY_C_CONFIG, "cc")

    # Check for binary_c

    BINARY_C_EXE = os.path.join(BINARY_C_DIR, "binary_c")

    if not os.path.isfile(BINARY_C_EXE):

        print("We require  binary_c executable; have you built binary_c?")

        raise NameError("BINARY_C executable doesnt exist")

    # TODO: debug

    libbinary_c = "-lbinary_c"

    binclibs = from_binary_c_config(BINARY_C_CONFIG, "libs")

    libdirs = "{} -L{}".format(

        from_binary_c_config(BINARY_C_CONFIG, "libdirs"), BINARY_C_SRC_DIR

    )

    bincflags = from_binary_c_config(BINARY_C_CONFIG, "cflags")

    bincincdirs = from_binary_c_config(BINARY_C_CONFIG, "incdirs")

    # combine

    binclibs = " {} {} {}".format(libdirs, libbinary_c, binclibs)

    # setup defaults:

    defaults = {

        "cc": "gcc",  # default compiler

        "ccflags": bincflags,

        "ld": "ld",  # 'ld': $Config{ld}, # default linker

        "debug": 0,

        "inc": "{} -I{}".format(bincincdirs, BINARY_C_SRC_DIR),

        # inc => ' '.($Config{inc}//' ').' '.$bincincdirs." -I$srcdir ", # include the defaults plus # GSL and binary_c

        # 'libname': libname, # libname is usually just binary_c corresponding to libbinary_c.so

        "libs": binclibs,

    }

    # set values with defaults. TODO: make other input possile.

    ld = defaults["ld"]

    debug = defaults["debug"]

    inc = defaults[

        "inc"

    ]  # = ($ENV{BINARY_GRID2_INC} // $defaults{inc}).' '.($ENV{BINARY_GRID2_EXTRAINC} // '');

    libs = defaults[

        "libs"

    ]  # = ($ENV{BINARY_GRID2_LIBS} // $defaults{libs}).' '.($ENV{BINARY_GRID2_EXTRALIBS}//'');

    ccflags = defaults[

        "ccflags"

    ]  #  = $ENV{BINARY_GRID2_CCFLAGS} // ($defaults{ccflags}) . ($ENV{BINARY_GRID2_EXTRACCFLAGS} // '');

    # you must define _SEARCH_H to prevent it being loaded twice

    ccflags += " -shared -D_SEARCH_H"

    # remove the visibility=hidden for this compilation

    ccflags = ccflags.replace("-fvisibility=hidden", "")

    # ensure library paths to the front of the libs:

    libs_content = libs.split(" ")

    library_paths = [el for el in libs_content if el.startswith("-L")]

    non_library_paths = [

        el for el in libs_content if (not el.startswith("-L") and not el == "")

    ]

    libs = "{} {}".format(" ".join(library_paths), " ".join(non_library_paths))

    if verbose:

        print(

            "Building shared library for custom logging with (binary_c.h) at {} on {}\n".format(

                BINARY_C_SRC_DIR, socket.gethostname()

            )

        )

        print(

            "With options:\n\tcc = {cc}\n\tccflags = {ccflags}\n\tld = {ld}\n\tlibs = {libs}\n\tinc = {inc}\n\n".format(

                cc=cc, ccflags=ccflags, ld=ld, libs=libs, inc=inc

            )

        )

    return {"cc": cc, "ld": ld, "ccflags": ccflags, "libs": libs, "inc": inc}

def compile_shared_lib(code, sourcefile_name, outfile_name, verbose=False):

    """

    Function to write the custom logging code to a file and then compile it.

    """

    # Write code to file

    binary_c_write_log_code(code, sourcefile_name)

    # create compilation command

    compilation_dict = return_compilation_dict()

    # Construct full command

    command = "{cc} {ccflags} {libs} -o {outfile_name} {sourcefile_name} {inc}".format(

        cc=compilation_dict["cc"],

        ccflags=compilation_dict["ccflags"],

        libs=compilation_dict["libs"],

        outfile_name=outfile_name,

        sourcefile_name=sourcefile_name,

        inc=compilation_dict["inc"],

    )

    # remove extra whitespaces:

    command = " ".join(command.split())

    # Execute compilation

    if verbose:

        print("Executing following command:\n{command}".format(command=command))

    res = subprocess.check_output("{command}".format(command=command), shell=True)

    if verbose:

        if res:

            print("Output of compilation command:\n{}".format(res))

def temp_custom_logging_dir():

    """

    Function to return the path the custom logging library shared object and script will be written to.

    Makes use of os.makedirs exist_ok which requires python 3.2+

    """

    tmp_dir = tempfile.gettempdir()

    path = os.path.join(tmp_dir, "binary_c_python")

    #

    os.makedirs(path, exist_ok=True)

    return path

def create_and_load_logging_function(custom_logging_code):

    """

    Function to automatically compile the shared library with the given custom logging code and load it with ctypes

    returns:

        memory adress of the custom logging function in a int type.

    """

    #

    compile_shared_lib(

        custom_logging_code,

        sourcefile_name=os.path.join(temp_custom_logging_dir(), "custom_logging.c"),

        outfile_name=os.path.join(temp_custom_logging_dir(), "libcustom_logging.so"),

    )

    # Loading library

    dll1 = ctypes.CDLL("libgslcblas.so", mode=ctypes.RTLD_GLOBAL)

    dll2 = ctypes.CDLL("libgsl.so", mode=ctypes.RTLD_GLOBAL)

    dll3 = ctypes.CDLL("libbinary_c.so", mode=ctypes.RTLD_GLOBAL)

    libmean = ctypes.CDLL(

        os.path.join(temp_custom_logging_dir(), "libcustom_logging.so"),

        mode=ctypes.RTLD_GLOBAL,

    )  # loads the shared library

    # Get memory adress of function. mimicking a pointer

    func_memaddr = ctypes.cast(libmean.custom_output_function, ctypes.c_void_p).value

    return func_memaddr

from collections import defaultdict

import binary_c_python_api

from binarycpython.utils.custom_logging_functions import (

    create_and_load_logging_function,

)

def create_arg_string(arg_dict):

    """

    Function that creates the arg string

    """

    arg_string = ""

    for key in arg_dict.keys():

        arg_string += "{key} {value} ".format(key=key, value=arg_dict[key])

    arg_string = arg_string.strip()

    return arg_string

def get_defaults():

    """

    Function that calls the binaryc get args function and cast it into a dictionary

    All the values are strings

    """

    default_output = binary_c_python_api.return_arglines()

    default_dict = {}

    for default in default_output.split("\n"):

        if not default in ["__ARG_BEGIN", "__ARG_END", ""]:

            key, value = default.split(" = ")

            # Filter out NULLS (not compiled anyway)

            if not value in ["NULL", "Function"]:

                if not value == "":

                    default_dict[key] = value

    return default_dict

def get_arg_keys():

    """

    Function that return the list of possible keys to give in the arg string

    """

    return get_defaults().keys()

def run_system(**kwargs):

    """

    Wrapper to run a system with settings 

    This function determines which underlying python-c api function will be called based upon the arguments that are passed via kwargs.

    - if custom_logging_code or custom_logging_dict is included in the kwargs then it will     

    - if 

    """

    # Load default args

    args = get_defaults()

    if "custom_logging_code" in kwargs:

        # Use kwarg value to override defaults and add new args

        for key in kwargs.keys():

            if not key == "custom_logging_code":

                args[key] = kwargs[key]

        # Generate library and get memaddr

        func_memaddr = create_and_load_logging_function(kwargs["custom_logging_code"])

        # Construct arguments string and final execution string

        arg_string = create_arg_string(args)

        arg_string = "binary_c {}".format(arg_string)

        # Run it and get output

        output = binary_c_python_api.run_binary_custom_logging(arg_string, func_memaddr)

        return output

    elif "log_filename" in kwargs:

        # Use kwarg value to override defaults and add new args

        for key in kwargs.keys():

            args[key] = kwargs[key]

        # Construct arguments string and final execution string

        arg_string = create_arg_string(args)

        arg_string = "binary_c {}".format(arg_string)

        # Run it and get output

        output = binary_c_python_api.run_binary_with_logfile(arg_string)

        return output

    else:  # run the plain basic type

        # Use kwarg value to override defaults and add new args

        for key in kwargs.keys():

            args[key] = kwargs[key]

        # Construct arguments string and final execution string

        arg_string = create_arg_string(args)

        arg_string = "binary_c {}".format(arg_string)

        # Run it and get output

        output = binary_c_python_api.run_binary(arg_string)

        return output

def run_system_with_log(**kwargs):

    """

    Wrapper to run a system with settings AND logs the files to a designated place defined by the log_filename parameter.

    """

    # Load default args

    args = get_defaults()

    # args = {}

    # For example

    # physics_args['M_1'] = 20

    # physics_args['separation'] = 0 # 0 = ignored, use period

    # physics_args['orbital_period'] = 100000000000 # To make it single

    # Use kwarg value to override defaults and add new args

    for key in kwargs.keys():

        args[key] = kwargs[key]

    # Construct arguments string and final execution string

    arg_string = create_arg_string(args)

    arg_string = "binary_c {}".format(arg_string)

    # print(arg_string)

    # Run it and get output

    buffer = ""

    output = binary_c_python_api.run_binary_with_log(arg_string)

    return output

def parse_output(output, selected_header):

    """

    Function that parses output of binary_c:

    This function works in two cases:

    if the caught line contains output like 'example_header time=12.32 mass=0.94 ..'

    or if the line contains output like 'example_header 12.32 0.94'

    You can give a 'selected_header' to catch any line that starts with that. 

    Then the values will be put into a dictionary.

    TODO: Think about exporting to numpy array or pandas instead of a defaultdict

    """

    value_dicts     = []

    val_lists       = []

    # split output on newlines

    for i, line in enumerate(output.split("\n")):

        # Skip any blank lines

        if not line == "":

            split_line = line.split()

            # Select parts

            header = split_line[0]

            values_list = split_line[1:]

            # print(values_list)

            # Catch line starting with selected header

            if header == selected_header:

                # Check if the line contains '=' symbols:

                value_dict = {}

                if all('=' in el for el in values_list):

                    for el in values_list:

                        key, val = el.split("=")

                        value_dict[key.strip()] = val.strip()

                    value_dicts.append(value_dict)

                else:

                    if any('=' in el for el in values_list):

                        raise ValueError('Caught line contains some = symbols but not all of them do. aborting run')

                    else:

                        for i, val in enumerate(values_list):

                            value_dict[i] = val

                        value_dicts.append(value_dict)

    if len(value_dicts) == 0:

        print(

            "Sorry, didnt find any line matching your header {}".format(selected_header)

        )

        return None

    keys = value_dicts[0].keys()

    # Construct final dict.

    final_values_dict = defaultdict(list)

    for value_dict in value_dicts:

        for key in keys:

            final_values_dict[key].append(value_dict[key])

    return final_values_dict

def load_logfile(logfile):

    with open(logfile, 'r') as f:

        logfile_data = f.readlines()

    time_list = []

    m1_list = []

    m2_list = []

    k1_list = []

    k2_list = []

    sep_list = []

    ecc_list = []

    rel_r1_list = []

    rel_r2_list = []

    event_list = []

    random_seed = logfile_data[0].split()[-2]

    random_count = logfile_data[0].split()[-1]

    probability = logfile_data[-1].split()

    for line in logfile_data[1:-1]:

        split_line = line.split()

        time_list.append(split_line[0])

        m1_list.append(split_line[1])

        m2_list.append(split_line[2])

        k1_list.append(split_line[3])

        k2_list.append(split_line[4])

        sep_list.append(split_line[5])

        ecc_list.append(split_line[6])

        rel_r1_list.append(split_line[7])

        rel_r2_list.append(split_line[8])

        event_list.append(' '.join(split_line[9:]))

    print(event_list)

 No newline at end of file