From 77cef2b18ce12f80b00b9290b77dfc1858125b52 Mon Sep 17 00:00:00 2001
From: David Hendriks <davidhendriks93@gmail.com>
Date: Wed, 20 Nov 2019 23:56:34 +0000
Subject: [PATCH] made the parse output a bit more functional
---
.../custom_logging_functions.py | 30 ++++++----
binaryc_python_utils/functions.py | 38 ++++++++----
examples/examples.py | 28 ++++++---
setup.py | 59 ++++++++++---------
4 files changed, 93 insertions(+), 62 deletions(-)
diff --git a/binaryc_python_utils/custom_logging_functions.py b/binaryc_python_utils/custom_logging_functions.py
index 3bb4d7f48..cd37988bc 100644
--- a/binaryc_python_utils/custom_logging_functions.py
+++ b/binaryc_python_utils/custom_logging_functions.py
@@ -122,7 +122,7 @@ def from_binary_c_config(config_file, flag):
return res
-def return_compilation_dict():
+def return_compilation_dict(verbose=False):
"""
Function to build the compile command for the shared library
@@ -206,21 +206,23 @@ def return_compilation_dict():
]
libs = "{} {}".format(" ".join(library_paths), " ".join(non_library_paths))
- print(
- "Building shared library for custom logging with (binary_c.h) at {} on {}\n".format(
- BINARY_C_SRC_DIR, socket.gethostname()
+
+ 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
+ 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):
+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.
"""
@@ -245,11 +247,13 @@ def compile_shared_lib(code, sourcefile_name, outfile_name):
command = " ".join(command.split())
# Execute compilation
- print("Executing following command:\n{command}".format(command=command))
+ if verbose:
+ print("Executing following command:\n{command}".format(command=command))
res = subprocess.check_output("{command}".format(command=command), shell=True)
- if res:
- print("Output of compilation command:\n{}".format(res))
+ if verbose:
+ if res:
+ print("Output of compilation command:\n{}".format(res))
def temp_custom_logging_dir():
diff --git a/binaryc_python_utils/functions.py b/binaryc_python_utils/functions.py
index c0b9ee155..cc7e3b954 100644
--- a/binaryc_python_utils/functions.py
+++ b/binaryc_python_utils/functions.py
@@ -136,16 +136,20 @@ def run_system_with_log(**kwargs):
def parse_output(output, selected_header):
"""
- Function that parses output of binaryc when it is construction like this:
- DAVID_SINGLE_ANALYSIS t=0 mass=20
+ 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
-
+
+ TODO: Think about exporting to numpy array or pandas instead of a defaultdict
"""
- value_dicts = []
- val_lists = []
+
+ value_dicts = []
+ val_lists = []
# split output on newlines
for i, line in enumerate(output.split("\n")):
@@ -155,17 +159,25 @@ def parse_output(output, selected_header):
# Select parts
header = split_line[0]
- value_array = split_line[1:]
+ values_list = split_line[1:]
+ # print(values_list)
# Catch line starting with selected header
if header == selected_header:
- # print(value_array)
- # Make a dict
+ # Check if the line contains '=' symbols:
value_dict = {}
- for el in value_array:
- key, val = el.split("=")
- value_dict[key] = val
- value_dicts.append(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(
diff --git a/examples/examples.py b/examples/examples.py
index a8609771c..7df0e0287 100644
--- a/examples/examples.py
+++ b/examples/examples.py
@@ -20,7 +20,6 @@ Use these as inspiration/base.
def run_example_binary():
"""
Function to run a binary system. Very basic approach which directly adresses the run_binary(..) python-c wrapper function.
-
"""
m1 = 15.0 # Msun
@@ -46,7 +45,6 @@ def run_example_binary():
output = binary_c.run_binary(argstring)
print(output)
-
# run_example_binary()
@@ -60,6 +58,8 @@ def run_example_binary_with_run_system():
run_system: mostly just makes passing arguments to the function easier. It also loads all the necessary defaults in the background
parse_output: Takes the raw output of binary_c and selects those lines that start with the given header.
Note, if you dont use the custom_logging functionality binary_c should be configured to have output that starts with that given header
+
+ The parsing of the output only works correctly if either all of the values are described inline like `mass=<number>' or none of them are.
"""
import pandas as pd
@@ -68,16 +68,31 @@ def run_example_binary_with_run_system():
# Run system. all arguments can be given as optional arguments.
output = run_system(M_1=10, M_2=20, separation=0, orbital_period=100000000000)
+ # print(output)
+
# Catch results that start with a given header. (Mind that binary_c has to be configured to print them if your not using a custom logging function)
- result_example_header = parse_output(output, "example_header")
+ result_example_header_1 = parse_output(output, selected_header="example_header_1")
+ result_example_header_2 = parse_output(output, selected_header="example_header_2")
+
+ # print(result_example_header_1)
#### Now do whatever you want with it:
# Put it in numpy arrays
# t_res = np.asarray(result_example_header['t'], dtype=np.float64, order='C')
# m_res = np.asarray(result_example_header['mass'], dtype=np.float64, order='C')
+ # Or put them into a pandas array
+
+
# Cast the data into a dataframe.
- df = pd.DataFrame.from_dict(result_example_header, dtype=np.float64)
+ # This example automatically catches the column names because the binary_c output line is constructed as 'example_header_1 time=<number>..'
+ df = pd.DataFrame.from_dict(result_example_header_1, dtype=np.float64)
+ print(df)
+
+ # This example has column headers which are numbered, but we can override that with custom headers.
+ df2 = pd.DataFrame.from_dict(result_example_header_2, dtype=np.float64)
+ df2.columns=['time', 'mass_1', 'mass_2', 'st1', 'st2', 'sep', 'ecc']
+ print(df2)
# print(df)
# sliced_df = df[df.t < 1000] # Cut off late parts of evolution
@@ -85,8 +100,7 @@ def run_example_binary_with_run_system():
# Some routine to plot.
-# run_example_binary_with_run_system()
-
+run_example_binary_with_run_system()
def run_example_binary_with_custom_logging():
"""
@@ -166,4 +180,4 @@ def run_example_binary_with_writing_logfile():
# Some routine to plot.
-# run_example_binary_with_writing_logfile()
+# run_example_binary_with_writing_logfile()
\ No newline at end of file
diff --git a/setup.py b/setup.py
index c2e18e378..88648bed4 100644
--- a/setup.py
+++ b/setup.py
@@ -1,6 +1,6 @@
-# from distutils.core import setup, Extension
+from distutils.core import setup, Extension
# from setuptools import find_packages
-from setuptools import setup, find_packages, Extension
+# from setuptools import setup, find_packages, Extension
import os
import subprocess
import re
@@ -57,11 +57,37 @@ API_h = os.environ["BINARY_C"] + "/src/API/binary_c_API.h"
binary_c_define_macros.extend([("BINARY_C_API_H", API_h)])
+binary_c_python_api_module = Extension(
+ "binary_c",
+ ["src/binary_c_python.c"],
+ include_dirs=[
+ os.environ["BINARY_C"] + "/src",
+ os.environ["BINARY_C"] + "/src/API",
+ "include",
+ ]
+ + binary_c_incdirs,
+ libraries=["binary_c"] + binary_c_libs + ["binary_c_api"],
+ library_dirs=[
+ os.environ["BINARY_C"] + "/src",
+ "./",
+ os.path.join(CWD, "lib/"),
+ ]
+ + binary_c_libdirs,
+ runtime_library_dirs=[
+ os.environ["BINARY_C"] + "/src",
+ "./",
+ os.path.join(CWD, "lib/"),
+ ]
+ + binary_c_libdirs,
+ define_macros=[] + binary_c_define_macros,
+ extra_objects=[],
+ extra_compile_args=[],
+)
+
def readme():
with open('README.md') as f:
return f.read()
-
setup(
name="binary_c",
version="1.0",
@@ -72,31 +98,6 @@ setup(
url="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python",
license="",
ext_modules=[
- Extension(
- "binary_c",
- ["src/binary_c_python.c"],
- include_dirs=[
- os.environ["BINARY_C"] + "/src",
- os.environ["BINARY_C"] + "/src/API",
- "include",
- ]
- + binary_c_incdirs,
- libraries=["binary_c"] + binary_c_libs + ["binary_c_api"],
- library_dirs=[
- os.environ["BINARY_C"] + "/src",
- "./",
- os.path.join(CWD, "lib/"),
- ]
- + binary_c_libdirs,
- runtime_library_dirs=[
- os.environ["BINARY_C"] + "/src",
- "./",
- os.path.join(CWD, "lib/"),
- ]
- + binary_c_libdirs,
- define_macros=[] + binary_c_define_macros,
- extra_objects=[],
- extra_compile_args=[],
- )
+ binary_c_python_api_module
], # binary_c must be loaded
)
--
GitLab