From 3bc0755e190b3abfb2393dfe83f58bd28eae409a Mon Sep 17 00:00:00 2001
From: David Hendriks <davidhendriks93@gmail.com>
Date: Thu, 23 Jan 2020 16:46:47 +0000
Subject: [PATCH] added functions for the grid. working on the automatic
generation of the grid code
---
binarycpython/utils/functions.py | 59 ++++++++++++++
binarycpython/utils/grid.py | 130 ++++++++++++++++++++++++++-----
2 files changed, 168 insertions(+), 21 deletions(-)
diff --git a/binarycpython/utils/functions.py b/binarycpython/utils/functions.py
index f5ebd8729..e045c5614 100644
--- a/binarycpython/utils/functions.py
+++ b/binarycpython/utils/functions.py
@@ -1,13 +1,72 @@
import copy
import json
+import os
+import h5py
from collections import defaultdict
+import numpy as np
import binary_c_python_api
from binarycpython.utils.custom_logging_functions import (
create_and_load_logging_function,
)
+def create_hdf5(data_dir):
+ """
+ Function to create an hdf5 file from the contents of a directory:
+ - settings file is selected by checking on files ending on settings
+ - data files are selected by checking on files ending with .dat
+ """
+
+ # Get content of data_dir
+ content_data_dir = os.listdir(data_dir)
+
+ # Settings
+ settings_file = [file for file in content_data_dir if file.endswith('_settings.json')][0]
+ with open(settings_file, 'r') as f:
+ settings_json = json.load(f)
+
+ # create basename for hdf5
+ base_name = settings_file.replace('_settings.json', '')
+
+ # Get data files
+ data_files = [el for el in content_data_dir if el.endswith('.dat')]
+
+ # Create the file
+ hdf5_filename = os.path.join(data_dir,'{base_name}.hdf5'.format(base_name=base_name))
+ f = h5py.File(hdf5_filename, 'w')
+
+ # Create settings group
+ settings_grp = f.create_group('settings')
+
+ # Write version_string to settings_group
+ settings_grp.create_dataset('used_settings', data=json.dumps(settings_json))
+
+ # Create the data group
+ data_grp = f.create_group('data')
+
+ print('Creating {}'.format(hdf5_filename))
+
+ # Write the data to the file:
+ # Make sure:
+ for data_file in data_files:
+ # filename stuff
+ filename = data_file
+ full_path = os.path.join(data_dir, filename)
+ base_name = os.path.splitext(os.path.basename(filename))[0]
+
+ # Get header info
+ header_name = '{base_name}_header'.format(base_name=base_name)
+ data_headers = np.genfromtxt(full_path, dtype='str', max_rows=1)
+ data_headers = np.char.encode(data_headers)
+ data_grp.create_dataset(header_name, data=data_headers)
+
+ # Add data
+ data = np.loadtxt(full_path, skiprows=1)
+ data_grp.create_dataset(base_name, data=data)
+
+ f.close()
+
def get_help_super(print_help=False, return_dict=True, fail_silently=True):
"""
Function that first runs get_help_all, and then per argument also run the help function to get as much information as possible.
diff --git a/binarycpython/utils/grid.py b/binarycpython/utils/grid.py
index 507983858..f09371556 100644
--- a/binarycpython/utils/grid.py
+++ b/binarycpython/utils/grid.py
@@ -11,6 +11,7 @@ from binarycpython.utils.custom_logging_functions import (
autogen_C_logging_code,
binary_c_log_code,
create_and_load_logging_function,
+ temp_custom_logging_dir,
)
from binarycpython.utils.functions import get_defaults
@@ -32,7 +33,7 @@ from binarycpython.utils.functions import get_defaults
# DONE: add functionality to return the evcode_version_string
# Make this function also an API call. Doest seem to get written to a buffer that is stored into a python object. rather its just written to stdout
# DONE: add functionality to return the evcode_args_list
-
+# TODO: add grid generation script
class Population(object):
def __init__(self):
@@ -107,7 +108,8 @@ class Population(object):
if not parameter_dict:
parameter_dict = self.bse_options
- argline = "binary_c "
+ argline = "binary_c "
+ # TODO: check if that sort actually works
for param_name in sorted(parameter_dict):
argline += "{} {} ".format(param_name, parameter_dict[param_name])
argline = argline.strip()
@@ -120,18 +122,7 @@ class Population(object):
pass
- def add_grid_variable(
- self,
- name,
- longname,
- range,
- resolution,
- spacingfunc,
- precode,
- probdist,
- dphasevol,
- condition,
- ):
+ def add_grid_variable(self, name, longname, valuerange, resolution, spacingfunc, precode, probdist, dphasevol, condition=None):
"""
Function to add grid variables to the grid_options.
@@ -173,9 +164,9 @@ class Population(object):
grid_variable = {
"name": name,
"longname": longname,
- "range": range, # TODO: change name
+ "valuerange": valuerange,
"resolution": resolution,
- "spacingfunction": spacingfunction,
+ "spacingfunc": spacingfunc,
"precode": precode,
"probdist": probdist,
"dphasevol": dphasevol,
@@ -253,19 +244,35 @@ class Population(object):
return all_info
- def export_all_info(self, outfile):
+ def export_all_info(self, use_datadir=False, outfile=None):
"""
Function that exports the all_info to a json file
TODO: if any of the values in the dicts here is of a not-serializable form, then we need to change that to a string or something
so, use a recursive function that goes over the all_info dict and finds those that fit
+
+ TODO: Fix to write things to the directory. which options do which etc
"""
all_info = self.return_all_info()
- # if not outfile.endswith('json'):
- with open(outfile, "w") as f:
- f.write(json.dumps(all_info, indent=4))
+ if use_datadir:
+ base_name = os.path.splitext(self.custom_options['base_filename'])[0]
+ settings_name = base_name + '_settings.json'
+
+ # Check directory, make if necessary
+ os.makedirs(self.custom_options['data_dir'], exist_ok=True)
+
+ settings_fullname = os.path.join(self.custom_options['data_dir'], settings_name)
+
+ # if not outfile.endswith('json'):
+ with open(settings_fullname, "w") as f:
+ f.write(json.dumps(all_info, indent=4))
+
+ else:
+ # if not outfile.endswith('json'):
+ with open(outfile, "w") as f:
+ f.write(json.dumps(all_info, indent=4))
def set_custom_logging(self):
"""
@@ -425,5 +432,86 @@ class Population(object):
print("\n\nBinary_c output:")
print(output)
+ ###################################################
+ # Unordered functions
+ ###################################################
+
+
+ def generate_grid_code(self):
+ """
+ Function that generates the code from which the population will be made.
+
+ # TODO: make a generator for this.
+ # TODO: Add correct logging everywhere
+ # TODO: add different types of grid.
+ """
+
+ code_string = ""
+ depth = 0
+ indent = ' '
+
+ # Set some values in the generated code:
+
+ # TODO: add imports
+ # TODO:
+
+ code_string += "starcount = 0\n"
+ code_string += "probsum = []\n"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ # Generate code
+ print("Generating grid code")
+ for el in sorted(self.grid_options["grid_variables"].items(), key=lambda x: x[1]['grid_variable_number']):
+ print("Constructing/adding: {}".format(el[0]))
+ grid_variable = el[1]
+
+ # Adding for loop structure
+ code_string += indent * depth + 'for {} in range({}, {}):'.format(grid_variable['name'], grid_variable['valuerange'][0], grid_variable['valuerange'][1]) + '\n'
+
+ # Add pre-code
+ code_string += indent * (depth + 1) + '{}'.format(grid_variable['precode'].replace('\n', '\n'+indent * (depth + 1))) + '\n'
+
+ # Calculate probability
+
+
+ # some testing line.
+ code_string += indent * (depth + 1) + 'print({})'.format(grid_variable['name']) + '\n'
+
+ # Add some space
+ code_string += "\n"
+
+ #
+ depth += 1
+
+
+ # Write to file
+ gridcode_filename = os.path.join(temp_custom_logging_dir(), 'example_grid.py')
+ with open(gridcode_filename, 'w') as f:
+ f.write(code_string)
+
+
-################################################################################################
\ No newline at end of file
+################################################################################################
--
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