def from_files(cls, template_filepath, additional_filepaths_list, tag='__KP'):
# Read in template
logger.info("Reading template from file:" + template_filepath)
content = json2dict(template_filepath)
# Get the filename and create a TaggedTemplate
template_filename = os.path.basename(template_filepath)
for additional_filepath in additional_filepaths_list:
print(additional_filepath)
logger.info("Reading additional events from file:" + additional_filepath)
additional_content = json2dict(additional_filepath)
content['Events'] += additional_content['Events']
return cls(template_filename, content, tag)
def from_files(cls, config_name, campaign_name=None, **kwargs):
"""
Build up a simulation configuration from the path to an existing
config.json and optionally a campaign.json file on disk.
Attributes:
config_name (string): Path to the config file to load.
campaign_name (string): Path to the campaign file to load.
kwargs (dict): Additional overrides of config parameters
"""
config = json2dict(config_name)
campaign = json2dict(
campaign_name) if campaign_name else empty_campaign
return cls(config, campaign, **kwargs)
def from_file(cls, template_filepath, tag='__KP'):
# Read in template
logger.info("Reading template from file:" + template_filepath)
content = json2dict(template_filepath)
# Get the filename and create a TaggedTemplate
template_filename = os.path.basename(template_filepath)
return cls(template_filename, content, tag)
def add_immune_overlays(cb, tags, directory=None, site=None):
"""
Add an immunity overlay.
To do so, reads the demographics files and find the corresponding immunity initialization overlay.
:param cb: The :py:class:`DTKConfigBuilder <dtk.utils.core.DTKConfigBuilder>` holding the configuration
:param tags: List of immunity tags that have corresponding initialization files
:param directory: Main directory where the ..._immune_init_x_...json files are stored
:param site: If the site is specified, the files will be expected to be found in the immune_init/site subdirectory.
:return: Nothing
"""
if not directory:
directory = SetupParser().get('input_root')
demogfiles = cb.get_param("Demographics_Filenames")
if len(demogfiles) != 1:
print(demogfiles)
raise Exception(
'add_immune_init function is expecting only a single demographics file.'
)
demog_filename = demogfiles[0]
subdirs, demog_filename = os.path.split(demog_filename)
if '2.5' not in demog_filename:
prefix = demog_filename.split('.')[0]
else:
prefix = '.'.join(demog_filename.split('.')[:2])
# e.g. DataFiles/Zambia/Sinamalima_single_node/immune_init/SinazongweConstant/..._immune_init_x_...json
if site:
subdirs = os.path.join(subdirs, 'immune_init', site)
if 'demographics' not in prefix:
raise Exception(
'add_immune_init function expecting a base demographics layer with demographics in the name.'
)
for tag in tags:
immune_init_name = prefix.replace("demographics", "immune_init_" + tag,
1)
if directory:
cb.add_demog_overlay(
immune_init_name,
json2dict(
os.path.join(directory, subdirs,
'%s.json' % immune_init_name)))
else:
cb.append_overlay(
os.path.join(subdirs, '%s.json' % immune_init_name))
cb.enable("Immunity_Initialization_Distribution"
) # compatibility with EMOD v2.0 and earlier
cb.set_param("Immunity_Initialization_Distribution_Type",
"DISTRIBUTION_COMPLEX")
def from_file(cls, template_filepath):
"""
Initialize a BaseTemplate from a file path.
:param template_file: Path to the file on disk.
"""
# Read in template
logger.info("Reading config template from file: %s" %
template_filepath)
contents = json2dict(template_filepath)
# Get the filename and create a ConfigTemplate
template_filename = os.path.basename(template_filepath)
return cls(template_filename, contents)