Source code for braviz.readAndFilter.config_file
##############################################################################
# Braviz, Brain Data interactive visualization #
# Copyright (C) 2014 Diego Angulo #
# #
# This program is free software: you can redistribute it and/or modify #
# it under the terms of the GNU Lesser General Public License as #
# published by the Free Software Foundation, either version 3 of the #
# License, or (at your option) any later version. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU Lesser General Public License for more details. #
# #
# You should have received a copy of the GNU Lesser General Public License#
# along with this program. If not, see <http://www.gnu.org/licenses/>. #
##############################################################################
"""Contains a class for accessing Braviz configuration from configuration files and functions to access such files"""
import os
from ConfigParser import RawConfigParser
import logging
import vtk
__author__ = 'Diego'
[docs]class BravizConfig(RawConfigParser):
"""Holds Braviz configuration"""
[docs] def get_background(self):
"""Background color from a configuration file
.. deprecated:: 3.0b
Use a gray or degraded gray background
Returns:
tuple : RGB value as a float tuple
"""
back_string = self.get('VTK', 'background')
back_list = back_string.split(' ')
back_nums = map(float, back_list)
return tuple(back_nums)
[docs] def get_interaction_style(self):
"""Interaction style from a configuration file
.. deprecated:: 3.0b
Use TrackballCamera
Checks if the intraction style is a valid vtk interaction style and returns vtk name
Returns:
vtkInteractorStyle class
"""
vtk_attrs = dir(vtk)
upper_vtk_attrs = map(lambda x: x.upper(), vtk_attrs)
custom_interactor_style = self.get('VTK', 'interaction_style')
interaction_style = 'vtkInteractorStyle%s' % custom_interactor_style
try:
idx = upper_vtk_attrs.index(interaction_style.upper())
except ValueError:
log = logging.getLogger(__name__)
log.error('Erroneous interactor_style value %s' %
custom_interactor_style)
raise Exception(
'Erroneous interactor_style value %s' % custom_interactor_style)
style = vtk_attrs[idx]
return style
[docs] def get_default_variables(self):
"""
Default variables from configuration file
Returns:
dict : A dictionary containing the default variables. The keys are
``{"nom1","nom2","ratio1","ratio2","lat"}``
"""
nom1 = self.get('Default_Variables', 'nominal1')
nom2 = self.get('Default_Variables', 'nominal2')
ratio1 = self.get('Default_Variables', 'numeric1')
ratio2 = self.get('Default_Variables', 'numeric2')
lat = self.get('Default_Variables', 'laterality')
return {"nom1": nom1, "nom2": nom2, "ratio1": ratio1, "ratio2": ratio2, "lat": lat}
[docs] def get_laterality(self):
"""
Laterality from configuration file
Returns:
A tuple ``(lat, left)`` where *lat* is the name of the nominal variable containing laterality information
and *left* is the label (integer) this variable takes for left-handed subjects.
"""
lat = self.get('Default_Variables', 'laterality')
left = self.getint('Default_Variables', 'left_handed_label')
return lat, left
[docs] def get_default_subject(self):
"""
Default subject from configuration file
Returns:
An integer containing the code for the chosen default subject
"""
return self.getint('Defaults', 'default_subject')
[docs] def get_reference_population(self):
"""
Reference population from configuration file
Returns:
A tuple ``(var,label)`` where *var* is the name of the nominal variable that separates the reference population
and *label* is the integer value this variable takes for the reference population
"""
var = self.get('Default_Variables', 'reference_pop_var')
label = self.getint('Default_Variables', 'reference_pop_label')
return var, label
def get_project_name(self):
return self.get("Braviz", "project")
[docs]def get_apps_config():
"""
Reads configuration from the 'braviz.applications' directory :class:`BravizConfig`
Args:
lala (str): mamama :class:`BravizConfig`
Returns:
BravizConfig : An instance of :class:`BravizConfig` containing the configuration specified in the file at
the applications directory
"""
apps_dir = os.path.join(os.path.dirname(__file__), "..", "applications")
return get_config(apps_dir)
[docs]def get_config(custom_dir=None):
"""
Read Braviz configuration file
A default configuration file is read at the library directory. A secondary configuration can also be read,
and in this case its values will overwrite default ones.
Args:
custom_dir (str) : Location of a secondary configuration file.
For convenience a file can also be passed and the directory containing it will be used
Returns:
BravizConfig : An instance of :class:`BravizConfig` containing the configuration specified in the file at
the specified directory
"""
config_dir = os.path.dirname(os.path.realpath(__file__))
config_file_name = 'braviz.cfg'
default_config_name = os.path.join(config_dir, config_file_name)
config_files = [default_config_name]
if custom_dir is not None:
if os.path.isfile(custom_dir):
custom_dir = os.path.dirname(custom_dir)
custom_dir = os.path.realpath(custom_dir)
full_config_name = os.path.join(custom_dir, config_file_name)
if not os.path.isfile(full_config_name):
make_default_config(full_config_name)
else:
config_files.append(full_config_name)
# print config_files
braviz_conf = BravizConfig()
braviz_conf.read(config_files)
return braviz_conf
[docs]def make_default_config(default_config_name=None):
"""Creates a configuration file with default parameters and stores it
Args:
default_config_name (str) : Name used to store the default configuration,
if ``None`` it stored as `braviz.cfg` in the directory containing this library
"""
if default_config_name is None:
config_dir = os.path.dirname(os.path.realpath(__file__))
config_file_name = 'braviz.cfg'
default_config_name = os.path.join(config_dir, config_file_name)
braviz_conf = BravizConfig()
braviz_conf.add_section('Braviz')
braviz_conf.set('Braviz', 'project', 'kmc400')
braviz_conf.set('Braviz', 'server_port', '8100')
braviz_conf.set('Braviz', 'logger', 'console')
braviz_conf.set('Braviz', 'web_logger_server', '127.0.0.1:8050')
braviz_conf.add_section("Default_Variables")
braviz_conf.set('Default_Variables', 'nominal1', 'ubicac')
braviz_conf.set('Default_Variables', 'nominal2', 'BIRTH_sexo5')
braviz_conf.set('Default_Variables', 'numeric1', 'WASI_FSIQ_4')
braviz_conf.set('Default_Variables', 'numeric2', 'BIRTH_peso5')
braviz_conf.set(
'Default_Variables', 'laterality', 'LAT_EdinburgHandedness')
braviz_conf.set('Default_Variables', 'left_handed_label', 3)
braviz_conf.set('Default_Variables', 'reference_pop_var', 'ubicac')
braviz_conf.set('Default_Variables', 'reference_pop_label', 3)
braviz_conf.add_section("Defaults")
braviz_conf.set('Defaults', 'default_subject', 119)
braviz_conf.add_section('VTK')
braviz_conf.set('VTK', 'Background', '0.1 0.1 0.2')
braviz_conf.set('VTK', 'Interaction_Style', 'TrackballCamera')
log = logging.getLogger(__name__)
try:
with open(default_config_name, 'w') as config_file:
braviz_conf.write(config_file)
log.info("default configuration file created in %s" %
default_config_name)
except IOError:
log.error("couldn't create default configuration file in %s" %
default_config_name)
return braviz_conf
[docs]def get_host_config(project, hostname=None):
"""
Reads host configuration for a given project
Args:
project (str) : The name of the project. This function will look for a file called ``<project>_hosts.cfg``
in the directory containing the module :mod:`braviz.applications`
hostname (str) : Name of host to get configuration. If ``None`` the name of the current host,
as returned by :func:`platform.node` will be used
Returns:
dict : A dictionary containing the requested configuration parameters.
"""
log = logging.getLogger(__name__)
if hostname is None:
import platform
hostname = platform.node()
config = RawConfigParser()
file_name = os.path.join(
os.path.dirname(__file__), "..", "applications", "%s_hosts.cfg" % project)
config.read(file_name)
if not config.has_section(hostname):
log.info("No exact match found, trying default")
hostname = "default"
if not config.has_section(hostname):
apps_dir = os.path.normpath(os.path.dirname(file_name))
raise KeyError("Unknown host %s\nPlease modify the %s_hosts.cfg file in %s" % (
hostname, project, apps_dir))
items = dict(config.items(hostname))
return items
if __name__ == "__main__":
config_dir = os.path.dirname(os.path.realpath(__file__))
config_file_name = 'braviz.cfg'
default_config_name = os.path.join(config_dir, config_file_name)
make_default_config(default_config_name)
# config_dir = os.path.join(config_dir, "..", "applications")
# default_config_name = os.path.join(config_dir, config_file_name)
# make_default_config(default_config_name)