def test_read_config():
"""Function to unit test the reading of the pipeline's JSON config files"""
config_file_path = '../../Config/config.json'
config = config_utils.read_config(config_file_path)
assert type(config) == type({'a': 1, 'b': 2})
assert 'proc_data' in config.keys()
config_file_path = '../../Config/inst_config.json'
config = config_utils.read_config(config_file_path)
assert type(config) == type({'a': 1, 'b': 2})
assert 'instrid' in config.keys()
def main():
print("Reading configuration")
config = read_config()
print("Fetching data")
raw_epc_data = get_epc_data(config.epc_data_url, True)
print("Cleaning data")
data = clean_data(raw_epc_data, config.data_columns)
print("Writing data")
# Wait for postgres to start ... should be handled at the infra level
time.sleep(5)
pg = Postgres(config)
pg.write_data(data, config.postgres_table_name)
print("Verifying data")
print(pg.read_data())
print("Complete")
def test_set_config_value():
test_key = 'proc_data'
new_value = '/Users/test/path'
config_file_path = path.join(TEST_DATA, 'config.json')
copyfile('../../Config/config.json', config_file_path)
init_config = config_utils.read_config(config_file_path)
status = config_utils.set_config_value(config_file_path, test_key,
new_value)
updated_config = config_utils.read_config(config_file_path)
assert updated_config[test_key]['value'] == new_value
remove(config_file_path)
def setup_options(self):
# setup the list of COMPorts
self.set_listofcomports(get_list_ports())
# Handel Config
try:
config_file = config_utils.read_config()
except Exception as e:
print(e)
config_file = False
if config_file:
# set up log bacse on config
if 'log_dir' in config_file and config_file['log_dir']:
if not os.path.exists(config_file['log_dir']):
os.makedirs(config_file['log_dir'])
self.ui.LogDir.setText(config_file['log_dir'])
else:
self.ui.LogDir.setText(self.make_log_dir())
# set up baudrate base on config
if 'baudrate' in config_file and config_file['baudrate']:
self.ui.Baudrate.setCurrentIndex(
config_utils.get_baudrate_index(config_file['baudrate']))
# set up font base on config
if 'font' in config_file and config_file['font']:
self.ui.fontComboBox_2.setCurrentIndex(
self.ui.fontComboBox_2.findText(config_file['font']))
if 'font_size' in config_file and config_file['font_size']:
self.ui.FontSize.setValue(config_file['font_size'])
# setup nightmode and log base on config
# night mode:
if 'nightmode' in config_file:
if not config_file['nightmode']:
self.ui.checkBox_2.setChecked(False)
# config setting
if 'logenabled' in config_file:
if not config_file['logenabled']:
self.ui.checkBox.setChecked(False)
if 'log_rotaion_enabled' in config_file:
if not config_file['log_rotaion_enabled']:
self.ui.LogRotation.setChecked(False)
if 'log_rotation_size' in config_file:
if isinstance(config_file['log_rotation_size'], int):
self.ui.LogSize.setValue(config_file['log_rotation_size'])
else:
self.ui.LogDir.setText(self.make_log_dir())
self.ui.Baudrate.setCurrentIndex(0)
self.ui.checkBox_2.setChecked(True)
self.ui.checkBox.setChecked(True)
# Setup defaul log name
self.ui.LogName.setText(self.make_log_name())
def show_config(self):
msg = QMessageBox()
msg.setStandardButtons(QMessageBox.Ok | QMessageBox.RestoreDefaults
| QMessageBox.Cancel)
if config_utils.read_config():
string_to_show = "Current Settings Saved:\n\n" + str(
config_utils.read_config()).replace(",", "\n")
msg.setDetailedText("Configuration File:\n{0}\n{1}".format(
config_utils.get_path_config_file(), string_to_show))
else:
msg.setDetailedText(
"No Config file found.\nSave Current config to start.")
current_logpath = self.get_log_dir()
current_baudrate = self.get_baud_rate()
current_font = self.get_font()
current_font_size = str(self.get_font_size())
if self.get_night_mode():
current_nightmode = "On"
else:
current_nightmode = "Off"
if self.get_logenabled():
current_logsetting = "On"
else:
current_logsetting = "Off"
if self.get_logrotation():
current_logrotation = "On"
log_rotation_size = self.get_logrotationsize()
else:
current_logrotation = "off"
log_rotation_size = "-"
msg.setWindowTitle("Current Configuration:")
msg.setText(
"Log Path: {0}\nBaudrate: {1}\nFont: {2}-{5}\nNight Mode: {3}\nLogging: {4}\nLog Rotation: {6} at {7} MB"
.format(current_logpath, current_baudrate, current_font,
current_nightmode, current_logsetting, current_font_size,
current_logrotation, log_rotation_size))
#msg.buttonClicked.connect(save_config_handler)
msg.buttonClicked.connect(self.save_config_handler)
retval = msg.exec_()
def generate_map():
"""Function to plot given pixel positions on a HEALpix map"""
# Get user optional parameters
options = get_args()
# Fetch configuration:
config = config_utils.read_config(options['config_file'])
# Initialze the HEALpix map
#ahp = HEALPix(nside=NSIDE, order='ring', frame=TETE())
# Load data on the locations of regions of interest depending on user selections:
if options['object_list'] == 'O':
regions = load_open_cluster_data(config)
elif options['object_list'] == 'G':
regions = load_globular_cluster_data(config)
elif options['object_list'] == 'M':
regions = load_Magellenic_Cloud_data(config)
elif options['object_list'] == 'GB':
regions = load_Galactic_Bulge_data(config)
elif options['object_list'] == 'GP':
regions = load_Galactic_Plane_data(config)
elif options['object_list'] == 'C':
regions = load_Clementini_region_data(config)
elif options['object_list'] == 'B':
regions = load_Bonito_SFR_data(config)
elif options['object_list'] == 'Z':
regions = load_SFR_data(config)
elif options['object_list'] == 'P':
regions = load_optimized_pencilbeams(config)
elif options['object_list'] == 'LP':
regions = load_larger_pencilbeams(config)
# Use the HEALpix map together with the regions of interest to calculate the
# HEALpixels included within those regions:
print('Generating sky map...')
for r in regions:
r.calc_hp_healpixels_for_region()
# Build a map combining the pixel regions of all regions of interest:
maps = build_sky_map(config, options, regions)
# Output the map data:
output_sky_map(config, maps, options)
def reset_module():
options = config_utils.read_config("./monk_adapter.conf","MonkAccount")
print options
monk_adapter.remove_all_data(options['accountid'],options['groupid01'])
options['groupid01'] = monk_adapter.add_group(options['accountid'],"group01","dataCollection01")
monk_adapter.remove_all_data(options['accountid'],options['groupid02'])
options['groupid02'] = monk_adapter.add_group(options['accountid'],"group02","dataCollection02")
#reCreate Categories
like_category_id = monk_adapter.add_category(options['groupid01'],'like')
unlike_category_id = monk_adapter.add_category(options['groupid01'],'unlike')
s_like_category_id = monk_adapter.add_category(options['groupid02'],'like')
s_unlike_category_id = monk_adapter.add_category(options['groupid02'],'unlike')
pairs = {'groupid01':options['groupid01'],'category_like':like_category_id,'category_unlike':unlike_category_id,
'groupid02':options['groupid02'],'s_category_like':s_like_category_id,'s_category_unlike':s_unlike_category_id}
config_utils.write_config("./monk_adapter.conf","MonkAccount",pairs)
best_curriculum_coefficient, best_saver, sess,
test_trajectories_dir, trainer, level):
print_and_log('end of level {} best: {} from step: {}'.format(
level, best_cost, best_cost_global_step))
restore_best(sess, best_saver, best_curriculum_coefficient, trainer)
# test all
test_trajectories_file = os.path.join(test_trajectories_dir,
'level{}_all.txt'.format(level))
endpoints_by_path = trainer.collect_test_data(level,
is_challenging=False)[-1]
serialize_compress(endpoints_by_path, test_trajectories_file)
print_and_log(os.linesep)
# test hard
test_trajectories_file = os.path.join(
test_trajectories_dir, 'level{}_challenging.txt'.format(level))
endpoints_by_path = trainer.collect_test_data(level,
is_challenging=True)[-1]
serialize_compress(endpoints_by_path, test_trajectories_file)
print_and_log(os.linesep)
def restore_best(sess, best_saver, best_curriculum_coefficient, trainer):
best_saver.restore(sess)
trainer.episode_runner.curriculum_coefficient = best_curriculum_coefficient
if __name__ == '__main__':
# read the config
config = read_config()
run_for_config(config)
import config_utils data = config_utils.read_config() print(data["SERVER_URL"])
config['wa_notebook']['notebook_fname'] + '\nreturn code: ' +
str(proc.returncode))
exit(1)
# copy output files to results dir
for fname in config['wa_notebook']['result_fnames']:
src = os.path.join(config['wa_notebook']['dirname'], fname)
dst = os.path.join(config['results_dirname'], fname)
copyfile(src, dst)
def run(config):
'''
execute analysis
:param config:
:return:
'''
df_stats, df_all_folds = combine_wcslp_results(config)
prepare_wa_improve_input_file(df_all_folds, config)
run_wa_improve_notebook(config)
if __name__ == '__main__':
config_file_name = 'config.json'
config = config_utils.read_config(config_file_name)
df_stats, df_all_folds = combine_wcslp_results(config)
prepare_wa_improve_input_file(df_all_folds, config)
run_wa_improve_notebook(config)
def build_priority_maps():
# Fetch configuration:
use_hp_maps = True
if len(argv) < 2:
config_file = input('Please enter the path to the configuration file: ')
else:
config_file = argv[1]
config = config_utils.read_config(config_file)
# Initialze the HEALpix map and storage array - this includes an extra
# column for the combined_map and the maps summed over all filters
#ahp = HEALPix(nside=config['NSIDE'], order='ring', frame=TETE())
NPIX = hp.nside2npix(config['NSIDE'])
# Build vote maps in each filter based on the stellar density of each HEALpix
vote_maps = {}
map_titles = ['combined_map']
for code in config['map_codes']:
map_title = config[code]['file_root_name']
map_titles.append(map_title)
for filter in config['filter_list']:
map = PriorityMap(npix=NPIX,filter=filter)
# Read in component maps for different science cases and add them
# to the combined map for this filter
for code in config['map_codes']:
file_name = path.join(config['output_dir'],
config[code]['file_root_name']+'_'+str(filter)+'.fits')
# map.map_dict contains the original science maps with the
# computed priority per-healpix, since this is calculated on
# various different scientific grounds
if use_hp_maps:
pix_data = hp.read_map(file_name)
map_title = config[code]['file_root_name']
else:
hdul = fits.open(file_name)
pix_data = hdul[1].data['HEALpix_values']
map_title = hdul[0].header['MAPTITLE']
# vote_map contains the sum of all of the maps.
# Note that no renormalization is performed at this stage because
# this has been done for the maps generated by generate_sky_maps.
map.vote_map += pix_data
map.map_dict[map_title] = pix_data
# The final vote_map for this filter is normalized to 1.
map.vote_map = map.vote_map/map.vote_map.max()
vote_maps[filter] = map
# Sum the priority per HEALpix of each science map over all filters
summed_maps = {}
for map_title in map_titles:
sum_map = np.zeros(NPIX)
for filter in config['filter_list']:
if map_title == 'combined_map':
sum_map += vote_maps[filter].vote_map
else:
sum_map += vote_maps[filter].map_dict[map_title]
summed_maps[map_title] = sum_map
# Output the priority map plots in both PNG and FITS formats, and the data
# as a FITS binary table
for filter in config['filter_list']:
map = vote_maps[filter]
fig = plt.figure(3,(10,10))
plot_max = map.vote_map.max()
if np.isnan(plot_max):
plot_max = 1.0
hp.mollview(map.vote_map, title="Regions of Interest "+str(filter)+"-band",
min=0.0, max=plot_max)
hp.graticule()
plt.tight_layout()
plt.savefig(path.join(config['output_dir'],config['output_file_name']+'_plot_'+str(filter)+'.png'))
plt.close(3)
hp.write_map(path.join(config['output_dir'],config['output_file_name']+'_plot_'+str(filter)+'.fits'), map.vote_map, overwrite=True)
# Header
hdr = fits.Header()
hdr['NSIDE'] = config['NSIDE']
hdr['NPIX'] = hp.nside2npix(config['NSIDE'])
hdr['MAPTITLE'] = 'Combined priority survey footprint'
for i,map_title in enumerate(map_titles):
hdr['SCIMAP'+str(i)] = map_title
hdr['VERSION'] = '1.1.0'
phdu = fits.PrimaryHDU(header=hdr)
hdu_list = [phdu]
# First table extension: combined vote map
col_list = []
col_list.append( fits.Column(name='combined_map', array=map.vote_map, format='E') )
# Subsequent extensions contain the component maps for different science cases:
for map_title, data in map.map_dict.items():
col_list.append( fits.Column(name=map_title, array=data, format='E') )
hdu = fits.BinTableHDU.from_columns(col_list)
hdu_list.append(hdu)
hdul = fits.HDUList(hdu_list)
hdul.writeto(path.join(config['output_dir'],
config['output_file_name']+'_data_'+str(filter)+'.fits'),
overwrite=True)
# Output summed maps
hdr = fits.Header()
hdr['NSIDE'] = config['NSIDE']
hdr['NPIX'] = hp.nside2npix(config['NSIDE'])
hdr['MAPTITLE'] = 'Total priority survey footprint'
hdr['VERSION'] = '1.1.0'
phdu = fits.PrimaryHDU(header=hdr)
hdu_list = [phdu]
col_list = []
for map_title in map_titles:
col_list.append( fits.Column(name=map_title, array=summed_maps[map_title], format='E') )
hdu = fits.BinTableHDU.from_columns(col_list)
hdu_list.append(hdu)
hdul = fits.HDUList(hdu_list)
hdul.writeto(path.join(config['output_dir'],
config['output_file_name']+'_data_sum.fits'),
overwrite=True)
close_log()
return best_cost
def end_of_level_test(best_cost, best_cost_global_step, best_curriculum_coefficient, best_saver, sess,
test_trajectories_dir, trainer):
print_and_log('end of run. best: {} from step: {}'.format(best_cost, best_cost_global_step))
restore_best(sess, best_saver, best_curriculum_coefficient, trainer)
# test all
test_trajectories_file = os.path.join(test_trajectories_dir, 'all.txt')
endpoints_by_path = trainer.collect_test_data(is_challenging=False)[-1]
serialize_compress(endpoints_by_path, test_trajectories_file)
print_and_log(os.linesep)
# test hard
test_trajectories_file = os.path.join(test_trajectories_dir, 'challenging.txt')
endpoints_by_path = trainer.collect_test_data(is_challenging=True)[-1]
serialize_compress(endpoints_by_path, test_trajectories_file)
print_and_log(os.linesep)
def restore_best(sess, best_saver, best_curriculum_coefficient, trainer):
best_saver.restore(sess)
trainer.episode_runner.curriculum_coefficient = best_curriculum_coefficient
if __name__ == '__main__':
# read the config
config_path = os.path.join(get_config_directory(), 'config_subgoal_sequential.yml')
config = read_config(config_path)
run_for_config(config)