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4th module is renamed. utils is updated. config is updated.
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@hoomanzabeti
hoomanzabeti committed Apr 7, 2021
1 parent 1e7f6ce commit 64f3519
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Showing 5 changed files with 65 additions and 76 deletions.
50 changes: 20 additions & 30 deletions config.yml
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Original file line number Diff line number Diff line change
@@ -1,72 +1,62 @@
---
design_param:
'general':
'seed':
'mode': 'range'
'values': [0,1,1]
'N':
'mode': 'scalar'
'values': [1000]
'm':
'mode': 'range'
'values': [10,30,10]
'verbose': False
'groups':
input: 'design_matrix.csv'
design:
groups:
#input: 'design_matrix.csv'
params:
seed: 10
N: 1000
'm':
'mode': 'range'
'values': [10,30,10]
'verbose': False
'run_ID': 'debugging'
'plotting': False
'saving': True
'graph_gen_method': 'no_multiple'
'group_size':
'mode': 'scalar'
'mode': 'list'
'values': [16]
'max_tests_per_individual':
'mode': 'scalar'
'mode': 'list'
'values': [16]
'individual_status':
input: 'individual_status.csv'
params:
's':
'mode': 'scalar'
'mode': 'list'
'values': [50]
'test_results':
'input': 'test_results.csv'
'params':
'test_noise_methods': ['permutation']
'permutation_noise_prob':
'mode': 'scalar'
'mode': 'list'
'values': [0.01]
'theta_l':
'mode': 'scalar'
'mode': 'list'
'values': [0.00]
'theta_u':
'mode': 'scalar'
'mode': 'list'
'values': [0.0625]
'binary_symmetric_noise_prob':
'mode': 'scalar'
'mode': 'list'
'values': [0.26]

decoder_param:
'decode':
decode:
'decoder':
'lambda_w': 1
'lambda_e':
'mode': 'scalar'
'values': [0.125,0.25,0.5,1,2,4,8]
'lambda_e': 0.25
'defective_num_lower_bound': null
'sensitivity_threshold': null
'specificity_threshold': null
'is_it_noiseless': False
'lp_relaxation': False
'solver_name': 'CPLEX_PY'
'solver_options':
'mode': 'exact'
'timeLimit': 1800
'lambda_selection':
'cross_validation': False
'lambda_selection': True
'number_of_folds': 2
'cv_param':
'mode': 'exact'
'lambda_e': [0.125,0.25,0.5,1,2,4,8]
#'mip':True
'evaluation':
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2 changes: 1 addition & 1 deletion group_testing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
from group_testing_optimizer import GT_optimizer
from group_testing_evaluation import decoder_evaluation
from group_testing_reporter import decoder_reporter
from model_preprocessing_with_pulp import *
from group_testing_decoder import *
import os
import decoder
import argparse
Expand Down
0 model_preprocessing_with_pulp.py → group_testing_decoder.py
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File renamed without changes.
3 changes: 1 addition & 2 deletions group_testing_mp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
from generate_groups import gen_measurement_matrix
from generate_individual_status import gen_status_vector
from group_testing_evaluation import decoder_evaluation
from model_preprocessing_with_pulp import *
from group_testing_decoder import *
from multiprocessing import Pool
from multiprocessing import cpu_count
import numpy as np
Expand Down Expand Up @@ -157,7 +157,6 @@ def multi_process_group_testing(design_param, decoder_param):
# param = config_decoder(config_dict['param'])
# lambda_selection = param['lambda_selection']
design_param, decoder_param = config_reader('config.yml')
print(design_param,decoder_param)
# output files path
path = os.getcwd()
currentDate = datetime.datetime.now()
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86 changes: 43 additions & 43 deletions utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,13 +34,15 @@ def config_decoder(config_inpt):
for keys, vals in config_inpt.items():
if isinstance(vals, dict):
#print(vals)
if config_inpt[keys]['mode'] == 'range':
config_inpt[keys] = np.arange(*config_inpt[keys]['values'])
elif config_inpt[keys]['mode'] == 'scalar':
config_inpt[keys] = config_inpt[keys]['values']
if 'mode' in config_inpt[keys].keys():
if config_inpt[keys]['mode'] == 'range':
config_inpt[keys] = np.arange(*config_inpt[keys]['values'])
elif config_inpt[keys]['mode'] == 'list':
config_inpt[keys] = config_inpt[keys]['values']
# TODO: remove mode = exact there is no need for it!
elif config_inpt[keys]['mode'] == 'exact':
config_inpt[keys].pop('mode')
#elif config_inpt[keys]['mode'] == 'dict':
else:
#config_inpt[keys].pop('mode')
config_inpt[keys] = [config_inpt[keys]]
else:
config_inpt[keys] = [vals]
Expand All @@ -66,26 +68,26 @@ def config_reader(config_file_name):
e = sys.exc_info()[0]
print("config file can not be found!")
print("Error:", e)
design_param = {'general': False, 'generate_groups': False, 'generate_individual_status': False,
design_param = {'generate_groups': False, 'generate_individual_status': False,
'generate_test_results': False, 'test_results': False}
decoder_param = {'decode': False, 'lambda_selection': False, 'evaluation': False}
decoder_param = {'decoder': False, 'lambda_selection': False, 'evaluation': False}
# Load params
if 'design_param' in config_dict.keys():
try:
# assert 'general' in config_dict['design_param'].keys(), "You should define general properties of design!"
general_param = config_dict['design_param']['general']
design_param['general'] = True
design_param.update(general_param)
except KeyError:
print("Warning: 'general' block is not found in the config file! We try to recover essential information "
"from the input files!")
assert 'groups' in config_dict['design_param'].keys(), \
if 'design' in config_dict.keys():
# try:
# # assert 'general' in config_dict['design_param'].keys(), "You should define general properties of design!"
# general_param = config_dict['design_param']['general']
# design_param['general'] = True
# design_param.update(general_param)
# except KeyError:
# print("Warning: 'general' block is not found in the config file! We try to recover essential information "
# "from the input files!")
assert 'groups' in config_dict['design'].keys(), \
"You should define the 'groups' block in the config file!"
generate_groups = config_input_or_params(config_dict['design_param']['groups'], 'groups', 'generate_groups')
generate_groups = config_input_or_params(config_dict['design']['groups'], 'groups', 'generate_groups')
design_param.update(generate_groups)
try:
generate_individual_status = config_input_or_params(
current_dict=config_dict['design_param']['individual_status'],
current_dict=config_dict['design']['individual_status'],
block_name='individual_status',
generate_label='generate_individual_status')
design_param.update(generate_individual_status)
Expand All @@ -94,46 +96,43 @@ def config_reader(config_file_name):
"if the results need to be evaluated!")
# if 'test_results' in config_dict['design_param'].keys():
try:
generate_test_results = config_input_or_params(config_dict['design_param']['test_results'], 'test_results',
generate_test_results = config_input_or_params(config_dict['design']['test_results'], 'test_results',
'generate_test_results')
design_param.update(generate_test_results)
design_param['test_results'] = True
except KeyError:
print("Warning: 'test_results' block is not found in the config file! Test results is necessary for"
" decoding!")
if 'decoder_param' in config_dict.keys():
if 'decode' in config_dict.keys():
assert design_param['test_results'], "It is not possible to decode without test results! Please define the " \
"'test_results' block in the config file."
if 'decode' in config_dict['decoder_param'].keys():
if 'decoder' in config_dict['decode'].keys():
try:
decode_param = config_dict['decoder_param']['decode']
decoder_param['decode'] = True
decode_param = config_dict['decode']['decoder']
decoder_param['decoder'] = True
decoder_param.update(decode_param)
except:
# TODO: this should be KeyError
e = sys.exc_info()[0]
print("config file format is not correct!")
print("Error1:", e)
if 'lambda_selection' in config_dict['decoder_param'].keys():
try:
lambda_selection_param = config_dict['decoder_param']['lambda_selection']
decoder_param['lambda_selection'] = True
decoder_param.update(lambda_selection_param)
except:
# TODO: this should be KeyError
print("decoder format in the config file is not correct!")
e = sys.exc_info()[0]
print("config file format is not correct!")
print("Error2:", e)
if 'evaluation' in config_dict['decoder_param'].keys():
print("Error:", e)
# if 'lambda_selection' in config_dict['decoder_param'].keys():
# try:
# lambda_selection_param = config_dict['decoder_param']['lambda_selection']
# decoder_param['lambda_selection'] = True
# decoder_param.update(lambda_selection_param)
# except:
# e = sys.exc_info()[0]
# print("config file format is not correct!")
# print("Error2:", e)
if 'evaluation' in config_dict['decode'].keys():
try:
evaluation_param = config_dict['decoder_param']['evaluation']
evaluation_param = config_dict['decode']['evaluation']
decoder_param['evaluation'] = True
decoder_param.update(evaluation_param)
except:
# TODO: this should be KeyError
print("evaluation format in the config file is not correct!")
e = sys.exc_info()[0]
print("config file format is not correct!")
print("Error3:", e)
print("Error:", e)

return config_decoder(design_param), config_decoder(decoder_param)

Expand All @@ -157,3 +156,4 @@ def path_generator(file_path, file_name, file_format):
if __name__ == '__main__':
design_param, decoder_param = config_reader('config.yml')
print(design_param, decoder_param)
print(len(design_param), len(decoder_param))

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