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import os
import glob
import json
import argparse
from typing import List, Dict, Any, Union
from collections import Counter
import numpy as np
def get_temp_qa(question_type, paraphrased_path):
"""
Load all question data and return a list of filtered template IDs based on question_type.
Args:
question_type (str): Type of question to filter by ('single-query', 'single-verify', etc., or 'all').
paraphrased_path (str): Base path for the dataset.
Returns:
List[int]: A list of unique template IDs matching the filter criteria.
"""
data = []
for split in ["train", "valid", "test"]:
file_pattern = os.path.join(paraphrased_path, split, "*.json")
for fname in sorted(glob.glob(file_pattern)):
with open(fname, "r") as f:
records = json.load(f)
data.extend(records)
print(f"Loaded {len(data)} samples!")
temp_list = []
if question_type != "all":
for item in data:
if item['question_type'] == question_type:
temp_list.append(item['template_id'])
else:
for item in data:
if "single-" in item['question_type']:
temp_list.append(item['template_id'])
temp_ids = list(set(temp_list))
# Filter template IDs to avoid conflict class
temp_ids = [i for i in temp_ids if i not in [17, 14, 26, 28, 4, 40, 31]]
return temp_ids
def prepare_ecg_qa_data(args):
if args.question_type == "all":
class_qa = get_class_qa("single-verify")
ecg_qa_list_1 = change_ecg_to_qa(
class_qa, "single-verify",
paraphrased_path=args.paraphrased_path,
dif_exp=args.dif_exp
)
class_qa += get_class_qa("single-choose")
ecg_qa_list_2 = change_ecg_to_qa(
class_qa, "single-choose",
paraphrased_path=args.paraphrased_path,
dif_exp=args.dif_exp
)
class_qa += get_class_qa("single-query")
ecg_qa_list_3 = change_ecg_to_qa(
class_qa, "single-query",
paraphrased_path=args.paraphrased_path,
dif_exp=args.dif_exp
)
ecg_qa_list = {**ecg_qa_list_1, **ecg_qa_list_2, **ecg_qa_list_3}
else:
class_qa = get_temp_qa(args.question_type, args.paraphrased_path)
ecg_qa_list = change_ecg_to_qa(
class_qa, args.question_type,
paraphrased_path=args.paraphrased_path,
dif_exp=args.dif_exp
)
all_ecg_qa_temp = list(ecg_qa_list.keys())
sample_size = int(len(all_ecg_qa_temp) * 0.8)
train_temp = np.random.choice(all_ecg_qa_temp, sample_size, replace=False).tolist()
test_temp = [i for i in all_ecg_qa_temp if i not in train_temp]
return class_qa, train_temp, test_temp
def change_ecg_to_qa(
sample_ids,
question_type,
paraphrased_path,
in_template=None,
dif_exp=1,
attr="",
test_dataset="ptb-xl"
):
"""
Process ECG data to create a dictionary of question-answer pairs categorized by template.
Args:
sample_ids (List[int]): List of template IDs to include.
question_type (str): Type of question to filter.
paraphrased_path (str): Base path for all data.
data_root_path (str, optional): Path to the data root directory.
in_template (List, optional): List of templates to include.
dif_exp (int, optional): Controls return format. Default is 1.
attr (str, optional): Attribute type filter.
test_dataset (str, optional): Dataset to use ('ptb-xl' or 'mimic'). Default is 'ptb-xl'.
Returns:
Dict: Dictionary of ECG QA data categorized by template.
"""
data = []
# Define subdirectories to process
subdirectories = ["train", "valid", "test"]
# Load data from all subdirectories
for subdir in subdirectories:
directory_path = os.path.join(paraphrased_path, subdir)
if not os.path.exists(directory_path):
print(f"Warning: Directory {directory_path} does not exist!")
continue
file_pattern = os.path.join(directory_path, "*.json")
files = sorted(glob.glob(file_pattern))
if not files:
print(f"Warning: No JSON files found in {directory_path}")
continue
for fname in files:
with open(fname, "r") as f:
json_data = json.load(f)
data.extend(json_data)
# Filter by attribute type if specified
if attr != "":
sample_data = [item for item in data if item['attribute_type'] == attr]
else:
sample_data = data
# Filter samples by file existence if using MIMIC dataset
if test_dataset == "mimic":
ecg_data_path = os.path.join(paraphrased_path, "mimic_iv_ecg/processed_test_30k/")
if not os.path.exists(ecg_data_path):
print(f"Warning: MIMIC ECG data path {ecg_data_path} does not exist!")
sample_data = [sample for sample in sample_data if os.path.isfile(os.path.join(ecg_data_path, f"{sample['ecg_id'][0]}.mat"))]
ecg_qa_dict = {}
if len(sample_data) == 0:
print(f"Cannot find template_id == {sample_ids} or no data available")
else:
for sample in sample_data:
template_id = sample['template_id']
if template_id in sample_ids:
process_sample_by_type(sample, template_id, ecg_qa_dict, in_template)
filter_ecg_qa_dict_by_question_type(ecg_qa_dict, question_type)
if dif_exp == 1:
return {key: [value] for key, value in ecg_qa_dict.items()}
return filter_by_question_frequency(ecg_qa_dict)
def process_sample_by_type(sample, template_id, ecg_qa_dict, in_template):
"""
Process a sample based on its question type.
Args:
sample (Dict): The sample data.
template_id (int): The template ID.
ecg_qa_dict (Dict): Dictionary to populate with processed data.
in_template (List, optional): List of templates to include.
"""
question_type = sample['question_type']
if question_type == 'single-verify':
process_single_verify_sample(sample, template_id, ecg_qa_dict, in_template)
elif question_type == 'single-choose':
process_single_choose_sample(sample, template_id, ecg_qa_dict, in_template)
elif question_type == 'single-query':
process_single_query_sample(sample, template_id, ecg_qa_dict, in_template)
def process_single_verify_sample(sample, template_id, ecg_qa_dict, in_template):
"""
Process a single-verify type sample.
Args:
sample (Dict): The sample data.
template_id (int): The template ID.
ecg_qa_dict (Dict): Dictionary to populate with processed data.
in_template (List, optional): List of templates to include.
"""
if sample['answer'][0] in ["yes", "no"]:
answer = sample['answer'][0]
all_attributes = "_".join(sorted(sample['attribute']))
dict_key = f"{template_id}_{all_attributes}_{answer}"
if in_template is None or dict_key in in_template:
if dict_key not in ecg_qa_dict:
ecg_qa_dict[dict_key] = [sample]
else:
ecg_qa_dict[dict_key].append(sample)
def process_single_choose_sample(sample, template_id, ecg_qa_dict, in_template):
"""
Process a single-choose type sample.
Args:
sample (Dict): The sample data.
template_id (int): The template ID.
ecg_qa_dict (Dict): Dictionary to populate with processed data.
in_template (List, optional): List of templates to include.
"""
if len(sample['answer']) == 1:
answer = sample['answer'][0]
elif len(sample['answer']) == 2:
answer = "both"
sample['answer'] = ["both"]
else:
print("single-choose data have more than 2 answers!")
return
all_attributes = "_".join(sorted(sample['attribute']))
if in_template is None:
handle_single_choose_without_template(sample, template_id, answer, all_attributes, ecg_qa_dict)
else:
handle_single_choose_with_template(sample, template_id, answer, all_attributes, in_template, ecg_qa_dict)
def handle_single_choose_without_template(sample, template_id, answer, all_attributes, ecg_qa_dict):
"""
Handle a single-choose type sample when no template is provided.
Args:
sample (Dict): The sample data.
template_id (int): The template ID.
answer (str): The answer string.
all_attributes (str): The joined attributes string.
ecg_qa_dict (Dict): Dictionary to populate with processed data.
"""
if answer == "both":
dict_key = f"{template_id}_{all_attributes}_{answer}"
add_to_ecg_qa_dict(dict_key, sample, ecg_qa_dict)
elif answer == "none":
for attr in sample['attribute']:
dict_key = f"{template_id}_{attr}_{answer}"
add_to_ecg_qa_dict(dict_key, sample, ecg_qa_dict)
else:
dict_key = f"{template_id}_{answer}_{answer}"
add_to_ecg_qa_dict(dict_key, sample, ecg_qa_dict)
def handle_single_choose_with_template(sample, template_id, answer, all_attributes, in_template, ecg_qa_dict):
"""
Handle a single-choose type sample when a template is provided.
Args:
sample (Dict): The sample data.
template_id (int): The template ID.
answer (str): The answer string.
all_attributes (str): The joined attributes string.
in_template (List): List of templates to include.
ecg_qa_dict (Dict): Dictionary to populate with processed data.
"""
full_key = f"{template_id}_{all_attributes}_{answer}"
short_key = f"{template_id}_{answer}"
if full_key in in_template or short_key in in_template:
if answer == "both":
dict_key = f"{template_id}_{all_attributes}_{answer}"
add_to_ecg_qa_dict(dict_key, sample, ecg_qa_dict)
elif answer == "none":
for attr in sample['attribute']:
dict_key = f"{template_id}_{attr}_{answer}"
add_to_ecg_qa_dict(dict_key, sample, ecg_qa_dict)
else:
dict_key = f"{template_id}_{answer}_{answer}"
add_to_ecg_qa_dict(dict_key, sample, ecg_qa_dict)
def process_single_query_sample(sample, template_id, ecg_qa_dict, in_template):
"""
Process a single-query type sample.
Args:
sample (Dict): The sample data.
template_id (int): The template ID.
ecg_qa_dict (Dict): Dictionary to populate with processed data.
in_template (List, optional): List of templates to include.
"""
if len(sample['answer']) == 1:
answer = sample['answer'][0]
elif len(sample['answer']) >= 2:
answer = ", ".join(sample['answer'])
sample['answer'] = [answer]
all_attributes = "_".join(sorted(sample['attribute']))
dict_key = f"{template_id}_{all_attributes}_{answer}"
if in_template is None or dict_key in in_template:
if dict_key not in ecg_qa_dict:
ecg_qa_dict[dict_key] = [sample]
else:
ecg_qa_dict[dict_key].append(sample)
def add_to_ecg_qa_dict(key, sample, ecg_qa_dict):
"""
Add a sample to the ECG QA dictionary.
Args:
key (str): The dictionary key.
sample (Dict): The sample data.
ecg_qa_dict (Dict): Dictionary to populate with processed data.
"""
if key not in ecg_qa_dict:
ecg_qa_dict[key] = [sample]
else:
ecg_qa_dict[key].append(sample)
def filter_ecg_qa_dict_by_question_type(ecg_qa_dict, question_type):
"""
Filter the ECG QA dictionary by question type and minimum sample counts.
Args:
ecg_qa_dict (Dict): Dictionary to filter.
question_type (str): Type of question to filter by.
"""
for key in list(ecg_qa_dict.keys()):
if question_type in ["single-verify", "single-choose", "single-query"]:
qt = question_type
elif question_type == "all":
if len(ecg_qa_dict[key]) == 0:
del ecg_qa_dict[key]
continue
qt = ecg_qa_dict[key][0]['question_type']
else:
continue
if qt == "single-verify" and len(ecg_qa_dict[key]) < 140:
del ecg_qa_dict[key]
elif qt == "single-choose" and len(ecg_qa_dict[key]) < 14:
del ecg_qa_dict[key]
elif qt == "single-query" and len(ecg_qa_dict[key]) < 50:
del ecg_qa_dict[key]
def filter_by_question_frequency(ecg_qa_dict):
"""
Filter the ECG QA dictionary by question frequency.
Args:
ecg_qa_dict (Dict): Dictionary to filter.
Returns:
Dict: Filtered dictionary.
"""
for key in list(ecg_qa_dict.keys()):
question_id_counter = Counter(sample['question_id'] for sample in ecg_qa_dict[key])
frequent_question_ids = [q_id for q_id, count in question_id_counter.items() if count >= 10]
all_samples_by_question = []
for question_id in frequent_question_ids:
question_samples = [sample for sample in ecg_qa_dict[key] if sample['question_id'] == question_id]
all_samples_by_question.append(question_samples)
if len(all_samples_by_question) != 0:
ecg_qa_dict[key] = all_samples_by_question
else:
del ecg_qa_dict[key]
return ecg_qa_dict
def validate_path(path):
"""
Validate if a path exists.
Args:
path (str): Path to validate.
Returns:
bool: True if path exists, False otherwise.
"""
if not os.path.exists(path):
return False
return True
def main():
"""
Main function to run the ECG data processing.
"""
parser = argparse.ArgumentParser(description='ECG Data Processor')
parser.add_argument('--paraphrased_path', type=str,
default='path/to/paraphrased',
help='path to ./paraphrased containing trian/val/test ECG-QA json files')
parser.add_argument('--test_dataset', type=str, default="ptb-xl", choices=["ptb-xl", "mimic"],
help='Dataset to use (ptb-xl or mimic)')
args = parser.parse_args()
paraphrased_path = args.paraphrased_path
# Process each question type
for q_type in ['single-verify', 'single-choose', 'single-query', 'all']:
print(f"\nProcessing {q_type} question type...")
# Get template IDs for the question type
temp_ids = get_temp_qa(q_type, paraphrased_path)
print(f"{q_type} temp_ids: {temp_ids} (total: {len(temp_ids)})")
# Get the QA dictionary
ecg_qa_dict = change_ecg_to_qa(
temp_ids,
q_type,
paraphrased_path=paraphrased_path,
test_dataset=args.test_dataset
)
print(f"ECG QA dictionary length: {len(ecg_qa_dict)}")
# Calculate total QA count
total_qa_count = 0
for category_key in ecg_qa_dict.keys():
category_values = ecg_qa_dict.get(category_key)
category_total = sum(len(item) for item in category_values)
total_qa_count += category_total
print(f"Total QA count for '{q_type}': {total_qa_count}")
print("-" * 40)
if __name__ == "__main__":
main() |