--- a
+++ b/preprocessOfApneaECG/mit2Segments.py
@@ -0,0 +1,370 @@
+"""
+	This file include some functions for converting raw Apnea-ECG database to many txt files, each txt file including
+	 a 60s ECG segment corresponding with labels came from raw Apnea-ECG database.
+
+	Before run this file, you first set path information.
+	
+	If you want to know more information about Apnea-ECG database, please see https://physionet.org/physiobank/database/apnea-ecg/.
+	
+"""
+
+__version__ = '0.2'
+__time__ = "2019.06.22"
+__author__ = "zzklove3344"
+
+import wfdb
+import os
+import numpy as np
+
+# path information
+# You need to set these file path before you run this file.
+# Raw apnea-ecg database. You must download firstly.
+APNEA_ECG_DATABASE_PATH = "G:/Apnea-ecg/raw records/"
+# Folder for writing apnea-ecg 60s segments
+SEGMENTS_BASE_PATH = "F:/Apnea-ecg/ecg segments/"
+
+# The number of segments in train set
+SEGMENTS_NUMBER_TRAIN = 17045
+# The number of segments in test set
+SEGMENTS_NUMBER_TEST = 17268
+
+APNEA_ECG_TRAIN_FILENAME = [
+	"a01", "a02", "a03", "a04", "a05", "a06", "a07", "a08", "a09", "a10",
+	"a11", "a12", "a13", "a14", "a15", "a16", "a17", "a18", "a19", "a20",
+	"b01", "b02", "b03", "b04", "b05",
+	"c01", "c02", "c03", "c04", "c05", "c06", "c07", "c08", "c09", "c10"
+]
+
+# The number of 60s segments for every subject in a01-a20, b01-b05, c01-c10
+TRAIN_LABEL_AMOUNT = [489, 528, 519, 492, 454,
+			  510, 511, 501, 495, 517,
+			  466, 577, 495, 509, 510,
+			  482, 485, 489, 502, 510,
+			  487, 517, 441, 429, 433,
+			  484, 502, 454, 482, 466,
+			  468, 429, 513, 468, 431]
+
+APNEA_ECG_TEST_FILENAME = [
+	"x01", "x02", "x03", "x04", "x05", "x06", "x07", "x08", "x09", "x10",
+	"x11", "x12", "x13", "x14", "x15", "x16", "x17", "x18", "x19", "x20",
+	"x21", "x22", "x23", "x24", "x25", "x26", "x27", "x28", "x29", "x30",
+	"x31", "x32", "x33", "x34", "x35"
+]
+
+# The number of 60s segments for every subject in x01-x35
+TEST_LABEL_AMOUNT = [523, 469, 465, 482, 505,
+			  450, 509, 517, 508, 510,
+			  457, 527, 506, 490, 498,
+			  515, 400, 459, 487, 513,
+			  510, 482, 527, 429, 510,
+			  520, 498, 495, 470, 511,
+			  557, 538, 473, 475, 483]
+
+ECG_RAW_FREQUENCY = 100
+
+
+class Mit2Segment:
+	"""
+	Mit to 60s segments.
+	"""
+	
+	def __init__(self):
+		self.raw_ecg_data = None  # list, raw ecg data
+		self.denoised_ecg_data = None 	# list, raw ecg data
+		r"""basic attributes"""
+		self.label = None  # int, 0 or 1
+		self.database_name = None  # string, "apnea ecg"
+		self.filename = None  # string, like "a01", "x02"
+		self.local_id = None  # int, the ID in filename, like 101 in "a01"
+		self.global_id = None  # int, global ID in database(train set or test set)
+		self.samplefrom = None  # int, sample from where
+		self.sampleto = None  # int, sample to where
+		self.base_file_path = None		# string
+		
+	def write_ecg_segment(self, rdf):
+		"""
+		Write minute-by-minute ECG segment to txt file.
+		:param int rdf: 0 means to write to raw ecg file, 1 means to write to denoised ecg file.
+		:return: None
+		"""
+		
+		# a01-a10, b01-b05 and c01-c10 belong to train set;
+		# x01-x35 belong to test set.
+		# if self.filename.find('x') >= 0:
+		# 	file_path = SEGMENTS_BASE_PATH + "test/" + str(self.global_id) + "/"
+		# else:
+		# 	file_path = SEGMENTS_BASE_PATH + "train/" + str(self.global_id) + "/"
+		if not os.path.exists(self.base_file_path):
+			os.makedirs(self.base_file_path)
+		if rdf == 0:
+			filename = "raw_ecg_segment_data.txt"
+			ecg_data = self.raw_ecg_data
+		elif rdf == 1:
+			filename = "denosing_ecg_segment_data.txt"
+			ecg_data = self.denoised_ecg_data
+		else:
+			raise Exception("Error rdf value.")
+		
+		attr_name = "database_name file_name local_id samplefrom sampleto global_id label\n"
+		# 将标签转化为数字
+		if self.label == 'A':
+			self.label = 1
+		elif self.label == 'N':
+			self.label = 0
+		
+		with open(self.base_file_path + filename, "w") as f:
+			r"""attributes name """
+			f.write(attr_name)
+			
+			r"""attributes value"""
+			f.write(
+				self.database_name[0] + " " + self.database_name[1] + " "
+				+ self.filename + " " + str(self.local_id) + " "
+				+ str(self.global_id) + " " + str(self.samplefrom) + " "
+				+ str(self.sampleto) + " " + str(self.label) + "\n")
+			
+			r"""data"""
+			for value in ecg_data:
+				f.write(str(value[0]) + "\n")
+	
+	def read_ecg_segment(self, rdf, database_name_or_path):
+		"""
+		Read Minute-by-minute ECG segment from TXT file
+		:param string or list database_name_or_path: the database or the file path you want to read
+		:param int rdf: 0 means to read to raw ecg file, 1 means to read to denoised ecg file.
+		:return: None
+		"""
+		
+		if rdf == 0:
+			filename = "raw_ecg_segment_data.txt"
+		elif rdf == 1:
+			filename = "denosing_ecg_segment_data.txt"
+		else:
+			raise Exception("Error rdf value.")
+		if database_name_or_path == ["apnea-ecg", "train"]:
+			file_path = SEGMENTS_BASE_PATH + "train/" + str(self.global_id) + "/" + filename
+		elif database_name_or_path == ["apnea-ecg", "test"]:
+			file_path = SEGMENTS_BASE_PATH + "test/" + str(self.global_id) + "/" + filename
+		else:
+			file_path = database_name_or_path
+		
+		with open(file_path) as f:
+			_ = f.readline()
+			
+			# attribute values
+			attrs_value = f.readline().replace("\n", "").split(" ")
+			self.database_name = [attrs_value[0], attrs_value[1]]
+			self.filename = attrs_value[2]
+			self.local_id = int(attrs_value[3])
+			self.global_id = int(attrs_value[4])
+			self.samplefrom = int(attrs_value[5])
+			self.sampleto = int(attrs_value[6])
+			self.label = int(attrs_value[7])
+			self.base_file_path = SEGMENTS_BASE_PATH + self.database_name[1] + "/" + str(self.global_id) + "/"
+			
+			# ECG segment data
+			ecg_data = []
+			data_value = f.readline().replace("\n", "")
+			while data_value != "":
+				ecg_data.append(float(data_value))
+				data_value = f.readline().replace("\n", "")
+			if rdf == 0:
+				self.raw_ecg_data = ecg_data
+			elif rdf == 1:
+				self.denoised_ecg_data = ecg_data
+	
+	def read_edr(self, flag):
+		"""
+		flag为0时读取原始edr信号,为1时读取下采样之后的edr信号.
+		:return: None
+		"""
+		
+		edr = []
+		if self.filename.find('x') >= 0:
+			if flag == 0:
+				file_path = SEGMENTS_BASE_PATH + "test/" + str(self.global_id) + "/edr.txt"
+			elif flag == 1:
+				file_path = SEGMENTS_BASE_PATH + "test/" + str(self.global_id) + "/downsampling_EDR.txt"
+			else:
+				file_path = ""
+				print("edr file path error....")
+		else:
+			if flag == 0:
+				file_path = SEGMENTS_BASE_PATH + "train/" + str(self.global_id) + "/edr.txt"
+			elif flag == 1:
+				file_path = SEGMENTS_BASE_PATH + "train/" + str(self.global_id) + "/downsampling_EDR.txt"
+			else:
+				file_path = ""
+				print("edr file path error....")
+		
+		with open(file_path) as f:
+			data_value = f.readline().replace("\n", "")
+			while data_value != "":
+				edr.append(float(data_value))
+				data_value = f.readline().replace("\n", "")
+			edr = np.array(edr)
+		
+		return edr
+
+
+def get_ecg_data_annotations(database_name, is_debug=False):
+	"""
+	Read files in specified database.
+	:param list database_name: Database you want to read.
+							    Reserved paras, it must be ["apnea-ecg", "train"] or ["apnea-ecg", "test"] now.
+	:param bool is_debug: whether is debug mode.
+	:return list: ecg data and annotations.
+
+	example: data_set = get_ecg_data_annotations("train", True)
+	"""
+	
+	data_annotations_set = []
+	file_name_set = None
+	no_apn = None
+	
+	if database_name[0] == "apnea-ecg":
+		root_file_path = APNEA_ECG_DATABASE_PATH
+		if database_name[1] == "train":
+			file_name_set = APNEA_ECG_TRAIN_FILENAME
+			no_apn = False
+		elif database_name[1] == "test":
+			file_name_set = APNEA_ECG_TEST_FILENAME
+			no_apn = True
+	
+	# if database name is test, we first read label file
+	test_label_set = []
+	if no_apn is True:
+		# read event-2.txt, which is test label downloading from PhysioNet
+		test_annotation_path = root_file_path + "event-2.txt"
+		with open(test_annotation_path) as f:
+			lines = f.readlines()
+			for line in lines:
+				line = line.replace("\n", "")
+				for index_str in range(len(line)):
+					if line[index_str] == "A" or line[index_str] == "N":
+						test_label_set.append(line[index_str])
+	
+	file_count = 0  # use when the database name is test.
+	test_label_index = 0  # use when the database name is test.
+	for name in file_name_set:
+		if is_debug:
+			print("process file " + name + "...")
+		
+		file_path = root_file_path + name
+		ecg_data = wfdb.rdrecord(file_path)  # use wfdb.rdrecord to read data
+		
+		if no_apn is False:
+			# use wfdb.rdann to read annotation
+			annotation = wfdb.rdann(file_path, "apn")
+			# annotation range
+			annotation_range_list = annotation.sample
+			# annotation
+			annotation_list = annotation.symbol
+		else:
+			annotation_range_list = []
+			annotation_list = []
+			for index_label in range(TEST_LABEL_AMOUNT[file_count]):
+				annotation_range_list.append(np.array(index_label * 6000))
+				annotation_list.append(test_label_set[test_label_index])
+				test_label_index += 1
+			file_count += 1
+			annotation_range_list = np.array(annotation_range_list)
+		
+		data_annotations_set.append([ecg_data, annotation_range_list, annotation_list, name])
+	
+	return data_annotations_set
+
+
+def process_ecg_data_segments(database_name, data_annotations_set, is_debug=False):
+	"""
+	Divide ECG data to minute-by-minute ECG segment.
+	:param list database_name: name of database.
+	                           Reserved paras, it must be ["apnea-ecg", "train"] or ["apnea-ecg", "test"] now.
+	:param list data_annotations_set: output of function get_ecg_data_annotations.
+	:param bool is_debug: whether is debug mode.
+	:return: None
+	"""
+	
+	data_set = []
+	global_counter = 0  # use for global id
+	
+	base_floder_path = None
+	
+	if database_name[0] == "apnea-ecg":
+		if database_name[1] == "train":
+			base_floder_path = SEGMENTS_BASE_PATH + "/train"
+		elif database_name[1] == "test":
+			base_floder_path = SEGMENTS_BASE_PATH + "/test"
+	
+	# ecg data segments divide
+	for data_annotation in data_annotations_set:
+		segment_amount = len(data_annotation[2])
+		for index_segment in range(segment_amount):
+			eds = Mit2Segment()
+			eds.database_name = database_name
+			eds.samplefrom = data_annotation[1][index_segment]
+			if (data_annotation[1][index_segment] + 6000) > len(data_annotation[0].p_signal):
+				eds.sampleto = len(data_annotation[0].p_signal)
+			else:
+				eds.sampleto = data_annotation[1][index_segment] + 6000
+			eds.raw_ecg_data = data_annotation[0].p_signal[eds.samplefrom:eds.sampleto]
+			eds.label = data_annotation[2][index_segment]
+			eds.filename = data_annotation[3]
+			eds.local_id = index_segment
+			eds.global_id = global_counter
+			eds.base_file_path = SEGMENTS_BASE_PATH + "/" + database_name[1] + "/" + str(eds.global_id) + "/"
+			eds.write_ecg_segment(rdf=0)
+			global_counter += 1
+			data_set.append(eds)
+			if is_debug:
+				print("---------------------------------------------------")
+				print(("global id: %s,  file name: %s, local id: %s") % (
+					str(eds.global_id), eds.filename, str(eds.local_id)))
+				print("---------------------------------------------------")
+	
+	if not os.path.exists(base_floder_path):
+		os.makedirs(base_floder_path)
+	
+	# extra_info, this file store number of all ECG segments.
+	with open(base_floder_path + "/extra_info.txt", "w") as f:
+		f.write("Number of ECG segments\n")
+		f.write(str(global_counter))
+	
+	return data_set
+
+
+def produce_database(database_name, is_debug):
+	"""
+	Produce database. It will write many txt files in SEGMENTS_BASE_PATH.
+	:param list database_name: name of database.
+	                           Reserved paras, it must be ["apnea-ecg", "train"] or ["apnea-ecg", "test"] now.
+	:param bool is_debug: whether is debug mode.
+	:return: None
+	"""
+	
+	# read files from a01-a35, every file including whole ecg data and the corresponding annotation
+	data_annotations_set = get_ecg_data_annotations(database_name, is_debug)
+	# divide ECG data to minute-by-minute ECG segments
+	_ = process_ecg_data_segments(database_name, data_annotations_set, is_debug)
+
+
+def produce_all_database(is_debug):
+	"""
+	Produce train database and test database.
+	:param bool is_debug: whether is debug mode.
+	:return: None
+	"""
+	produce_database(["apnea-ecg", "train"], is_debug)
+	produce_database(["apnea-ecg", "test"], is_debug)
+
+
+if __name__ == '__main__':
+	print("fileIO test statements")
+	# if you want to generate train database, you can run follow statement.
+	# produce_database(["apnea-ecg", "train"], is_debug)
+	
+	# if you want to generate test database, you can run follow statement.
+	# produce_database(["apnea-ecg", "test"], is_debug)
+	
+	# if you want to generate train and test database, you can run follow statement.
+	produce_all_database(True)