peterlu14
683 lines
24 KiB
Python
683 lines
24 KiB
Python
import base64
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import re
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import zlib
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import sys
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import gc
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from collections import Counter
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from typing import Iterable
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from time import time, sleep
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from biopro.devlib.data import *
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from json import loads as json_parse, dumps as _json_stringify
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from typing import Dict, Optional, Any
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from datetime import datetime
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import threading
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from biopro.recording.file import RecordingMetaFile, RecordingFile, RecordingMini, RecordingFileWriter
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from biopro.devlib.data import DataDecodeFormat
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from biopro.util.logger import logging_info, Logger
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from biopro.util.json import JSON_OBJECT
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from .socket import ServerThread
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from multiprocessing import Process, Queue
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from .mqtt import MqttDataMessageHandler, MqttThread
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import biopro.server._identify
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from concurrent.futures import ThreadPoolExecutor, as_completed
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_RUNTIME_COMPILE = False
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def json_stringify(o: Any) -> str:
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return _json_stringify(o, separators=(',', ':'))
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# noinspection PyUnusedLocal
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class RecordingProcess(Process):
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"""
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connect to DB and send sql command
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"""
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def __init__(self, client_id: str, log_verbose, device_id, queue_rec, queue_ds, queue_msg, meta_path,
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device_info, parameter, parent, recording_file_name, data_format,
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mqtt_ip, mqtt_port,
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name = 'Recording-Process', database = None):
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super(RecordingProcess, self).__init__(name = name)
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self._database = database
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self._device = device_id
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self._meta_file = RecordingMetaFile.load(meta_path, self._database)
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self._meta_file._device = device_info
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self._meta_file._filepath = meta_path
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self._meta_file._parameter = parameter
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self._meta_file._parent = parent
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self._meta_file._recording_file_name = recording_file_name
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self._meta_file._device_id = device_id
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print(self._meta_file._device, self._meta_file._parameter, self._meta_file._parent, self._meta_file._filepath)
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self._meta_file.write(self._database)
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self._data_format = data_format
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self._timer = None
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self.sync_file_request = False
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self._sync_started = False
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self._writer = None
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self.log_verbose = log_verbose
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self._mqtt_thread = MqttThread(None,
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mqtt_ip,
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mqtt_port,
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'device-' + str(self._device) + '-' + str(self._meta_file._file_uuid),
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self.log_verbose,
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'MQTT-device-' + str(self._device),
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is_sub = False)
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# self._mqtt_thread.start()
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self._mqtt_send_data_ch_level = {}
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self._queue_rec = queue_rec
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self._queue_ds = queue_ds
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self._queue_msg = queue_msg
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self.queue_flag = True
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self._is_close = True
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self._prev_data = []
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self._prev_delta_time = []
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self._prev_time_stamp = []
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self._isTimeOut = False
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# section use
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self._skip_ram_cnt = 0
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self._get_first_last_cnt = [True, True, True, True, True, True, True, True]
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self._last_cnt = [-1, -1, -1, -1, -1, -1, -1, -1]
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self._wrong_cnt = 0
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# elite data length
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self._elite_data_len = 40
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self._mem_header_len = 3
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self._mem_tailer_len = 6
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self._single_data_len = self._elite_data_len + self._mem_header_len + self._mem_tailer_len
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def ensure_data_format(self) -> DataDecodeFormat:
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if isinstance(self._data_format, (str, bytes)):
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self._data_format = DataDecodeFormat.parse(self._data_format)
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# add device information
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if isinstance(self._data_format, RecDataDecoder):
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self._data_format.device = self._device
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return self._data_format
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def data_format(self) -> DataDecodeFormat:
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decoder = self.ensure_data_format()
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# transmit calibration gain level to decoder
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if isinstance(decoder, TDC4VAF2DataDecoder):
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# get amp_gain from meta file
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decoder.amp_gain = self._meta_file.configuration.amp_gain
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elif isinstance(decoder, TDC4VCDataDecoder):
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# get amp_gain from meta file
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decoder.amp_gain = self._meta_file.configuration.amp_gain
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decoder._channel = self._meta_file.configuration.channel
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decoder._adc_clock = self._meta_file.configuration.get_parameter('ADC_CLOCK')
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# decoder._time_stamp_list = self._time_stamp_list
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decoder._axis_ch = self._meta_file.configuration.get_parameter('AXIS_CH')
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decoder._prev_data = self._prev_data
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decoder._prev_delta_time = self._prev_delta_time
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decoder._prev_time_stamp = self._prev_time_stamp
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# elif isinstance(decoder, I4V4Z4T4DataDecoder):
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# get cycle_time from meta file
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# decoder._mode = self._meta_file.configuration.MODE
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# decoder._cycle_start_time = self._cycle_start_time
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elif isinstance(decoder, NeuliveThreeOneDataDecoder):
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# get amp_gain from meta file
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decoder.amp_gain = self._meta_file.configuration.amp_gain
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decoder._channel = self._meta_file.configuration.channel
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decoder._adc_clock = self._meta_file.configuration.get_parameter('ADC_CLOCK')
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# decoder._time_stamp_list = self._time_stamp_list
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decoder._axis_ch = self._meta_file.configuration.get_parameter('AXIS_CH')
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decoder._accelerator_sensitivity = self._meta_file.configuration.get_parameter('ACCELERATOR_S')
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decoder._prev_data = self._prev_data
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decoder._prev_delta_time = self._prev_delta_time
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decoder._prev_time_stamp = self._prev_time_stamp
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elif isinstance(decoder, EISZeroOneDataDecoder):
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# get amp_gain from meta file
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decoder._ac_amp = self._meta_file.configuration.get_parameter('AC_AMP')
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decoder._mode = self._meta_file.configuration.get_parameter('MODE')
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decoder._freq_start = self._meta_file.configuration.get_parameter('FREQ_START')
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decoder._freq_stop = self._meta_file.configuration.get_parameter('FREQ_STOP')
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return decoder
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def recv_data_foreach_runtime(self) -> bool:
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"""foreach data runtime to receive data. called by :class:`DataRuntimeThread`.
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:return: has runtime received data
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"""
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q = None
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try:
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# now = time()
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q = self._queue_rec.get()
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# get_queue_time_cost = time() - now
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# if get_queue_time_cost > 2:
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# print('get queue cost time', get_queue_time_cost)
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except:
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return False
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finally:
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if self._queue_rec.qsize() > 10:
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print('qsize: ', self._device, self._queue_rec.qsize())
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if q == 'close':
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self.log_verbose('RecordingProcess file close:', self._device)
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self.rec_update()
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self.final_write()
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self.is_closed = True
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return False
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else:
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self.rec_update()
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self.sync_data(q)
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del q
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return True
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def sync_data(self, data = None):
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self._isTimeOut = False
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current_time = time()
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if self._timer is not None:
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if current_time - self._timer > 1.5:
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print('time, sync_data routine_time', 'device:', self._device, datetime.now(), current_time, current_time - self._timer)
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self._isTimeOut = True
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self._timer = current_time
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decoder = self.data_format()
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# print('sync_data')
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# print('data',data)
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# print('server/data', self._prev_delta_time,self._prev_time_stamp, self._prev_data)
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if data is None or len(data) == 0:
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result = decoder.decode(b'')
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if result is not None:
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ret = result
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else:
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return None
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else:
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ret = []
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# print('decoder data')
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for offset, section in self._foreach_data_section(data):
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# for section in self._neu_foreach_data_section(data):
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result = decoder.decode(section)
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# if self._isTimeOut:
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# try:
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# print('result: ', result.data_size)
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# except:
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# pass
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try:
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if isinstance(decoder, I4V4Z4T4DataDecoder) or isinstance(decoder, EISZeroOneDataDecoder):
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if decoder.isFinishMode is not None and decoder.isFinishMode() == 1:
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self._queue_msg.put(['ds', self._device, 'interrupt'])
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# content = {}
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# content['header'] = 'device_instruction/0'
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# content['device'] = result.device
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# content['instruction'] = 'interrupt'
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# self._mqtt_thread.publish('device_instruction',json_stringify(content), True)
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# self.server.stop_sync(self.device)
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except RuntimeError as e:
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print(e)
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if result is not None:
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##
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if len(self._mqtt_send_data_ch_level) == 0:
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for ch in result.channels():
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self._mqtt_send_data_ch_level[ch] = MqttDataMessageHandler(self._mqtt_thread, 'data_server/device_data_stream/' + str(result.device) + '/' + str(ch) )
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ret.append(result)
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else:
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continue
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# write back
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# ctime1 = time()
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if self._writer is not None and len(ret) > 0:
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if len(self._writer.channel_list) == 0:
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self._writer.channels_update(ret[0].channels())
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self._writer.write(ret, self._mqtt_send_data_ch_level)
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# print('write time: ', time() - ctime1)
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# print(ret)
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del ret
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del data
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return
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def _check_cnt(self, raw_data: bytes, device: int):
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# check memory board cnt, if jump cnt, don't save data
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save = True
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head = raw_data[0]
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head_counter = raw_data[1]
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device_id = raw_data[3]
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try:
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# assign last_data_cnt value and handle first last_data_cnt
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if (device == 4):
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if (self._get_first_last_cnt[4] == True):
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self._get_first_last_cnt[4] = False
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self._last_cnt[4] = head_counter - 1
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last_data_cnt = self._last_cnt[4]
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elif (device == 5):
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if (self._get_first_last_cnt[5] == True):
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self._get_first_last_cnt[5] = False
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self._last_cnt[5] = head_counter - 1
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last_data_cnt = self._last_cnt[5]
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elif (device == 6):
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if (self._get_first_last_cnt[6] == True):
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self._get_first_last_cnt[6] = False
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self._last_cnt[6] = head_counter - 1
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last_data_cnt = self._last_cnt[6]
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elif (device == 7):
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if (self._get_first_last_cnt[7] == True):
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self._get_first_last_cnt[7] = False
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self._last_cnt[7] = head_counter - 1
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last_data_cnt = self._last_cnt[7]
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# dont save to section when head or id is wrong
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if (head != 255 or device_id != device):
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save = False
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last_data_cnt = last_data_cnt + 1
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return save
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if (last_data_cnt == 255):
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if (head_counter - last_data_cnt != -255):
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save = False
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last_data_cnt = 0
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else:
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last_data_cnt = head_counter
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else:
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if (head_counter - last_data_cnt != 1):
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save = False
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last_data_cnt = last_data_cnt + 1
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else:
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last_data_cnt = head_counter
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finally:
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if (device == 4):
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self._last_cnt[4] = last_data_cnt
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elif (device == 5):
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self._last_cnt[5] = last_data_cnt
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elif (device == 6):
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self._last_cnt[6] = last_data_cnt
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elif (device == 7):
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self._last_cnt[7] = last_data_cnt
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if (save == False):
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self._wrong_cnt += 1
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print('jump cnt', self._wrong_cnt, 'times, device:', device, ',', datetime.now())
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return save
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def _check_jump_ram(self, raw_data: bytes, colum_now: int, colum_total: int, save: bool, device: int, data_len: int):
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col = colum_now
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save = False
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if raw_data[col][0] != 255 or raw_data[col][3] != device:
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return save
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if colum_total == 1:
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print('this ram data < 3 records, colum_total = ', colum_total)
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print('raw_data[0]', raw_data[0])
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return save
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elif colum_total == 2:
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print('this ram data < 3 records, colum_total = ', colum_total)
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print('raw_data[0]', raw_data[0])
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print('raw_data[1]', raw_data[1])
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if (raw_data[col + 1][1] - raw_data[col][1] == 1) or (raw_data[col][1] == 255 and raw_data[col + 1][1] == 0):
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save = True
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elif colum_total >= 3:
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if (raw_data[col + 1][1] - raw_data[col][1] == 1 and raw_data[col + 2][1] - raw_data[col + 1][1] == 1) or\
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(raw_data[col][1] == 255 and raw_data[col + 1][1] == 0 and raw_data[col + 2][1] == 1) or\
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(raw_data[col][1] == 254 and raw_data[col + 1][1] == 255 and raw_data[col + 2][1] == 0):
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save = True
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if save == True:
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self._skip_ram_cnt += 1
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last_data_cnt = raw_data[col][1]
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if (device == 4):
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print('self._last_cnt[4]:', self._last_cnt[4], ', last_data_cnt:', last_data_cnt)
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if (device == 5):
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print('self._last_cnt[5]:', self._last_cnt[5], ', last_data_cnt:', last_data_cnt)
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if (device == 6):
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print('self._last_cnt[6]:', self._last_cnt[6], ', last_data_cnt:', last_data_cnt)
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if (device == 7):
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print('self._last_cnt[7]:', self._last_cnt[7], ', last_data_cnt:', last_data_cnt)
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print('skip RAM, but data is right, solve data', list(raw_data[col][0:3]),'|', list(raw_data[colum_total-1][0:3]), 'skip Ram', self._skip_ram_cnt, 'times \n')
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if (device == 4):
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self._last_cnt[4] = last_data_cnt
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elif (device == 5):
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self._last_cnt[5] = last_data_cnt
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elif (device == 6):
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self._last_cnt[6] = last_data_cnt
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elif (device == 7):
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self._last_cnt[7] = last_data_cnt
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return save
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def _neu_foreach_data_section(self, data: bytes):
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"""
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:param data:
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:return:
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"""
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_device = 6
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offset = 0
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ret = [_device]
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total_sample = 0
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ble_packet_end = 0
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header = None
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# packet header format
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# - header (0xFF)
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# - data counter
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# - data content len (ble_packet_end)
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# - chip id
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def _discard_packet_header(offset: int, data: bytes) -> List[int, int]:
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while offset < len(data):
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data_header = data[offset]
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if data_header != 0xFF:
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offset += 1
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continue
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head_counter = data[offset + 1]
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ble_packet_len = data[offset + 2]
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device_id = data[offset + 3]
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if device_id != _device:
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offset += 1
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continue
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else:
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ble_packet_end = offset + ble_packet_len + 3
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# print("head_counter", head_counter)
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return offset+4, ble_packet_end
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return len(data), 0
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# decoder header format:
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# - timestamp (LSB)
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# - channnel data number
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# - delta time
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def _get_ret_header(offset: int, data: bytes) -> List[int, int, Optional[bytes]]:
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total_sample = data[offset + 4]
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decoder_header = data[offset : offset+7]
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offset += 7
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return [offset, total_sample, decoder_header]
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def _is_ret_need_header(ret: bytes) -> bool:
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if len(ret) < 7:
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return True
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else:
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return False
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def _is_ret_complete(ret: bytes) -> bool:
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if len(ret) < 8:
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return False
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sample_length = 3
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sample_number = int((len(ret) - 8) / sample_length)
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if sample_number >= total_sample:
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return True
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else:
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return False
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def _extend_ret(ret: bytes, offset: int, data: bytes) -> List[int, bytes]:
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expect_ret_len = 8 + total_sample*3 # header_len = 8
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extend_len = expect_ret_len - len(ret)
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if (offset + extend_len) < ble_packet_end:
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ret.extend(data[offset : offset + extend_len])
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offset += extend_len
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else:
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ret.extend(data[offset : ble_packet_end])
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offset = ble_packet_end
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return offset, ret
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# print("pre decode data len = ", len(data))
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# print("pre decode data = ", list(data))
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while offset < len(data):
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if offset >= ble_packet_end:
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offset, ble_packet_end = _discard_packet_header(offset, data)
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if _is_ret_need_header(ret):
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# get ret header
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offset, total_sample, header = _get_ret_header(offset, data)
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total_sample += 2 # acc data can be view as two sample
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ret.extend(header)
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# extend ret
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offset, ret = _extend_ret(ret, offset, data)
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# is ret complete?
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if _is_ret_complete(ret):
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# print("ret = ", ret)
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# print("\n")
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yield bytes(ret)
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ret = [_device]
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def log_data_receive_statistics(self, logger: Logger):
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c = self._data_counter
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def _foreach_data_section(self, data: bytes):
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"""
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:param data:
|
|
:return:
|
|
"""
|
|
raw_data = []
|
|
records = 0
|
|
print_flag = False
|
|
device = self._device
|
|
single_data_len = self._single_data_len
|
|
mem_header_len = self._mem_header_len
|
|
|
|
# packet section data use two microarray
|
|
for i in range(0, len(data), single_data_len):
|
|
records = records + 1
|
|
raw_data.append(data[i : i + single_data_len])
|
|
if len(data[i : i + 10]) < 10:
|
|
print('data dont be package:', raw_data[records - 1], 'index:', records - 1)
|
|
del raw_data[records - 1]
|
|
records = records - 1
|
|
|
|
# check cnt
|
|
for i in range(records):
|
|
|
|
# if jump cnt, don't save data
|
|
save = self._check_cnt(raw_data[i], device)
|
|
|
|
# # if jump Ram, also can handle data
|
|
if save == False:
|
|
save = self._check_jump_ram(raw_data, i, records, save, device, single_data_len)
|
|
|
|
if (save == True):
|
|
section = raw_data[i]
|
|
|
|
check_sum = sum(section[0 : single_data_len - 1]) & 0b11111111
|
|
|
|
if (check_sum != section[single_data_len - 1]):
|
|
print('check number not match,',
|
|
list(section[0 : mem_header_len]), section[-1], '!=', check_sum, 'device:', device, ',', datetime.now())
|
|
if (i-1 >= 0):
|
|
print('check number not match', list(raw_data[i-1]), 'raw:', i-1)
|
|
|
|
print('check number not match', list(raw_data[i]), 'raw:', i)
|
|
|
|
if (i+1 <= records):
|
|
print('check number not match', list(raw_data[i+1]), 'raw:', i+1, '\n')
|
|
section = section + b'\x01'
|
|
|
|
print('delete data:', list(raw_data[i][0:3]), 'raw:', i, '\n')
|
|
continue
|
|
else:
|
|
section = section + b'\x00'
|
|
|
|
# section = section[3:]
|
|
yield None, section
|
|
|
|
else:
|
|
print_flag = True
|
|
print('delete data:', list(raw_data[i][0:3]), 'raw:', i, '\n')
|
|
|
|
# if print_flag:
|
|
# print('delete data context:')
|
|
# for i in range(0, len(data), single_data_len):
|
|
# print(list(data[i:i+single_data_len]))
|
|
# print()
|
|
|
|
return
|
|
|
|
def run(self) -> None:
|
|
self.setup()
|
|
# self.routine()
|
|
|
|
def setup(self) -> None:
|
|
self.log_verbose('RecordingProcess setup:', self._device)
|
|
self._is_close = False
|
|
if self._mqtt_thread is not None:
|
|
self._mqtt_thread.start()
|
|
self._writer = RecordingFileWriter(self._meta_file, self._device, self._database)
|
|
self.routine()
|
|
|
|
def routine(self) -> None:
|
|
self.log_verbose('RecordingProcess routine:', self._device)
|
|
self._sync_started = True
|
|
running = True
|
|
while running:
|
|
running = self.recv_data_foreach_runtime()
|
|
self.log_verbose('RecordingProcess routine done:', self._device)
|
|
if self._mqtt_thread is not None:
|
|
self._mqtt_thread.shutdown()
|
|
return None
|
|
|
|
def shutdown(self) -> None:
|
|
self.log_verbose('RecordingProcess shutdown:', self._device)
|
|
self._sync_started = False
|
|
self._queue_rec.put('close')
|
|
self.queue_flag = True
|
|
|
|
|
|
def final_write(self):
|
|
if self._writer is not None:
|
|
return self._writer.close()
|
|
else:
|
|
return False
|
|
|
|
# def put_queue(self, request: list) -> None:
|
|
# self._queue.put(request)
|
|
# del request
|
|
# return
|
|
|
|
@property
|
|
def filepath(self):
|
|
return self._meta_file.filepath
|
|
|
|
@property
|
|
def meta_file(self) -> RecordingMetaFile:
|
|
return self._meta_file
|
|
|
|
@property
|
|
def file_writer(self) -> Optional[RecordingFileWriter]:
|
|
return self._writer
|
|
|
|
@property
|
|
def device(self) -> int:
|
|
return self._device
|
|
|
|
@property
|
|
def sync_started(self) -> bool:
|
|
return self._sync_started
|
|
|
|
# @sync_started.setter
|
|
# def sync_started(self, value: bool):
|
|
# self._sync_started = value
|
|
|
|
# if value:
|
|
# self._open()
|
|
# else:
|
|
# self._close()
|
|
|
|
def put_rec_queue(self, data) -> None:
|
|
self._queue_rec.put(data)
|
|
return
|
|
|
|
def rec_update(self) -> bool:
|
|
while self._queue_ds.qsize() > 0:
|
|
try:
|
|
q = self._queue_ds.get(block=False)
|
|
except:
|
|
return False
|
|
if q is not None:
|
|
func_name = q[0]
|
|
args = q[1:]
|
|
try:
|
|
self.solve_for(func_name, args = args)
|
|
except RuntimeError as e:
|
|
print('solve func error', func_name, args)
|
|
return False
|
|
return True
|
|
|
|
def solve_for(self, name: str, args: list):
|
|
do = f"{name}"
|
|
if callable(getattr(self, do)):
|
|
try:
|
|
getattr(self, do)(*args)
|
|
except:
|
|
pass
|
|
return None
|
|
|
|
def update_meta_id(self, _uuid, _id):
|
|
if self._writer is not None:
|
|
self._writer.update_meta_id(_id)
|
|
return
|
|
|
|
def update_raw_dict_id(self, _uuid, _channel, _id):
|
|
if self._writer is not None:
|
|
self._writer.update_raw_dict_id(_channel, _id)
|
|
return
|
|
|
|
def update_mini_dict_id(self, _uuid, _scale, _channel, _id):
|
|
if self._writer is not None:
|
|
self._writer.update_mini_dict_id(_scale, _channel, _id)
|
|
return
|
|
|