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rsh_parser.py
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"""Parser for Troitsk Rsh data files."""
import os
import struct
import sys
from datetime import datetime
import dateutil
import numpy as np
from df_data.type_codes import (channel_control, synchro_channel_control,
synchro_channel_types, synchro_control)
CUR_DIR = os.path.dirname(os.path.realpath(__file__))
if CUR_DIR not in sys.path:
sys.path.append(CUR_DIR)
del CUR_DIR
def serialise_to_rsh(params: dict) -> str:
"""Преобразование конфигурационного файла в формате JSON в текстовый хедер.
rsh. Хедер можно использовать как конфигурационный файл для lan10-12base
@params -- параметры в формате JSON (dfparser.def_values.DEF_RSH_PARAMS)
@return -- текстовый хедер
"""
out = "// Generated at %s\n\n" % (datetime.now())
def add_val(field, value):
"""Add value to multiple line in rsh format."""
if isinstance(value, bytes):
value = value.decode("cp1251")
val = ''.join('%s, ' % (v) for v in value) if isinstance(value, list) \
else value
if isinstance(val, str) and val.endswith(', '):
val = val[:-2]
return '%s -- %s\n' % (val, field)
for param in params:
if param == "channel":
for i, channel in enumerate(params[param]):
for ch_par in channel:
val = "%s_%s[%s]" % (param, ch_par, i)
if ch_par == "params":
val = "%ss_%s[%s]" % (param, ch_par, i)
out += add_val(val, channel[ch_par])
elif param == "synchro_channel":
for sync_ch_par in params[param]:
if sync_ch_par == "type":
out += add_val(param, params[param][sync_ch_par])
else:
out += add_val("%s_%s" % (param, sync_ch_par),
params[param][sync_ch_par])
else:
out += add_val(param, params[param])
return out
def parse_from_rsb(header: bytearray) -> dict:
"""Парсинг бинарного хедера rsb в JSON.
@header -- бинарный хедер (2048 bytes)
@return -- параметры в формате JSON (dfparser.def_values.DEF_RSH_PARAMS)
"""
params = {}
params["text_header_size"] = struct.unpack('I', header[0:4])[0]
params["events_num"] = struct.unpack('i', header[8:12])[0]
start_time = struct.unpack('Q', header[16:24])[0]
params["start_time"] = datetime.fromtimestamp(start_time).isoformat()
end_time = struct.unpack('Q', header[24:32])[0]
params["end_time"] = datetime.fromtimestamp(end_time).isoformat()
params["filepath"] = header[32: 32 + 255].rstrip(b'\0').decode("cp1251")
params["num_blocks"] = struct.unpack('i', header[288:292])[0]
params["aquisition_time"] = struct.unpack('i', header[292:296])[0]
params["blocks_in_file"] = struct.unpack('i', header[296:300])[0]
params["waitTime"] = struct.unpack('i', header[300:304])[0]
params["threshold"] = struct.unpack('d', header[312:320])[0]
sync_params_num = struct.unpack('I', header[336:340])[0]
sync_params = np.unique(np.frombuffer(header[320:336], np.uint32)
[:sync_params_num])
params["synchro_control"] = []
for param in sync_params:
if param == 0:
params["synchro_control"].append("Default")
else:
params["synchro_control"].append(list(synchro_control.keys())
[list(synchro_control.values())
.index(param)])
params["sample_freq"] = struct.unpack('d', header[344:352])[0]
params["pre_history"] = struct.unpack('I', header[352:356])[0]
params["packet_number"] = struct.unpack('i', header[356:360])[0]
params["b_size"] = struct.unpack('I', header[360:364])[0]
params["hysteresis"] = struct.unpack('I', header[364:368])[0]
params["channel_number"] = struct.unpack('I', header[368:372])[0]
ch_params = []
for i in range(params["channel_number"]):
ch_data = header[372 + 56 * i: 372 + 56 * (i + 1)]
ch_param = {}
param_num = struct.unpack('I', ch_data[36:40])[0]
ch_params_raw = np.unique(np.frombuffer(ch_data[4:36],
np.uint32)[:param_num])
ch_param["params"] = []
for param in ch_params_raw:
if param == 0:
ch_param["params"].append("Default")
else:
ch_param["params"].append(list(channel_control.keys())
[list(channel_control.values())
.index(param)])
ch_param["adjustment"] = struct.unpack('d', ch_data[44:52])[0]
ch_param["gain"] = struct.unpack('I', ch_data[52:56])[0]
ch_params.append(ch_param)
params["channel"] = ch_params
synchro_channel = {}
sync_ch_par_num = struct.unpack('I', header[632:636])[0]
sync_ch_params_raw = np.unique(np.frombuffer(header[600:632],
np.uint32)[:sync_ch_par_num])
synchro_channel["params"] = []
for param in sync_ch_params_raw:
if param == 0:
synchro_channel["params"].append("Default")
else:
synchro_channel["params"] \
.append(list(synchro_channel_control.keys())
[list(synchro_channel_control.values()).index(param)])
synchro_channel_type = struct.unpack('I', header[304:308])[0]
synchro_channel["type"] = list(synchro_channel_types.keys())[
list(synchro_channel_types.values()).index(synchro_channel_type)]
synchro_channel["gain"] = struct.unpack('I', header[636:640])[0]
params["synchro_channel"] = synchro_channel
params["err_lang"] = struct.unpack('I', header[640:644])[0]
params["board_name"] = header[644:644 + 255].rstrip(b'\0').decode("cp1251")
params["board_id"] = struct.unpack('I', header[900:904])[0]
return params
def serialize_to_rsb(params: dict) -> bytes:
"""Сериализация JSON хедера rsb.
@params -- параметры в формате JSON (dfparser.def_values.DEF_RSH_PARAMS)
@return -- бинарный хедер (2048 bytes)
"""
header = bytearray(np.zeros(2048, np.byte).tostring())
if "text_header_size" in params:
header[0:4] = struct.pack('I', params["text_header_size"])
if "events_num" in params:
header[8:12] = struct.pack('i', params["events_num"])
if "start_time" in params:
start_time = dateutil.parser.parse(params["start_time"]).timestamp()
header[16:24] = struct.pack('Q', int(start_time))
if "end_time" in params:
end_time = dateutil.parser.parse(params["end_time"]).timestamp()
header[24:32] = struct.pack('Q', int(end_time))
header[32:32 + len(params["filepath"])
] = params['filepath'].encode('cp1251')
header[288:292] = struct.pack('i', params["num_blocks"])
header[292:296] = struct.pack('i', int(params["aquisition_time"]))
header[296:300] = struct.pack('i', params["blocks_in_file"])
header[300:304] = struct.pack('i', int(params["waitTime"]))
header[312:320] = struct.pack('d', params["threshold"])
sync_params = params["synchro_control"]
sync_params_num = len(sync_params)
header[336:340] = struct.pack('I', sync_params_num)
for i in range(sync_params_num):
if sync_params[i] == 'Default':
code = 0
else:
code = synchro_control[sync_params[i]]
header[320 + i * 4:320 + (i + 1) * 4] = struct.pack('I', code)
header[344:352] = struct.pack('d', params["sample_freq"])
header[352:356] = struct.pack('I', params["pre_history"])
header[356:360] = struct.pack('i', params["packet_number"])
header[360:364] = struct.pack('I', params["b_size"])
header[364:368] = struct.pack('I', params["hysteresis"])
header[368:372] = struct.pack('I', params["channel_number"])
for i in range(params["channel_number"]):
off = 372 + 56 * i
ch_param = params['channel'][i]
header[off + 44: off + 52] = struct.pack('d', ch_param["adjustment"])
header[off + 52: off + 56] = struct.pack('I', ch_param["gain"])
header[off + 36: off + 40] = struct.pack('I', len(ch_param['params']))
for j, param in enumerate(ch_param['params']):
if param == 'Default':
code = 0
else:
code = channel_control[param]
header[off + 4 + j * 4:
off + 4 + (j + 1) * 4] = struct.pack('I', code)
synchro_channel = params['synchro_channel']
header[632:636] = struct.pack('I', len(synchro_channel['params']))
for i, param in enumerate(synchro_channel['params']):
if param == 'Default':
code = 0
else:
code = synchro_channel_control[param]
header[600 + i * 4: 600 + (i + 1) * 4] = struct.pack('I', code)
sync_type = synchro_channel_types[synchro_channel['type']]
header[304:308] = struct.pack('I', sync_type)
header[636:640] = struct.pack('I', synchro_channel["gain"])
if "err_lang" in params:
header[640:644] = struct.pack('I', params["err_lang"])
if "board_name" in params:
header[644:644 + len(params["board_name"])] = \
params['board_name'].encode('cp1251')
if "board_id" in params:
header[900: 904] = struct.pack('I', params["board_id"])
return bytes(header)
def dump_to_rsb(params: dict, times: np.ndarray, data: np.ndarray) -> bytes:
"""Сохранение данных в формате rsb.
@params -- параметры набора
@times -- абсолютные времена блоков в наносекундах
@data -- данные блоков (block_num, block_size)
@return -- сериализованные данные
"""
assert isinstance(times, np.ndarray)
assert times.ndim == 1
assert isinstance(data, np.ndarray)
assert data.ndim == 2
assert len(data) == len(times)
params['b_size'] = data.shape[1]
params['events_num'] = data.shape[0]
start = int(times.min() * 1e-9)
end = int(times.max() * 1e-9)
if 'start_time' not in params:
params['start_time'] = datetime.fromtimestamp(start).isoformat()
if 'end_time' not in params:
params['end_time'] = datetime.fromtimestamp(end).isoformat()
text_header = bytearray(5120)
text = serialise_to_rsh(params).encode('cp1251')
text_header[:len(text)] = text
params['text_header_size'] = len(text)
binary_header = serialize_to_rsb(params)
bin_data = b''
ch_num = params['channel_number']
ev_size = params['b_size']
for i, event_data in enumerate(data):
event = bytearray(
np.zeros(96 + 2 * ch_num * ev_size, np.byte).tostring())
text_hdr = datetime.fromtimestamp(int(times[i] * 10e-9)).isoformat()
event[:len(text_hdr)] = text_hdr.encode('cp1251')
event[64:68] = struct.pack('I', i)
event[72:80] = struct.pack('Q', int(times[i] * 10e-9))
event[80:88] = struct.pack('Q', int(times[i]))
event[96:] = event_data.astype(np.int16).tostring()
bin_data += event
return bytes(text_header + binary_header + bin_data)
class RshPackage(object):
"""Rsh package object."""
def __init__(self, file):
"""Load from file or fp.
@file -- filename or opened file
"""
if isinstance(file, str):
self.file = open(file, "rb+")
else:
self.file = file
self.file.seek(0)
self.text_header = self.file.read(5120).decode("cp1251").rstrip('\0')
header = self.file.read(2048)
self.params = parse_from_rsb(header)
def get_event(self, num):
"""Extract event from dataset."""
if num < 0 or num >= self.params["events_num"]:
raise IndexError("Index out of range [0:%s]" %
(self.params["events_num"]))
ch_num = self.params['channel_number']
ev_size = self.params['b_size']
event = {}
self.file.seek(7168 + num * (96 + 2 * ch_num * ev_size))
event["text_hdr"] = self.file.read(64)
event["ev_num"] = struct.unpack('I', self.file.read(4))[0]
self.file.read(4)
start_time = struct.unpack('Q', self.file.read(8))[0]
event["start_time"] = datetime.fromtimestamp(start_time)
ns_since_epoch = struct.unpack('Q', self.file.read(8))[0]
if ns_since_epoch:
event['ns_since_epoch'] = ns_since_epoch
self.file.read(8)
event_data = self.file.read(2 * ev_size * ch_num)
event["data"] = np.fromstring(event_data, np.short)
return event
def update_event_data(self, num, data):
"""Update event data in dataset."""
if num < 0 or num >= self.params["events_num"]:
raise IndexError("Index out of range [0:%s]" %
(self.params["events_num"]))
if isinstance(data, np.ndarray):
raise TypeError("data should be np.ndarray")
if data.dtype != np.short:
raise TypeError("data array dtype should be dtype('int16')")
ch_num = self.params['channel_number']
ev_size = self.params['b_size']
if data.shape != (ch_num * ev_size,):
raise Exception("data should contain same number of elements "
"(%s)" % (ch_num * ev_size))
self.file.seek(7168 + num * (96 + 2 * ch_num * ev_size) + 96)
self.file.write(data.tostring())
self.file.flush()