diff --git a/sohstationviewer/model/mseed/read_mseed_experiment/mseed_reader.py b/sohstationviewer/model/mseed/read_mseed_experiment/mseed_reader.py
index 2dff217ac9f295c9f2e982443fe2732c6280d334..3cfd423dc5f336765f9349c4e969821bbfdc4938 100644
--- a/sohstationviewer/model/mseed/read_mseed_experiment/mseed_reader.py
+++ b/sohstationviewer/model/mseed/read_mseed_experiment/mseed_reader.py
@@ -1,10 +1,14 @@
+from numbers import Number, Real
+from typing import BinaryIO, Optional, List
+
import obspy
+from obspy import UTCDateTime
from decode_mseed import (
decode_ieee_float, decode_ieee_double, decode_steim, decode_int16,
decode_int24, decode_int32,
)
-from help_do_stuff import (
+from mseed_helper import (
FixedHeader, Blockette1000, get_data_endianness, Unpacker,
get_record_metadata, get_header_endianness, RecordMetadata,
EncodingFormat,
@@ -12,19 +16,66 @@ from help_do_stuff import (
class RecordReader:
- def __init__(self, file):
+ """
+ This class reads one data record from an MSEED file.
+ """
+
+ def __init__(self, file: BinaryIO) -> None:
+ # The MSEED file object to read from. The file pointer needs to be
+ # located at the start of a data record.
self.file = file
- self.fixed_header: FixedHeader = None
- self.blockette_1000: Blockette1000 = None
- # Utility object that helps unpack byte string in fixed header.
+
+ self.fixed_header: Optional[FixedHeader] = None
+ self.blockette_1000: Optional[Blockette1000] = None
+ self.other_blockettes: List[str] = []
+ # Utility object that helps unpack byte strings in the header (the
+ # fixed header and the blockettes).
# Separate from the one for data in case the header has a different
# byte order.
# TODO: change blockettes to use this unpacker as well.
- self.fixed_header_unpacker: Unpacker = Unpacker()
+ self.header_unpacker: Unpacker = Unpacker()
+
self.data_unpacker: Unpacker = Unpacker()
- self.record_metadata: RecordMetadata = None
+ self.record_metadata: Optional[RecordMetadata] = None
+
+ self.read_header()
+
+ def read_header(self) -> None:
+ """
+ Read the header of the current data record. The header includes the
+ fixed portion, blockette 1000, and any blockettes that follow.
+ """
+ # Save the start of the record so that we can go back after reading the
+ # header.
+ record_start = self.file.tell()
+
+ self.read_fixed_header()
+ self.read_blockette_1000()
+
+ header_endianness = get_header_endianness(self.fixed_header)
+ if header_endianness == 'little':
+ self.header_unpacker.byte_order_char = '<'
+ else:
+ self.header_unpacker.byte_order_char = '>'
+
+ data_endianness = get_data_endianness(self.blockette_1000)
+ if data_endianness == 'little':
+ self.data_unpacker.byte_order_char = '<'
+ else:
+ self.data_unpacker.byte_order_char = '>'
+
+ self.record_metadata = get_record_metadata(self.fixed_header,
+ self.header_unpacker)
+
+ self.apply_time_correction()
+ self.read_blockettes()
+ self.file.seek(record_start)
- def read_fixed_header(self):
+ def read_fixed_header(self) -> None:
+ """
+ Read the fixed header of the current data record and store it in
+ self.fixed_header.
+ """
byte_counts = [6, 1, 1, 5, 2, 3, 2, 10, 2, 2, 2, 1, 1, 1, 1, 4, 2, 2]
fixed_header_sections_values = []
@@ -32,23 +83,74 @@ class RecordReader:
fixed_header_sections_values.append(self.file.read(byte_count))
self.fixed_header = FixedHeader(*fixed_header_sections_values)
- def read_blockette_500(self):
+ def read_blockette_500(self) -> None:
"""
- Read blockette 500. Only read more precise start time. Assumes that the
- file pointer is at the start of the blockette.
- # TODO: find out what VCO correction is.
+ Read blockette 500 and format its content. The result is stored for
+ future uses. Assumes that the file pointer is at the start of the
+ blockette.
"""
- self.file.seek(18, 1)
- start_time_microsecond = self.file.read(1)
- start_time_microsecond = self.data_unpacker.unpack(
- 'b', start_time_microsecond
+ blockette_content = {}
+ # Skip the first four bytes because they contain meta-information about
+ # the blockettes.
+ self.file.read(4)
+
+ vco_correction = self.file.read(4)
+ blockette_content['VCO correction'] = self.header_unpacker.unpack(
+ 'f', vco_correction
)[0]
- # Convert from microsecond to second so that UTCDateTime can handle it.
- start_time_microsecond /= (10 ** 6)
- self.record_metadata.start_time += start_time_microsecond
- self.file.seek(181, 1)
- def read_blockette_1000(self):
+ exception_time_bytes = self.file.read(10)
+ exception_time_tuple = self.header_unpacker.unpack(
+ 'HHBBBBH', exception_time_bytes)
+ exception_time = UTCDateTime(year=exception_time_tuple[0],
+ julday=exception_time_tuple[1],
+ hour=exception_time_tuple[2],
+ minute=exception_time_tuple[3],
+ second=exception_time_tuple[4],
+ microsecond=exception_time_tuple[6] * 100)
+ blockette_content['Time of exception'] = exception_time.strftime(
+ '%Y:%j:%H:%M:%S:%f'
+ )
+
+ microsecond = self.file.read(1)
+ microsecond = self.header_unpacker.unpack('B', microsecond)[0]
+ start_time_adjustment = microsecond / (10 ** 6)
+ self.record_metadata.start_time += start_time_adjustment
+ blockette_content['Micro sec'] = microsecond
+
+ reception_quality = self.file.read(1)
+ blockette_content['Reception Quality'] = self.header_unpacker.unpack(
+ 'B', reception_quality
+ )[0]
+
+ exception_count = self.file.read(4)
+ blockette_content['Exception Count'] = self.header_unpacker.unpack(
+ 'I', exception_count
+ )[0]
+
+ exception_type = self.file.read(16)
+ blockette_content['Exception Type'] = self.header_unpacker.unpack(
+ '16s', exception_type
+ )[0].decode('utf-8').strip()
+
+ clock_model = self.file.read(32)
+ blockette_content['Clock Model'] = self.header_unpacker.unpack(
+ '32s', clock_model
+ )[0].decode('utf-8').strip()
+
+ clock_status = self.file.read(128)
+ blockette_content['Clock Status'] = self.header_unpacker.unpack(
+ '128s', clock_status
+ )[0].decode('utf-8').strip()
+
+ formatted_blockette = '\n'.join([f'{key}: {value}' for key, value in blockette_content.items()])
+ self.other_blockettes.append(formatted_blockette)
+
+ def read_blockette_1000(self) -> None:
+ """
+ Read blockette 1000 of the current data record and store it in
+ self.blockette_1000.
+ """
blockette_1000_section_lengths = [2, 2, 1, 1, 1, 1]
blockette_1000_values = []
for section_length in blockette_1000_section_lengths:
@@ -56,7 +158,7 @@ class RecordReader:
self.blockette_1000 = Blockette1000(*blockette_1000_values)
- def read_blockette_1001(self):
+ def read_blockette_1001(self) -> None:
"""
Read blockette 1001. The only valuable thing in this blockette is the
more precise start time. Assumes that the file pointer is at the start
@@ -64,19 +166,25 @@ class RecordReader:
"""
self.file.read(5)
start_time_microsecond = self.file.read(1)
- start_time_microsecond = self.data_unpacker.unpack(
+ start_time_microsecond = self.header_unpacker.unpack(
'b', start_time_microsecond
)[0]
# Convert from microsecond to second so that UTCDateTime can handle it.
- start_time_microsecond /= (10**6)
+ start_time_microsecond /= (10 ** 6)
self.record_metadata.start_time += start_time_microsecond
self.file.read(2)
- def apply_time_correction(self):
+ def read_blockette_2000(self) -> None:
+ pass
+
+ def apply_time_correction(self) -> None:
+ """
+ Apply the time correction found in the fixed header to the start time.
+ """
# format() is used here instead of bin() because we need to pad the
# resulting bit string with 0 to the left.
activity_flags = format(
- self.fixed_header_unpacker.unpack(
+ self.header_unpacker.unpack(
'B', self.fixed_header.activity_flags)[0],
'0>8b'
)
@@ -84,15 +192,20 @@ class RecordReader:
if is_time_correction_applied:
return
- time_correction = self.fixed_header_unpacker.unpack(
+ time_correction = self.header_unpacker.unpack(
'L', self.fixed_header.time_correction
)[0]
# We need to convert the unit from 0.0001 seconds to seconds
time_correction *= 0.0001
self.record_metadata.start_time += time_correction
- def read_blockettes(self):
- blockette_count = self.fixed_header_unpacker.unpack(
+ def read_blockettes(self) -> None:
+ """
+ Read all the blockettes in the current data record aside from blockette
+ 1000, which has beem read previously. Currently only handle blockettes
+ 500, 1001, and 2000.
+ """
+ blockette_count = self.header_unpacker.unpack(
'B', self.fixed_header.blockette_count
)[0]
for i in range(1, blockette_count):
@@ -101,49 +214,38 @@ class RecordReader:
next_blockette_type = self.file.read(2)
# Move file pointer back to start of blockette
self.file.seek(-2, 1)
- next_blockette_type = self.data_unpacker.unpack(
+ next_blockette_type = self.header_unpacker.unpack(
'H', next_blockette_type
)[0]
- if next_blockette_type not in (1000, 1001, 500):
+ if next_blockette_type not in (500, 1000, 1001):
print('We currently only handle blockettes 500, 1000, and'
'1001.')
continue
- if next_blockette_type == 1001:
- self.read_blockette_1001()
- elif next_blockette_type == 500:
+ if next_blockette_type == 500:
self.read_blockette_500()
+ elif next_blockette_type == 1001:
+ self.read_blockette_1001()
+ elif next_blockette_type == 2000:
+ self.read_blockette_2000()
- def get_first_data_point(self):
+ def get_first_data_point(self) -> Real:
+ """
+ Get the first data point of the current data record.
+ :return: the first data point of the current data record, whose type is
+ determined based on the encoding type stored in blockette 1000.
+ """
record_start = self.file.tell()
- self.read_fixed_header()
- self.read_blockette_1000()
-
- header_endianness = get_header_endianness(self.fixed_header)
- if header_endianness == 'little':
- self.fixed_header_unpacker.byte_order_char = '<'
- else:
- self.fixed_header_unpacker.byte_order_char = '>'
-
- data_endianness = get_data_endianness(self.blockette_1000)
- if data_endianness == 'little':
- self.data_unpacker.byte_order_char = '<'
- else:
- self.data_unpacker.byte_order_char = '>'
-
- self.record_metadata = get_record_metadata(self.fixed_header,
- self.fixed_header_unpacker)
-
- self.apply_time_correction()
- self.read_blockettes()
- data_start = self.fixed_header_unpacker.unpack('H', self.fixed_header.data_offset)[0]
- # It is most convenient to seek to the start of the record, then seek
- # to the start of the data. Any other way would involve some
- # calculation to determine which point to seek to.
- self.file.seek(record_start)
+ data_start = self.header_unpacker.unpack(
+ 'H', self.fixed_header.data_offset
+ )[0]
+ # The data start byte is defined as an offset from the start of the
+ # data record. Seeing as we should be at the start of the data record
+ # by seeking there at the end of every major step, we can simply seek
+ # to the start of the data.
self.file.seek(data_start, 1)
encoding_format = self.blockette_1000.encoding_format
- encoding_format = self.data_unpacker.unpack('b', encoding_format)[0]
+ encoding_format = self.header_unpacker.unpack('b', encoding_format)[0]
encoding_format = EncodingFormat(encoding_format)
# Currently, we are extracting only the first data point in each
@@ -153,6 +255,7 @@ class RecordReader:
# the whole buffer.
buffer = self.file.read(8)
encoding_to_decoder = {
+ EncodingFormat.ASCII: (lambda a1, a2: int(1)),
EncodingFormat.INT_16_BIT: decode_int16,
EncodingFormat.INT_24_BIT: decode_int24,
EncodingFormat.INT_32_BIT: decode_int32,
@@ -161,50 +264,61 @@ class RecordReader:
EncodingFormat.STEIM_1: decode_steim,
EncodingFormat.STEIM_2: decode_steim,
}
- first_data_point = encoding_to_decoder[encoding_format](buffer, self.data_unpacker)
-
+ first_data_point = encoding_to_decoder[encoding_format](buffer,
+ self.data_unpacker)
+ # Seek back to the start of the record so we can call this method again
+ # if needed.
+ self.file.seek(record_start)
return first_data_point
+class MSeedReader:
+ def __init__(self, file: BinaryIO) -> None:
+ self.file = file
+
+ def read(self):
+ trace = []
+ while 1:
+ # We know that end of file is reached when read() returns an empty
+ # string.
+ is_eof = (self.file.read(1) == b'')
+ if is_eof:
+ break
+ # We need to move the file pointer back to its position after we do
+ # the end of file check. Otherwise, we would be off by one byte for all
+ # the reads afterward.
+ self.file.seek(-1, 1)
+
+ # We save the start of the current record so that after we are done
+ # reading the record, we can move back. This makes moving to the next
+ # record a lot easier, seeing as we can simply move the file pointer
+ # a distance the size of the current record.
+ current_record_start = self.file.tell()
+
+ reader = RecordReader(self.file)
+ trace.append(reader.get_first_data_point())
+ print(reader.other_blockettes[0])
+ # sample_count = reader.record_metadata.sample_count
+ # sample_rate = reader.record_metadata.sample_rate
+ # record_time_taken = sample_count / sample_rate
+ # record_end_time = reader.record_metadata.start_time + record_time_taken
+
+ # MSEED stores the size of a data record as an exponent of a power of
+ # two, so we have to convert that to actual size before doing anything
+ # else.
+ record_length_exp = reader.header_unpacker.unpack(
+ 'B', reader.blockette_1000.record_length
+ )[0]
+ record_size = 2 ** record_length_exp
+
+ self.file.seek(current_record_start)
+ self.file.seek(record_size, 1)
+ print(trace)
+
+
if __name__ == '__main__':
# numpy.set_printoptions(threshold=sys.maxsize)
- file_path = '/Users/kle/PycharmProjects/sohstationviewer/tests/test_data/potato.sdr/XX.KC01..VCO.D.2020.145'
+ file_path = '/Users/kle/PycharmProjects/sohstationviewer/tests/test_data/DT0001__.ACE'
file = open(file_path, 'rb')
stream = obspy.read(file_path)
-
- trace = []
- while 1:
- # We know that end of file is reached when read() returns an empty
- # string.
- is_eof = (file.read(1) == b'')
- if is_eof:
- break
- # We need to move the file pointer back to its position before we do
- # the end of file check. Otherwise, we would be off by one byte for all
- # the reads afterward.
- file.seek(-1, 1)
-
- # We save the start of the current record so that after we are done
- # reading the record, we can move back. This makes moving to the next
- # record a lot easier, seeing as we can simply move the file pointer
- # a distance the size of the current record.
- current_record_start = file.tell()
-
- reader = RecordReader(file)
- trace.append(reader.get_first_data_point())
- sample_count = reader.record_metadata.sample_count
- sample_rate = reader.record_metadata.sample_rate
- record_time_taken = sample_count / sample_rate
- record_end_time = reader.record_metadata.start_time + record_time_taken
-
- # MSEED stores the size of a data record as an exponent of a power of
- # two, so we have to convert that to actual size before doing anything
- # else.
- record_length_exp = reader.data_unpacker.unpack(
- 'B', reader.blockette_1000.record_length
- )[0]
- record_size = 2 ** record_length_exp
-
- file.seek(current_record_start)
- file.seek(record_size, 1)
- print(trace)
+ MSeedReader(file).read()