You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
177 lines
6.8 KiB
177 lines
6.8 KiB
# -*- coding: utf-8 -*-
|
|
|
|
import array
|
|
from collections import namedtuple
|
|
import struct
|
|
from StringIO import StringIO
|
|
|
|
field_of_view = namedtuple('FOV', ['number', 'x', 'y', 'z', 'pfs_offset'])
|
|
|
|
|
|
class Nd2Parser(object):
|
|
"""
|
|
Reads .nd2 files, provides an interface to the metadata, and generates numpy arrays from the image data.
|
|
|
|
"""
|
|
CHUNK_HEADER = 0xabeceda
|
|
CHUNK_MAP_START = "ND2 FILEMAP SIGNATURE NAME 0001!"
|
|
CHUNK_MAP_END = "ND2 CHUNK MAP SIGNATURE 0000001!"
|
|
|
|
def __init__(self, filename):
|
|
self._absolute_start = None
|
|
self._filename = filename
|
|
self._fh = None
|
|
self._chunk_map_start_location = None
|
|
self._cursor_position = 0
|
|
self._dimension_text = None
|
|
self._label_map = {}
|
|
self.metadata = {}
|
|
self._read_map()
|
|
self._parse_metadata()
|
|
|
|
@property
|
|
def _file_handle(self):
|
|
if self._fh is None:
|
|
self._fh = open(self._filename, "rb")
|
|
return self._fh
|
|
|
|
@property
|
|
def _dimensions(self):
|
|
if self._dimension_text is None:
|
|
for line in self.metadata['ImageTextInfo']['SLxImageTextInfo'].values():
|
|
if "Dimensions:" in line:
|
|
metadata = line
|
|
break
|
|
else:
|
|
raise ValueError("Could not parse metadata dimensions!")
|
|
for line in metadata.split("\r\n"):
|
|
if line.startswith("Dimensions:"):
|
|
self._dimension_text = line
|
|
break
|
|
else:
|
|
raise ValueError("Could not parse metadata dimensions!")
|
|
return self._dimension_text
|
|
|
|
@property
|
|
def _image_count(self):
|
|
return self.metadata['ImageAttributes']['SLxImageAttributes']['uiSequenceCount']
|
|
|
|
@property
|
|
def _sequence_count(self):
|
|
return self.metadata['ImageEvents']['RLxExperimentRecord']['uiCount']
|
|
|
|
def _parse_metadata(self):
|
|
for label in self._label_map.keys():
|
|
if label.endswith("LV!") or "LV|" in label:
|
|
data = self._read_chunk(self._label_map[label])
|
|
stop = label.index("LV")
|
|
self.metadata[label[:stop]] = self._read_metadata(data, 1)
|
|
|
|
def _read_map(self):
|
|
"""
|
|
Every label ends with an exclamation point, however, we can't directly search for those to find all the labels
|
|
as some of the bytes contain the value 33, which is the ASCII code for "!". So we iteratively find each label,
|
|
grab the subsequent data (always 16 bytes long), advance to the next label and repeat.
|
|
|
|
"""
|
|
self._file_handle.seek(-8, 2)
|
|
chunk_map_start_location = struct.unpack("Q", self._file_handle.read(8))[0]
|
|
self._file_handle.seek(chunk_map_start_location)
|
|
raw_text = self._file_handle.read(-1)
|
|
label_start = raw_text.index(Nd2Parser.CHUNK_MAP_START) + 32
|
|
|
|
while True:
|
|
data_start = raw_text.index("!", label_start) + 1
|
|
key = raw_text[label_start: data_start]
|
|
location, length = struct.unpack("QQ", raw_text[data_start: data_start + 16])
|
|
if key == Nd2Parser.CHUNK_MAP_END:
|
|
# We've reached the end of the chunk map
|
|
break
|
|
self._label_map[key] = location
|
|
label_start = data_start + 16
|
|
|
|
def _read_chunk(self, chunk_location):
|
|
"""
|
|
Gets the data for a given chunk pointer
|
|
|
|
"""
|
|
self._file_handle.seek(chunk_location)
|
|
# The chunk metadata is always 16 bytes long
|
|
chunk_metadata = self._file_handle.read(16)
|
|
header, relative_offset, data_length = struct.unpack("IIQ", chunk_metadata)
|
|
if header != Nd2Parser.CHUNK_HEADER:
|
|
raise ValueError("The ND2 file seems to be corrupted.")
|
|
# We start at the location of the chunk metadata, skip over the metadata, and then proceed to the
|
|
# start of the actual data field, which is at some arbitrary place after the metadata.
|
|
self._file_handle.seek(chunk_location + 16 + relative_offset)
|
|
return self._file_handle.read(data_length)
|
|
|
|
def _z_level_count(self):
|
|
st = self._read_chunk(self._label_map["CustomData|Z!"])
|
|
return len(array.array("d", st))
|
|
|
|
def _parse_unsigned_char(self, data):
|
|
return struct.unpack("B", data.read(1))[0]
|
|
|
|
def _parse_unsigned_int(self, data):
|
|
return struct.unpack("I", data.read(4))[0]
|
|
|
|
def _parse_unsigned_long(self, data):
|
|
return struct.unpack("Q", data.read(8))[0]
|
|
|
|
def _parse_double(self, data):
|
|
return struct.unpack("d", data.read(8))[0]
|
|
|
|
def _parse_string(self, data):
|
|
value = data.read(2)
|
|
while not value.endswith("\x00\x00"):
|
|
# the string ends at the first instance of \x00\x00
|
|
value += data.read(2)
|
|
return value.decode("utf16")[:-1].encode("utf8")
|
|
|
|
def _parse_char_array(self, data):
|
|
array_length = struct.unpack("Q", data.read(8))[0]
|
|
return array.array("B", data.read(array_length))
|
|
|
|
def _parse_metadata_item(self, data):
|
|
new_count, length = struct.unpack("<IQ", data.read(12))
|
|
length -= data.tell() - self._cursor_position
|
|
next_data_length = data.read(length)
|
|
value = self._read_metadata(next_data_length, new_count)
|
|
# Skip some offsets
|
|
data.read(new_count * 8)
|
|
return value
|
|
|
|
def _get_value(self, data, data_type):
|
|
parser = {1: self._parse_unsigned_char,
|
|
2: self._parse_unsigned_int,
|
|
3: self._parse_unsigned_int,
|
|
5: self._parse_unsigned_long,
|
|
6: self._parse_double,
|
|
8: self._parse_string,
|
|
9: self._parse_char_array,
|
|
11: self._parse_metadata_item}
|
|
return parser[data_type](data)
|
|
|
|
def _read_metadata(self, data, count):
|
|
data = StringIO(data)
|
|
metadata = {}
|
|
for _ in xrange(count):
|
|
self._cursor_position = data.tell()
|
|
header = data.read(2)
|
|
if not header:
|
|
break
|
|
data_type, name_length = map(ord, header)
|
|
name = data.read(name_length * 2).decode("utf16")[:-1].encode("utf8")
|
|
value = self._get_value(data, data_type)
|
|
if name not in metadata.keys():
|
|
metadata[name] = value
|
|
else:
|
|
if not isinstance(metadata[name], list):
|
|
# We have encountered this key exactly once before. Since we're seeing it again, we know we
|
|
# need to convert it to a list before proceeding.
|
|
metadata[name] = [metadata[name]]
|
|
# We've encountered this key before so we're guaranteed to be dealing with a list. Thus we append
|
|
# the value to the already-existing list.
|
|
metadata[name].append(value)
|
|
return metadata
|