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sorta built new parser

feature/load_slices
Jim Rybarski 10 years ago
parent
commit
872255c61c
5 changed files with 138 additions and 3 deletions
  1. +109
    -3
      nd2reader/model/__init__.py
  2. +9
    -0
      tests.py
  3. +0
    -0
      tests/__init__.py
  4. +20
    -0
      tests/model/__init__.py
  5. +0
    -0
      tests/service/__init__.py

+ 109
- 3
nd2reader/model/__init__.py View File

@ -1,6 +1,10 @@
import numpy as np
import skimage.io
import logging
from io import BytesIO
import array
import struct
log = logging.getLogger("nd2reader")
@ -76,9 +80,111 @@ class Image(object):
skimage.io.show()
from io import BytesIO
import array
import struct
class MetadataItem(object):
def __init__(self, start, data):
self._datatype = ord(data[start])
self._label_length = 2 * ord(data[start + 1])
self._data = data
@property
def is_valid(self):
return self._datatype > 0
@property
def key(self):
return self._data[2:self._label_length].decode("utf16").encode("utf8")
@property
def length(self):
return self._length
@property
def data_start(self):
return self._label_length + 2
@property
def _body(self):
"""
All data after the header.
"""
return self._data[self.data_start:]
def _get_bytes(self, count):
return self._data[self.data_start: self.data_start + count]
@property
def value(self):
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,
}
return parser[self._datatype]()
def _parse_unsigned_char(self):
self._length = 1
return self._unpack("B", self._get_bytes(self._length))
def _parse_unsigned_int(self):
self._length = 4
return self._unpack("I", self._get_bytes(self._length))
def _parse_unsigned_long(self):
self._length = 8
return self._unpack("Q", self._get_bytes(self._length))
def _parse_double(self):
self._length = 8
return self._unpack("d", self._get_bytes(self._length))
def _parse_string(self):
# the string is of unknown length but ends at the first instance of \x00\x00
stop = self._body.index("\x00\x00")
self._length = stop
return self._body[:stop - 1].decode("utf16").encode("utf8")
def _parse_char_array(self):
array_length = self._unpack("Q", self._get_bytes(8))
self._length = array_length + 8
return array.array("B", self._body[8:array_length])
def _parse_metadata_item(self):
count, length = struct.unpack("<IQ", self._get_bytes(12))
metadata_set = MetadataSet(self._body, 0, count)
def _unpack(self, kind, data):
"""
:param kind: the datatype to interpret the bytes as (see: https://docs.python.org/2/library/struct.html#struct-format-strings)
:type kind: str
:param data: the bytes to be converted
:type data: bytes
Parses a sequence of bytes and converts them to a Python data type.
struct.unpack() returns a tuple but we only want the first element.
"""
return struct.unpack(kind, data)[0]
class MetadataSet(object):
"""
A container of metadata items. Can contain other MetadataSet objects.
"""
def __init__(self, data, start, item_count):
self._items = []
self._parse(data, start, item_count)
def _parse(self, data, start, item_count):
for item in range(item_count):
metadata_item = MetadataItem(start, data)
if not metadata_item.is_valid:
break
start += metadata_item.length
class Chunkmap(object):


+ 9
- 0
tests.py View File

@ -0,0 +1,9 @@
"""
Auto-discovers all unittests in the tests directory and runs them
"""
import unittest
loader = unittest.TestLoader()
tests = loader.discover('tests', pattern='*.py', top_level_dir='.')
testRunner = unittest.TextTestRunner()
testRunner.run(tests)

+ 0
- 0
tests/__init__.py View File


+ 20
- 0
tests/model/__init__.py View File

@ -0,0 +1,20 @@
import unittest
from nd2reader.model import MetadataSet, MetadataItem
class MetadataItemTests(unittest.TestCase):
def test_is_valid(self):
data = b'\x0b\x13S\x00L\x00x\x00P\x00i\x00c\x00t\x00u\x00r\x00e\x00M\x00e\x00t\x00a\x00d\x00a\x00t\x00a\x00\x00\x00!\x00\x00\x00\xd5]\x00\x00\x00\x00\x00\x00\x06\nd\x00T\x00i\x00m\x00e\x00M\x00S\x00e\x00c\x00\x00\x00\x00\xc0T\x1c\x9b#\xbb@\x06\x0ed\x00T\x00i\x00m\x00e\x00A\x00b\x00s\x00o\x00l\x00u\x00t\x00e\x00\x00\x00Sf\xf5\xa6\xa7\xbeBA\x02\x0ce\x00T\x00i\x00m\x00e\x00S\x00o\x00u\x00r\x00c\x00e\x00\x00\x00\x00\x00\x00\x00\x06\x06d\x00X\x00P\x00o\x00s\x00\x00\x00\x00\x00\x00\x00\x00$\x9d\xc0\x06\x06d\x00Y\x00P\x00o\x00s\x00\x00\x00\x00\x00\x00\x00\xe0\r\xe5@\x03\x06u\x00i\x00R\x00o\x00w\x00\x00\x00\x00\x00\x00\x00\x03\nu\x00i\x00C\x00o\x00n\x002\x000\x00(\x00L\x00\x00\x00\x00\x00\x00\x00\x06\x06d\x00Z\x00P\x00o\x00s\x00\x00\x00\x9a\x99\x99\x99Y\x8d\xb8@\x01\x0eb\x00Z\x00P\x00o\x00s\x00A\x00b\x00s\x00o\x00l\x00u\x00t\x00e\x00\x00\x00\x01\x06\x07d\x00A\x00n\x00g'
item = MetadataItem(0, data)
self.assertTrue(item.is_valid)
def test_key(self):
data = b'\x0b\x13S\x00L\x00x\x00P\x00i\x00c\x00t\x00u\x00r\x00e\x00M\x00e\x00t\x00a\x00d\x00a\x00t\x00a\x00\x00\x00!\x00\x00\x00\xd5]\x00\x00\x00\x00\x00\x00\x06\nd\x00T\x00i\x00m\x00e\x00M\x00S\x00e\x00c\x00\x00\x00\x00\xc0T\x1c\x9b#\xbb@\x06\x0ed\x00T\x00i\x00m\x00e\x00A\x00b\x00s\x00o\x00l\x00u\x00t\x00e\x00\x00\x00Sf\xf5\xa6\xa7\xbeBA\x02\x0ce\x00T\x00i\x00m\x00e\x00S\x00o\x00u\x00r\x00c\x00e\x00\x00\x00\x00\x00\x00\x00\x06\x06d\x00X\x00P\x00o\x00s\x00\x00\x00\x00\x00\x00\x00\x00$\x9d\xc0\x06\x06d\x00Y\x00P\x00o\x00s\x00\x00\x00\x00\x00\x00\x00\xe0\r\xe5@\x03\x06u\x00i\x00R\x00o\x00w\x00\x00\x00\x00\x00\x00\x00\x03\nu\x00i\x00C\x00o\x00n\x002\x000\x00(\x00L\x00\x00\x00\x00\x00\x00\x00\x06\x06d\x00Z\x00P\x00o\x00s\x00\x00\x00\x9a\x99\x99\x99Y\x8d\xb8@\x01\x0eb\x00Z\x00P\x00o\x00s\x00A\x00b\x00s\x00o\x00l\x00u\x00t\x00e\x00\x00\x00\x01\x06\x07d\x00A\x00n\x00g'
item = MetadataItem(0, data)
self.assertEqual(item.key, "SLxPictureMetadata")
def test_parse_double(self):
data = b'\x06\nd\x00T\x00i\x00m\x00e\x00M\x00S\x00e\x00c\x00\x00\x00\x00\xc0T\x1c\x9b#\xbb@\x06\x0e'
item = MetadataItem(0, data)
self.assertEqual(item.value, 6947.605901047587)

+ 0
- 0
tests/service/__init__.py View File


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