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Merge pull request #47 from jimrybarski/dev 

Python 3 support
feature/load_slices
Jim Rybarski 10 years ago
parent
9222a340dd b8c75b2aba
commit
7593b5ac3a
4 changed files with 44 additions and 38 deletions
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  1. +7
    -6
      nd2reader/__init__.py
  2. +29
    -28
      nd2reader/parser.py
  3. +2
    -1
      requirements.txt
  4. +6
    -3
      setup.py

+ 7
- 6
nd2reader/__init__.py View File

@ -2,6 +2,7 @@
from nd2reader.model import Image, ImageSet from nd2reader.model import Image, ImageSet
from nd2reader.parser import Nd2Parser from nd2reader.parser import Nd2Parser
import six
class Nd2(Nd2Parser): class Nd2(Nd2Parser):
@ -18,7 +19,7 @@ class Nd2(Nd2Parser):
"Created: %s" % self._absolute_start.strftime("%Y-%m-%d %H:%M:%S"), "Created: %s" % self._absolute_start.strftime("%Y-%m-%d %H:%M:%S"),
"Image size: %sx%s (HxW)" % (self.height, self.width), "Image size: %sx%s (HxW)" % (self.height, self.width),
"Image cycles: %s" % self._time_index_count, "Image cycles: %s" % self._time_index_count,
"Channels: %s" % ", ".join(["'%s'" % channel for channel in self._channels]),
"Channels: %s" % ", ".join(["'%s'" % str(channel) for channel in self._channels]),
"Fields of View: %s" % self._field_of_view_count, "Fields of View: %s" % self._field_of_view_count,
"Z-Levels: %s" % self._z_level_count "Z-Levels: %s" % self._z_level_count
]) ])
@ -30,7 +31,7 @@ class Nd2(Nd2Parser):
:rtype: int :rtype: int
""" """
return self.metadata['ImageAttributes']['SLxImageAttributes']['uiHeight']
return self.metadata[six.b('ImageAttributes')][six.b('SLxImageAttributes')][six.b('uiHeight')]
@property @property
def width(self): def width(self):
@ -39,7 +40,7 @@ class Nd2(Nd2Parser):
:rtype: int :rtype: int
""" """
return self.metadata['ImageAttributes']['SLxImageAttributes']['uiWidth']
return self.metadata[six.b('ImageAttributes')][six.b('SLxImageAttributes')][six.b('uiWidth')]
def __iter__(self): def __iter__(self):
""" """
@ -67,11 +68,11 @@ class Nd2(Nd2Parser):
:return: model.ImageSet() :return: model.ImageSet()
""" """
for time_index in xrange(self._time_index_count):
for time_index in range(self._time_index_count):
image_set = ImageSet() image_set = ImageSet()
for fov in range(self._field_of_view_count): for fov in range(self._field_of_view_count):
for channel_name in self._channels: for channel_name in self._channels:
for z_level in xrange(self._z_level_count):
for z_level in range(self._z_level_count):
image = self.get_image(time_index, fov, channel_name, z_level) image = self.get_image(time_index, fov, channel_name, z_level)
if image is not None: if image is not None:
image_set.add(image) image_set.add(image)
@ -101,4 +102,4 @@ class Nd2(Nd2Parser):
except TypeError: except TypeError:
return None return None
else: else:
return image
return image

+ 29
- 28
nd2reader/parser.py View File

@ -1,15 +1,11 @@
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
import array import array
from collections import namedtuple
from datetime import datetime from datetime import datetime
import numpy as np import numpy as np
import re import re
import struct import struct
from StringIO import StringIO
field_of_view = namedtuple('FOV', ['number', 'x', 'y', 'z', 'pfs_offset'])
import six
class Nd2Parser(object): class Nd2Parser(object):
@ -19,9 +15,9 @@ class Nd2Parser(object):
""" """
CHUNK_HEADER = 0xabeceda CHUNK_HEADER = 0xabeceda
CHUNK_MAP_START = "ND2 FILEMAP SIGNATURE NAME 0001!"
CHUNK_MAP_END = "ND2 CHUNK MAP SIGNATURE 0000001!"
CHUNK_MAP_START = six.b("ND2 FILEMAP SIGNATURE NAME 0001!")
CHUNK_MAP_END = six.b("ND2 CHUNK MAP SIGNATURE 0000001!")
def __init__(self, filename): def __init__(self, filename):
self._filename = filename self._filename = filename
self._fh = None self._fh = None
@ -51,7 +47,7 @@ class Nd2Parser(object):
:return: (int, array.array()) or None :return: (int, array.array()) or None
""" """
chunk = self._label_map["ImageDataSeq|%d!" % image_group_number]
chunk = self._label_map[six.b("ImageDataSeq|%d!" % image_group_number)]
data = self._read_chunk(chunk) data = self._read_chunk(chunk)
# All images in the same image group share the same timestamp! So if you have complicated image data, # All images in the same image group share the same timestamp! So if you have complicated image data,
# your timestamps may not be entirely accurate. Practically speaking though, they'll only be off by a few # your timestamps may not be entirely accurate. Practically speaking though, they'll only be off by a few
@ -82,18 +78,20 @@ class Nd2Parser(object):
""" """
if self._dimension_text is None: if self._dimension_text is None:
for line in self.metadata['ImageTextInfo']['SLxImageTextInfo'].values():
if "Dimensions:" in line:
for line in self.metadata[six.b('ImageTextInfo')][six.b('SLxImageTextInfo')].values():
if six.b("Dimensions:") in line:
metadata = line metadata = line
break break
else: else:
raise ValueError("Could not parse metadata dimensions!") raise ValueError("Could not parse metadata dimensions!")
for line in metadata.split("\r\n"):
if line.startswith("Dimensions:"):
for line in metadata.split(six.b("\r\n")):
if line.startswith(six.b("Dimensions:")):
self._dimension_text = line self._dimension_text = line
break break
else: else:
raise ValueError("Could not parse metadata dimensions!") raise ValueError("Could not parse metadata dimensions!")
if six.PY3:
return self._dimension_text.decode("utf8")
return self._dimension_text return self._dimension_text
@property @property
@ -105,19 +103,19 @@ class Nd2Parser(object):
:rtype: str :rtype: str
""" """
metadata = self.metadata['ImageMetadataSeq']['SLxPictureMetadata']['sPicturePlanes']
metadata = self.metadata[six.b('ImageMetadataSeq')][six.b('SLxPictureMetadata')][six.b('sPicturePlanes')]
try: try:
validity = self.metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx'][''][0]['ppNextLevelEx'][''][0]['pItemValid']
validity = self.metadata[six.b('ImageMetadata')][six.b('SLxExperiment')][six.b('ppNextLevelEx')][six.b('')][0][six.b('ppNextLevelEx')][six.b('')][0][six.b('pItemValid')]
except KeyError: except KeyError:
# If none of the channels have been deleted, there is no validity list, so we just make one # If none of the channels have been deleted, there is no validity list, so we just make one
validity = [True for _ in metadata] validity = [True for _ in metadata]
# Channel information is contained in dictionaries with the keys a0, a1...an where the number # Channel information is contained in dictionaries with the keys a0, a1...an where the number
# indicates the order in which the channel is stored. So by sorting the dicts alphabetically # indicates the order in which the channel is stored. So by sorting the dicts alphabetically
# we get the correct order. # we get the correct order.
for (label, chan), valid in zip(sorted(metadata['sPlaneNew'].items()), validity):
for (label, chan), valid in zip(sorted(metadata[six.b('sPlaneNew')].items()), validity):
if not valid: if not valid:
continue continue
yield chan['sDescription']
yield chan[six.b('sDescription')].decode("utf8")
def _calculate_image_group_number(self, time_index, fov, z_level): def _calculate_image_group_number(self, time_index, fov, z_level):
""" """
@ -154,17 +152,18 @@ class Nd2Parser(object):
:rtype: datetime.datetime() :rtype: datetime.datetime()
""" """
for line in self.metadata['ImageTextInfo']['SLxImageTextInfo'].values():
for line in self.metadata[six.b('ImageTextInfo')][six.b('SLxImageTextInfo')].values():
line = line.decode("utf8")
absolute_start_12 = None absolute_start_12 = None
absolute_start_24 = None absolute_start_24 = None
# ND2s seem to randomly switch between 12- and 24-hour representations. # ND2s seem to randomly switch between 12- and 24-hour representations.
try: try:
absolute_start_24 = datetime.strptime(line, "%m/%d/%Y %H:%M:%S") absolute_start_24 = datetime.strptime(line, "%m/%d/%Y %H:%M:%S")
except ValueError:
except (TypeError, ValueError):
pass pass
try: try:
absolute_start_12 = datetime.strptime(line, "%m/%d/%Y %I:%M:%S %p") absolute_start_12 = datetime.strptime(line, "%m/%d/%Y %I:%M:%S %p")
except ValueError:
except (TypeError, ValueError):
pass pass
if not absolute_start_12 and not absolute_start_24: if not absolute_start_12 and not absolute_start_24:
continue continue
@ -182,7 +181,7 @@ class Nd2Parser(object):
pattern = r""".*?λ\((\d+)\).*?""" pattern = r""".*?λ\((\d+)\).*?"""
try: try:
count = int(re.match(pattern, self._dimensions).group(1)) count = int(re.match(pattern, self._dimensions).group(1))
except AttributeError:
except AttributeError as e:
return 1 return 1
else: else:
return count return count
@ -246,7 +245,7 @@ class Nd2Parser(object):
:rtype: int :rtype: int
""" """
return self.metadata['ImageAttributes']['SLxImageAttributes']['uiSequenceCount']
return self.metadata[six.b('ImageAttributes')][six.b('SLxImageAttributes')][six.b('uiSequenceCount')]
def _parse_metadata(self): def _parse_metadata(self):
""" """
@ -254,9 +253,9 @@ class Nd2Parser(object):
""" """
for label in self._label_map.keys(): for label in self._label_map.keys():
if label.endswith("LV!") or "LV|" in label:
if label.endswith(six.b("LV!")) or six.b("LV|") in label:
data = self._read_chunk(self._label_map[label]) data = self._read_chunk(self._label_map[label])
stop = label.index("LV")
stop = label.index(six.b("LV"))
self.metadata[label[:stop]] = self._read_metadata(data, 1) self.metadata[label[:stop]] = self._read_metadata(data, 1)
def _read_map(self): def _read_map(self):
@ -273,7 +272,7 @@ class Nd2Parser(object):
label_start = raw_text.index(Nd2Parser.CHUNK_MAP_START) + 32 label_start = raw_text.index(Nd2Parser.CHUNK_MAP_START) + 32
while True: while True:
data_start = raw_text.index("!", label_start) + 1
data_start = raw_text.index(six.b("!"), label_start) + 1
key = raw_text[label_start: data_start] key = raw_text[label_start: data_start]
location, length = struct.unpack("QQ", raw_text[data_start: data_start + 16]) location, length = struct.unpack("QQ", raw_text[data_start: data_start + 16])
if key == Nd2Parser.CHUNK_MAP_END: if key == Nd2Parser.CHUNK_MAP_END:
@ -312,7 +311,7 @@ class Nd2Parser(object):
def _parse_string(self, data): def _parse_string(self, data):
value = data.read(2) value = data.read(2)
while not value.endswith("\x00\x00"):
while not value.endswith(six.b("\x00\x00")):
# the string ends at the first instance of \x00\x00 # the string ends at the first instance of \x00\x00
value += data.read(2) value += data.read(2)
return value.decode("utf16")[:-1].encode("utf8") return value.decode("utf16")[:-1].encode("utf8")
@ -354,14 +353,16 @@ class Nd2Parser(object):
Iterates over each element some section of the metadata and parses it. Iterates over each element some section of the metadata and parses it.
""" """
data = StringIO(data)
data = six.BytesIO(data)
metadata = {} metadata = {}
for _ in xrange(count):
for _ in range(count):
self._cursor_position = data.tell() self._cursor_position = data.tell()
header = data.read(2) header = data.read(2)
if not header: if not header:
# We've reached the end of some hierarchy of data # We've reached the end of some hierarchy of data
break break
if six.PY3:
header = header.decode("utf8")
data_type, name_length = map(ord, header) data_type, name_length = map(ord, header)
name = data.read(name_length * 2).decode("utf16")[:-1].encode("utf8") name = data.read(name_length * 2).decode("utf16")[:-1].encode("utf8")
value = self._get_value(data, data_type) value = self._get_value(data, data_type)


+ 2
- 1
requirements.txt View File

@ -1 +1,2 @@
numpy>=1.9.2
numpy>=1.9.2
six

+ 6
- 3
setup.py View File

@ -1,14 +1,16 @@
from distutils.core import setup from distutils.core import setup
VERSION = "1.0.1"
setup( setup(
name="nd2reader", name="nd2reader",
packages=['nd2reader', 'nd2reader.model'], packages=['nd2reader', 'nd2reader.model'],
version="1.0.0",
version=VERSION,
description='A tool for reading ND2 files produced by NIS Elements', description='A tool for reading ND2 files produced by NIS Elements',
author='Jim Rybarski', author='Jim Rybarski',
author_email='jim@rybarski.com', author_email='jim@rybarski.com',
url='https://github.com/jimrybarski/nd2reader', url='https://github.com/jimrybarski/nd2reader',
download_url='https://github.com/jimrybarski/nd2reader/tarball/1.0.0',
download_url='https://github.com/jimrybarski/nd2reader/tarball/%s' % VERSION,
keywords=['nd2', 'nikon', 'microscopy', 'NIS Elements'], keywords=['nd2', 'nikon', 'microscopy', 'NIS Elements'],
classifiers=['Development Status :: 5 - Production/Stable', classifiers=['Development Status :: 5 - Production/Stable',
'Intended Audience :: Science/Research', 'Intended Audience :: Science/Research',
@ -16,6 +18,7 @@ setup(
'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)', 'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
'Operating System :: POSIX :: Linux', 'Operating System :: POSIX :: Linux',
'Programming Language :: Python :: 2.7', 'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3.4',
'Topic :: Scientific/Engineering', 'Topic :: Scientific/Engineering',
] ]
)
)

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