From ebe9b854b6c93c1562961f85af328fb8738a1496 Mon Sep 17 00:00:00 2001 From: Jim Rybarski Date: Tue, 26 May 2015 03:10:02 +0000 Subject: [PATCH 1/2] resolves #43: removed unused NamedTuple --- nd2reader/parser.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/nd2reader/parser.py b/nd2reader/parser.py index a794627..58914a3 100644 --- a/nd2reader/parser.py +++ b/nd2reader/parser.py @@ -1,7 +1,6 @@ # -*- coding: utf-8 -*- import array -from collections import namedtuple from datetime import datetime import numpy as np import re @@ -9,9 +8,6 @@ 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. From 06d6a2158692743c81763f37e16761787120d010 Mon Sep 17 00:00:00 2001 From: Jim Rybarski Date: Sun, 31 May 2015 01:21:47 +0000 Subject: [PATCH 2/2] resolves #37: Python 3 support! --- nd2reader/__init__.py | 13 ++++++----- nd2reader/parser.py | 53 +++++++++++++++++++++++-------------------- requirements.txt | 3 ++- setup.py | 9 +++++--- 4 files changed, 44 insertions(+), 34 deletions(-) diff --git a/nd2reader/__init__.py b/nd2reader/__init__.py index 26a6f1b..ca14b22 100644 --- a/nd2reader/__init__.py +++ b/nd2reader/__init__.py @@ -2,6 +2,7 @@ from nd2reader.model import Image, ImageSet from nd2reader.parser import Nd2Parser +import six class Nd2(Nd2Parser): @@ -18,7 +19,7 @@ class Nd2(Nd2Parser): "Created: %s" % self._absolute_start.strftime("%Y-%m-%d %H:%M:%S"), "Image size: %sx%s (HxW)" % (self.height, self.width), "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, "Z-Levels: %s" % self._z_level_count ]) @@ -30,7 +31,7 @@ class Nd2(Nd2Parser): :rtype: int """ - return self.metadata['ImageAttributes']['SLxImageAttributes']['uiHeight'] + return self.metadata[six.b('ImageAttributes')][six.b('SLxImageAttributes')][six.b('uiHeight')] @property def width(self): @@ -39,7 +40,7 @@ class Nd2(Nd2Parser): :rtype: int """ - return self.metadata['ImageAttributes']['SLxImageAttributes']['uiWidth'] + return self.metadata[six.b('ImageAttributes')][six.b('SLxImageAttributes')][six.b('uiWidth')] def __iter__(self): """ @@ -67,11 +68,11 @@ class Nd2(Nd2Parser): :return: model.ImageSet() """ - for time_index in xrange(self._time_index_count): + for time_index in range(self._time_index_count): image_set = ImageSet() for fov in range(self._field_of_view_count): 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) if image is not None: image_set.add(image) @@ -101,4 +102,4 @@ class Nd2(Nd2Parser): except TypeError: return None else: - return image \ No newline at end of file + return image diff --git a/nd2reader/parser.py b/nd2reader/parser.py index 58914a3..a5961bc 100644 --- a/nd2reader/parser.py +++ b/nd2reader/parser.py @@ -5,7 +5,7 @@ from datetime import datetime import numpy as np import re import struct -from StringIO import StringIO +import six class Nd2Parser(object): @@ -15,9 +15,9 @@ class Nd2Parser(object): """ 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): self._filename = filename self._fh = None @@ -47,7 +47,7 @@ class Nd2Parser(object): :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) # 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 @@ -78,18 +78,20 @@ class Nd2Parser(object): """ 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 break else: 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 break else: raise ValueError("Could not parse metadata dimensions!") + if six.PY3: + return self._dimension_text.decode("utf8") return self._dimension_text @property @@ -101,19 +103,19 @@ class Nd2Parser(object): :rtype: str """ - metadata = self.metadata['ImageMetadataSeq']['SLxPictureMetadata']['sPicturePlanes'] + metadata = self.metadata[six.b('ImageMetadataSeq')][six.b('SLxPictureMetadata')][six.b('sPicturePlanes')] 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: # If none of the channels have been deleted, there is no validity list, so we just make one validity = [True for _ in metadata] # 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 # 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: continue - yield chan['sDescription'] + yield chan[six.b('sDescription')].decode("utf8") def _calculate_image_group_number(self, time_index, fov, z_level): """ @@ -150,17 +152,18 @@ class Nd2Parser(object): :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_24 = None # ND2s seem to randomly switch between 12- and 24-hour representations. try: absolute_start_24 = datetime.strptime(line, "%m/%d/%Y %H:%M:%S") - except ValueError: + except (TypeError, ValueError): pass try: absolute_start_12 = datetime.strptime(line, "%m/%d/%Y %I:%M:%S %p") - except ValueError: + except (TypeError, ValueError): pass if not absolute_start_12 and not absolute_start_24: continue @@ -178,7 +181,7 @@ class Nd2Parser(object): pattern = r""".*?λ\((\d+)\).*?""" try: count = int(re.match(pattern, self._dimensions).group(1)) - except AttributeError: + except AttributeError as e: return 1 else: return count @@ -242,7 +245,7 @@ class Nd2Parser(object): :rtype: int """ - return self.metadata['ImageAttributes']['SLxImageAttributes']['uiSequenceCount'] + return self.metadata[six.b('ImageAttributes')][six.b('SLxImageAttributes')][six.b('uiSequenceCount')] def _parse_metadata(self): """ @@ -250,9 +253,9 @@ class Nd2Parser(object): """ 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]) - stop = label.index("LV") + stop = label.index(six.b("LV")) self.metadata[label[:stop]] = self._read_metadata(data, 1) def _read_map(self): @@ -269,7 +272,7 @@ class Nd2Parser(object): label_start = raw_text.index(Nd2Parser.CHUNK_MAP_START) + 32 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] location, length = struct.unpack("QQ", raw_text[data_start: data_start + 16]) if key == Nd2Parser.CHUNK_MAP_END: @@ -308,7 +311,7 @@ class Nd2Parser(object): def _parse_string(self, data): 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 value += data.read(2) return value.decode("utf16")[:-1].encode("utf8") @@ -350,14 +353,16 @@ class Nd2Parser(object): Iterates over each element some section of the metadata and parses it. """ - data = StringIO(data) + data = six.BytesIO(data) metadata = {} - for _ in xrange(count): + for _ in range(count): self._cursor_position = data.tell() header = data.read(2) if not header: # We've reached the end of some hierarchy of data break + if six.PY3: + header = header.decode("utf8") 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) diff --git a/requirements.txt b/requirements.txt index ccee7d9..ed8da63 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1 +1,2 @@ -numpy>=1.9.2 \ No newline at end of file +numpy>=1.9.2 +six diff --git a/setup.py b/setup.py index 1aee9c5..d250eec 100644 --- a/setup.py +++ b/setup.py @@ -1,14 +1,16 @@ from distutils.core import setup +VERSION = "1.0.1" + setup( name="nd2reader", packages=['nd2reader', 'nd2reader.model'], - version="1.0.0", + version=VERSION, description='A tool for reading ND2 files produced by NIS Elements', author='Jim Rybarski', author_email='jim@rybarski.com', 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'], classifiers=['Development Status :: 5 - Production/Stable', 'Intended Audience :: Science/Research', @@ -16,6 +18,7 @@ setup( 'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)', 'Operating System :: POSIX :: Linux', 'Programming Language :: Python :: 2.7', + 'Programming Language :: Python :: 3.4', 'Topic :: Scientific/Engineering', ] -) \ No newline at end of file +)