Pypi refactorzolfa-add_slices_loading
@ -0,0 +1,4 @@ | |||||
Author: Jim Rybarski <jim@rybarski.com> | |||||
nd2reader is based on the read_nd2 module from the SLOTH library (http://pythonhosted.org/SLOTH/_modules/sloth/read_nd2.html). | |||||
Thanks to M.Kauer and B.Kauer for solving the hardest part of parsing ND2s. |
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FROM ubuntu | |||||
MAINTAINER Jim Rybarski <jim@rybarski.com> | |||||
RUN mkdir -p /var/nds2 | |||||
RUN apt-get update && apt-get install -y \ | |||||
python-numpy | |||||
COPY . /opt/nd2reader | |||||
WORKDIR /opt/nd2reader | |||||
RUN python setup.py install | |||||
WORKDIR /var/nd2s | |||||
CMD /usr/bin/python2.7 |
@ -0,0 +1,7 @@ | |||||
.PHONY: build shell | |||||
build: | |||||
docker build -t jimrybarski/nd2reader . | |||||
shell: | |||||
docker run --rm -v ~/Documents/nd2s:/var/nd2s -it jimrybarski/nd2reader |
@ -1,20 +1,116 @@ | |||||
nd2reader | |||||
========= | |||||
# nd2reader | |||||
## Simple access to hierarchical .nd2 files | |||||
### About | |||||
# About | |||||
`nd2reader` is a pure-Python package that reads images produced by NIS Elements. | |||||
`nd2reader` is a pure-Python package that reads images produced by Nikon microscopes. Though it more or less works, it is currently under development and is not quite ready for use by the general public. Version 1.0 should be released in early 2015. | |||||
.nd2 files contain images and metadata, which can be split along multiple dimensions: time, fields of view (xy-plane), focus (z-plane), and filter channel. | |||||
.nd2 files contain images and metadata, which can be split along multiple dimensions: time, fields of view (xy-axis), focus (z-axis), and filter channel. `nd2reader` allows you to view any subset of images based on any or all of these dimensions. | |||||
`nd2reader` produces data in numpy arrays, which makes it trivial to use with the image analysis packages such as `scikit-image` and `OpenCV`. | |||||
`nd2reader` holds data in numpy arrays, which makes it trivial to use with the image analysis packages `scikit-image` and `OpenCV`. | |||||
### Installation | |||||
# Dependencies | |||||
Just use pip: | |||||
numpy | |||||
`pip install nd2reader` | |||||
# Installation | |||||
If you want to install via git, clone the repo and run: | |||||
I'll write this eventually. | |||||
`python setup.py install` | |||||
### ND2s | |||||
A quick summary of ND2 metadata can be obtained as shown below. | |||||
```python | |||||
>>> import nd2reader | |||||
>>> nd2 = nd2reader.Nd2("/path/to/my_images.nd2") | |||||
>>> nd2 | |||||
<ND2 /path/to/my_images.nd2> | |||||
Created: 2014-11-11 15:59:19 | |||||
Image size: 1280x800 (HxW) | |||||
Image cycles: 636 | |||||
Channels: '', 'GFP' | |||||
Fields of View: 8 | |||||
Z-Levels: 3 | |||||
``` | |||||
### Simple Iteration | |||||
For most cases, you'll just want to iterate over each image: | |||||
```python | |||||
import nd2reader | |||||
nd2 = nd2reader.Nd2("/path/to/my_images.nd2") | |||||
for image in nd2: | |||||
do_something(image.data) | |||||
``` | |||||
### Image Sets | |||||
If you have complicated hierarchical data, it may be easier to use image sets, which groups images together if they | |||||
share the same time index and field of view: | |||||
```python | |||||
import nd2reader | |||||
nd2 = nd2reader.Nd2("/path/to/my_complicated_images.nd2") | |||||
for image_set in nd2.image_sets: | |||||
# you can select images by channel | |||||
gfp_image = image_set.get("GFP") | |||||
do_something_gfp_related(gfp_image) | |||||
# you can also specify the z-level. this defaults to 0 if not given | |||||
out_of_focus_image = image_set.get("Bright Field", z_level=1) | |||||
do_something_out_of_focus_related(out_of_focus_image) | |||||
``` | |||||
### Direct Image Access | |||||
There is a method, `get_image`, which allows random access to images. This might not always return an image, however, | |||||
if you acquired different numbers of images in each cycle of a program. For example, if you acquire GFP images every | |||||
other minute, but acquire bright field images every minute, `get_image` will return `None` at certain time indexes. | |||||
### Images | |||||
`Image` objects provide several pieces of useful data. | |||||
```python | |||||
>>> import nd2reader | |||||
>>> nd2 = nd2reader.Nd2("/path/to/my_images.nd2") | |||||
>>> image = nd2.get_image(14, 2, "GFP", 1) | |||||
>>> image.data | |||||
array([[1809, 1783, 1830, ..., 1923, 1920, 1914], | |||||
[1687, 1855, 1792, ..., 1986, 1903, 1889], | |||||
[1758, 1901, 1849, ..., 1911, 2010, 1954], | |||||
..., | |||||
[3363, 3370, 3570, ..., 3565, 3601, 3459], | |||||
[3480, 3428, 3328, ..., 3542, 3461, 3575], | |||||
[3497, 3666, 3635, ..., 3817, 3867, 3779]]) | |||||
>>> image.channel | |||||
'GFP' | |||||
>>> image.timestamp | |||||
1699.7947813408175 | |||||
>>> image.field_of_view | |||||
2 | |||||
>>> image.z_level | |||||
1 | |||||
# You can also get a quick summary of image data: | |||||
>>> image | |||||
<ND2 Image> | |||||
1280x800 (HxW) | |||||
Timestamp: 1699.79478134 | |||||
Field of View: 2 | |||||
Channel: GFP | |||||
Z-Level: 1 | |||||
``` | |||||
### Bug Reports and Features | |||||
If this fails to work exactly as expected, please open a Github issue. If you get an unhandled exception, please | |||||
paste the entire stack trace into the issue as well. | |||||
### Contributing | |||||
Please feel free to submit a pull request with any new features you think would be useful. You can also create an | |||||
issue if you'd just like to propose or discuss a potential idea. |
@ -1,47 +1,104 @@ | |||||
import logging | |||||
from nd2reader.service import BaseNd2 | |||||
# -*- coding: utf-8 -*- | |||||
from nd2reader.model import Image, ImageSet | from nd2reader.model import Image, ImageSet | ||||
from nd2reader.parser import Nd2Parser | |||||
log = logging.getLogger(__name__) | |||||
log.setLevel(logging.DEBUG) | |||||
class Nd2(Nd2Parser): | |||||
""" | |||||
Allows easy access to NIS Elements .nd2 image files. | |||||
class Nd2(BaseNd2): | |||||
""" | |||||
def __init__(self, filename): | def __init__(self, filename): | ||||
super(Nd2, self).__init__(filename) | super(Nd2, self).__init__(filename) | ||||
self._filename = filename | |||||
def __repr__(self): | |||||
return "\n".join(["<ND2 %s>" % self._filename, | |||||
"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]), | |||||
"Fields of View: %s" % self._field_of_view_count, | |||||
"Z-Levels: %s" % self._z_level_count | |||||
]) | |||||
def get_image(self, time_index, fov, channel_name, z_level): | |||||
image_set_number = self._calculate_image_set_number(time_index, fov, z_level) | |||||
timestamp, raw_image_data = self._reader.get_raw_image_data(image_set_number, self.channel_offset[channel_name]) | |||||
return Image(timestamp, raw_image_data, fov, channel_name, z_level, self.height, self.width) | |||||
@property | |||||
def height(self): | |||||
""" | |||||
:return: height of each image, in pixels | |||||
:rtype: int | |||||
""" | |||||
return self.metadata['ImageAttributes']['SLxImageAttributes']['uiHeight'] | |||||
@property | |||||
def width(self): | |||||
""" | |||||
:return: width of each image, in pixels | |||||
:rtype: int | |||||
""" | |||||
return self.metadata['ImageAttributes']['SLxImageAttributes']['uiWidth'] | |||||
def __iter__(self): | def __iter__(self): | ||||
""" | """ | ||||
Just return every image in order (might not be exactly the order that the images were physically taken, but it will | |||||
be within a few seconds). A better explanation is probably needed here. | |||||
Iterates over every image, in the order they were taken. | |||||
:return: model.Image() | |||||
""" | """ | ||||
for i in range(self._image_count): | for i in range(self._image_count): | ||||
for fov in range(self.field_of_view_count): | |||||
for z_level in range(self.z_level_count): | |||||
for channel in self.channels: | |||||
image = self.get_image(i, fov, channel.name, z_level) | |||||
if image.is_valid: | |||||
for fov in range(self._field_of_view_count): | |||||
for z_level in range(self._z_level_count): | |||||
for channel_name in self._channels: | |||||
image = self.get_image(i, fov, channel_name, z_level) | |||||
if image is not None: | |||||
yield image | yield image | ||||
def image_sets(self, field_of_view, time_indices=None, channels=None, z_levels=None): | |||||
""" | |||||
Gets all the images for a given field of view and | |||||
@property | |||||
def image_sets(self): | |||||
""" | """ | ||||
timepoint_set = xrange(self.time_index_count) if time_indices is None else time_indices | |||||
channel_set = [channel.name for channel in self.channels] if channels is None else channels | |||||
z_level_set = xrange(self.z_level_count) if z_levels is None else z_levels | |||||
Iterates over groups of related images. This is useful if your ND2 contains multiple fields of view. | |||||
A typical use case might be that you have, say, four areas of interest that you're monitoring, and every | |||||
minute you take a bright field and GFP image of each one. For each cycle, this method would produce four | |||||
ImageSet objects, each containing one bright field and one GFP image. | |||||
:return: model.ImageSet() | |||||
for timepoint in timepoint_set: | |||||
""" | |||||
for time_index in xrange(self._time_index_count): | |||||
image_set = ImageSet() | image_set = ImageSet() | ||||
for channel_name in channel_set: | |||||
for z_level in z_level_set: | |||||
image = self.get_image(timepoint, field_of_view, channel_name, z_level) | |||||
if image.is_valid: | |||||
image_set.add(image) | |||||
yield image_set | |||||
for fov in range(self._field_of_view_count): | |||||
for channel_name in self._channels: | |||||
for z_level in xrange(self._z_level_count): | |||||
image = self.get_image(time_index, fov, channel_name, z_level) | |||||
if image is not None: | |||||
image_set.add(image) | |||||
yield image_set | |||||
def get_image(self, time_index, field_of_view, channel_name, z_level): | |||||
""" | |||||
Returns an Image if data exists for the given parameters, otherwise returns None. In general, you should avoid | |||||
using this method unless you're very familiar with the structure of ND2 files. If you have a use case that | |||||
cannot be met by the `__iter__` or `image_sets` methods above, please create an issue on Github. | |||||
:param time_index: the frame number | |||||
:type time_index: int | |||||
:param field_of_view: the label for the place in the XY-plane where this image was taken. | |||||
:type field_of_view: int | |||||
:param channel_name: the name of the color of this image | |||||
:type channel_name: str | |||||
:param z_level: the label for the location in the Z-plane where this image was taken. | |||||
:type z_level: int | |||||
:rtype: nd2reader.model.Image() or None | |||||
""" | |||||
image_set_number = self._calculate_image_group_number(time_index, field_of_view, z_level) | |||||
try: | |||||
timestamp, raw_image_data = self._get_raw_image_data(image_set_number, self._channel_offset[channel_name]) | |||||
image = Image(timestamp, raw_image_data, field_of_view, channel_name, z_level, self.height, self.width) | |||||
except TypeError: | |||||
return None | |||||
else: | |||||
return image |
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# -*- coding: utf-8 -*- | |||||
import array | |||||
from collections import namedtuple | |||||
from datetime import datetime | |||||
import numpy as np | |||||
import re | |||||
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. | |||||
You should not ever need to instantiate this class manually unless you're a developer. | |||||
""" | |||||
CHUNK_HEADER = 0xabeceda | |||||
CHUNK_MAP_START = "ND2 FILEMAP SIGNATURE NAME 0001!" | |||||
CHUNK_MAP_END = "ND2 CHUNK MAP SIGNATURE 0000001!" | |||||
def __init__(self, filename): | |||||
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 | |||||
def _get_raw_image_data(self, image_group_number, channel_offset): | |||||
""" | |||||
Reads the raw bytes and the timestamp of an image. | |||||
:param image_group_number: groups are made of images with the same time index, field of view and z-level. | |||||
:type image_group_number: int | |||||
:param channel_offset: the offset in the array where the bytes for this image are found. | |||||
:type channel_offset: int | |||||
:return: (int, array.array()) or None | |||||
""" | |||||
chunk = self._label_map["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 | |||||
# seconds unless you're doing something super weird. | |||||
timestamp = struct.unpack("d", data[:8])[0] | |||||
image_group_data = array.array("H", data) | |||||
image_data_start = 4 + channel_offset | |||||
# The images for the various channels are interleaved within the same array. For example, the second image | |||||
# of a four image group will be composed of bytes 2, 6, 10, etc. If you understand why someone would design | |||||
# a data structure that way, please send the author of this library a message. | |||||
image_data = image_group_data[image_data_start::self._channel_count] | |||||
# Skip images that are all zeros! This is important, since NIS Elements creates blank "gap" images if you | |||||
# don't have the same number of images each cycle. We discovered this because we only took GFP images every | |||||
# other cycle to reduce phototoxicity, but NIS Elements still allocated memory as if we were going to take | |||||
# them every cycle. | |||||
if np.any(image_data): | |||||
return timestamp, image_data | |||||
return None | |||||
@property | |||||
def _dimensions(self): | |||||
""" | |||||
While there are metadata values that represent a lot of what we want to capture, they seem to be unreliable. | |||||
Sometimes certain elements don't exist, or change their data type randomly. However, the human-readable text | |||||
is always there and in the same exact format, so we just parse that instead. | |||||
:rtype: str | |||||
""" | |||||
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 _channels(self): | |||||
""" | |||||
These are labels created by the NIS Elements user. Typically they may a short description of the filter cube | |||||
used (e.g. "bright field", "GFP", etc.) | |||||
:rtype: str | |||||
""" | |||||
metadata = self.metadata['ImageMetadataSeq']['SLxPictureMetadata']['sPicturePlanes'] | |||||
try: | |||||
validity = self.metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx'][''][0]['ppNextLevelEx'][''][0]['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): | |||||
if not valid: | |||||
continue | |||||
yield chan['sDescription'] | |||||
def _calculate_image_group_number(self, time_index, fov, z_level): | |||||
""" | |||||
Images are grouped together if they share the same time index, field of view, and z-level. | |||||
:type time_index: int | |||||
:type fov: int | |||||
:type z_level: int | |||||
:rtype: int | |||||
""" | |||||
return time_index * self._field_of_view_count * self._z_level_count + (fov * self._z_level_count + z_level) | |||||
@property | |||||
def _channel_offset(self): | |||||
""" | |||||
Image data is interleaved for each image set. That is, if there are four images in a set, the first image | |||||
will consist of pixels 1, 5, 9, etc, the second will be pixels 2, 6, 10, and so forth. | |||||
:rtype: dict | |||||
""" | |||||
channel_offset = {} | |||||
for n, channel in enumerate(self._channels): | |||||
channel_offset[channel] = n | |||||
return channel_offset | |||||
@property | |||||
def _absolute_start(self): | |||||
""" | |||||
The date and time when acquisition began. | |||||
:rtype: datetime.datetime() | |||||
""" | |||||
for line in self.metadata['ImageTextInfo']['SLxImageTextInfo'].values(): | |||||
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: | |||||
pass | |||||
try: | |||||
absolute_start_12 = datetime.strptime(line, "%m/%d/%Y %I:%M:%S %p") | |||||
except ValueError: | |||||
pass | |||||
if not absolute_start_12 and not absolute_start_24: | |||||
continue | |||||
return absolute_start_12 if absolute_start_12 else absolute_start_24 | |||||
raise ValueError("This ND2 has no recorded start time. This is probably a bug.") | |||||
@property | |||||
def _channel_count(self): | |||||
""" | |||||
The number of different channels used, including bright field. | |||||
:rtype: int | |||||
""" | |||||
pattern = r""".*?λ\((\d+)\).*?""" | |||||
try: | |||||
count = int(re.match(pattern, self._dimensions).group(1)) | |||||
except AttributeError: | |||||
return 1 | |||||
else: | |||||
return count | |||||
@property | |||||
def _field_of_view_count(self): | |||||
""" | |||||
The metadata contains information about fields of view, but it contains it even if some fields | |||||
of view were cropped. We can't find anything that states which fields of view are actually | |||||
in the image data, so we have to calculate it. There probably is something somewhere, since | |||||
NIS Elements can figure it out, but we haven't found it yet. | |||||
:rtype: int | |||||
""" | |||||
pattern = r""".*?XY\((\d+)\).*?""" | |||||
try: | |||||
count = int(re.match(pattern, self._dimensions).group(1)) | |||||
except AttributeError: | |||||
return 1 | |||||
else: | |||||
return count | |||||
@property | |||||
def _time_index_count(self): | |||||
""" | |||||
The number of cycles. | |||||
:rtype: int | |||||
""" | |||||
pattern = r""".*?T'\((\d+)\).*?""" | |||||
try: | |||||
count = int(re.match(pattern, self._dimensions).group(1)) | |||||
except AttributeError: | |||||
return 1 | |||||
else: | |||||
return count | |||||
@property | |||||
def _z_level_count(self): | |||||
""" | |||||
The number of different levels in the Z-plane. | |||||
:rtype: int | |||||
""" | |||||
pattern = r""".*?Z\((\d+)\).*?""" | |||||
try: | |||||
count = int(re.match(pattern, self._dimensions).group(1)) | |||||
except AttributeError: | |||||
return 1 | |||||
else: | |||||
return count | |||||
@property | |||||
def _image_count(self): | |||||
""" | |||||
The total number of images in the ND2. Warning: this may be inaccurate as it includes "gap" images. | |||||
:rtype: int | |||||
""" | |||||
return self.metadata['ImageAttributes']['SLxImageAttributes']['uiSequenceCount'] | |||||
def _parse_metadata(self): | |||||
""" | |||||
Reads all metadata. | |||||
""" | |||||
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 _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): | |||||
""" | |||||
Reads hierarchical data, analogous to a Python dict. | |||||
""" | |||||
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): | |||||
""" | |||||
ND2s use various codes to indicate different data types, which we translate here. | |||||
""" | |||||
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): | |||||
""" | |||||
Iterates over each element some section of the metadata and parses it. | |||||
""" | |||||
data = StringIO(data) | |||||
metadata = {} | |||||
for _ in xrange(count): | |||||
self._cursor_position = data.tell() | |||||
header = data.read(2) | |||||
if not header: | |||||
# We've reached the end of some hierarchy of data | |||||
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 |
@ -1,439 +0,0 @@ | |||||
# -*- coding: utf-8 -*- | |||||
import array | |||||
import numpy as np | |||||
import struct | |||||
import re | |||||
from StringIO import StringIO | |||||
from collections import namedtuple | |||||
import logging | |||||
from nd2reader.model import Channel | |||||
from datetime import datetime | |||||
log = logging.getLogger(__name__) | |||||
log.setLevel(logging.DEBUG) | |||||
chunk = namedtuple('Chunk', ['location', 'length']) | |||||
field_of_view = namedtuple('FOV', ['number', 'x', 'y', 'z', 'pfs_offset']) | |||||
class BaseNd2(object): | |||||
def __init__(self, filename): | |||||
self._reader = Nd2Reader(filename) | |||||
self._channel_offset = None | |||||
@property | |||||
def height(self): | |||||
""" | |||||
:return: height of each image, in pixels | |||||
""" | |||||
return self._metadata['ImageAttributes']['SLxImageAttributes']['uiHeight'] | |||||
@property | |||||
def width(self): | |||||
""" | |||||
:return: width of each image, in pixels | |||||
""" | |||||
return self._metadata['ImageAttributes']['SLxImageAttributes']['uiWidth'] | |||||
@property | |||||
def absolute_start(self): | |||||
return self._reader.absolute_start | |||||
@property | |||||
def channels(self): | |||||
metadata = self._metadata['ImageMetadataSeq']['SLxPictureMetadata']['sPicturePlanes'] | |||||
try: | |||||
validity = self._metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx'][''][0]['ppNextLevelEx'][''][0]['pItemValid'] | |||||
except KeyError: | |||||
# If none of the channels have been deleted, there is no validity list, so we just make one | |||||
validity = [True for i 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): | |||||
if not valid: | |||||
continue | |||||
name = chan['sDescription'] | |||||
exposure_time = metadata['sSampleSetting'][label]['dExposureTime'] | |||||
camera = metadata['sSampleSetting'][label]['pCameraSetting']['CameraUserName'] | |||||
yield Channel(name, camera, exposure_time) | |||||
@property | |||||
def channel_names(self): | |||||
""" | |||||
A convenience method for getting an alphabetized list of channel names. | |||||
:return: list[str] | |||||
""" | |||||
for channel in sorted(self.channels, key=lambda x: x.name): | |||||
yield channel.name | |||||
@property | |||||
def _image_count(self): | |||||
return self._metadata['ImageAttributes']['SLxImageAttributes']['uiSequenceCount'] | |||||
@property | |||||
def _sequence_count(self): | |||||
return self._metadata['ImageEvents']['RLxExperimentRecord']['uiCount'] | |||||
@property | |||||
def time_index_count(self): | |||||
""" | |||||
The number of images for a given field of view, channel, and z_level combination. | |||||
Effectively the number of frames. | |||||
:rtype: int | |||||
""" | |||||
return self._reader.time_index_count | |||||
@property | |||||
def z_level_count(self): | |||||
return self._reader.z_level_count | |||||
@property | |||||
def field_of_view_count(self): | |||||
""" | |||||
The metadata contains information about fields of view, but it contains it even if some fields | |||||
of view were cropped. We can't find anything that states which fields of view are actually | |||||
in the image data, so we have to calculate it. There probably is something somewhere, since | |||||
NIS Elements can figure it out, but we haven't found it yet. | |||||
""" | |||||
return self._reader.field_of_view_count | |||||
@property | |||||
def channel_count(self): | |||||
return self._reader.channel_count | |||||
@property | |||||
def channel_offset(self): | |||||
if self._channel_offset is None: | |||||
self._channel_offset = {} | |||||
for n, channel in enumerate(self.channels): | |||||
self._channel_offset[channel.name] = n | |||||
return self._channel_offset | |||||
@property | |||||
def _metadata(self): | |||||
return self._reader.metadata | |||||
def _calculate_image_set_number(self, time_index, fov, z_level): | |||||
return time_index * self.field_of_view_count * self.z_level_count + (fov * self.z_level_count + z_level) | |||||
class Nd2Reader(object): | |||||
""" | |||||
Reads .nd2 files, provides an interface to the metadata, and generates numpy arrays from the image data. | |||||
""" | |||||
def __init__(self, filename): | |||||
self._absolute_start = None | |||||
self._filename = filename | |||||
self._file_handler = None | |||||
self._chunk_map_start_location = None | |||||
self._label_map = {} | |||||
self._metadata = {} | |||||
self._read_map() | |||||
self._parse_dict_data() | |||||
self.__dimensions = None | |||||
@property | |||||
def _dimensions(self): | |||||
if self.__dimensions is None: | |||||
# The particular slot that this data shows up in changes (seemingly) randomly | |||||
for line in self._metadata['ImageTextInfo']['SLxImageTextInfo'].values(): | |||||
if "Dimensions:" in line: | |||||
metadata = line | |||||
break | |||||
else: | |||||
raise Exception("Could not parse metadata dimensions!") | |||||
for line in metadata.split("\r\n"): | |||||
if line.startswith("Dimensions:"): | |||||
self.__dimensions = line | |||||
break | |||||
return self.__dimensions | |||||
@property | |||||
def absolute_start(self): | |||||
if self._absolute_start is None: | |||||
for line in self._metadata['ImageTextInfo']['SLxImageTextInfo'].values(): | |||||
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: | |||||
pass | |||||
try: | |||||
absolute_start_12 = datetime.strptime(line, "%m/%d/%Y %I:%M:%S %p") | |||||
except ValueError: | |||||
pass | |||||
if not absolute_start_12 and not absolute_start_24: | |||||
continue | |||||
self._absolute_start = absolute_start_12 if absolute_start_12 else absolute_start_24 | |||||
return self._absolute_start | |||||
@property | |||||
def fh(self): | |||||
if self._file_handler is None: | |||||
self._file_handler = open(self._filename, "rb") | |||||
return self._file_handler | |||||
@property | |||||
def time_index_count(self): | |||||
""" | |||||
The number of images for a given field of view, channel, and z_level combination. | |||||
Effectively the number of frames. | |||||
:rtype: int | |||||
""" | |||||
pattern = r""".*?T'\((\d+)\).*?""" | |||||
try: | |||||
count = int(re.match(pattern, self._dimensions).group(1)) | |||||
except AttributeError: | |||||
return 1 | |||||
else: | |||||
return count | |||||
@property | |||||
def z_level_count(self): | |||||
pattern = r""".*?Z\((\d+)\).*?""" | |||||
try: | |||||
count = int(re.match(pattern, self._dimensions).group(1)) | |||||
except AttributeError: | |||||
return 1 | |||||
else: | |||||
return count | |||||
@property | |||||
def field_of_view_count(self): | |||||
""" | |||||
The metadata contains information about fields of view, but it contains it even if some fields | |||||
of view were cropped. We can't find anything that states which fields of view are actually | |||||
in the image data, so we have to calculate it. There probably is something somewhere, since | |||||
NIS Elements can figure it out, but we haven't found it yet. | |||||
""" | |||||
pattern = r""".*?XY\((\d+)\).*?""" | |||||
try: | |||||
count = int(re.match(pattern, self._dimensions).group(1)) | |||||
except AttributeError: | |||||
return 1 | |||||
else: | |||||
return count | |||||
@property | |||||
def channel_count(self): | |||||
pattern = r""".*?λ\((\d+)\).*?""" | |||||
try: | |||||
count = int(re.match(pattern, self._dimensions).group(1)) | |||||
except AttributeError: | |||||
return 1 | |||||
else: | |||||
return count | |||||
def get_raw_image_data(self, image_set_number, channel_offset): | |||||
chunk = self._label_map["ImageDataSeq|%d!" % image_set_number] | |||||
data = self._read_chunk(chunk.location) | |||||
timestamp = struct.unpack("d", data[:8])[0] | |||||
# The images for the various channels are interleaved within each other. Yes, this is an incredibly unintuitive and nonsensical way | |||||
# to store data. | |||||
image_data = array.array("H", data) | |||||
image_data_start = 4 + channel_offset | |||||
return timestamp, image_data[image_data_start::self.channel_count] | |||||
def _parse_dict_data(self): | |||||
# TODO: Don't like this name | |||||
for label in self._top_level_dict_labels: | |||||
chunk_location = self._label_map[label].location | |||||
data = self._read_chunk(chunk_location) | |||||
stop = label.index("LV") | |||||
self._metadata[label[:stop]] = self.read_lv_encoding(data, 1) | |||||
@property | |||||
def metadata(self): | |||||
return self._metadata | |||||
@property | |||||
def _top_level_dict_labels(self): | |||||
# TODO: I don't like this name either | |||||
for label in self._label_map.keys(): | |||||
if label.endswith("LV!") or "LV|" in label: | |||||
yield label | |||||
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. | |||||
""" | |||||
raw_text = self._get_raw_chunk_map_text() | |||||
label_start = self._find_first_label_offset(raw_text) | |||||
while True: | |||||
data_start = self._get_data_start(label_start, raw_text) | |||||
label, value = self._extract_map_key(label_start, data_start, raw_text) | |||||
if label == "ND2 CHUNK MAP SIGNATURE 0000001!": | |||||
# We've reached the end of the chunk map | |||||
break | |||||
self._label_map[label] = value | |||||
label_start = data_start + 16 | |||||
@staticmethod | |||||
def _find_first_label_offset(raw_text): | |||||
""" | |||||
The chunk map starts with some number of (seemingly) useless bytes, followed | |||||
by "ND2 FILEMAP SIGNATURE NAME 0001!". We return the location of the first character after this sequence, | |||||
which is the actual beginning of the chunk map. | |||||
""" | |||||
return raw_text.index("ND2 FILEMAP SIGNATURE NAME 0001!") + 32 | |||||
@staticmethod | |||||
def _get_data_start(label_start, raw_text): | |||||
""" | |||||
The data for a given label begins immediately after the first exclamation point | |||||
""" | |||||
return raw_text.index("!", label_start) + 1 | |||||
@staticmethod | |||||
def _extract_map_key(label_start, data_start, raw_text): | |||||
""" | |||||
Chunk map entries are a string label of arbitrary length followed by 16 bytes of data, which represent | |||||
the byte offset from the beginning of the file where that data can be found. | |||||
""" | |||||
key = raw_text[label_start: data_start] | |||||
location, length = struct.unpack("QQ", raw_text[data_start: data_start + 16]) | |||||
return key, chunk(location=location, length=length) | |||||
@property | |||||
def chunk_map_start_location(self): | |||||
""" | |||||
The position in bytes from the beginning of the file where the chunk map begins. | |||||
The chunk map is a series of string labels followed by the position (in bytes) of the respective data. | |||||
""" | |||||
if self._chunk_map_start_location is None: | |||||
# Put the cursor 8 bytes before the end of the file | |||||
self.fh.seek(-8, 2) | |||||
# Read the last 8 bytes of the file | |||||
self._chunk_map_start_location = struct.unpack("Q", self.fh.read(8))[0] | |||||
return self._chunk_map_start_location | |||||
def _read_chunk(self, chunk_location): | |||||
""" | |||||
Gets the data for a given chunk pointer | |||||
""" | |||||
self.fh.seek(chunk_location) | |||||
chunk_data = self._read_chunk_metadata() | |||||
header, relative_offset, data_length = self._parse_chunk_metadata(chunk_data) | |||||
return self._read_chunk_data(chunk_location, relative_offset, data_length) | |||||
def _read_chunk_metadata(self): | |||||
""" | |||||
Gets the chunks metadata, which is always 16 bytes | |||||
""" | |||||
return self.fh.read(16) | |||||
def _read_chunk_data(self, chunk_location, relative_offset, data_length): | |||||
""" | |||||
Reads the actual data for a given chunk | |||||
""" | |||||
# 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.fh.seek(chunk_location + 16 + relative_offset) | |||||
return self.fh.read(data_length) | |||||
@staticmethod | |||||
def _parse_chunk_metadata(chunk_data): | |||||
""" | |||||
Finds out everything about a given chunk. Every chunk begins with the same value, so if that's ever | |||||
different we can assume the file has suffered some kind of damage. | |||||
""" | |||||
header, relative_offset, data_length = struct.unpack("IIQ", chunk_data) | |||||
if header != 0xabeceda: | |||||
raise ValueError("The ND2 file seems to be corrupted.") | |||||
return header, relative_offset, data_length | |||||
def _get_raw_chunk_map_text(self): | |||||
""" | |||||
Reads the entire chunk map and returns it as a string. | |||||
""" | |||||
self.fh.seek(self.chunk_map_start_location) | |||||
return self.fh.read(-1) | |||||
@staticmethod | |||||
def as_numpy_array(arr): | |||||
return np.frombuffer(arr) | |||||
def _z_level_count(self): | |||||
name = "CustomData|Z!" | |||||
st = self._read_chunk(self._label_map[name].location) | |||||
res = array.array("d", st) | |||||
return len(res) | |||||
def read_lv_encoding(self, data, count): | |||||
data = StringIO(data) | |||||
res = {} | |||||
total_count = 0 | |||||
for c in range(count): | |||||
lastpos = data.tell() | |||||
total_count += 1 | |||||
hdr = data.read(2) | |||||
if not hdr: | |||||
break | |||||
typ = ord(hdr[0]) | |||||
bname = data.read(2*ord(hdr[1])) | |||||
name = bname.decode("utf16")[:-1].encode("utf8") | |||||
if typ == 1: | |||||
value, = struct.unpack("B", data.read(1)) | |||||
elif typ in [2, 3]: | |||||
value, = struct.unpack("I", data.read(4)) | |||||
elif typ == 5: | |||||
value, = struct.unpack("Q", data.read(8)) | |||||
elif typ == 6: | |||||
value, = struct.unpack("d", data.read(8)) | |||||
elif typ == 8: | |||||
value = data.read(2) | |||||
while value[-2:] != "\x00\x00": | |||||
value += data.read(2) | |||||
value = value.decode("utf16")[:-1].encode("utf8") | |||||
elif typ == 9: | |||||
cnt, = struct.unpack("Q", data.read(8)) | |||||
value = array.array("B", data.read(cnt)) | |||||
elif typ == 11: | |||||
newcount, length = struct.unpack("<IQ", data.read(12)) | |||||
length -= data.tell()-lastpos | |||||
nextdata = data.read(length) | |||||
value = self.read_lv_encoding(nextdata, newcount) | |||||
# Skip some offsets | |||||
data.read(newcount * 8) | |||||
else: | |||||
assert 0, "%s hdr %x:%x unknown" % (name, ord(hdr[0]), ord(hdr[1])) | |||||
if not name in res: | |||||
res[name] = value | |||||
else: | |||||
if not isinstance(res[name], list): | |||||
res[name] = [res[name]] | |||||
res[name].append(value) | |||||
x = data.read() | |||||
assert not x, "skip %d %s" % (len(x), repr(x[:30])) | |||||
return res |
@ -0,0 +1 @@ | |||||
numpy>=1.9.2 |
@ -0,0 +1,2 @@ | |||||
[metadata] | |||||
description-file = README.md |
@ -1,10 +1,21 @@ | |||||
from setuptools import setup, find_packages | |||||
from distutils.core import setup | |||||
setup( | setup( | ||||
name="nd2reader", | name="nd2reader", | ||||
packages=find_packages(), | |||||
version="0.9.7", | |||||
install_requires=[ | |||||
'numpy', | |||||
], | |||||
packages=['nd2reader', 'nd2reader.model'], | |||||
version="1.0.0", | |||||
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', | |||||
keywords=['nd2', 'nikon', 'microscopy', 'NIS Elements'], | |||||
classifiers=['Development Status :: 5 - Production/Stable', | |||||
'Intended Audience :: Science/Research', | |||||
'License :: Freely Distributable', | |||||
'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)', | |||||
'Operating System :: POSIX :: Linux', | |||||
'Programming Language :: Python :: 2.7', | |||||
'Topic :: Scientific/Engineering', | |||||
] | |||||
) | ) |
@ -1,9 +0,0 @@ | |||||
""" | |||||
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) |
@ -1,20 +0,0 @@ | |||||
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) | |||||