@ -0,0 +1,4 @@ | |||
[submodule "docs"] | |||
path = docs | |||
url = https://github.com/rbnvrw/nd2reader.git | |||
branch = gh-pages |
@ -1,23 +1,33 @@ | |||
env: | |||
global: | |||
- CC_TEST_REPORTER_ID=8582900c285e4da0f253555b1bac1ba501bd6ff07850b0f227166b3cdac59ecc | |||
language: python | |||
git: | |||
depth: 3 | |||
notifications: | |||
email: false | |||
addons: | |||
code_climate: | |||
repo_token: 8582900c285e4da0f253555b1bac1ba501bd6ff07850b0f227166b3cdac59ecc | |||
python: | |||
- "2.7" | |||
- "3.4" | |||
- "3.5" | |||
- "3.5-dev" # 3.5 development branch | |||
- "3.6" | |||
- "3.6-dev" # 3.6 development branch | |||
- "3.7-dev" # 3.7 development branch | |||
- "nightly" # currently points to 3.7-dev | |||
- 3.5 | |||
- 3.6 | |||
- 3.7 | |||
- 3.8 | |||
install: | |||
- pip install --upgrade pip setuptools wheel | |||
- pip install --only-binary=numpy numpy | |||
- pip install -r requirements.txt | |||
- pip install codeclimate-test-reporter coverage | |||
- pip install 'coverage>=4.0,<4.4' --force-reinstall # Upstream bug: https://github.com/nedbat/coveragepy/issues/578 | |||
before_script: | |||
- curl -L https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64 > ./cc-test-reporter | |||
- chmod +x ./cc-test-reporter | |||
- ./cc-test-reporter before-build | |||
script: python ./test.py | |||
script: python ./test.py && CODECLIMATE_REPO_TOKEN=8582900c285e4da0f253555b1bac1ba501bd6ff07850b0f227166b3cdac59ecc codeclimate-test-reporter | |||
after_script: | |||
- ./cc-test-reporter after-build --exit-code $TRAVIS_TEST_RESULT |
@ -0,0 +1,76 @@ | |||
# Contributor Covenant Code of Conduct | |||
## Our Pledge | |||
In the interest of fostering an open and welcoming environment, we as | |||
contributors and maintainers pledge to making participation in our project and | |||
our community a harassment-free experience for everyone, regardless of age, body | |||
size, disability, ethnicity, sex characteristics, gender identity and expression, | |||
level of experience, education, socio-economic status, nationality, personal | |||
appearance, race, religion, or sexual identity and orientation. | |||
## Our Standards | |||
Examples of behavior that contributes to creating a positive environment | |||
include: | |||
* Using welcoming and inclusive language | |||
* Being respectful of differing viewpoints and experiences | |||
* Gracefully accepting constructive criticism | |||
* Focusing on what is best for the community | |||
* Showing empathy towards other community members | |||
Examples of unacceptable behavior by participants include: | |||
* The use of sexualized language or imagery and unwelcome sexual attention or | |||
advances | |||
* Trolling, insulting/derogatory comments, and personal or political attacks | |||
* Public or private harassment | |||
* Publishing others' private information, such as a physical or electronic | |||
address, without explicit permission | |||
* Other conduct which could reasonably be considered inappropriate in a | |||
professional setting | |||
## Our Responsibilities | |||
Project maintainers are responsible for clarifying the standards of acceptable | |||
behavior and are expected to take appropriate and fair corrective action in | |||
response to any instances of unacceptable behavior. | |||
Project maintainers have the right and responsibility to remove, edit, or | |||
reject comments, commits, code, wiki edits, issues, and other contributions | |||
that are not aligned to this Code of Conduct, or to ban temporarily or | |||
permanently any contributor for other behaviors that they deem inappropriate, | |||
threatening, offensive, or harmful. | |||
## Scope | |||
This Code of Conduct applies both within project spaces and in public spaces | |||
when an individual is representing the project or its community. Examples of | |||
representing a project or community include using an official project e-mail | |||
address, posting via an official social media account, or acting as an appointed | |||
representative at an online or offline event. Representation of a project may be | |||
further defined and clarified by project maintainers. | |||
## Enforcement | |||
Instances of abusive, harassing, or otherwise unacceptable behavior may be | |||
reported by contacting the project team at development@lighthacking.nl. All | |||
complaints will be reviewed and investigated and will result in a response that | |||
is deemed necessary and appropriate to the circumstances. The project team is | |||
obligated to maintain confidentiality with regard to the reporter of an incident. | |||
Further details of specific enforcement policies may be posted separately. | |||
Project maintainers who do not follow or enforce the Code of Conduct in good | |||
faith may face temporary or permanent repercussions as determined by other | |||
members of the project's leadership. | |||
## Attribution | |||
This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, | |||
available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html | |||
[homepage]: https://www.contributor-covenant.org | |||
For answers to common questions about this code of conduct, see | |||
https://www.contributor-covenant.org/faq |
@ -0,0 +1,621 @@ | |||
GNU GENERAL PUBLIC LICENSE | |||
Version 3, 29 June 2007 | |||
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> | |||
Everyone is permitted to copy and distribute verbatim copies | |||
of this license document, but changing it is not allowed. | |||
Preamble | |||
The GNU General Public License is a free, copyleft license for | |||
software and other kinds of works. | |||
The licenses for most software and other practical works are designed | |||
to take away your freedom to share and change the works. By contrast, | |||
the GNU General Public License is intended to guarantee your freedom to | |||
share and change all versions of a program--to make sure it remains free | |||
software for all its users. We, the Free Software Foundation, use the | |||
GNU General Public License for most of our software; it applies also to | |||
any other work released this way by its authors. You can apply it to | |||
your programs, too. | |||
When we speak of free software, we are referring to freedom, not | |||
price. Our General Public Licenses are designed to make sure that you | |||
have the freedom to distribute copies of free software (and charge for | |||
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To protect your rights, we need to prevent others from denying you | |||
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you modify it: responsibilities to respect the freedom of others. | |||
For example, if you distribute copies of such a program, whether | |||
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Developers that use the GNU GPL protect your rights with two steps: | |||
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For the developers' and authors' protection, the GPL clearly explains | |||
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Some devices are designed to deny users access to install or run | |||
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stand ready to extend this provision to those domains in future versions | |||
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Finally, every program is threatened constantly by software patents. | |||
States should not allow patents to restrict development and use of | |||
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patents cannot be used to render the program non-free. | |||
The precise terms and conditions for copying, distribution and | |||
modification follow. | |||
TERMS AND CONDITIONS | |||
0. Definitions. | |||
"This License" refers to version 3 of the GNU General Public License. | |||
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works, such as semiconductor masks. | |||
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A "covered work" means either the unmodified Program or a work based | |||
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To "propagate" a work means to do anything with it that, without | |||
permission, would make you directly or secondarily liable for | |||
infringement under applicable copyright law, except executing it on a | |||
computer or modifying a private copy. Propagation includes copying, | |||
distribution (with or without modification), making available to the | |||
public, and in some countries other activities as well. | |||
To "convey" a work means any kind of propagation that enables other | |||
parties to make or receive copies. Mere interaction with a user through | |||
a computer network, with no transfer of a copy, is not conveying. | |||
An interactive user interface displays "Appropriate Legal Notices" | |||
to the extent that it includes a convenient and prominently visible | |||
feature that (1) displays an appropriate copyright notice, and (2) | |||
tells the user that there is no warranty for the work (except to the | |||
extent that warranties are provided), that licensees may convey the | |||
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menu, a prominent item in the list meets this criterion. | |||
1. Source Code. | |||
The "source code" for a work means the preferred form of the work | |||
for making modifications to it. "Object code" means any non-source | |||
form of a work. | |||
A "Standard Interface" means an interface that either is an official | |||
standard defined by a recognized standards body, or, in the case of | |||
interfaces specified for a particular programming language, one that | |||
is widely used among developers working in that language. | |||
The "System Libraries" of an executable work include anything, other | |||
than the work as a whole, that (a) is included in the normal form of | |||
packaging a Major Component, but which is not part of that Major | |||
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"Major Component", in this context, means a major essential component | |||
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(if any) on which the executable work runs, or a compiler used to | |||
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The "Corresponding Source" for a work in object code form means all | |||
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work) run the object code and to modify the work, including scripts to | |||
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The Corresponding Source need not include anything that users | |||
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The Corresponding Source for a work in source code form is that | |||
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All rights granted under this License are granted for the term of | |||
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You may make, run and propagate covered works that you do not | |||
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Conveying under any other circumstances is permitted solely under | |||
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No covered work shall be deemed part of an effective technological | |||
measure under any applicable law fulfilling obligations under article | |||
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similar laws prohibiting or restricting circumvention of such | |||
measures. | |||
When you convey a covered work, you waive any legal power to forbid | |||
circumvention of technological measures to the extent such circumvention | |||
is effected by exercising rights under this License with respect to | |||
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modification of the work as a means of enforcing, against the work's | |||
users, your or third parties' legal rights to forbid circumvention of | |||
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4. Conveying Verbatim Copies. | |||
You may convey verbatim copies of the Program's source code as you | |||
receive it, in any medium, provided that you conspicuously and | |||
appropriately publish on each copy an appropriate copyright notice; | |||
keep intact all notices stating that this License and any | |||
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keep intact all notices of the absence of any warranty; and give all | |||
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You may charge any price or no price for each copy that you convey, | |||
and you may offer support or warranty protection for a fee. | |||
5. Conveying Modified Source Versions. | |||
You may convey a work based on the Program, or the modifications to | |||
produce it from the Program, in the form of source code under the | |||
terms of section 4, provided that you also meet all of these conditions: | |||
a) The work must carry prominent notices stating that you modified | |||
it, and giving a relevant date. | |||
b) The work must carry prominent notices stating that it is | |||
released under this License and any conditions added under section | |||
7. This requirement modifies the requirement in section 4 to | |||
"keep intact all notices". | |||
c) You must license the entire work, as a whole, under this | |||
License to anyone who comes into possession of a copy. This | |||
License will therefore apply, along with any applicable section 7 | |||
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regardless of how they are packaged. This License gives no | |||
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invalidate such permission if you have separately received it. | |||
d) If the work has interactive user interfaces, each must display | |||
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You may convey a covered work in object code form under the terms | |||
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"Additional permissions" are terms that supplement the terms of this | |||
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Additional permissions that are applicable to the entire Program shall | |||
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11. Patents. | |||
A "contributor" is a copyright holder who authorizes use under this | |||
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work thus licensed is called the contributor's "contributor version". | |||
A contributor's "essential patent claims" are all patent claims | |||
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Each contributor grants you a non-exclusive, worldwide, royalty-free | |||
patent license under the contributor's essential patent claims, to | |||
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propagate the contents of its contributor version. | |||
In the following three paragraphs, a "patent license" is any express | |||
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If the disclaimer of warranty and limitation of liability provided | |||
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END OF TERMS AND CONDITIONS |
@ -0,0 +1,6 @@ | |||
include MANIFEST.in | |||
include VERSION | |||
include setup.py | |||
include README.md | |||
include LICENSE | |||
include COPYING |
@ -1,3 +1,5 @@ | |||
from os import path | |||
from nd2reader.reader import ND2Reader | |||
from nd2reader.legacy import Nd2 | |||
__version__ = '2.1.3' | |||
__version__ = '3.2.3' |
@ -0,0 +1,280 @@ | |||
"""Functions to create artificial nd2 data for testing purposes | |||
""" | |||
import six | |||
import numpy as np | |||
import struct | |||
from nd2reader.common import check_or_make_dir | |||
from os import path | |||
global_labels = ['image_attributes', 'image_text_info', 'image_metadata', | |||
'image_metadata_sequence', 'image_calibration', 'x_data', | |||
'y_data', 'z_data', 'roi_metadata', 'pfs_status', 'pfs_offset', | |||
'guid', 'description', 'camera_exposure_time', 'camera_temp', | |||
'acquisition_times', 'acquisition_times_2', | |||
'acquisition_frames', 'lut_data', 'grabber_settings', | |||
'custom_data', 'app_info', 'image_frame_0'] | |||
global_file_labels = ["ImageAttributesLV!", "ImageTextInfoLV!", | |||
"ImageMetadataLV!", "ImageMetadataSeqLV|0!", | |||
"ImageCalibrationLV|0!", "CustomData|X!", "CustomData|Y!", | |||
"CustomData|Z!", "CustomData|RoiMetadata_v1!", | |||
"CustomData|PFS_STATUS!", "CustomData|PFS_OFFSET!", | |||
"CustomData|GUIDStore!", "CustomData|CustomDescriptionV1_0!", | |||
"CustomData|Camera_ExposureTime1!", "CustomData|CameraTemp1!", | |||
"CustomData|AcqTimesCache!", "CustomData|AcqTimes2Cache!", | |||
"CustomData|AcqFramesCache!", "CustomDataVar|LUTDataV1_0!", | |||
"CustomDataVar|GrabberCameraSettingsV1_0!", | |||
"CustomDataVar|CustomDataV2_0!", "CustomDataVar|AppInfo_V1_0!", | |||
"ImageDataSeq|0!"] | |||
class ArtificialND2(object): | |||
"""Artificial ND2 class (for testing purposes) | |||
""" | |||
header = 0xabeceda | |||
relative_offset = 0 | |||
data_types = {'unsigned_char': 1, | |||
'unsigned_int': 2, | |||
'unsigned_int_2': 3, | |||
'unsigned_long': 5, | |||
'double': 6, | |||
'string': 8, | |||
'char_array': 9, | |||
'metadata_item': 11, | |||
} | |||
def __init__(self, file, version=(3, 0), skip_blocks=None): | |||
self.version = version | |||
self.raw_text, self.locations, self.data = b'', None, None | |||
check_or_make_dir(path.dirname(file)) | |||
self._fh = open(file, 'w+b', 0) | |||
self.write_file(skip_blocks) | |||
def __enter__(self): | |||
return self | |||
def __exit__(self, exc_type, exc_value, traceback): | |||
self.close() | |||
@property | |||
def file_handle(self): | |||
"""The file handle to the binary file | |||
Returns: | |||
file: the file handle | |||
""" | |||
return self._fh | |||
def close(self): | |||
"""Correctly close the file handle | |||
""" | |||
if self._fh is not None: | |||
self._fh.close() | |||
def write_file(self, skip_blocks=None): | |||
if skip_blocks is None: | |||
skip_blocks = [] | |||
if 'version' not in skip_blocks: | |||
# write version header at start of the file | |||
self.write_version() | |||
if 'label_map' not in skip_blocks: | |||
# write label map + data in the center | |||
self.locations, self.data = self.write_label_map() | |||
if 'label_map_marker' not in skip_blocks: | |||
# write start position of label map at the end of the file | |||
self.write_label_map_info() | |||
# write all to file | |||
self._fh.write(self.raw_text) | |||
def write_version(self): | |||
"""Write file header | |||
""" | |||
# write 16 empty bytes | |||
self.raw_text += bytearray(16) | |||
# write version info | |||
self.raw_text += self._get_version_string() | |||
def write_label_map_info(self): | |||
"""Write the location of the start of the label map at the end of the file | |||
""" | |||
location = self._get_version_byte_length() | |||
self.raw_text += struct.pack("Q", location) | |||
def _get_version_string(self): | |||
return six.b('ND2 FILE SIGNATURE CHUNK NAME01!Ver%s.%s' % self.version) | |||
def _get_version_byte_length(self): | |||
return 16 + len(self._get_version_string()) | |||
def write_label_map(self): | |||
raw_text, locations, data = self.create_label_map_bytes() | |||
self.raw_text += raw_text | |||
return locations, data | |||
def create_label_map_bytes(self): | |||
"""Construct a binary label map | |||
Returns: | |||
tuple: (binary data, dictionary data) | |||
""" | |||
raw_text = six.b('') | |||
labels = global_labels | |||
file_labels = global_file_labels | |||
file_data, file_data_dict = self._get_file_data(labels) | |||
locations = {} | |||
# generate random positions and lengths | |||
version_length = self._get_version_byte_length() | |||
# calculate data length | |||
label_length = np.sum([len(six.b(l)) + 16 for l in file_labels]) | |||
# write label map | |||
cur_pos = version_length + label_length | |||
for label, file_label, data in zip(labels, file_labels, file_data): | |||
raw_text += six.b(file_label) | |||
data_length = len(data) | |||
raw_text += struct.pack('QQ', cur_pos, data_length) | |||
locations[label] = (cur_pos, data_length) | |||
cur_pos += data_length | |||
# write data | |||
raw_text += six.b('').join(file_data) | |||
return raw_text, locations, file_data_dict | |||
def _pack_data_with_metadata(self, data): | |||
packed_data = self._pack_raw_data_with_metadata(data) | |||
raw_data = struct.pack("IIQ", self.header, self.relative_offset, len(packed_data)) | |||
raw_data += packed_data | |||
return raw_data | |||
def _pack_raw_data_with_metadata(self, data): | |||
raw_data = b'' | |||
if isinstance(data, dict): | |||
raw_data = self._pack_dict_with_metadata(data) | |||
elif isinstance(data, int): | |||
raw_data = struct.pack('I', data) | |||
elif isinstance(data, float): | |||
raw_data = struct.pack('d', data) | |||
elif isinstance(data, str): | |||
raw_data = self._str_to_padded_bytes(data) | |||
return raw_data | |||
def _get_data_type(self, data): | |||
if isinstance(data, dict): | |||
return self.data_types['metadata_item'] | |||
elif isinstance(data, int): | |||
return self.data_types['unsigned_int'] | |||
elif isinstance(data, str): | |||
return self.data_types['string'] | |||
else: | |||
return self.data_types['double'] | |||
@staticmethod | |||
def _str_to_padded_bytes(data): | |||
return six.b('').join([struct.pack('cx', six.b(s)) for s in data]) + struct.pack('xx') | |||
def _pack_dict_with_metadata(self, data): | |||
raw_data = b'' | |||
for data_key in data.keys(): | |||
# names have always one character extra and are padded in zero bytes??? | |||
b_data_key = self._str_to_padded_bytes(data_key) | |||
# header consists of data type and length of key name, it is represented by 2 unsigned chars | |||
raw_data += struct.pack('BB', self._get_data_type(data[data_key]), len(data_key) + 1) | |||
raw_data += b_data_key | |||
sub_data = self._pack_raw_data_with_metadata(data[data_key]) | |||
if isinstance(data[data_key], dict): | |||
# Pack: the number of keys and the length of raw data until now, sub data | |||
# and the 12 bytes that we add now | |||
raw_data += struct.pack("<IQ", len(data[data_key].keys()), len(sub_data) + len(raw_data) + 12) | |||
raw_data += sub_data | |||
if isinstance(data[data_key], dict): | |||
# apparently there is also a huge empty space | |||
raw_data += b''.join([struct.pack('x')] * len(data[data_key].keys()) * 8) | |||
return raw_data | |||
@staticmethod | |||
def _get_slx_img_attrib(): | |||
return {'uiWidth': 128, | |||
'uiWidthBytes': 256, | |||
'uiHeight': 128, | |||
'uiComp': 1, | |||
'uiBpcInMemory': 16, | |||
'uiBpcSignificant': 12, | |||
'uiSequenceCount': 70, | |||
'uiTileWidth': 128, | |||
'uiTileHeight': 128, | |||
'eCompression': 2, | |||
'dCompressionParam': -1.0, | |||
'ePixelType': 1, | |||
'uiVirtualComponents': 1 | |||
} | |||
@staticmethod | |||
def _get_slx_picture_metadata(): | |||
return {'sPicturePlanes': | |||
{ | |||
'sPlaneNew': { | |||
# channels are numbered a0, a1, ..., aN | |||
'a0': { | |||
'sDescription': 'TRITC' | |||
} | |||
} | |||
} | |||
} | |||
def _get_file_data(self, labels): | |||
file_data = [ | |||
{'SLxImageAttributes': self._get_slx_img_attrib()}, # ImageAttributesLV!", | |||
7, # ImageTextInfoLV!", | |||
7, # ImageMetadataLV!", | |||
{'SLxPictureMetadata': self._get_slx_picture_metadata()}, # ImageMetadataSeqLV|0!", | |||
7, # ImageCalibrationLV|0!", | |||
7, # CustomData|X!", | |||
7, # CustomData|Y!", | |||
7, # CustomData|Z!", | |||
7, # CustomData|RoiMetadata_v1!", | |||
7, # CustomData|PFS_STATUS!", | |||
7, # CustomData|PFS_OFFSET!", | |||
7, # CustomData|GUIDStore!", | |||
7, # CustomData|CustomDescriptionV1_0!", | |||
7, # CustomData|Camera_ExposureTime1!", | |||
7, # CustomData|CameraTemp1!", | |||
[0], # CustomData|AcqTimesCache!", | |||
[0], # CustomData|AcqTimes2Cache!", | |||
[0], # CustomData|AcqFramesCache!", | |||
7, # CustomDataVar|LUTDataV1_0!", | |||
7, # CustomDataVar|GrabberCameraSettingsV1_0!", | |||
7, # CustomDataVar|CustomDataV2_0!", | |||
7, # CustomDataVar|AppInfo_V1_0!", | |||
7, # ImageDataSeq|0!" | |||
] | |||
file_data_dict = {l: d for l, d in zip(labels, file_data)} | |||
# convert to bytes | |||
file_data = [self._pack_data_with_metadata(d) for d in file_data] | |||
return file_data, file_data_dict |
@ -0,0 +1,111 @@ | |||
import six | |||
import warnings | |||
from nd2reader.common import get_from_dict_if_exists | |||
def parse_if_not_none(to_check, callback): | |||
if to_check is not None: | |||
return callback() | |||
return None | |||
def parse_dimension_text_line(line): | |||
if six.b("Dimensions:") in line: | |||
entries = line.split(six.b("\r\n")) | |||
for entry in entries: | |||
if entry.startswith(six.b("Dimensions:")): | |||
return entry | |||
return None | |||
def parse_roi_shape(shape): | |||
if shape == 3: | |||
return 'rectangle' | |||
elif shape == 9: | |||
return 'circle' | |||
return None | |||
def parse_roi_type(type_no): | |||
if type_no == 4: | |||
return 'stimulation' | |||
elif type_no == 3: | |||
return 'reference' | |||
elif type_no == 2: | |||
return 'background' | |||
return None | |||
def get_loops_from_data(loop_data): | |||
# special ND experiment | |||
if six.b('pPeriod') not in loop_data: | |||
return [] | |||
if six.b('uiPeriodCount') in loop_data and loop_data[six.b('uiPeriodCount')] > 0: | |||
loops = [] | |||
for i, period in enumerate(loop_data[six.b('pPeriod')]): | |||
# exclude invalid periods | |||
if six.b('pPeriodValid') in loop_data: | |||
try: | |||
if loop_data[six.b('pPeriodValid')][i] == 1: | |||
loops.append(loop_data[six.b('pPeriod')][period]) | |||
except IndexError: | |||
continue | |||
else: | |||
# we can't be sure, append all | |||
loops.append(loop_data[six.b('pPeriod')][period]) | |||
return [loop_data] | |||
def guess_sampling_from_loops(duration, loop): | |||
""" In some cases, both keys are not saved. Then try to calculate it. | |||
Args: | |||
duration: the total duration of the loop | |||
loop: the raw loop data | |||
Returns: | |||
float: the guessed sampling interval in milliseconds | |||
""" | |||
number_of_loops = get_from_dict_if_exists('uiCount', loop) | |||
number_of_loops = number_of_loops if number_of_loops is not None and number_of_loops > 0 else 1 | |||
interval = duration / number_of_loops | |||
return interval | |||
def determine_sampling_interval(duration, loop): | |||
"""Determines the loop sampling interval in milliseconds | |||
Args: | |||
duration: loop duration in milliseconds | |||
loop: loop dictionary | |||
Returns: | |||
float: the sampling interval in milliseconds | |||
""" | |||
interval = get_from_dict_if_exists('dPeriod', loop) | |||
avg_interval = get_from_dict_if_exists('dAvgPeriodDiff', loop) | |||
if interval is None or interval <= 0: | |||
interval = avg_interval | |||
else: | |||
avg_interval_set = avg_interval is not None and avg_interval > 0 | |||
if round(avg_interval) != round(interval) and avg_interval_set: | |||
message = ("Reported average frame interval (%.1f ms) doesn't" | |||
" match the set interval (%.1f ms). Using the average" | |||
" now.") | |||
warnings.warn(message % (avg_interval, interval), RuntimeWarning) | |||
interval = avg_interval | |||
if interval is None or interval <= 0: | |||
# In some cases, both keys are not saved. Then try to calculate it. | |||
interval = guess_sampling_from_loops(duration, loop) | |||
return interval |
@ -1,15 +1,21 @@ | |||
class InvalidVersionError(Exception): | |||
""" | |||
We don't know how to parse the version of ND2 that we were given. | |||
class InvalidFileType(Exception): | |||
"""Non .nd2 extension file. | |||
File does not have an extension .nd2. | |||
""" | |||
pass | |||
class InvalidVersionError(Exception): | |||
"""Unknown version. | |||
We don't know how to parse the version of ND2 that we were given. | |||
class NoImageError(Exception): | |||
""" | |||
Some apparent images in ND2s are just completely blank placeholders. These are used when the number of images per | |||
cycle are unequal (e.g. if you take fluorescent images every 2 minutes, and bright field images every minute). | |||
pass | |||
class EmptyFileError(Exception): | |||
"""This .nd2 file seems to be empty. | |||
Raised if no axes are found in the file. | |||
""" | |||
pass |
@ -0,0 +1,167 @@ | |||
""" | |||
Legacy class for backwards compatibility | |||
""" | |||
import warnings | |||
from nd2reader import ND2Reader | |||
class Nd2(object): | |||
""" Warning: this module is deprecated and only maintained for backwards compatibility with the non-PIMS version of | |||
nd2reader. | |||
""" | |||
def __init__(self, filename): | |||
warnings.warn( | |||
"The 'Nd2' class is deprecated, please consider using the new ND2Reader interface which uses pims.", | |||
DeprecationWarning) | |||
self.reader = ND2Reader(filename) | |||
def __repr__(self): | |||
return "\n".join(["<Deprecated ND2 %s>" % self.reader.filename, | |||
"Created: %s" % (self.date if self.date is not None else "Unknown"), | |||
"Image size: %sx%s (HxW)" % (self.height, self.width), | |||
"Frames: %s" % len(self.frames), | |||
"Channels: %s" % ", ".join(["%s" % str(channel) for channel in self.channels]), | |||
"Fields of View: %s" % len(self.fields_of_view), | |||
"Z-Levels: %s" % len(self.z_levels) | |||
]) | |||
def __enter__(self): | |||
return self | |||
def __exit__(self, exc_type, exc_val, exc_tb): | |||
if self.reader is not None: | |||
self.reader.close() | |||
def __len__(self): | |||
return len(self.reader) | |||
def __getitem__(self, item): | |||
return self.reader[item] | |||
def select(self, fields_of_view=None, channels=None, z_levels=None, start=0, stop=None): | |||
"""Select images based on criteria. | |||
Args: | |||
fields_of_view: the fields of view | |||
channels: the color channels | |||
z_levels: the z levels | |||
start: the starting frame | |||
stop: the last frame | |||
Returns: | |||
ND2Reader: Sliced ND2Reader which contains the frames | |||
""" | |||
if stop is None: | |||
stop = len(self.frames) | |||
return self.reader[start:stop] | |||
def get_image(self, frame_number, field_of_view, channel_name, z_level): | |||
"""Deprecated. Returns the specified image from the ND2Reader class. | |||
Args: | |||
frame_number: the frame number | |||
field_of_view: the field of view number | |||
channel_name: the name of the color channel | |||
z_level: the z level number | |||
Returns: | |||
Frame: the specified image | |||
""" | |||
return self.reader.parser.get_image_by_attributes(frame_number, field_of_view, channel_name, z_level, | |||
self.height, self.width) | |||
def close(self): | |||
"""Closes the ND2Reader | |||
""" | |||
if self.reader is not None: | |||
self.reader.close() | |||
@property | |||
def height(self): | |||
"""Deprecated. Fetches the height of the image. | |||
Returns: | |||
int: the pixel height of the image | |||
""" | |||
return self._get_width_or_height("height") | |||
@property | |||
def width(self): | |||
"""Deprecated. Fetches the width of the image. | |||
Returns: | |||
int: the pixel width of the image | |||
""" | |||
return self._get_width_or_height("width") | |||
def _get_width_or_height(self, key): | |||
return self.reader.metadata[key] if self.reader.metadata[key] is not None else 0 | |||
@property | |||
def z_levels(self): | |||
"""Deprecated. Fetches the available z levels. | |||
Returns: | |||
list: z levels. | |||
""" | |||
return self.reader.metadata["z_levels"] | |||
@property | |||
def fields_of_view(self): | |||
"""Deprecated. Fetches the fields of view. | |||
Returns: | |||
list: fields of view. | |||
""" | |||
return self.reader.metadata["fields_of_view"] | |||
@property | |||
def channels(self): | |||
"""Deprecated. Fetches all color channels. | |||
Returns: | |||
list: the color channels. | |||
""" | |||
return self.reader.metadata["channels"] | |||
@property | |||
def frames(self): | |||
"""Deprecated. Fetches all frames. | |||
Returns: | |||
list: list of frames | |||
""" | |||
return self.reader.metadata["frames"] | |||
@property | |||
def date(self): | |||
"""Deprecated. Fetches the acquisition date. | |||
Returns: | |||
string: the date | |||
""" | |||
return self.reader.metadata["date"] | |||
@property | |||
def pixel_microns(self): | |||
"""Deprecated. Fetches the amount of microns per pixel. | |||
Returns: | |||
float: microns per pixel | |||
""" | |||
return self.reader.metadata["pixel_microns"] |
@ -0,0 +1,54 @@ | |||
# -*- coding: utf-8 -*- | |||
import numpy as np # type: ignore | |||
import warnings | |||
def get_unwanted_bytes_ids(image_group_data, image_data_start, height, width): | |||
# Check if the byte array size conforms to the image axes size. If not, check | |||
# that the number of unexpected (unwanted) bytes is a multiple of the number of | |||
# rows (height), as the same unmber of unwanted bytes is expected to be | |||
# appended at the end of each row. Then, returns the indexes of the unwanted | |||
# bytes. | |||
number_of_true_channels = int(len(image_group_data[4:]) / (height * width)) | |||
n_unwanted_bytes = (len(image_group_data[image_data_start:])) % (height * width) | |||
if not n_unwanted_bytes: | |||
return np.arange(0) | |||
assert 0 == n_unwanted_bytes % height, ( | |||
"An unexpected number of extra bytes was encountered based on the expected" | |||
+ " frame size, therefore the file could not be parsed." | |||
) | |||
return np.arange( | |||
image_data_start + height * number_of_true_channels, | |||
len(image_group_data) - n_unwanted_bytes + 1, | |||
height * number_of_true_channels, | |||
) | |||
def remove_bytes_by_id(byte_ids, image_group_data, height): | |||
# Remove bytes by ID. | |||
bytes_per_row = len(byte_ids) // height | |||
warnings.warn( | |||
f"{len(byte_ids)} ({bytes_per_row}*{height}) unexpected zero " | |||
+ "bytes were found in the ND2 file and removed to allow further parsing." | |||
) | |||
for i in range(len(byte_ids)): | |||
del image_group_data[byte_ids[i] : (byte_ids[i] + bytes_per_row)] | |||
def remove_parsed_unwanted_bytes(image_group_data, image_data_start, height, width): | |||
# Stitched ND2 files have been reported to contain unexpected (according to | |||
# image shape) zero bytes at the end of each image data row. This hinders | |||
# proper reshaping of the data. Hence, here the unwanted zero bytes are | |||
# identified and removed. | |||
unwanted_byte_ids = get_unwanted_bytes_ids( | |||
image_group_data, image_data_start, height, width | |||
) | |||
if 0 != len(unwanted_byte_ids): | |||
assert np.all( | |||
image_group_data[unwanted_byte_ids + np.arange(len(unwanted_byte_ids))] == 0 | |||
), ( | |||
f"{len(unwanted_byte_ids)} unexpected non-zero bytes were found" | |||
+ " in the ND2 file, the file could not be parsed." | |||
) | |||
remove_bytes_by_id(unwanted_byte_ids, image_group_data, height) | |||
return image_group_data |
@ -0,0 +1,17 @@ | |||
Update version in 'nd2reader/__init__.py' file | |||
Rebuild sphinx documentation | |||
Commit & push both master and docs | |||
Check if travis unittests are passing | |||
Publish new release on GitHub | |||
Run `python setup.py sdist bdist_wheel` | |||
Run `twine upload dist/*` | |||
Update the version in nd2reader-feedstock to update the conda version: in recipe/meta.yaml, update version and checksum using `sha256sum` | |||
Create & merge PR in nd2reader-feedstock |
@ -1,2 +1,5 @@ | |||
[metadata] | |||
description-file = README.md | |||
description-file = README.md | |||
[bdist_wheel] | |||
universal=1 |
@ -0,0 +1,20 @@ | |||
# Makefile for Sphinx documentation | |||
# | |||
# You can set these variables from the command line. | |||
SPHINXBUILD = python3 -msphinx | |||
BUILDDIR = ../docs | |||
# Internal variables. | |||
ALLSPHINXOPTS = . | |||
.PHONY: help | |||
help: | |||
@echo "Please use \`make <target>' where <target> is one of" | |||
@echo " html to make standalone HTML files" | |||
.PHONY: html | |||
html: | |||
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR) | |||
@echo | |||
@echo "Build finished. The HTML pages are in $(BUILDDIR)." |
@ -0,0 +1 @@ | |||
{% extends "!layout.html" %} |
@ -0,0 +1,164 @@ | |||
#!/usr/bin/env python3 | |||
# -*- coding: utf-8 -*- | |||
import sphinx_bootstrap_theme | |||
from recommonmark.parser import CommonMarkParser | |||
from nd2reader import __version__ as VERSION | |||
# -- General configuration ------------------------------------------------ | |||
# If your documentation needs a minimal Sphinx version, state it here. | |||
# | |||
# needs_sphinx = '1.0' | |||
# Add any Sphinx extension module names here, as strings. They can be | |||
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom | |||
# ones. | |||
extensions = ['sphinx.ext.autodoc', | |||
'sphinx.ext.todo', | |||
'sphinx.ext.viewcode', | |||
'sphinx.ext.napoleon'] | |||
# Add any paths that contain templates here, relative to this directory. | |||
templates_path = ['_templates'] | |||
# The suffix(es) of source filenames. | |||
# You can specify multiple suffix as a list of string: | |||
# | |||
# source_suffix = ['.rst', '.md'] | |||
source_parsers = { | |||
'.md': CommonMarkParser, | |||
} | |||
source_suffix = ['.rst', '.md'] | |||
# The master toctree document. | |||
master_doc = 'index' | |||
# General information about the project. | |||
project = 'nd2reader' | |||
copyright = '2017 - 2019, Ruben Verweij' | |||
author = 'Ruben Verweij' | |||
# The version info for the project you're documenting, acts as replacement for | |||
# |version| and |release|, also used in various other places throughout the | |||
# built documents. | |||
# | |||
# The short X.Y version. | |||
version = VERSION | |||
# The full version, including alpha/beta/rc tags. | |||
release = VERSION | |||
# The language for content autogenerated by Sphinx. Refer to documentation | |||
# for a list of supported languages. | |||
# | |||
# This is also used if you do content translation via gettext catalogs. | |||
# Usually you set "language" from the command line for these cases. | |||
language = 'en' | |||
# List of patterns, relative to source directory, that match files and | |||
# directories to ignore when looking for source files. | |||
# This patterns also effect to html_static_path and html_extra_path | |||
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] | |||
# The name of the Pygments (syntax highlighting) style to use. | |||
pygments_style = 'sphinx' | |||
# If true, `todo` and `todoList` produce output, else they produce nothing. | |||
todo_include_todos = True | |||
# -- Options for HTML output ---------------------------------------------- | |||
# The theme to use for HTML and HTML Help pages. See the documentation for | |||
# a list of builtin themes. | |||
# | |||
html_theme = 'bootstrap' | |||
html_theme_path = sphinx_bootstrap_theme.get_html_theme_path() | |||
# Theme options are theme-specific and customize the look and feel of a theme | |||
# further. For a list of options available for each theme, see the | |||
# documentation. | |||
# | |||
html_theme_options = { | |||
'navbar_links': [ | |||
("Lighthacking", "http://lighthacking.nl", True), | |||
], | |||
} | |||
# Add any paths that contain custom static files (such as style sheets) here, | |||
# relative to this directory. They are copied after the builtin static files, | |||
# so a file named "default.css" will overwrite the builtin "default.css". | |||
html_static_path = [] | |||
# -- Options for HTMLHelp output ------------------------------------------ | |||
# Output file base name for HTML help builder. | |||
htmlhelp_basename = 'nd2readerdoc' | |||
# -- Options for LaTeX output --------------------------------------------- | |||
latex_elements = { | |||
# The paper size ('letterpaper' or 'a4paper'). | |||
# | |||
# 'papersize': 'letterpaper', | |||
# The font size ('10pt', '11pt' or '12pt'). | |||
# | |||
# 'pointsize': '10pt', | |||
# Additional stuff for the LaTeX preamble. | |||
# | |||
# 'preamble': '', | |||
# Latex figure (float) alignment | |||
# | |||
# 'figure_align': 'htbp', | |||
} | |||
# Grouping the document tree into LaTeX files. List of tuples | |||
# (source start file, target name, title, | |||
# author, documentclass [howto, manual, or own class]). | |||
latex_documents = [ | |||
(master_doc, 'nd2reader.tex', 'nd2reader Documentation', | |||
'Ruben Verweij', 'manual'), | |||
] | |||
# -- Options for manual page output --------------------------------------- | |||
# One entry per manual page. List of tuples | |||
# (source start file, name, description, authors, manual section). | |||
man_pages = [ | |||
(master_doc, 'nd2reader', 'nd2reader Documentation', | |||
[author], 1) | |||
] | |||
# -- Options for Texinfo output ------------------------------------------- | |||
# Grouping the document tree into Texinfo files. List of tuples | |||
# (source start file, target name, title, author, | |||
# dir menu entry, description, category) | |||
texinfo_documents = [ | |||
(master_doc, 'nd2reader', 'nd2reader Documentation', | |||
author, 'nd2reader', 'One line description of project.', | |||
'Miscellaneous'), | |||
] | |||
# -- Options for Epub output ---------------------------------------------- | |||
# Bibliographic Dublin Core info. | |||
epub_title = project | |||
epub_author = author | |||
epub_publisher = author | |||
epub_copyright = copyright | |||
# The unique identifier of the text. This can be a ISBN number | |||
# or the project homepage. | |||
# | |||
# epub_identifier = '' | |||
# A unique identification for the text. | |||
# | |||
# epub_uid = '' | |||
# A list of files that should not be packed into the epub file. | |||
epub_exclude_files = ['search.html'] |
@ -0,0 +1,20 @@ | |||
``nd2reader``: a pure-Python package for reading Nikon .nd2 files | |||
================================================================= | |||
`nd2reader` is a pure-Python package that reads images produced by NIS Elements 4.0+. It has only been definitively tested on NIS Elements 4.30.02 Build 1053. Support for older versions is being actively worked on. | |||
The reader is written in the `pims <https://github.com/soft-matter/pims>`_ framework, enabling easy access to multidimensional files, lazy slicing, and nice display in IPython. To get started, see the quick start tutorial. | |||
.. toctree:: | |||
:maxdepth: 4 | |||
:caption: Contents: | |||
nd2reader quick start tutorial <tutorial> | |||
nd2reader API reference <nd2reader> | |||
Indices and tables | |||
================== | |||
* :ref:`genindex` | |||
* :ref:`modindex` | |||
* :ref:`search` |
@ -0,0 +1,55 @@ | |||
@ECHO OFF | |||
REM Command file for Sphinx documentation | |||
pushd %~dp0 | |||
if "%SPHINXBUILD%" == "" ( | |||
set SPHINXBUILD=python3 -msphinx | |||
) | |||
set BUILDDIR=../docs | |||
set ALLSPHINXOPTS= . | |||
if "%1" == "" goto help | |||
if "%1" == "help" ( | |||
:help | |||
echo.Please use `make ^<target^>` where ^<target^> is one of | |||
echo. html to make standalone HTML files | |||
goto end | |||
) | |||
REM Check if sphinx-build is available and fallback to Python version if any | |||
%SPHINXBUILD% 1>NUL 2>NUL | |||
if errorlevel 9009 goto sphinx_python | |||
goto sphinx_ok | |||
:sphinx_python | |||
set SPHINXBUILD=python3 -m sphinx.__init__ | |||
%SPHINXBUILD% 2> nul | |||
if errorlevel 9009 ( | |||
echo. | |||
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx | |||
echo.installed, then set the SPHINXBUILD environment variable to point | |||
echo.to the full path of the 'sphinx-build' executable. Alternatively you | |||
echo.may add the Sphinx directory to PATH. | |||
echo. | |||
echo.If you don't have Sphinx installed, grab it from | |||
echo.http://sphinx-doc.org/ | |||
exit /b 1 | |||
) | |||
:sphinx_ok | |||
if "%1" == "html" ( | |||
%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR% | |||
if errorlevel 1 exit /b 1 | |||
echo. | |||
echo.Build finished. The HTML pages are in %BUILDDIR%. | |||
goto end | |||
) | |||
:end | |||
popd |
@ -0,0 +1,72 @@ | |||
nd2reader package | |||
================= | |||
In general, you should only have to use the ``nd2reader.reader`` module. The rest of the submodules are for internal | |||
use only. | |||
Submodules | |||
---------- | |||
nd2reader.reader module | |||
----------------------- | |||
.. automodule:: nd2reader.reader | |||
:members: | |||
:undoc-members: | |||
:show-inheritance: | |||
nd2reader.parser module | |||
----------------------- | |||
.. automodule:: nd2reader.parser | |||
:members: | |||
:undoc-members: | |||
:show-inheritance: | |||
nd2reader.raw_metadata module | |||
----------------------------- | |||
.. automodule:: nd2reader.raw_metadata | |||
:members: | |||
:undoc-members: | |||
:show-inheritance: | |||
nd2reader.label_map module | |||
-------------------------- | |||
.. automodule:: nd2reader.label_map | |||
:members: | |||
:undoc-members: | |||
:show-inheritance: | |||
nd2reader.common module | |||
----------------------- | |||
.. automodule:: nd2reader.common | |||
:members: | |||
:undoc-members: | |||
:show-inheritance: | |||
nd2reader.exceptions module | |||
--------------------------- | |||
.. automodule:: nd2reader.exceptions | |||
:members: | |||
:undoc-members: | |||
:show-inheritance: | |||
nd2reader.artificial module | |||
------------------------------- | |||
.. automodule:: nd2reader.artificial | |||
:members: | |||
:undoc-members: | |||
:show-inheritance: | |||
nd2reader.legacy module | |||
----------------------- | |||
.. automodule:: nd2reader.legacy | |||
:members: | |||
:undoc-members: | |||
:show-inheritance: |
@ -0,0 +1,119 @@ | |||
# Tutorial | |||
### Installation | |||
The package is available on PyPi. Install it using: | |||
``` | |||
pip install nd2reader | |||
``` | |||
If you don't already have the packages `numpy`, `pims`, `six` and `xmltodict`, they will be installed automatically if you use the `setup.py` script. | |||
`nd2reader` is an order of magnitude faster in Python 3. I recommend using it unless you have no other choice. Python 2.7 and Python >= 3.4 are supported. | |||
#### Installation via Conda Forge | |||
Installing `nd2reader` from the `conda-forge` channel can be achieved by adding `conda-forge` to your channels with: | |||
``` | |||
conda config --add channels conda-forge | |||
``` | |||
Once the `conda-forge` channel has been enabled, `nd2reader` can be installed with: | |||
``` | |||
conda install nd2reader | |||
``` | |||
It is possible to list all of the versions of `nd2reader` available on your platform with: | |||
``` | |||
conda search nd2reader --channel conda-forge | |||
``` | |||
### Opening ND2s | |||
`nd2reader` follows the [pims](https://github.com/soft-matter/pims) framework. To open a file and show the first frame: | |||
```python | |||
from nd2reader import ND2Reader | |||
import matplotlib.pyplot as plt | |||
with ND2Reader('my_directory/example.nd2') as images: | |||
plt.imshow(images[0]) | |||
``` | |||
After opening the file, all `pims` features are supported. Please refer to the [pims documentation](http://soft-matter.github.io/pims/). | |||
### ND2 metadata | |||
The ND2 file contains various metadata, such as acquisition information, | |||
regions of interest and custom user comments. Most of this metadata is parsed | |||
and available in dictionary form. For example: | |||
```python | |||
from nd2reader import ND2Reader | |||
with ND2Reader('my_directory/example.nd2') as images: | |||
# width and height of the image | |||
print('%d x %d px' % (images.metadata['width'], images.metadata['height'])) | |||
``` | |||
All metadata properties are: | |||
* `width`: the width of the image in pixels | |||
* `height`: the height of the image in pixels | |||
* `date`: the date the image was taken | |||
* `fields_of_view`: the fields of view in the image | |||
* `frames`: a list of all frame numbers | |||
* `z_levels`: the z levels in the image | |||
* `total_images_per_channel`: the number of images per color channel | |||
* `channels`: the color channels | |||
* `pixel_microns`: the amount of microns per pixel | |||
* `rois`: the regions of interest (ROIs) defined by the user | |||
* `experiment`: information about the nature and timings of the ND experiment | |||
### Iterating over fields of view | |||
Using `NDExperiments` in the Nikon software, it is possible to acquire images on different `(x, y)` positions. | |||
This is referred to as different fields of view. Using this reader, the fields of view are on the `v` axis. | |||
For example: | |||
```python | |||
from nd2reader import ND2Reader | |||
with ND2Reader('my_directory/example.nd2') as images: | |||
# width and height of the image | |||
print(images.metadata) | |||
``` | |||
will output | |||
```python | |||
{'channels': ['BF100xoil-1x-R', 'BF+RITC'], | |||
'date': datetime.datetime(2017, 10, 30, 14, 35, 18), | |||
'experiment': {'description': 'ND Acquisition', | |||
'loops': [{'duration': 0, | |||
'sampling_interval': 0.0, | |||
'start': 0, | |||
'stimulation': False}]}, | |||
'fields_of_view': [0, 1], | |||
'frames': [0], | |||
'height': 1895, | |||
'num_frames': 1, | |||
'pixel_microns': 0.09214285714285715, | |||
'total_images_per_channel': 6, | |||
'width': 2368, | |||
'z_levels': [0, 1, 2]} | |||
``` | |||
for our example file. As you can see from the metadata, it has two fields of view. We can also look at the sizes of the axes: | |||
```python | |||
print(images.sizes) | |||
``` | |||
```python | |||
{'c': 2, 't': 1, 'v': 2, 'x': 2368, 'y': 1895, 'z': 3} | |||
``` | |||
As you can see, the fields of view are listed on the `v` axis. It is therefore possible to loop over them like this: | |||
```python | |||
images.iter_axes = 'v' | |||
for fov in images: | |||
print(fov) # Frame containing one field of view | |||
``` | |||
For more information on axis bundling and iteration, refer to the [pims documentation](http://soft-matter.github.io/pims/v0.4/multidimensional.html#axes-bundling). |
@ -0,0 +1,22 @@ | |||
import unittest | |||
from os import path | |||
import six | |||
import struct | |||
from nd2reader.artificial import ArtificialND2 | |||
from nd2reader.common import get_version, parse_version, parse_date, _add_to_metadata, _parse_unsigned_char, \ | |||
_parse_unsigned_int, _parse_unsigned_long, _parse_double, check_or_make_dir | |||
from nd2reader.exceptions import InvalidVersionError | |||
class TestArtificial(unittest.TestCase): | |||
def setUp(self): | |||
dir_path = path.dirname(path.realpath(__file__)) | |||
check_or_make_dir(path.join(dir_path, 'test_data/')) | |||
self.test_file = path.join(dir_path, 'test_data/test.nd2') | |||
self.create_test_nd2() | |||
def create_test_nd2(self): | |||
with ArtificialND2(self.test_file) as artificial: | |||
self.assertIsNotNone(artificial.file_handle) | |||
artificial.close() |
@ -0,0 +1,79 @@ | |||
import unittest | |||
from nd2reader.label_map import LabelMap | |||
from nd2reader.artificial import ArtificialND2 | |||
class TestLabelMap(unittest.TestCase): | |||
def setUp(self): | |||
self.nd2 = ArtificialND2('test_data/test_nd2_label_map001.nd2') | |||
self.raw_text, self.locations = self.nd2.raw_text, self.nd2.locations | |||
self.label_map = LabelMap(self.raw_text) | |||
def test_image_data_location(self): | |||
self.assertEqual(self.locations['image_frame_0'][0], self.label_map.get_image_data_location(0)) | |||
def test_image_text_info(self): | |||
self.assertEqual(self.locations['image_text_info'][0], self.label_map.image_text_info) | |||
def test_image_metadata(self): | |||
self.assertEqual(self.locations['image_metadata'][0], self.label_map.image_metadata) | |||
def test_image_attributes(self): | |||
self.assertEqual(self.locations['image_attributes'][0], self.label_map.image_attributes) | |||
def test_image_metadata_sequence(self): | |||
self.assertEqual(self.locations['image_metadata_sequence'][0], self.label_map.image_metadata_sequence) | |||
def test_image_calibration(self): | |||
self.assertEqual(self.locations['image_calibration'][0], self.label_map.image_calibration) | |||
def test_x_data(self): | |||
self.assertEqual(self.locations['x_data'][0], self.label_map.x_data) | |||
def test_y_data(self): | |||
self.assertEqual(self.locations['y_data'][0], self.label_map.y_data) | |||
def test_z_data(self): | |||
self.assertEqual(self.locations['z_data'][0], self.label_map.z_data) | |||
def test_roi_metadata(self): | |||
self.assertEqual(self.locations['roi_metadata'][0], self.label_map.roi_metadata) | |||
def test_pfs_status(self): | |||
self.assertEqual(self.locations['pfs_status'][0], self.label_map.pfs_status) | |||
def test_pfs_offset(self): | |||
self.assertEqual(self.locations['pfs_offset'][0], self.label_map.pfs_offset) | |||
def test_guid(self): | |||
self.assertEqual(self.locations['guid'][0], self.label_map.guid) | |||
def test_description(self): | |||
self.assertEqual(self.locations['description'][0], self.label_map.description) | |||
def test_camera_exposure_time(self): | |||
self.assertEqual(self.locations['camera_exposure_time'][0], self.label_map.camera_exposure_time) | |||
def test_camera_temp(self): | |||
self.assertEqual(self.locations['camera_temp'][0], self.label_map.camera_temp) | |||
def test_acquisition_times(self): | |||
self.assertEqual(self.locations['acquisition_times'][0], self.label_map.acquisition_times) | |||
def test_acquisition_times_2(self): | |||
self.assertEqual(self.locations['acquisition_times_2'][0], self.label_map.acquisition_times_2) | |||
def test_acquisition_frames(self): | |||
self.assertEqual(self.locations['acquisition_frames'][0], self.label_map.acquisition_frames) | |||
def test_lut_data(self): | |||
self.assertEqual(self.locations['lut_data'][0], self.label_map.lut_data) | |||
def test_grabber_settings(self): | |||
self.assertEqual(self.locations['grabber_settings'][0], self.label_map.grabber_settings) | |||
def test_custom_data(self): | |||
self.assertEqual(self.locations['custom_data'][0], self.label_map.custom_data) | |||
def test_app_info(self): | |||
self.assertEqual(self.locations['app_info'][0], self.label_map.app_info) |
@ -0,0 +1,38 @@ | |||
import unittest | |||
import warnings | |||
from nd2reader.legacy import Nd2 | |||
from nd2reader.reader import ND2Reader | |||
from nd2reader.artificial import ArtificialND2 | |||
class TestLegacy(unittest.TestCase): | |||
def test_init(self): | |||
with ArtificialND2('test_data/legacy.nd2'): | |||
with warnings.catch_warnings(record=True) as w: | |||
# Cause all warnings to always be triggered. | |||
warnings.simplefilter("always") | |||
with Nd2('test_data/legacy.nd2') as reader: | |||
self.assertIsInstance(reader.reader, ND2Reader) | |||
self.assertTrue(issubclass(w[0].category, DeprecationWarning)) | |||
self.assertEquals(str(w[0].message), "The 'Nd2' class is deprecated, please consider using the new" + | |||
" ND2Reader interface which uses pims.") | |||
def test_misc(self): | |||
with ArtificialND2('test_data/legacy.nd2'): | |||
with Nd2('test_data/legacy.nd2') as reader: | |||
representation = "\n".join(["<Deprecated ND2 %s>" % reader.reader.filename, | |||
"Created: Unknown", | |||
"Image size: %sx%s (HxW)" % (reader.height, reader.width), | |||
"Frames: %s" % len(reader.frames), | |||
"Channels: %s" % ", ".join(["%s" % str(channel) for channel | |||
in reader.channels]), | |||
"Fields of View: %s" % len(reader.fields_of_view), | |||
"Z-Levels: %s" % len(reader.z_levels) | |||
]) | |||
self.assertEquals(representation, str(reader)) | |||
# not implemented yet | |||
self.assertEquals(reader.pixel_microns, None) | |||
self.assertEquals(len(reader), 1) |
@ -0,0 +1,36 @@ | |||
import unittest | |||
from os import path | |||
from nd2reader.artificial import ArtificialND2 | |||
from nd2reader.common import check_or_make_dir | |||
from nd2reader.parser import Parser | |||
import urllib.request | |||
class TestParser(unittest.TestCase): | |||
def create_test_nd2(self): | |||
with ArtificialND2(self.test_file) as artificial: | |||
artificial.close() | |||
def setUp(self): | |||
dir_path = path.dirname(path.realpath(__file__)) | |||
check_or_make_dir(path.join(dir_path, "test_data/")) | |||
self.test_file = path.join(dir_path, "test_data/test.nd2") | |||
self.create_test_nd2() | |||
def test_can_open_test_file(self): | |||
self.create_test_nd2() | |||
with open(self.test_file, "rb") as fh: | |||
parser = Parser(fh) | |||
self.assertTrue(parser.supported) | |||
def test_get_image(self): | |||
stitched_path = "test_data/test_stitched.nd2" | |||
if not path.isfile(stitched_path): | |||
file_name, header = urllib.request.urlretrieve( | |||
"https://downloads.openmicroscopy.org/images/ND2/karl/sample_image.nd2", | |||
stitched_path, | |||
) | |||
with open(stitched_path, "rb") as fh: | |||
parser = Parser(fh) | |||
parser.get_image(0) |
@ -1,18 +1,81 @@ | |||
import unittest | |||
import six | |||
from nd2reader.artificial import ArtificialND2 | |||
from nd2reader.label_map import LabelMap | |||
from nd2reader.raw_metadata import RawMetadata | |||
from nd2reader.common_raw_metadata import parse_roi_shape, parse_roi_type, parse_dimension_text_line | |||
class TestRawMetadata(unittest.TestCase): | |||
def setUp(self): | |||
self.metadata = RawMetadata(None, None) | |||
self.nd2 = ArtificialND2('test_data/test_nd2_raw_metadata001.nd2') | |||
self.raw_text, self.locations, self.file_data = self.nd2.raw_text, self.nd2.locations, self.nd2.data | |||
self.label_map = LabelMap(self.raw_text) | |||
self.metadata = RawMetadata(self.nd2.file_handle, self.label_map) | |||
def test_parse_roi_shape(self): | |||
self.assertEqual(self.metadata._parse_roi_shape(3), 'rectangle') | |||
self.assertEqual(self.metadata._parse_roi_shape(9), 'circle') | |||
self.assertIsNone(self.metadata._parse_roi_shape(-1)) | |||
self.assertEqual(parse_roi_shape(3), 'rectangle') | |||
self.assertEqual(parse_roi_shape(9), 'circle') | |||
self.assertIsNone(parse_roi_shape(-1)) | |||
def test_parse_roi_type(self): | |||
self.assertEqual(self.metadata._parse_roi_type(3), 'reference') | |||
self.assertEqual(self.metadata._parse_roi_type(2), 'background') | |||
self.assertEqual(self.metadata._parse_roi_type(4), 'stimulation') | |||
self.assertIsNone(self.metadata._parse_roi_type(-1)) | |||
self.assertEqual(parse_roi_type(3), 'reference') | |||
self.assertEqual(parse_roi_type(2), 'background') | |||
self.assertEqual(parse_roi_type(4), 'stimulation') | |||
self.assertIsNone(parse_roi_type(-1)) | |||
def test_parse_dimension_text(self): | |||
line = six.b('Metadata:\r\nDimensions: T(443) x \xce\xbb(1)\r\nCamera Name: Andor Zyla VSC-01537') | |||
self.assertEqual(parse_dimension_text_line(line), six.b('Dimensions: T(443) x \xce\xbb(1)')) | |||
self.assertIsNone(parse_dimension_text_line(six.b('Dim: nothing'))) | |||
def test_parse_z_levels(self): | |||
# smokescreen test to check if the fallback to z_coordinates is working | |||
# for details, see RawMetadata._parse_z_levels() | |||
dimension_text = self.metadata._parse_dimension_text() | |||
z_levels = self.metadata._parse_dimension(r""".*?Z\((\d+)\).*?""", dimension_text) | |||
z_coords = self.metadata._parse_z_coordinates() | |||
self.assertEqual(len(dimension_text), 0) | |||
self.assertEqual(len(z_levels), 0) | |||
self.assertEqual(len(self.metadata._parse_z_levels()), len(z_coords)) | |||
def test_dict(self): | |||
self.assertTrue(type(self.metadata.__dict__) is dict) | |||
def test_parsed_metadata_has_all_keys(self): | |||
metadata = self.metadata.get_parsed_metadata() | |||
self.assertTrue(type(metadata) is dict) | |||
required_keys = ["height", "width", "date", "fields_of_view", "frames", "z_levels", "total_images_per_channel", | |||
"channels", "pixel_microns"] | |||
for required in required_keys: | |||
self.assertTrue(required in metadata) | |||
def test_cached_metadata(self): | |||
metadata_one = self.metadata.get_parsed_metadata() | |||
metadata_two = self.metadata.get_parsed_metadata() | |||
self.assertEqual(metadata_one, metadata_two) | |||
def test_pfs_status(self): | |||
self.assertEqual(self.file_data['pfs_status'], self.metadata.pfs_status[0]) | |||
def _assert_dicts_equal(self, parsed_dict, original_dict): | |||
for attribute in original_dict.keys(): | |||
parsed_key = six.b(attribute) | |||
self.assertIn(parsed_key, parsed_dict.keys()) | |||
if isinstance(parsed_dict[parsed_key], dict): | |||
self._assert_dicts_equal(parsed_dict[parsed_key], original_dict[attribute]) | |||
else: | |||
self.assertEqual(parsed_dict[parsed_key], original_dict[attribute]) | |||
def test_image_attributes(self): | |||
parsed_dict = self.metadata.image_attributes | |||
self._assert_dicts_equal(parsed_dict, self.file_data['image_attributes']) | |||
def test_color_channels(self): | |||
parsed_channels = self.metadata.get_parsed_metadata()['channels'] | |||
self.assertEquals(parsed_channels, ['TRITC']) |
@ -0,0 +1,79 @@ | |||
import unittest | |||
import numpy as np | |||
import struct | |||
from pims import Frame | |||
from nd2reader.artificial import ArtificialND2 | |||
from nd2reader.exceptions import EmptyFileError, InvalidFileType | |||
from nd2reader.reader import ND2Reader | |||
from nd2reader.parser import Parser | |||
class TestReader(unittest.TestCase): | |||
def test_invalid_file_extension(self): | |||
self.assertRaises(InvalidFileType, lambda: ND2Reader('test_data/invalid_extension_file.inv')) | |||
def test_extension(self): | |||
self.assertTrue('nd2' in ND2Reader.class_exts()) | |||
def cmp_two_readers(self, r1, r2): | |||
attributes = r1.data['image_attributes']['SLxImageAttributes'] | |||
self.assertEqual(r2.metadata['width'], attributes['uiWidth']) | |||
self.assertEqual(r2.metadata['height'], attributes['uiHeight']) | |||
self.assertEqual(r2.metadata['width'], r2.sizes['x']) | |||
self.assertEqual(r2.metadata['height'], r2.sizes['y']) | |||
self.assertEqual(r2.pixel_type, np.float64) | |||
self.assertEqual(r2.iter_axes, ['t']) | |||
def test_init_and_init_axes(self): | |||
with ArtificialND2('test_data/test_nd2_reader.nd2') as artificial: | |||
with ND2Reader('test_data/test_nd2_reader.nd2') as reader: | |||
self.cmp_two_readers(artificial, reader) | |||
def test_init_from_handler(self): | |||
with ArtificialND2('test_data/test_nd2_reader.nd2') as artificial: | |||
with open('test_data/test_nd2_reader.nd2', "rb") as FH: | |||
with ND2Reader(FH) as reader: | |||
self.cmp_two_readers(artificial, reader) | |||
def test_init_empty_file(self): | |||
with ArtificialND2('test_data/empty.nd2', skip_blocks=['label_map_marker']): | |||
with self.assertRaises(EmptyFileError) as exception: | |||
with ND2Reader('test_data/empty.nd2'): | |||
pass | |||
self.assertEqual(str(exception.exception), "No axes were found for this .nd2 file.") | |||
def test_get_parser(self): | |||
with ArtificialND2('test_data/test_nd2_reader.nd2') as _: | |||
with ND2Reader('test_data/test_nd2_reader.nd2') as reader: | |||
self.assertIsInstance(reader.parser, Parser) | |||
def test_get_timesteps(self): | |||
with ArtificialND2('test_data/test_nd2_reader.nd2') as _: | |||
with ND2Reader('test_data/test_nd2_reader.nd2') as reader: | |||
timesteps = reader.timesteps | |||
self.assertEquals(len(timesteps), 0) | |||
def test_get_frame_zero(self): | |||
# Best test we can do for now: | |||
# test everything up to the actual unpacking of the frame data | |||
with ArtificialND2('test_data/test_nd2_reader.nd2') as _: | |||
with ND2Reader('test_data/test_nd2_reader.nd2') as reader: | |||
with self.assertRaises(struct.error) as exception: | |||
frame = reader[0] | |||
self.assertIn('unpack', str(exception.exception)) | |||
def test_get_frame_2D(self): | |||
# Best test we can do for now: | |||
# test everything up to the actual unpacking of the frame data | |||
with ArtificialND2('test_data/test_nd2_reader.nd2') as _: | |||
with ND2Reader('test_data/test_nd2_reader.nd2') as reader: | |||
with self.assertRaises(struct.error) as exception: | |||
frame = reader.get_frame_2D(c=0, t=0, z=0, x=0, y=0, v=0) | |||
self.assertIn('unpack', str(exception.exception)) |
@ -1,12 +1,8 @@ | |||
import nd2reader | |||
import unittest | |||
from setup import VERSION | |||
from nd2reader import __version__ as VERSION | |||
class TestVersion(unittest.TestCase): | |||
def test_module_version_type(self): | |||
# just make sure the version number exists and is the type we expect | |||
self.assertEqual(type(nd2reader.__version__), str) | |||
def test_versions_in_sync(self): | |||
self.assertEqual(nd2reader.__version__, VERSION) | |||
self.assertEqual(type(VERSION), str) |