ome-tiled 0.1.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- ome_tiled-0.1.0/.gitignore +122 -0
- ome_tiled-0.1.0/LICENSE +201 -0
- ome_tiled-0.1.0/PKG-INFO +194 -0
- ome_tiled-0.1.0/README.md +166 -0
- ome_tiled-0.1.0/pyproject.toml +144 -0
- ome_tiled-0.1.0/src/ome_tiled/__init__.py +4 -0
- ome_tiled-0.1.0/src/ome_tiled/_adapter.py +104 -0
- ome_tiled-0.1.0/src/ome_tiled/_ngff.py +98 -0
- ome_tiled-0.1.0/src/ome_tiled/py.typed +0 -0
|
@@ -0,0 +1,122 @@
|
|
|
1
|
+
# Byte-compiled / optimized / DLL files
|
|
2
|
+
__pycache__/
|
|
3
|
+
*.py[cod]
|
|
4
|
+
*$py.class
|
|
5
|
+
|
|
6
|
+
# C extensions
|
|
7
|
+
*.so
|
|
8
|
+
|
|
9
|
+
# Distribution / packaging
|
|
10
|
+
.Python
|
|
11
|
+
env/
|
|
12
|
+
build/
|
|
13
|
+
develop-eggs/
|
|
14
|
+
dist/
|
|
15
|
+
downloads/
|
|
16
|
+
eggs/
|
|
17
|
+
.eggs/
|
|
18
|
+
lib/
|
|
19
|
+
lib64/
|
|
20
|
+
parts/
|
|
21
|
+
sdist/
|
|
22
|
+
var/
|
|
23
|
+
wheels/
|
|
24
|
+
*.egg-info/
|
|
25
|
+
.installed.cfg
|
|
26
|
+
*.egg
|
|
27
|
+
|
|
28
|
+
# PyInstaller
|
|
29
|
+
# Usually these files are written by a python script from a template
|
|
30
|
+
# before PyInstaller builds the exe, so as to inject date/other infos into it.
|
|
31
|
+
*.manifest
|
|
32
|
+
*.spec
|
|
33
|
+
|
|
34
|
+
# Installer logs
|
|
35
|
+
pip-log.txt
|
|
36
|
+
pip-delete-this-directory.txt
|
|
37
|
+
|
|
38
|
+
# Unit test / coverage reports
|
|
39
|
+
htmlcov/
|
|
40
|
+
.tox/
|
|
41
|
+
.coverage
|
|
42
|
+
.coverage.*
|
|
43
|
+
.cache
|
|
44
|
+
nosetests.xml
|
|
45
|
+
coverage.xml
|
|
46
|
+
*.cover
|
|
47
|
+
.hypothesis/
|
|
48
|
+
.pytest_cache/
|
|
49
|
+
.ruff_cache/
|
|
50
|
+
.nox/
|
|
51
|
+
|
|
52
|
+
# Translations
|
|
53
|
+
*.mo
|
|
54
|
+
*.pot
|
|
55
|
+
|
|
56
|
+
# Django stuff:
|
|
57
|
+
*.log
|
|
58
|
+
local_settings.py
|
|
59
|
+
|
|
60
|
+
# Flask stuff:
|
|
61
|
+
instance/
|
|
62
|
+
.webassets-cache
|
|
63
|
+
|
|
64
|
+
# Scrapy stuff:
|
|
65
|
+
.scrapy
|
|
66
|
+
|
|
67
|
+
# Sphinx documentation
|
|
68
|
+
docs/_build/
|
|
69
|
+
|
|
70
|
+
# PyBuilder
|
|
71
|
+
target/
|
|
72
|
+
|
|
73
|
+
# Jupyter Notebook
|
|
74
|
+
.ipynb_checkpoints
|
|
75
|
+
|
|
76
|
+
# Dask worker cache
|
|
77
|
+
dask-worker-space/
|
|
78
|
+
|
|
79
|
+
# pyenv
|
|
80
|
+
.python-version
|
|
81
|
+
|
|
82
|
+
# celery beat schedule file
|
|
83
|
+
celerybeat-schedule
|
|
84
|
+
|
|
85
|
+
# SageMath parsed files
|
|
86
|
+
*.sage.py
|
|
87
|
+
|
|
88
|
+
# dotenv
|
|
89
|
+
.env
|
|
90
|
+
|
|
91
|
+
# virtualenv
|
|
92
|
+
.venv
|
|
93
|
+
venv/
|
|
94
|
+
ENV/
|
|
95
|
+
|
|
96
|
+
# Spyder project settings
|
|
97
|
+
.spyderproject
|
|
98
|
+
.spyproject
|
|
99
|
+
|
|
100
|
+
# Rope project settings
|
|
101
|
+
.ropeproject
|
|
102
|
+
|
|
103
|
+
# mkdocs documentation
|
|
104
|
+
/site
|
|
105
|
+
|
|
106
|
+
# mypy
|
|
107
|
+
.mypy_cache/
|
|
108
|
+
|
|
109
|
+
# IDE settings
|
|
110
|
+
.vscode/
|
|
111
|
+
.idea/
|
|
112
|
+
|
|
113
|
+
# local test configs
|
|
114
|
+
test_configs/*
|
|
115
|
+
|
|
116
|
+
# MkDocs build output
|
|
117
|
+
site/
|
|
118
|
+
|
|
119
|
+
# claude
|
|
120
|
+
.claude/settings.local.json
|
|
121
|
+
.claude/plans
|
|
122
|
+
CLAUDE.local.md
|
ome_tiled-0.1.0/LICENSE
ADDED
|
@@ -0,0 +1,201 @@
|
|
|
1
|
+
Apache License
|
|
2
|
+
Version 2.0, January 2004
|
|
3
|
+
http://www.apache.org/licenses/
|
|
4
|
+
|
|
5
|
+
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
|
|
6
|
+
|
|
7
|
+
1. Definitions.
|
|
8
|
+
|
|
9
|
+
"License" shall mean the terms and conditions for use, reproduction,
|
|
10
|
+
and distribution as defined by Sections 1 through 9 of this document.
|
|
11
|
+
|
|
12
|
+
"Licensor" shall mean the copyright owner or entity authorized by
|
|
13
|
+
the copyright owner that is granting the License.
|
|
14
|
+
|
|
15
|
+
"Legal Entity" shall mean the union of the acting entity and all
|
|
16
|
+
other entities that control, are controlled by, or are under common
|
|
17
|
+
control with that entity. For the purposes of this definition,
|
|
18
|
+
"control" means (i) the power, direct or indirect, to cause the
|
|
19
|
+
direction or management of such entity, whether by contract or
|
|
20
|
+
otherwise, or (ii) ownership of fifty percent (50%) or more of the
|
|
21
|
+
outstanding shares, or (iii) beneficial ownership of such entity.
|
|
22
|
+
|
|
23
|
+
"You" (or "Your") shall mean an individual or Legal Entity
|
|
24
|
+
exercising permissions granted by this License.
|
|
25
|
+
|
|
26
|
+
"Source" form shall mean the preferred form for making modifications,
|
|
27
|
+
including but not limited to software source code, documentation
|
|
28
|
+
source, and configuration files.
|
|
29
|
+
|
|
30
|
+
"Object" form shall mean any form resulting from mechanical
|
|
31
|
+
transformation or translation of a Source form, including but
|
|
32
|
+
not limited to compiled object code, generated documentation,
|
|
33
|
+
and conversions to other media types.
|
|
34
|
+
|
|
35
|
+
"Work" shall mean the work of authorship, whether in Source or
|
|
36
|
+
Object form, made available under the License, as indicated by a
|
|
37
|
+
copyright notice that is included in or attached to the work
|
|
38
|
+
(an example is provided in the Appendix below).
|
|
39
|
+
|
|
40
|
+
"Derivative Works" shall mean any work, whether in Source or Object
|
|
41
|
+
form, that is based on (or derived from) the Work and for which the
|
|
42
|
+
editorial revisions, annotations, elaborations, or other modifications
|
|
43
|
+
represent, as a whole, an original work of authorship. For the purposes
|
|
44
|
+
of this License, Derivative Works shall not include works that remain
|
|
45
|
+
separable from, or merely link (or bind by name) to the interfaces of,
|
|
46
|
+
the Work and Derivative Works thereof.
|
|
47
|
+
|
|
48
|
+
"Contribution" shall mean any work of authorship, including
|
|
49
|
+
the original version of the Work and any modifications or additions
|
|
50
|
+
to that Work or Derivative Works thereof, that is intentionally
|
|
51
|
+
submitted to Licensor for inclusion in the Work by the copyright owner
|
|
52
|
+
or by an individual or Legal Entity authorized to submit on behalf of
|
|
53
|
+
the copyright owner. For the purposes of this definition, "submitted"
|
|
54
|
+
means any form of electronic, verbal, or written communication sent
|
|
55
|
+
to the Licensor or its representatives, including but not limited to
|
|
56
|
+
communication on electronic mailing lists, source code control systems,
|
|
57
|
+
and issue tracking systems that are managed by, or on behalf of, the
|
|
58
|
+
Licensor for the purpose of discussing and improving the Work, but
|
|
59
|
+
excluding communication that is conspicuously marked or otherwise
|
|
60
|
+
designated in writing by the copyright owner as "Not a Contribution."
|
|
61
|
+
|
|
62
|
+
"Contributor" shall mean Licensor and any individual or Legal Entity
|
|
63
|
+
on behalf of whom a Contribution has been received by Licensor and
|
|
64
|
+
subsequently incorporated within the Work.
|
|
65
|
+
|
|
66
|
+
2. Grant of Copyright License. Subject to the terms and conditions of
|
|
67
|
+
this License, each Contributor hereby grants to You a perpetual,
|
|
68
|
+
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
|
|
69
|
+
copyright license to reproduce, prepare Derivative Works of,
|
|
70
|
+
publicly display, publicly perform, sublicense, and distribute the
|
|
71
|
+
Work and such Derivative Works in Source or Object form.
|
|
72
|
+
|
|
73
|
+
3. Grant of Patent License. Subject to the terms and conditions of
|
|
74
|
+
this License, each Contributor hereby grants to You a perpetual,
|
|
75
|
+
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
|
|
76
|
+
(except as stated in this section) patent license to make, have made,
|
|
77
|
+
use, offer to sell, sell, import, and otherwise transfer the Work,
|
|
78
|
+
where such license applies only to those patent claims licensable
|
|
79
|
+
by such Contributor that are necessarily infringed by their
|
|
80
|
+
Contribution(s) alone or by combination of their Contribution(s)
|
|
81
|
+
with the Work to which such Contribution(s) was submitted. If You
|
|
82
|
+
institute patent litigation against any entity (including a
|
|
83
|
+
cross-claim or counterclaim in a lawsuit) alleging that the Work
|
|
84
|
+
or a Contribution incorporated within the Work constitutes direct
|
|
85
|
+
or contributory patent infringement, then any patent licenses
|
|
86
|
+
granted to You under this License for that Work shall terminate
|
|
87
|
+
as of the date such litigation is filed.
|
|
88
|
+
|
|
89
|
+
4. Redistribution. You may reproduce and distribute copies of the
|
|
90
|
+
Work or Derivative Works thereof in any medium, with or without
|
|
91
|
+
modifications, and in Source or Object form, provided that You
|
|
92
|
+
meet the following conditions:
|
|
93
|
+
|
|
94
|
+
(a) You must give any other recipients of the Work or
|
|
95
|
+
Derivative Works a copy of this License; and
|
|
96
|
+
|
|
97
|
+
(b) You must cause any modified files to carry prominent notices
|
|
98
|
+
stating that You changed the files; and
|
|
99
|
+
|
|
100
|
+
(c) You must retain, in the Source form of any Derivative Works
|
|
101
|
+
that You distribute, all copyright, patent, trademark, and
|
|
102
|
+
attribution notices from the Source form of the Work,
|
|
103
|
+
excluding those notices that do not pertain to any part of
|
|
104
|
+
the Derivative Works; and
|
|
105
|
+
|
|
106
|
+
(d) If the Work includes a "NOTICE" text file as part of its
|
|
107
|
+
distribution, then any Derivative Works that You distribute must
|
|
108
|
+
include a readable copy of the attribution notices contained
|
|
109
|
+
within such NOTICE file, excluding those notices that do not
|
|
110
|
+
pertain to any part of the Derivative Works, in at least one
|
|
111
|
+
of the following places: within a NOTICE text file distributed
|
|
112
|
+
as part of the Derivative Works; within the Source form or
|
|
113
|
+
documentation, if provided along with the Derivative Works; or,
|
|
114
|
+
within a display generated by the Derivative Works, if and
|
|
115
|
+
wherever such third-party notices normally appear. The contents
|
|
116
|
+
of the NOTICE file are for informational purposes only and
|
|
117
|
+
do not modify the License. You may add Your own attribution
|
|
118
|
+
notices within Derivative Works that You distribute, alongside
|
|
119
|
+
or as an addendum to the NOTICE text from the Work, provided
|
|
120
|
+
that such additional attribution notices cannot be construed
|
|
121
|
+
as modifying the License.
|
|
122
|
+
|
|
123
|
+
You may add Your own copyright statement to Your modifications and
|
|
124
|
+
may provide additional or different license terms and conditions
|
|
125
|
+
for use, reproduction, or distribution of Your modifications, or
|
|
126
|
+
for any such Derivative Works as a whole, provided Your use,
|
|
127
|
+
reproduction, and distribution of the Work otherwise complies with
|
|
128
|
+
the conditions stated in this License.
|
|
129
|
+
|
|
130
|
+
5. Submission of Contributions. Unless You explicitly state otherwise,
|
|
131
|
+
any Contribution intentionally submitted for inclusion in the Work
|
|
132
|
+
by You to the Licensor shall be under the terms and conditions of
|
|
133
|
+
this License, without any additional terms or conditions.
|
|
134
|
+
Notwithstanding the above, nothing herein shall supersede or modify
|
|
135
|
+
the terms of any separate license agreement you may have executed
|
|
136
|
+
with Licensor regarding such Contributions.
|
|
137
|
+
|
|
138
|
+
6. Trademarks. This License does not grant permission to use the trade
|
|
139
|
+
names, trademarks, service marks, or product names of the Licensor,
|
|
140
|
+
except as required for reasonable and customary use in describing the
|
|
141
|
+
origin of the Work and reproducing the content of the NOTICE file.
|
|
142
|
+
|
|
143
|
+
7. Disclaimer of Warranty. Unless required by applicable law or
|
|
144
|
+
agreed to in writing, Licensor provides the Work (and each
|
|
145
|
+
Contributor provides its Contributions) on an "AS IS" BASIS,
|
|
146
|
+
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
|
|
147
|
+
implied, including, without limitation, any warranties or conditions
|
|
148
|
+
of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
|
|
149
|
+
PARTICULAR PURPOSE. You are solely responsible for determining the
|
|
150
|
+
appropriateness of using or redistributing the Work and assume any
|
|
151
|
+
risks associated with Your exercise of permissions under this License.
|
|
152
|
+
|
|
153
|
+
8. Limitation of Liability. In no event and under no legal theory,
|
|
154
|
+
whether in tort (including negligence), contract, or otherwise,
|
|
155
|
+
unless required by applicable law (such as deliberate and grossly
|
|
156
|
+
negligent acts) or agreed to in writing, shall any Contributor be
|
|
157
|
+
liable to You for damages, including any direct, indirect, special,
|
|
158
|
+
incidental, or consequential damages of any character arising as a
|
|
159
|
+
result of this License or out of the use or inability to use the
|
|
160
|
+
Work (including but not limited to damages for loss of goodwill,
|
|
161
|
+
work stoppage, computer failure or malfunction, or any and all
|
|
162
|
+
other commercial damages or losses), even if such Contributor
|
|
163
|
+
has been advised of the possibility of such damages.
|
|
164
|
+
|
|
165
|
+
9. Accepting Warranty or Additional Liability. While redistributing
|
|
166
|
+
the Work or Derivative Works thereof, You may choose to offer,
|
|
167
|
+
and charge a fee for, acceptance of support, warranty, indemnity,
|
|
168
|
+
or other liability obligations and/or rights consistent with this
|
|
169
|
+
License. However, in accepting such obligations, You may act only
|
|
170
|
+
on Your own behalf and on Your sole responsibility, not on behalf
|
|
171
|
+
of any other Contributor, and only if You agree to indemnify,
|
|
172
|
+
defend, and hold each Contributor harmless for any liability
|
|
173
|
+
incurred by, or claims asserted against, such Contributor by reason
|
|
174
|
+
of your accepting any such warranty or additional liability.
|
|
175
|
+
|
|
176
|
+
END OF TERMS AND CONDITIONS
|
|
177
|
+
|
|
178
|
+
APPENDIX: How to apply the Apache License to your work.
|
|
179
|
+
|
|
180
|
+
To apply the Apache License to your work, attach the following
|
|
181
|
+
boilerplate notice, with the fields enclosed by brackets "[]"
|
|
182
|
+
replaced with your own identifying information. (Don't include
|
|
183
|
+
the brackets!) The text should be enclosed in the appropriate
|
|
184
|
+
comment syntax for the file format. We also recommend that a
|
|
185
|
+
file or class name and description of purpose be included on the
|
|
186
|
+
same "printed page" as the copyright notice for easier
|
|
187
|
+
identification within third-party archives.
|
|
188
|
+
|
|
189
|
+
Copyright 2024 - 2026, Leibniz Institute of Photonic Technology
|
|
190
|
+
|
|
191
|
+
Licensed under the Apache License, Version 2.0 (the "License");
|
|
192
|
+
you may not use this file except in compliance with the License.
|
|
193
|
+
You may obtain a copy of the License at
|
|
194
|
+
|
|
195
|
+
http://www.apache.org/licenses/LICENSE-2.0
|
|
196
|
+
|
|
197
|
+
Unless required by applicable law or agreed to in writing, software
|
|
198
|
+
distributed under the License is distributed on an "AS IS" BASIS,
|
|
199
|
+
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
|
200
|
+
See the License for the specific language governing permissions and
|
|
201
|
+
limitations under the License.
|
ome_tiled-0.1.0/PKG-INFO
ADDED
|
@@ -0,0 +1,194 @@
|
|
|
1
|
+
Metadata-Version: 2.5
|
|
2
|
+
Name: ome-tiled
|
|
3
|
+
Version: 0.1.0
|
|
4
|
+
Summary: A tiled adapter that serves OME-Zarr images with their axis names.
|
|
5
|
+
Project-URL: bugs, https://github.com/redsun-acquisition/ome-tiled/issues
|
|
6
|
+
Project-URL: changelog, https://github.com/redsun-acquisition/ome-tiled/blob/main/CHANGELOG.md
|
|
7
|
+
Project-URL: homepage, https://github.com/redsun-acquisition/ome-tiled
|
|
8
|
+
Author-email: Jacopo Abramo <jacopo.abramo@gmail.com>
|
|
9
|
+
Maintainer-email: Jacopo Abramo <jacopo.abramo@gmail.com>
|
|
10
|
+
License: Apache-2.0
|
|
11
|
+
License-File: LICENSE
|
|
12
|
+
Classifier: Development Status :: 3 - Alpha
|
|
13
|
+
Classifier: Intended Audience :: Developers
|
|
14
|
+
Classifier: Intended Audience :: Science/Research
|
|
15
|
+
Classifier: License :: OSI Approved :: Apache Software License
|
|
16
|
+
Classifier: Programming Language :: Python :: 3
|
|
17
|
+
Classifier: Programming Language :: Python :: 3.11
|
|
18
|
+
Classifier: Programming Language :: Python :: 3.12
|
|
19
|
+
Classifier: Programming Language :: Python :: 3.13
|
|
20
|
+
Classifier: Programming Language :: Python :: Implementation :: CPython
|
|
21
|
+
Classifier: Topic :: Scientific/Engineering
|
|
22
|
+
Classifier: Typing :: Typed
|
|
23
|
+
Requires-Python: <3.14,>=3.11
|
|
24
|
+
Requires-Dist: tiled[server]>=0.2.18
|
|
25
|
+
Requires-Dist: yaozarrs>=0.3.2
|
|
26
|
+
Requires-Dist: zarr>=3.1.6
|
|
27
|
+
Description-Content-Type: text/markdown
|
|
28
|
+
|
|
29
|
+
[](https://pypi.org/project/ome-tiled)
|
|
30
|
+
[](https://pypi.org/project/ome-tiled)
|
|
31
|
+
[](https://codecov.io/gh/redsun-acquisition/ome-tiled)
|
|
32
|
+
[](https://github.com/astral-sh/ruff)
|
|
33
|
+
[](https://mypy-lang.org/)
|
|
34
|
+
[](https://opensource.org/licenses/Apache-2.0)
|
|
35
|
+
|
|
36
|
+
# ome-tiled
|
|
37
|
+
|
|
38
|
+
An adapter for [`tiled`](https://github.com/bluesky/tiled) that serves OME-Zarr
|
|
39
|
+
images as arrays with their axis names, which `tiled`'s own Zarr adapter
|
|
40
|
+
leaves out.
|
|
41
|
+
|
|
42
|
+
## Install
|
|
43
|
+
|
|
44
|
+
With `uv` (recommended):
|
|
45
|
+
|
|
46
|
+
```console
|
|
47
|
+
uv add ome-tiled
|
|
48
|
+
```
|
|
49
|
+
|
|
50
|
+
With `pip`:
|
|
51
|
+
|
|
52
|
+
```console
|
|
53
|
+
pip install ome-tiled
|
|
54
|
+
```
|
|
55
|
+
|
|
56
|
+
Install it on the server, and also wherever `tiled register` runs: registering
|
|
57
|
+
opens each store through the adapter on the registering side.
|
|
58
|
+
|
|
59
|
+
## Usage
|
|
60
|
+
|
|
61
|
+
Serve a directory, letting `ome-tiled` find the OME-Zarr stores in it:
|
|
62
|
+
|
|
63
|
+
```console
|
|
64
|
+
tiled serve directory data/ \
|
|
65
|
+
--adapter application/x-ome-zarr=ome_tiled:OmeZarrAdapter \
|
|
66
|
+
--mimetype-hook ome_tiled:detect
|
|
67
|
+
```
|
|
68
|
+
|
|
69
|
+
Each image then reads as one array whose `dims` are its axis names:
|
|
70
|
+
|
|
71
|
+
```python
|
|
72
|
+
from tiled.client import from_uri
|
|
73
|
+
|
|
74
|
+
client = from_uri("http://localhost:8000", api_key="...")
|
|
75
|
+
client["stack"].structure().dims # ('t', 'z', 'y', 'x')
|
|
76
|
+
```
|
|
77
|
+
|
|
78
|
+
The hook recognizes a store by its metadata, whatever it is called. Stores
|
|
79
|
+
named `*.ome.zarr` can be routed by name instead, with
|
|
80
|
+
`--ext .ome.zarr=application/x-ome-zarr` in place of `--mimetype-hook`.
|
|
81
|
+
|
|
82
|
+
### From a configuration file
|
|
83
|
+
|
|
84
|
+
Register the adapter in the server's configuration:
|
|
85
|
+
|
|
86
|
+
```yaml
|
|
87
|
+
# config.yml
|
|
88
|
+
trees:
|
|
89
|
+
- tree: catalog
|
|
90
|
+
path: /
|
|
91
|
+
args:
|
|
92
|
+
uri: ./catalog.db
|
|
93
|
+
init_if_not_exists: true
|
|
94
|
+
readable_storage:
|
|
95
|
+
- data/
|
|
96
|
+
adapters_by_mimetype:
|
|
97
|
+
application/x-ome-zarr: ome_tiled:OmeZarrAdapter
|
|
98
|
+
```
|
|
99
|
+
|
|
100
|
+
Then start the server and register the directory:
|
|
101
|
+
|
|
102
|
+
```console
|
|
103
|
+
tiled serve config config.yml --api-key secret
|
|
104
|
+
tiled register http://localhost:8000 data/ --api-key secret \
|
|
105
|
+
--adapter application/x-ome-zarr=ome_tiled:OmeZarrAdapter \
|
|
106
|
+
--mimetype-hook ome_tiled:detect
|
|
107
|
+
```
|
|
108
|
+
|
|
109
|
+
### From Python
|
|
110
|
+
|
|
111
|
+
```python
|
|
112
|
+
from tiled.catalog import from_uri
|
|
113
|
+
|
|
114
|
+
catalog = from_uri(
|
|
115
|
+
"catalog.db",
|
|
116
|
+
readable_storage=["data/"],
|
|
117
|
+
init_if_not_exists=True,
|
|
118
|
+
adapters_by_mimetype={"application/x-ome-zarr": "ome_tiled:OmeZarrAdapter"},
|
|
119
|
+
)
|
|
120
|
+
```
|
|
121
|
+
|
|
122
|
+
`tiled.server.simple.SimpleTiledServer` takes no adapters, so add the adapter to
|
|
123
|
+
its catalog after starting the server and before registering anything:
|
|
124
|
+
|
|
125
|
+
```python
|
|
126
|
+
from tiled.server.simple import SimpleTiledServer
|
|
127
|
+
|
|
128
|
+
from ome_tiled import OME_ZARR_MIMETYPE, OmeZarrAdapter
|
|
129
|
+
|
|
130
|
+
server = SimpleTiledServer(readable_storage=["data/"])
|
|
131
|
+
server.catalog.context.adapters_by_mimetype.maps[0][OME_ZARR_MIMETYPE] = OmeZarrAdapter
|
|
132
|
+
```
|
|
133
|
+
|
|
134
|
+
### Registering by hand
|
|
135
|
+
|
|
136
|
+
`tiled` answers a registered node's structure and metadata from its database,
|
|
137
|
+
so a registration made with `client.new` has to store the adapter's own, or the
|
|
138
|
+
node reads without its axis names:
|
|
139
|
+
|
|
140
|
+
```python
|
|
141
|
+
from tiled.structures.core import StructureFamily
|
|
142
|
+
from tiled.structures.data_source import Asset, DataSource, Management
|
|
143
|
+
|
|
144
|
+
from ome_tiled import OME_ZARR_MIMETYPE, OmeZarrAdapter
|
|
145
|
+
|
|
146
|
+
uri = "file:///data/stack.ome.zarr"
|
|
147
|
+
adapter = OmeZarrAdapter.from_uris(uri)
|
|
148
|
+
client.new(
|
|
149
|
+
key="stack",
|
|
150
|
+
structure_family=StructureFamily.array,
|
|
151
|
+
data_sources=[
|
|
152
|
+
DataSource(
|
|
153
|
+
management=Management.external,
|
|
154
|
+
mimetype=OME_ZARR_MIMETYPE,
|
|
155
|
+
structure_family=StructureFamily.array,
|
|
156
|
+
structure=adapter.structure(),
|
|
157
|
+
assets=[Asset(data_uri=uri, is_directory=True, parameter="data_uri")],
|
|
158
|
+
)
|
|
159
|
+
],
|
|
160
|
+
metadata=dict(adapter.metadata()),
|
|
161
|
+
specs=[],
|
|
162
|
+
)
|
|
163
|
+
```
|
|
164
|
+
|
|
165
|
+
The URI may name the image group or its full-resolution array; both read the
|
|
166
|
+
same way.
|
|
167
|
+
|
|
168
|
+
## What it reads
|
|
169
|
+
|
|
170
|
+
- NGFF 0.4 and 0.5 images and label images, validated with
|
|
171
|
+
[`yaozarrs`](https://github.com/imaging-formats/yaozarrs). The axes, with their
|
|
172
|
+
types and units, are under `axes` in the node's metadata.
|
|
173
|
+
- A Zarr group holding several such images, each presented as its own array.
|
|
174
|
+
- The full-resolution level only. Pyramids read at level `0`.
|
|
175
|
+
|
|
176
|
+
Anything else is served as `tiled`'s Zarr adapter serves it, with a log line
|
|
177
|
+
saying why: other NGFF layouts such as `bioformats2raw` series, plates, wells
|
|
178
|
+
and label groups, and any group whose NGFF metadata fails validation.
|
|
179
|
+
Validation is strict, so a file that breaks the NGFF specification, for example
|
|
180
|
+
a dataset without `coordinateTransformations`, reads as plain Zarr rather than
|
|
181
|
+
as an image.
|
|
182
|
+
|
|
183
|
+
Axes of a custom kind, such as a scan pattern, keep their names too. NGFF
|
|
184
|
+
orders axes as time, then channel or custom, then space, so a file that puts a
|
|
185
|
+
custom axis after the spatial ones fails validation and reads as plain Zarr.
|
|
186
|
+
|
|
187
|
+
## More
|
|
188
|
+
|
|
189
|
+
The `tiled` documentation explains adapters, mimetypes and detection hooks in
|
|
190
|
+
more detail: [Serve Files with Custom Formats](https://blueskyproject.io/tiled/user-guide/read-custom-formats.html).
|
|
191
|
+
|
|
192
|
+
## License
|
|
193
|
+
|
|
194
|
+
Apache License 2.0. See [`LICENSE`](LICENSE).
|
|
@@ -0,0 +1,166 @@
|
|
|
1
|
+
[](https://pypi.org/project/ome-tiled)
|
|
2
|
+
[](https://pypi.org/project/ome-tiled)
|
|
3
|
+
[](https://codecov.io/gh/redsun-acquisition/ome-tiled)
|
|
4
|
+
[](https://github.com/astral-sh/ruff)
|
|
5
|
+
[](https://mypy-lang.org/)
|
|
6
|
+
[](https://opensource.org/licenses/Apache-2.0)
|
|
7
|
+
|
|
8
|
+
# ome-tiled
|
|
9
|
+
|
|
10
|
+
An adapter for [`tiled`](https://github.com/bluesky/tiled) that serves OME-Zarr
|
|
11
|
+
images as arrays with their axis names, which `tiled`'s own Zarr adapter
|
|
12
|
+
leaves out.
|
|
13
|
+
|
|
14
|
+
## Install
|
|
15
|
+
|
|
16
|
+
With `uv` (recommended):
|
|
17
|
+
|
|
18
|
+
```console
|
|
19
|
+
uv add ome-tiled
|
|
20
|
+
```
|
|
21
|
+
|
|
22
|
+
With `pip`:
|
|
23
|
+
|
|
24
|
+
```console
|
|
25
|
+
pip install ome-tiled
|
|
26
|
+
```
|
|
27
|
+
|
|
28
|
+
Install it on the server, and also wherever `tiled register` runs: registering
|
|
29
|
+
opens each store through the adapter on the registering side.
|
|
30
|
+
|
|
31
|
+
## Usage
|
|
32
|
+
|
|
33
|
+
Serve a directory, letting `ome-tiled` find the OME-Zarr stores in it:
|
|
34
|
+
|
|
35
|
+
```console
|
|
36
|
+
tiled serve directory data/ \
|
|
37
|
+
--adapter application/x-ome-zarr=ome_tiled:OmeZarrAdapter \
|
|
38
|
+
--mimetype-hook ome_tiled:detect
|
|
39
|
+
```
|
|
40
|
+
|
|
41
|
+
Each image then reads as one array whose `dims` are its axis names:
|
|
42
|
+
|
|
43
|
+
```python
|
|
44
|
+
from tiled.client import from_uri
|
|
45
|
+
|
|
46
|
+
client = from_uri("http://localhost:8000", api_key="...")
|
|
47
|
+
client["stack"].structure().dims # ('t', 'z', 'y', 'x')
|
|
48
|
+
```
|
|
49
|
+
|
|
50
|
+
The hook recognizes a store by its metadata, whatever it is called. Stores
|
|
51
|
+
named `*.ome.zarr` can be routed by name instead, with
|
|
52
|
+
`--ext .ome.zarr=application/x-ome-zarr` in place of `--mimetype-hook`.
|
|
53
|
+
|
|
54
|
+
### From a configuration file
|
|
55
|
+
|
|
56
|
+
Register the adapter in the server's configuration:
|
|
57
|
+
|
|
58
|
+
```yaml
|
|
59
|
+
# config.yml
|
|
60
|
+
trees:
|
|
61
|
+
- tree: catalog
|
|
62
|
+
path: /
|
|
63
|
+
args:
|
|
64
|
+
uri: ./catalog.db
|
|
65
|
+
init_if_not_exists: true
|
|
66
|
+
readable_storage:
|
|
67
|
+
- data/
|
|
68
|
+
adapters_by_mimetype:
|
|
69
|
+
application/x-ome-zarr: ome_tiled:OmeZarrAdapter
|
|
70
|
+
```
|
|
71
|
+
|
|
72
|
+
Then start the server and register the directory:
|
|
73
|
+
|
|
74
|
+
```console
|
|
75
|
+
tiled serve config config.yml --api-key secret
|
|
76
|
+
tiled register http://localhost:8000 data/ --api-key secret \
|
|
77
|
+
--adapter application/x-ome-zarr=ome_tiled:OmeZarrAdapter \
|
|
78
|
+
--mimetype-hook ome_tiled:detect
|
|
79
|
+
```
|
|
80
|
+
|
|
81
|
+
### From Python
|
|
82
|
+
|
|
83
|
+
```python
|
|
84
|
+
from tiled.catalog import from_uri
|
|
85
|
+
|
|
86
|
+
catalog = from_uri(
|
|
87
|
+
"catalog.db",
|
|
88
|
+
readable_storage=["data/"],
|
|
89
|
+
init_if_not_exists=True,
|
|
90
|
+
adapters_by_mimetype={"application/x-ome-zarr": "ome_tiled:OmeZarrAdapter"},
|
|
91
|
+
)
|
|
92
|
+
```
|
|
93
|
+
|
|
94
|
+
`tiled.server.simple.SimpleTiledServer` takes no adapters, so add the adapter to
|
|
95
|
+
its catalog after starting the server and before registering anything:
|
|
96
|
+
|
|
97
|
+
```python
|
|
98
|
+
from tiled.server.simple import SimpleTiledServer
|
|
99
|
+
|
|
100
|
+
from ome_tiled import OME_ZARR_MIMETYPE, OmeZarrAdapter
|
|
101
|
+
|
|
102
|
+
server = SimpleTiledServer(readable_storage=["data/"])
|
|
103
|
+
server.catalog.context.adapters_by_mimetype.maps[0][OME_ZARR_MIMETYPE] = OmeZarrAdapter
|
|
104
|
+
```
|
|
105
|
+
|
|
106
|
+
### Registering by hand
|
|
107
|
+
|
|
108
|
+
`tiled` answers a registered node's structure and metadata from its database,
|
|
109
|
+
so a registration made with `client.new` has to store the adapter's own, or the
|
|
110
|
+
node reads without its axis names:
|
|
111
|
+
|
|
112
|
+
```python
|
|
113
|
+
from tiled.structures.core import StructureFamily
|
|
114
|
+
from tiled.structures.data_source import Asset, DataSource, Management
|
|
115
|
+
|
|
116
|
+
from ome_tiled import OME_ZARR_MIMETYPE, OmeZarrAdapter
|
|
117
|
+
|
|
118
|
+
uri = "file:///data/stack.ome.zarr"
|
|
119
|
+
adapter = OmeZarrAdapter.from_uris(uri)
|
|
120
|
+
client.new(
|
|
121
|
+
key="stack",
|
|
122
|
+
structure_family=StructureFamily.array,
|
|
123
|
+
data_sources=[
|
|
124
|
+
DataSource(
|
|
125
|
+
management=Management.external,
|
|
126
|
+
mimetype=OME_ZARR_MIMETYPE,
|
|
127
|
+
structure_family=StructureFamily.array,
|
|
128
|
+
structure=adapter.structure(),
|
|
129
|
+
assets=[Asset(data_uri=uri, is_directory=True, parameter="data_uri")],
|
|
130
|
+
)
|
|
131
|
+
],
|
|
132
|
+
metadata=dict(adapter.metadata()),
|
|
133
|
+
specs=[],
|
|
134
|
+
)
|
|
135
|
+
```
|
|
136
|
+
|
|
137
|
+
The URI may name the image group or its full-resolution array; both read the
|
|
138
|
+
same way.
|
|
139
|
+
|
|
140
|
+
## What it reads
|
|
141
|
+
|
|
142
|
+
- NGFF 0.4 and 0.5 images and label images, validated with
|
|
143
|
+
[`yaozarrs`](https://github.com/imaging-formats/yaozarrs). The axes, with their
|
|
144
|
+
types and units, are under `axes` in the node's metadata.
|
|
145
|
+
- A Zarr group holding several such images, each presented as its own array.
|
|
146
|
+
- The full-resolution level only. Pyramids read at level `0`.
|
|
147
|
+
|
|
148
|
+
Anything else is served as `tiled`'s Zarr adapter serves it, with a log line
|
|
149
|
+
saying why: other NGFF layouts such as `bioformats2raw` series, plates, wells
|
|
150
|
+
and label groups, and any group whose NGFF metadata fails validation.
|
|
151
|
+
Validation is strict, so a file that breaks the NGFF specification, for example
|
|
152
|
+
a dataset without `coordinateTransformations`, reads as plain Zarr rather than
|
|
153
|
+
as an image.
|
|
154
|
+
|
|
155
|
+
Axes of a custom kind, such as a scan pattern, keep their names too. NGFF
|
|
156
|
+
orders axes as time, then channel or custom, then space, so a file that puts a
|
|
157
|
+
custom axis after the spatial ones fails validation and reads as plain Zarr.
|
|
158
|
+
|
|
159
|
+
## More
|
|
160
|
+
|
|
161
|
+
The `tiled` documentation explains adapters, mimetypes and detection hooks in
|
|
162
|
+
more detail: [Serve Files with Custom Formats](https://blueskyproject.io/tiled/user-guide/read-custom-formats.html).
|
|
163
|
+
|
|
164
|
+
## License
|
|
165
|
+
|
|
166
|
+
Apache License 2.0. See [`LICENSE`](LICENSE).
|
|
@@ -0,0 +1,144 @@
|
|
|
1
|
+
[build-system]
|
|
2
|
+
requires = ["hatchling", "hatch-vcs"]
|
|
3
|
+
build-backend = "hatchling.build"
|
|
4
|
+
|
|
5
|
+
[project]
|
|
6
|
+
name = "ome-tiled"
|
|
7
|
+
dynamic = ["version"]
|
|
8
|
+
description = "A tiled adapter that serves OME-Zarr images with their axis names."
|
|
9
|
+
readme = "README.md"
|
|
10
|
+
authors = [{ name = "Jacopo Abramo", email = "jacopo.abramo@gmail.com" }]
|
|
11
|
+
maintainers = [{ name = "Jacopo Abramo", email = "jacopo.abramo@gmail.com" }]
|
|
12
|
+
classifiers = [
|
|
13
|
+
"Development Status :: 3 - Alpha",
|
|
14
|
+
"Intended Audience :: Developers",
|
|
15
|
+
"Intended Audience :: Science/Research",
|
|
16
|
+
"Topic :: Scientific/Engineering",
|
|
17
|
+
"Programming Language :: Python :: Implementation :: CPython",
|
|
18
|
+
"Programming Language :: Python :: 3",
|
|
19
|
+
"Programming Language :: Python :: 3.11",
|
|
20
|
+
"Programming Language :: Python :: 3.12",
|
|
21
|
+
"Programming Language :: Python :: 3.13",
|
|
22
|
+
# no 3.14 until tiled installs there: https://github.com/bluesky/tiled/issues/1144
|
|
23
|
+
"Typing :: Typed",
|
|
24
|
+
"License :: OSI Approved :: Apache Software License",
|
|
25
|
+
]
|
|
26
|
+
license = { text = "Apache-2.0" }
|
|
27
|
+
requires-python = ">=3.11,<3.14"
|
|
28
|
+
dependencies = [
|
|
29
|
+
"tiled[server]>=0.2.18",
|
|
30
|
+
"yaozarrs>=0.3.2",
|
|
31
|
+
"zarr>=3.1.6",
|
|
32
|
+
]
|
|
33
|
+
|
|
34
|
+
[project.urls]
|
|
35
|
+
bugs = "https://github.com/redsun-acquisition/ome-tiled/issues"
|
|
36
|
+
changelog = "https://github.com/redsun-acquisition/ome-tiled/blob/main/CHANGELOG.md"
|
|
37
|
+
homepage = "https://github.com/redsun-acquisition/ome-tiled"
|
|
38
|
+
|
|
39
|
+
[tool.hatch.version]
|
|
40
|
+
source = "vcs"
|
|
41
|
+
|
|
42
|
+
[tool.hatch.build.targets.wheel]
|
|
43
|
+
packages = ["src/ome_tiled"]
|
|
44
|
+
|
|
45
|
+
[tool.hatch.build.targets.sdist]
|
|
46
|
+
include = ["src/ome_tiled/**"]
|
|
47
|
+
|
|
48
|
+
[tool.mypy]
|
|
49
|
+
files = "."
|
|
50
|
+
disable_error_code = [
|
|
51
|
+
"import-untyped",
|
|
52
|
+
"no-untyped-call"
|
|
53
|
+
]
|
|
54
|
+
pretty = true
|
|
55
|
+
strict = true
|
|
56
|
+
warn_unreachable = true
|
|
57
|
+
warn_no_return = true
|
|
58
|
+
|
|
59
|
+
[tool.coverage.run]
|
|
60
|
+
source = ["ome_tiled"]
|
|
61
|
+
|
|
62
|
+
# CI combines data from Linux, macOS and Windows runners, each checking out
|
|
63
|
+
# the repository under a different absolute path
|
|
64
|
+
[tool.coverage.paths]
|
|
65
|
+
source = ["src/", "*/src/"]
|
|
66
|
+
|
|
67
|
+
[tool.ruff]
|
|
68
|
+
fix = true
|
|
69
|
+
|
|
70
|
+
[tool.ruff.format]
|
|
71
|
+
docstring-code-format = true
|
|
72
|
+
|
|
73
|
+
[tool.ruff.lint]
|
|
74
|
+
extend-select = [
|
|
75
|
+
"D", # enable docstring checks
|
|
76
|
+
"I", # enable imports checks
|
|
77
|
+
"TC", # enable type check imports
|
|
78
|
+
"FA102", # force __future__ imports
|
|
79
|
+
]
|
|
80
|
+
ignore = ["D100","D104"] # https://docs.astral.sh/ruff/rules/undocumented-public-package/
|
|
81
|
+
|
|
82
|
+
[tool.ruff.lint.per-file-ignores]
|
|
83
|
+
"tests/*.py" = [
|
|
84
|
+
# ignore missing docstrings in tests
|
|
85
|
+
"D101",
|
|
86
|
+
"D102",
|
|
87
|
+
"D103",
|
|
88
|
+
# ignore type check imports in tests
|
|
89
|
+
"TC",
|
|
90
|
+
]
|
|
91
|
+
|
|
92
|
+
[tool.ruff.lint.pydocstyle]
|
|
93
|
+
convention = "numpy"
|
|
94
|
+
|
|
95
|
+
[tool.tox]
|
|
96
|
+
requires = ["tox>=4.28", "tox-uv-bare>=1.36"]
|
|
97
|
+
env_list = ["lint", "mypy", "tests"]
|
|
98
|
+
|
|
99
|
+
[tool.tox.env_run_base]
|
|
100
|
+
runner = "uv-venv-lock-runner"
|
|
101
|
+
dependency_groups = ["dev"]
|
|
102
|
+
|
|
103
|
+
[tool.tox.env.lint]
|
|
104
|
+
commands = [
|
|
105
|
+
["ruff", "check", "--fix", "."],
|
|
106
|
+
["ruff", "format", "."],
|
|
107
|
+
]
|
|
108
|
+
|
|
109
|
+
[tool.tox.env.mypy]
|
|
110
|
+
commands = [["mypy"]]
|
|
111
|
+
|
|
112
|
+
[tool.tox.env.tests]
|
|
113
|
+
commands = [["pytest", "-q", { replace = "posargs", extend = true }]]
|
|
114
|
+
|
|
115
|
+
# https://coverage.readthedocs.io/en/latest/config.html
|
|
116
|
+
[tool.coverage.report]
|
|
117
|
+
exclude_lines = [
|
|
118
|
+
"@abstractmethod",
|
|
119
|
+
"if TYPE_CHECKING:",
|
|
120
|
+
"@overload",
|
|
121
|
+
"class .*Protocol",
|
|
122
|
+
"except ImportError",
|
|
123
|
+
"except PackageNotFoundError",
|
|
124
|
+
"raise NotImplementedError()",
|
|
125
|
+
]
|
|
126
|
+
|
|
127
|
+
[tool.pytest.ini_options]
|
|
128
|
+
minversion = "6.0"
|
|
129
|
+
testpaths = [
|
|
130
|
+
"tests",
|
|
131
|
+
]
|
|
132
|
+
addopts = "-p no:warnings"
|
|
133
|
+
|
|
134
|
+
[dependency-groups]
|
|
135
|
+
dev = [
|
|
136
|
+
"acquire-zarr>=0.10.0",
|
|
137
|
+
"mypy>=2.3.1",
|
|
138
|
+
"ome-writers[acquire-zarr,zarr-python]>=0.3.2",
|
|
139
|
+
"prek>=0.5.3",
|
|
140
|
+
"pytest>=9.1.1",
|
|
141
|
+
"pytest-cov>=7.1.0",
|
|
142
|
+
"ruff>=0.16.8",
|
|
143
|
+
"tox-uv-bare>=1.36.0",
|
|
144
|
+
]
|
|
@@ -0,0 +1,104 @@
|
|
|
1
|
+
from __future__ import annotations
|
|
2
|
+
|
|
3
|
+
import logging
|
|
4
|
+
from typing import TYPE_CHECKING, Any
|
|
5
|
+
|
|
6
|
+
import zarr
|
|
7
|
+
from tiled.adapters.zarr import ZarrArrayAdapter, ZarrGroupAdapter
|
|
8
|
+
from tiled.structures.array import ArrayStructure
|
|
9
|
+
from tiled.utils import path_from_uri
|
|
10
|
+
from zarr.errors import GroupNotFoundError
|
|
11
|
+
|
|
12
|
+
from ome_tiled._ngff import NgffImage, NgffSkipped, classify
|
|
13
|
+
|
|
14
|
+
if TYPE_CHECKING:
|
|
15
|
+
from pathlib import Path
|
|
16
|
+
|
|
17
|
+
logger = logging.getLogger(__name__)
|
|
18
|
+
|
|
19
|
+
|
|
20
|
+
# tiled ships no type information, so its classes are Any to mypy
|
|
21
|
+
class OmeZarrAdapter(ZarrGroupAdapter): # type: ignore[misc]
|
|
22
|
+
"""Serve OME-Zarr images as arrays with their axis names.
|
|
23
|
+
|
|
24
|
+
Register it under ``OME_ZARR_MIMETYPE``. An image registered by its group
|
|
25
|
+
or by its full-resolution array reads as one array whose ``dims`` are the
|
|
26
|
+
axes' names, with the axes in the metadata under ``axes``. A group holding
|
|
27
|
+
images presents each as such an array. Any other group, including NGFF
|
|
28
|
+
layouts this package does not read and metadata that fails validation, is
|
|
29
|
+
served as ``tiled``'s Zarr adapter serves it.
|
|
30
|
+
"""
|
|
31
|
+
|
|
32
|
+
def __getitem__(self, key: str) -> Any:
|
|
33
|
+
value = self._zarr_group[key]
|
|
34
|
+
if isinstance(value, zarr.Group):
|
|
35
|
+
return open_group(value)
|
|
36
|
+
return super().__getitem__(key)
|
|
37
|
+
|
|
38
|
+
@classmethod
|
|
39
|
+
def from_uris(cls, data_uri: str, **kwargs: Any) -> Any:
|
|
40
|
+
"""Open the group or array at *data_uri*."""
|
|
41
|
+
return open_path(path_from_uri(data_uri), **kwargs)
|
|
42
|
+
|
|
43
|
+
@classmethod
|
|
44
|
+
def from_catalog(cls, data_source: Any, node: Any, /, **kwargs: Any) -> Any:
|
|
45
|
+
"""Open a registered asset, keeping the structure stored with it."""
|
|
46
|
+
return open_path(
|
|
47
|
+
path_from_uri(data_source.assets[0].data_uri),
|
|
48
|
+
structure=data_source.structure,
|
|
49
|
+
metadata=node.metadata_,
|
|
50
|
+
specs=node.specs,
|
|
51
|
+
**kwargs,
|
|
52
|
+
)
|
|
53
|
+
|
|
54
|
+
|
|
55
|
+
def open_path(
|
|
56
|
+
path: Path, *, structure: ArrayStructure | None = None, **kwargs: Any
|
|
57
|
+
) -> Any:
|
|
58
|
+
"""Return the adapter for the group or array at *path*."""
|
|
59
|
+
node = zarr.open(path, mode="r")
|
|
60
|
+
if isinstance(node, zarr.Group):
|
|
61
|
+
return open_group(node, structure=structure, **kwargs)
|
|
62
|
+
try:
|
|
63
|
+
parent = zarr.open_group(path.parent, mode="r")
|
|
64
|
+
except GroupNotFoundError:
|
|
65
|
+
image = None
|
|
66
|
+
else:
|
|
67
|
+
image = classify(parent.attrs.asdict())
|
|
68
|
+
if isinstance(image, NgffImage):
|
|
69
|
+
return open_image(node, image, structure=structure, **kwargs)
|
|
70
|
+
return ZarrArrayAdapter(
|
|
71
|
+
node, structure or ArrayStructure.from_array(node), **kwargs
|
|
72
|
+
)
|
|
73
|
+
|
|
74
|
+
|
|
75
|
+
def open_group(
|
|
76
|
+
group: zarr.Group, *, structure: ArrayStructure | None = None, **kwargs: Any
|
|
77
|
+
) -> Any:
|
|
78
|
+
"""Return an image's array adapter for an image group, a group adapter otherwise."""
|
|
79
|
+
image = classify(group.attrs.asdict())
|
|
80
|
+
if isinstance(image, NgffImage):
|
|
81
|
+
array = group.get(image.path)
|
|
82
|
+
if isinstance(array, zarr.Array):
|
|
83
|
+
return open_image(array, image, structure=structure, **kwargs)
|
|
84
|
+
image = NgffSkipped(f"dataset {image.path!r} is not an array")
|
|
85
|
+
if isinstance(image, NgffSkipped):
|
|
86
|
+
logger.info("Serving %s as plain Zarr: %s", group.store_path, image.reason)
|
|
87
|
+
return OmeZarrAdapter(group, **kwargs)
|
|
88
|
+
|
|
89
|
+
|
|
90
|
+
def open_image(
|
|
91
|
+
array: zarr.Array[Any],
|
|
92
|
+
image: NgffImage,
|
|
93
|
+
*,
|
|
94
|
+
structure: ArrayStructure | None = None,
|
|
95
|
+
metadata: dict[str, Any] | None = None,
|
|
96
|
+
**kwargs: Any,
|
|
97
|
+
) -> Any:
|
|
98
|
+
"""Return an array adapter carrying the image's axis names and axes."""
|
|
99
|
+
return ZarrArrayAdapter(
|
|
100
|
+
array,
|
|
101
|
+
structure or ArrayStructure.from_array(array, dims=image.dims),
|
|
102
|
+
metadata={**(metadata or {}), "axes": [dict(axis) for axis in image.axes]},
|
|
103
|
+
**kwargs,
|
|
104
|
+
)
|
|
@@ -0,0 +1,98 @@
|
|
|
1
|
+
from __future__ import annotations
|
|
2
|
+
|
|
3
|
+
from dataclasses import dataclass
|
|
4
|
+
from typing import TYPE_CHECKING, Any, Final
|
|
5
|
+
|
|
6
|
+
import yaozarrs
|
|
7
|
+
import zarr
|
|
8
|
+
from pydantic import ValidationError
|
|
9
|
+
from yaozarrs import v04, v05
|
|
10
|
+
from zarr.errors import ContainsArrayError, GroupNotFoundError
|
|
11
|
+
|
|
12
|
+
if TYPE_CHECKING:
|
|
13
|
+
from collections.abc import Mapping
|
|
14
|
+
from pathlib import Path
|
|
15
|
+
|
|
16
|
+
OME_ZARR_MIMETYPE: Final = "application/x-ome-zarr"
|
|
17
|
+
"""Mimetype under which a catalog routes OME-Zarr data to ``OmeZarrAdapter``."""
|
|
18
|
+
|
|
19
|
+
IMAGES: Final = (v04.Image, v04.LabelImage, v05.Image, v05.LabelImage)
|
|
20
|
+
|
|
21
|
+
|
|
22
|
+
@dataclass(frozen=True)
|
|
23
|
+
class NgffImage:
|
|
24
|
+
"""An OME-Zarr image, reduced to what serving it as one array needs.
|
|
25
|
+
|
|
26
|
+
Attributes
|
|
27
|
+
----------
|
|
28
|
+
dims : tuple[str, ...]
|
|
29
|
+
Axis names, in array order.
|
|
30
|
+
axes : tuple[Mapping[str, Any], ...]
|
|
31
|
+
Each axis as the metadata writes it: ``name``, ``type`` and ``unit``
|
|
32
|
+
when present.
|
|
33
|
+
path : str
|
|
34
|
+
Path of the full-resolution array, relative to the image group.
|
|
35
|
+
"""
|
|
36
|
+
|
|
37
|
+
dims: tuple[str, ...]
|
|
38
|
+
axes: tuple[Mapping[str, Any], ...]
|
|
39
|
+
path: str
|
|
40
|
+
|
|
41
|
+
|
|
42
|
+
@dataclass(frozen=True)
|
|
43
|
+
class NgffSkipped:
|
|
44
|
+
"""An OME-Zarr group this package does not serve, and why."""
|
|
45
|
+
|
|
46
|
+
reason: str
|
|
47
|
+
|
|
48
|
+
|
|
49
|
+
def classify(attributes: Mapping[str, Any]) -> NgffImage | NgffSkipped | None:
|
|
50
|
+
"""Classify a Zarr group by its attributes.
|
|
51
|
+
|
|
52
|
+
Returns
|
|
53
|
+
-------
|
|
54
|
+
NgffImage | NgffSkipped | None
|
|
55
|
+
``NgffImage`` for an NGFF 0.4 or 0.5 image or label image,
|
|
56
|
+
``NgffSkipped`` for any other NGFF layout and for NGFF metadata that
|
|
57
|
+
fails validation, and ``None`` for a group that is not NGFF.
|
|
58
|
+
"""
|
|
59
|
+
try:
|
|
60
|
+
node = yaozarrs.validate_ome_object(dict(attributes))
|
|
61
|
+
except ValidationError as error:
|
|
62
|
+
# the errors do not tell a plain group from a broken image, so the keys
|
|
63
|
+
# decide whether the group claimed to be NGFF at all
|
|
64
|
+
if "ome" in attributes or "multiscales" in attributes:
|
|
65
|
+
return NgffSkipped(f"NGFF metadata failed validation: {error}")
|
|
66
|
+
return None
|
|
67
|
+
if isinstance(node, v05.OMEAttributes):
|
|
68
|
+
node = node.ome
|
|
69
|
+
if not isinstance(node, IMAGES):
|
|
70
|
+
return NgffSkipped(type(node).__name__)
|
|
71
|
+
multiscale = node.multiscales[0]
|
|
72
|
+
axes = tuple(axis.model_dump(exclude_none=True) for axis in multiscale.axes)
|
|
73
|
+
return NgffImage(
|
|
74
|
+
dims=tuple(axis["name"] for axis in axes),
|
|
75
|
+
axes=axes,
|
|
76
|
+
path=multiscale.datasets[0].path,
|
|
77
|
+
)
|
|
78
|
+
|
|
79
|
+
|
|
80
|
+
def detect(path: Path, mimetype: str | None) -> str | None:
|
|
81
|
+
"""Return ``OME_ZARR_MIMETYPE`` for an OME-Zarr store, *mimetype* for anything else.
|
|
82
|
+
|
|
83
|
+
A directory is an OME-Zarr store when its root group carries NGFF metadata,
|
|
84
|
+
or when a group directly under a plain root is an NGFF image. Pass it to
|
|
85
|
+
``tiled`` as ``mimetype_detection_hook``.
|
|
86
|
+
"""
|
|
87
|
+
if not path.is_dir():
|
|
88
|
+
return mimetype
|
|
89
|
+
try:
|
|
90
|
+
root = zarr.open_group(path, mode="r")
|
|
91
|
+
except (GroupNotFoundError, ContainsArrayError):
|
|
92
|
+
return mimetype
|
|
93
|
+
if classify(root.attrs.asdict()) is not None:
|
|
94
|
+
return OME_ZARR_MIMETYPE
|
|
95
|
+
for _, child in root.groups():
|
|
96
|
+
if isinstance(classify(child.attrs.asdict()), NgffImage):
|
|
97
|
+
return OME_ZARR_MIMETYPE
|
|
98
|
+
return mimetype
|
|
File without changes
|