blob: 880fb71f55efb5c702db58b3563e0f1d5383e979 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
|
%global _empty_manifest_terminate_build 0
Name: python-napatrackmater
Version: 3.5.4
Release: 1
Summary: Import Trackmate XML files for Track Visualization and analysis in Napari.
License: MIT License
URL: https://github.com/kapoorlab/NapaTrackMater/
Source0: https://mirrors.nju.edu.cn/pypi/web/packages/14/91/848e4bd2bf71766c7a51f45a2c9ad8cff42f9349b27024ec4f37e476df42/napatrackmater-3.5.4.tar.gz
BuildArch: noarch
Requires: python3-lxml
Requires: python3-vollseg
Requires: python3-napari
Requires: python3-natsort
Requires: python3-seaborn
%description
# NapaTrackMater
Napari Visualization tool for Trackmate > 6.0 and bTrackmate XML files for 3D + time tracks.
This repository is the bridge between the Fiji and Napari world for exporting and viewing the track XML files using [Napari track layer](https://napari.org/tutorials/fundamentals/tracks.html).
[](https://travis-ci.com/github/kapoorlab/napatrackmater)
[](https://pypi.org/project/napatrackmater/)
## Installation
This package can be installed with:
`pip install --user napatrackmater`
If you are building this from the source, clone the repository and install via
```bash
git clone https://github.com/kapoorlab/NapaTrackMater/
cd NapaTrackMater
pip install --user -e .
# or, to install in editable mode AND grab all of the developer tools
# (this is required if you want to contribute code back to NapaTrackMater)
pip install --user -r requirements.txt
```
### Pipenv install
Pipenv allows you to install dependencies in a virtual environment.
```bash
# install pipenv if you don't already have it installed
pip install --user pipenv
# clone the repository and sync the dependencies
git clone https://github.com/kapoorlab/NapaTrackMater/
cd NapaTrackMater
pipenv sync
# make the current package available
pipenv run python setup.py develop
# you can run the example notebooks by starting the jupyter notebook inside the virtual env
pipenv run jupyter notebook
```
## Docker
A Docker image can be used to run the code in a container. Once inside the project's directory, build the image with:
~~~bash
docker build -t kapoorlab/NapaTrackMater .
~~~
Now to run the `track` command:
~~~bash
# show help
docker run --rm -it kapoorlab/NapaTrackMater
# run it with example data
docker run --rm -it -v $(pwd)/examples/data:/input kapoorlab/NapaTrackMater track -f /input -r /input/Raw.tif -s /input/Seg.tif -s /input/Mask.tif -n test
~~~
## Requirements
- Python 3.9 and above.
## License
Under MIT license. See [LICENSE](LICENSE).
## Authors
- Varun Kapoor <randomaccessiblekapoor@gmail.com>
- Mari Tolonen
%package -n python3-napatrackmater
Summary: Import Trackmate XML files for Track Visualization and analysis in Napari.
Provides: python-napatrackmater
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-napatrackmater
# NapaTrackMater
Napari Visualization tool for Trackmate > 6.0 and bTrackmate XML files for 3D + time tracks.
This repository is the bridge between the Fiji and Napari world for exporting and viewing the track XML files using [Napari track layer](https://napari.org/tutorials/fundamentals/tracks.html).
[](https://travis-ci.com/github/kapoorlab/napatrackmater)
[](https://pypi.org/project/napatrackmater/)
## Installation
This package can be installed with:
`pip install --user napatrackmater`
If you are building this from the source, clone the repository and install via
```bash
git clone https://github.com/kapoorlab/NapaTrackMater/
cd NapaTrackMater
pip install --user -e .
# or, to install in editable mode AND grab all of the developer tools
# (this is required if you want to contribute code back to NapaTrackMater)
pip install --user -r requirements.txt
```
### Pipenv install
Pipenv allows you to install dependencies in a virtual environment.
```bash
# install pipenv if you don't already have it installed
pip install --user pipenv
# clone the repository and sync the dependencies
git clone https://github.com/kapoorlab/NapaTrackMater/
cd NapaTrackMater
pipenv sync
# make the current package available
pipenv run python setup.py develop
# you can run the example notebooks by starting the jupyter notebook inside the virtual env
pipenv run jupyter notebook
```
## Docker
A Docker image can be used to run the code in a container. Once inside the project's directory, build the image with:
~~~bash
docker build -t kapoorlab/NapaTrackMater .
~~~
Now to run the `track` command:
~~~bash
# show help
docker run --rm -it kapoorlab/NapaTrackMater
# run it with example data
docker run --rm -it -v $(pwd)/examples/data:/input kapoorlab/NapaTrackMater track -f /input -r /input/Raw.tif -s /input/Seg.tif -s /input/Mask.tif -n test
~~~
## Requirements
- Python 3.9 and above.
## License
Under MIT license. See [LICENSE](LICENSE).
## Authors
- Varun Kapoor <randomaccessiblekapoor@gmail.com>
- Mari Tolonen
%package help
Summary: Development documents and examples for napatrackmater
Provides: python3-napatrackmater-doc
%description help
# NapaTrackMater
Napari Visualization tool for Trackmate > 6.0 and bTrackmate XML files for 3D + time tracks.
This repository is the bridge between the Fiji and Napari world for exporting and viewing the track XML files using [Napari track layer](https://napari.org/tutorials/fundamentals/tracks.html).
[](https://travis-ci.com/github/kapoorlab/napatrackmater)
[](https://pypi.org/project/napatrackmater/)
## Installation
This package can be installed with:
`pip install --user napatrackmater`
If you are building this from the source, clone the repository and install via
```bash
git clone https://github.com/kapoorlab/NapaTrackMater/
cd NapaTrackMater
pip install --user -e .
# or, to install in editable mode AND grab all of the developer tools
# (this is required if you want to contribute code back to NapaTrackMater)
pip install --user -r requirements.txt
```
### Pipenv install
Pipenv allows you to install dependencies in a virtual environment.
```bash
# install pipenv if you don't already have it installed
pip install --user pipenv
# clone the repository and sync the dependencies
git clone https://github.com/kapoorlab/NapaTrackMater/
cd NapaTrackMater
pipenv sync
# make the current package available
pipenv run python setup.py develop
# you can run the example notebooks by starting the jupyter notebook inside the virtual env
pipenv run jupyter notebook
```
## Docker
A Docker image can be used to run the code in a container. Once inside the project's directory, build the image with:
~~~bash
docker build -t kapoorlab/NapaTrackMater .
~~~
Now to run the `track` command:
~~~bash
# show help
docker run --rm -it kapoorlab/NapaTrackMater
# run it with example data
docker run --rm -it -v $(pwd)/examples/data:/input kapoorlab/NapaTrackMater track -f /input -r /input/Raw.tif -s /input/Seg.tif -s /input/Mask.tif -n test
~~~
## Requirements
- Python 3.9 and above.
## License
Under MIT license. See [LICENSE](LICENSE).
## Authors
- Varun Kapoor <randomaccessiblekapoor@gmail.com>
- Mari Tolonen
%prep
%autosetup -n napatrackmater-3.5.4
%build
%py3_build
%install
%py3_install
install -d -m755 %{buildroot}/%{_pkgdocdir}
if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
pushd %{buildroot}
if [ -d usr/lib ]; then
find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/lib64 ]; then
find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/bin ]; then
find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/sbin ]; then
find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
fi
touch doclist.lst
if [ -d usr/share/man ]; then
find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
fi
popd
mv %{buildroot}/filelist.lst .
mv %{buildroot}/doclist.lst .
%files -n python3-napatrackmater -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Fri May 05 2023 Python_Bot <Python_Bot@openeuler.org> - 3.5.4-1
- Package Spec generated
|
