PyHaloXML
Python code to read/write .annotation files from Halo. Can export as .geojson for further analysis.
Examples
Example 1 : Move rectangles to a different layer and save as .annotation.
Example 2 : Check if annotations have holes in them and save as .geojson.
Example 3 : Show the wkt representation of the shapely polygon.
Example 4 : Create a .annotation file from coordinates.
Installation
pip install pyhaloxml
Note on version 3
The matching of negative to positive regions now needs to be done by the user after loading the data. The examples have been updated. This needed to happen because negative regions can be unmatched in Halo. This would cause errors when loading.
Loading speed
Rust is used to match the negative regions to positive regions, thanks to Wim Pomp!
It takes 41 seconds to load a 30.9MB file with 856454 vertices in 5769 regions with 731 holes.
Development
- Install Rust
- Clone the repository
pip install -e .
Notes on development
- The xml is relatively simple. There are Annotations and an annotation contains regions.
- Regions can be either positive or negative. However regions in an annotation are not hierarchical. So there is no telling what negative region should go with what positive region.
- This package expects a negative region to be fully enclosed by one positive region. The matching is done by taking a single point that is inside or on the border of the negative region and checking if it is inside a positive region.
Metadata
Release files for pyhaloxml 3.1.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| pyhaloxml-3.1.2.tar.gz | 845.2 kB | Details |
Built distributions (wheels)
Total release size: 1.3 MB
Release files / pyhaloxml-3.1.2.tar.gz
| Download URL | pyhaloxml-3.1.2.tar.gz |
|---|---|
| Size | 845.2 kB |
| Tags | Source |
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twine/5.1.1 CPython/3.12.7
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Release files / pyhaloxml-3.1.2-pp310-pypy310_pp73-win_amd64.whl
| Download URL | pyhaloxml-3.1.2-pp310-pypy310_pp73-win_amd64.whl |
|---|---|
| Size | 25.1 kB |
| Tags | PyPy 3.10 PyPy 3.10 7.3 Windows x86-64 |
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| Uploaded via |
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Release files / pyhaloxml-3.1.2-pp310-pypy310_pp73-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | pyhaloxml-3.1.2-pp310-pypy310_pp73-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Uploaded via |
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Release files / pyhaloxml-3.1.2-pp310-pypy310_pp73-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl
| Download URL | pyhaloxml-3.1.2-pp310-pypy310_pp73-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl |
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Release files / pyhaloxml-3.1.2-pp310-pypy310_pp73-macosx_11_0_arm64.whl
| Download URL | pyhaloxml-3.1.2-pp310-pypy310_pp73-macosx_11_0_arm64.whl |
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| Size | 12.7 kB |
| Tags | PyPy 3.10 PyPy 3.10 7.3 macOS 11.0+ ARM64 |
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Release files / pyhaloxml-3.1.2-pp310-pypy310_pp73-macosx_10_15_x86_64.whl
| Download URL | pyhaloxml-3.1.2-pp310-pypy310_pp73-macosx_10_15_x86_64.whl |
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Release files / pyhaloxml-3.1.2-cp313-cp313-win_amd64.whl
| Download URL | pyhaloxml-3.1.2-cp313-cp313-win_amd64.whl |
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| Size | 25.0 kB |
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Release files / pyhaloxml-3.1.2-cp313-cp313-musllinux_1_2_x86_64.whl
| Download URL | pyhaloxml-3.1.2-cp313-cp313-musllinux_1_2_x86_64.whl |
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| Tags | CPython 3.13 Linux musl 1.2+ x86-64 |
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Release files / pyhaloxml-3.1.2-cp313-cp313-musllinux_1_2_i686.whl
| Download URL | pyhaloxml-3.1.2-cp313-cp313-musllinux_1_2_i686.whl |
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| Size | 14.4 kB |
| Tags | CPython 3.13 Linux musl 1.2+ x86-32 |
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Release files / pyhaloxml-3.1.2-cp313-cp313-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | pyhaloxml-3.1.2-cp313-cp313-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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Release files / pyhaloxml-3.1.2-cp313-cp313-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl
| Download URL | pyhaloxml-3.1.2-cp313-cp313-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl |
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Release files / pyhaloxml-3.1.2-cp313-cp313-macosx_11_0_arm64.whl
| Download URL | pyhaloxml-3.1.2-cp313-cp313-macosx_11_0_arm64.whl |
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| Size | 12.7 kB |
| Tags | CPython 3.13 macOS 11.0+ ARM64 |
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Release files / pyhaloxml-3.1.2-cp313-cp313-macosx_10_13_x86_64.whl
| Download URL | pyhaloxml-3.1.2-cp313-cp313-macosx_10_13_x86_64.whl |
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| Tags | CPython 3.13 macOS 10.13+ x86-64 |
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Release files / pyhaloxml-3.1.2-cp312-cp312-win_amd64.whl
| Download URL | pyhaloxml-3.1.2-cp312-cp312-win_amd64.whl |
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| Size | 25.0 kB |
| Tags | CPython 3.12 Windows x86-64 |
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Release files / pyhaloxml-3.1.2-cp312-cp312-musllinux_1_2_x86_64.whl
| Download URL | pyhaloxml-3.1.2-cp312-cp312-musllinux_1_2_x86_64.whl |
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| Tags | CPython 3.12 Linux musl 1.2+ x86-64 |
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Release files / pyhaloxml-3.1.2-cp312-cp312-musllinux_1_2_i686.whl
| Download URL | pyhaloxml-3.1.2-cp312-cp312-musllinux_1_2_i686.whl |
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| Size | 14.4 kB |
| Tags | CPython 3.12 Linux musl 1.2+ x86-32 |
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Release files / pyhaloxml-3.1.2-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | pyhaloxml-3.1.2-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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Release files / pyhaloxml-3.1.2-cp312-cp312-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl
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Release files / pyhaloxml-3.1.2-cp312-cp312-macosx_11_0_arm64.whl
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Release files / pyhaloxml-3.1.2-cp312-cp312-macosx_10_13_x86_64.whl
| Download URL | pyhaloxml-3.1.2-cp312-cp312-macosx_10_13_x86_64.whl |
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Release files / pyhaloxml-3.1.2-cp311-cp311-win_amd64.whl
| Download URL | pyhaloxml-3.1.2-cp311-cp311-win_amd64.whl |
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| Size | 25.0 kB |
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Release files / pyhaloxml-3.1.2-cp311-cp311-musllinux_1_2_x86_64.whl
| Download URL | pyhaloxml-3.1.2-cp311-cp311-musllinux_1_2_x86_64.whl |
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| Size | 14.1 kB |
| Tags | CPython 3.11 Linux musl 1.2+ x86-64 |
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Release files / pyhaloxml-3.1.2-cp311-cp311-musllinux_1_2_i686.whl
| Download URL | pyhaloxml-3.1.2-cp311-cp311-musllinux_1_2_i686.whl |
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| Size | 14.4 kB |
| Tags | CPython 3.11 Linux musl 1.2+ x86-32 |
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Release files / pyhaloxml-3.1.2-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | pyhaloxml-3.1.2-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Tags | CPython 3.11 Linux glibc 2.17+ x86-64 Linux glibc 2.5+ x86-64 |
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Release files / pyhaloxml-3.1.2-cp311-cp311-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl
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| Size | 13.7 kB |
| Tags | CPython 3.11 Linux glibc 2.17+ x86-32 Linux glibc 2.5+ x86-32 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.7
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Release files / pyhaloxml-3.1.2-cp311-cp311-macosx_11_0_arm64.whl
| Download URL | pyhaloxml-3.1.2-cp311-cp311-macosx_11_0_arm64.whl |
|---|---|
| Size | 12.7 kB |
| Tags | CPython 3.11 macOS 11.0+ ARM64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.7
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Release files / pyhaloxml-3.1.2-cp311-cp311-macosx_10_9_x86_64.whl
| Download URL | pyhaloxml-3.1.2-cp311-cp311-macosx_10_9_x86_64.whl |
|---|---|
| Size | 12.3 kB |
| Tags | CPython 3.11 macOS 10.9+ x86-64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.7
|
Release files / pyhaloxml-3.1.2-cp310-cp310-win_amd64.whl
| Download URL | pyhaloxml-3.1.2-cp310-cp310-win_amd64.whl |
|---|---|
| Size | 25.0 kB |
| Tags | CPython 3.10 Windows x86-64 |
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SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.7
|
Release files / pyhaloxml-3.1.2-cp310-cp310-musllinux_1_2_x86_64.whl
| Download URL | pyhaloxml-3.1.2-cp310-cp310-musllinux_1_2_x86_64.whl |
|---|---|
| Size | 14.1 kB |
| Tags | CPython 3.10 Linux musl 1.2+ x86-64 |
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SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.7
|
Release files / pyhaloxml-3.1.2-cp310-cp310-musllinux_1_2_i686.whl
| Download URL | pyhaloxml-3.1.2-cp310-cp310-musllinux_1_2_i686.whl |
|---|---|
| Size | 14.4 kB |
| Tags | CPython 3.10 Linux musl 1.2+ x86-32 |
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SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.7
|
Release files / pyhaloxml-3.1.2-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | pyhaloxml-3.1.2-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 13.6 kB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 Linux glibc 2.5+ x86-64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.7
|
Release files / pyhaloxml-3.1.2-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl
| Download URL | pyhaloxml-3.1.2-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl |
|---|---|
| Size | 13.7 kB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-32 Linux glibc 2.5+ x86-32 |
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SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.7
|
Release files / pyhaloxml-3.1.2-cp310-cp310-macosx_11_0_arm64.whl
| Download URL | pyhaloxml-3.1.2-cp310-cp310-macosx_11_0_arm64.whl |
|---|---|
| Size | 12.7 kB |
| Tags | CPython 3.10 macOS 11.0+ ARM64 |
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SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.7
|
Release files / pyhaloxml-3.1.2-cp310-cp310-macosx_10_9_x86_64.whl
| Download URL | pyhaloxml-3.1.2-cp310-cp310-macosx_10_9_x86_64.whl |
|---|---|
| Size | 12.3 kB |
| Tags | CPython 3.10 macOS 10.9+ x86-64 |
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SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.12.7
|