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Commit c2314caa authored by Simon Wittl's avatar Simon Wittl
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readme update

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.gitlab-ci.yml 0 → 100644
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image: ubuntu:latest
stages:
- code_embed
- ruff
variables:
GIT_STRATEGY: clone
code_embedder:
stage: code_embed
script:
- cd code-embedder/
- poetry install --only main
- README_PATHS=$(find .. -maxdepth 1 -name "*.md" -print)
- poetry run python ./src/main.py --readme-paths $README_PATHS
- cd ..
- README_PATHS=$(find . -maxdepth 1 -name "*.md" -print)
- git add $README_PATHS
- git diff --staged
- export BRANCH_NAME="${CI_MERGE_REQUEST_SOURCE_BRANCH_NAME:-$CI_COMMIT_REF_NAME}"
- echo "branch name $BRANCH_NAME"
- git remote set-url origin "https://oauth2:${PERSONAL_ACCESS_TOKEN}@${CI_SERVER_HOST}/${CI_PROJECT_PATH}.git"
- echo "https://oauth2:${PERSONAL_ACCESS_TOKEN}@${CI_SERVER_HOST}/${CI_PROJECT_PATH}.git"
- if ! git diff --cached --exit-code; then
git commit -m "Apply Code Embedder";
git push origin HEAD:$BRANCH_NAME;
else
echo "No changes to commit";
fi
before_script:
- apt-get update && apt-get install -y curl git python3 python3-pip
- curl -sSL https://install.python-poetry.org | python3 -
- export PATH="$HOME/.local/bin:$PATH"
- git clone https://github.com/kvankova/code-embedder.git --branch "v0.5.2"
- git config --global user.email $GITLAB_USER_EMAIL
- git config --global user.name $GITLAB_USER_NAME
only:
- merge_requests
ruff_linter:
stage: ruff
script:
- curl -LsSf https://astral.sh/uv/install.sh | sh
- source $HOME/.local/bin/env
- uv tool run ruff check
before_script:
- apt-get update && apt-get install -y curl
only:
- merge_requests
README.md
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− 2
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# Json Datadefinition
![](./examples/logo.svg)
This repository contains `.h5` I/O utilities for the RoboCT group at Deggendorf. The data structure is auto generated from [THD JSON](https://mygit.th-deg.de/roboct/definitions/json_schemas).
For information of the data structure please look at `THD JSON`.
This repository contains `.h5` I/O utilities for the RoboCT group at Deggendorf. The data structure is auto generated from [THD JSON](https://mygit.th-deg.de/roboct-public/roboct-schemas).
For information of the data structure / group names please look at `THD JSON`.
## Examples
The main groups for a RoboCT project can be seen here [here](./examples/README.md).
You can explore small dataset with the HDF5 Viewer.
![](./examples/h5_viewer.png)
## Usage
### Initialize a File
```python:../scripts/generate_example_projection.py
from h5py import File
import numpy as np
from h5schemas.projection.add_projection import (
init_projection_dataset,
add_projection_sample,
)
def main():
# Generate a file in write mode.
test_file = File("./examples/projection.h5", "w")
# Initialize the .H5 structure
init_projection_dataset(test_file, False, (128, 128), (0.139, 0.139))
# Add dummy projections
add_projection_sample(
test_file,
1e5 * np.random.random((128, 128)),
[0.0, 1.0, 2.0],
[3.0, 4.0, 5.0, 6.0],
[7.0, 8.0, 9.0],
[10.0, 11.0, 12.0, 13],
)
add_projection_sample(
test_file,
1e5 * np.random.random((128, 128)),
np.array([0.0, 1.0, 2.0]),
np.array([3.0, 4.0, 5.0, 6.0]),
np.array([7.0, 8.0, 9.0]),
np.array([10.0, 11.0, 12.0, 13]),
voltage_kv=100,
)
# Access data
print(test_file["/image/image_array"][...])
if __name__ == "__main__":
main()
```
### Append new Group
```python:../scripts/add_joint_states_to_projection.py
from h5py import File
import numpy as np
from h5schemas.projection.add_projection import (
add_projection_sample,
)
from h5schemas.thd_joint_states.add_thd_joint_states import (
init_thd_joint_states,
add_thd_joint_states_sample,
)
def main():
# Generate a file in write mode.
test_file = File("./examples/projection.h5", "a")
# Add a new projection sample
add_projection_sample(
test_file,
1e5 * np.random.random((128, 128)),
[0.0, 1.0, 2.0],
[3.0, 4.0, 5.0, 6.0],
[7.0, 8.0, 9.0],
[10.0, 11.0, 12.0, 13],
)
# Add a new group
init_thd_joint_states(test_file)
add_thd_joint_states_sample(test_file, *np.arange(15))
if __name__ == "__main__":
main()
```
### Slice / Load a Dataset
```python:../scripts/load_slice.py
from h5py import File
from h5schemas.load_utilities.projection import extract_projection, GeomOptions
def main():
# Load the second projection from the dataset
test_file = File("./examples/projection.h5", "r")
projection = extract_projection(test_file, 1, GeomOptions.PROJECTION_GEOMETRY)
print(projection.image_array.shape)
# Load the first to projections an slice the projection data [20:50, 50:100:2]
projection = extract_projection(
test_file,
slice(0, 2),
GeomOptions.PROJECTION_GEOMETRY,
crop=(slice(20, 50), slice(50, 100, 2)),
)
print(projection.image_array.shape)
if __name__ == "__main__":
main()
```
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examples/README.md 0 → 100644
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```bash
.\examples\projection.h5 (5 objects)
├── detector (2 objects)
│ ├── image_dimensions_px (2 objects)
│ │ ├── u (1,), int32
│ │ └── v (1,), int32
│ └── pixel_pitch_mm (2 objects)
│ ├── u (1,), float64
│ └── v (1,), float64
├── image (2 objects)
│ ├── header (2 objects)
│ │ ├── timestamp (2,), float64
│ │ └── uuid (2,), |S100
│ └── image_array (2, 128, 128), uint16
├── projection_geometry (6 objects)
│ ├── detector_center_orientation_quat (4 objects)
│ │ ├── w (2,), float64
│ │ ├── x (2,), float64
│ │ ├── y (2,), float64
│ │ └── z (2,), float64
│ ├── detector_center_position_mm (3 objects)
│ │ ├── x (2,), float64
│ │ ├── y (2,), float64
│ │ └── z (2,), float64
│ ├── detector_center_rotation_matrix (2 objects)
│ │ ├── u (3 objects)
│ │ │ ├── x (0,), float64
│ │ │ ├── y (0,), float64
│ │ │ └── z (0,), float64
│ │ └── v (3 objects)
│ │ ├── x (0,), float64
│ │ ├── y (0,), float64
│ │ └── z (0,), float64
│ ├── focal_spot_orientation_quat (4 objects)
│ │ ├── w (2,), float64
│ │ ├── x (2,), float64
│ │ ├── y (2,), float64
│ │ └── z (2,), float64
│ ├── focal_spot_position_mm (3 objects)
│ │ ├── x (2,), float64
│ │ ├── y (2,), float64
│ │ └── z (2,), float64
│ └── header (2 objects)
│ ├── timestamp (2,), float64
│ └── uuid (2,), |S100
├── projection_geometry_nominal (6 objects)
│ ├── detector_center_orientation_quat (4 objects)
│ │ ├── w (2,), float64
│ │ ├── x (2,), float64
│ │ ├── y (2,), float64
│ │ └── z (2,), float64
│ ├── detector_center_position_mm (3 objects)
│ │ ├── x (2,), float64
│ │ ├── y (2,), float64
│ │ └── z (2,), float64
│ ├── detector_center_rotation_matrix (2 objects)
│ │ ├── u (3 objects)
│ │ │ ├── x (0,), float64
│ │ │ ├── y (0,), float64
│ │ │ └── z (0,), float64
│ │ └── v (3 objects)
│ │ ├── x (0,), float64
│ │ ├── y (0,), float64
│ │ └── z (0,), float64
│ ├── focal_spot_orientation_quat (4 objects)
│ │ ├── w (2,), float64
│ │ ├── x (2,), float64
│ │ ├── y (2,), float64
│ │ └── z (2,), float64
│ ├── focal_spot_position_mm (3 objects)
│ │ ├── x (2,), float64
│ │ ├── y (2,), float64
│ │ └── z (2,), float64
│ └── header (2 objects)
│ ├── timestamp (2,), float64
│ └── uuid (2,), |S100
└── source (2 objects)
├── current_ma (256,), float64
└── voltage_kv (256,), float64
```
\ No newline at end of file
examples/h5_viewer.png 0 → 100644
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examples/h5_viewer.png

268 KiB

examples/projection.h5
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pyproject.toml
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......@@ -9,6 +9,7 @@ authors = [
requires-python = ">=3.10"
dependencies = [
"h5py>=3.13.0",
"h5tree>=1.0",
"jsonref>=1.1.0",
"numpy==2.0.2",
"pandas>=2.2.3",
......
scripts/add_joint_states_to_projection.py
+ 4
− 26
View file @ c2314caa
from h5py import File
import numpy as np
from h5schemas.projection.add_projection import (
init_projection_dataset,
add_projection_sample,
)
from h5schemas.thd_joint_states.add_thd_joint_states import (
......@@ -14,16 +13,7 @@ def main():
# Generate a file in write mode.
test_file = File("./examples/projection.h5", "a")
# Initialize the .H5 structure
init_projection_dataset(test_file, False, (128, 128), (0.139, 0.139))
# # Add joint states group
# joint_states_group = test_file.require_group("/joint_states/")
# Init joint states group
init_thd_joint_states(test_file)
# Add dummy projections 1
# Add a new projection sample
add_projection_sample(
test_file,
1e5 * np.random.random((128, 128)),
......@@ -32,22 +22,10 @@ def main():
[7.0, 8.0, 9.0],
[10.0, 11.0, 12.0, 13],
)
add_thd_joint_states_sample(test_file, *np.arange(15))
# # Add dummy projections 2
# add_projection_sample(
# test_file,
# 1e5 * np.random.random((128, 128)),
# np.array([0.0, 1.0, 2.0]),
# np.array([3.0, 4.0, 5.0, 6.0]),
# np.array([7.0, 8.0, 9.0]),
# np.array([10.0, 11.0, 12.0, 13]),
# voltage_kv=100,
# )
# add_thd_joint_states_sample(joint_states_group, *np.arange(15, 30))
# # Access data
# print(test_file["/image/image_array"][...])
# Add a new group
init_thd_joint_states(test_file)
add_thd_joint_states_sample(test_file, *np.arange(15))
if __name__ == "__main__":
......
scripts/load_slice.py 0 → 100644
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− 0
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from h5py import File
from h5schemas.load_utilities.projection import extract_projection, GeomOptions
def main():
# Load the second projection from the dataset
test_file = File("./examples/projection.h5", "r")
projection = extract_projection(test_file, 1, GeomOptions.PROJECTION_GEOMETRY)
print(projection.image_array.shape)
# Load the first to projections an slice the projection data [20:50, 50:100:2]
projection = extract_projection(
test_file,
slice(0, 2),
GeomOptions.PROJECTION_GEOMETRY,
crop=(slice(20, 50), slice(50, 100, 2)),
)
print(projection.image_array.shape)
if __name__ == "__main__":
main()
src/h5schemas/load_utilities/projection.py
+ 19
− 4
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from h5schemas.load_utilities.projection_geometry import extract_projection_geometry, ProjectionGeometry
from h5schemas.load_utilities.projection_geometry import (
extract_projection_geometry,
ProjectionGeometry,
)
from h5py import Group
import numpy as np
from typing import NamedTuple, ClassVar, Literal
......@@ -24,13 +27,20 @@ class Projection(NamedTuple):
timestamp: np.ndarray
def extract_projection(h5_group: Group, indices: slice | int, projection_geometry_group: str = GeomOptions.PROJECTION_GEOMETRY, crop: list[slice] | None = None) -> Projection:
def extract_projection(
h5_group: Group,
indices: slice | int,
projection_geometry_group: str = GeomOptions.PROJECTION_GEOMETRY,
crop: list[slice] | None = None,
) -> Projection:
if crop is None:
crop = (slice(0, None, 1), slice(0, None, 1))
if len(crop) != 3 and isinstance(indices, slice):
crop = (slice(0, None), crop[0], crop[1])
projection_geometry = extract_projection_geometry(h5_group[projection_geometry_group], indices)
projection_geometry = extract_projection_geometry(
h5_group[projection_geometry_group], indices
)
uuid = h5_group["image"]["header"]["uuid"][indices]
timestamp = h5_group["image"]["header"]["timestamp"][indices]
image = h5_group["image"]["image_array"][indices][crop]
......@@ -51,6 +61,11 @@ if __name__ == "__main__":
print(projection)
print(projection.image_array.shape)
projection = extract_projection(test_file, slice(0, 2), GeomOptions.PROJECTION_GEOMETRY, crop=(slice(20, 50), slice(50, 100)))
projection = extract_projection(
test_file,
slice(0, 2),
GeomOptions.PROJECTION_GEOMETRY,
crop=(slice(20, 50), slice(50, 100)),
)
print(projection)
print(projection.image_array.shape)
src/h5schemas/load_utilities/projection_geometry.py
+ 3
− 1
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......@@ -14,7 +14,9 @@ class ProjectionGeometry(NamedTuple):
timestamp: np.ndarray
def extract_projection_geometry(h5_group: Group, indices: slice | int) -> ProjectionGeometry:
def extract_projection_geometry(
h5_group: Group, indices: slice | int
) -> ProjectionGeometry:
detector_center_position_mm = extract_vector(
h5_group["detector_center_position_mm"], indices, CommonVectors.XYZ
)
......
uv.lock
+ 24
− 0
View file @ c2314caa
......@@ -97,6 +97,7 @@ version = "0.1.22"
source = { editable = "." }
dependencies = [
{ name = "h5py" },
{ name = "h5tree" },
{ name = "jsonref" },
{ name = "numpy" },
{ name = "pandas" },
......@@ -107,6 +108,7 @@ dependencies = [
[package.metadata]
requires-dist = [
{ name = "h5py", specifier = ">=3.13.0" },
{ name = "h5tree", specifier = ">=1.0" },
{ name = "jsonref", specifier = ">=1.1.0" },
{ name = "numpy", specifier = "==2.0.2" },
{ name = "pandas", specifier = ">=2.2.3" },
......@@ -114,6 +116,19 @@ requires-dist = [
{ name = "thd-json", git = "https://mygit.th-deg.de/roboct-public/roboct-schemas" },
]
[[package]]
name = "h5tree"
version = "1.0"
source = { registry = "https://pypi.org/simple" }
dependencies = [
{ name = "h5py" },
{ name = "termcolor" },
]
sdist = { url = "https://files.pythonhosted.org/packages/ab/9b/ea46f715d5c5059de88ca2f87a63e7cb9a54f2a6e6cf56e88234730b179a/h5tree-1.0.tar.gz", hash = "sha256:d3c6ac2c647ebf4ba37ee91bdbd30ba147e68b0449c05ce1fe2ff9e7e61d8e12", size = 3418 }
wheels = [
{ url = "https://files.pythonhosted.org/packages/d6/f6/949bb1616da797ffe2badb6d09ee9664387c27105c28bac59917467c6254/h5tree-1.0-py3-none-any.whl", hash = "sha256:e7b83c6ea25fbd40dc05e8cf182aa43bde9bae19d88f7bed0308ff621d5c337e", size = 3466 },
]
[[package]]
name = "hatchling"
version = "1.27.0"
......@@ -697,6 +712,15 @@ wheels = [
{ url = "https://files.pythonhosted.org/packages/89/fd/62f31643596f6ab71fc6d2a87acdee0bc01a03fbe1a7f3f6dc0c91e2546d/tables-3.10.1-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:757c6ea257c174af8036cf8f273ede756bbcd6db5ac7e2a4d64e788b0f371152", size = 7527953 },
]
[[package]]
name = "termcolor"
version = "2.5.0"
source = { registry = "https://pypi.org/simple" }
sdist = { url = "https://files.pythonhosted.org/packages/37/72/88311445fd44c455c7d553e61f95412cf89054308a1aa2434ab835075fc5/termcolor-2.5.0.tar.gz", hash = "sha256:998d8d27da6d48442e8e1f016119076b690d962507531df4890fcd2db2ef8a6f", size = 13057 }
wheels = [
{ url = "https://files.pythonhosted.org/packages/7f/be/df630c387a0a054815d60be6a97eb4e8f17385d5d6fe660e1c02750062b4/termcolor-2.5.0-py3-none-any.whl", hash = "sha256:37b17b5fc1e604945c2642c872a3764b5d547a48009871aea3edd3afa180afb8", size = 7755 },
]
[[package]]
name = "thd-json"
version = "0.1.14"
......
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