.gitignore

+__pycache__
+.ruff_cache
+.hypothesis
+.venv
+dist

.gitlab-ci.yml

+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

.python-version

+3.10

README.md

+# Json Datadefinition
+![](./examples/logo.svg)
+
+This repository contains data structure definitions for the RoboCT group at Deggendorf. It includes custom data structure schemas, example data files, and validation scripts.
+- Example Files: Stored in the `example` folder, these files demonstrate data structure usage.
+- Validation Scripts: Located in the `scripts` folder, these scripts validate `thd_json` data structure definitions against their schemas.
+
+## THD JSON
+
+This data structure use always a human-readable `.json` for storing header information.
+
+## CLI
+
+CLI tools for the validation of folder are automatically created. 
+To install the current tools just use:
+```ps1
+uv tool install --from git+https://mygit.th-deg.de/roboct/definitions/json_schemas thd-json
+
+```
+After the installation the validators are available as CLI:
+```ps1
+projection_validator(.exe) --help 
+```
+
+### Projection
+
+This schema defines the properties for projection data in THD JSON format.
+
+| Property                      | Type     | Description                                             | Constraints               | Required |
+|-------------------------------|----------|---------------------------------------------------------|---------------------------|----------|
+| `header`                      | header   | Header to identify File.                                | format: Header            | Yes      |
+| `focal_spot_position_mm`      | array    | Position of the focal spot in millimeters               | 3 numbers                 | Yes      |
+| `focal_spot_orientation_quat` | array    | Quaternion representing the focal spots orientation     | 4 numbers                 | No       |
+| `detector_center_position_mm` | array    | Center position of the detector in millimeters          | 3 numbers                 | Yes      |
+| `detector_horizontal_vector`  | array    | Horizontal orientation vector of the detector           | 3 numbers                 | No       |
+| `detector_vertical_vector`    | array    | Vertical orientation vector of the detector             | 3 numbers                 | No       |
+| `detector_center_orientation_quat` | array | Quaternion representing the detector's center orientation | 4 numbers             | Yes      |
+| `pixel_pitch_width_mm`        | number   | Pixel pitch in millimeters (width)                      | Minimum 0.001             | Yes      |
+| `pixel_pitch_height_mm`       | number   | Pixel pitch in millimeters (height)                     | Minimum 0.001             | Yes      |
+| `image_width_px`              | integer  | Width of the image in pixels                            | Minimum 1                 | Yes      |
+| `image_height_px`             | integer  | Height of the image in pixels                           | Minimum 1                 | Yes      |
+| `projection_matrix_cera`      | array    | Projection matrix for CERA, representing transformations | 3 arrays of 4 numbers    | No       |
+
+### Header
+
+| Property   | Type   | Description                                      | Constraints              | Required |
+|------------|--------|--------------------------------------------------|--------------------------|----------|
+| `timestamp`| string | Timestamp, e.g., 2018-11-13T20:20:39+00:00       | format: date-time        | Yes      |
+| `uuid`     | string | Unique identifier                                | format: uuid             | Yes      |
+
+
+### Examples
+
+Python example to validate a projection file:
+
+```python:../scripts/validate_file.py 
+from thd_json.projection import get_projection_validator
+from pathlib import Path
+
+
+FILE = Path("./examples/generated/example_projection.json")
+
+
+def main():
+    projection_validator = get_projection_validator()
+    projection_validator.file(FILE)
+
+
+if __name__ == "__main__":
+    main()
+
+```
+
+Python example to validate a folder of projections
+
+```python:../scripts/validate_folder.py:o:main
+def main():
+    projection_validator = get_projection_validator()
+    projection_validator.folder(FOLDER)
+``` 
+
+## Contribute
+
+- For changes please make a pull request.
+- Update the version and date number of the schema.
+- Add a new datatyp:
+    - add a moulde to `src`\ `thd_json`\ `new_data_type`
+    - add a validation function to the `__init__.py` of the `new_data_typ`. Example of [`projection`.\__init\__.py"](./src/thd_json/projection/__init__.py):
+
+```python:../src/thd_json/projection/__init__.py
+from thd_json import Validator
+from thd_json.header import JsonHeader, generate_header
+from thd_json.projection_geometry import get_projection_geometry_dict
+from thd_json.detector import get_detector_dict
+
+
+from pathlib import Path
+import argparse
+import numpy as np
+
+
+def get_projection_validator(json_suffix: str = "*.json") -> Validator:
+    return Validator(Path(__file__).parent / Path("projection.json"), json_suffix)
+
+
+def projection_cli():
+    parser = argparse.ArgumentParser(
+        description="JSON THD Projection Geometry Validator CLI with uv."
+    )
+    parser.add_argument("folder", help="Folder to check.", type=str)
+    parser.add_argument(
+        "suffix", help="Projection suffix.", default="*.json", type=Path, nargs="?"
+    )
+    args = parser.parse_args()
+
+    suffix = str(args.suffix)
+    if not suffix.startswith("*"):
+        raise ValueError(f'The suffix must always start with: "*". \nIt is: {suffix}')
+
+    validator = get_projection_validator(suffix)
+
+    folder = Path(args.folder)
+    if not folder.exists():
+        raise FileNotFoundError(f"Folder: {folder} does not exist")
+
+    validator.folder(Path(args.folder))
+
+
+def get_projection_dict(
+    image_path: Path,
+    focal_spot_position_mm: np.ndarray,
+    detector_center_position_mm: np.ndarray,
+    detector_center_orientation_quat: np.ndarray,
+    image_dimensions_px: np.ndarray,
+    pixel_pitch_mm: np.ndarray,
+    header: JsonHeader | None = None,
+):
+    if header is None:
+        header = generate_header()
+
+    projection = dict()
+    projection["projection_geometry"] = get_projection_geometry_dict(
+        focal_spot_position_mm,
+        detector_center_position_mm,
+        detector_center_orientation_quat,
+        header,
+    )
+
+    projection["detector"] = get_detector_dict(image_dimensions_px, pixel_pitch_mm)
+    projection["image"] = {"image_path", str(image_path)}
+
+    return projection
+
+
+if __name__ == "__main__":
+    projection_cli()
+
+```
+- add the CLI script to the `pyproject.toml` 
+```toml
+[project.scripts]
+projection_validator = "thd_json.projection:projection_cli"
+...
+new_data_typ_validator = "thd_json.new_data_typ:new_data_typ_cli"
+
+``` 
+

examples/artist/1c32ae9b-ad9a-11ef-af9a-f46d3febaf33_projection.json

+{
+    "projection_geometry": {
+        "focal_spot_position_mm": {
+            "x": 0.0,
+            "y": 0.0,
+            "z": 100.0
+        },
+        "detector_center_position_mm": {
+            "x": 0.0,
+            "y": 0.0,
+            "z": 0.0
+        },
+        "detector_center_orientation_quat": {
+            "x": 0.0,
+            "y": 0.0,
+            "z": 0.0,
+            "w": 1.0
+        },
+        "focal_spot_orientation_quat": {
+            "x": 0.0,
+            "y": 0.0,
+            "z": 0.0,
+            "w": 1.0
+        },
+        "header": {
+            "uuid": "1c32ae9b-ad9a-11ef-af9a-f46d3febaf33"
+        }
+    },
+    "detector": {
+        "pixel_pitch_mm": {
+            "u": 0.10000000149011612,
+            "v": 0.10000000149011612
+        },
+        "image_dimensions_px": {
+            "u": 1000,
+            "v": 1000
+        }
+    },
+    "image": {
+        "image_path": "1c32ae9b-ad9a-11ef-af9a-f46d3febaf33_projection.tif"
+    }
+}
\ No newline at end of file

examples/generated/example_detector.json

+{
+    "image_dimensions_px": {
+        "u": 1,
+        "v": 1
+    },
+    "pixel_pitch_mm": {
+        "u": 0.001,
+        "v": 0.001
+    }
+}
\ No newline at end of file

examples/generated/example_header.json

+{
+    "uuid": ""
+}
\ No newline at end of file

examples/generated/example_projection.json

+{
+    "detector": {
+        "image_dimensions_px": {
+            "u": 1,
+            "v": 1
+        },
+        "pixel_pitch_mm": {
+            "u": 0.001,
+            "v": 0.001
+        }
+    },
+    "image": {
+        "image_path": ".tif"
+    },
+    "projection_geometry": {
+        "detector_center_orientation_quat": {
+            "w": 0.0,
+            "x": 0.0,
+            "y": 0.0,
+            "z": 0.0
+        },
+        "detector_center_position_mm": {
+            "x": 0.0,
+            "y": 0.0,
+            "z": 0.0
+        },
+        "focal_spot_position_mm": {
+            "x": 0.0,
+            "y": 0.0,
+            "z": 0.0
+        },
+        "header": {
+            "uuid": ""
+        }
+    }
+}
\ No newline at end of file

examples/generated/example_roi.json

+{
+    "header": {
+        "uuid": ""
+    },
+    "roi_center_position_mm": [
+        0.0,
+        0.0,
+        0.0
+    ],
+    "roi_orientation_quat": [
+        0.0,
+        0.0,
+        0.0,
+        0.0
+    ],
+    "roi_resolution_mm": [
+        0.0,
+        0.0,
+        0.0
+    ],
+    "roi_voxels": [
+        1,
+        1,
+        1
+    ]
+}
\ No newline at end of file

examples/generated/example_source.json

+{
+    "current_ma": 0.001,
+    "voltage_kv": 0.001
+}
\ No newline at end of file

examples/logo.svg

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+   height="100mm"
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+       gradientTransform="matrix(-4.9612089,1.5676235,-1.4017317,-4.4361952,234.55247,439.48857)" />
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+       id="rect2"
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+       height="100"
+       x="0"
+       y="0" />
+    <text
+       xml:space="preserve"
+       style="font-size:25.4px;letter-spacing:2.64583px;fill:#1eb7be;fill-opacity:1;stroke-width:0.264583"
+       x="47.415554"
+       y="21.421324"
+       id="text9"><tspan
+         sodipodi:role="line"
+         id="tspan9"
+         style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:25.4px;font-family:'Cascadia Code';-inkscape-font-specification:'Cascadia Code';letter-spacing:2.64583px;fill:#ffffff;fill-opacity:1;stroke-width:0.264583"
+         x="47.415554"
+         y="21.421324">THD</tspan></text>
+    <text
+       xml:space="preserve"
+       style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:7.05556px;font-family:'Cascadia Code';-inkscape-font-specification:'Cascadia Code';letter-spacing:2.38125px;word-spacing:0px;fill:#ffffff;fill-opacity:1;stroke-width:0.264583"
+       x="2.3253708"
+       y="94.57032"
+       id="text10"><tspan
+         sodipodi:role="line"
+         id="tspan10"
+         style="font-size:7.05556px;letter-spacing:2.38125px;word-spacing:0px;stroke-width:0.264583"
+         x="2.3253708"
+         y="94.57032"
+         dx="0">TWIN ROBOTIC CT</tspan></text>
+    <text
+       xml:space="preserve"
+       style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:12.7px;font-family:'Cascadia Code';-inkscape-font-specification:'Cascadia Code';letter-spacing:0px;word-spacing:0px;fill:#ffffff;fill-opacity:1;stroke-width:0.264583"
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+       y="49.816677"
+       id="text10-8"><tspan
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+         x="50.820835"
+         y="49.816677"
+         id="tspan1">JSON<tspan
+   style="text-align:center;letter-spacing:1.49225px;text-anchor:middle"
+   id="tspan3" /></tspan><tspan
+         sodipodi:role="line"
+         style="font-size:12.7px;text-align:center;letter-spacing:0px;word-spacing:0px;text-anchor:middle;stroke-width:0.264583"
+         x="50.820835"
+         y="65.691673"
+         id="tspan2">SCHEMAS</tspan></text>
+  </g>
+</svg>

examples/thd_json/test_thd.json

+{
+    "header":
+    {
+        "uuid": "b83d81a1-333f-448e-af75-7c7db317fd96",
+        "timestamp": "2018-11-13T20:20:39+00:00"
+    },
+    "image":
+    {
+        "uuid": "b83d81a1-333f-448e-af75-7c7db317fd96",
+        "timestamp": "2018-11-13T20:20:39+00:00",
+        "image_path": "test_thd.tif"
+    },
+    "projection_geometry": {
+        "focal_spot_position_mm": [
+            2724.71682,
+            1690.5,
+            193.29345
+        ],
+        "detector_center_position_mm": [
+            1902.85619,
+            1690.5,
+            121.38996
+        ],
+        "detector_horizontal_vector": [
+            -0.08715574274765814,
+            0.0,
+            0.9961946980917458
+        ],
+        "detector_vertical_vector": [
+            -0.0,
+            -1.0000000000000002,
+            0.0
+        ],
+        "detector_center_orientation_quat": [
+            0.6755902076156602,
+            -0.0,
+            0.737277336810124,
+            0.0
+        ]
+    },
+    "detector": {
+        "pixel_pitch_width_mm": 0.07479989711934157,
+        "pixel_pitch_height_mm": 0.07479989711934157,
+        "image_width_px": 1944,
+        "image_height_px": 1536
+    }
+}
\ No newline at end of file

pyproject.toml

+[project]
+name = "thd-json"
+version = "0.1.9"
+description = "THD JSON schema and validation tools."
+authors = [
+    { name = "swittl", email = "simon.wittl@th-deg.de" }
+]
+requires-python = ">=3.10"
+dependencies = [
+    "hypothesis>=6.119.0",
+    "hypothesis-jsonschema>=0.23.1",
+    "json-schema>=0.3",
+    "jsonschema>=4.23.0",
+    "numpy>=2.1.3",
+    "pillow>=11.0.0",
+    "hatchling>=1.26.3",
+]
+
+[project.scripts]
+projection_validator = "thd_json.projection:projection_cli"
+header_validator = "thd_json.header:header_cli"
+generate_header = "thd_json.header:generate_header_cli"
+image_validator = "thd_json.image:image_cli"
+detector_validator = "thd_json.detector:detector_cli"
+source_validator = "thd_json.source:source_cli"
+projection_geometry_validator = "thd_json.projection_geometry:projection_geometry_cli"
+
+[project.optional-dependencies]
+load = [
+    "numpy>=2.1.3",
+    "pillow>=11.0.0",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"

scripts/generate_example_data.py

+from hypothesis_jsonschema import from_schema
+from thd_json.projection import get_projection_validator
+from thd_json.header import get_header_validator
+from thd_json.source import get_source_validator
+from thd_json.detector import get_detector_validator
+from thd_json.roi import get_roi_validator
+from hypothesis import given, settings
+import json
+from pathlib import Path
+
+
+SAVE_FOLDER = Path("./examples/generated")
+
+
+def main():
+    for name, get_validator in [
+        ("projection", get_projection_validator),
+        ("header", get_header_validator),
+        ("source", get_source_validator),
+        ("detector", get_detector_validator),
+        ("roi", get_roi_validator),
+    ]:
+        validator = get_validator()
+        schema = validator.get_schema()
+        strategy = from_schema(schema)
+
+        @settings(max_examples=1)
+        @given(strategy)
+        def schema(data):
+            with open(SAVE_FOLDER / f"example_{name}.json", "w") as f:
+                json.dump(data, f, indent=4)
+            return
+
+        schema()
+
+
+if __name__ == "__main__":
+    main()

scripts/get_projection_geometry.py

+from thd_json.projection_geometry import get_projection_geometry_dict
+import numpy as np
+
+
+def main():
+    focal_spot_position_mm = np.array([100.0, 50.0, 75.0])  # Example 3D position
+    detector_center_position_mm = np.array([200.0, 150.0, 250.0])  # Example 3D position
+    detector_center_orientation_quat = np.array(
+        [0.0, 0.0, 0.0, 1.0]
+    )  # Quaternion (w, x, y, z)
+
+    result = get_projection_geometry_dict(
+        focal_spot_position_mm=focal_spot_position_mm,
+        detector_center_position_mm=detector_center_position_mm,
+        detector_center_orientation_quat=detector_center_orientation_quat,
+        header=None,
+    )
+
+    # Print the result
+    print(result)
+
+
+if __name__ == "__main__":
+    main()

scripts/load_projection.py

+from thd_json.load_projection import load_thd_projection
+from pathlib import Path
+
+
+LOAD_PATH = Path(
+    "./examples/artist/856cbbd8-ad99-11ef-8841-f46d3febaf33_projection.json"
+)
+
+
+def main():
+    meta_data, projection = load_thd_projection(LOAD_PATH)
+    print(meta_data)
+    print(f"Projection Shape: {projection.shape}")
+
+
+if __name__ == "__main__":
+    main()

scripts/set_schema_versions_and_date.py

+import json
+from pathlib import Path
+from importlib.metadata import version
+from datetime import datetime
+
+"""
+This script updates the version and date metadata in all JSON files 
+found within the './src/thd_json' directory and its subdirectories.
+
+It performs the following:
+1. Reads each JSON file.
+2. Updates the "version" field with the version of the installed 'thd_json' package.
+3. Updates the "date" field with the current date formatted as DD.MM.YYYY.
+4. Writes the updated JSON data back to the file.
+
+Usage:
+- Ensure the 'thd_json' package is installed in your environment.
+- Run the script, and it will process all JSON files within the specified directory.
+
+Dependencies:
+- json: To handle JSON data.
+- pathlib.Path: For traversing the file system.
+- importlib.metadata.version: To retrieve the version of the 'thd_json' package.
+- datetime: To get and format the current date.
+
+"""
+
+
+def change_version(file_path: Path):
+    with open(file_path, "r") as f:
+        schema_dict = json.load(f)
+    current_datetime = datetime.now()
+
+    formatted_date = current_datetime.strftime("%d.%m.%Y")
+    schema_dict["version"] = version("thd_json")
+    schema_dict["date"] = formatted_date
+
+    with open(file_path, "w") as f:
+        json.dump(schema_dict, f, indent=2)
+
+
+def main():
+    for file in Path("./src/thd_json").rglob("*.json"):
+        change_version(file)
+    print(version("thd_json"))
+
+
+if __name__ == "__main__":
+    main()