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README.md
View file @ 54962797
......@@ -55,15 +55,25 @@ Python example to validate a projection file:
```python:../scripts/validate_file.py
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 pathlib import Path
FILE = Path("./examples/generated/example_projection.json")
FILE_H = Path("./examples/generated/example_header.json")
FILE_P = Path("./examples/generated/example_projection.json")
FILE_S = Path("./examples/generated/example_source.json")
def main():
source_validator = get_source_validator()
source_validator.file(FILE_S)
projection_validator = get_projection_validator()
projection_validator.file(FILE)
projection_validator.file(FILE_P)
header_validator = get_header_validator()
header_validator.file(FILE_H)
if __name__ == "__main__":
......
examples/generated/example_header.json
View file @ 54962797
{
"uuid": ""
"uuid": "0060361f-056d-11f0-b60b-f46d3febaf36"
}
\ No newline at end of file
examples/generated/example_projection.json
View file @ 54962797
......@@ -24,13 +24,19 @@
"y": 0.0,
"z": 0.0
},
"focal_spot_orientation_quat": {
"w": 0.0,
"x": 0.0,
"y": 0.0,
"z": 0.0
},
"focal_spot_position_mm": {
"x": 0.0,
"y": 0.0,
"z": 0.0
},
"header": {
"uuid": ""
"uuid": "005f11bd-056d-11f0-b60b-f46d3febaf36"
}
}
}
\ No newline at end of file
examples/generated/example_roi.json
View file @ 54962797
{
"header": {
"uuid": ""
"uuid": "00670fe0-056d-11f0-b60b-f46d3febaf36"
},
"roi_center_position_mm": [
0.0,
......
pyproject.toml
View file @ 54962797
[project]
name = "thd-json"
version = "0.1.10"
version = "0.1.11"
description = "THD JSON schema and validation tools."
authors = [
{ name = "swittl", email = "simon.wittl@th-deg.de" }
......@@ -14,6 +14,7 @@ dependencies = [
"numpy>=2.1.3",
"pillow>=11.0.0",
"hatchling>=1.26.3",
"jsonref>=1.1.0",
]
[project.scripts]
......
scripts/generate_example_data.py
View file @ 54962797
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.header import get_header_validator, generate_header
from thd_json.source import get_source_validator
from thd_json.detector import get_detector_validator
from thd_json.roi import get_roi_validator
......@@ -12,6 +12,16 @@ from pathlib import Path
SAVE_FOLDER = Path("./examples/generated")
def set_uuid(src: dict):
for k, v in src.items():
if isinstance(v, dict):
set_uuid(v)
if k == "uuid":
header = generate_header()
src[k] = header.uuid
def main():
for name, get_validator in [
("projection", get_projection_validator),
......@@ -28,6 +38,7 @@ def main():
@given(strategy)
def schema(data):
with open(SAVE_FOLDER / f"example_{name}.json", "w") as f:
set_uuid(data)
json.dump(data, f, indent=4)
return
......
scripts/validate_file.py
View file @ 54962797
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 pathlib import Path
FILE = Path("./examples/generated/example_projection.json")
FILE_H = Path("./examples/generated/example_header.json")
FILE_P = Path("./examples/generated/example_projection.json")
FILE_S = Path("./examples/generated/example_source.json")
def main():
source_validator = get_source_validator()
source_validator.file(FILE_S)
projection_validator = get_projection_validator()
projection_validator.file(FILE)
projection_validator.file(FILE_P)
header_validator = get_header_validator()
header_validator.file(FILE_H)
if __name__ == "__main__":
......
src/thd_json/detector/detector.json
View file @ 54962797
......@@ -2,8 +2,8 @@
"$schema": "http://json-schema.org/draft-07/schema#",
"title": "THD Detector File Schema",
"type": "object",
"version": "0.1.9",
"date": "28.11.2024",
"version": "0.1.11",
"date": "20.03.2025",
"properties": {
"pixel_pitch_mm": {
"type": "object",
......
src/thd_json/header/header.json
View file @ 54962797
......@@ -2,8 +2,8 @@
"$schema": "http://json-schema.org/draft-07/schema#",
"title": "THD Data Metadata Header File Schema",
"type": "object",
"version": "0.1.9",
"date": "28.11.2024",
"version": "0.1.11",
"date": "20.03.2025",
"properties": {
"timestamp": {
"type": "string",
......
src/thd_json/image/image.json
View file @ 54962797
......@@ -2,8 +2,8 @@
"$schema": "http://json-schema.org/draft-07/schema#",
"title": "THD Projection Image File Schema",
"type": "object",
"version": "0.1.9",
"date": "28.11.2024",
"version": "0.1.11",
"date": "20.03.2025",
"properties": {
"header": {
"$ref": "../header/header.json"
......
src/thd_json/projection/projection.json
View file @ 54962797
......@@ -2,24 +2,23 @@
"$schema": "http://json-schema.org/draft-07/schema#",
"title": "THD Projection File Schema",
"type": "object",
"version": "0.1.9",
"date": "28.11.2024",
"version": "0.1.11",
"date": "20.03.2025",
"properties": {
"image": {
"$ref": "./image/image.json"
"$ref": "../image/image.json"
},
"projection_geometry": {
"$ref": "./projection_geometry/projection_geometry.json"
"$ref": "../projection_geometry/projection_geometry.json"
},
"projection_geometry_nominal":
{
"$ref": "./projection_geometry/projection_geometry.json"
"projection_geometry_nominal": {
"$ref": "../projection_geometry/projection_geometry.json"
},
"detector": {
"$ref": "./detector/detector.json"
"$ref": "../detector/detector.json"
},
"source": {
"$ref": "./source/source.json"
"$ref": "../source/source.json"
}
},
"required": [
......
src/thd_json/projection_geometry/projection_geometry.json
View file @ 54962797
......@@ -2,8 +2,8 @@
"$schema": "http://json-schema.org/draft-07/schema#",
"title": "THD Projection Geometry File Schema",
"type": "object",
"version": "0.1.9",
"date": "28.11.2024",
"version": "0.1.11",
"date": "20.03.2025",
"properties": {
"header": {
"$ref": "../header/header.json"
......
src/thd_json/roi/roi.json
View file @ 54962797
......@@ -2,14 +2,14 @@
"$schema": "http://json-schema.org/draft-07/schema#",
"title": "THD ROI File Schema",
"type": "object",
"version": "0.1.9",
"date": "28.11.2024",
"version": "0.1.11",
"date": "20.03.2025",
"properties": {
"header": {
"$ref": "./header/header.json"
"$ref": "../header/header.json"
},
"volume": {
"$ref": "./volume/volume.json"
"$ref": "../volume/volume.json"
},
"roi_center_position_mm": {
"type": "array",
......
src/thd_json/source/source.json
View file @ 54962797
......@@ -2,8 +2,8 @@
"$schema": "http://json-schema.org/draft-07/schema#",
"title": "THD X-Ray Source File Schema",
"type": "object",
"version": "0.1.9",
"date": "28.11.2024",
"version": "0.1.11",
"date": "20.03.2025",
"properties": {
"voltage_kv": {
"type": "number",
......@@ -12,7 +12,7 @@
},
"current_ma": {
"type": "number",
"description": "Source current in µA.",
"description": "Source current in \u00c2\u00b5A.",
"minimum": 0.001
}
},
......
src/thd_json/validation.py
View file @ 54962797
import json
from pathlib import Path
from jsonschema import ValidationError, RefResolver
from jsonschema import ValidationError
from jsonschema.validators import Draft202012Validator
import jsonref
class Validator:
......@@ -11,20 +12,14 @@ class Validator:
print(f"Validator for schema: {json_schema} \nSuffix: {json_suffix}\n")
def file(self, file_path: Path) -> bool:
with (
open(str(self.json_schema)) as schema_file,
open(str(file_path)) as data_file,
):
schema = json.load(schema_file)
with open(str(file_path)) as data_file:
data = json.load(data_file)
schema_path = self.json_schema.parent.absolute().as_uri()
resolver = RefResolver(base_uri=schema_path, referrer=schema)
self.json_schema.parent.absolute().as_uri() + "/"
schema = self.get_schema()
try:
Draft202012Validator(
schema=schema,
format_checker=Draft202012Validator.FORMAT_CHECKER,
resolver=resolver,
).validate(data)
print(f"Validate file: {file_path.parent} / {file_path.name}\n")
......@@ -40,29 +35,7 @@ class Validator:
return True
def get_schema(self):
schema_path = self.json_schema.parent.absolute().as_uri()
schema_path = self.json_schema.parent.absolute().as_uri() + "/"
with open(str(self.json_schema)) as schema_file:
schema = json.load(schema_file)
resolver = RefResolver(base_uri=schema_path, referrer=schema)
return self.resolve_ref(resolver, schema)
def resolve_ref(self, resolver, schema_part):
if isinstance(schema_part, dict) and "$ref" in schema_part:
# Resolve the reference
ref = schema_part["$ref"]
with resolver.resolving(ref) as resolved:
return self.resolve_ref(
resolver, resolved
) # Recursively resolve nested references
elif isinstance(schema_part, dict):
# Resolve each value in the dictionary
return {
key: self.resolve_ref(resolver, value)
for key, value in schema_part.items()
}
elif isinstance(schema_part, list):
# Resolve each item in the list
return [self.resolve_ref(resolver, item) for item in schema_part]
return schema_part
schema = jsonref.load(schema_file, schema_path)
return schema
src/thd_json/volume/volume.json
View file @ 54962797
......@@ -2,8 +2,8 @@
"$schema": "http://json-schema.org/draft-07/schema#",
"title": "THD Projection Volume File Schema",
"type": "object",
"version": "0.1.9",
"date": "28.11.2024",
"version": "0.1.11",
"date": "20.03.2025",
"properties": {
"header": {
"$ref": "../header/header.json"
......
uv.lock
View file @ 54962797
......@@ -68,6 +68,15 @@ version = "0.3"
source = { registry = "https://pypi.org/simple" }
sdist = { url = "https://files.pythonhosted.org/packages/2a/04/855eecfdd379ff774ce86770808c6663ad4fdf14c43ed4e6fd7156aa5cf9/json_schema-0.3.tar.gz", hash = "sha256:a164efbb405f535615e58aff191b55fbfdad61d2ff0e7bfce6acf086358ca4b3", size = 5425 }
[[package]]
name = "jsonref"
version = "1.1.0"
source = { registry = "https://pypi.org/simple" }
sdist = { url = "https://files.pythonhosted.org/packages/aa/0d/c1f3277e90ccdb50d33ed5ba1ec5b3f0a242ed8c1b1a85d3afeb68464dca/jsonref-1.1.0.tar.gz", hash = "sha256:32fe8e1d85af0fdefbebce950af85590b22b60f9e95443176adbde4e1ecea552", size = 8814 }
wheels = [
{ url = "https://files.pythonhosted.org/packages/0c/ec/e1db9922bceb168197a558a2b8c03a7963f1afe93517ddd3cf99f202f996/jsonref-1.1.0-py3-none-any.whl", hash = "sha256:590dc7773df6c21cbf948b5dac07a72a251db28b0238ceecce0a2abfa8ec30a9", size = 9425 },
]
[[package]]
name = "jsonschema"
version = "4.23.0"
......@@ -347,13 +356,14 @@ wheels = [
[[package]]
name = "thd-json"
version = "0.1.9"
version = "0.1.11"
source = { editable = "." }
dependencies = [
{ name = "hatchling" },
{ name = "hypothesis" },
{ name = "hypothesis-jsonschema" },
{ name = "json-schema" },
{ name = "jsonref" },
{ name = "jsonschema" },
{ name = "numpy" },
{ name = "pillow" },
......@@ -371,6 +381,7 @@ requires-dist = [
{ name = "hypothesis", specifier = ">=6.119.0" },
{ name = "hypothesis-jsonschema", specifier = ">=0.23.1" },
{ name = "json-schema", specifier = ">=0.3" },
{ name = "jsonref", specifier = ">=1.1.0" },
{ name = "jsonschema", specifier = ">=4.23.0" },
{ name = "numpy", specifier = ">=2.1.3" },
{ name = "numpy", marker = "extra == 'load'", specifier = ">=2.1.3" },
......