From 860457cdc6189dd5313fc688d145afa14e36ea95 Mon Sep 17 00:00:00 2001
From: swittl <simon.wittl@th-deg.de>
Date: Fri, 21 Mar 2025 10:54:27 +0100
Subject: [PATCH] added overwrite / inserts
---
examples/header.h5 | Bin 24928 -> 800 bytes
examples/projection_geometry.h5 | Bin 186352 -> 186352 bytes
pyproject.toml | 2 +-
src/h5schemas/header/add_header.py | 4 +-
src/h5schemas/header/overwrite_header.py | 14 +++
src/h5schemas/image/overwrite_image.py | 20 ++++
.../add_projection_geometry.py | 11 +++
.../overwrite_projection_geometry.py | 88 ++++++++++++++++++
8 files changed, 137 insertions(+), 2 deletions(-)
create mode 100644 src/h5schemas/header/overwrite_header.py
create mode 100644 src/h5schemas/image/overwrite_image.py
create mode 100644 src/h5schemas/projection_geometry/overwrite_projection_geometry.py
diff --git a/examples/header.h5 b/examples/header.h5
index 55f849af30b411def5615dca45ce8811be91d386..82daee09f5d9bab4d4ef6cf1c24d6067e7457f8a 100644
GIT binary patch
delta 63
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literal 24928
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diff --git a/examples/projection_geometry.h5 b/examples/projection_geometry.h5
index 33fa0d029f9c06080eb024291a542da0e34bbf58..881fcc6f7961040df0d860fa0471cbe8ddce7644 100644
GIT binary patch
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diff --git a/pyproject.toml b/pyproject.toml
index e4a6fac..75d5612 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
[project]
name = "h5schemas"
-version = "0.1.15"
+version = "0.1.16"
description = "Add your description here"
readme = "README.md"
authors = [
diff --git a/src/h5schemas/header/add_header.py b/src/h5schemas/header/add_header.py
index d95bc9e..892043a 100644
--- a/src/h5schemas/header/add_header.py
+++ b/src/h5schemas/header/add_header.py
@@ -48,10 +48,12 @@ def uuid_time_from_json_header(json_header_obj: header.JsonHeader) -> tuple[str,
if __name__ == "__main__":
- test_file = File("./examples/header.h5", "w")
+ from h5schemas.header.overwrite_header import overwrite_header_at_index
+ test_file = File("./examples/header.h5", "a")
init_header(test_file)
add_header_sample(test_file, None)
add_header_sample(test_file, None)
add_header_sample(test_file, None)
add_header_sample(test_file, *uuid_time_from_json_header(header.generate_header()))
+ overwrite_header_at_index(test_file, 0, 'test', 0.0)
\ No newline at end of file
diff --git a/src/h5schemas/header/overwrite_header.py b/src/h5schemas/header/overwrite_header.py
new file mode 100644
index 0000000..9e5ee8c
--- /dev/null
+++ b/src/h5schemas/header/overwrite_header.py
@@ -0,0 +1,14 @@
+from h5py import File, Group
+from h5schemas.header.add_header import check_uuid_time_stamp
+
+
+def overwrite_header_at_index(
+ h5_file: File | Group, index: int, uuid: str | None, timestamp: float | None = None
+):
+ uuid, timestamp = check_uuid_time_stamp(uuid, timestamp)
+
+ dst = h5_file["uuid"]
+ dst[index] = uuid
+
+ dst = h5_file["timestamp"]
+ dst[index] = timestamp
\ No newline at end of file
diff --git a/src/h5schemas/image/overwrite_image.py b/src/h5schemas/image/overwrite_image.py
new file mode 100644
index 0000000..e9238c0
--- /dev/null
+++ b/src/h5schemas/image/overwrite_image.py
@@ -0,0 +1,20 @@
+from h5py import File, Group
+import numpy as np
+from pathlib import Path
+
+from h5schemas.header.overwrite_header import overwrite_header_at_index
+
+def overwrite_image_at_index(h5_file: File | Group,
+ image: Path | np.ndarray,
+ index: int,
+ uuid: str | None = None,
+ timestamp: int | None = None,
+):
+ if isinstance(image, Path):
+ dst = h5_file["image_path"]
+ dst[index] = str(image)
+ else:
+ dst = h5_file["image_array"]
+ dst[index] = image
+
+ overwrite_header_at_index(h5_file["header"], index, uuid, timestamp)
\ No newline at end of file
diff --git a/src/h5schemas/projection_geometry/add_projection_geometry.py b/src/h5schemas/projection_geometry/add_projection_geometry.py
index 45a608c..32f8bff 100644
--- a/src/h5schemas/projection_geometry/add_projection_geometry.py
+++ b/src/h5schemas/projection_geometry/add_projection_geometry.py
@@ -101,6 +101,7 @@ def add_projection_geometry_sample(
if __name__ == "__main__":
+ from h5schemas.projection_geometry.overwrite_projection_geometry import overwrite_projection_geometry_at_index
test_file = File("./examples/projection_geometry.h5", "w")
init_projection_geometry(test_file)
add_projection_geometry_sample(
@@ -113,3 +114,13 @@ if __name__ == "__main__":
add_projection_geometry_sample(
test_file, [0.0, 1.0, 2.0], [3.0, 4.0, 5.0, 6.0], [7.0, 8.0, 9.0]
)
+
+ overwrite_projection_geometry_at_index(
+ test_file,
+ 0,
+ [1.0, 1.0, 1.0],
+ [3.0, 4.0, 5.0, 6.0],
+ [1.0, 1.0, 1.0],
+ [10.0, 11.0, 12.0, 13],
+ uuid='test',
+ )
\ No newline at end of file
diff --git a/src/h5schemas/projection_geometry/overwrite_projection_geometry.py b/src/h5schemas/projection_geometry/overwrite_projection_geometry.py
new file mode 100644
index 0000000..3a216af
--- /dev/null
+++ b/src/h5schemas/projection_geometry/overwrite_projection_geometry.py
@@ -0,0 +1,88 @@
+from h5py import File, Group
+import numpy as np
+from h5schemas.header.overwrite_header import overwrite_header_at_index
+
+
+
+
+def overwrite_projection_geometry_at_index(
+ h5_file: File | Group,
+ index: int,
+ detector_center_position_mm: tuple[float, float, float],
+ detector_center_orientation_quat: tuple[float, float, float, float],
+ focal_spot_position_mm: tuple[float, float, float],
+ focal_spot_orientation_quat: tuple[float, float, float, float] | None = None,
+ uuid: str | None = None,
+ timestamp: float | None = None,
+):
+ update_values = list()
+
+ def insert_update(values):
+ dst, value = values
+ dst[index] = value
+
+ update_values.append(
+ [h5_file["detector_center_position_mm/x"], detector_center_position_mm[0]]
+ )
+ update_values.append(
+ [h5_file["detector_center_position_mm/y"], detector_center_position_mm[1]]
+ )
+ update_values.append(
+ [h5_file["detector_center_position_mm/z"], detector_center_position_mm[2]]
+ )
+
+ update_values.append(
+ [
+ h5_file["detector_center_orientation_quat/x"],
+ detector_center_orientation_quat[0],
+ ]
+ )
+ update_values.append(
+ [
+ h5_file["detector_center_orientation_quat/y"],
+ detector_center_orientation_quat[1],
+ ]
+ )
+ update_values.append(
+ [
+ h5_file["detector_center_orientation_quat/z"],
+ detector_center_orientation_quat[2],
+ ]
+ )
+ update_values.append(
+ [
+ h5_file["detector_center_orientation_quat/w"],
+ detector_center_orientation_quat[3],
+ ]
+ )
+
+ update_values.append(
+ [h5_file["focal_spot_position_mm/x"], focal_spot_position_mm[0]]
+ )
+ update_values.append(
+ [h5_file["focal_spot_position_mm/y"], focal_spot_position_mm[1]]
+ )
+ update_values.append(
+ [h5_file["focal_spot_position_mm/z"], focal_spot_position_mm[2]]
+ )
+
+ if focal_spot_orientation_quat is None:
+ focal_spot_orientation_quat = (0.0, 0.0, 0.0, 1.0)
+
+ update_values.append(
+ [h5_file["focal_spot_orientation_quat/x"], focal_spot_orientation_quat[0]]
+ )
+ update_values.append(
+ [h5_file["focal_spot_orientation_quat/y"], focal_spot_orientation_quat[1]]
+ )
+ update_values.append(
+ [h5_file["focal_spot_orientation_quat/z"], focal_spot_orientation_quat[2]]
+ )
+ update_values.append(
+ [h5_file["focal_spot_orientation_quat/w"], focal_spot_orientation_quat[3]]
+ )
+
+ for value in update_values:
+ insert_update(value)
+
+ overwrite_header_at_index(h5_file['header'], index, uuid, timestamp)
\ No newline at end of file
--
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