diff --git a/src/artist_pythonlib/api.py b/src/artist_pythonlib/api.py
index 5ed2e43bb4de23ac43f44fcf0124bcf454095db3..f28c0ccd6631ea0833602f400b2141f0c822017a 100644
--- a/src/artist_pythonlib/api.py
+++ b/src/artist_pythonlib/api.py
@@ -23,13 +23,17 @@ from h5py import File, Group
from artist_pythonlib.geometries import projection_geometry, thd_projection_geometry
from artist_pythonlib.common_types import PROJECTIONGEOMETRIES, SAVEMODES
from artist_pythonlib.remote_connection import Junction, _rc
-from h5schemas.projection.add_projection import init_projection_dataset, add_projection_sample
+from h5schemas.projection.add_projection import (
+ init_projection_dataset,
+ add_projection_sample,
+)
import tempfile
from artist_pythonlib.utility import load_projection
H5_INIT = True
+
class API:
def __init__(self, remote_control: Junction = None) -> None:
if remote_control is None:
@@ -68,10 +72,10 @@ class API:
if save_projection_geometry == PROJECTIONGEOMETRIES.THD:
geom = self.projection_geometry(save_projection_geometry)
- name = f'{geom["image"]["image_path"][:-4]}_{save_path.stem}'
+ name = f"{geom['image']['image_path'][:-4]}_{save_path.stem}"
save_path = save_path.parent / f"{name}.tif"
save_path_json = save_path.parent / f"{name}.json"
- geom['image']['image_path'] = save_path.name
+ geom["image"]["image_path"] = save_path.name
elif save_projection_geometry == PROJECTIONGEOMETRIES.STANDARD:
save_path_json = save_path.parent / f"{save_path.stem}.json"
@@ -90,61 +94,68 @@ class API:
self._save_image_png(save_path)
return save_path
- def save_hdf5(self,
- save_path: Path | File | Group,
- initialize_dataset: bool = False):
-
+ def save_hdf5(
+ self, save_path: Path | File | Group, initialize_dataset: bool = False
+ ):
global H5_INIT
if isinstance(save_path, Path):
- save_path = File(save_path, 'a')
+ save_path = File(save_path, "a")
- file = Path(tempfile.gettempdir()) / 'image.tif'
+ file = Path(tempfile.gettempdir()) / "image.tif"
file = self.save_image(file, save_projection_geometry=PROJECTIONGEOMETRIES.THD)
projection, current_geometry = load_projection(file)
if H5_INIT or initialize_dataset:
H5_INIT = False
- image_dimensions_px = [current_geometry['detector']['image_dimensions_px']['u'], current_geometry['detector']['image_dimensions_px']['v']]
- pixel_pitch_mm = [current_geometry['detector']['pixel_pitch_mm']['u'], current_geometry['detector']['pixel_pitch_mm']['v']]
- init_projection_dataset(save_path, False, image_dimensions_px, pixel_pitch_mm)
-
-
+ image_dimensions_px = [
+ current_geometry["detector"]["image_dimensions_px"]["u"],
+ current_geometry["detector"]["image_dimensions_px"]["v"],
+ ]
+ pixel_pitch_mm = [
+ current_geometry["detector"]["pixel_pitch_mm"]["u"],
+ current_geometry["detector"]["pixel_pitch_mm"]["v"],
+ ]
+ init_projection_dataset(
+ save_path, False, image_dimensions_px, pixel_pitch_mm
+ )
source_pos = [
- current_geometry['projection_geometry']['focal_spot_position_mm']['x'],
- current_geometry['projection_geometry']['focal_spot_position_mm']['y'],
- current_geometry['projection_geometry']['focal_spot_position_mm']['z'],
+ current_geometry["projection_geometry"]["focal_spot_position_mm"]["x"],
+ current_geometry["projection_geometry"]["focal_spot_position_mm"]["y"],
+ current_geometry["projection_geometry"]["focal_spot_position_mm"]["z"],
]
detector_pos = [
- current_geometry['projection_geometry']['detector_center_position_mm']['x'],
- current_geometry['projection_geometry']['detector_center_position_mm']['y'],
- current_geometry['projection_geometry']['detector_center_position_mm']['z'],
+ current_geometry["projection_geometry"]["detector_center_position_mm"]["x"],
+ current_geometry["projection_geometry"]["detector_center_position_mm"]["y"],
+ current_geometry["projection_geometry"]["detector_center_position_mm"]["z"],
]
source_ori = [
- current_geometry['projection_geometry']['focal_spot_orientation_quat']['x'],
- current_geometry['projection_geometry']['focal_spot_orientation_quat']['y'],
- current_geometry['projection_geometry']['focal_spot_orientation_quat']['z'],
- current_geometry['projection_geometry']['focal_spot_orientation_quat']['w'],
+ current_geometry["projection_geometry"]["focal_spot_orientation_quat"]["x"],
+ current_geometry["projection_geometry"]["focal_spot_orientation_quat"]["y"],
+ current_geometry["projection_geometry"]["focal_spot_orientation_quat"]["z"],
+ current_geometry["projection_geometry"]["focal_spot_orientation_quat"]["w"],
]
detector_ori = [
- current_geometry['projection_geometry']['detector_center_orientation_quat']['x'],
- current_geometry['projection_geometry']['detector_center_orientation_quat']['y'],
- current_geometry['projection_geometry']['detector_center_orientation_quat']['z'],
- current_geometry['projection_geometry']['detector_center_orientation_quat']['w'],
+ current_geometry["projection_geometry"]["detector_center_orientation_quat"][
+ "x"
+ ],
+ current_geometry["projection_geometry"]["detector_center_orientation_quat"][
+ "y"
+ ],
+ current_geometry["projection_geometry"]["detector_center_orientation_quat"][
+ "z"
+ ],
+ current_geometry["projection_geometry"]["detector_center_orientation_quat"][
+ "w"
+ ],
]
-
add_projection_sample(
- save_path,
- projection,
- detector_pos,
- detector_ori,
- source_pos,
- source_ori
+ save_path, projection, detector_pos, detector_ori, source_pos, source_ori
)
def _save_image_uint16(self, save_path: Path):
@@ -156,7 +167,7 @@ class API:
# self.rc.send('set imgList [Engine::Go]')
save_path_projection = str(save_path.absolute()).replace("\\", "\\\\")
self.rc.send(
- f'set imgList [Engine::Go]; Image::SaveFloatTIFF [lindex $imgList 0] {save_path_projection} True; {r"foreach i $imgList {$i Delete}"}'
+ f"set imgList [Engine::Go]; Image::SaveFloatTIFF [lindex $imgList 0] {save_path_projection} True; {r'foreach i $imgList {$i Delete}'}"
)
def _save_image_uint8(self, save_path: Path):
@@ -171,7 +182,7 @@ class API:
save_path.parent / (save_path.stem + ".json")
) # Image::SaveFile [lindex $imgList 0] [file join $env(HOME) Pictures/artistlib2.tif] true',
self.rc.send(
- f'set imgList [Engine::Go]; Image::SaveFloatTIFF [lindex $imgList 0] {save_path_projection} True; {r"foreach i $imgList {$i Delete}"}'
+ f"set imgList [Engine::Go]; Image::SaveFloatTIFF [lindex $imgList 0] {save_path_projection} True; {r'foreach i $imgList {$i Delete}'}"
)
with open(str(save_path_json), "w") as f:
@@ -186,7 +197,7 @@ class API:
# self.rc.send('set imgList [Engine::Go]')
save_path_projection = str(save_path.absolute()).replace("\\", "\\\\")
self.rc.send(
- f'set imgList [Engine::Go]; Image::SaveFloatTIFF [lindex $imgList 0] {save_path_projection} True; {r"foreach i $imgList {$i Delete}"}'
+ f"set imgList [Engine::Go]; Image::SaveFloatTIFF [lindex $imgList 0] {save_path_projection} True; {r'foreach i $imgList {$i Delete}'}"
)
# self.rc.send('foreach i $imgList {$i Delete}')
@@ -202,7 +213,7 @@ class API:
save_path.parent / (save_path.stem + ".json")
) # Image::SaveFile [lindex $imgList 0] [file join $env(HOME) Pictures/artistlib2.tif] true',
self.rc.send(
- f'set imgList [Engine::Go]; Image::SaveFloatTIFF [lindex $imgList 0] {save_path_projection} True; {r"foreach i $imgList {$i Delete}"}'
+ f"set imgList [Engine::Go]; Image::SaveFloatTIFF [lindex $imgList 0] {save_path_projection} True; {r'foreach i $imgList {$i Delete}'}"
)
with open(str(save_path_json), "w") as f:
@@ -217,7 +228,7 @@ class API:
# self.rc.send('set imgList [Engine::Go]')
save_path_projection = str(save_path.absolute()).replace("\\", "\\\\")
self.rc.send(
- f'set imgList [Engine::Go]; Image::SaveFloatTIFF [lindex $imgList 0] {save_path_projection} True; {r"foreach i $imgList {$i Delete}"}'
+ f"set imgList [Engine::Go]; Image::SaveFloatTIFF [lindex $imgList 0] {save_path_projection} True; {r'foreach i $imgList {$i Delete}'}"
)
def translate(
@@ -450,4 +461,4 @@ class API:
)
self.rc.send(
f'::XRayProject::LoadProject "{self.path_to_artist(project_file)}"'
- )
\ No newline at end of file
+ )
diff --git a/src/artist_pythonlib/geometries/thd_format.py b/src/artist_pythonlib/geometries/thd_format.py
index 5d850a31c0809a45c5813c5014a70cd26c465bf3..d0f83dd25bed4bfb895dce9f541d8418705b5996 100644
--- a/src/artist_pythonlib/geometries/thd_format.py
+++ b/src/artist_pythonlib/geometries/thd_format.py
@@ -40,7 +40,7 @@ def thd_projection_geometry(api) -> dict:
np.asarray(detector_pixel_count),
np.asarray(detector_resolution),
json_header,
- Rotation.from_matrix(source_orientation).as_quat())
-
+ Rotation.from_matrix(source_orientation).as_quat(),
+ )
return data_dict
diff --git a/uv.lock b/uv.lock
index 7e75d2e672a94703b3940e9b8b22213adf7f1b0e..a405b310156e27afd134ca4f1a77dfa972efecb8 100644
--- a/uv.lock
+++ b/uv.lock
@@ -22,7 +22,7 @@ thd = [
[package.metadata]
requires-dist = [
- { name = "h5schemas", git = "https://mygit.th-deg.de/roboct/definitions/h5schemas" },
+ { name = "h5schemas", git = "https://mygit.th-deg.de/roboct-public/roboct-h5" },
{ name = "matplotlib", specifier = "<=3.9" },
{ name = "numpy", specifier = ">=1.23" },
{ name = "pillow", specifier = ">=10.0" },
@@ -249,7 +249,7 @@ wheels = [
[[package]]
name = "h5schemas"
version = "0.1.0"
-source = { git = "https://mygit.th-deg.de/roboct/definitions/h5schemas#3624c61163e3230bd2ac42884aa7b39d2cfcdeb8" }
+source = { git = "https://mygit.th-deg.de/roboct-public/roboct-h5#3624c61163e3230bd2ac42884aa7b39d2cfcdeb8" }
dependencies = [
{ name = "h5py" },
{ name = "jsonref" },