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  • roboct-public/artist-api
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pyproject.toml
View file @ 5b27a608
......@@ -28,4 +28,4 @@ build-backend = "hatchling.build"
[tool.uv.sources]
thd-json = { git = "https://mygit.th-deg.de/roboct-public/roboct-schemas" }
h5schemas = { git = "https://mygit.th-deg.de/roboct/definitions/h5schemas" }
h5schemas = { git = "https://mygit.th-deg.de/roboct-public/roboct-h5" }
src/artist_pythonlib/api.py
View file @ 5b27a608
......@@ -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
)
src/artist_pythonlib/geometries/thd_format.py
View file @ 5b27a608
......@@ -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
uv.lock
View file @ 5b27a608
......@@ -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" },
......