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Adding a capability of changing the bit depth of saved tiffs in sweep run #739

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Merged
dkazanc merged 2 commits into from
Jul 10, 2026
Merged

Adding a capability of changing the bit depth of saved tiffs in sweep run #739

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9b03526
adding a capability of changing the bit depth of saved tiffs in sweep…
dkazanc Jul 10, 2026
cfcfa4b
Merge branch 'main' into sweepimages_bit
dkazanc Jul 10, 2026
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13 changes: 12 additions & 1 deletion httomo/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -178,6 +178,12 @@ def check(pipeline: Union[Path, str], in_data_file: Optional[Path] = None):
is_flag=True,
help="Save intermediate images (snapshots) from some methods in the pipeline.",
)
@click.option(
"--bits_sweep_images",
type=click.INT,
default=32,
help="Change the bit depth of saved tiff images in the sweep run from default 32 bit to 16 or 8 bit tiffs.",
)
@click.option(
"--monitor",
type=click.STRING,
Expand Down Expand Up @@ -257,6 +263,7 @@ def run(
output_folder_name: Optional[Path],
gpu_id: int,
save_all: bool,
bits_sweep_images: int,
reslice_dir: Union[Path, None],
max_cpu_slices: int,
max_memory: str,
Expand Down Expand Up @@ -320,6 +327,7 @@ def run(
else pipeline
),
save_all,
bits_sweep_images,
method_wrapper_comm,
format_enum,
)
Expand Down Expand Up @@ -491,6 +499,7 @@ def generate_pipeline(
in_data_file: Path,
pipeline: Union[Path, str],
save_all: bool,
bits_sweep_images: int,
method_wrapper_comm: MPI.Comm,
pipeline_format: PipelineFormat,
) -> Pipeline:
Expand All @@ -504,7 +513,9 @@ def generate_pipeline(
pipeline_object = init_UiLayer.build_pipeline()

# perform transformations on pipeline
tr = TransformLayer(comm=method_wrapper_comm, save_all=save_all)
tr = TransformLayer(
comm=method_wrapper_comm, save_all=save_all, bits_sweep_images=bits_sweep_images
)
pipeline_object = tr.transform(pipeline_object)

return pipeline_object
Expand Down
3 changes: 3 additions & 0 deletions httomo/transform_layer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,10 +28,12 @@ def __init__(
comm: MPI.Comm,
repo=MethodDatabaseRepository(),
save_all=False,
bits_sweep_images=32,
out_dir: Optional[os.PathLike] = None,
):
self._repo = repo
self._save_all = save_all
self._bits_sweep_images = bits_sweep_images
self._comm = comm
self._out_dir = out_dir if out_dir is not None else httomo.globals.run_out_dir

Expand Down Expand Up @@ -162,6 +164,7 @@ def insert_save_images_after_sweep(self, pipeline: Pipeline) -> Pipeline:
task_id=f"saveimage_sweep_{m.task_id}",
subfolder_name="images_sweep_" + str(m.method_name),
axis=1,
bit_depth=self._bits_sweep_images,
),
)
sweep_before = True
Expand Down
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