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fix attenuation + root #881

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Merged
dsarrut merged 4 commits into from
Jan 15, 2026
Merged

fix attenuation + root #881

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74b4419
Fix unit conversion in photon attenuation script (mm^-1 to cm^-1)
dsarrut Jan 9, 2026
ef76069
replace root mktree with brackets
dsarrut Jan 14, 2026
e4132f0
Fix escape character in ASCII art and adjust gantry angle shape for n…
dsarrut Jan 14, 2026
9a8c968
Refactor gantry_angles_deg to use nested lists in test054_parallel_ge…
dsarrut Jan 15, 2026
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2 changes: 1 addition & 1 deletion opengate/bin/opengate_photon_attenuation_image.py
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Original file line number Diff line number Diff line change
Expand Up @@ -106,7 +106,7 @@ def go(
)
if mm:
arr = itk.array_view_from_image(image)
arr = arr * 10
arr = arr / 10
new_image = itk.image_from_array(arr)
new_image.SetSpacing(image.GetSpacing())
new_image.SetOrigin(image.GetOrigin())
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9 changes: 6 additions & 3 deletions opengate/contrib/root_helpers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -222,9 +222,11 @@ def root_split_tree_by_branch(
)

with uproot.recreate(high_val_path) as high_file:
high_file.mktree(tree_name, high_val_events)
# high_file.mktree(tree_name, high_val_events)
high_file[tree_name] = high_val_events
with uproot.recreate(low_val_path) as low_file:
low_file.mktree(tree_name, low_val_events)
# low_file.mktree(tree_name, low_val_events)
low_file[tree_name] = low_val_events

if verbose:
logger.info(f"Successfully wrote high-value events to '{high_val_path}'.")
Expand Down Expand Up @@ -287,7 +289,8 @@ def root_merge_trees(
merged_data = ak.concatenate(all_data_to_merge)

with uproot.recreate(output_path) as output_file:
output_file.mktree(tree_name, merged_data)
# output_file.mktree(tree_name, merged_data)
output_file[tree_name] = merged_data

if verbose:
logger.info(
Expand Down
2 changes: 1 addition & 1 deletion opengate/tests/src/actors/test030_dose_motion_dynamic_param.py
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Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,7 @@
sim.run_timing_intervals = [
(i * interval_length, (i + 1) * interval_length) for i in range(n)
]
gantry_angles_deg = [i * 20 for i in range(n)]
gantry_angles_deg = [[i * 20] for i in range(n)]
(
dynamic_translations,
dynamic_rotations,
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5 changes: 3 additions & 2 deletions opengate/tests/src/actors/test030_dose_motion_dynamic_param_custom.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ def print_face():
print("**** ^^^ ^^^ ****")
print("**** O O ****")
print("**** L ****")
print("**** \_____/ ****")
print("**** \\_____/ ****")
print("**** V ****")
print("*******************")

Expand Down Expand Up @@ -148,7 +148,8 @@ def apply_change(self, run_id):
sim.run_timing_intervals = [
(i * interval_length, (i + 1) * interval_length) for i in range(n)
]
gantry_angles_deg = [i * 20 for i in range(n)]
# Wrap in brackets to create shape (N, 1) for newer scipy
gantry_angles_deg = [[i * 20] for i in range(n)]
# use a helper function
(
dynamic_translations,
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2 changes: 1 addition & 1 deletion opengate/tests/src/geometry/test054_parallel_geometry_proj.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@
sim.run_timing_intervals = [
(i * interval_length, (i + 1) * interval_length) for i in range(n)
]
gantry_angles_deg = [i * 20 for i in range(n)]
gantry_angles_deg = [[i * 20] for i in range(n)]
(
dynamic_translations,
dynamic_rotations,
Expand Down
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