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Add polar transform and pair distribution function analysis #177

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10901b8
adding support for 3d dm4 files --> 4dstem
cophus Dec 2, 2025
9de8ec3
initial construction of polar4dstem class
cophus Dec 3, 2025
a1c4f7f
Changing sampling direction for polar4dstem
cophus Dec 4, 2025
bb68208
initial commit for RDF class
cophus Dec 4, 2025
f982a28
initial pdf code + f parameters
ehrhardtkm Dec 16, 2025
dad7523
origin finding and pdf updates
ehrhardtkm Jan 8, 2026
b9e79c7
pixel calibration bug fix
ehrhardtkm Jan 12, 2026
f9a26ab
make torch native and general cleanup
ehrhardtkm Feb 20, 2026
1150740
additional cleanup
ehrhardtkm Feb 20, 2026
fb0e5c7
added comments for increased clarity
ehrhardtkm Feb 27, 2026
0384cf7
minor fixes
ehrhardtkm Mar 17, 2026
30807c9
origin finding speedup
ehrhardtkm Mar 17, 2026
2c81b59
Merge branch 'nanobeam' into polar4dstem
ehrhardtkm Mar 17, 2026
3603d71
make calculate_Gr use precomputed bg
ehrhardtkm Mar 17, 2026
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19 changes: 15 additions & 4 deletions src/quantem/core/datastructures/dataset4dstem.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,12 @@

from quantem.core.datastructures.dataset2d import Dataset2d
from quantem.core.datastructures.dataset4d import Dataset4d
from quantem.core.datastructures.polar4dstem import dataset4dstem_polar_transform

from quantem.core.datastructures.polar4dstem import (
auto_origin_id as _auto_origin_id,
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)
from quantem.core.datastructures.polar4dstem import (
dataset4dstem_polar_transform as _dataset4dstem_polar_transform,
)
from quantem.core.utils.validators import ensure_valid_array
from quantem.core.visualization import show_2d
from quantem.core.visualization.visualization_utils import ScalebarConfig
Expand Down Expand Up @@ -74,7 +78,7 @@ def __init__(
_token : object | None, optional
Token to prevent direct instantiation, by default None
"""
mdata_keys_4dstem = ["q_to_r_rotation_ccw_deg", 'q_transpose', "ellipticity"]
mdata_keys_4dstem = ["q_to_r_rotation_ccw_deg", "q_transpose", "ellipticity"]
for k in mdata_keys_4dstem:
if k not in metadata.keys():
metadata[k] = None
Expand Down Expand Up @@ -754,5 +758,12 @@ def median_filter_masked_pixels(self, mask: np.ndarray, kernel_width: int = 3):
self.array[:, :, x_min:x_max, y_min:y_max], axis=(2, 3)
)

def auto_origin_id(self, **kwargs):
"""Find diffraction centers by minimizing angular intensity variation.

Delegates to the module-level ``auto_origin_id`` function.
See its docstring for full parameter details.
"""
return _auto_origin_id(self, **kwargs)

polar_transform = dataset4dstem_polar_transform
polar_transform = _dataset4dstem_polar_transform
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