Skip to content

change kwargs in read4stem #166

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
smribet wants to merge 1 commit into
base: dev
Choose a base branch
from
+16 −12
Open

change kwargs in read4stem #166

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
28 changes: 16 additions & 12 deletions src/quantem/core/io/file_readers.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ def read_4dstem(
Index of the dataset to load if file contains multiple datasets.
If None, automatically selects the first 4D dataset found.
**kwargs: dict
Additional keyword arguments to pass to the Dataset4dstem constructor.
Additional keyword arguments to pass to the file reader.

Copy link

@CSSFrancis CSSFrancis Jan 29, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I'd add sampling, Orgin and Units as Other Parameters:

Suggested change
Other Parameters
----------------
name : str | None, optional
A descriptive name for the dataset. If None, defaults to "4D-STEM dataset"
origin : NDArray | tuple | list | float | int | None, optional
The origin coordinates for each dimension. If None, defaults to zeros
sampling : NDArray | tuple | list | float | int | None, optional
The sampling rate/spacing for each dimension. If None, defaults to ones
units : list[str] | tuple | list | None, optional
Units for each dimension. If None, defaults to ["pixels"] * 4
signal_units : str, optional
Units for the array values, by default "arb. units"

Returns
--------
Expand All @@ -39,8 +39,12 @@ def read_4dstem(
if file_type is None:
file_type = Path(file_path).suffix.lower().lstrip(".")

sampling_override = kwargs.pop("sampling", None)
origin_override = kwargs.pop("origin", None)
units_override = kwargs.pop("units", None)

Copy link

@CSSFrancis CSSFrancis Jan 29, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
name_override = kwargs.pop("name", None)

file_reader = importlib.import_module(f"rsciio.{file_type}").file_reader
data_list = file_reader(file_path)
data_list = file_reader(file_path, **kwargs)

# If specific index provided, use it
if dataset_index is not None:
Expand Down Expand Up @@ -69,25 +73,25 @@ def read_4dstem(

imported_axes = imported_data["axes"]

sampling = kwargs.pop(
"sampling",
[ax["scale"] for ax in imported_axes],
sampling = (
sampling_override
if sampling_override is not None
else [ax["scale"] for ax in imported_axes]
Copy link

@CSSFrancis CSSFrancis Jan 29, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Not all axes have offsets and scales. For example sometimes there will be axes with non-linear scales. Then you can acess the non-linear axis via ax["axis"]

Suggested change
else [ax["scale"] for ax in imported_axes]
else [ax.get("scale", 1) for ax in imported_axes]

)
origin = kwargs.pop(
"origin",
[ax["offset"] for ax in imported_axes],
origin = (
origin_override if origin_override is not None else [ax["offset"] for ax in imported_axes]
Copy link

@CSSFrancis CSSFrancis Jan 29, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Same as above:

Not sure the policy on logging but you could output a warning that the scale is non-linear.

Suggested change
origin_override if origin_override is not None else [ax["offset"] for ax in imported_axes]
origin_override if origin_override is not None else [ax.get("offset", 0) for ax in imported_axes]

)
units = kwargs.pop(
"units",
["pixels" if ax["units"] == "1" else ax["units"] for ax in imported_axes],
units = (
Copy link

@CSSFrancis CSSFrancis Jan 29, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

All axes will have units :) and a name. That is the minimal definition.

units_override
if units_override is not None
else ["pixels" if ax["units"] == "1" else ax["units"] for ax in imported_axes]
)

dataset = Dataset4dstem.from_array(
array=imported_data["data"],
sampling=sampling,
origin=origin,
units=units,
Copy link

@CSSFrancis CSSFrancis Jan 29, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
units=units,
units=units,
name = name,

**kwargs,
)

return dataset
Expand Down