playnano.io.formats.read_aris module

Module to decode and load .aris high-speed AFM data files into an AFMImageStack object.

The Asylum Reseach ARIS files contain multiple frames that may differ in pixel resolution. The global pixel size (from the first frame) is stored in pixel_size_nm, while per-frame overrides are stored in each entry of frame_metadata under the key frame_pixel_size_nm.

playnano.io.formats.read_aris.load_aris(file_path: Path | str, channel: str) → AFMImageStack[source]

Load image stack from a Asylum Research .aris file, scaled to nanometers.

The images are loaded, reshaped into frames, and have timestamps generated.

Parameters:

  • file_path (Path | str) – Path to the .aris file.

  • channel (str) – Channel to extract.

Returns:

Loaded AFM image stack with metadata and per-frame info.

Return type:

AFMImageStack

Notes

Pixel size may vary between frames in ARIS files. The global pixel_size_nm attribute corresponds to the first frame, while per-frame values are stored in frame_metadata.

playnano.io.formats.read_aris.load_frames_and_scaling(data: Group, info: Group, selected_ch: str) → tuple[ndarray, list[float]][source]

Load all frames for the given channel and compute per-frame pixel sizes.

Parameters:

  • data (h5py.Group) – HDF5 group with frame/channel image data.

  • info (h5py.Group) – HDF5 group containing metadata and per-frame overrides.

  • selected_ch (str) – Channel name to extract.

Returns:

3D stack array and per-frame pixel-size values (nm).

Return type:

(ndarray, list of float)