diff --git a/.gitignore b/.gitignore
index d87d85c8..e51818a0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -191,3 +191,9 @@ ipynb-playground/
# widget (JS build artifacts)
node_modules/
widget/src/quantem/widget/static/
+
+# Playwright testing
+playwright-report/
+playwright/
+test-results/
+playwright*.config.ts
diff --git a/src/quantem/core/io/file_readers.py b/src/quantem/core/io/file_readers.py
index cb36f1de..91d93eeb 100644
--- a/src/quantem/core/io/file_readers.py
+++ b/src/quantem/core/io/file_readers.py
@@ -138,6 +138,41 @@ def read_2d(
return dataset
+def _find_4d_dataset(group: h5py.Group, path: list[str] | None = None) -> tuple[list[str], h5py.Dataset] | None:
+ """Recursively search for a 4D dataset in an HDF5 group."""
+ if path is None:
+ path = []
+ for key in group.keys():
+ item = group[key]
+ current_path = path + [key]
+ if isinstance(item, h5py.Dataset):
+ if item.ndim == 4:
+ return current_path, item
+ elif isinstance(item, h5py.Group):
+ result = _find_4d_dataset(item, current_path)
+ if result is not None:
+ return result
+ return None
+
+
+def _find_calibration(group: h5py.Group, path: list[str] | None = None) -> tuple[list[str], h5py.Group] | None:
+ """Recursively search for a calibration group containing R_pixel_size and Q_pixel_size."""
+ if path is None:
+ path = []
+ for key in group.keys():
+ item = group[key]
+ current_path = path + [key]
+ if isinstance(item, h5py.Group):
+ # Check if this group has calibration keys
+ if "R_pixel_size" in item and "Q_pixel_size" in item:
+ return current_path, item
+ # Recurse into subgroups
+ result = _find_calibration(item, current_path)
+ if result is not None:
+ return result
+ return None
+
+
def read_emdfile_to_4dstem(
file_path: str | PathLike,
data_keys: list[str] | None = None,
@@ -146,42 +181,73 @@ def read_emdfile_to_4dstem(
"""
File reader for legacy `emdFile` / `py4DSTEM` files.
+ If data_keys and calibration_keys are not provided, the function will
+ automatically search for a 4D dataset and calibration metadata.
+
Parameters
----------
file_path: str | PathLike
Path to data
+ data_keys: list[str], optional
+ List of keys to navigate to the data. If None, auto-detects.
+ calibration_keys: list[str], optional
+ List of keys to navigate to calibration. If None, auto-detects.
Returns
--------
Dataset4dstem
"""
with h5py.File(file_path, "r") as file:
- # Access the data directly
- data_keys = ["datacube_root", "datacube", "data"] if data_keys is None else data_keys
- print("keys: ", data_keys)
- try:
- data = file
- for key in data_keys:
- data = data[key] # type: ignore
- except KeyError:
- raise KeyError(f"Could not find key {data_keys} in {file_path}")
-
- # Access calibration values directly
- calibration_keys = (
- ["datacube_root", "metadatabundle", "calibration"]
- if calibration_keys is None
- else calibration_keys
- )
- try:
- calibration = file
- for key in calibration_keys:
- calibration = calibration[key] # type: ignore
- except KeyError:
- raise KeyError(f"Could not find calibration key {calibration_keys} in {file_path}")
- r_pixel_size = calibration["R_pixel_size"][()] # type: ignore
- q_pixel_size = calibration["Q_pixel_size"][()] # type: ignore
- r_pixel_units = calibration["R_pixel_units"][()] # type: ignore
- q_pixel_units = calibration["Q_pixel_units"][()] # type: ignore
+ # Auto-detect or use provided data keys
+ if data_keys is None:
+ result = _find_4d_dataset(file)
+ if result is None:
+ raise KeyError(f"Could not find any 4D dataset in {file_path}")
+ data_keys, data = result
+ else:
+ try:
+ data = file
+ for key in data_keys:
+ data = data[key] # type: ignore
+ except KeyError:
+ raise KeyError(f"Could not find key {data_keys} in {file_path}")
+
+ # Auto-detect or use provided calibration keys
+ if calibration_keys is None:
+ result = _find_calibration(file)
+ if result is None:
+ # No calibration found, use defaults
+ r_pixel_size = 1.0
+ q_pixel_size = 1.0
+ r_pixel_units = "pixels"
+ q_pixel_units = "pixels"
+ else:
+ calibration_keys, calibration = result
+ r_pixel_size = calibration["R_pixel_size"][()] # type: ignore
+ q_pixel_size = calibration["Q_pixel_size"][()] # type: ignore
+ r_pixel_units = calibration.get("R_pixel_units", [()])
+ if hasattr(r_pixel_units, "__getitem__"):
+ r_pixel_units = r_pixel_units[()]
+ q_pixel_units = calibration.get("Q_pixel_units", [()])
+ if hasattr(q_pixel_units, "__getitem__"):
+ q_pixel_units = q_pixel_units[()]
+ else:
+ try:
+ calibration = file
+ for key in calibration_keys:
+ calibration = calibration[key] # type: ignore
+ except KeyError:
+ raise KeyError(f"Could not find calibration key {calibration_keys} in {file_path}")
+ r_pixel_size = calibration["R_pixel_size"][()] # type: ignore
+ q_pixel_size = calibration["Q_pixel_size"][()] # type: ignore
+ r_pixel_units = calibration["R_pixel_units"][()] # type: ignore
+ q_pixel_units = calibration["Q_pixel_units"][()] # type: ignore
+
+ # Decode bytes to string if needed
+ if isinstance(r_pixel_units, bytes):
+ r_pixel_units = r_pixel_units.decode("utf-8")
+ if isinstance(q_pixel_units, bytes):
+ q_pixel_units = q_pixel_units.decode("utf-8")
dataset = Dataset4dstem.from_array(
array=data,
diff --git a/src/quantem/core/utils/validators.py b/src/quantem/core/utils/validators.py
index 02f8a935..33c2c83e 100644
--- a/src/quantem/core/utils/validators.py
+++ b/src/quantem/core/utils/validators.py
@@ -1,3 +1,5 @@
+from __future__ import annotations
+
import os
from pathlib import Path
from typing import TYPE_CHECKING, Any, Optional, TypeAlias, Union, overload
@@ -12,6 +14,7 @@
if TYPE_CHECKING:
import cupy as cp
import torch
+
TensorLike: TypeAlias = ArrayLike | torch.Tensor
else:
TensorLike: TypeAlias = ArrayLike
@@ -20,6 +23,7 @@
if config.get("has_cupy"):
import cupy as cp
+
# --- Dataset Validation Functions ---
def ensure_valid_array(
array: "np.ndarray | cp.ndarray", dtype: DTypeLike = None, ndim: int | None = None
diff --git a/uv.lock b/uv.lock
index 29931da7..66714a13 100644
--- a/uv.lock
+++ b/uv.lock
@@ -2619,10 +2619,16 @@ version = "0.0.1"
source = { editable = "widget" }
dependencies = [
{ name = "anywidget" },
+ { name = "numpy" },
+ { name = "traitlets" },
]
[package.metadata]
-requires-dist = [{ name = "anywidget", specifier = ">=0.9.0" }]
+requires-dist = [
+ { name = "anywidget", specifier = ">=0.9.0" },
+ { name = "numpy", specifier = ">=2.0.0" },
+ { name = "traitlets", specifier = ">=5.0.0" },
+]
[[package]]
name = "referencing"
diff --git a/widget/js/index.jsx b/widget/js/index.jsx
deleted file mode 100644
index a3341f63..00000000
--- a/widget/js/index.jsx
+++ /dev/null
@@ -1,33 +0,0 @@
-import * as React from "react";
-import * as ReactDOM from "react-dom/client";
-
-function Widget({ model }) {
- const [count, setCount] = React.useState(model.get("count"));
-
- React.useEffect(() => {
- const onChange = () => setCount(model.get("count"));
- model.on("change:count", onChange);
- return () => model.off("change:count", onChange);
- }, [model]);
-
- const handleClick = () => {
- model.set("count", count + 1);
- model.save_changes();
- };
-
- return (
-
-
quantem.widget
-
Count: {count}
-
-