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Load/make thumbnail for any 2D image #56

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Jul 31, 2024
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Load/make thumbnail for any 2D image #56

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25 changes: 20 additions & 5 deletions src/opera_utils/h5explorer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,13 @@ def __dir__(self):
return list(self._attr_cache.keys())


def create_explorer_widget(hf: h5py.File, load_less_than: float = 1e3):
def create_explorer_widget(
hf: h5py.File,
load_less_than: float = 1e3,
subsample: tuple[int, int] = (10, 10),
cmap: str = "gray",
interpolation: str = "nearest",
):
"""Make a widget in Jupyter to explore a h5py file.

Requires `ipywidgets` and `matplotlib` to be installed.
Expand All @@ -88,10 +94,17 @@ def create_explorer_widget(hf: h5py.File, load_less_than: float = 1e3):
import ipywidgets as widgets
import matplotlib.pyplot as plt

sub_row, sub_col = subsample

def _make_thumbnail(image):
# Create a thumbnail of the dataset
fig, ax = plt.subplots(figsize=(5, 5))
ax.imshow(image, cmap="gray", vmax=np.nanpercentile(image, 99))
ax.imshow(
image,
cmap=cmap,
interpolation=interpolation,
vmax=np.nanpercentile(image, 99),
)
ax.axis("off")
buf = BytesIO()
plt.savefig(buf, format="png", dpi=150)
Expand Down Expand Up @@ -120,10 +133,12 @@ def _add_widgets(item, level: int = 0):
content += f"<br>Value: {item[()]}"
html_widget = widgets.HTML(content)

if not item.ndim == 2 or not item.dtype == np.complex64:
if not item.ndim == 2:
return html_widget
# If the dataset is a 2D complex array, make a thumbnail
image_widget = _make_thumbnail(np.abs(item[::5, ::10]))
# If the dataset is a 2D array, make a thumbnail
# Handle the real or complex the same
data = np.abs(item[::sub_row, ::sub_col])
image_widget = _make_thumbnail(data)
return widgets.VBox([image_widget, html_widget])

else:
Expand Down