Note

This page was generated from a Jupyter notebook. Download: interactive_features.ipynb

Interactive Features in cdiutils#

This notebook demonstrates the interactive visualisation and data exploration tools available in cdiutils:

  1. ``plot_3d_isosurface``: Interactive 3D isosurface plotting with multiple quantities

  2. ``ThreeDViewer``: Widget for exploring complex 3D arrays (amplitude + phase)

  3. ``TabPlotData``: Interactive browser for exploring CDI reconstruction results

Installation#

These features require additional dependencies:

pip install cdiutils[interactive]

Or install individually:

pip install plotly scikit-image scipy ipywidgets h5glance

[ ]:

import numpy as np

import cdiutils
from cdiutils.interactive import TabPlotData, ThreeDViewer, plot_3d_isosurface

cdiutils.update_plot_params()

[ ]:

# load reconstruction data from CXI file (here, we assume it has been generated by CDIutils pipeline)
data_path = ""
data = cdiutils.io.load_cxi(
    data_path,
    "amplitude",
    "phase",
    "het_strain",
    "lattice_parameter",
    "dspacing",
    "support",
)
voxel_size = cdiutils.io.load_cxi(data_path, "voxel_size")

print(f"Data shape: {data['amplitude'].shape}")
print(f"Voxel size: {voxel_size} nm")

plot_3d_isosurface#

Interactive isosurface plot with multiple quantities. Features:

  • Threshold slider: control isosurface level

  • Quantity dropdown: switch between different data arrays

  • Colormap dropdown: choose from 20+ colormaps

  • Colorbar controls: auto-scale, symmetric mode, or manual limits

  • Replace NaN checkbox: replace NaN values with mean to avoid artefacts

[ ]:

plot_3d_isosurface(
    data["amplitude"],
    data,
    voxel_size=voxel_size,
)

ThreeDViewer Class#

A widget for exploring complex 3D arrays (amplitude + phase). Features:

  • Threshold slider: control isosurface level based on amplitude

  • Phase/Amplitude toggle: switch between phase and amplitude display

  • Colormap dropdown: choose from 20+ colormaps

  • Colorbar controls: auto-scale, symmetric mode, or manual limits

  • Replace NaN checkbox: replace NaN values with mean

  • Rotation toggle: enable continuous rotation animation

  • Theme toggle: switch between light and dark themes

[ ]:

# create complex 3D array
complex_3d = data["amplitude"] * np.exp(1j * data["phase"])

# create viewer
viewer = ThreeDViewer(complex_3d, voxel_size=voxel_size, figsize=(9, 6))
viewer.show()

Notes#

  • Try adjusting the threshold slider to explore different isosurface levels

  • Use the colormap dropdown to find the best visualisation for your data

  • Enable “Replace NaN with mean” if you see unusual colours (NaN artefacts)

  • For strain data, use symmetric colorbar with diverging colormaps like “cet_CET_D13”

  • The dark theme can be helpful when working in low-light environments

TabPlotData Class#

An interactive browser for exploring CDI reconstruction results from a folder structure. Features:

  • Tab navigation: browse through different scans and reconstructions

  • Interactive plots: 2D slices and 3D visualisations

  • Data inspection: view metadata and reconstruction parameters

  • Quick comparison: easily compare results from different scans

[ ]:

path_to_results_dir = ""
tab = TabPlotData(path_to_results_dir)
tab.show()