Progress Viewer (autoplot)

The Progress Viewer is a GUI for monitoring EMC reconstruction progress. It displays volume slices (3D mode) or class averages (2D mode) alongside plots of reconstruction metrics as a function of iteration.

Launch

From within a reconstruction directory:

dragonfly.autoplot

With a specific config file:

dragonfly.autoplot -c config.ini

To view slices of a particular volume file without tracking a running reconstruction:

dragonfly.autoplot -f data/output_050.h5

Command-line Options

usage: dragonfly.autoplot [-c CONFIG_FILE] [-f VOLUME_FILE]

-c, --config_file   Path to config file (default: config.ini)
-f, --volume_file   Show slices of a particular file instead of tracking output

Display Areas

The window is split into three panels:

Volume slices (top left)

In 3D mode, three orthogonal slices through the reconstructed volume at the current layer number. The slice planes can be rotated by Ctrl+dragging or Alt+dragging on a slice panel, and the normal vectors can be set explicitly via right-click.

In 2D mode, a grid of all class averages is shown on the left with an enlarged view of the selected class on the right. Click a class thumbnail to select it.

Metrics plots (bottom left)

Plots of reconstruction metrics parsed from the log file:

• RMS change of the 3D volume between iterations

• Mutual information between frames and orientations

• Average log-likelihood

• Orientation convergence showing the most likely orientation for each frame as a function of iteration (sorted and colored by the last iteration)

White dashed lines mark changes in beta (annealing schedule). Orange dashed lines mark changes in the number of rotation samples.

Options panel (right)

Controls for log file path, volume file path, color scale range, exponent (gamma), iteration/layer/mode sliders, and action buttons.

Controls

Iteration slider

Select which iteration’s output to display.

Layer slider (3D mode)

Select the layer number for the orthogonal slices.

Mode slider (multi-mode reconstructions)

Select which mode to display. In 2D mode, clicking a class thumbnail also selects the mode.

Check / Keep checking

Check reads the log file to detect new completed iterations and updates all plots. Keep checking polls the log file every 5 seconds for automatic updates during a running reconstruction.

Plot / Reparse

Plot re-renders with current settings. Reparse forces re-reading of the volume file from disk.

VRange / Exp

Set the minimum and maximum of the color scale, and the exponent (gamma) for the power-law normalization. Enter log for symmetric logarithmic normalization.

Keyboard Shortcuts

Shortcut	Action
Enter	Plot / refresh
Ctrl+S	Save slices image
Ctrl+K	Check for new iterations
Ctrl+Q	Quit

Menu Reference

File

• Load Volume – Open a volume file (HDF5 or binary) for viewing.

• Load Config – Reload the GUI with a different config file.

• Quit – Close the application.

Image

• Save Slices Image – Save the current volume slices plot as a PNG.

• Save Log Plot – Save the metrics panel as a PNG.

• Save Layer Movie – Save an MP4 animation sweeping through all layers.

• Save Iteration Movie – Save an MP4 animation sweeping through all iterations.

• Color Map – Choose from coolwarm, cubehelix, CMRmap, gray, gray_r, jet.

Analysis

• Open Frameviewer – Launch the Frame Viewer showing frames assigned to the current mode (in multi-mode reconstructions).

• Subtract radial minimum – Remove the radial minimum from the current volume to highlight anisotropic features.

• Normalize high q (2D only) – Normalize the outer region of all classes to 1.

• Align models (2D only) – Align principal axes of all class averages.

• Mode selection – Toggle mode selection for generating a blacklist file. Click class thumbnails to mark good classes, then save a blacklist that flags frames not belonging to the selected classes.

• Open CLPCA – Launch the Common-Line PCA analysis window.

• 2D Class Phaser (2D only) – Launch 2D phasing of class averages.