ctfgroup.py

Assign micrographs to defocus groups - ctfgroup.py -

Usage: ctfgroup.py [-s] def_sort.dat

The optional -s flag uses small fonts in the display.

Overview
Input files
Selecting defocus groups
Plotting power spectra
Saving your selections
Defocus spread

In the main window, ctfgroup.py displays a point for each micrograph, sorted by defocus.

You can put points/micrographs into defocus groups by outlining them with the left mouse button.

The power spectra of color-coded defocus groups can be viewed in Gnuplot with the right mouse button.

The objective is to assign all micrographs to a set of defocus groups using two constraints:
1) Maximize the number of micrographs in each group. SNR increases with the number of particles.
2) Keep defocus values within each group as small as possible (minimize defocus spread). Power spectra of micrographs from the same defocus group should be plotted together, to ensure that their zeroes (minima) line up, and do not cancel out.

Inputs

ctfgroup.py reads a SPIDER document file with Micrograph numbers and their corresponding defocus values in the 1st and 2nd data columns, respectively. An example is the file def_sort.ext created by the procedure defsort.spi, during single particle reconstruction. If there is a third column with defocus group numbers, ctfgroup.py will use these numbers to color the data points. This doc file should be named on the command line:
```
ctfgroup.py def_sort.dat
```
To display power spectra, ctfgroup.py also reads document files specified in the plot files: box in the lower right corner of the main window. The default files for plotting are the power/ctf***.ext files created by the procedure defsort.spi. These files are displayed in Gnuplot with the pyplot interface.

Assigning micrographs to defocus groups

A defocus group should contain a set of points that are vertically aligned, as far as that is possible. That is, they should have nearly the same defocus. Group points by dragging the left mouse button to outline a box around them. Selected points will be assigned a new color. You may reselect points as often as you wish.

Plotting power spectra

Once points are colored (assigned), their corresponding power spectra doc files can be plotted, by clicking the right mouse button over a group. This opens a Gnuplot window and a pyplot control window. pyplot reads the file template in the lower left corner of the main window (next to the plot files: button). By default, columns 1 vs 5 are plotted from the power/ctf*** doc files. You can enter a different doc file template in the entry box. You can change which columns are plotted in the pyplot control window. The current set of micrographs being plotted are displayed as plus signs in the main ctfgroup window.

Saving your selections

ctfgroup.py lets you save your selections in a doc file with the same data columns as the def_sort file: Micrographs, Defocus, Defocus_Groups. Under the File menu, select Save as, and specify a file name.

Defocus spread

Enabling the defocus spread plot (under the File menu) displays the envelope computed by setting
defocus spread = max(defocus) - min(defocus) within a group. The X axis for this plot is spatial frequency.

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