~~NOTOC~~
[{{ ::ctf_punisher_blue2.png?275|CTF Punisher}}]
===== sp_ctf_punish =====
Apply trapped CTF : Multiplies images by the contrast transfer function only after the first extremum.

\\
===== Usage =====

Usage in command line:

  sp_ctf_punish.py input_stack output_directory --plot --singlehdf --verbosity --debug 

\\
===== Typical usage =====
The purpose of sp_ctf_punish.py is to: 
  : multiply images by the contrast transfer function (CTF) only after the first extremum

The general choices for CTF-correction include (among others):
  : doing nothing
  : phase-flipping
  : multiplying by the CTF

Multiplying by the CTF has the effect of flipping the phases where the CTF is negative, while avoiding the sharp filter edges during phase-flipping. (See 1D profile plot.)

However, multiplying by the CTF also dampens the data near the origin, which often adversely affects particle-recognition and alignment. 

This program multiplies by the CTF, but only after the first extremum of the CTF. Before this extremum, the amplitudes are preserved. This strategy was referred to as a "trapped CTF" in SPIDER, or "ignore CTF until first peak" in RELION.

{{ :plotctf.png?600 |1D profiles of different CTF-correction strategies}}
\\ __Standard usage: __

  sp_ctf_punish.py input_stack output_directory
[{{ ::trapped_ctf_examples.png?200|1) Padded image.2) CTF-multiplied image. 3) Phase-flipped image. 4) CTF-punished image. Images are low-pass filtered for clarity.}}]
\\
===== Input =====
=== Main Parameters ===
  ; input_stack : Set of images. (default required string)
  ; output_directory : Directory where outputs will be written. (default required string)
  ; %%--%%plot : Writes plot of example CTF profiles (machine-specific, may not work)
  ; %%--%%singlehdf : Writes a single HDF stack instead of a BDB stack pointing to MRC stacks.
  ; %%--%%debug : Writes example of various CTF-correction strategies.

\\
===== Output =====
  ; bdb:ctfpunished : Filtered BDB stack
  ; stkctfpunished.hdf : (optional) Filtered HDF stack
  ; plotctf.png : 1D profiles of example CTF

\\

===== Description =====

\\
==== Method ====

\\
==== Reference ====
SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs.
Shaikh TR, Gao H, Baxter WT, Asturias FJ, Boisset N, Leith A, Frank J. Nat Protoc. 2008;3(12):1941-74. doi: 10.1038/nprot.2008.156.
\\
==== Developer Notes ====

\\
==== Author / Maintainer ====
Tapu Shaikh

\\
==== Keywords ====
Category 1:: APPLICATIONS

\\
==== Files ====
sphire/bin/sp_ctf_punish.py

\\
==== See also ====

\\
==== Maturity ====
Beta:: Under evaluation and testing. Please let us know if there are any bugs.

\\
==== Bugs ====
On some machines, the 1D profiles cannot be plotted.

\\