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+~~NOTOC~~
+[{{ ::ctf_punisher_blue2.png?275|CTF Punisher}}]
+===== sp_ctf_punisher =====
+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_punisher.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_punisher.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.
+\\

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