Xmipp

xmipp_angular_projection_matching (v3.0)

Usage

Perform a discrete angular assignment using projection matching in real space. This program is relatively fast, using polar coordinates for the in-plane angular searches and the 5-dimensional search of rotation angles and origin offsets is broken in two: first the angles are search in a 3D-search; then, for the optimal orientation the origin offsets are searched (2D).

The output of the program consists of a document file with all assigned angles and rotations. This file also contains a column for the maximum cross-correlation coefficient. Note that the program does not alter the image headers. The recommended use of this program is within the python script of the xmipp_protocol_projmatch.py

See also
angular_discrete_assign angular_continuous_assign angular_project_library

Parameters

-i <doc_file>
Docfile with input images
-o <output_filename>
Output filename
-r, --ref <stackFile>
Reference projections
--search5d_shift <s5dshift=0>
Search range (in +/- pix) for 5D shift search
--search5d_step <s5dstep=2>
Step size for 5D shift search (in pix)
--Ri <ri=1>
Inner radius to limit rotational search
--Ro <ro=-1>
Outer radius to limit rotational search ro = -1 -> dim/2-1
-s, --scale <step=1> <n_steps=3>
scale step factor (1 means 0.01 in/de-crements) and number of steps around 1. with default values: 1 0.01 | 0.02 | 0.03

Extra parameters

--mem <mem=1>
Available memory for reference library (Gb)
--max_shift <max_shift=-1>
Max. change in origin offset (+/- pixels; neg= no limit)
--ctf <filename>
CTF to apply to the reference projections, either a CTF parameter file or a 2D image with the CTF amplitudes
--pad <pad=1>
Padding factor (for CTF correction only)
--phase_flipped
Use this if the experimental images have been phase flipped
--thr <threads=1>
Number of concurrent threads
--append
Append (versus overwrite) data to the output file

Examples and notes

Example of use: Sample at 2 pixel step size for 5D shift search
xmipp_angular_projection_matching -i experimental.doc -o assigned_angles.doc --ref reference.stk --search5d_step 2

User's comments

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