radsum3d Average 2D Radon transforms into 3D Radon transforms.
(Also works for Fourier Radon transforms)
image format: SPIDER
USAGE: radsum3d
.Input (empty) 3D Radon transform: rad3d001
[Enter the name of a 3D Radon transform to which the 2D projection
transforms should be added (averaged)]
.File name pattern for 2D projection transforms: rad2d00001
[Typically enter the file name of the first projection transform.
In the example "00001" serves as a pattern only and is substituted
with the real numbers. Do not use * or [..] expression.]
.Should the projections be added or substracted: +
[Enter - if the projection transforms ahould be subtracted and
+ if they should be averaged into the transform. The subtraction
can be interesting fot iterative projection alignment.]
.Use equalized sampling or polar sampling: P
[You can shose between polar sampling, and (E) a sampling that equalizes
the sampling points by diluting them with the cos of the latitudinal
coordinate.]
.Are the radon transforms real or Fourier: R
[Since there is no indication is the file if the Radon transforms
are real valued or Fourier transformed it has to be indicated here.
The 3D and 3D transforms both must have the same type
(Fourier or real)]
.Set line value to 0 when counter is on 0 (Y/N=default): N
[Enter Y if the values in the line should be set to 0 when the counter
at the end of the line is on 0, meaning that there are not projection
transforms averaged into this line. This can occur when the - option
is used to subtract projection transforms. After multiple iterations
numerical errors may leave small values in a line, even though they
should be 0.]
.Input selection document file or *: sel001
[Optional, enter the name of a selection document file that tells
the program which images to use and whic ones to leav out.
*Typically, this file has the file number as key, and in the first
column a 1 if the projection should be used and 0 if not.
*Alternatively the first column may contain any value, and the
decision if a projection is used or not depends on a threshold
(see below). This can be used in alignment procedures where one
can take the cross-correlation coefficient as collumn 1 and give
a threshold as a criterium for removing projection transforms that
show a cross-correlation coefficient below a certain threshold.
*Second alternative: The document file contains a key followed by the
image file number, followed by one or more numbers indicating the
set membership(s) of the particle. This format was created for the
use of new data partitioning methods under development.]
If a selection file was specified:
.Column with image number, Set number to reconstruct: 0,0
[If the document file is not a selection file, but contains the image
numbers insteadt provide a column number other than 0. If
the document file contains multiple sets, enter the set that should be
reconstructed. The document file created by hex3drm has multiple sets.]
if the column number and set number were 0(the normal situation):
.Threshold for selection document file (def 0.5): 0.5
[Enter a threshold value for the value from the selection document
file. Below this value projections are rejected, above accepted.
0.5 works well for the simple 0 / 1 index. If a 0 is entered other
questions follow]
If the threshold is specified as 0:
.Sigma to calculate the selection cutoff (def -0.2): -0.5
[If no threshold was given, the program determined the
sigma and average of the selection column. Specifying
0.5 her means that all images with a slection value of
less than average-0.5*sigma are rejected.]
If no selection file was specified:
.Enter file numbers (style: 1-100,120-134,137,150-1000): 1-10594
[Enter the numbers of the files that should be averaged into the
3D Redon transform. At this time it is not clear if there is
a limit to the line length or if continuation lines a possible
(probably not).]
.Randomization with replacement (Y/N=default): N
[Enter if you want to do a reconstruction using randomization with
replacement. This can be used to obtain an approximation of the
3D variance. Default is N]
If Y was answered:
.Number of draws: 9000
[Enter the number of projections that should be drawn randomly
from the available projection set.]
.Name of statistics output doc file: statdoc001
[This document file will have the information about which
porjections were drawn.]
.Angle set number in projection header (1=def, 2 or 3): 1
[The spider image file contains 3 locations to store euler angle sets
and x-y shifts (although the shift locations have been used also for
other purposes in the later versions of SPIDER. Typically the valid
Euler angles can be found in position 1. The purpose of multiple
location more redundancy for alignments. When 2D Radon trasnforms
are aligned to 3D Radon transforms (or 2D polar Fouriers to 3D
polar Fouriers which is the same), then the new angle can be saved
in a position other than 1, and a reconstruction can be first
calculated to possibley verify the validity of the alignment, before
overwriting the default position.]
.Symmetry to impose 0=none=def, 1 around z-axis, 4 icosahedral: 0
[Enter 0 for asymmetrical particles, 1 for particles with proven
symmetry around the z-axis, which must be well aligned, and 4 for
icosahedral symmetry enforcement. Other symmetries are in the
works.]
Programs: radsum3d.py, put2drads, cputrmn_plus.f, putrmrealn.f, getsym.f
Author: M. Radermacher