This program (EWBP, elliptical-square weighted backprojection) computes the weighted backprojection (WBP) reconstruction of a volume from a mass normalized and aligned series of projections. WBP is a linear shift-invariant algorithm, hence the reconstruction can be described by its point spread function. The only thing one can manipulate with this algorithm is its weighting function. The reconstruction is computed by multiplying the Fourier transform of each projection with its weighting function and backprojecting the weighted values into the reconstruction volume.
The current program provides a set of weighting functions. Besides the conventional r*-weighting function which is valid for a regular tilt series, there is the so-called elliptical-square weighting function which applies to arbitrary tilting geometry of the projection set and also takes care of the scaling problem (that is, the scales of the reconstruction and that of the projections correspond to each other). The elliptical-square weighting function is recommended for all situations.
Here's an example command file for EWBP:
(time /mama/weipingtprog/ewbp /mama/weiping/progtjunk.MnAln \
/mama/weiping/prog/junk.xzyw -dimxz= 128:150 -iy=0:127:1 \
-filter-2 -reconxz=128:150 -moderec=2 -hdfilt \
-no_hrfilt -positivity ) > /mama/weiping/emrecon.log
IdatFile | OrecFile | NX:NY:NV | reconXZ | iY | Weighting function | sizeXZ | modeRec | HatFilt | no_HrwFilt | positivity
Priism | Reconstruction | MASSNORM | APPL_PRM | TAPIR | Alignment
This is the name of the input file which contains the mass normalized and aligned projection series created by APPL_PRM.
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This is the name of the file that will contain the data for the reconstructed volume.
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The first two values are, respectively, the x and y dimensions of the data in the input projection series. The last value is the number of projections in the series.
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These two values set the x and z dimensions, in pixels, of the reconstructed volume (the volume is written as slices parallel to the xz plane so these values are the dimensions of a single slice). The z dimension should be greater than the specimen thickness. When the reconstructed volume is used as an input for TAPIR, the z dimension should be twice the specimen thickness to limit contamination of the TAPIR reconstruction by volatile projection direct components; also, the sizes for the TAPIR reconstruction and the initial reconstruction should be the same.
On the command line, the dimensions of the reconstruction are set with
-reconxz=nx:ny. When the
dimensions are not set, nx is taken to be the same size as the
x dimension of an input projection, and nz is set to one-third
of nx.
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These three values set which projections in the input file, IdatFile, are used in the reconstruction. The first is the first index (running from 0 to the number of projections minus one) to use, the second is the last possible index to use, and the third is the index step.
From the command line, use
-iy=start_index:last_index:step to set the range of projection used in the
reconstruction. When the range of indices is not set, the whole projection
series is used: start_index is set to zero, last_index
is set to the number of projections minus one, and step is one.
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There are three choices for the weighting function to use in the weighted backprojection:
To specify the weighting function from the command line use
-filter=code where code is
one of the following:
When no weighting function is specified on the command line, the default is to use the elliptical-square function.
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These two values are, respectively, the x and z dimensions in pixels of the particle and are used when computing the elliptical or elliptical-square weighting functions.
To specify the particle dimensions from the command line, use
-sizexz=nx:nz. If the
particle size is not set, the program uses the x and z dimensions of a
reconstruction slice for the dimensions of the particle.
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Use this switch to set the data type used to represent the values in the reconstructed volume. You have the choice of using a four byte floating-point representation (Mode=2: Real*4) or a two byte signed integer representation (Mode=1: Int*2).
To set the output data type from the command line, use
-moderec=2 for the floating-point representation or
-moderec=1 for the signed integer representation. If neither
is set, the floating-point representation is used.
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When the toggle is on, a Hamming filter is applied to the data
before the reconstruction; when it is off, no Hamming filter is applied.
On the command line, the way to turn on the Hamming filter applied before
the reconstruction is to use -hfil_d. The default behavior
is not to apply the initial Hamming filter.
This switch is normally not used.
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This toggle only affects the reconstruction when the r*-weighting function
is used. When the toggle is on, no Hamming filter is applied to the
r*-weighting function for reconstruction; when it is off, a Hamming filter
is applied. On the command line, the way to turn off the Hamming filter
applied to the r*-weighting function is to use -no_hfilr. The
default behavior is to apply the Hamming filter.
This switch is normally not used.
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When this switch is on, data values in reconstructed volume which are
less than zero are coerced to zero (a positivity constraint). No such
constraint is applied when the switch is off (the default behavior). On
the command line, the way to force the positivity constraint is to supply
a -positivity option.
This switch is normally not used.
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