TAPIR (Tomographic Alternating Projecting Iterative Reconstruction) uses a constrained iterative reconstruction algorithm. Its goal is to minimize the difference between the reconstruction and the tilted projections. The constraints are compact support, positivity and smoothness of the reconstruction. In each cycle of refinement, this algorithm simply calculates the difference between the reprojection of the reconstruction and its corresponding projection, and the difference is applied to the reconstruction by backprojection.
The improvement of TAPIR over weighted backprojection (WBP) is dramatic if the object is sparsely distributed. It can remove the backprojection strips around isolated features with the positivity constraint being a strong information source (it is always applied in TAPIR). The strip-like artifacts are mainly due to the missing wedge problem, i.e., we can only collect data up to tilt of +-75 degree (in contrast, a tilt range of +-90 degree avoids the problem).
Here's a sample command file for TAPIR:
(time tapir \
/mama/weiping/prog/junk.MnAln \
/mama/weiping/prog/junk.xzy \
-istrfile=/mama/weiping/prog/junk.xzyw \
-reconxz=128:150 -iy=0:127 -smooth=.9 \
-cycles=3 -moderec=2 -positivity=1 -proj_pos=1 ) \
> /mama/weiping/emrecon.log
Aligned series | Reconstruction | NX:NY:NV | Initial guess | Output XZ size | Y range | Smooth | Cycles | Output format | Statistics | Positivity | Coerce input | Resolution | Resolution scale | Add multires | Guess resolution
Priism | Alignment and reconstruction | MASSNORM | APPL_PRM | EWBP | Alignment with markers
This is the name of the input file which contains the mass normalized and aligned projection series created by APPL_PRM. On the command line, the name of the file with mass-normalized and aligned data is the first argument.
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This is the name of the file that will contain the data for the reconstructed volume. On the command line, the name of for the output image data is the second argument.
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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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This is the name of a file containing the initial reconstruction guess; the file could be created by EWBP. The initial guess is optional; when none is used as the file name, it is assumed that there is no initial guess available.
If the initial guess is supplied, its dimensions must match the dimensions of the output reconstruction as set by the output XZ size and y range input parameters.
To set the file name for the initial guess on the command line, use
-istrfile=filename. If the -istrfile
option is not supplied, it is assumed that no initial guess is available.
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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). If the initial reconstruction guess is supplied as an input (with the initial guess parameter), then these dimensions should match the x and z dimensions of that file. Otherwise, the z dimensions should be set to be at least twice the specimen thickness to limit contamination of the TAPIR reconstruction by the volatile projection direct components.
On the command line, the dimensions of the reconstruction are set with
-reconxz=nx:nz. When
nx is not set, the x dimension of the reconstructed volume is the
same as the x dimension of the input data. When nz is not set,
the z dimension of the reconstructed volume is one fourth of the x dimension
of the input data.
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These two values set the range of y pixels from the aligned tilt series to use in the reconstruction. The first is the first index (running from 0 to the number of y pixels minus one) to use, and the second is the last possible index to use. If you supply an initial guess, the y dimension of the guess must match that specified with these values.
The range of indices used is set on the command line with
-iy=start_index:last_index.
If you do not specify a range, all y pixels are used:
start_index is set to zero and last_index is set to
the number of y pixels minus one.
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This parameter constrains how smooth the reconstruction should be. This is achieved by smoothing the reconstruction after every round of correcting it by how it compared with the projection data. Smoothing is normally used to minimize the interpolation error and/or quantum noise. The smoothing is done by applying a Gaussian filter (restricted to a five by five region and renormalized) to the reconstructed data. The smoothing parameter sets the sigma for this Gaussian filter; a value of 0.9 works well.
On the command line use -smooth=sigma to
set the smoothing constant. If is not set, no smoothing is done.
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This parameter sets the maximum number of iterations that are performed. When asked to perform zero iterations, tapir will backproject the input tilt series to generate the reconstruction.
On the command line use -cycles=n to set the
number of iterations. If -cycles is not supplied, tapir will
perform one iteration.
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This parameter controls the data type used to represent values in the reconstructed volume. You have the choice of using a four byte floating-point representation or a two byte signed integer representation.
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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tapir can write summary results for reconstruction statistics as a function of iteration. The resulting file is a text file which is compatible with Priism's 2D Plot. It contains four quantities as a function of iteration: the R-factor (sum of the absolute value of the differences between the input projections and the projections computed from the reconstruction divided by the sum of the absolute values of the input projections), Npos (the fraction of the volume where the positivity constraint caused a value to be coerced to zero), the correlation coefficient between the input projections and the projections computed from the reconstruction, and the statistic that tapir in versions of Priism prior to 4.2.3 called the R-factor (sum of the absolue value of the differences between the input projections and the projections computed from the reconstruction divided by the sum of the absolute values in the input projections added to the sum of the absolute values in the projections from the reconstruction). To have tapir write these summary results, enter a file name that is not "none" in the "Statistics" field. As a shortcut, you can turn on the toggle button adjacent to the "Statistics" field to insert the base name for the input tilt series plus a .tapir_stat extension. From the command line, use
-statfile=name
to specify the file name for the summary statistics; if you do not use
a -statfile option, tapir will assume name was "none"
and will not write the summary statistics in a separate file.
The results in the summary statistics file reflect all xz slices through the reconstruction. In its log file, tapir always includes the statistics for each xz slice followed by the combined result for all slices that were generated in that run of tapir. For parallel runs of tapir, the log file will have a final set of summary statistics merging the results from the tapir runs used to generate the full reconstruction.
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When this toggle is on, the pixel values in the reconstruction are forced to be non-negative. This a priori constraint is a powerful way to improve the reconstruction so it isn't generally useful to turn off the positivity constraint.
From the command line, the positivity constraint is turned on by specifying
-positivity=any value. If this is omitted, no
positivity constraint is applied.
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When this toggle is on, the values from the mass-normalized projection data are forced to be non-negative (negative values are set to zero). This is almost always the right thing to do.
From the command line, the positivity condition is imposed on the input
data by specifying -proj_pos=any value.
If this is omitted, no positivity condition is applied.
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The resolution parameter selects which resolution to process from the input tilt series. Normally, the tilt series has been preprocessed with apply parameters, and the highest resolution in the tilt series corresponds to the resolution you want. In those situations, you would set the resolution parameter to zero (the default value) to select the highest resolution from the tilt series.
On the command line, use
-res=i
to have the reconstruction use the ith resolution from the tilt series. When run from the command line and no resolution is selected, the reconstruction will use the highest resolution present in the input tilt series.
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The resolution scale parameter controls the scale factor applied to the reconstruction size and smoothing parameters. In the typical case where you select a resolution level to process from the main dialog of EMTAR, the graphical interface will automatically fill in the resolution scale correctly. In the case where you are running the reconstruction directly on a downsampled tilt series but still specify the reconstruction size and smoothing in terms of the full resolution, you should set the resolution scale to be the same as the downsampling factor (if the data is scaled down by a factor of four set the resolution scale parameter to four).
On the command line, use
-rscale=i
to set the resolution scale to be i. When run from the command line without the -rscale option, tapir will use a scale factor equal to two raised to the power of the resolution level selected with -res.
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Turn on the "Add multires" toggle button to cause tapir to add lower resolutions to the reconstruction if the x and y dimensions of the reconstruction are large enough. Turn off the "Add multires" toggle button to cause tapir to generate a reconstruction with a single resolution.
On the command line, include
-multires
in the command-line options for tapir to cause tapir to add lower resolutions to the reconstruction if the x and y dimensions of the reconstruction are large enough.
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The guess resolution parameter allows you to select which resolution to use from the file containing the initial guess. The dimensions of the resolution you select must be compatible with the dimensions you've specified for the reconstruction.
On the command line, use
-gres=i
in the command-line options for tapir to use the ith resolution from the initial guess file. When run from the command line without the -gres option, tapir will use the highest resolution present in the initial guess file.
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