fitpatches(1) General Commands Manual fitpatches(1)
NAME
fitpatches - manage and fit to patch vector files for supermontaging
SYNOPSIS
fitpatches options supermontage_info_file
DESCRIPTION
Fitpatches is a Python program that assists with the evaluation and
editing of patch vector files produced by Edgepatches and provides
information on aberrant vectors to Stitchalign. It uses Refine-
match(1) to fit a single linear transformation to the original patch
vectors and produce a set of "reduced" vectors with the often large
linear component removed. The resulting patch vector file retains the
correlation coefficients originally produced by Corrsearch3d. The
program also runs Findwarp on these reduced vectors and shows the
mean and maximum residual and outlier information provided by fitting
in Findwarp. The resulting patch vector file contains a residual
value for each vector and a value for the fraction of fits on which the
vector was excluded as an outlier. This file will be used by
Stitchalign to determine which vectors to exclude as outliers or
because of their high residuals. Fitpatches also manages making vector
models from the patch files when the latter are newly derived, and con-
verting vector models back to patch files after they have been edited.
The files managed by this program have the following names:
edgename.patch - Original patch vectors with CCCs
edgename_ccc.mod - Original vector model with CCCs
edgename_reduce.patch - Reduced patch vectors with CCCs
edgename_reduce.mod - Reduced vector model with CCCs
edgename_resid.patch - Reduced vectors with residuals/outlier fractions
edgename_resid.mod - Reduced vector model with residuals
The program is designed to perform appropriate operations after you
edit any one of the patch vector models. Specifically, each time it is
run, it first determines whether the vector model corresponding to each
of the three kinds of patch files has been edited; i.e., whether it
contains fewer vectors than the current patch file does. If so, that
vector model is converted back to a patch file, and the current file is
saved as a backup by adding "~" to its name.
Next, the program determines whether to make new reduced vectors from
the original vectors. It will do this if the reduced vectors do not
yet exist, or if the original vectors have been edited while the
reduced vectors have not been edited, either now or on a previous run
of the program. In other words, once you have edited the reduced vec-
tors with CCCs, they are protected from being overwritten. When the
program makes a new set of reduced vectors, it will also make a vector
model from the patch file.
Finally, the program always runs Findwarp to make a new set of vec-
tors with residual and outlier information. The input patch vectors
for this are either the reduced vectors or the existing set of vectors
with residuals. The reduced vectors are used if the vectors with
residuals do not exist yet, or if the vectors with residuals have not
been edited yet and the reduced vectors are new in some manner (i.e.,
have just been edited, or have just been produced from the original
vectors). Otherwise, the residual vectors themselves are used as input
to Findwarp to make a new set of vectors with residuals. In other
words, once you have edited the vectors with residuals, they will not
be overwritten by running Findwarp on the reduced vectors. After
running Findwarp, the program makes a new vector model from the
patch file.
If you go back to Edgepatches to make new original patches,
Edgepatches will remove the entries for the derived patches from the
supermontage info file, and Fitpatches will make new patch files uncon-
ditionally when you run it again.
You should run Fitpatches immediately after Edgepatches, and also
after any editing of the vector models, to ensure that Stitchalign
has up-to-date information on the residuals and outliers. You are free
to edit any of the vector models in any sequence, but there is no rea-
son to edit the original vectors, since it is easier to see problems in
reduced vectors. It is probably more useful to edit the patches with
residuals than the reduced patches with CCCs. If you do want to edit
both kinds of patches, it is recommended that you first edit the
reduced patches with CCCs, then run Fitpatches to make new patches with
residuals, then edit the patches with residuals.
OPTIONS
Fitpatches uses the PIP package for input (see the manual page for
pip). Options can be specified either as command line arguments
(with the -) or one per line in a command file (without the -).
Options can be abbreviated to unique letters; the currently valid
abbreviations for short names are shown in parentheses.
-info (-i) OR -InfoFile File name
Name of a supermontage info file in which all data about files
is be stored. It will be read in when the program starts, and
renamed to filename~ before writing a new version when the pro-
gram exits. If this option is not entered, the first non-option
argument will be taken as the name of the info file.
-xrun (-x) OR -XRunStartEnd Two integers
Starting and ending frame number in X for patch files to analyze
-yrun (-y) OR -YRunStartEnd Two integers
Starting and ending frame number in Y for patch files to analyze
-zrun (-z) OR -ZRunStartEnd Two integers
Starting and ending Z value for patch files to analyze
-target (-t) OR -TargetMeanResidual Multiple floats
One or more mean residual values to try to reach when Find-
warp(1) searches for the best warping. Multiple values should
be entered in increasing order. Findwarp will try to find a
warping with the largest number of included patches that gives a
mean residual below the first value; then it tries again with
the second value, etc. The default values are designed to pro-
duce a successful fit even with rather bad patches.
-clip (-c) OR -ClippingPlaneBoxSize Integer
Four clipping planes will be added to the reduced and residual
models to allow a small square of the patch vector model to be
viewed in isolation. Use this option to change the size from
the default of 600 pixels.
-scale (-s) OR -ScaleFactor Floating point
Factor for scaling vectors in reduced and residual models. The
default is 10, is is used for vectors when combining tomograms.
Note that the original vectors are always scaled by 5 in
Edgepatches because they tend to be so long.
-rescale (-r) OR -RescaleModels
Remake the reduced and residual models with the current scale
factor.
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input
FILES
The files managed by the program are listed above. Every time the info
file is modified, the existing copy is renamed to a backup with the ~
extension.
AUTHOR
David Mastronarde
SEE ALSO
corrsearch3d, edgepatches, patch2imod, imod2patch,
stitchalign
Email bug reports to mast at colorado dot edu.
IMOD 5.0.2 fitpatches(1)