imodinfo(1) General Commands Manual imodinfo(1)
NAME
imodinfo - Prints information about IMOD files.
SYNOPSIS
imodinfo [options] IMOD_filename
DESCRIPTION
Prints information about an IMOD model to standard output. The types
of information output vary, depending upon the options. Typical uses
include printing out lists of objects, contours and point data in an
IMOD file; printing out areas, lengths and centroids of contours; and
printing out surface areas and volumes of objects or surfaces. The
measurements of lengths, areas, and volumes are generally expressed in
terms of the units of the pixel size defined in the model header (e.g.,
nm or microns), if one is defined. A Z-scale in the model header is
also applied as appropriate. However, reported positions are always in
pixels.
The program computes surface area and volume in several different ways,
depending upon whether an object is meshed or not:
1) If there is no mesh information, volume is computed by taking
the area of each contour times the thickness of the sections (defined
by pixel size and Z-scale), summed over all of the contours. This is
referred to as cylinder volume. It will be inaccurate if you skipped
sections in modeling, especially if you skipped sections routinely.
Other than this, it will be very close to correct.
2) If there is no mesh information, surface area is computed by
taking the length of each contour times the section thickness, summed
over all contours. This is referred to as cylinder surface area and it
is grossly inaccurate.
3) With mesh information, the program determines which contours
are connected to other contours or to cap points by a mesh, and sums
the area of contours times the distance to the connected contours in Z.
This measure is now referred to as the contour volume. (It used to be
referred to as mesh volume because it uses mesh information, even
though it is not the volume inside the mesh.) It handles the problem
of skipped sections and also gives a slightly more accurate volume mea-
surement for the capped regions because it integrates with a trape-
zoidal approximation. This computation is valid only for closed con-
tour, planar objects.
4) With a mesh, the program also computes a volume from the mesh
by summing the volumes of tetrahedra formed between each mesh triangle
and a single point at the center of the mesh. This is referred to as
the volume inside the mesh. It will be slightly more accurate than the
contour volume if the mesh completely encloses the volume, but it can
be quite inaccurate if the mesh is not capped. This computation is
valid for any fully meshed volume, including tubular meshes around an
open contour, as well as saved isosurface objects. Such a volume can
be computed for each surface if the option to use surface information
was used when meshing.
5) With a mesh, surface area is computed by adding the areas of
all the triangles in the mesh. This is referred to as mesh surface
area and it is an exact measure of the area of the mesh. However, to
the extent that the mesh is not smooth, it can overestimate the true
surface area of the object.
If any of your model objects has complex topology, with contours inside
of other contours, the computed volumes will not be correct unless the
program analyzes for inside contours, which it does not do by default.
Use -i option to have the program do this analysis. However, if you
use -x or -y to specify a subset range in X or Y, or use -t to restrict
the analysis with clipping planes, the inside-contour analysis is done
automatically and you do not need to specify -i separately. With these
other options, the program will give the same outputs as with the -i
option.
The options -a , -c , -e , -l , -L , -F , -p , -r and -s are mutually
exclusive.
OPTIONS
-a Print ascii readable IMOD output. Not all of the types of data
stored in a binary model are printed in an ascii model file, but
all contour and mesh data are printed. Also, slicer angles,
clipping planes, and general values assigned to contours and
points will be printed.
-c Print volume, surface area, and center of gravity for each
object in column output. For closed contour objects, the cen-
troid is computed from the area enclosed inside each contour.
For open contour objects, the centroid is computed from the line
segments themselves.
-l Print lengths of open contours in column output.
-L Print lengths of contours broken out by fine-grained color, if
any, and excluding gaps. For each object, a table is printed
for each color used. This table shows the contour number and
the length of the portion assigned that color, for each contour
that uses the color. If the -h option is given, only summary
information on total and mean lengths os printed. Unlike in
other length reports, this one excludes gaps from the total
length, so this option is useful for getting correct lengths of
what is drawn when there are gaps, even if there are no fine-
grained colors.
-s Print volumes and surface areas for each separate surface in an
object, as defined by contour surface numbers and possibly by
mesh surface numbers. The maximum extent, or biggest distance
between any two points in the surface contours, is also
reported. If a mesh is available, the cylinder surface area is
omitted from the report. If any meshes have a surface number
greater than 0, the volume inside the mesh (mesh volume) will be
reported for each surface. If such information seems to be
available for all surfaces, the cylinder volume will be omitted.
To get mesh volumes, be sure to cap and to select the option to
use surface information when meshing.
-p Print point size information, including a summary of mean
radius, and the implied total surface area and volume of scat-
tered points. There will be a size output for every point in
any contour that has points with non-zero size. If there is a
default point size for the object, that size will be listed when
there is no size defined for an individual point. For closed
and open contour objects, points will be output only for con-
tours having points of non-zero size, unless the -v option is
given, in which case they will be output for all points in an
object with a non-zero object point size defined. These sizes
will be in the model units. Note that the ascii model output
will also show point sizes in pixels for each point that has one
defined.
-r Print ratio of length to area for closed contours.
-e Print properties of equivalent ellipses for closed contours.
The equivalent ellipse is the one with the same second moments
as the area enclosed by a contour. If limits are entered with
-x, -y, or -z, only contours with center coordinates within the
limits are in reported. Only the X and Y coordinates of the
points are considered when computing these ellipses. For each
contour, the values reported are the X and Y center coordinates
of the ellipse (i.e, the centroid of the contour area), the
average Z coordinate of the contour points, all in pixels, the
semi-major and semi-minor axes in scaled units, the eccentricity
as usually defined (a value between 0 for a circle and 1 for a
maximally elongated ellipse), and the angle of the semi-major
axis (a value between 0 and 180 except as described next). If
the range of angles is less than 80 degrees, then numbers will
be reported that are suitable for simple averaging. This is
accomplished based on the angle of the first contour for an
object: if it is less than 44, then all subsequent angles
greater than 136 will have 180 subtracted to give negative
angles; if it is greater than 136, 180 is then added to angles
less than 45. Means and standard deviations are also reported
for these four measures; the mean of the angles will be adjusted
to be between 0 and 180. BEWARE: if the range of angles is
greater than 88 degrees, the mean will be meaningless unless the
distribution of angles does not wrap around at 0 or 180, so you
need to examine the individual angles before using the mean.
-F Print full report on the objects, a collection of summary infor-
mation.
-o list
Print data only from the objects given in the list, a comma-sep-
arated list of ranges.
-g # Print data only from objects in the object group with the given
number, numbered from 1 as in the 3dmod Model View-Edit-Object
List dialog. This option cannot be entered along with -o.
-i Analyze for inside contours and adjust computed volume by sub-
tracting rather than adding the areas of contours that represent
inside-out surfaces. This option works only for closed con-
tours. It is invoked automatically if you analyze a subset in X
or Y, or use clipping planes. Individual contour data will not
be printed for closed contour objects.
-x min,max
-y min,max
-z min,max
Compute areas and volumes within the subvolume specified by the
minimum and maximum values. One or two of these three options
may be entered if desired. Subvolume analysis works only with
closed contour and scattered point objects. It works for
options that print surface areas and volumes and with the -p
option. In the standard output, the number of scattered points
within the subvolume will be reported for each object.
-t 1/-1
Truncate objects by their respective clipping planes; enter -t 1
or -t -1 to use region shown or not shown by the clipping
planes, respectively. All currently active object clipping
planes will be applied, as well as any active global clipping
planes for objects that do not have the setting to skip the
global planes. Like the subvolume analysis, this option works
only with closed contour and scattered point objects, and for
options that print surface areas and volumes and with the -p
option. Clipping plane truncation can be used together with
subvolume analysis.
-v[v] Print more verbose output. The -vv option will increase the
level of output information even further. These options over-
ride the -h option. Without other options for specific output,
-v will give some summary information about each closed contour,
including: length; area; centroid; bounding box in X and Y
(lower left then upper right coordinates); circularity based on
the ratio of perimeter squared to area, where a circle has a
value of 1; and four measures based on rotating the contour to
maximize the aspect ratio of its bounding box: the orientation,
aspect ratio, and length and width of that bounding box, and an
"ellipse" measure based on a ratio of contour area to area of an
ellipse with that length and width. These measures of elliptic-
ity and orientation are not as accurate as the ones provided by
the -e option.
-h Suppress the information about each contour in the standard
model output. Use this option to extract summary information
more easily from large models.
-f filename
Write output to given filename instead of to standard output.
AUTHORS
Jim Kremer
David Mastronarde
SEE ALSO
3dmod
BUGS
Cylinder surface areas are erroneous because they do not account for
the obliquity of the surface; for a sphere the area will be underesti-
mated by 22%. Use mesh surface areas whenever possible.
Email bug reports to mast at colorado dot edu.
IMOD 4.12.61 imodinfo(1)