Public web page of
ContourTopologyChecker
ContourTopoologyChecker Project Definition ( v1x01 )
Overview
Restrictions, Exclusions, Limitations
- Only contour and surface files supported by the ShapeTools? libary are supported.
- java 1.5 is expected.
- The suface mesh must be formed only of triangular faces.
People Affected
| Person | Initials | Role | Notes |
|---|
| Bae Cheol | BC | programmer | |
| Craig Schwartz | CS | project supervisor and programmer | |
| Ryan Cabeen | RC | advisor | |
| Roger Woods | RW | project sponsor | |
Version
1.0.1
Assumptions
- if both test and reference contours are present, the N'th element of the test list is the same anatomical contour as the N'th element of the reference list.
Requirements
- Java 1.5 is used to implement this program
Requirements Change Procedure
- Changes to be mutually agreed upon by __ and __.
- Changes and their date will be entered in a 'requirements change' list.
Requirements Changes
Add table output alternative
- Change Date: 26 Feb 2008
- Approved by
- Ryan Cabeen
- Craig Schwartz
The output table may optionally contain all input files. Each line of the output table will
contain:
- the path to the input file
- A string indicating if the file passed or failed the test.
The text used to indicate "passed" or "failed" may be changed by the user via
the command line arguments
- -passedText text
- -failedText text
If these arguments are not found, the default values will be
- Passed - "Passed"
- Failed - "Failed"
The two elements of the output lines of the table will be separated by a text delimiter
whose default value is a tab. This delimiter may be changed via a runtime argument
of
Add table output alternative
Change Date: 24 March 2008
Approved by
- Ryan Cabeen
- Craig Schwartz
Change Details
Add an optional additional test for pass/fail - specify a set of atlas sulcal curves
whose vertices (Vs) will each be compared with the homologous points in all the subject sulcal curves (Vh).
If the distance between these two vertices iseither
- significantly larger than the distance between two sucessive points of the same sulcal curve (Vh0, Vh1) then fail.
- larger than a threshold value (defaults to 64) then fail.
Assumptions:
the file base names in the subject sulcal curves and in the set of atlas sulcal curves are the same,
allowing the proper curve to be selected for comparison
this assumption is not yet validated
example of new usage
java -jar checker.jar -atlas list_of_atlas_curves -files list_of_subject_sulcal_curves -passed -report report.out
Add distance to map edge test
Change Date: 9 April 08
Approved by
- Ryan Cabeen (approval pending)
- Craig Schwartz
Completed Date: 10 April 08
Change Details
Add to the "pass" testing the requirement that each vertex of the contour being tested be
further than a specified distance from the edge of the flattend space.
- This distance will default to 1
- this distance may be changed at runtime by the user.
- this test may be disabled at runtime by the user
- the distance metric used is a Euclidean distance
Test reference contour vertices for boundary and inclusion on manifold.
Change Date: 11 April 08
Approved by
- Ryan Cabeen
- Craig Schwartz
Completed Date: 11 April 08
Change details
if present, each vertex of the reference contour homologous to the test contour
is tested for
- being on the manifold
- being too close to the border of the mainfold.
These tests are exactly the same as those applied to the test contour references, except that
the test contour vertices are also checked for closeness to the reference contour vertices.
"homologous to" means:
if contour #N in the list of test contours is being checked, also check reference contour #N.
example of new usage
Reject contours containing vertices whose distance to the map edge is 5 or less
java -jar checker.jar -distanceToEdge 5 -files list_of_subject_sulcal_curves -passed -report report.out
Disable the distance to edge test
java -jar checker.jar -disableDistanceToEdge -atlas list_of_atlas_curves -files list_of_subject_sulcal_curves -passed -report report.out
Allow for null elements that always fail
Change Date: 14 May 2008
Approved by
- Ryan Cabeen
- Craig Schwartz
Change Details
The user will specify a symbol on the command line that when encountered at the i-th element in either the target or the reference lists, the i-th element of the report will be the fail symbol.
example of new usage
Suppose we have the null symbol be "NULL" with the following lists:
$ cat tart_files.txt
target_a.obj
target_b.obj
target_c.obj
$ cat ref_files.txt
reference_a.obj
NULL
reference_c.obj
Then the following call:
java -jar checker.jar -null "NULL" -atlas tar_files.txt -files ref_files.txt -passed -report report.out
Would produce output where the second element of 'report.out' would be a fail.
Products
This project will result in the following products:
- An application program that maps contours to a 2d grid
- a pipleline wrapper (.pipe) file for the GRID build
- A Twiki user web page describing the topology checking algorithm
Typical Usage
java -jar
BlendFlatmap in.rdd inDual.rdd out.rdd
Lessons Learned
(filled out after the post-project review)
Contour Topology Checker
Overview
This program examines a group of flattened contours (see
MapContour to flatten the contours) to determine
if any contours in the group cross the edges of the two dimensional map obtained by flattening
the three dimensional surface (flatmap).
Applications that attempt to create averages from such contours will fail unless the original
three dimensional topology (implied by the flattened map) is fully accounted for; such lines may
be referred to as having 'fallen off' the edge of the two dimensional flattened surface.
This program is useful to determine whether a particular contour may be properly handled by
warping protocols that do not account for all these special case topologies. This enables
a user of such protocols to prune troublesome contours before starting the time consuming warping
process.
Project Components
A sample shell script
This C- Shell script determines which contours contain segments that extend over the
edges of the 2d square onto which they are flattened.
#!/bin/csh
# this script determines which of a set of input contours
# contain segments that cross the bounds of the 2D, 256x256 space onto
# which they are flattened.
# version 7 January 2008
set verboseArg="-verbose "
# directory wth contour lines
set linesDir=data/10580/lines/R
set outputDir=output
mkdir -p ${outputDir}
# the surface on which these lines were drawn
set surface=data/10580/surface/10580_n3_305_6p_450_R.obj
# path to the output report
set report="10580.fallen.txt"
# define the applications to use
# directory containing application jar files.
set jarDir=/nethome/users/shapetls/ShapeTools
# path to MapContour
set flattenContour=${jarDir}/MapContour.jar
# path to ContourTopologyCheck
set checkTopology=${jarDir}/ContourTopologyCheck.jar
foreach i ($linesDir/*.obj)
set output=${outputDir}/$i:t
echo "flattening contour $i into ${output}"
java -jar ${flattenContour} ${verboseArg} -overwrite -shape ${surface} -contour ${i} -output ${output}
set output=$i:t
set output=$output:r.dual.obj
set output=${outputDir}/$output
echo "flattening contour $i dual into ${output}"
java -jar ${flattenContour} ${verboseArg} -dual -overwrite -shape ${surface} -contour ${i} -output ${output}end
# check for flattened lines containiing vertices not in standard 2d flatmap space ('falling off')
echo "checking for contour(s) that will fail"
java -jar ${checkTopology} ${verboseArg} -overwrite -directory ${outputDir} -failed -report ${report}
echo "Done. The output report is in file ${report}"
