pcj

SYNOPSIS

Used to manipulate parameter/geometry files

SYNTAX 

    pcj    -commands    file

DESCRIPTION

This program is used to form .pot, .fac and .pts files which have a a form described in cjmaps and cvrti . Features provided include volume reduction, parameter extraction by key list, automatic triangulation and file format conversion from Pollard-style map/mesh file to parameter/geometry files.

Volume Reduction

pcj takes a description of a reduced volume as one set of arguments. With this description, pcj attempts to locate all nodes which are within the reduced volume. Volume reduction also includes changes to the spatial discretization resolution. With this option, it is possible to generate a coarse mesh for display or post-processing from a fine mesh used in simulation or data acquisition. The extracted nodal coordinates from the reduced volume are written to an output .pts file. The initial node numbers are written to an output .key file.

Parameter Extraction by Key List

pcj allows parameter extraction based on a key list generated in a previous invocation of pcj . This procedure can be used to generate a new .pot file from an existing .pot file.

Automatic Triangulation

pcj will perform limited triangulation of the extracted nodes on a uniform grid. The triangle list based on the extracted node numbers is written to a .fac file.

File Conversion

pcj takes Pollard style mesh/map files and converts these files to geometry/parameter files. When the mesh file is used, automatic triangulation is attempted on the resultant coordinate set.

Key Comparisions

pcj will take two key files and compare the contents to generate an output key file which contains the entries on both lists. The output file will contain each intersection entry listed as a pair so the output file may be used as a vector list with cvrti .

Commands

-bx,by,bz
Lower left corner coordinate of the extracted volume
-cx,cy,cz
Upper right corner coordinate of the extracted volume
-dx,dy,dz
Discretization resolution of the extracted volume
-e
Tolerance for the extraction search.
-fk
Specify the name for the generated/previously defined extraction key list
-fkt
Specify the name for the comparison step vector file
-fm
Specify the name for a generated .pot file
-fp
Specify the name for a generated .pts file
-ft
Specify the name for a generated .fac file
-rkt
Specify the name for the comparison key list
-rm
Specify the name for an input .pot file for parameter extraction
-rp
Specify the name for an input .pts file for parameter extraction
-wk
Only write the key list for the reduced volume
-fkt
Perform a comparison key list step
-wm
Only write the potential map (pot) for the reduced volume
-wp
Only write the nodal coordinates list (x,y,z) for the reduced volume
-wt
Only write the triangle list for the reduced volume
-wpd
Write pdraw file header and nodal coordinates (x,y,pot) for the reduced volume
-f
Specify a FileRoot name for the created output files
-m
Specify a Pollard type map.* input file
-n
Specify a map number for extraction for a Pollard *.map file file A Pollard type conprs.* file (omitted otherwise)

pcj works like a number of UNIX filter functions and provides no internal manipulation. All operations are specified at the command line.

Examples

pcj -bx -0.720 -by -0.360 -bz -0.180  
    -cx  0.720 -cy  0.360 -cz -0.180  
    -dx  0.045 -dy  0.045 -dz  0.045 -e 0.1  
    -m map.ua3d0700 conprs.ua3d07
Generate all geometry/parameter files with automatic triangulation from a Pollard style mesh description in conprs.ua3d07 and a Pollard style map description in map.ua3d0700. A 2-D sheet built from the x-y plane at the specified z layer will result. The first map in the map.ua3d0700 file is extracted. 
pcj -bx -0.720 -by -0.360 -bz -0.180  
    -cx  0.720 -cy -0.360 -cz  0.180  
    -dx  0.045 -dy  0.045 -dz  0.045 -e 0.1  
    -m map.ua3d0700 conprs.ua3d07
Generate all geometry/parameter files with automatic triangulation from a Pollard style mesh description in conprs.ua3d07 and a Pollard style map description in map.ua3d0700. A 2-D sheet built from the x-z plane at the specified y layer will result. The first map in the map.ua3d0700 file is extracted. 
pcj -bx -0.720 -by -0.360 -bz -0.180  
    -cx -0.720 -cy  0.360 -cz  0.180  
    -dx  0.045 -dy  0.045 -dz  0.045 -e 0.1  
    -m map.ua3d0700 conprs.ua3d07
Generate all geometry/parameter files with automatic triangulation from a Pollard style mesh description in conprs.ua3d07 and a Pollard style map description in map.ua3d0700. A 2-D sheet built from the y-z plane at the specified x layer will result. The first map in the map.ua3d0700 file is extracted. 
pcj -fk pcj.key -rm pcj.pot -rp pcj.pts  
    -dx  0.090 -dy  0.090 -dz  0.090 -e 0.1  
    -fm ex4.pot -fp ex4.pts -ft ex4.fac
Resample the results from a previous invocation of pcj in which the files pcj.pot and pcj.pts were constructed. Store the results from the resampling and the new triangulation in files ex4.*. 
pcj -fk pcj.key  
    -fm ex5.pot  -fp ex5.pts  -ft  ex5.fac  
    -n 1 -m map.ua3d0700
Extract the second map from the mapfile map.ua3d0700 using the keys from an earlier invocation of pcj as stored in pcj.key. Place the output in files with names ex5.*. 

pcj -bx -100.0 -e 1.0 -m map.ua2d1900 conprs.ua2d19

Perform default sampling on a 2-D mesh. By specifying a very low value for bx and a high value for tolerance e, all points in the mesh conprs.ua2d19 will be extracted and triangulated.

-generate with the Makefile. -the PCJxxx.c files -the pcj.h include file

Notes

1. There are upper limits on the max number of nodes and triangles. If you specify input parametrs which exceed these limits, the most straightforward way to work around the limits is to increase the spatial resolution for extraction.

2. The triangulation is very limited. It will only work on uniform grids and with discretization resolutions that are multiples of the internal resolution of the input grid.

AUTHOR

Andrew E. Pollard, Assistant Professor
Computational Electrophysiology - 536 Boggs
Tulane University Biomedical Engineering
New Orleans, LA 70118
andrew.pollard@tulane.edu