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case4.13/case4.13_3sph.in: Use 3 sphere test data set


  

Input Data Options special purpose data requiring pre-processing (0) tomographic data (1) segmented data (2) burn data (3) medial axis data (4) throat data (5) Enter choice: 4

Data Processing Options plot MA (1) plot MA with MS (2) convert MS files to segmented file type (3) histogram and fit pore MA burn data (4) embed search tree(s) (5) shortest paths (6) min cut/max flow (7) convert data to/from ascii format (9) convert MA list to/from node/path formats (10) modify MA (11) histogram MA info (12) throat calculation (13) test throat calculation (19) identify fibers (14) convert to graph format (15) construct neuron (16) reconstruct burn layers (17) isolate neuron soma/dendrite structures (18) Enter choice: 13

Files assumed to be labelled basename.ext, basename is limited to 255 characters maximum, ext is a numerical designator lying between 000 and 999 It is assumed that the files have consecutively numbered extensions ie. 000 -> 056, or 021 -> 049

Enter basename for Medial structure files: ../../Examples/data/3_spheres/ma/ma Are files compressed? [y,n]: y

Resize information selection. NOTE, row and column numbers begin from 0

For each slice, enter first and last column of data to use (x-dir): 0 44 enter first and last row of data to use (y-dir): 0 54

enter first and last slice of data to use (z-dir): 1 25

Trim medial structure voxels on volume edges? (y,n(dflt)): n Enter basename for burn files: ../../Examples/data/3_spheres/brn/brn Are files compressed? [y,n]: y

Is the data 2_dimensional (y,n(dflt): n

By default 7 (maximum burn number) burn steps are done before abandoning a search for throats along a medial axispath. You however have a choice of changing this value (c) opting for a local criteria based on each path (p) leaving it unchanged (u). Enter choice (c,p,u(dflt)): c

Enter maximum number of burn steps to be done before abandoning a search for throats along a medial axis path: 26

Average burn number on Medial Axis is 6

By default throat calculation is attempted for paths which are at least 6 (average burn number) long. Do you wish to specify a new length (y,n(dflt)): y Input new lower limit for length: 6

Enter basename for singlet loc/burn files: ../../Examples/data/3_spheres/ma/sngl Enter basename for cluster/path loc/burn files: ../../Examples/data/3_spheres/ma/cp_loc Enter basename for cluster/path list files: ../../Examples/data/3_spheres/ma/cp_list

Are files compressed? [y,n]: y

There are 3 ma paths. Compute throats for all? (y,n): y Compute throats for branch-branch paths[n,y(dft)]: y branch-leaf paths[n,y(dft)]: y leaf-leaf paths[n,y(dft)]: y

Subdivide non monotonic paths to find multiple throats on the same path (y(dflt),n): y

If non monotonic paths are not subdivided satisfactorily, attempt to find a single throat for the path? (y(dflt),n): y

Ignore branch-branch and branch-leaf paths if their length is less than the maximum burn number on the clusters to which they attach? (n(dflt),y): y

Compute throats for monotonic branch-branch paths? [y,n(dft)]: y

Choices for dealing with naturally monotonic branch-branch paths. 1) Calculate throats for all of them 2) Ignore all of them for throat calculations 3) Calculate throat for a monotonic path if one of the two ends has a burn number <= a chosen value. Enter choice (1,2,3): 3

Any naturally monotonic branch-branch path with a burn number <= the threshold value atone of the two ends will be considered forthroat calculations Enter threshold value: 2

Choices for dealing with barrier induced monotonic branch-branch paths. 1) Calculate throats for all of them 2) Ignore all of them for throat calculations 3) Calculate throat for a monotonic path if a non barrier end has a burn number <= a chosen value. Enter choice (1,2,3): 3

Any barrier induced monotonic branch-branch path with a burn number <= the threshold value ata non barrier end will be considered forthroat calculations Enter threshold value: 2

Compute throats for monotonic branch-leaf paths? [y,n(dft)]: y

Choices for dealing with naturally monotonic branch-leaf paths. 1) Calculate throats for all of them 2) Ignore all of them for throat calculations 3) Calculate throat for a monotonic path if at least one end has a burn number <= a threshold value 4) Calculate throat for a monotonic path if the branch end has a burn number <= a threshold value. Enter choice (1,2,3,4): 3

Any naturally monotonic branch-leaf path with a burn number <= the threshold value atat least one end will be considered forthroat calculations Enter threshold value: 3

Choices for dealing with barrier induced monotonic branch-leaf paths. 1) Calculate throats for all of them 2) Ignore all of them for throat calculations 3) Calculate throat for a monotonic path if a non barrier end has a burn number <= a threshold value 4) Calculate throat for a monotonic path if the branch end is away from a barrier and has a burn number <= a threshold value. Enter choice (1,2,3,4): 4

Any barrier induced monotonic branch-leaf path with a burn number <= the threshold value ata non barrier end will be considered forthroat calculations Enter threshold value: 2

Compute throats for monotonic leaf-leaf paths? [y,n(dft)]: y

Choices for dealing with leaf-leaf monotonic leaf-leaf paths. 1) Calculate throats for all of them 2) Ignore all of them for throat calculations 3) Calculate throat for a monotonic path if one of the ends has a burn number <= a threshold value. Enter choice (1,2,3): 3

Any leaf-leaf monotonic leaf-leaf path with a burn number <= the threshold value atone of the ends will be considered forthroat calculations Enter threshold value: 2

Choices for dealing with leaf-leaf monotonic leaf-leaf paths. 1) Calculate throats for all of them 2) Ignore all of them for throat calculations 3) Calculate throat for a monotonic path if a non barrier end has a burn number <= a threshold value. Enter choice (1,2,3): 3

Any leaf-leaf monotonic leaf-leaf path with a burn number <= the threshold value ata non barrier end will be considered forthroat calculations Enter threshold value: 2

Compute throats for constant burn number paths? [y,n(dft)]: y

Any constant burn number path with burn numbers <= a threshold value will be considered for throat calculations. Enter the threshold value: 6

Request throat debugging output in ma style files? (y,n(dflt)): n Enter basename for throat files: thr_3sph Are files to be compressed? [y,n]: y

Print intermediate results to file (y(dflt),n): y

Intermediate results can be periodically printed after a certain number of paths have been examined. Input the periodicity (default 50): 50 Output burn steps file? (n(dflt),y): n

Enter connectivity to be used for throat surface (6(dflt),26): 6



next up previous contents
Next: case4.13/case4.13_nl.in: Use 5 sphere Up: Main Menu 4: Analyses Previous: case4.13: Compute Throat Size

Brent Lindquist
Thu Sep 30 12:33:54 EDT 1999