DVC Executable

Whether you have installed the full gui, or just the executable, you are able to run the DVC from the command line, in the environment where you have installed it.

DVC Commands

The DVC executable can be called using the following commands:

dvc dvc_in - execute dvc code with dvc_in (a txt dvc input file) controlling the run

dvc help - provide additional detail about running the dvc code

dvc example - print dvc_in_example with brief keyword descriptions

dvc manual - print dvc_manual with more detailed information

Example DVC Input File

This is the contents of the dvc_in_example file mentioned above:

###############################################################################
#
#
#               example dvc process control file
#
#
###############################################################################

# all lines beginning with a # character are ignored
# some parameters are conditionally required, depending on the setting of other parameters
# for example, if subvol_thresh is off, the threshold description parameters are not required

### file names

reference_filename      frame_000_f.npy         ### reference tomography image volume
correlate_filename      frame_010_f.npy         ### correlation tomography image volume

point_cloud_filename    central_grid_5.roi      ### file of search point locations
output_filename         central_grid_5_test             ### base name for output files

### description of the image data files, all must be the same size and structure

vol_bit_depth           8                       ### 8 or 16
vol_hdr_lngth           96              ### fixed-length header size, may be zero
vol_wide                1520                    ### width in pixels of each slice
vol_high                1257                    ### height in pixels of each slice
vol_tall                1260                    ### number of slices in the stack

### parameters defining the subvolumes that will be created at each search point

subvol_geom             sphere                  ### cube, sphere
subvol_size             80                      ### side length or diameter, in voxels
subvol_npts             8000                    ### number of points to distribute within the subvol

subvol_thresh           off                     ### on or off, evaluate subvolumes based on threshold
gray_thresh_min 27                      ### lower limit of a gray threshold range if subvol_thresh is on
gray_thresh_max 127                     ### upper limit of a gray threshold range if subvol_thresh is on
min_vol_fract   0.2                     ### only search if subvol fraction is greater than

### required parameters defining the basic the search process

disp_max                38                      ### in voxels, used for range checking and global search limits
num_srch_dof            6                       ### 3, 6, or 12
obj_function            znssd                   ### sad, ssd, zssd, nssd, znssd
interp_type             tricubic                ### trilinear, tricubic

### optional parameters tuning and refining the search process

rigid_trans             34.0 4.0 0.0            ### rigid body offset of target volume, in voxels
basin_radius            0.0                     ### coarse-search resolution, in voxels, 0.0 = none
subvol_aspect           1.0 1.0 1.0             ### subvolume aspect ratio

DVC Configuration

Details about most of the options can be found in the Running DVC Analysis section.

However, the DVC executable has some options which have not yet made their way into the app. These are as follows:

subvol_thresh

examplar: subvol_thresh off required: yes suitable: on, off

Defines the state of subvolume thresholding to active (on) or inactive (off).

Useful if there is a simple gray level segmentation between foreground and background.

Subvolumes with little foreground content are not searched and flagged on output.

gray_thresh_min

examplar: gray_thresh_min 25

required: If subvol_thresh is on

suitable: 0 <= int <= 2^vol_bit_depth, and < gray_thresh_max

Defines the lower limit of a gray scale threshold range.

Voxels between (min) and (max) are included in the threshold range.

gray_thresh_max

examplar: gray_thresh_max 125

required: If subvol_thresh is on

suitable: 0 <= int <= 2^vol_bit_depth, and > gray_thresh_min

Defines the upper limit of a gray scale threshold range.

Voxels between (min) and (max) are included in the threshold range.

min_vol_fract

examplar: min_vol_fract 0.2

required: If subvol_thresh is on

suitable: 0.000000 <= double <= 1.000000

Defines a parameter for pre-checking subvolumes for content.

The fraction of subvolume points within the gray_thresh_min/max range is determined.

If below min_vol_fract, the subvolume is likely in a void or in a background region.

A point failing the test is not searched and flagged on output.

More detailed information about all parameters can be found in by running the dvc_manual command.