The following are commands will be processed by libvoxel when reading images. They shall be given in after ElementDataFile keyword in the .mhd files to avoid incompatibility with Fiji-is-ImageJ and Paraview. Furthermore, any additional application specific keywords shall be provided after these since libvoxel stops processing the commands once it encounters any unrecognised keyword (i.e. other than comments and keywords below).
The list of supported commands by libvxel can be obtained from voxelImageProcess app by running:
voxelImageProcess ?
Specific commands' usage can be shown by running:
voxelImageProcess ? command
Note these are in additional to the mhd header data provided in the top of .mhd files:
ObjectType = Image
NDims = 3
ElementType = MET_UCHAR
ElementByteOrderMSB = False
DimSize = 1000 1000 1000
ElementSize = 1.6 1.6 1.6
Offset = 0 0 0
ElementDataFile = Image.raw.gz
//HeaderSize = 0
//CompressedData = True
//OutputFormat = .raw.gz // alias for DefaultImageFormat, not part of MHD specification
Additional MHD rules:
- The order of the first 6 keywords should not be changed for compatibility with third-party software (ImageJ and Paraview).
- Use
#or//for commenting and deactivating commads/lines. - Each keyword and its data should be given in a single line. This is because libvoxel currently does not rely on the more user friendly InputFile.h syntax, used by pnextract and pnflow ... codes.
- Libvoxel detects only basic data/keywords provided in Image.am files and Image.tif files, without the need for a .mhd file. However, the commands bellow can only be provided in a separate .mhd (text) file, in which the name of Image.tif or Image.am file is given as an argument to ElementDataFile keyword (see above).
info:
Show image information/stats
info
pore:
Pore/selectPore thresholds image and sets the given range to zero (pore voxel values)
pore 0 150
threshold:
Same as selectPore
threshold 0 150
threshold101:
Same as selectPore, 101 means inside the range will be set to zero and outside to 1
threshold101 0 150
direction:
Re-interprets the image direction so that the flow direction becomes in the given direction
direction z
crop:
Crops the image, from a lower I, J, K and before an upper bound I J K values
crop 100 100 0 900 900 1000
resampleMean:
Resamples the image while setting the new values to the mean of original voxel values in case of refining (ratio<1)
resampleMean 2
resampleMax:
Resample the image while setting the new values to the max of original voxels in case of refining (ratio<1)
resampleMax 2
resampleMode:
Resample the image while setting the new values to the mode of original voxels in case of refining (ratio<1)
resampleMode 2
resliceZ:
Same as resample but only in z direction (for correcting CT images, limited)
resliceZ
replaceRange:
Sets range [min max] to a given value
replaceRange 200 255 1
keepLargest0:
Keeps the largest connected region with value of 0, sets the rest to maxT-1 (=254 for 8bit images).
Use this to compute effective porosity.
write:
Write the image into file
write image_copy.raw
write image_copy.am
write image_copy.mhd
write8bit:
Write the image as unsigned char
write8bit image_8bit.raw
write8bit image_8bit.am
write8bit image_8bit.mhd
modeFilter:
Apply few iterations (first argument) of mode filter, reject mode if frequency less than second argument
modeFilter 1 2 // 1 iterations, 2 for the threshold mode frequency to change a voxel
medianFilter:
Apply a median filter
medianFilter 1
medianX:
Apply few iterations of median filter only in x direction ( can help reduce file size of grey images when compressed)
medianX 1
FaceMedian06:
Median filter over 6 closest adjacent voxels
FaceMedian06 1
PointMedian032:
Median filter over 32 closest adjacent voxels
PointMedian032 1 //<- one iterations
mapFrom:
Assigns voxel values from another image based on their physical location (X0+ijk*dX). Image offsets should be assigned correctly.
mapFrom "image_name.mhd" ;
mapFrom "image_name.mhd" 0 65536 0 0 ; //<- \[vv_min vv_max\] increase-factor shift
operation:
Apply a mathematical unary (!, &, ~) or binary (+, -, *, b, e). Here b stands for begin or min and e stands for maximum or end for voxel values. The second argument shall be empty in case of unary operations, or a number or an image file name in case of binary operators.
operation + 10 //<- add 10 to voxel values
operation + image2.mhd -50 //<- -50 is a shift value to avoid overfow/capping
operation b 1 //<- set voxel values below <10 to 10
operation e 250 //<- set voxel values above 250> to 250
operat:
operat is an alias for operation keyword
read:
Read an image, overwriting any previously loaded data
read input_image.tif
read input_image.am
read input_image.mhd
reset:
Reset N ( image size) dx (voxel size) or X0 (offset/origin)
reset N 100 100 100
reset dx 3e-6 3e-6 3e-6
reset X0 0. 0. 0.
reset Nd0 100 100 100 3e-6 3e-6 3e-6 0. 0. 0.
reset dx 3e-6
Paint:
Paint a 3D shape into the image
Paint s 30 30 30 10 //<- shape-type(sphere) Centre:Xc(30,30,30) and radius R=10
PaintAdd:
Paints over a 3D shape on the image, increasing the previous voxel values (brightness), otherwise same as Paint
PaintAdd s 30 30 30 10 //<- shape-type(sphere) Centre:Xc(30,30,30) and radius R=10
The following keywords fate in further libvoxel versions shall be reviewed
cropD:
Same as crop, D is a reminder for [) meaning beginning of range is included but end is not
cropD 100 100 0 900 900 1000
rescale:
Adjust voxel values brightness /contrast (redundant, use operat keyword instead)
rescale 0 10000
Offset:
Change the image origin
Offset 0 0 0
delense032:
Primitive lens artefact remover, obsolete(?)
delense032
circleOut:
Set voxels outside a circles (cylinder) of radius R centrrd at Xc Yc
circleOut ; //<- centre set to centre of image and radius to half of image (width+height)/2
circleOut 500 500 450 ; //<- centre_X=500 Y=500, radius=450 voxels
growLabel:
Propagate a voxel value iteratively to its adjacent ones, obsolete
growLabel 0 5
fillHoles:
Filter out small features (obsolete feature)
fillHoles 2
readAtZ:
Read a new image and assign it at the beginning of the given slice number (obsolete, see mapFrom instead)
readAtZ 1150
maskWriteFraction:
writes fraction of voxels of two images having the same value (TODO remove?)
maskWriteFraction "maskname.mhd" "outName.txt" 0 2 1000000