convertVol

Usage: convertVol [input] [output]Allowed options are:

Positionals:
  1 TEXT:FILE REQUIRED                  volumetric file (.pgm3d, .vol, .longvol).
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         volumetric file (.pgm3d, .vol, .longvol).
  -o,--output TEXT                      volumetric file (.pgm3d, .vol, .longvol)

Examples:

$ convertVol ${DGtal}/examples/samples/lobster.vol convertedVol.p3d

DGtal

Definition ATu0v1.h:57

To upgrade a "Version-2" vol file to a "Version-3" (default Vol writer):

$ convertVol ${DGtal}/examples/samples/lobster.vol ${DGtal}/examples/samples/lobster.vol

See also: convertVol.cpp

dicom2vol

Usage: dicom2vol [input] [output]Allowed options are:

Positionals:
  1 TEXT:FILE REQUIRED                  dicom image  (.dcm).
  2 TEXT:FILE                           volumetric file (.vol, .longvol .pgm3d, .raw).
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         dicom image  (.dcm).
  -o,--output TEXT                      volumetric file (.vol, .longvol .pgm3d, .raw)
  --dicomMin INT                        set minimum density threshold on Hounsfield scale
  --dicomMax INT                        set maximum density threshold on Hounsfield scale

Example:

$ dicom2vol -i ${DGtal}/tests/samples/dicomSample/1629.dcm --dicomMin 0 --dicomMax 300 -o sample.vol

See also: dicom2vol.cpp

freeman2img

The transformation can fill shapes with hole by using the freemanchain orientation. The interior is considered on the left according to a freeman chain move, i.e. a clockwise oriented contour represents a hole in the shape.Usage: freeman2img [input] [output]Allowed options are:

Positionals:
  1 TEXT:FILE REQUIRED                  Input freeman chain file name.
  2 TEXT:FILE                           the output file name.
 
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         Input freeman chain file name.
  -b,--border UINT                      add a border in the resulting image (used only in the automatic mode i.e when --space is not used.
  -o,--output TEXT=result.pgm           the output file name
  -s,--space INT x 4                    Define the space from its bounding box (lower and upper coordinates) else the space is automatically defined from the freemanchain bounding boxes.

Example:

$freeman2img ${DGtal}/tests/samples/contourS.fc sample.pgm

You will obtain such image:

Resulting image

Example with several contours: The file located in $DGtal/examples/samples/contourS2.fc contains different contours with some ones corresponds to hole. We can apply the same conversion as the previous example:

$ freeman2img $DGtal/examples/samples/contourS2.fc sample2.pgm

You will obtain such image:

Resulting image

See also: img2freeman freeman2img.cpp

freeman2sdp

Usage: freeman2sdp [input] > output.sdpAllowed options are:

Positionals:
  1 TEXT:FILE REQUIRED                  Input freeman chain file name.
 
  Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         Input freeman chain file name.
  -o,--oneLine                          output the digital contour in one line like: X0 Y0 X1 Y1 ... XN YN
  --info                                adds some info as comments at the beginning of the file.
 
   @b Example:
   @code
   freeman2sdp -i ${DGtal}/tests/samples/contourS.fc > contourS.sdp

You will obtain such result:

   $ more contourS.sdp  
   # grid curve 1/1 closed
   13 60
   14 60
   14 59
   14 58
   15 58
   15 57
   16 57
   16 56
   17 56
   17 55
   17 54
   18 54
   ...

See also: freeman2sdp.cpp

HDF52vol

Usage: HDF52vol [input] [output]Allowed options are:

Positionals:
  1 TEXT:FILE REQUIRED                  volumetric file (.pgm3d, .vol, .longvol).
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         the input FreemanChain file name
  -o,--output TEXT                      the output filename

Example:

$HDF52vol -i ${DGtal}/tests/samples/ex_image2.h5 -o out.vol

See also: HDF52vol.cpp

heightfield2shading

You can choose between lambertian model (diffuse reflectance) and specular model (Nayar reflectance model). You can also choose between a single directional light source (using -l{x,y,z} options) or use light source which emits in all direction (by specifying the light source position with -p{x,y,z} option). Another rendering mode is given from a bitmap reflectance map which represents the rendering for a normal vector value (mapped according the x/y coordinates).Usage: heightfield2shading [input] [output]Allowed options are:

Positionals:
  1 TEXT:FILE REQUIRED                  mesh file (.off)
  2 TEXT=result.pgm                     sequence of discrete point file (.sdp)
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         mesh file (.off)
  -o,--output TEXT=result.pgm           sequence of discrete point file (.sdp)
  -s,--meshScale FLOAT                  change the default mesh scale (each vertex multiplied by the scale)
  -a,--remeshMinArea FLOAT=0.01         ajust the remeshing min triangle are used to avoid empty areas
  --heightFieldMaxScan INT=255          set the maximal scan deep.
  -x,--centerX INT=0                    choose x center of the projected image.
  -y,--centerY INT=0                    choose y center of the projected image.
  -z,--centerZ INT=200                  choose z center of the projected image.
  --nx FLOAT=0                          set the x component of the projection direction.
  --ny FLOAT=0                          set the y component of the projection direction.
  --nz FLOAT=1                          set the z component of the projection direction.
  -v,--invertNormals                    invert normal vector of the mesh
  --width FLOAT=500                     set the width of the area to be extracted as an height field image. (note that the resulting image width also depends of the scale parameter (option --meshScale))
  --height FLOAT=500                    set the height of the area to extracted  as an height field image. (note that the resulting image height also depends of the scale parameter (option --meshScale))
  --orientAutoFrontX                    automatically orients the camera in front according the x axis.
  --orientAutoFrontY                    automatically orients the camera in front according the y axis.
  --orientAutoFrontZ                    automatically orients the camera in front according the z axis.
  --orientBack                          change the camera direction to back instead front as given in  orientAutoFront{X,Y,Z} options.
  --exportNormals                       export mesh normal vectors (given in the image height field basis).
  --backgroundNormalBack                set the normals of background in camera opposite direction (to obtain a black background in rendering).
  --setBackgroundLastDepth              change the default background (black with the last filled intensity).

Example:

$ heightfield2shading ${DGtal}/examples/samples/bunnyHeightField.pgm shading.pgm --lDir 0.0 1.0 1.0 --importNormal ${DGtal}/examples/samples/bunnyHeightField_normals.sdp -s 1.0 0.2 0.8

You will obtain such image:

Resulting image with a 90° ccw rotation

Other example:

$ heightfield2shading ${DGtal}/examples/samples/bunnyHeightField.pgm shading.ppm --importNormal ${DGtal}/examples/samples/bunnyHeightField_normals.sdp --hsvShading

You will obtain such image:

Resulting image with a 90° ccw rotation (and conversion to png)

See also: heightfield2shading.cpp

heightfield2vol

Usage: heightfield2vol [OPTIONS] 1 [2]Allowed options are:

Positionals:
  1 TEXT REQUIRED                       input heightfield file (2D image).
  2 TEXT                                output volumetric file.
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT REQUIRED              input heightfield file (2D image).
  -o,--output TEXT                      output volumetric file.
  -s,--scale FLOAT                      set the scale factor on height values (default 1.0)
  -z,--volZ UINT                        set the Z max value of domain.
  -f,--foregroundValue UINT             specify the foreground value of the resulting voxel.
  -b,--backgroundValue UINT             specify the background value of the resulting volumetric file.

Example:

$ heightfield2vol ${DGtal}/examples/samples/church.pgm volResu.vol -s 0.3 -z 50

You will obtain such image:

Resulting image.

See also: heightfield2vol.cpp

img2freeman

Allowed options are:

Positionals:
  1 TEXT:FILE REQUIRED                  input image file name (any 2D image format accepted by DGtal::GenericReader).
  contourSelect INT x 3                 Select contour according reference point and maximal distance:  ex. --contourSelect X Y distanceMax
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         input image file name (any 2D image format accepted by DGtal::GenericReader).
  -m,--min FLOAT                        min image threshold value (default 128)
  -M,--max FLOAT                        max image threshold value (default 255)
  --sort                                to sort the resulting freemanchain by decreasing size.
  -s,--minSize UINT                     minSize of the extracted freeman chain (default 0)
  -r,--thresholdRangeMin INT x 3        use a range interval as threshold (from min) : --thresholdRangeMin min increment max : for each possible i, it define a digital sets [min, min+((i+1)*increment)] such that min+((i+1)*increment)< max  and extract their boundary.
  -R,--thresholdRangeMax INT x 3        use a range interval as threshold (from max) : --thresholdRangeMax min increment max : for each possible i, it define a digital sets [ max-((i)*increment), max] such that max-((i)*increment)>min  and extract their boundary.

Example:

$ img2freeman ${DGtal}/examples/samples/church.pgm > contours.fc

You will obtain such results:

more contours.fc
0 138 032
0 155 032
0 202 032
0 265 010122
0 268 0030100323232232
0 300 01101003223303222
0 395 012
0 398 0001012111111111110111111011222232
0 408 032
0 425 012
0 428 010323003301032330001032300030003030003003000032323033322332322332230333333322221222222223000000030000033323332323032230321233003323322300322223223032322121110011223232110012211111111112
1 131 00100032322221
1 277 103321
2 393 112330
2 288 00032221
2 296 0321
2 373 0321
3 424 1230
3 192 0321
390 767 3303000000030030333333001011033333230003323223233030303010111003303233010332332233000333000010103033030330030101110030333230301003332321233223322222123233303322332333330030330303322321211212123222332330010003222332233010033232300030111011010032323032233333303301030010033033321221222332300033212....

See also: img2freeman.cpp

imgAddNoise

Allowed options are:

Positionals:
  1 TEXT:FILE REQUIRED                  input image file name (any 2D image format accepted by DGtal::GenericReader).
  2 TEXT=result.png                     output image file name (any 2D image format accepted by DGtal::GenericWriter)
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         input image file name (any 2D image format accepted by DGtal::GenericReader).
  -o,--output TEXT=result.png           output image file name (any 2D image format accepted by DGtal::GenericWriter)
  -n,--noise FLOAT=0.5                  Kanungo noise level in ]0,1[ (default 0.5)

Example:

$ imgAddNoise ${DGtal}/examples/samples/klokan.pgm noise.pgm

You will obtain such image:

Resulting image.

See also: imgAddNoise.cpp

itk2vol

Allowed options are:

Positionals:
  1 TEXT:FILE REQUIRED                  Any file format in the ITK library (mhd, mha, ...).
  2 TEXT                                volumetric file (.vol, .pgm3d).
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         Any file format in the ITK library (mhd, mha, ...).
  -o,--output TEXT                      volumetric file (.vol, .pgm3d).
  -m,--maskImage TEXT                   Use a mask image to remove image part (where mask is 0). The default mask value can be changed using mask default value.
  -r,--maskRemoveLabel INT              Change the label value that defines the part of input image to be removed by the option --maskImage.
  --inputMin INT                        set minimum density threshold on Hounsfield scale.
  --inputMax INT                        set maximum density threshold on Hounsfield scale.
  -t,--inputType TEXT:{int,double}      to sepcify the input image type (int or double).
 
@b Example:
@code
$itk2vol image.mhd sample.vol  --dicomMin -500 --dicomMax -100

See also: itk2vol.cpp

longvol2vol

Usage: longvol2vol [input] [output]Allowed options are:

Positionals:
  1 TEXT:FILE REQUIRED                  Input longvol filename ( .longvol)
  2 TEXT                                Output vol filename.
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         Input longvol filename ( .longvol)
  -o,--output TEXT                      Output vol filename.
  -m,--mode UINT:{0,1,2}                Conversion mode:
                                                 0 = cast (default)
                                                 1 = Linear Scaling
                                                 2 = Grayscale cycle (32 steps, except 0 values).

Example:

$ longvol2vol ${DGtal}/tests/samples/test.longvol out.vol

See also: longvol2vol.cpp

mesh2heightfield

The 3D mesh is discretized and scanned in the normal direction N, starting from P with a step 1.Usage: mesh2heightfield [input] [output]Allowed options are:

Positionals:
  1 TEXT:FILE                           input heightfield file (2D image).
  2 TEXT                                output image.
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE                  input heightfield file (2D image).
  -d,--domain UINT x 2                  specify the domain (required when normal are imported and if --inout is not given).
  -o,--output TEXT                      output image.
  --importNormal TEXT                   import normals from file.
  --orderedNormalsImport                Use ordered normals.
  --lightDir,--lDir,--ld FLOAT x 3      light source direction: lx ly lz.
  --lightPos,--lPos,--lp FLOAT x 3      light source position: px py pz.
  -s,--specularModel FLOAT x 3          use specular Nayar model with 3 param Kdiff, Kspec, sigma.
  -r,--reflectanceMap TEXT:FILE         specify a image as reflectance map.
  --hsvShading                          use shading with HSV shading (given from the normal vector)
  --normalMap                           generates normal map.
  -v,--invertNormals                    invert normal orientations.

Example:

$ mesh2heightfield -i ${DGtal}/examples/samples/tref.off heighfield.pgm

You will obtain such image:

Resulting heightfield.

See also: mesh2heightfield.cpp

mesh2vol

Usage: mesh2vol [input]Allowed options are:

positionals:
  1 TEXT:FILE REQUIRED                  mesh file (.off).
  2 TEXT=result.vol                     filename of ouput volumetric file (vol, pgm3d, ...).
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         mesh file (.off).
  -o,--output TEXT=result.vol           filename of ouput volumetric file (vol, pgm3d, ...).
  -m,--margin UINT                      add volume margin around the mesh bounding box.
  -d,--objectDomainBB                   use the digitization space defined from bounding box of input mesh. If seleted, the option --resolution will have no effect.
  -s,--separation UINT:{6,26}=6         voxelization 6-separated or 26-separated.
  -f,--fillValue                                        change the default output  volumetric image value in [1...255].
  -r,--resolution UINT=128              digitization domain size (e.g. 128). The mesh will be scaled such that its bounding box maps to [0,resolution)^3.

Example:

$ mesh2vol -i ${DGtal}/examples/samples/tref.off --separation 26 --resolution 256 -o output.vol

See also: mesh2vol.cpp

ofs2off

Usage: ofs2off [input] [output]Allowed options are:

Positionals:
  1 TEXT:FILE REQUIRED                  ofs file (.ofs).
  2 TEXT:FILE                           ofs file (.ofs).
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         ofs file (.ofs).
  -o,--output TEXT                      ofs file (.off)

Example:

$ ofs2off input.ofs output.off

See also: ofs2off.cpp

raw2HDF5

Usage: raw2HDF5 [input] [output]Allowed options are:

Positionals:
  1 TEXT:FILE REQUIRED                  Input raw file.
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         Input raw file.
  -o,--output TEXT=result.hdf5           Output hdf5 filename.
  --x UINT REQUIRED                     x extent.
  --y UINT REQUIRED                     y extent.
  --z UINT REQUIRED                     z extent.

Example:

$ raw2HDF5 -x 128 -y 128 -z 128 -i input.raw -o output.hd

See also: raw2HDF5.cpp

raw2vol

Allowed options are:

Allowed options are: :
 
Positionals:
  1 TEXT:FILE REQUIRED                  Input raw file.
  2 TEXT:FILE REQUIRED                  Input raw file.
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         Input raw file.
  -o,--output TEXT=result.vol           Output vol filename.
  --x UINT REQUIRED                     x extent.
  --y UINT REQUIRED                     y extent.
  --z UINT REQUIRED                     z extent.

Example:

$ raw2vol -x 128 -y 128 -z 128 -i input.raw -o output.vol

See also: raw2vol.cpp

sdp2vol

Allowed options are:

Positionals:
  1 TEXT:FILE REQUIRED                  Sequence of 3d Discrete points (.sdp).
  2 TEXT                                Vol file  (.vol, .longvol, .pgm3d) 
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         Sequence of 3d Discrete points (.sdp).
  -o,--output TEXT                      Vol file  (.vol, .longvol, .pgm3d) 
  -f,--foregroundVal INT                value which will represent the foreground object in the resulting image (default 128)
  -b,--backgroundVal INT                value which will represent the background outside the  object in the resulting image (default 0)
  -d,--domain INT x 6                   customizes the domain of the resulting image xmin ymin zmin xmax ymax zmax (computed automatically by default)
  --invertY                             Invert the Y axis (image flip in the y direction)

Example:

$ sdp2vol volumePoints.sdp volume.vol -d 0 0 0 10 10 10

See also: sdp2vol.cpp

slice2vol

Allowed options are:

Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT ... REQUIRED          input 2D files (.pgm)
  -o,--output TEXT                      volumetric file (.vol, .longvol .pgm3d)
  -s,--sliceOrientation UINT:{0,1,2}=2  specify the slice orientation for which the slice are defined (by default =2 (Z direction))

Example:

$ slice2vol -i slice1.pgm slice2.pgm slice3.pgm -o out.vol

See also: slice2vol.cpp

vol2heightfield

Usage: vol2heightfield [input] [output]Allowed options are:

Positionals:
  1 TEXT:FILE REQUIRED                  vol file (.vol, .longvol .p3d, .pgm3d and if DGTAL_WITH_ITK is selected: dicom, dcm, mha, mhd). For longvol, dicom, dcm, mha or mhd formats, the input values are linearly scaled between 0 and 255.
  2 TEXT=result.pgm                     resulting image filename (in pgm or other).
 
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         vol file (.vol, .longvol .p3d, .pgm3d and if DGTAL_WITH_ITK is selected: dicom, dcm, mha, mhd). For longvol, dicom, dcm, mha or mhd formats, the input values are linearly scaled between 0 and 255.
  -o,--output TEXT                      resulting image filename (in pgm or other)
  -m,--thresholdMin INT=128             threshold min (excluded) to define binary shape.
  -M,--thresholdMax INT=255             threshold max (included) to define binary shape.
  --rescaleInputMin INT=0               min value used to rescale the input intensity (to avoid basic cast into 8  bits image).
  --rescaleInputMax INT=255             max value used to rescale the input intensity (to avoid basic cast into 8  bits image).
  --nx FLOAT=0                          set the x component of the projection direction.
  --ny FLOAT=0                          set the y component of the projection direction.
  --nz FLOAT=1                          set the z component of the projection direction.
  -x,--centerX UINT=0                   choose x center of the projected image.
  -y,--centerY UINT=0                   choose y center of the projected image.
  -z,--centerZ UINT=0                   choose z center of the projected image.
  -w,--width UINT=100                   set the width of the resulting height Field image.
  --height UINT=100                     set the height of the resulting height Field image.
  --heightFieldMaxScan UINT             set the maximal scan deep.
  --setBackgroundLastDepth              change the default background (black with the last filled intensity).

Example:

$ vol2heightfield ${DGtal}/examples/samples/lobster.vol resultingHeightMap.pgm -m 60 -M 500 --nx 0 --ny 0.7 --nz -1 -x 150 -y 0 -z 150 --width 300 --height 300 --heightFieldMaxScan 350 resultingHeightMap.pgm

You should obtain such a resulting image:

resulting image.

See also: vol2heightfield.cpp

vol2obj

Usage: ./converters/vol2obj [OPTIONS] 1 [2]Allowed options are:

Positionals:
  1 TEXT:FILE REQUIRED                  vol file (.vol, .longvol .p3d, .pgm3d or .sdp and if DGTAL_WITH_ITK is selected: dicom, dcm, mha, mhd). For longvol, dicom, dcm, mha or mhd formats, the input values are linearly scaled between 0 and 255.
  2 TEXT                                output file (.obj or .off).
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         vol file (.vol, .longvol .p3d, .pgm3d or .sdp and if DGTAL_WITH_ITK is selected: dicom, dcm, mha, mhd). For longvol, dicom, dcm, mha or mhd formats, the input values are linearly scaled between 0 and 255.
  -o,--output TEXT                      output file (.obj or .off).
  -m,--thresholdMin INT=128             threshold min (excluded) to define binary shape.
  -M,--thresholdMax INT=255             threshold max (included) to define binary shape.
  --rescaleInputMin INT=0               min value used to rescale the input intensity (to avoid basic cast into 8  bits image).
  --rescaleInputMax INT=255             max value used to rescale the input intensity (to avoid basic cast into 8  bits image).

See also: vol2obj.cpp

vol2raw

Allowed options are:

Usage: ./converters/vol2raw [OPTIONS] 1 [2]
 
Positionals:
  1 TEXT:FILE REQUIRED                  vol file (.vol, .longvol .p3d, .pgm3d and if DGTAL_WITH_ITK is selected: dicom, dcm, mha, mhd). For longvol, dicom, dcm, mha or mhd formats, the input values are linearly scaled between 0 and 255.
  2 TEXT                                output file (.raw).
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         vol file (.vol, .longvol .p3d, .pgm3d and if DGTAL_WITH_ITK is selected: dicom, dcm, mha, mhd). For longvol, dicom, dcm, mha or mhd formats, the input values are linearly scaled between 0 and 255.
  -o,--output TEXT                      output file (.raw).
  --rescaleInputMin INT=0               min value used to rescale the input intensity (to avoid basic cast into 8  bits image).
  --rescaleInputMax INT=255             max value used to rescale the input intensity (to avoid basic cast into 8  bits image).

Example:

vol2raw input.vol out.raw

See also: vol2raw.cpp

vol2sdp

Allowed options are:

 vol2sdp  ${DGtal}/examples/samples/lobster.vol volumeList.sdp
 Usage: ./converters/vol2sdp [OPTIONS] 1 [2]
 
 Positionals:
 1 TEXT:FILE REQUIRED        vol file (.vol, .longvol .p3d, .pgm3d and if DGTAL_WITH_ITK is selected: dicom, dcm, mha, mhd) or sdp (sequence of discrete points). For longvol, dicom, dcm, mha or mhd formats, the input values are linearly scaled between 0 and 255.
 2 TEXT=result.sdp           sequence of discrete point file (.sdp)
 
 Options:
 -h,--help                   Print this help message and exit
 -i,--input TEXT:FILE REQUIRED
                            vol file (.vol, .longvol .p3d, .pgm3d and if DGTAL_WITH_ITK is selected: dicom, dcm, mha, mhd) or sdp (sequence of discrete points). 
                            For longvol, dicom, dcm, mha or mhd formats, the input values are linearly scaled between 0 and 255.
-o,--output TEXT=result.sdp sequence of discrete point file (.sdp)
-e,--exportImageValues      option to export also the image value of the voxel in a fourth field.
-m,--thresholdMin INT=128   threshold min (excluded) to define binary shape.
-M,--thresholdMax INT=255   threshold max (included) to define binary shape.
--rescaleInputMin INT=0     min value used to rescale the input intensity (to avoid basic cast into 8  bits image).
--rescaleInputMax INT=255   max value used to rescale the input intensity (to avoid basic cast into 8  bits image).

Example:

$ vol2sdp  ${DGtal}/examples/samples/lobster.vol volumeList.sdp -m 70
# Visualisation:
$ 3dSDPViewer volumeList.sdp

You should obtain such a visualization:

resulting visualisation.

See also: vol2sdp.cpp

vol2slice

Usage: vol2slice [input] [output]Allowed options are:

 Typical use: to extract all slices defined in Y plane (y=cst): 
 vol2slice -i image3d.vol -s 1  -o slice.pgm 
 
Usage: ./converters/vol2slice [OPTIONS] 1 [2]
 
Positionals:
  1 TEXT:FILE REQUIRED                  vol file (.vol, .longvol .p3d, .pgm3d and if DGTAL_WITH_ITK is selected: dicom, dcm, mha, mhd). For longvol, dicom, dcm, mha                                         or mhd formats, the input values are linearly scaled between 0 and 255.
  2 TEXT=result.pgm                     base_name.extension:  extracted 2D slice volumetric files (will result n files base_name_xxx.extension)
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         vol file (.vol, .longvol .p3d, .pgm3d and if DGTAL_WITH_ITK is selected: dicom, dcm, mha, mhd). For longvol, dicom, dcm, mha                                         or mhd formats, the input values are linearly scaled between 0 and 255.
  -o,--output TEXT=result.pgm           base_name.extension:  extracted 2D slice volumetric files (will result n files base_name_xxx.extension)
  -f,--setFirstSlice INT:NUMBER=0       Set the first slice index to be extracted.
  -l,--setLastSlice INT:NUMBER          Set the last slice index to be extracted (by default set to maximal value according to the given volume).
  -s,--sliceOrientation UINT:{0,1,2}=2  specify the slice orientation for which the slice are defined (by default =2 (Z direction))
  --rescaleInputMin INT=0               min value used to rescale the input intensity (to avoid basic cast into 8  bits image).
  --rescaleInputMax INT=255             max value used to rescale the input intensity (to avoid basic cast into 8  bits image).

Example:

# Export Z slice images (-s 2):

$ vol2slice ${DGtal}/examples/samples/lobster.vol slice.pgm -f 10 -l 15 -s 2

You should obtain such a visualization:

resulting visualisation.

See also: vol2slice.cpp

vol2vox

Usage: vo2vox -i [input] -o [output]Allowed options are:

Positionals:
 1 TEXT:FILE REQUIRED                  Input vol file.
 2 TEXT=result.vox                     Output filename.
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         Input vol file.
  -o,--output TEXT=result.vox           Output filename.

Example:

$ vol2vox ${DGtal}/examples/samples/Al.100.vol Al.100.vox

volBoundary2obj

Usage: converters/volBoundary2obj [OPTIONS] 1 [2]Allowed options are:

Positionals:
  1 TEXT:FILE REQUIRED                  vol file (.vol, .longvol .p3d, .pgm3d and if DGTAL_WITH_ITK is selected: dicom, dcm, mha, mhd). For longvol, dicom, dcm, mha or mhd formats, the input values are linearly scaled between 0 and 255.
  2 TEXT                                output file (.obj or .off).
 
Options:
  -h,--help                             Print this help message and exit
  -i,--input TEXT:FILE REQUIRED         vol file (.vol, .longvol .p3d, .pgm3d and if DGTAL_WITH_ITK is selected: dicom, dcm, mha, mhd). For longvol, dicom, dcm, mha or mhd formats, the input values are linearly scaled between 0 and 255.
  -o,--output TEXT                      output file (.obj or .off).
  -m,--thresholdMin INT=128             threshold min (excluded) to define binary shape.
  -M,--thresholdMax INT=255             threshold max (included) to define binary shape.
  --rescaleInputMin INT=0               min value used to rescale the input intensity (to avoid basic cast into 8  bits image).
  --rescaleInputMax INT=255             max value used to rescale the input intensity (to avoid basic cast into 8  bits image).
  -c,--customDiffuse UINT=[230,230,230,255] x 4
                                        set the R, G, B, A components of the diffuse colors of the mesh faces.
  -t,--triangulatedSurface              save the dual triangulated surface instead instead the default digital surface.

Example:

$ volBoundary2obj $DGtal/examples/samples/lobster.vol out.obj -m 80

You should obtain such a visualization:

resulting visualisation.

See also: volBoundary2obj.cpp

vox2vol

Usage: vox2vol -i [input] -o [output]Allowed options are:

Positionals:
1 TEXT:FILE REQUIRED                  
2 TEXT=result.vol                     
 
Options:
-h,--help                             Print this help message and exit
-i,--input TEXT:FILE REQUIRED         
-o,--ouput TEXT=result.vol            

Example:

$ vox2vol Al.100.vox Al.100.vol