PARTAG_SRCOBJDIST

Defines: distance in mm between X-ray source and origin (rotation center)
Value type: float
Default value: 500

PARTAG_SRCDETDIST

Defines: distance in mm between X-ray source and detector
Value type: float
Default value: 1000

PARTAG_SCANANGLE

Defines: scan angle in degrees (angle of rotation of the gantry or rotational table)
Value type: float
Default value: 360

PARTAG_STARTANGLE

Defines: angle in degrees where scan was started (controls angular orientation of the object in the output cube)
Value type: float
Default value: 0

PARTAG_INVERSEANGLE

Defines: If set to 1 then angle counts in the angle.bin file must be inverted (to support different angle.bin conventions). Not relevant when angle.bin is not present.
Value type: integer (can be 0 or 1)
Default value: 0

PARTAG_PROJRECON

Defines: Number of projections (input views) to reconstruct
Value type: integer
Default value: 360

PARTAG_DETOFFSETU

Defines: Detector position horizontal offset in pixels (distance between the point where the central ray intersects the detector and the physical center of the detector)
Value type: float
Default value: 0

PARTAG_DETOFFSETV

Defines: Detector position vertical offset in pixels (distance between the point where central ray intersects the detector and the physical center of the detector)
Value type: float
Default value: 0

PARTAG_DETPIVOT

Defines: Detector pivot (tilt) in degrees (detector rotation angle around an axis through its center and parallel to the axis of rotation)
Value type: float
Default value: 0

PARTAG_ROTATIONDIR

Defines: Gantry or turntable direction of rotation
Value type: integer (can be 0,1, or –1; 0 or 1 means CW; -1 means CCW)
Default value: 0

PARTAG_DETSIZEU

Defines: Projection size in pixels in horizontal direction (perpendicular to the axis of rotation)
Value type: integer
Default value: 512

PARTAG_DETSIZEV

Defines: Projection size in pixels in horizontal direction (parallel to the axis of rotation)
Value type: integer
Default value: 512

PARTAG_DETPITCHU

Defines: Projection element size (pixel size) in mm in horizontal direction (perpendicular to the axis of rotation)
Value type: float
Default value: 1.0

PARTAG_DETPITCHV

Defines: Projection element size (pixel size) in mm in vertical direction (parallel to the axis of rotation)
Value type: float
Default value: 1.0

PARTAG_INPUTHEADERLEN

Defines: length of the header (in bytes) of a projection file.
Value type: integer
Default value: 0

PARTAG_INPUTLOGGEDFLOAT

Defines: If set to 1 then projection files contain logged attenuation data
Value type: integer (can be 0 or 1)
Default value: 0

PARTAG_INPUTISUNSIGNED

Defines: If set to 1 then projection files contain unsigned 16-bit integers
Value type: integer (can be 0 or 1)
Default value: 0

PARTAG_INPUTREQSWAP

Defines: If set to 1 then projection files contain big-endian 16-bit integers
Value type: integer (can be 0 or 1)
Default value: 0

PARTAG_TRANSPOSED_PRJ

Defines: If set to 1 then projection files contain transposed projections
Value type: integer (can be 0 or 1)
Default value: 0

PARTAG_INPUTDOWNSAMPLE_X

Defines: Input projection will be down-sampled (binned) along the U (horizontal) axis by defined factor before any further processing actions applied
Value type: integer (can be 0,1,2,4,8; 0 or 1 means no down-sampling applied)
Default value: 0

PARTAG_INPUTDOWNSAMPLE_Y

Defines: Input projection will be down-sampled (binned) along the V (vertical) axis by defined factor before any further processing actions applied
Value type: integer (can be 0,1,2,4,8; 0 or 1 means no down-sampling applied)
Default value: 0

PARTAG_CROP_UP

Defines: The projection top margin (of this width, in pixels) will be internally cropped out before any further processing actions applied
Value type: integer
Default value: 0

PARTAG_CROP_DOWN

Defines: The projection bottom margin (of this width, in pixels) will be internally cropped out before any further processing actions applied
Value type: integer
Default value: 0

PARTAG_CROP_LEFT

Defines: The projection left margin (of this width, in pixels) will be internally cropped out before any further processing actions applied
Value type: integer
Default value: 0

PARTAG_CROP_RIGHT

Defines: The projection right margin (of this width, in pixels) will be internally cropped out before any further processing actions applied
Value type: integer
Default value: 0

OPTTAG_DEADPIXDETECT

Defines: If set to 1 then auto detection of dead detector pixels is active. The auto detection process is applied to AirRaw file (if one exists).
Value type: integer (can be 0 or 1)
Default value: 0

PARTAG_SLICE_AUTOWATER

If set to a value larger than 0 then the dynamic slice scale calibration algorithm is activated. The algorithm allows aligning density profiles automatically. It is based on reconstructed volume histogram analysis and controlled by this tag. The tag should be set to a value of density between the observed densities of air and water. Please note that the value is supposed to be set in mg/cm³ (HU+1000).
Value type: integer
Default value: 0

PARTAG_POSTPROFACTOR

COBRA provides 3-dimensional smoothing as a post-processing feature, controlled by a set of parameters. This is a boundary-preserving de-noising procedure. It is assumed that reconstruction is being performed into a bigger slice size cube. Using of an increased cube typically is beneficial for the further steps. (The final cube size is defined by PARTAG_CUBESIZEX, PAR-TAG_CUBESIZEY). The alignment of a cube size (down-sampling from an intermediate size to a final one) is the internal step of the algorithm.
PARTAG_POSTPROFACTOR is to set a smoothing sigma factor, a good estimate for this parameter is the standard deviation of noise in the image.
Value type: integer
Default value: 0

PARTAG_POSTPROAPRTHRZ

PARTAG_POSTPROAPRTHRZ is to set a horizontal aperture of a smoothing 3D filter.
Value type: integer
Default value: 3

PARTAG_POSTPROAPRTVRT

PARTAG_POSTPROAPRTVRT is to set a vertical aperture of a smoothing 3D filter.
Value type: integer
Default value: 3

PARTAG_POSTPROMEDIANAPRT

PARTAG_POSTPROMEDIANAPRT is to set the aperture of 2D median filter.
Value type: integer
Default value: 3

PARTAG_POSTPROFILTERMODE

Currently this parameter is for internal Cobra use. Must be kept 0
Value type: integer
Default value: 0

PARTAG_INTERCUBESIZE

Value type: integer
Default value: equal to PARTAG_CUBESIZEX setting

PARTAG_CUBESIZEX

Defines: Reconstruction volume size along X in pixels
Value type: integer
Default value: 512

PARTAG_CUBESIZEY

Defines: Reconstruction volume size along Y in pixels
Value type: integer
Default value: 512

PARTAG_CUBESIZEZ

Defines: Reconstruction volume size along Z in pixels
Value type: integer
Default value: 512

PARTAG_CUBEPITCHX

Defines: Volume element size (voxel pitch) along X, mm
Value type: float
Default value: 1

PARTAG_CUBEPITCHY

Defines: Volume element size (voxel pitch) along Y, mm
Value type: float
Default value: 1

PARTAG_CUBEPITCHZ

Defines: Volume element size (voxel pitch) along Z, mm
Value type: float
Default value: 1

PARTAG_CUBEORIGINX

Defines: Reconstruction volume center offset, relatively origin, along X, pixels (One can reconstruct an eccentric cube)
Value type: integer
Default value: 0

PARTAG_CUBEORIGINY

Defines: Reconstruction volume center offset, relatively origin, along Y, pixels (One can reconstruct an eccentric cube)
Value type: integer
Default value: 0

PARTAG_CUBEORIGINZ

Defines: Reconstruction volume center offset, relatively origin, along Z, pixels (One can reconstruct an eccentric cube)
Value type: integer
Default value: 0

PARTAG_DICOM

Defines: Volume file output format (0 – raw; 1 – uncompressed DICOM; 2 – compressed loss-less DICOM; 3 - compressed lossy DICOM)
Value type: integer
Default value: 0

PARTAG_OFFSET

Defines: a constant value as ADC offset (constant uniform dark field)
Value type: integer
Default value: 0

PARTAG_AIRLEVEL

Defines: a constant value as the air intensity
Value type: integer
Default value: 32000

PARTAG_SCALEFACTOR

Factor for fitting the dynamic range of the filtered projections into signed word scale
Value type: float
Default value: 700

OPTTAG_AIRCAL

Defines: If set to 1 then air raw (bright field) calibration in Feldkamp filtering phase is being applied
Value type: integer (can be 0 or 1)
Default value: 1

OPTTAG_LOG

Defines: If set to 1 then logarithm operation in Feldkamp filtering phase is being applied
Value type: integer (can be 0 or 1)
Default value: 1

OPTTAG_OFFSET

Defines: If set to 1 then ADC offset (dark field) calibration in Feldkamp filtering phase is being applied
Value type: integer (can be 0 or 1)
Default value: 1

OPTTAG_FFT

Defines: If set to 1 then filtering operation in Feldkamp filtering phase is being applied
Value type: integer (can be 0 or 1)
Default value: 1

OPTTAG_PARKER

Defines: If set to 1 then filtering operation in Feldkamp filtering phase is being applied
Value type: integer (can be 0 or 1)
Default value: 1

OPTTAG_SLVERTFILT

Defines: If set to 1 then a vertical smoothing (along axis of rotation) in Feldkamp filtering phase is being applied. Smoothing aperture = 3.
Value type: integer (can be 0 or 1)
Default value: 1

OPTTAG_VRTSMOOTH

Defines: If set to 1 then a vertical smoothing (along axis of rotation) in Feldkamp filtering phase is being applied. Smoothing aperture = 5.
Value type: integer (can be 0 or 1)
Default value: 0

PARTAG_PREPROSMOOTHFACTOR

Defines: When PARTAG_PREPROSMOOTHFACTOR is set to a number different than 0 then a 2-dimensional non-linear filter is being applied. This filter has the following parameters: hori-zontal and vertical aperture and a signal standard deviation to control a boundary-preserving behavior (to set the level of noise). This filter is being applied in the spatial domain on pre-FFT stage (on the logged attenuation signal representation) to normalized preprocessed signal. The filter is defined by three parameters: Ax (horizontal aperture), Ay (vertical aperture), V (signal variation).
Use PARTAG_PREPROSMOOTHFACTOR to set up the value of V. Since the procedure is being applied on the normalized integer signal please make multiple experiments with various V to find out an optimal value. It should provide the best compromise between keeping all boundaries preserved and the signal value. A particular setup depends on the application and the scale factor.
Value type: integer (0-255)
Default value: 3

PARTAG_PREPROSMOOTHAPRTHRZ

Defines: When PARTAG_PREPROSMOOTHFACTOR is set to a number different than 0 then 2-dimensional non-linear filter is being applied. This filter has the following parameters: horizon-tal and vertical aperture and a signal standard deviation to control boundary-preserving behavior (to set the noise level). This filter is being applied in the spatial domain, pre-FFT stage (on the logged attenuation signal representation) to normalized preprocessed signal. The filter is defined by three parameters:
Ax (horizontal aperture), Ay (vertical aperture), V (signal variation). Use PARTAG_ PREPROSMOOTHAPRTHRZ to control Ax.
Value type: integer (0-11)
Default value: 0

PARTAG_PREPROSMOOTHAPRTVRT

Defines: When PARTAG_PREPROSMOOTHFACTOR is set to a number different than 0 then 2-dimensional non-linear filter is being applied. This filter has the following parameters: horizon-tal and vertical aperture and a signal standard deviation to control boundary-preserving behavior (to set the noise level). This filter is being applied in the spatial domain, pre-FFT stage (on the logged attenuation signal representation) to normalized preprocessed signal. The filter is defined by three parameters: Ax (horizontal aperture), Ay (vertical aperture), V (signal variation). Use PARTAG_PREPROSMOOTHAPRTVRT to control Ay
Value type: integer (0-11)
Default value: 3

OPTTAG_ZFILTER<NN>

Defines: Coefficients 0-15 for V (vertical) axis filter (<NN> stands for any number 0-15).
Value type: integer (0-255)
Default value: 0

OPTTAG_FILTERNUM

Defines: a particular filter kernel (frequency amplification profile) applied in the frequency domain of the Feldkamp filtering phase.
Value type: integer
Default value: 1 (Shepp-Logan)

PARTAG_BHFACTOR<N>

Defines: a simple beam-hardening correction. <N> stands for indexes 0-3 of coefficients determining a polynomial pre-distortion of logged attenuation signal
Value type: float
Default value: 0

OPTTAG_PROTRUSIONCMODE

Defines: COBRA’s protrusion correction algorithm. Tag can have 3 different values, 0, 1 and 2. When it is set to 0, there will be no protrusion correction. Mode 1 assumes that image is linearly decaying outside the detector field of view. Mode 2 assumes that the object has nearly cylindrical shape and a non-linear arch-shape function is used for the extrapolation.
Value type: integer (0-2)
Default value: 1

PARTAG_SCATTERCORRFACTOR_P<N>

Internal COBRA use (reserved)

OPTTAG_CFA

Feldkamp algorithm is an approximate algorithm and as such can produce artifacts known as Feldkamp artifacts. The artifact comes from the nature of the algorithm itself and is independent of its implementation. It is more critical in half beam mode, because of lack of projections from the opposite sides. Feldkamp artifact correction algorithm is an iterative method that significantly reduces this artifact This method is 1.5-2 times slower than standard Feldkamp algorithm in halfbeam mode. It is activated by OPTTAG_CFA tag.
Value type: integer (0-1)
Default value: 0

SAMARATAG_HIGHCONTRASTLEVEL

Defines: Behavior of SAR method (part of SAMARA). SAMARA stands for Streak Artifact and Metal Artifact Reduction Algorithm. It is an iterative algorithm for 3D reconstruction, which is more tolerant against input data imperfections than the standard Feldkamp method.
Value type: integer (0-255)
Default value: 0

SAMARATAG_LOWCONTRASTLEVEL

Value type: integer (0-255)
Default value: 0

SAMARATAG_HIDENSLEVEL

Value type: integer (1000-16000)
Default value: 0

SAMARATAG_TOOTHDENSLEVEL

The tag is used to set a density level threshold. Densities between SAMARATAG_TOOTHDENSLEVEL and SAMARATAG_HIDENSLEVEL do not get negative corrections.
Value type: integer (0-255)
Default value: 0

SAMARATAG_SMALLDETAILSIZE

Defines: Behavior of MAR method (part of SAMARA). The tag is used to set an object size threshold. Small dense objects are considered not causing non-linearity.
Value type: integer (0-255)
Default value: 0

PARTAG_PRJSTARTFROM

The projection counter starts from this number
Value type: integer (0-255)
Default value: 0

PARTAG_UNIFSLICELOCATION

If set to 0 then Cobra 6.5.x naming conventions are supported (results of MAR and CFA corrections are being saved into separate volumes). Not relevant if SAR/MAR/CFA are not used.
Value type: integer (0 or 1)
Default value: 1

PARTAG_SRCDATAPATH

Defines: Source data folder (folder where files with input views are located)
Value type: character
Default value: The folder where the current xxm file exists

OPTTAG_PRJNAMEFORMAT

Defines: Format string for source file in C-syntax (projection name convention)
Value type: character
Default value: raw.%04i

PARTAG_DSTDATAPATH

Reconstructed volume data folder (folder where files with reconstructed slices are located)
Value type: character
Default value: The folder where the current xxm file exists

OPTTAG_SLCNAMEFORMAT

Defines: Format string for source file in C-syntax (slice name convention)
Value type: character
Default value: %04i.slice

BPMODETAG_LINITRP

Presence of this keyword in parameter file defines a fine reconstruction mode. Applicable for CPU-reconstruction only.
Value type: not applicable
Default value: both BPMODETAG_LINITRP and BPMODETAG_NRSTNBR are missing a draft reconstruction mode is being applied

BPMODETAG_NRSTNBR

Presence of this keyword in parameter file defines a draft reconstruction mode. Applicable for CPU-reconstruction only.
Value type: not applicable
Default value: when both BPMODETAG_LINITRP and BPMODETAG_NRSTNBR are missing a draft reconstruction mode is being applied

PARTAG_DUMPVOLBG

Applicable if reconstruction engine is working in multi-pass (multi-slab) mode (the reconstructed volume is too big to fit RAM). When set to 1 then the slices from a slab N-1 are being saved in parallel with reconstructing a slab N. Basically useful for cluster solutions.
Value type: integer (0 or 1)
Default value: 0

MODE_OFFLINE

Presence of this keyword in parameter file defines offline reconstruction mode when all projections exist on a disk at the moment of start of reconstruction.
Value type: not applicable
Default value: both MODE_OFFLINE and MODE_INLINE are missing offline reconstruction mode is being applied

MODE_INLINE

Presence of this keyword in parameter file defines inline reconstruction mode when existence of projection is being synchronized with the reconstruction process (for speedup)
Value type: not applicable
Default value: both MODE_OFFLINE and MODE_INLINE are missing offline reconstruction mode is being applied

PARTAG_SHOWEXTRA

Defines: the fraction of partially illuminated areas on the top and bottom of the field of view that will be shown in the reconstructed slices.
Value type: integer (0-2)
Default value: 1

PARTAG_EXTRAFOVSLICE

Defines: if set to 1 then all voxels in the slice periphery beyond FOV will be shown (not set to zero) in the reconstructed slices.
Value type: integer (0 or 1)
Default value: 0

PARTAG_HBTC

Defines: if set to 1 then half-beam geometry and reconstruction algorithm are effective.
Value type: integer (0 or 1)
Default value: 0

PARTAG_3XVIEW

Defines: if set to 1 then 3x view geometry and reconstruction algorithm are effective.
Value type: integer (0 or 1)
Default value: 0

PARTAG_FASTEXTVIEW

Defines: if set to 1 then half-beam reconstruction algorithm is being performed in draft mode (faster but density values are less accurate).
Value type: integer (0 or 1)
Default value: 0

PARTAG_STACKEDVOLQTY

Defines: If set to value 2 or bigger then stack-volume hardware setup and reconstruction algorithm are effective. It allows combining (stacking) several (from 2 to 12) cylindrical sub-volumes one on top of the other, thus increasing the effective detector size in V. Several scans must be performed and the object should be moved in vertical z-direction in between the scans.
Value type: integer (1-12)
Default value: 1

PARTAG_STACKEDVOLMODE

If PARTAG_STACKEDVOLQTY is set to value 2 or bigger then stack-volume hardware setup and reconstruction algorithm are effective. It allows combining (stacking) several (from 2 to 12) cylindrical sub-volumes one on top of the other, thus increasing the effective detector size in V. Several scans must be performed and the object should be moved in vertical z-direction in between the scans.
If PARTAG_STACKEDVOLMODE =0 then no angular alignment = 0, adjusting volumes only in x,y,z translation;
If PARTAG_STACKEDVOLMODE =1 then adjusting volumes in all 6 degrees of freedom.
Value type: integer (0-1)
Default value: 0

PARTAG_STACKEDVOLOVERLAP

PARTAG_STACKEDVOLOVERLAP defines an upper limit of overlap of stacked subvolumes (%). COBRA will look for 2 slices with maximum similarity and will stitch sub-volumes there.
Value type: integer (1-100)
Default value: 40

PARTAG_STACKEDVOLDIRECTION

If PARTAG_STACKEDVOLQTY is set to value 2 or bigger then stack-volume hardware setup and reconstruction algorithm is effective. It allows combining (stacking) several (from 2 to 12) cylindrical sub-volumes one on top of the other, thus increasing the effective detector size in V. Several scans must be performed and the object should be moved in vertical z-direction in between the scans.
PARTAG_STACKEDVOLDIRECTION defines a direction of object/gantry motion during making sub-volumes. Setting PARTAG_STACKEDVOLDIRECTION to 1 means sub-volume #0 will get highest slice numbers in a combined volume
Value type: integer (0-1)
Default value: 0

PARTAG_STACKEDVOLADJUSTFACTOR

PARTAG_STACKEDVOLADJUSTFACTOR defines a direction of object/gantry motion during making of sub-volumes. Setting PARTAG_STACKEDVOLDIRECTION to 1 means sub-volume #0 will get the highest slice numbers in a combined volume
Value type: integer (0-1)
Default value: 0

PARTAG_STACKEDVOLSEAMLOCATION

PARTAG_ STACKEDVOLSEAMLOCATION defines a slice number where sub-volumes have approximately same slice content. If set, it makes the sub-volume adjustment procedure more reliable and fast.
Value type: integer (0-number of slices in sub-volume)
Default value: 0

PARTAG_PROJ_RECON<NN>

PARTAG_PROJ_RECON defines number of projections to reconstruct, corresponds sub-volume ( #0, #1,…#11)
Value type: integer (0-11)
Default value: 512

PARTAG_PRJ_STARTFROM_3X

When PARTAG_3XVIEW is set to 1 then 3x view hardware setup and reconstruction algorithm are effective. It means that there is a second gantry (object) revolution with a different detector position. PARTAG_PRJ_STARTFROM_3X defines a first projection number belonging to the second gantry revolution.
Value type: integer
Default value: 512

PARTAG_PRJ_RECON_FORWARD_3X

When PARTAG_PRJ_RECON_FORWARD_3X is set to 1 then it is assumed that revolution with the outer detector position has been made first.
Value type: integer (0-1)
Default value: 0

PARTAG_DET_OFFSET_U_3XEXT

PARTAG_DET_OFFSET_U_3XEXT defines the detector position in the direction perpendicular to the axis of rotation.
Value type: float
Default value: 0

PARTAG_DET_OFFSET_V_3XEXT

PARTAG_DET_OFFSET_V_3XEXT defines the detector position in the direction parallel to the axis of rotation.
Value type: float
Default value: 0

OPTTAG_SLICESCALE

For performing a scaling of output volume values to calibrate the whole system to Hounsfield units or mg/sm³
Value type: float
Default value: 1.0

OPTTAG_GAMMASLICESCALE

is used to correct for nonlinearity resulting from beam hardening and scattering according to the following formula
Cube(x,y,z) =  Cube(x,y,z)  |  Cube(x,y,z)<1300
Cube(x,y,z) =  1300 + {Cube(x,y,z)-1300}*Gamma  |  Cube(x,y,z)<1300
Value type: float
Default value: 1.0

PARTAG_MINUS1000

Converting reconstructed volume values from density units (mg/cm3) to Hounsfield units if set to 1
Value type: integer (0 or 1)
Default value: 0

PARTAG_SLICEOFFSETVALUE

Numerical offset of reconstructed volume values. It overrides PARTAG_MINUS1000. It is typically used to increase a contrast keeping air level below –1000 Hounsfield units
Value type: integer
Default value: 0

PARTAG_NEGATIVE_DENIED

If set to 1 then negative densities below 0 mg/cm3 in the reconstructed volume values are converted to 0
Value type: integer
Default value: 0

PARTAG_SLICEFLIPX

Flips the cube about X-axis at output if set to 1
Value type: integer (0 or 1)
Default value: 0

PARTAG_SLICEFLIPY

Flips the cube abpout Y-axis at output if set to 1
Value type: integer (0 or 1)
Default value: 0

PARTAG_SLICEFLIPZ

Flips the cube about Z-axis at output if set to 1
Value type: integer (0 or 1)
Default value: 0

BPMODETAG_USE_GPU

Defines : using graphics accelerating unit (GPU) for performing the back-projecting phase of Felkamp algorithm
Value type: integer (0-1)
Default value: 0

PARTAG_FP_GPU

Defines: Performing re-projecting step on GPU. Relevant for Feldkamp artifact correction algorithm.
Value type: integer (0-1)
Default value: 0

OPTTAG_3DBUFFERSIZE

Defines : 3D buffer size (in MB) for performing the back-projecting phase of Felkamp algorithm
Value type: integer
Default value: auto (depends on available RAM)

OPTTAG_ENGINEQTY

Reserved. Currently used as COBRA internal non-documented tag
Value type: integer (1 or 2)
Default value: 1

OPTTAG_WORKDIR

Setting the folder for intermediate output files (SDK only)
Value type: character
Default value: The folder where Cobra is installed.