nipype.interfaces.niftyseg.maths module¶
Nipype interface for seg_maths.
The maths module provides higher-level interfaces to some of the operations that can be performed with the niftysegmaths (seg_maths) command-line program.
BinaryMaths¶
Bases: MathsCommand
Wrapped executable:
seg_maths
.Binary mathematical operations.
See also
Examples
>>> import copy >>> from nipype.interfaces import niftyseg >>> binary = niftyseg.BinaryMaths() >>> binary.inputs.in_file = 'im1.nii' >>> binary.inputs.output_datatype = 'float'>>> # Test sub operation >>> binary_sub = copy.deepcopy(binary) >>> binary_sub.inputs.operation = 'sub' >>> binary_sub.inputs.operand_file = 'im2.nii' >>> binary_sub.cmdline 'seg_maths im1.nii -sub im2.nii -odt float im1_sub.nii' >>> binary_sub.run()>>> # Test mul operation >>> binary_mul = copy.deepcopy(binary) >>> binary_mul.inputs.operation = 'mul' >>> binary_mul.inputs.operand_value = 2.0 >>> binary_mul.cmdline 'seg_maths im1.nii -mul 2.00000000 -odt float im1_mul.nii' >>> binary_mul.run()>>> # Test llsnorm operation >>> binary_llsnorm = copy.deepcopy(binary) >>> binary_llsnorm.inputs.operation = 'llsnorm' >>> binary_llsnorm.inputs.operand_file = 'im2.nii' >>> binary_llsnorm.cmdline 'seg_maths im1.nii -llsnorm im2.nii -odt float im1_llsnorm.nii' >>> binary_llsnorm.run()>>> # Test splitinter operation >>> binary_splitinter = copy.deepcopy(binary) >>> binary_splitinter.inputs.operation = 'splitinter' >>> binary_splitinter.inputs.operand_str = 'z' >>> binary_splitinter.cmdline 'seg_maths im1.nii -splitinter z -odt float im1_splitinter.nii' >>> binary_splitinter.run()
- in_filea pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument:
%s
(position: 2).- operand_filea pathlike object or string representing an existing file
Second image to perform operation with. Maps to a command-line argument:
%s
(position: 5). Mutually exclusive with inputs:operand_value
,operand_str
.- operand_str‘x’ or ‘y’ or ‘z’
String value to perform operation splitinter. Maps to a command-line argument:
%s
(position: 5). Mutually exclusive with inputs:operand_value
,operand_file
.- operand_valuea float
Float value to perform operation with. Maps to a command-line argument:
%.8f
(position: 5). Mutually exclusive with inputs:operand_file
,operand_str
.- operation‘mul’ or ‘div’ or ‘add’ or ‘sub’ or ‘pow’ or ‘thr’ or ‘uthr’ or ‘smo’ or ‘edge’ or ‘sobel3’ or ‘sobel5’ or ‘min’ or ‘smol’ or ‘geo’ or ‘llsnorm’ or ‘masknan’ or ‘hdr_copy’ or ‘splitinter’
Operation to perform:
mul - <float/file> - Multiply image <float> value or by other image.
div - <float/file> - Divide image by <float> or by other image.
add - <float/file> - Add image by <float> or by other image.
sub - <float/file> - Subtract image by <float> or by other image.
pow - <float> - Image to the power of <float>.
thr - <float> - Threshold the image below <float>.
uthr - <float> - Threshold image above <float>.
smo - <float> - Gaussian smoothing by std <float> (in voxels and up to 4-D).
edge - <float> - Calculate the edges of the image using a threshold <float>.
sobel3 - <float> - Calculate the edges of all timepoints using a Sobel filter with a 3x3x3 kernel and applying <float> gaussian smoothing.
sobel5 - <float> - Calculate the edges of all timepoints using a Sobel filter with a 5x5x5 kernel and applying <float> gaussian smoothing.
min - <file> - Get the min per voxel between <current> and <file>.
smol - <float> - Gaussian smoothing of a 3D label image.
geo - <float/file> - Geodesic distance according to the speed function <float/file>
llsnorm <file_norm> - Linear LS normalisation between current and <file_norm>
masknan <file_norm> - Assign everything outside the mask (mask==0) with NaNs
hdr_copy <file> - Copy header from working image to <file> and save in <output>.
splitinter <x/y/z> - Split interleaved slices in direction <x/y/z> into separate time points
Maps to a command-line argument:
-%s
(position: 4).
- argsa string
Additional parameters to the command. Maps to a command-line argument:
%s
.- environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value:
{}
)- out_filea pathlike object or string representing a file
Image to write. Maps to a command-line argument:
%s
(position: -2).- output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’
Datatype to use for output (default uses input type). Maps to a command-line argument:
-odt %s
(position: -3).
- out_filea pathlike object or string representing a file
Image written after calculations.
BinaryMathsInteger¶
Bases: MathsCommand
Wrapped executable:
seg_maths
.Integer mathematical operations.
See also
Examples
>>> import copy >>> from nipype.interfaces.niftyseg import BinaryMathsInteger >>> binaryi = BinaryMathsInteger() >>> binaryi.inputs.in_file = 'im1.nii' >>> binaryi.inputs.output_datatype = 'float' >>> # Test dil operation >>> binaryi_dil = copy.deepcopy(binaryi) >>> binaryi_dil.inputs.operation = 'dil' >>> binaryi_dil.inputs.operand_value = 2 >>> binaryi_dil.cmdline 'seg_maths im1.nii -dil 2 -odt float im1_dil.nii' >>> binaryi_dil.run() >>> # Test dil operation >>> binaryi_ero = copy.deepcopy(binaryi) >>> binaryi_ero.inputs.operation = 'ero' >>> binaryi_ero.inputs.operand_value = 1 >>> binaryi_ero.cmdline 'seg_maths im1.nii -ero 1 -odt float im1_ero.nii' >>> binaryi_ero.run() >>> # Test pad operation >>> binaryi_pad = copy.deepcopy(binaryi) >>> binaryi_pad.inputs.operation = 'pad' >>> binaryi_pad.inputs.operand_value = 4 >>> binaryi_pad.cmdline 'seg_maths im1.nii -pad 4 -odt float im1_pad.nii' >>> binaryi_pad.run()
- in_filea pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument:
%s
(position: 2).- operand_valuean integer
Int value to perform operation with. Maps to a command-line argument:
%d
(position: 5).- operation‘dil’ or ‘ero’ or ‘tp’ or ‘equal’ or ‘pad’ or ‘crop’
Operation to perform:
equal - <int> - Get voxels equal to <int>
dil - <int> - Dilate the image <int> times (in voxels).
ero - <int> - Erode the image <int> times (in voxels).
tp - <int> - Extract time point <int>
crop - <int> - Crop <int> voxels around each 3D volume.
pad - <int> - Pad <int> voxels with NaN value around each 3D volume.
Maps to a command-line argument:
-%s
(position: 4).
- argsa string
Additional parameters to the command. Maps to a command-line argument:
%s
.- environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value:
{}
)- out_filea pathlike object or string representing a file
Image to write. Maps to a command-line argument:
%s
(position: -2).- output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’
Datatype to use for output (default uses input type). Maps to a command-line argument:
-odt %s
(position: -3).
- out_filea pathlike object or string representing a file
Image written after calculations.
MathsCommand¶
Bases: NiftySegCommand
Wrapped executable:
seg_maths
.Base Command Interface for seg_maths interfaces.
The executable seg_maths enables the sequential execution of arithmetic operations, like multiplication (-mul), division (-div) or addition (-add), binarisation (-bin) or thresholding (-thr) operations and convolution by a Gaussian kernel (-smo). It also allows mathematical morphology based operations like dilation (-dil), erosion (-ero), connected components (-lconcomp) and hole filling (-fill), Euclidean (- euc) and geodesic (-geo) distance transforms, local image similarity metric calculation (-lncc and -lssd). Finally, it allows multiple operations over the dimensionality of the image, from merging 3D images together as a 4D image (-merge) or splitting (-split or -tp) 4D images into several 3D images, to estimating the maximum, minimum and average over all time-points, etc.
- in_filea pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument:
%s
(position: 2).
- argsa string
Additional parameters to the command. Maps to a command-line argument:
%s
.- environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value:
{}
)- out_filea pathlike object or string representing a file
Image to write. Maps to a command-line argument:
%s
(position: -2).- output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’
Datatype to use for output (default uses input type). Maps to a command-line argument:
-odt %s
(position: -3).
- out_filea pathlike object or string representing a file
Image written after calculations.
Merge¶
Bases: MathsCommand
Wrapped executable:
seg_maths
.Merge image files.
See also
Examples
>>> from nipype.interfaces import niftyseg >>> node = niftyseg.Merge() >>> node.inputs.in_file = 'im1.nii' >>> files = ['im2.nii', 'im3.nii'] >>> node.inputs.merge_files = files >>> node.inputs.dimension = 2 >>> node.inputs.output_datatype = 'float' >>> node.cmdline 'seg_maths im1.nii -merge 2 2 im2.nii im3.nii -odt float im1_merged.nii'
- dimensionan integer
Dimension to merge the images.
- in_filea pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument:
%s
(position: 2).- merge_filesa list of items which are a pathlike object or string representing an existing file
List of images to merge to the working image <input>. Maps to a command-line argument:
%s
(position: 4).
- argsa string
Additional parameters to the command. Maps to a command-line argument:
%s
.- environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value:
{}
)- out_filea pathlike object or string representing a file
Image to write. Maps to a command-line argument:
%s
(position: -2).- output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’
Datatype to use for output (default uses input type). Maps to a command-line argument:
-odt %s
(position: -3).
- out_filea pathlike object or string representing a file
Image written after calculations.
TupleMaths¶
Bases: MathsCommand
Wrapped executable:
seg_maths
.Mathematical operations on tuples.
See also
Examples
>>> import copy >>> from nipype.interfaces import niftyseg >>> tuple = niftyseg.TupleMaths() >>> tuple.inputs.in_file = 'im1.nii' >>> tuple.inputs.output_datatype = 'float'>>> # Test lncc operation >>> tuple_lncc = copy.deepcopy(tuple) >>> tuple_lncc.inputs.operation = 'lncc' >>> tuple_lncc.inputs.operand_file1 = 'im2.nii' >>> tuple_lncc.inputs.operand_value2 = 2.0 >>> tuple_lncc.cmdline 'seg_maths im1.nii -lncc im2.nii 2.00000000 -odt float im1_lncc.nii' >>> tuple_lncc.run()>>> # Test lssd operation >>> tuple_lssd = copy.deepcopy(tuple) >>> tuple_lssd.inputs.operation = 'lssd' >>> tuple_lssd.inputs.operand_file1 = 'im2.nii' >>> tuple_lssd.inputs.operand_value2 = 1.0 >>> tuple_lssd.cmdline 'seg_maths im1.nii -lssd im2.nii 1.00000000 -odt float im1_lssd.nii' >>> tuple_lssd.run()>>> # Test lltsnorm operation >>> tuple_lltsnorm = copy.deepcopy(tuple) >>> tuple_lltsnorm.inputs.operation = 'lltsnorm' >>> tuple_lltsnorm.inputs.operand_file1 = 'im2.nii' >>> tuple_lltsnorm.inputs.operand_value2 = 0.01 >>> tuple_lltsnorm.cmdline 'seg_maths im1.nii -lltsnorm im2.nii 0.01000000 -odt float im1_lltsnorm.nii' >>> tuple_lltsnorm.run()
- in_filea pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument:
%s
(position: 2).- operand_file1a pathlike object or string representing an existing file
Image to perform operation 1 with. Maps to a command-line argument:
%s
(position: 5). Mutually exclusive with inputs:operand_value1
.- operand_file2a pathlike object or string representing an existing file
Image to perform operation 2 with. Maps to a command-line argument:
%s
(position: 6). Mutually exclusive with inputs:operand_value2
.- operand_value1a float
Float value to perform operation 1 with. Maps to a command-line argument:
%.8f
(position: 5). Mutually exclusive with inputs:operand_file1
.- operand_value2a float
Float value to perform operation 2 with. Maps to a command-line argument:
%.8f
(position: 6). Mutually exclusive with inputs:operand_file2
.- operation‘lncc’ or ‘lssd’ or ‘lltsnorm’
Operation to perform:
lncc <file> <std> Local CC between current img and <file> on a kernel with <std>
lssd <file> <std> Local SSD between current img and <file> on a kernel with <std>
lltsnorm <file_norm> <float> Linear LTS normalisation assuming <float> percent outliers
Maps to a command-line argument:
-%s
(position: 4).
- argsa string
Additional parameters to the command. Maps to a command-line argument:
%s
.- environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value:
{}
)- out_filea pathlike object or string representing a file
Image to write. Maps to a command-line argument:
%s
(position: -2).- output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’
Datatype to use for output (default uses input type). Maps to a command-line argument:
-odt %s
(position: -3).
- out_filea pathlike object or string representing a file
Image written after calculations.
UnaryMaths¶
Bases: MathsCommand
Wrapped executable:
seg_maths
.Unary mathematical operations.
See also
Examples
>>> import copy >>> from nipype.interfaces import niftyseg >>> unary = niftyseg.UnaryMaths() >>> unary.inputs.output_datatype = 'float' >>> unary.inputs.in_file = 'im1.nii'>>> # Test sqrt operation >>> unary_sqrt = copy.deepcopy(unary) >>> unary_sqrt.inputs.operation = 'sqrt' >>> unary_sqrt.cmdline 'seg_maths im1.nii -sqrt -odt float im1_sqrt.nii' >>> unary_sqrt.run()>>> # Test sqrt operation >>> unary_abs = copy.deepcopy(unary) >>> unary_abs.inputs.operation = 'abs' >>> unary_abs.cmdline 'seg_maths im1.nii -abs -odt float im1_abs.nii' >>> unary_abs.run()>>> # Test bin operation >>> unary_bin = copy.deepcopy(unary) >>> unary_bin.inputs.operation = 'bin' >>> unary_bin.cmdline 'seg_maths im1.nii -bin -odt float im1_bin.nii' >>> unary_bin.run()>>> # Test otsu operation >>> unary_otsu = copy.deepcopy(unary) >>> unary_otsu.inputs.operation = 'otsu' >>> unary_otsu.cmdline 'seg_maths im1.nii -otsu -odt float im1_otsu.nii' >>> unary_otsu.run()>>> # Test isnan operation >>> unary_isnan = copy.deepcopy(unary) >>> unary_isnan.inputs.operation = 'isnan' >>> unary_isnan.cmdline 'seg_maths im1.nii -isnan -odt float im1_isnan.nii' >>> unary_isnan.run()
- in_filea pathlike object or string representing an existing file
Image to operate on. Maps to a command-line argument:
%s
(position: 2).- operation‘sqrt’ or ‘exp’ or ‘log’ or ‘recip’ or ‘abs’ or ‘bin’ or ‘otsu’ or ‘lconcomp’ or ‘concomp6’ or ‘concomp26’ or ‘fill’ or ‘euc’ or ‘tpmax’ or ‘tmean’ or ‘tmax’ or ‘tmin’ or ‘splitlab’ or ‘removenan’ or ‘isnan’ or ‘subsamp2’ or ‘scl’ or ‘4to5’ or ‘range’
Operation to perform:
sqrt - Square root of the image).
exp - Exponential root of the image.
log - Log of the image.
recip - Reciprocal (1/I) of the image.
abs - Absolute value of the image.
bin - Binarise the image.
otsu - Otsu thresholding of the current image.
lconcomp - Take the largest connected component
concomp6 - Label the different connected components with a 6NN kernel
concomp26 - Label the different connected components with a 26NN kernel
fill - Fill holes in binary object (e.g. fill ventricle in brain mask).
euc - Euclidean distance transform
tpmax - Get the time point with the highest value (binarise 4D probabilities)
tmean - Mean value of all time points.
tmax - Max value of all time points.
tmin - Mean value of all time points.
splitlab - Split the integer labels into multiple timepoints
removenan - Remove all NaNs and replace then with 0
isnan - Binary image equal to 1 if the value is NaN and 0 otherwise
subsamp2 - Subsample the image by 2 using NN sampling (qform and sform scaled)
scl - Reset scale and slope info.
4to5 - Flip the 4th and 5th dimension.
range - Reset the image range to the min max.
Maps to a command-line argument:
-%s
(position: 4).
- argsa string
Additional parameters to the command. Maps to a command-line argument:
%s
.- environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value:
{}
)- out_filea pathlike object or string representing a file
Image to write. Maps to a command-line argument:
%s
(position: -2).- output_datatype‘float’ or ‘char’ or ‘int’ or ‘short’ or ‘double’ or ‘input’
Datatype to use for output (default uses input type). Maps to a command-line argument:
-odt %s
(position: -3).
- out_filea pathlike object or string representing a file
Image written after calculations.