3 d:@sdZddlZddlZddlmZmZmZmZm Z ddlm Z m Z Gddde Z Gd d d eZ Gd d d e ZGd dde ZGdddeZGddde ZGdddeZGddde ZGdddeZGddde ZGdddeZGddde ZGdd d eZGd!d"d"e ZGd#d$d$eZGd%d&d&e ZGd'd(d(eZGd)d*d*e ZGd+d,d,eZGd-d.d.e ZGd/d0d0eZ Gd1d2d2e Z!Gd3d4d4eZ"Gd5d6d6e Z#Gd7d8d8eZ$Gd9d:d:e Z%Gd;d<dd>e Z'Gd?d@d@e'Z(GdAdBdBeZ)GdCdDdDe'Z*GdEdFdFeZ+GdGdHdHe'Z,GdIdJdJeZ-GdKdLdLe Z.GdMdNdNeZ/GdOdPdPe Z0GdQdRdReZ1GdSdTdTe Z2GdUdVdVeZ3GdWdXdXe Z4GdYdZdZeZ5dS)[z The maths module provides higher-level interfaces to some of the operations that can be performed with the fslmaths command-line program. N) TraitedSpecFiletraitsInputMultiPath isdefined) FSLCommandFSLCommandInputSpecc@sxeZdZeddddddZeddddddZd d d d d dgZejeddddZ ejeddddZ ej ddddZ dS) MathsInputrz%sTzimage to operate on)positionargstrexists mandatorydesczimage to writeF)Zgenfiler r rZ hash_filesfloatcharintshortdoubleinputrz-dt %sz3datatype to use for calculations (default is float))r r rz-odt %sz4datatype to use for output (default uses input type)z-nanz*change NaNs to zeros before doing anythingN) __name__ __module__ __qualname__rin_fileout_file_dtypesrEnumZinternal_datatypeoutput_datatypeBoolZ nan2zerosr#r#=/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/fsl/maths.pyr s"  r c@seZdZeddZdS) MathsOutputz image written after calculations)rN)rrrrrr#r#r#r$r%*sr%c@s,eZdZdZeZeZdZddZ ddZ dS) MathsCommandZfslmathsZ_mathscCsT|jj}|jj|d<t|jjs<|j|jj|jd|d<tj j |d|d<|S)Nr)suffix) output_specgetinputsrrZ _gen_fnamer_suffixospathabspath)selfoutputsr#r#r$ _list_outputs6s   zMathsCommand._list_outputscCs|dkr|jdSdS)Nr)r1)r/namer#r#r$ _gen_filename@s zMathsCommand._gen_filenameN) rrrZ_cmdr input_specr%r(r+r1r3r#r#r#r$r&/s  r&c@s2eZdZddddddgZejed dd d d Zd S)ChangeDataTypeInputrrrrrrrz-odt %sTzoutput data type)r r rrNr)rrrrrr r!r#r#r#r$r5Fsr5c@seZdZdZeZdZdS)ChangeDataTypez0Use fslmaths to change the datatype of an image.Z_chdtN)rrr__doc__r5r4r+r#r#r#r$r6Nsr6c@sLeZdZejdddddZejddddd Zejd d Z ejd d gdZ dS)ThresholdInputSpecTz%szthreshold value)rr r rZbelowabovez+zero-out either below or above thresh value) usedefaultrz6interpret thresh as percentage (0-100) of robust range)rz,use nonzero voxels to calculate robust rangeuse_robust_range)rrequiresN) rrrrFloatthreshr directionr"r<use_nonzero_voxelsr#r#r#r$r8Usr8cs(eZdZdZeZdZfddZZS) ThresholdzCUse fslmaths to apply a threshold to an image in a variety of ways.Z_threshcs|dkrpd}|j}|jjdkr&|d7}|d7}t|jr`|jr`t|jrX|jrX|d7}n|d7}|d|7}|Stt|j|||S) Nr?-r:uZthrPpz %.10f)r*r@rr<rAsuperrB _format_arg)r/r2specvalueargZ_si) __class__r#r$rHos   zThreshold._format_arg) rrrr7r8r4r+rH __classcell__r#r#)rLr$rBisrBc @s&eZdZejddddddddd Zd S) StdImageInputTXYZTz-%sstdr9z$dimension to standard deviate across)r;r r rN)rrrrr dimensionr#r#r#r$rNsrNc@seZdZdZeZdZdS)StdImagez\Use fslmaths to generate a standard deviation in an image across a given dimension. Z_stdN)rrrr7rNr4r+r#r#r#r$rTsrTc @s&eZdZejddddddddd Zd S) MeanImageInputrOrPrQrRTz-%smeanr9zdimension to mean across)r;r r rN)rrrrr rSr#r#r#r$rUsrUc@seZdZdZeZdZdS) MeanImagez?Use fslmaths to generate a mean image across a given dimension.Z_meanN)rrrr7rUr4r+r#r#r#r$rVsrVc @s&eZdZejddddddddd Zd S) MaxImageInputrOrPrQrRTz-%smaxr9zdimension to max across)r;r r rN)rrrrr rSr#r#r#r$rWsrWc@seZdZdZeZdZdS)MaxImagearUse fslmaths to generate a max image across a given dimension. Examples -------- >>> from nipype.interfaces.fsl.maths import MaxImage >>> maxer = MaxImage() >>> maxer.inputs.in_file = "functional.nii" # doctest: +SKIP >>> maxer.dimension = "T" >>> maxer.cmdline # doctest: +SKIP 'fslmaths functional.nii -Tmax functional_max.nii' Z_maxN)rrrr7rWr4r+r#r#r#r$rXs rXc @s:eZdZejddddddddd Zejd d d d ddZdS)PercentileImageInputrOrPrQrRTz-%spercr9zdimension to percentile across)r;r r rrdz%fz5nth percentile (0-100) of FULL RANGE across dimension)lowhighr r rN)rrrrr rSZRangepercr#r#r#r$rYsrYc@seZdZdZeZdZdS)PercentileImageaUse fslmaths to generate a percentile image across a given dimension. Examples -------- >>> from nipype.interfaces.fsl.maths import MaxImage >>> percer = PercentileImage() >>> percer.inputs.in_file = "functional.nii" # doctest: +SKIP >>> percer.dimension = "T" >>> percer.perc = 90 >>> percer.cmdline # doctest: +SKIP 'fslmaths functional.nii -Tperc 90 functional_perc.nii' Z_percN)rrrr7rYr4r+r#r#r#r$r_s r_c @s&eZdZejddddddddd Zd S) MaxnImageInputrOrPrQrRTz-%smaxnr9zdimension to index max across)r;r r rN)rrrrr rSr#r#r#r$r`sr`c@seZdZdZeZdZdS) MaxnImagezUUse fslmaths to generate an image of index of max across a given dimension. Z_maxnN)rrrr7r`r4r+r#r#r#r$rasrac @s&eZdZejddddddddd Zd S) MinImageInputrOrPrQrRTz-%sminr9zdimension to min across)r;r r rN)rrrrr rSr#r#r#r$rb srbc@seZdZdZeZdZdS)MinImagezBUse fslmaths to generate a minimum image across a given dimension.Z_minN)rrrr7rbr4r+r#r#r#r$rcsrcc @s&eZdZejddddddddd Zd S) MedianImageInputrOrPrQrRTz -%smedianr9zdimension to median across)r;r r rN)rrrrr rSr#r#r#r$rd!srdc@seZdZdZeZdZdS) MedianImagezAUse fslmaths to generate a median image across a given dimension.Z_medianN)rrrr7rdr4r+r#r#r#r$re/srec @s&eZdZejddddddddd Zd S) AR1ImageInputrOrPrQrRTz-%sar1r9z)dimension to find AR(1) coefficientacross)r;r r rN)rrrrr rSr#r#r#r$rf6srfc@seZdZdZeZdZdS)AR1ImagezUse fslmaths to generate an AR1 coefficient image across a given dimension. (Should use -odt float and probably demean first) Z_ar1N)rrrr7rfr4r+r#r#r#r$rgDsrgc@s8eZdZejddgddddZejddgddddZd S) IsotropicSmoothInputTsigmar9z-s %.5fzfwhm of smoothing kernel [mm])rxorr r rfwhmzsigma of smoothing kernel [mm]N)rrrrr>rkrir#r#r#r$rhNsrhcs(eZdZdZeZdZfddZZS)IsotropicSmoothzAUse fslmaths to spatially smooth an image with a gaussian kernel.Z_smoothcsB|dkr.t|tjdtjd}|j|Stt|j|||S)Nrkr)rnpsqrtlogr rGrlrH)r/r2rIrJri)rLr#r$rHfs zIsotropicSmooth._format_arg) rrrr7rhr4r+rHrMr#r#)rLr$rl`srlc@seZdZeddddddZdS)ApplyMaskInputTz-mas %sr9z binary image defining mask space)rrr r rN)rrrrZ mask_filer#r#r#r$rqms rqc@seZdZdZeZdZdS) ApplyMaskz5Use fslmaths to apply a binary mask to another image.Z_maskedN)rrrr7rqr4r+r#r#r#r$rrxsrrc @sReZdZejddddddddd d d Zejd d dgddZeddd dgddZ dS) KernelInputZ3DZ2DZboxZboxvgaussZspherefilez -kernel %sr9zkernel shape to use)r r rz%.4fr[ kernel_filezDkernel size - voxels for box/boxv, mm for sphere, mm sigma for gauss)r r rjrTz%s kernel_sizezuse external file for kernel)rr r rjrN) rrrrr Z kernel_shaper>rwrrvr#r#r#r$rss,rsc @s$eZdZejddddddddZd S) DilateInputmeanmodalmaxz-dil%sTz*filtering operation to perfoem in dilation)r r rrN)rrrrr operationr#r#r#r$rxsrxcs(eZdZdZeZdZfddZZS) DilateImagez7Use fslmaths to perform a spatial dilation of an image.Z_dilcs4|dkr |jtdddd|Stt|j|||S)Nr}MDF)ryrzr{)r dictrGr~rH)r/r2rIrJ)rLr#r$rHszDilateImage._format_arg) rrrr7rxr4r+rHrMr#r#)rLr$r~sr~c@s eZdZejddddddZdS) ErodeInputz%sr|TFz:if true, minimum filter rather than erosion by zeroing-out)r r r; default_valuerN)rrrrr"minimum_filterr#r#r#r$rs rcs(eZdZdZeZdZfddZZS) ErodeImagez6Use fslmaths to perform a spatial erosion of an image.Z_erocs(|dkr|rdSdStt|j|||S)Nrz-eroFz-ero)rGrrH)r/r2rIrJ)rLr#r$rHs zErodeImage._format_arg) rrrr7rr4r+rHrMr#r#)rLr$rsrc @s$eZdZejddddddddZd S) SpatialFilterInputryZmedianZmeanuz-f%sr|Tzoperation to filter with)r r rrN)rrrrr r}r#r#r#r$rsrc@seZdZdZeZdZdS) SpatialFilterz*Use fslmaths to spatially filter an image._filtN)rrrr7rr4r+r#r#r#r$rsrc@sLeZdZejddddddddd d d d d dddddddddddddddZdS)UnaryMathsInputexprpsincostanasinacosatanZsqrroZrecipabsbinZbinvZfillhZfillh26indexZedgenanZnanmZrandZrandnrangez-%sr9Tzoperation to perform)r r rrN)rrrrr r}r#r#r#r$rs8rcs$eZdZdZeZfddZZS) UnaryMathszHUse fslmaths to perorm a variety of mathematical operations on an image.csd|jj|_tt|jS)N_)r*r}r+rGrr1)r/)rLr#r$r1 szUnaryMaths._list_outputs)rrrr7rr4r1rMr#r#)rLr$rsrc @sXeZdZejddddddddd d d d Zedd dddgddZejddddgddZ dS)BinaryMathsInputaddsubmuldivremr{minTz-%sr9zoperation to perform)rr r rz%sr[ operand_valuez&second image to perform operation with)rr rr rjrz%.8f operand_filezvalue to perform operation with)r rr rjrN) rrrrr r}rrr>rr#r#r#r$rs2rc@seZdZdZeZdS) BinaryMathszbUse fslmaths to perform mathematical operations using a second image or a numeric value. N)rrrr7rr4r#r#r#r$r/src@s2eZdZejdddddZeedddddZd S) MultiImageMathsInputr9z%sTz0python formatted string of operations to perform)r r rr)rz)list of file names to plug into op string)rrN) rrrrString op_stringrr operand_filesr#r#r#r$r8srcs$eZdZdZeZfddZZS)MultiImageMathsaUse fslmaths to perform a sequence of mathematical operations. Examples -------- >>> from nipype.interfaces.fsl import MultiImageMaths >>> maths = MultiImageMaths() >>> maths.inputs.in_file = "functional.nii" >>> maths.inputs.op_string = "-add %s -mul -1 -div %s" >>> maths.inputs.operand_files = ["functional2.nii", "functional3.nii"] >>> maths.inputs.out_file = "functional4.nii" >>> maths.cmdline 'fslmaths functional.nii -add functional2.nii -mul -1 -div functional3.nii functional4.nii' cs,|dkr|t|jjStt|j|||S)Nr)tupler*rrGrrH)r/r2rIrJ)rLr#r$rHYszMultiImageMaths._format_arg)rrrr7rr4rHrMr#r#)rLr$rGsrc@s4eZdZejd dddddZejd dddd dZd S) TemporalFilterInputrz%.6fr[Tz!lowpass filter sigma (in volumes))r r r;rz -bptf %.6fr9z"highpass filter sigma (in volumes)Nrr)rrrrr>Z lowpass_sigmaZhighpass_sigmar#r#r#r$r_src@seZdZdZeZdZdS)TemporalFilterzYUse fslmaths to apply a low, high, or bandpass temporal filter to a timeseries. rN)rrrr7rr4r+r#r#r#r$rqsr)6r7r,numpyrnbaserrrrrr r r r%r&r5r6r8rBrNrTrUrVrWrXrYr_r`rarbrcrdrerfrgrhrlrqrrrsrxr~rrrrrrrrrrrrr#r#r#r$s\         !