[f2ca4d]: / utils / resizeScans.pyc

Download this file

49 lines (47 with data), 4.5 kB

ó
M6žYc@s-ddlZddlZddlZddlZddlZddlZddlZddl	Z	ddl
Z
ddlZddlmZddlZddlZddl
Z
ddlmZddlZddljZddlZddlZdZeeddƒZedZedZed	Zed
ZedZedZed
ZddgZ e!edƒZ"ejedƒZ#edj$dƒZ%ej&ge%D]Z'e!e'ƒ^qœƒZ%dd„Z(dd„Z)ed„Z*e+dkr)x?e#D]4Z,ej-j.e,ƒZ/ej-j0ede/deƒZ1ej-j0ede/eƒZ2ej-j0ede/eƒZ3ej-j0ede/eƒZ4e1j5dedƒZ6e2j5dedƒZ7e3j5dedƒZ8e4j5dedƒZ9e)e1e6e%ƒe"róe*e6e6ƒne)e2e7e%dƒesîe)e3e8e%dƒqîqîWndS(iÿÿÿÿN(trandint(tdocopts_Write something here

Usage: 
    resizeScans.py [options]

Options:
    -h, --help                  Print this message
    --mainFolderPath=<str>      Main folder path [default: ../../Data/MS2017b/]
    --FLAIR_name=<str>          FLAIR prefix [default: FLAIR.nii.gz]
    --WMH_name=<str>            WMH prefix [default: wmh.nii.gz]
    --GIF_name=<str>            GIF prefix [default: parcellation.nii.gz]
    --CIRC_name=<str>           CIRC prefix [default: circumference.nii.gz]
    --gpu0=<int>                GPU number [default: 0]
    --useGPU=<int>              Use GPU [default: 0]
    --size=<str>                Shape to resize to [default: 200x200x100]
    --noGIFS                    Dont Resize GIFS
    --postfix=<str>             Postfix name to add [default: _200x200x100orig]
    --withNorm=<int>            Include normalization [default: 1]
tversionsv0.1s--noGIFSs--mainFolderPaths--FLAIR_names
--WMH_names
--GIF_names--CIRC_names	--postfixthisttinsubjectvars
--withNormsscans/*s--sizetxtinterpolatecCsÕtj|ƒ}|j}|dt|dƒ}|dt|dƒ}|dt|dƒ}d|d|dt|ƒdt|ƒdt|ƒd|}	|	GHtj|	jƒdtjƒ}
|
j	ƒdS(	Niiismri_convert t s -ds s -rt tstdout(
tPPt
numpyFromScantshapetfloattstrt
subprocesstPopentsplittPIPEtcommunicate(t	from_pathtto_pathtnew_sizet
interpolationtimgRtr1tr2tr3tcommandtprocess((s.//utils/resizeScans.pytconvertSizeAs	DcCsA|dkrdg}n|dkr0dg}ntj|dtƒ\}}|j}tj|ƒ}t|dƒ|d}	t|dƒ|d}
t|dƒ|d}|dd…dfc|	:<|dd…dfc|
:<|dd…dfc|:<tj|g|	|
|g|ƒdj	ƒ}tj
|||ƒ|S(NRitnearestit
get_affinei(R	R
tTrueRtnptcopyRtAUGMt
applyScaletsqueezetsaveScan(RRRRtspline_ordertimg_nptaffineRt
new_affineRRR((s.//utils/resizeScans.pytconvertSize2Ms 	+cCs‚tj|dtƒ\}}tj|jƒtdtdd|ƒ}tj|jƒtdtdd|ƒ}tj|||ƒdS(NRtnorm_methoditmain_folder_pathi(	R	R
R tNORMtapplyNormalizeR%tpostfixt	norm_typeR&(RRR-R(R)((s.//utils/resizeScans.pyt
normalizeScanbs((t__main__tscanstpretgifss.nii.gzR(:tostnumpyR!tnibabeltnibttimetmathtrandomtglobtcollectionstsysRtdatetimeRRR	t
nilearn.imagetimagetnimgtnormalizationsR.t
augmentationsR#tdocstrtargstnoGIFSR-t
FLAIR_nametWMH_nametGIF_namet	CIRC_nameR0R1tintt	with_normtglob_foldersRRtarraytiRR+R2t__name__tscan_foldertpathtbasenamet
folder_numtjoint
flair_pathtwmh_pathtgif_patht	circ_pathtreplacet
to_flair_pathtto_wmh_pathtto_gif_pathtto_circ_path(((s.//utils/resizeScans.pyt<module>sh






(