[b5be3a]: / 1 - Methods with Improved Results / __pycache__ / SegmentationFunctions.cpython-38.pyc

Download this file

110 lines (106 with data), 11.2 kB

U

ÓmbÆ=ã@sžddlZddlZddlZddlZddlZddlmZ	ddl
mZddlm
Z
ddlmZmZmZmZmZmZmZddlmZmZddlmZddlmZddlmZdd	l m!Z!d
Z"dZ#dZ$e	j%d
e"de	j%de"de	j%de#de	j%de"de	j%de"de	j%de#de	j%de$dde	j&d<dd„Z'dd„Z(d1dd„Z)d2dd „Z*d3d!d"„Z+d4d#d$„Z,d5d%d&„Z-d6d'd(„Z.d7d)d*„Z/d8d+d,„Z0d-d.„Z1d9d/d0„Z2dS):éN)Ú	Rectangle)ÚKMeans)ÚerosionÚopeningÚclosingÚsquareÚdiskÚconvex_hull_imageÚremove_small_holes)ÚlabelÚregionprops)Úsobel)Úcanny)Úndimage)Ú	watershedé
ééZfont)ÚsizeÚaxes)Z	titlesize)Z	labelsizeZxtickZytickZlegend)ZfontsizeÚfigure©é
ézfigure.figsizecCs‚g}t |¡D]}| |dd…d|¡q|jdd„d|d|d d¡d|d d¡…}td	|t|ƒfƒ||fS)
Néú/cSs t|| d¡d| d¡…ƒS)NÚ_éÚ.)ÚintÚfind)Ús©r"ú–/home/nushkash/PES1UG19CS078/4 IPCV Lab/Project - Cardiac Segmentation/cardiac-segmentation/1 - Methods with Improved Results/SegmentationFunctions.pyÚ<lambda>'óz"readSortedSlices.<locals>.<lambda>©Úkeyrrrz,CT scan of Patient %s consists of %d slices.)ÚosÚlistdirÚappendÚsortr ÚprintÚlen)ÚpathÚslicesr!ÚIDr"r"r#ÚreadSortedSlices"s(r1cCsttt|ƒƒS)N)ÚlistÚmapÚreadImg)r/r"r"r#ÚgetSliceImages,sr5cCs<t d|¡}t |tj¡}|r8t d¡tj|dd|S)Nz../zA CT Scan Image SliceÚgray©Zcmap)Úcv2ZimreadZcvtColorZCOLOR_RGB2GRAYÚpltÚtitleÚimshow)r.Ú
showOutputÚimgr"r"r#r40s
r4cst ||jd|jd¡ dd¡}t|dd}| |¡}|j}|j}ttt 	|¡|ƒƒ‰t 
‡fdd„|Dƒ¡}	|	 |jd|jd¡ t¡}	|rüt
jddddd	d
\}
}| ¡}|dj|dd|d d
¡|d |	¡|d dt|ƒd¡ˆ|	fS)zº
    Apply KMeans on an image with the number of clusters K
    Input: Image, Number of clusters K
    Output: Dictionary of cluster center labels and points, Output segmented image
    rréÿÿÿÿ)Z
n_clustersÚverbosecsg|]}ˆ|‘qSr"r")Ú.0r©Z
center_labelsr"r#Ú
<listcomp>KszimgKMeans.<locals>.<listcomp>éTr©ÚsharexÚshareyÚfigsizer6r7úOriginal ImagezImage after KMeans (K = ú))ÚnpZreshapeÚshaperZfitZlabels_Zcluster_centers_ÚdictÚzipZarangeÚarrayZastyperr9ÚsubplotsÚravelr;Ú	set_titleÚstr)r=ÚKr<Z
showHistogramZimgflatZkmeansZkmmodelÚlabelsZcentersÚoutputÚfigrr"rAr#Ú	imgKMeans:s $
rWc
Cs¾t|ddd\}}tdd„| ¡Dƒƒ}|d|dd}t ||d	tj¡\}}|r¶tjd
ddddd
\}}	|	 ¡}	|	dj	|dd|	d 
d¡|	d
j	|dd|	d
 
d¡||fS)z~
    Preprocess the image by applying truncated thresholding using KMeans
    Input: Image
    Output: Preprocessed image
    rr©r<cSsg|]}|d‘qS)rr")r@Úir"r"r#rBcsz#preprocessImage.<locals>.<listcomp>r>éþÿÿÿrCéÿrTrrDr6r7rHz$Processed Image - After Thresholding)rWÚsortedÚvaluesr8Ú	thresholdZ
THRESH_TOZEROr9rOrPr;rQ)
r=r<Ú	centroidsZ
segmented_imgZsorted_center_valuesr^ÚretvalÚprocImgrVrr"r"r#ÚpreprocessImage[srbcCs.t ||dtj¡\}}t|tdƒƒ}t|tdƒƒ}t|ƒ}t |¡}|r*t	j
dddddd\}	}
|
 ¡}
|
d d	¡|
dj
|d
d|
d d
¡|
dj
|d
d|
d d¡|
dj
|d
d|
d d¡|
dj
|d
d|
d d¡|
dj
|d
d|
d d¡|
dj
|d
d|S)Nr[rérCT)érrDrrHr6r7rzOn Performing Thresholding'súOn Opening with Square SE (3)zOn Opening with Disk SE (4)z'Outer Boundary Delineation with Canny'srzForeground Mask)r8r^Ú
THRESH_BINARYrrrrÚndiÚbinary_fill_holesr9rOrPrQr;)r=Úfg_thresholdr<r`Zinit_fg_maskZfg_mask_openedZfg_mask_opened2ZedgesÚfg_maskrVrr"r"r#ÚgetForegroundMaskvs*
rkcCsœ| ¡}t|jdƒD]4}t|jdƒD] }|||dkr(d|||<q(qt ||dtj¡\}}t|tdƒƒ}	t|	t	dƒƒ}
t
 |
¡}t|ƒ}t
|ƒ}
g}|
D]}|jdkr | |j¡q tj|jtjd}t|jdƒD]4}t|jdƒD] }||||krîd|||<qîqÜ|t |¡}tt|ƒƒdkr<t|ƒ}n| ¡}|t |¡t |¡}t|tdƒƒ}t|t	d	ƒƒ}t|ƒ}t
|ƒ}i}|D]}|j||j<q|rØt||jd
}t ||kt d¡t d¡¡}ntj|jtjd}|rtjd	dddd
d\}}| ¡}|d d¡|dj|dd|d d¡|dj|dd|d d¡|dj|dd|d d¡|dj|	dd|d	 d¡|d	j|
dd|d d¡|dj|dd|d d¡|dj|dd|d d¡|dj|dd|d d¡|dj|dd|d d¡|dj|dd|d d¡|dj|dd|d  d!¡|d j|dd||||fS)"Nrrr[rCéiÜ©Zdtyperrcr&rT)érnrDrHr6r7zEnhanced ImagezInitial Lung MaskzOn Opening with Square SE (2)zOn Closing with Disk SE (6)zOn Filling RegionszTrachea Mask/Primary Bronchiéú	Lung MaskézConvex Hull of Lung Maské	zInitial Intermediate Heart MaskrreézIntermediate heart mask)ÚcopyÚrangerKr8r^ZTHRESH_BINARY_INVrrrrrgrhrrÚarear*rJÚzerosÚuint8ÚinvertÚsumr	ÚmaxÚgetÚwherer9rOrPrQr;)r=rjrir<ZenhancedrYÚjr`Zinitial_lung_maskZlung_mask_opZlung_mask_opclZlung_mask_opclrmZ	label_imgZlung_regionsZtrachea_labelsÚtrachea_maskZrowZcolÚ	lung_maskÚch_lung_maskZinitial_int_heart_maskZint_heart_mask_op1Zint_heart_mask_op2Zheart_label_imgÚ
heart_regionsÚareasZheart_labelÚint_heart_maskrVrr"r"r#ÚgetLungTracheaMasks›s€


 r…c"Cs| ¡s||fS| ¡}t|jdƒD]4}t|jdƒD] }|||dkr8d|||<q8q&t|ddd\}}t| ¡ƒd}t ||dtj	¡\}	}
t
|
tdƒƒ}t|ƒ}t
|ƒ}
g}i}i}|
D]2}| |j¡|j||j<|j|j|jg||j<qÂt||jd}| |¡t ||kt d¡t d¡¡}t|ƒ}t
|ƒ}|dj}||}|||}|dkr|tj|jtjd	}d}næd}||d\}}||d}|t |¡d
||d}|t |¡d
||d}| ¡}tt |¡|jdƒD]\}|t |¡kr.t|jdƒD]}d|||<qn"tt |¡ƒD]}d|||<q<qö|t |¡}|rtjddddd
d\} }!|!  ¡}!|!d !d¡|!dj"|dd|!d !d¡|!dj"|dd|!d !d¡|!d "|¡|!d !d¡|!dj"|
dd|!d !d¡|!dj"|dd|!d !d¡|!dj"|dd|!d !d¡|!dj"|dd|rÖ|!dj#||f||fddd|!dj#||ddd|!dj#||d dd|!d! !d"¡|!d!j"|ddn |!d! !d"¡|!d!j"|dd|!d# !d$¡|!d#j"|dd||fS)%NrrrrXr[rnr&gà?rmg333333ã?rCT)rrrDzIntermediate Heart Maskr6r7zIntermediate Heart Segmentz-Intermediate Heart Segment on K-Means (K = 3)z
Spine MaskrczOn Closing with Disk SE (20)rzOn Opening with Square SE (4)rlzCentroid and uppermost pointz-rgø?)Z	linewidthz.g)Z
markersizez.brozConvex Hull of Spine Maskrqú
Heart Mask)$ÚanyrtrurKrWr{r]r8r^rfrrrrr*rvZcentroidÚorientationZaxis_major_lengthr|ÚremoverJr}rxrwÚmathZsinZcosZceilryr9rOrPrQr;Zplot)"r=r„r<Zint_heart_pixelrYr~r_Zsegmented_heart_imgZspine_thresholdr`Zinitial_spine_maskZ	bone_maskZlabel_spineZ
spine_regionsrTrƒZgeometric_measuresZspine_labelÚ
spine_maskZlabel_heartr‚Zheart_region_areaZspine_region_areaZ
frac_heartÚ
heart_maskZmake_spine_maskZy0Zx0rˆZx2Zy2Zchull_spine_maskrVrr"r"r#ÚchullSpineMasks


rcCs<tj|||d}|r8tjddt d¡tj|dd|S)N©Úmaskr©rGúSegmented Heartr6r7)r8Úbitwise_andr9rr:r;)r=rŒr<Ú	seg_heartr"r"r#ÚsegmentHeartƒs
r”cCs¤tj|||d}tj|||d}tj|||d}|rštjdddddd\}\}	}
}|	 d¡|	j|d	d
|
 d¡|
j|d	d
| d¡|j|d	d
|||fS)
NrŽrr)érlTF)rGrErFr‘r6r7zSegmented LungszSegmented Trachea)r8r’r9rOrQr;)r=rŒr€rr<r“Z	seg_lungsZseg_trachearVZax1Zax2Zax3r"r"r#ÚsegmentHeartLungsTracheas


r–csPtj‡fdd„|Dƒdd}t |¡}t |¡}||dkr@|S|||}|S)Ncsg|]}ˆdtjf|‘qS).)rJZnewaxis)r@ZcolorrŽr"r#rB¤sz"applyMaskColor.<locals>.<listcomp>rC)Zaxisr)rJZconcatenateZamaxZamin)rZ
mask_colorZmaskedZmaxValueZminValuer"rŽr#ÚapplyMaskColor¢s

r—cCsút dddg¡}t dddg¡}t dddg¡}t||ƒ}t||ƒ}	t||ƒ}
||	|
}|rîtjdddd\}}
|
 ¡}|d d¡|dj|dd|d	 d
¡|d	 |¡|d d¡|d |	¡|d d
¡|d |¡||	|
|fS)NérrC)rrrrHr6r7rr†rprZMasks)rJrNr—r9rOrPrQr;)r=rŒr€rr<Zheart_mask_colorZlung_mask_colorZtrachea_mask_colorÚ
heart_coloredÚlung_coloredÚtrachea_coloredÚ
colored_masksrVrZaxr"r"r#ÚgetColoredMasks²s&


r)r)rr)r)r)r)r)r)r)r)3r(r8rŠZnumpyrJZpandasZpdZmatplotlib.pyplotZpyplotr9Zmatplotlib.patchesrZsklearn.clusterrZskimage.morphologyrrrrrr	r
Zskimage.measurerrZskimage.filtersr
Zskimage.featurerZscipyrrgZskimage.segmentationrZ
SMALL_FONTZMEDIUM_FONTZ
LARGE_FONTZrcZrcParamsr1r5r4rWrbrkr…rr”r–r—rr"r"r"r#Ú<module>sH$




!

%
l
|