[b5be3a]: / 1 - Methods with Improved Results / __pycache__ / SegmentationFunctions.cpython-37.pyc

Download this file

114 lines (110 with data), 11.4 kB

B

¢‚mbº=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$„Z,d5d%d&„Z-d6d'd(„Z.d7d)d*„Z/d8d+d,„Z0d-d.„Z1d9d/d0„Z2dS):éN)Ú	Rectangle)ÚKMeans)ÚerosionÚopeningÚclosingÚsquareÚdiskÚconvex_hull_imageÚremove_small_holes)ÚlabelÚregionprops)Úsobel)Úcanny)Úndimage)Ú	watershedé
ééZfont)ÚsizeÚaxes)Z	titlesize)Z	labelsizeZxtickZytickZlegend)ZfontsizeÚfigure)é
ézfigure.figsizecCs~g}x$t |¡D]}| |d|¡qW|jdd„d|d|d d¡d|d d¡…}td|t|ƒfƒ||fS)	Nú/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.)ÚosÚlistdirÚappendÚsortrÚprintÚlen)ÚpathÚslicesrÚIDr r r!ÚreadSortedSlices"s(r.cCsttt|ƒƒS)N)ÚlistÚmapÚreadImg)r,r r r!ÚgetSliceImages,sr2cCs8t |¡}t |tj¡}|r4t d¡tj|dd|S)NzA CT Scan Image SliceÚgray)Úcmap)Úcv2ZimreadZcvtColorZCOLOR_RGB2GRAYÚpltÚtitleÚimshow)r+Ú
showOutputÚimgr r r!r10s

r1c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)Ú
center_labelsr r!ú
<listcomp>KszimgKMeans.<locals>.<listcomp>éT)rr)ÚsharexÚshareyÚfigsizer3)r4zOriginal ImagezImage after KMeans (K = ú))ÚnpZreshapeÚshaperZfitZlabels_Zcluster_centers_ÚdictÚzipZarangeÚarrayZastyperr6ÚsubplotsÚravelr8Ú	set_titleÚstr)r:ÚKr9Z
showHistogramZimgflatZkmeansZkmmodelÚlabelsZcentersÚoutputÚfigrr )r>r!Ú	imgKMeans:s $
rRc
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
    ér)r9cSsg|]}|d‘qS)rr )r=Úir r r!r?csz#preprocessImage.<locals>.<listcomp>r;éþÿÿÿr@éÿrT)rr)rArBrCr3)r4zOriginal Imagez$Processed Image - After Thresholding)rRÚsortedÚvaluesr5Ú	thresholdZ
THRESH_TOZEROr6rJrKr8rL)
r:r9Ú	centroidsZ
segmented_imgZsorted_center_valuesrYÚretvalÚprocImgrQrr r r!ÚpreprocessImage[sr]cCs.t ||dtj¡\}}t|tdƒƒ}t|tdƒƒ}t|ƒ}t |¡}|r*t	j
dddddd\}	}
|
 ¡}
|
d d	¡|
dj
|d
d|
d d
¡|
dj
|d
d|
d d¡|
dj
|d
d|
d d¡|
dj
|d
d|
d d¡|
dj
|d
d|
d d¡|
dj
|d
d|S)NrVrSér@T)ér)rArBrCrzOriginal Imager3)r4rzOn Performing Thresholding'szOn Opening with Square SE (3)zOn Opening with Disk SE (4)z'Outer Boundary Delineation with Canny'srzForeground Mask)r5rYÚ
THRESH_BINARYrrrrÚndiÚbinary_fill_holesr6rJrKrLr8)r:Úfg_thresholdr9r[Zinit_fg_maskZfg_mask_openedZfg_mask_opened2ZedgesÚfg_maskrQrr r r!ÚgetForegroundMaskvs*
recCs´| ¡}xJt|jdƒD]8}x2t|jdƒD] }|||dkr,d|||<q,WqWt ||dtj¡\}}t|tdƒƒ}	t|	t	dƒƒ}
t
 |
¡}t|ƒ}t
|ƒ}
g}x"|
D]}|jdkrª| |j¡qªWtj|jtjd}xJt|jdƒD]8}x2t|jdƒD] }||||krþd|||<qþWqêW|t |¡}tt|ƒƒdkrPt|ƒ}n| ¡}|t |¡t |¡}t|tdƒƒ}t|t	d	ƒƒ}t|ƒ}t
|ƒ}i}x|D]}|j||j<q¦W|rðt||jd
}t ||kt d¡t d¡¡}ntj|jtjd}|r¨tjd	dddd
d\}}| ¡}|d d¡|dj|dd|d d¡|dj|dd|d d¡|dj|dd|d d¡|dj|	dd|d	 d¡|d	j|
dd|d d¡|dj|dd|d d¡|dj|dd|d d¡|dj|dd|d d¡|dj|dd|d d¡|dj|dd|d d¡|dj|dd|d  d!¡|d j|dd||||fS)"NrrrVr@éiÜ)Údtyperr^)r$rST)érh)rArBrCzOriginal Imager3)r4zEnhanced ImagezInitial Lung MaskzOn Opening with Square SE (2)zOn Closing with Disk SE (6)zOn Filling RegionszTrachea Mask/Primary Bronchiéz	Lung MaskézConvex Hull of Lung Maské	zInitial Intermediate Heart MaskrzOn Opening with Square SE (3)ézIntermediate heart mask)ÚcopyÚrangerFr5rYZTHRESH_BINARY_INVrrrrrarbrrÚarear'rEÚzerosÚuint8ÚinvertÚsumr	ÚmaxÚgetÚwherer6rJrKrLr8)r:rdrcr9ZenhancedrTÚjr[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_maskrQrr r r!ÚgetLungTracheaMasks›s€




 r~c"Cs6| ¡s||fS| ¡}xJt|jdƒD]8}x2t|jdƒD] }|||dkr<d|||<q<Wq(Wt|ddd\}}t| ¡ƒd}t ||dtj	¡\}	}
t
|
tdƒƒ}t|ƒ}t
|ƒ}
g}i}i}x:|
D]2}| |j¡|j||j<|j|j|jg||j<qÌWt||jd}| |¡t ||kt d¡t d¡¡}t|ƒ}t
|ƒ}|dj}||}|||}|dkrˆtj|jtjd	}d}nòd}||d\}}||d}|t |¡d
||d}|t |¡d
||d}| ¡}x~tt |¡|jdƒD]d}|t |¡kr@xLt|jdƒD]}d|||<q(Wn&x$tt |¡ƒD]}d|||<qPWqW|t |¡}|r.tjddddd
d\} }!|!  ¡}!|!d !d¡|!dj"|dd|!d !d¡|!dj"|dd|!d !d¡|!d "|¡|!d !d¡|!dj"|
dd|!d !d¡|!dj"|dd|!d !d¡|!dj"|dd|!d !d¡|!dj"|dd|rî|!dj#||f||fddd|!dj#||ddd|!dj#||d dd|!d! !d"¡|!d!j"|ddn |!d! !d"¡|!d!j"|dd|!d# !d$¡|!d#j"|dd||fS)%NrrrS)r9rVrh)r$gà?)rgg333333ã?r@T)rr)rArBrCzIntermediate Heart Maskr3)r4zIntermediate Heart Segmentz-Intermediate Heart Segment on K-Means (K = 3)z
Spine Maskr^zOn Closing with Disk SE (20)rzOn Opening with Square SE (4)rfzCentroid and uppermost pointz-rgø?)Z	linewidthz.g)Z
markersizez.brizConvex Hull of Spine Maskrjz
Heart Mask)$ÚanyrmrnrFrRrtrXr5rYr`rrrrr'roZcentroidÚorientationZaxis_major_lengthruÚremoverErvrqrpÚmathZsinZcosZceilrrr6rJrKrLr8Zplot)"r:r}r9Zint_heart_pixelrTrwrZZsegmented_heart_imgZspine_thresholdr[Zinitial_spine_maskZ	bone_maskZlabel_spineZ
spine_regionsrOr|Zgeometric_measuresZspine_labelÚ
spine_maskZlabel_heartr{Zheart_region_areaZspine_region_areaZ
frac_heartÚ
heart_maskZmake_spine_maskZy0Zx0r€Zx2Zy2Zchull_spine_maskrQrr r r!ÚchullSpineMasks



r…cCs<tj|||d}|r8tjddt d¡tj|dd|S)N)Úmask)rr)rCzSegmented Heartr3)r4)r5Úbitwise_andr6rr7r8)r:r„r9Ú	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)
N)r†rrS)érfTF)rCrArBzSegmented Heartr3)r4zSegmented LungszSegmented Trachea)r5r‡r6rJrLr8)r:r„ryrxr9rˆZ	seg_lungsZseg_trachearQZax1Zax2Zax3r r r!ÚsegmentHeartLungsTracheas


r‹csPtj‡fdd„|Dƒdd}t |¡}t |¡}||dkr@|S|||}|S)Ncsg|]}ˆdtjf|‘qS).)rEZnewaxis)r=Zcolor)r†r r!r?¤sz"applyMaskColor.<locals>.<listcomp>r@)Zaxisr)rEZconcatenateZamaxZamin)r†Z
mask_colorZmaskedZmaxValueZminValuer )r†r!ÚapplyMaskColor¢s

rŒcCsút 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)Nérr@)rr)rCzOriginal Imager3)r4rz
Heart Maskz	Lung MaskrSZMasks)rErIrŒr6rJrKrLr8)r:r„ryrxr9Zheart_mask_colorZlung_mask_colorZtrachea_mask_colorÚ
heart_coloredÚlung_coloredÚtrachea_coloredÚ
colored_masksrQrZaxr r r!ÚgetColoredMasks²s&


r’)r)rr)r)r)r)r)r)r)r)3r%r5r‚ZnumpyrEZpandasZpdZmatplotlib.pyplotZpyplotr6Zmatplotlib.patchesrZsklearn.clusterrZskimage.morphologyrrrrrr	r
Zskimage.measurerrZskimage.filtersr
Zskimage.featurerZscipyrraZskimage.segmentationrZ
SMALL_FONTZMEDIUM_FONTZ
LARGE_FONTZrcZrcParamsr.r2r1rRr]rer~r…r‰r‹rŒr’r r r r!Ú<module>sH$




!

%
l
|