import sys
import os
import SimpleITK
import numpy
import matplotlib.pyplot
import subprocess
import json
import config
import getData

sys.path.append(os.path.join(os.path.expanduser('~'),'software','src','nixSuite','wrapper'))
import nixWrapper
nixWrapper.loadLibrary('labkeyInterface')
import labkeyInterface
import labkeyFileBrowser
import labkeyDatabaseBrowser

#manipulate segmentations
#rewrite this
#nim=getPatientNIM(pId)

def guessPixelPosition(sx=-1,sy=-1,sz=-1):
    #guess position of segments
    if sx<0:
        sx=12
    if sy<0:
        sy=28
    if sz<0:
        sz=32
    rz=4
    oz=0

    slc=[sx,sy,sz]
    p1=[sx,sy,sz]

    #tip
    fp={'0':[\
            [sx,sy,sz],   
            [sx-5,sy,sz],\
            [sx-2,sy,sz-rz],\
            [sx+3,sy,sz-rz],\
            [sx-2,sy,sz+rz-1],\
            [sx+3,sy,sz+rz]],\
        '1':[\
            [sx,sy,sz],  
            [sx-5,sy,sz],\
            [sx-1,sy-rz,sz],\
            [sx-1,sy+rz-1,sz],\
            [sx+3,sy-rz,sz],\
            [sx+3,sy+rz,sz]],\
        '2':[\
            [sx,sy,sz],
            [sx,sy+rz+oz,sz],\
            [sx,sy+0.3*rz+oz,sz-rz],\
            [sx,sy-0.3*rz+oz,sz-rz],\
            [sx,sy-rz+oz,sz],\
            [sx,sy-0.3*rz+oz,sz+rz],\
            [sx,sy+0.3*rz+oz,sz+rz]]}
    return fp

    
def getPatientNIM(r,setup):
    locDir=config.getLocalDir(r,setup)
    fileName=config.getNodeName(r,setup,'NM',19)+'.nrrd'
    f=os.path.join(locDir,fileName)
    im=SimpleITK.ReadImage(f)
    nim=SimpleITK.GetArrayFromImage(im)
    return nim

def writeSegmentation(db,r,setup):
    locDir=config.getLocalDir(r,setup)
    fileName='{}_Segmentation.txt'.format(config.getCode(r,setup))
    idFilter={'variable':'PatientId','value':config.getPatientId(r,setup),'oper':'eq'}
    visitFilter={'variable':'visitName','value':config.getVisitId(r,setup),'oper':'eq'}
    rows=getData.getSegmentation(db,setup,[idFilter,visitFilter])
    v=numpy.zeros((len(rows),3))
    for qr in rows:
        region=int(qr['regionId'])
        v[region,2]=float(qr['x'])
        v[region,1]=float(qr['y'])
        v[region,0]=float(qr['z'])
    #for i in range(len(rows)):
    #    print(v[i,:])
    numpy.savetxt(os.path.join(locDir,fileName),v)
    

#

fsetup='../template/cardiacSPECT.json'
with open(fsetup,'r') as f:
    setup=json.load(f)
    
net=labkeyInterface.labkeyInterface()
fconfig=os.path.join(os.path.expanduser('~'),'.labkey',setup['network'])
net.init(fconfig)
#net.getCSRF()
db=labkeyDatabaseBrowser.labkeyDB(net)
fb=labkeyFileBrowser.labkeyFileBrowser(net)
#rewrite this
#nim=getPatientNIM(pId)

pId='po1982022'
cx={}
cx[pId]=[32,31,31]
pId='pred15052022'
cx[pId]=[30,32,31]
#order
#[green,blue,red]

fp={'0':[],'1':[],'2':[]}

visitId='MIR'
idFilter={'variable':'PatientId','value':pId,'oper':'eq'}
visitFilter={'variable':'visitName','value':visitId,'oper':'eq'}

rows=getData.getPatients(db,setup,[idFilter,visitFilter])
for r in rows:
    print(r)

r=rows[0]
nim=getPatientNIM(r,setup)
#i labels segments
#ns=16
#for i in numpy.arange(ns):
#    sNum=r['SequenceNum']+0.0100*i
#seqFilter={'variable':'SequenceNum','value':'{:.2f}'.format(sNum),'oper':'eq'}
rows=getData.getSegmentation(db,setup,[idFilter,visitFilter])
    
if len(rows)==0:
    print('Not found for s={}'.format(sNum))
    fp=guessPixelPosition(*cx[pId])
else:
    for q in rows:
        print(q)
        slices=q['sliceId'].split(';')
        for s in slices:
            fp[s].append([float(x) for x in [q['x'],q['y'],q['z']]])
        #first point is (sx,sy,sz)

oz=0
rz=4
#update last 6 points 
sx=fp['0'][0][0]
sy=fp['0'][0][1]
sz=fp['0'][0][2]
slc=[int(x) for x in fp['0'][0]]
print('Center ({})'.format(slc))

cut0=20
w0=20
cut1=20
w1=20
cut2=20
w2=20
vmax=1000
vmin=0
fig,ax=matplotlib.pyplot.subplots(3,9,figsize=(20,12))
for i in numpy.arange(0,9):
    ax[0,i].imshow(nim[cut2:cut2+w2,slc[1]-4+i,cut0:cut0+w0],cmap='gray_r',vmax=vmax,vmin=vmin)
    ax[1,i].imshow(nim[cut2:cut2+w2,cut0:cut0+w0,slc[2]-4+i].T,cmap='gray_r',vmax=vmax,vmin=vmin)
    ax[2,i].imshow(nim[slc[0]-4+i,cut1:cut1+w1,cut1:cut1+w1],cmap='gray_r',vmax=vmax,vmin=vmin)
    if i==4:
        pt=fp['0']
        ax[0,i].scatter([x[2]-cut0 for x in pt],[x[0]-cut2 for x in pt])
        pt=fp['1']
        ax[1,i].scatter([x[0]-cut2 for x in pt],[x[1]-cut0 for x in pt])
        pt=fp['2']
        ax[2,i].scatter([x[2]-cut1 for x in pt],[x[1]-cut1 for x in pt])
        
    if i==0:
        ax[0,i].text(2,2,pId,fontsize='large')
          
        

rows=getData.getPatients(db,setup)
for r in rows:
    print('******{}******'.format(config.getCode(r,setup)))
    writeSegmentation(db,r,setup)