import numpy
import config
import SimpleITK
import os
import getData
import matplotlib.pyplot
def guessPixelPosition15(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]
pts={
'0':[sx-5,sy,sz],\
'1':[sx-2,sy,sz-rz],\
'2':[sx-2,sy,sz+rz-1],\
'3':[sx-1,sy-rz,sz],\
'4':[sx-1,sy+rz-1,sz],\
'5':[sx,sy-rz+oz,sz],\
'6':[sx,sy-0.3*rz+oz,sz-rz],\
'7':[sx,sy-0.3*rz+oz,sz+rz],\
'8':[sx,sy,sz],\
'9':[sx,sy+0.3*rz+oz,sz-rz],\
'10':[sx,sy+0.3*rz+oz,sz+rz],\
'11':[sx,sy+rz+oz,sz],\
'12':[sx+3,sy-rz,sz],\
'13':[sx+3,sy,sz-rz],\
'14':[sx+3,sy,sz+rz],\
'15':[sx+3,sy+rz,sz]}
slices={'0':['8','0','1','13','2','14'],\
'1':['8','0','3','4','12','15'],\
'2':['8','11','9','6','5','7','10']}
print(slices['0'])
fp={x:[pts[q] for q in slices[x]] for x in slices}
sliceIds={x:[] for x in pts}
for p in pts:
for s in slices:
if p in slices[s]:
sliceIds[p].append(s)
sliceCode={x:';'.join(sliceIds[x]) for x in sliceIds}
print(fp)
print(sliceCode)
return fp
#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 guessPixelPosition4(sx=-1,sy=-1,sz=-1):
#guess position of segments
if sx<0:
sx=32
if sy<0:
sy=31
if sz<0:
sz=31
rz=4
pts={
'0':[sx,sy,sz],\
'1':[sx,sy,sz-rz],\
'2':[sx,sy,sz+rz],\
'3':[sx,sy-rz,sz],\
'4':[sx,sy+rz,sz]}
slices={
'0':['0','1','2'],\
'1':['0','3','4'],\
'2':['0','1','2','3','4']}
print(slices['0'])
fp={x:[pts[q] for q in slices[x]] for x in slices}
sliceIds={x:[] for x in pts}
for p in pts:
for s in slices:
if p in slices[s]:
sliceIds[p].append(s)
sliceCode={x:';'.join(sliceIds[x]) for x in sliceIds}
print(fp)
print(sliceCode)
return [{'regionId':x,'x':pts[x][0],'y':pts[x][1],'z':pts[x][2],'sliceId':sliceCode[x]} for x in pts]
def updateSegmentation(db,setup,r,pixels):
copyFields=['PatientId','visitCode']
for x in pixels:
for c in copyFields:
x[c]=r[c]
x['SequenceNum']=r['SequenceNum']+0.01*int(x['regionId'])
filterVar=['PatientId','SequenceNum']
qFilter=[{'variable':y,'value':'{}'.format(x[y]),'oper':'eq'} for y in filterVar]
ds=db.selectRows(setup['project'],'study','Segmentation',qFilter)
entry={}
mode='insert'
if len(ds['rows'])>0:
entry=ds['rows'][0]
mode='update'
for q in x:
entry[q]=x[q]
db.modifyRows(mode,setup['project'],'study','Segmentation',[entry])
print('Done')
def getSegmentationFileName(r,setup,db=None):
if not db:
db,fb=getData.connectDB(setup['network'])
if setup['segmentationMode']=='TXT':
return '{}_Segmentation.txt'.format(config.getCode(r,setup))
if setup['segmentationMode']=='NRRD':
copyFields=['PatientId','visitCode']
qFilter=[{'variable':x,'value':r[x],'oper':'eq'} for x in copyFields]
qFilter.append({'variable':'User','value':setup['targetUser'],'oper':'eq'})
rows=getData.getSegmentation(db,setup,qFilter)
r=rows[0]
return r['latestFile']
def getURL(fb,r,setup,name):
remoteDir=fb.buildPathURL(setup['project'],config.getPathList(r,setup))
return '/'.join([remoteDir,'Segmentations',name])
def copyFromServer(fb,r,setup,names):
try:
forceReload=setup['forceReload']
except KeyError:
forceReload=False
getData.getLocalDir(r,setup,createIfMissing=True)
remoteDir=fb.buildPathURL(setup['project'],config.getPathList(r,setup))
for n in names:
localPath=getData.getLocalPath(r,setup,n)
if os.path.isfile(localPath) and not forceReload:
continue
remotePath='/'.join([remoteDir,'Segmentations',n])
fb.readFileToFile(remotePath,localPath)
def copyToServer(fb,r,setup,names):
remoteDir=fb.buildPathURL(setup['project'],config.getPathList(r,setup))
for n in names:
localPath=getLocalPath(r,setup,n)
remotePath='/'.join([remoteDir,'Segmentations',n])
fb.writeFileToFile(localPath,remotePath)
def writeSegmentation(db,fb,r,setup):
if setup['segmentationMode']=='NRRD':
print('Failed to load segmentation')
return
fileName=getSegmentationFileName(db,r,setup)
idFilter={'variable':'PatientId','value':config.getPatientId(r,setup),'oper':'eq'}
visitFilter={'variable':'visitCode','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(getData.getLocalPath(r,setup,fileName),v)
getData.copyToServer(fb,r,setup,[fileName])
def getNC(r,xsetup):
if xsetup['segmentationMode']=='TXT':
getNCTxt(r,xsetup)
if xsetup['segmentationMode']=='NRRD':
return xsetup['NC']
def getNCTxt(r,xsetup):
sName=getSegmentationFileName(db=None,r=r,setup=xsetup)
fName=getData.getLocalPath(r,xsetup,sName)
x=numpy.loadtxt(fName)
nc=x.shape[0]
return nc
def loadSegmentation(db,fb,r,setup):
sName=getSegmentationFileName(db,r,setup)
print(f'Looking for {sName}')
fName=getData.getLocalPath(r,setup,sName)
print(f'Local {fName}')
if not os.path.isfile(fName):
fURL=getData.getURL(fb,r,setup,sName)
if fb.entryExists(fURL):
getData.copyFromServer(fb,r,setup,[sName])
if os.path.isfile(fName):
print(f'Copied {fURL} to {fName}')
else:
print(f'Failed to load {fName} from {fURL}')
else:
#this creates local and global file
writeSegmentation(db,fb,r,setup)
if setup['segmentationMode']=='TXT':
return numpy.loadtxt(fName)
def plotSegmentation(db,fb,r,setup,vmax=1000):
copyFields=['PatientId','visitCode']
qFilter=[{'variable':x,'value':r[x],'oper':'eq'} for x in copyFields]
nim=getData.getPatientNIM(fb,r,setup)
rows=getData.getSegmentation(db,setup,qFilter)
if len(rows)==0:
pId=r['PatientId']
visitCode=r['visitCode']
print(f'Not found for id={pId}/{visitCode}')
return
fp={}
for q in rows:
if q['regionId']==0:
slc=[q['x'],q['y'],q['z']]
slc=[int(x) for x in slc]
slices=q['sliceId'].split(';')
for s in slices:
try:
fp[s].append([float(x) for x in [q['x'],q['y'],q['z']]])
except KeyError:
fp[s]=[]
fp[s].append([float(x) for x in [q['x'],q['y'],q['z']]])
cut0=20
w0=20
cut1=20
w1=20
cut2=20
w2=20
vmin=0
nd=3
fig,ax=matplotlib.pyplot.subplots(3,2*nd+1,figsize=(20,12))
for i in numpy.arange(0,2*nd+1):
ax[0,i].set_xlabel('z')
ax[0,i].set_ylabel('x')
ax[0,i].imshow(nim[cut2:cut2+w2,slc[1]-nd+i,cut0:cut0+w0],cmap='gray_r',vmax=vmax,vmin=vmin)
ax[1,i].set_xlabel('x')
ax[1,i].set_ylabel('y')
ax[1,i].imshow(nim[cut2:cut2+w2,cut0:cut0+w0,slc[2]-nd+i].T,cmap='gray_r',vmax=vmax,vmin=vmin)
ax[2,i].set_xlabel('z')
ax[2,i].set_ylabel('y')
ax[2,i].imshow(nim[slc[0]-nd+i,cut1:cut1+w1,cut1:cut1+w1],cmap='gray_r',vmax=vmax,vmin=vmin)
if i==nd:
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')
name='{}_segmentation.png'.format(config.getCode(r,setup))
fPath=getData.getLocalPath(r,setup,name)
fig.savefig(fPath)
getData.copyToServer(fb,r,setup,[name])
def getNRRDImage(r,setup,names=None):
if names:
localFile=getData.getLocalPath(r,setup,names['segmentation'][0])
else:
localFile=getData.getLocalPath(r,setup,getSegmentationFileName(r,setup))
segImg=SimpleITK.ReadImage(localFile)
seg=SimpleITK.GetArrayFromImage(segImg)
return seg