print ca.MinMax(weights)
ca.Div_I(blocks, weights)
else: # best
imagedir = '/home/sci/crottman/korenberg/results/'
blocks = cc.LoadMHA(
imagedir + 'BFI_2D_Reg/block1_as_MRI_' + col + '_256.mha', ca.MEM_HOST)
blk = cc.LoadMHA(imagedir + 'BFI_2D_Reg/block2_as_MRI_' + col + '_256.mha',
ca.MEM_HOST)
blocks += blk
blk = cc.LoadMHA(imagedir + 'landmark/block3_as_MRI_' + col + '.mha',
ca.MEM_HOST)
blocks += blk
blk = cc.LoadMHA(imagedir + 'landmark/block4_as_MRI_' + col + '.mha',
ca.MEM_HOST)
blocks += blk
imagedir = '/home/sci/crottman/korenberg/results/best/'
# Save Blocks
maxval = ca.MinMax(blocks)[1]
blocks /= maxval
fname_out = imagedir + 'blocks' + fname_end
cc.WriteMHA(blocks, fname_out)
if col == 'rgb':
fname_out = imagedir + 'blocks_as_MRI_rgba_' + str(sz) + '.mha'
cc.WriteColorMHA(blocks, fname_out)
BFIfname = 'block{0}_reg_fillblanks_{1}_hd4.mha'.format(block, color)
# BFI = cc.LoadMHA(BFIdir + BFIfname, mType)
# outimage = common.ExtractSliceIm(BFI,100)
cd.Disp3Pane(BFI_aff)
if color in ['bw', 've', 'weight']:
BFIdef = ca.ManagedImage3D(MRIgrid, mType) # these should be small enough
else:
BFIdef = ca.ManagedField3D(MRIgrid, mType)
cc.ApplyHReal(BFIdef, BFI_aff, h)
if sz == MRIsizes[-1] and color == colors[-1]:
cd.Disp3Pane(BFIdef)
# write data
if Write:
if color == 'rgb':
fname = 'block{0}_as_MRI_rgba_{1}.mha'.format(block, sz)
cc.WriteColorMHA(BFIdef, outdir + fname)
fname = 'block{0}_as_MRI_rgb_{1}.mha'.format(block, sz)
cc.WriteMHA(BFIdef, outdir + fname)
else:
#fname = 'block{0}_as_MRI_{1}_{2}_NEWLANDMARKS.mha'.format(block, color, sz)
fname = 'M15_01_to_MRI_TPS_bw_256_VE.mha'
cc.WriteMHA(BFIdef, outdir + fname)
cc.WriteMHA(h, outdir + 'M15_01_to_MRI_TPS_def_256.mha')
# cc.WriteMHA(h, outdir + 'block{0}_TPS_HField_{1}.mha'.format(block,sz))
cd.Disp3Pane(BFIdef)
common.DebugHere()
del BFIdef, BFI
del h
def Fragmenter():
tmpOb = Config.Load(
frgSpec,
pth.expanduser(
'~/korenbergNAS/3D_database/Working/configuration_files/SidescapeRelateBlockface/M{0}/section_{1}/section_{1}_frag0.yaml'
.format(secOb.mkyNum, secOb.secNum)))
dictBuild = {}
#Load in the whole image so that the fragment can cropped out
ssiSrc, bfiSrc, ssiMsk, bfiMsk = Loader(tmpOb, ca.MEM_HOST)
#Because some of the functions only woth with gray images
bfiGry = ca.Image3D(bfiSrc.grid(), bfiSrc.memType())
ca.Copy(bfiGry, bfiSrc, 1)
lblSsi, _ = ndimage.label(np.squeeze(ssiMsk.asnp()) > 0)
lblBfi, _ = ndimage.label(np.squeeze(bfiMsk.asnp()) > 0)
seedPt = np.squeeze(pp.LandmarkPicker([lblBfi, lblSsi]))
subMskBfi = common.ImFromNPArr(lblBfi == lblBfi[seedPt[0, 0],
seedPt[0,
1]].astype('int8'),
sp=bfiSrc.spacing(),
orig=bfiSrc.origin())
subMskSsi = common.ImFromNPArr(lblSsi == lblSsi[seedPt[1, 0],
seedPt[1,
1]].astype('int8'),
sp=ssiSrc.spacing(),
orig=ssiSrc.origin())
bfiGry *= subMskBfi
bfiSrc *= subMskBfi
ssiSrc *= subMskSsi
#Pick points that are the bounding box of the desired subvolume
corners = np.array(
pp.LandmarkPicker(
[np.squeeze(bfiGry.asnp()),
np.squeeze(ssiSrc.asnp())]))
bfiCds = corners[:, 0]
ssiCds = corners[:, 1]
#Extract the region from the source images
bfiRgn = cc.SubVol(bfiSrc,
xrng=[bfiCds[0, 0], bfiCds[1, 0]],
yrng=[bfiCds[0, 1], bfiCds[1, 1]])
ssiRgn = cc.SubVol(ssiSrc,
xrng=[ssiCds[0, 0], ssiCds[1, 0]],
yrng=[ssiCds[0, 1], ssiCds[1, 1]])
#Extract the region from the mask images
rgnMskSsi = cc.SubVol(subMskSsi,
xrng=[ssiCds[0, 0], ssiCds[1, 0]],
yrng=[ssiCds[0, 1], ssiCds[1, 1]])
rgnMskBfi = cc.SubVol(subMskBfi,
xrng=[bfiCds[0, 0], bfiCds[1, 0]],
yrng=[bfiCds[0, 1], bfiCds[1, 1]])
dictBuild['rgnBfi'] = np.divide(
bfiCds, np.array(bfiSrc.size().tolist()[0:2], 'float')).tolist()
dictBuild['rgnSsi'] = np.divide(
ssiCds, np.array(ssiSrc.size().tolist()[0:2], 'float')).tolist()
#Check the output directory for the source files of the fragment
if not pth.exists(
pth.expanduser(secOb.ssiSrcPath + 'frag{0}'.format(frgNum))):
os.mkdir(pth.expanduser(secOb.ssiSrcPath + 'frag{0}'.format(frgNum)))
if not pth.exists(
pth.expanduser(secOb.bfiSrcPath + 'frag{0}'.format(frgNum))):
os.mkdir(pth.expanduser(secOb.bfiSrcPath + 'frag{0}'.format(frgNum)))
#Check the output directory for the mask files of the fragment
if not pth.exists(
pth.expanduser(secOb.ssiMskPath + 'frag{0}'.format(frgNum))):
os.mkdir(pth.expanduser(secOb.ssiMskPath + 'frag{0}'.format(frgNum)))
if not pth.exists(
pth.expanduser(secOb.bfiMskPath + 'frag{0}'.format(frgNum))):
os.mkdir(pth.expanduser(secOb.bfiMskPath + 'frag{0}'.format(frgNum)))
dictBuild[
'ssiSrcName'] = 'frag{0}/M{1}_01_ssi_section_{2}_frag1.tif'.format(
frgNum, secOb.mkyNum, secOb.secNum)
dictBuild[
'bfiSrcName'] = 'frag{0}/M{1}_01_bfi_section_{2}_frag1.mha'.format(
frgNum, secOb.mkyNum, secOb.secNum)
dictBuild[
'ssiMskName'] = 'frag{0}/M{1}_01_ssi_section_{2}_frag1_mask.tif'.format(
frgNum, secOb.mkyNum, secOb.secNum)
dictBuild[
'bfiMskName'] = 'frag{0}/M{1}_01_bfi_section_{2}_frag1_mask.tif'.format(
frgNum, secOb.mkyNum, secOb.secNum)
#Write out the masked and cropped images so that they can be loaded from the YAML file
#The BFI region needs to be saved as color and mha format so that the grid information is carried over.
common.SaveITKImage(
ssiRgn, pth.expanduser(secOb.ssiSrcPath + dictBuild['ssiSrcName']))
cc.WriteColorMHA(
bfiRgn, pth.expanduser(secOb.bfiSrcPath + dictBuild['bfiSrcName']))
common.SaveITKImage(
rgnMskSsi, pth.expanduser(secOb.ssiMskPath + dictBuild['ssiMskName']))
common.SaveITKImage(
rgnMskBfi, pth.expanduser(secOb.bfiMskPath + dictBuild['bfiMskName']))
frgOb = Config.MkConfig(dictBuild, frgSpec)
updateFragOb(frgOb)
return None