Exemplos de Elastix em Python

Exemplo n.º 1

Arquivo: test_elastix_transform.py Projeto: ChristophKirst/ClearMap

print "Aligned images: result directory: %s" % resultDirectory



##############################################################################
# Test Transform Points
############################################################################## 

import iDISCO.Visualization.Plot as Plot;

import iDISCO.Alignment.Elastix as elx;

import iDISCO.Analysis.Voxelization as vox
import iDISCO.IO.IO as io

elx.initializeElastix('/home/ckirst/programs/elastix')
elx.ElastixSettings.printInfo()

verbose = True;

parameter.Alignment.AlignmentDirectory = os.path.join(basedirectory, 'Synthetic/elastix');

rcenters = numpy.array([[0,0,0],[0,52,0], [0,0,23], [74,0,0],[74,52,0]]);

#acenters = elx.transformPoints(rcenters, alignmentdirectory = parameter.Alignment.AlignmentDirectory, outdirectory = pointsdir);
acenters = elx.transformPoints(rcenters, alignmentdirectory = parameter.Alignment.AlignmentDirectory);

print acenters

Exemplo n.º 2

Arquivo: test_chain_data.py Projeto: MoritzNegwer/FriendlyClearmap

print("Aligned cfos with autofluo: result directory: %s" % resultDirectory)

##############################################################################
# Test Transform data auto to cfos
##############################################################################

from iDISCO.Parameter import *
import iDISCO.Alignment.Elastix as elx
import iDISCO.Visualization.Plot as Plot
import iDISCO.IO.IO as io

basedirectory = '/home/mtllab/Documents/whiskers/2ndgroup/C'

resultdir = os.path.join(basedirectory, 'elastix_cfos_auto')
transformfile = elx.getTransformParameterFile(resultdir)

# tranform points according to alignment of data and reference
resamplefile = os.path.join(basedirectory, 'autofluo_for_cfos_resample.tif')
transformdir = os.path.join(basedirectory, 'transform_data_cfos_auto')

elx.initializeElastix('/usr/local/elastix')
elx.ElastixSettings.printInfo()

#elx.transformData(dataresname, alignmentdirectory = resultdir, outdirectory = dataalgname)
elx.transformData(resamplefile,
                  transformparameterfile=transformfile,
                  outdirectory=transformdir)

##############################################################################
# Transform Points from Cfos to Autofluo

Exemplo n.º 3

Arquivo: test_chain_data.py Projeto: ChristophKirst/ClearMap

##############################################################################
# Test Transform data auto to cfos
############################################################################## 

from iDISCO.Parameter import *
import iDISCO.Alignment.Elastix as elx
import iDISCO.Visualization.Plot as Plot
import iDISCO.IO.IO as io

basedirectory = '/home/mtllab/Documents/whiskers/2ndgroup/C';

resultdir = os.path.join(basedirectory, 'elastix_cfos_auto');
transformfile = elx.getTransformParameterFile(resultdir)

# tranform points according to alignment of data and reference 
resamplefile = os.path.join(basedirectory, 'autofluo_for_cfos_resample.tif');
transformdir = os.path.join(basedirectory, 'transform_data_cfos_auto')

elx.initializeElastix('/usr/local/elastix')
elx.ElastixSettings.printInfo()

#elx.transformData(dataresname, alignmentdirectory = resultdir, outdirectory = dataalgname)
elx.transformData(resamplefile, transformparameterfile = transformfile, outdirectory = transformdir)
   

Exemplo n.º 4

Arquivo: test_chain_synthetic.py Projeto: MoritzNegwer/FriendlyClearmap

import iDISCO.Alignment.Elastix as elx;

verbose = True;

# directory in with elastix alignment result 
transformDirectory  =  os.path.join(baseDirectory, 'Synthetic/elastix');

#result diectory to write transformed points to (None = read back as array)
resultDirectory    = os.path.join(baseDirectory, 'Synthetic/transformix')

#define (y,x,z) coordinates for testing
points = numpy.array([[0,0,0],[74,0,0],[0,52,0],[0,0,23],[74,52,0]]);

#acenters = elx.transformPoints(rcenters, alignmentdirectory = parameter.Alignment.AlignmentDirectory, outdirectory = pointsdir);
pointsa = elx.transformPoints(points, resultDirectory = resultDirectory, transformDirectory = transformDirectory);

print(pointsa)



##############################################################################
# Test Transform Reference to Resampled Data
############################################################################## 

import os

import iDISCO.Settings as settings

import iDISCO.IO.IO as io
import iDISCO.Alignment.Elastix as elx

Exemplo n.º 5

print("Aligned images: result directory: %s" % resultDirectory)



##############################################################################
# Test Transform Points
############################################################################## 

import iDISCO.Visualization.Plot as Plot;

import iDISCO.Alignment.Elastix as elx;

import iDISCO.Analysis.Voxelization as vox
import iDISCO.IO.IO as io

elx.initializeElastix('/home/ckirst/programs/elastix')
elx.ElastixSettings.printInfo()

verbose = True;

parameter.Alignment.AlignmentDirectory = os.path.join(basedirectory, 'Synthetic/elastix');

rcenters = numpy.array([[0,0,0],[0,52,0], [0,0,23], [74,0,0],[74,52,0]]);

#acenters = elx.transformPoints(rcenters, alignmentdirectory = parameter.Alignment.AlignmentDirectory, outdirectory = pointsdir);
acenters = elx.transformPoints(rcenters, alignmentdirectory = parameter.Alignment.AlignmentDirectory);

print(acenters)

Exemplo n.º 6

Arquivo: test_chain_synthetic.py Projeto: ChristophKirst/ClearMap

import iDISCO.Alignment.Elastix as elx;

verbose = True;

# directory in with elastix alignment result 
transformDirectory  =  os.path.join(baseDirectory, 'Synthetic/elastix');

#result diectory to write transformed points to (None = read back as array)
resultDirectory    = os.path.join(baseDirectory, 'Synthetic/transformix')

#define (y,x,z) coordinates for testing
points = numpy.array([[0,0,0],[74,0,0],[0,52,0],[0,0,23],[74,52,0]]);

#acenters = elx.transformPoints(rcenters, alignmentdirectory = parameter.Alignment.AlignmentDirectory, outdirectory = pointsdir);
pointsa = elx.transformPoints(points, resultDirectory = resultDirectory, transformDirectory = transformDirectory);

print pointsa



##############################################################################
# Test Transform Reference to Resampled Data
############################################################################## 

import os

import iDISCO.Settings as settings

import iDISCO.IO.IO as io
import iDISCO.Alignment.Elastix as elx