Python alignData Beispiele

Beispiel #1

Datei: Run.py Projekt: ChristophKirst/ClearMap

def runAlignment(parameter):
    """Align data"""
    
    pa = parameter.Alignment;
    
    fi = pa.FixedImage;
    mi = pa.MovingImage;
    
    af = pa.AffineParameterFile;
    bf = pa.BSplineParameterFile;
    
    od = pa.AlignmentDirectory;
    
    alignData(fi, mi, af, bf, od);
        
    return od;

Beispiel #2

Datei: Run.py Projekt: MoritzNegwer/FriendlyClearmap

def runAlignment(parameter):
    """Align data"""

    pa = parameter.Alignment

    fi = pa.FixedImage
    mi = pa.MovingImage

    af = pa.AffineParameterFile
    bf = pa.BSplineParameterFile

    od = pa.AlignmentDirectory

    alignData(fi, mi, af, bf, od)

    return od

Beispiel #3

Datei: test_chain_synthetic.py Projekt: MoritzNegwer/FriendlyClearmap

alignmentParameter = {            
    #moving and reference images
    "movingImage" : os.path.join(baseDirectory, 'Synthetic/test_iDISCO_reference.tif'),
    "fixedImage"  : os.path.join(baseDirectory, 'Synthetic/test_iDISCO_resample.tif'),
    
    #elastix parameter files for alignment
    "affineParameterFile"  : os.path.join(alignmentDirectory, 'ElastixParameterAffine.txt'),
    "bSplineParameterFile" : None,
    
    #directory of the alignment result
    "resultDirectory" : alignmentDirectory
    };



result = alignData(**alignmentParameter);

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




##############################################################################
# Test Detect Points
############################################################################## 

import os

import iDISCO.Settings as settings

from iDISCO.ImageProcessing.CellDetection import detectCells

Beispiel #4

Datei: test_chain_synthetic.py Projekt: ChristophKirst/ClearMap

alignmentParameter = {            
    #moving and reference images
    "movingImage" : os.path.join(baseDirectory, 'Synthetic/test_iDISCO_reference.tif'),
    "fixedImage"  : os.path.join(baseDirectory, 'Synthetic/test_iDISCO_resample.tif'),
    
    #elastix parameter files for alignment
    "affineParameterFile"  : os.path.join(alignmentDirectory, 'ElastixParameterAffine.txt'),
    "bSplineParameterFile" : None,
    
    #directory of the alignment result
    "resultDirectory" : alignmentDirectory
    };



result = alignData(**alignmentParameter);

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




##############################################################################
# Test Detect Points
############################################################################## 

import os

import iDISCO.Settings as settings

from iDISCO.ImageProcessing.CellDetection import detectCells