afterProjectPath = fc.cleanLinuxPath(
projectPath.replace('EMProject.', 'ToBeElasticAlignedEMProject.'))
IJ.log('afterProjectPath ' + str(afterProjectPath))
project, loader, layerset, nLayers = fc.openTrakemProject(projectPath)
for l, layer in enumerate(layerset.getLayers()):
transformPath = os.path.join(
resultRigidAlignmentFolder,
'stitchedDownsampledEM_' + str(l).zfill(4) + '.xml')
aff = fc.getAffFromRVSTransformPath(transformPath)
# aff.scale(float(downsamplingFactor), float(downsamplingFactor)) # cannot be used because it is not a simple scaling
aff = AffineTransform(aff.getScaleX(), aff.getShearY(), aff.getShearX(),
aff.getScaleY(),
aff.getTranslateX() * float(downsamplingFactor),
aff.getTranslateY() * float(downsamplingFactor))
for patch in layer.getDisplayables(Patch):
currentAff = patch.getAffineTransform()
currentAff.preConcatenate(aff)
patch.setAffineTransform(currentAff)
IJ.log(
'The real EM project is now rigidly aligned. Saving and closing the project.'
)
fc.resizeDisplay(layerset)
project.save()
project.saveAs(afterProjectPath, True)
fc.closeProject(project)
time.sleep(2)
# For 2D, java offers an AffineTransform class that addresses this issue
# quite trivially, with the method rotate that takes an origin of rotation
# as argument.
# BEWARE that positive angles rotate to the right (rather than to the left)
# in the AffineTransform, so we use radians(45) instead of radians(-45).
# And BEWARE that AffineTransform.getMatrix fills a double[] array in
# an order that you wouldn't expect (see the javadoc), so instead
# we call each value of the matrix, one by one, to fill our matrix.
aff = AffineTransform() # initialized as the identity transform
cx = imp.getWidth() / 2.0
cy = imp.getHeight() / 2.0
aff.rotate(radians(45), cx, cy)
rotate45easy = AffineTransform2D()
rotate45easy.set(aff.getScaleX(), aff.getShearX(), aff.getTranslateX(),
aff.getShearY(), aff.getScaleY(), aff.getTranslateY())
print rotate45easy
viewTransformed(imp, rotate45easy, title=imp.getTitle() + " rotate45easy")
# An alternative that works also for 3D transformations exploits
# a nice property of transformation matrices: that they can be combined.
# That is, instead of applying a transform to an image, an then applying
# a second transform to the resulting image, instead the transformation
# matrices can be multiplied, and a single transform applied to the image.
# This is desirable not only for performance reasons, but primarily
# because it avoids the accumulation of interpolation errors.
# In addition, ImgLib2 realtransform classes offer a "rotate" method
# which simplies operations further: no more explicit sin and cos!
################################################
IJ.log('Aligning the highEM with the new rigid transforms')
downsamplingFactor = MagCParameters['downsample_EM']['downsamplingFactor']
IJ.log('The LM/EM pixel scale factor is ' + str(downsamplingFactor))
projectPath = fc.cleanLinuxPath(os.path.join(MagCFolder, 'MagC_EM', 'EMProject.xml')) # the high res EM project
afterProjectPath = fc.cleanLinuxPath(projectPath.replace('EMProject.', 'ToBeElasticAlignedEMProject.'))
IJ.log('afterProjectPath ' + str(afterProjectPath))
project, loader, layerset, nLayers = fc.openTrakemProject(projectPath)
for l, layer in enumerate(layerset.getLayers()):
transformPath = os.path.join(resultRigidAlignmentFolder, 'stitchedDownsampledEM_' + str(l).zfill(4) + '.xml')
aff = fc.getAffFromRVSTransformPath(transformPath)
# aff.scale(float(downsamplingFactor), float(downsamplingFactor)) # cannot be used because it is not a simple scaling
aff = AffineTransform(aff.getScaleX(), aff.getShearY(), aff.getShearX(), aff.getScaleY(), aff.getTranslateX() * float(downsamplingFactor), aff.getTranslateY() * float(downsamplingFactor))
for patch in layer.getDisplayables(Patch):
currentAff = patch.getAffineTransform()
currentAff.preConcatenate(aff)
patch.setAffineTransform(currentAff)
IJ.log('The real EM project is now rigidly aligned. Saving and closing the project.')
fc.resizeDisplay(layerset)
project.save()
project.saveAs(afterProjectPath, True)
fc.closeProject(project)
time.sleep(2)
fc.terminatePlugin(namePlugin, MagCFolder)