Merge pull request #459 from richardbeare/BuildTemplateFix

updated build_template with affine shape correction

ants/lib/CMakeLists.txt

@@ -94,6 +94,9 @@ pybind11_add_module(ResampleImage antscore/ResampleImage.cxx WRAP_ResampleImage.
 pybind11_add_module(ThresholdImage antscore/ThresholdImage.cxx WRAP_ThresholdImage.cxx)
 pybind11_add_module(TileImages antscore/TileImages.cxx WRAP_TileImages.cxx)
 
+pybind11_add_module(AverageAffineTransform antscore/AverageAffineTransform.cxx WRAP_AverageAffineTransform.cxx)
+pybind11_add_module(AverageAffineTransformNoRigid antscore/AverageAffineTransformNoRigid.cxx WRAP_AverageAffineTransformNoRigid.cxx)
+
 ## CONTRIB ##
 pybind11_add_module(antsImageAugment CONTRIB_antsImageAugment.cxx)
 
@@ -167,6 +170,8 @@ target_link_libraries(N4BiasFieldCorrection PRIVATE ${ITK_LIBRARIES} antsUtiliti
 target_link_libraries(ResampleImage PRIVATE ${ITK_LIBRARIES} antsUtilities)
 target_link_libraries(ThresholdImage PRIVATE ${ITK_LIBRARIES} antsUtilities)
 target_link_libraries(TileImages PRIVATE ${ITK_LIBRARIES} antsUtilities)
+target_link_libraries(AverageAffineTransform PRIVATE ${ITK_LIBRARIES} antsUtilities registrationUtilities)
+target_link_libraries(AverageAffineTransformNoRigid PRIVATE ${ITK_LIBRARIES} antsUtilities registrationUtilities)
 
 ## CONTRIB ##
 target_link_libraries(antsImageAugment PRIVATE ${ITK_LIBRARIES})

ants/lib/LOCAL_antsTransform.h

@@ -49,6 +49,7 @@
 #include "itkWindowedSincInterpolateImageFunction.h"
 #include "itkLabelImageGaussianInterpolateImageFunction.h"
 #include "itkTransformFileWriter.h"
+#include "itkTransformFactory.h"
 
 #include "itkMacro.h"
 #include "itkImage.h"
@@ -62,6 +63,7 @@
 #include "antscore/antsUtilities.h"
 #include "itkAffineTransform.h"
 #include "LOCAL_antsImage.h"
+#include "register_transforms.h"
 
 namespace py = pybind11;
 
@@ -377,6 +379,8 @@ py::capsule composeTransforms( std::vector<void *> tformlist,
 template <typename TransformBaseType, class PrecisionType, unsigned int Dimension>
 py::capsule readTransform( std::string filename, unsigned int dimension, std::string precision )
 {
+    register_transforms();
+
     typedef typename TransformBaseType::Pointer               TransformBasePointerType;
     typedef typename itk::CompositeTransform<PrecisionType, Dimension> CompositeTransformType;
 

ants/lib/LOCAL_readTransform.cxx

@@ -54,11 +54,13 @@
 
 #include "LOCAL_readTransform.h"
 
-namespace py = pybind11;
+#include "register_transforms.h"
 
+namespace py = pybind11;
 
 unsigned int getTransformDimensionFromFile( std::string filename )
 {
+    register_transforms();
     typedef itk::TransformFileReader TransformReaderType1;
     typedef typename TransformReaderType1::Pointer TransformReaderType;
     TransformReaderType reader = itk::TransformFileReader::New();
@@ -71,6 +73,7 @@ unsigned int getTransformDimensionFromFile( std::string filename )
 
 std::string getTransformNameFromFile( std::string filename )
 {
+    register_transforms();
     typedef itk::TransformFileReader TransformReaderType1;
     typedef typename TransformReaderType1::Pointer TransformReaderType;
     TransformReaderType reader = itk::TransformFileReader::New();

ants/lib/WRAP_AverageAffineTransform.cxx

@@ -0,0 +1,17 @@
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+
+#include "antscore/AverageAffineTransform.h"
+#include "antscore/AverageAffineTransformNoRigid.h"
+
+namespace py = pybind11;
+
+int AverageAffineTransform( std::vector<std::string> instring )
+{
+    return ants::AverageAffineTransform(instring, NULL);
+}
+
+PYBIND11_MODULE(AverageAffineTransform, m)
+{
+  m.def("AverageAffineTransform", &AverageAffineTransform);
+}

ants/lib/WRAP_AverageAffineTransformNoRigid.cxx

@@ -0,0 +1,16 @@
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+
+#include "antscore/AverageAffineTransformNoRigid.h"
+
+namespace py = pybind11;
+
+int AverageAffineTransformNoRigid( std::vector<std::string> instring )
+{
+    return ants::AverageAffineTransformNoRigid(instring, NULL);
+}
+
+PYBIND11_MODULE(AverageAffineTransformNoRigid, m)
+{
+  m.def("AverageAffineTransformNoRigid", &AverageAffineTransformNoRigid);
+}

ants/lib/__init__.py

@@ -55,7 +55,8 @@
 from .ThresholdImage import *
 from .integrateVelocityField import *
 from .TileImages import *
-
+from .AverageAffineTransform import *
+from .AverageAffineTransformNoRigid import *
 
 ## CONTRIB ##
 # NOTE: contrib contains code which is experimental

ants/lib/register_transforms.h

@@ -0,0 +1,22 @@
+#ifndef ANTS_REGISTER_TRANSFORM_H_
+#define ANTS_REGISTER_TRANSFORM_H_
+
+#include "itkTransform.h"
+#include "itkTransformFactory.h"
+
+void register_transforms()
+{
+    using MatrixOffsetTransformTypeA = itk::MatrixOffsetTransformBase<double, 3, 3>;
+    itk::TransformFactory<MatrixOffsetTransformTypeA>::RegisterTransform();
+
+    using MatrixOffsetTransformTypeB = itk::MatrixOffsetTransformBase<float, 3, 3>;
+    itk::TransformFactory<MatrixOffsetTransformTypeB>::RegisterTransform();
+
+    using MatrixOffsetTransformTypeC = itk::MatrixOffsetTransformBase<double, 2, 2>;
+    itk::TransformFactory<MatrixOffsetTransformTypeC>::RegisterTransform();
+
+    using MatrixOffsetTransformTypeD = itk::MatrixOffsetTransformBase<float, 2, 2>;
+    itk::TransformFactory<MatrixOffsetTransformTypeC>::RegisterTransform();
+}
+
+#endif

ants/registration/build_template.py

@@ -1,24 +1,25 @@
 __all__ = ["build_template"]
 
 import numpy as np
-
+import os
 from tempfile import mktemp
 
 from .reflect_image import reflect_image
 from .interface import registration
 from .apply_transforms import apply_transforms
 from .resample_image import resample_image_to_target
 from ..core import ants_image_io as iio
+from ..core import ants_transform_io as tio
 from .. import utils
 
-
 def build_template(
     initial_template=None,
     image_list=None,
     iterations=3,
     gradient_step=0.2,
     blending_weight=0.75,
     weights=None,
+    useNoRigid=False,
     **kwargs
 ):
     """
@@ -46,6 +47,9 @@ def build_template(
     weights : vector
         weight for each input image
 
+    useNoRigid : boolean
+        equivalent of -y in the script. Template update
+        step will not use the rigid component if this is True.
     kwargs : keyword args
         extra arguments passed to ants registration
 
@@ -79,22 +83,45 @@ def build_template(
 
     xavg = initial_template.clone()
     for i in range(iterations):
+        affinelist = []
         for k in range(len(image_list)):
             w1 = registration(
                 xavg, image_list[k], type_of_transform=type_of_transform, **kwargs
             )
+            L = len(w1["fwdtransforms"])
+            # affine is the last one
+            affinelist.append(w1["fwdtransforms"][L-1])
+
             if k == 0:
-                wavg = iio.image_read(w1["fwdtransforms"][0]) * weights[k]
+                if L == 2:
+                    wavg = iio.image_read(w1["fwdtransforms"][0]) * weights[k]
                 xavgNew = w1["warpedmovout"] * weights[k]
             else:
-                wavg = wavg + iio.image_read(w1["fwdtransforms"][0]) * weights[k]
+                if L == 2:
+                    wavg = wavg + iio.image_read(w1["fwdtransforms"][0]) * weights[k]
                 xavgNew = xavgNew + w1["warpedmovout"] * weights[k]
-        print(wavg.abs().mean())
-        wscl = (-1.0) * gradient_step
-        wavg = wavg * wscl
-        wavgfn = mktemp(suffix=".nii.gz")
-        iio.image_write(wavg, wavgfn)
-        xavg = apply_transforms(xavgNew, xavgNew, wavgfn)
+
+        if useNoRigid:
+            avgaffine = utils.average_affine_transform_no_rigid(affinelist)
+        else:
+            avgaffine = utils.average_affine_transform(affinelist)
+        afffn = mktemp(suffix=".mat")
+        tio.write_transform(avgaffine, afffn)
+
+        if L == 2:
+            print(wavg.abs().mean())
+            wscl = (-1.0) * gradient_step
+            wavg = wavg * wscl
+            # apply affine to the nonlinear?
+            # need to save the average
+            wavgA = apply_transforms(fixed = xavgNew, moving = wavg, imagetype=1, transformlist=afffn, whichtoinvert=[1])
+            wavgfn = mktemp(suffix=".nii.gz")
+            iio.image_write(wavgA, wavgfn)
+            xavg = apply_transforms(fixed=xavgNew, moving=xavgNew, transformlist=[wavgfn, afffn], whichtoinvert=[0, 1])
+        else:
+            xavg = apply_transforms(fixed=xavgNew, moving=xavgNew, transformlist=[afffn], whichtoinvert=[1])
+
+        os.remove(afffn)
         if blending_weight is not None:
             xavg = xavg * blending_weight + utils.iMath(xavg, "Sharpen") * (
                 1.0 - blending_weight

ants/utils/__init__.py

@@ -39,3 +39,4 @@
 from .smooth_image import *
 from .threshold_image import *
 from .weingarten_image_curvature import *
+from .average_transform import *

ants/utils/average_transform.py

@@ -0,0 +1,43 @@
+from .. import utils, core
+from tempfile import mktemp
+import os
+
+
+
+def _average_affine_transform_driver(transformlist, referencetransform=None, funcname="AverageAffineTransform"):
+    """
+    takes a list of transforms (files at the moment)
+    and returns the average
+    """
+
+    # AverageAffineTransform deals with transform files,
+    # so this function will need to deal with already
+    # loaded files. Doesn't look like the magic
+    # available for images has been added for transforms.
+    res_temp_file = mktemp(suffix='.mat')
+
+    # could do some stuff here to cope with transform lists that
+    # aren't files
+
+    # load one of the transforms to figure out the dimension
+    tf = core.ants_transform_io.read_transform(transformlist[0])
+    if referencetransform is None:
+        args = [tf.dimension, res_temp_file] + transformlist
+    else:
+        args = [tf.dimension, res_temp_file] + ['-R',  referencetransform] + transformlist
+    pargs = utils._int_antsProcessArguments(args)
+    print(pargs)
+    libfun = utils.get_lib_fn(funcname)
+    status = libfun(pargs)
+
+    res = core.ants_transform_io.read_transform(res_temp_file)
+    os.remove(res_temp_file)
+    return res
+
+def average_affine_transform(transformlist, referencetransform=None):
+    return _average_affine_transform_driver(transformlist, referencetransform, "AverageAffineTransform")
+
+
+def average_affine_transform_no_rigid(transformlist, referencetransform=None):
+    return _average_affine_transform_driver(transformlist, referencetransform, "AverageAffineTransformNoRigid")
+