antspymm 1.5.2__tar.gz → 1.5.3__tar.gz

{antspymm-1.5.2/antspymm.egg-info → antspymm-1.5.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: antspymm
-Version: 1.5.2
+Version: 1.5.3
 Summary: multi-channel/time-series medical image processing with antspyx
 Author-email: "Avants, Gosselin, Tustison, Reardon" <stnava@gmail.com>
 License: Apache-2.0

{antspymm-1.5.2 → antspymm-1.5.3}/antspymm/mm.py

@@ -2198,9 +2198,10 @@ def dti_numpy_to_image( reference_image, tensorarray, upper_triangular=True):
 def transform_and_reorient_dti( fixed, moving_dti, composite_transform, py_based=True, verbose=False, **kwargs):
     """
     apply a transform to DTI in the style of ants.apply_transforms. this function
-        expects a pre-computed composite transform which it will use to reorient 
-        the DTI using preservation of principle directions.
-    
+        expects a pre-computed composite transform which it will use to reorient
+        the DTI using preservation of principle directions.  BUG fix by cookpa 2025 
+        06 18.
+
     fixed : antsImage reference space
 
     moving_dti : antsImage DTI in upper triangular format
@@ -2224,34 +2225,36 @@ def transform_and_reorient_dti( fixed, moving_dti, composite_transform, py_based
     dtiw = []
     for k in range(len(dtsplit)):
         dtiw.append( ants.apply_transforms( fixed, dtsplit[k], composite_transform ) )
-    dtiw=ants.merge_channels(dtiw)
+    dtiw=ants.merge_channels(dtiw) # resampled into fixed space but still based in moving index space
     if verbose:
         print("reorient tensors locally: compose and get reo image")
-    locrot = ants.deformation_gradient( ants.image_read(composite_transform), 
+    locrot = ants.deformation_gradient( ants.image_read(composite_transform),
         to_rotation = True, py_based=py_based ).numpy()
-    rebaser = np.dot( np.transpose( fixed.direction  ), moving_dti.direction )
+    # rebases from moving index to fixed index space. Not quite what we need here
+    # rebaser = np.dot( np.transpose( fixed.direction  ), moving_dti.direction )
     if verbose:
         print("convert UT to full tensor")
     dtiw2tensor = triangular_to_tensor( dtiw )
     if verbose:
-        print("rebase tensors to new space via iterator")
+        print("rebase tensors to new space and apply reorientation via iterator")
     it = np.ndindex( fixed.shape )
     for i in it:
-        # direction * dt * direction.transpose();
         mmm = dtiw2tensor[i]
-        # transform rebase
+        # Rebase mmm to physical space
+        mmm = np.dot( mmm, np.transpose( moving_dti.direction ) )
+        mmm = np.dot( moving_dti.direction, mmm )
+        # Now apply local rotation
         locrotx = np.reshape( locrot[i], [3,3] )
         mmm = np.dot( mmm, np.transpose( locrotx ) )
         mmm = np.dot( locrotx, mmm )
-        # physical space rebase
-        mmm = np.dot( mmm, np.transpose( rebaser ) )
-        mmm = np.dot( rebaser, mmm )
+        # Now rebase to fixed index space
+        mmm = np.dot( mmm, np.transpose( fixed.direction ) )
+        mmm = np.dot( fixed.direction, mmm )
         dtiw2tensor[i] = mmm
     if verbose:
         print("done with rebasing")
     return dti_numpy_to_image( fixed, dtiw2tensor )
 
-
 def dti_reg(
     image,
     avg_b0,

{antspymm-1.5.2 → antspymm-1.5.3/antspymm.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: antspymm
-Version: 1.5.2
+Version: 1.5.3
 Summary: multi-channel/time-series medical image processing with antspyx
 Author-email: "Avants, Gosselin, Tustison, Reardon" <stnava@gmail.com>
 License: Apache-2.0

{antspymm-1.5.2 → antspymm-1.5.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "antspymm"
-version = "1.5.2"
+version = "1.5.3"
 description = "multi-channel/time-series medical image processing with antspyx"
 readme = "README.md"
 requires-python = ">=3.9"

antspymm-1.5.3/tests/dwi_run_ptbp_scrub.py

@@ -0,0 +1,80 @@
+import sys, os
+import unittest
+
+os.environ["TF_NUM_INTEROP_THREADS"] = "8"
+os.environ["TF_NUM_INTRAOP_THREADS"] = "8"
+os.environ["ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS"] = "8"
+
+import tempfile
+import shutil
+import tensorflow as tf
+import antspymm
+import antspyt1w
+import antspynet
+import ants
+from dipy.io.gradients import read_bvals_bvecs                                 
+
+import glob
+from typing import List
+
+downloaddir = os.path.expanduser( "~/data/PTBP/images/" )
+
+import glob
+import os
+from typing import List
+
+def extract_dti_prefix_paths(base_pattern: str) -> List[str]:
+    """
+    Find DTI-related files matching a pattern and extract the full path
+    with the filename minus its extension.
+
+    Args:
+        base_pattern (str): Glob pattern to find files (e.g., *.bval, *.nii.gz)
+
+    Returns:
+        List[str]: List of full prefix paths (without file extension)
+    """
+    files = glob.glob(base_pattern)
+    prefix_paths = []
+
+    for filepath in files:
+        root, _ = os.path.splitext(filepath)  # removes .bval, .nii.gz, etc.
+        prefix_paths.append(root)
+
+    return sorted(prefix_paths)
+
+files = extract_dti_prefix_paths(downloaddir + 'PEDS*/20*/DWI/*.bval')
+
+
+testingClass = unittest.TestCase( )
+islocal = False
+if not "prefix" in globals():
+    prefix = files[0]
+    print( "process: " + prefix )
+    # prefix = downloaddir + "PEDS097/20130215/DWI/PEDS097_20130215_0021_DTI_1_1x0_30x1000." # has problems
+    # prefix = downloaddir + "PEDS022/20131101/DWI/PEDS022_20131101_0015_DTI_1_1x0_30x1000." # "normal" quality
+    imgfn = prefix + ".nii.gz"
+    dwi = ants.image_read( imgfn )
+    dwi = ants.motion_correction( dwi )['motion_corrected']
+    dd = antspymm.dipy_dti_recon( dwi, prefix + ".bval", prefix + ".bvec", verbose=True )
+
+bvalr, bvecr = read_bvals_bvecs( prefix + ".bval", prefix + ".bvec" )
+mask=None
+mask=dd['dwi_mask']
+th=0.20
+# th=0.05
+for mask in [None,dd['dwi_mask']]:
+    print("Mask is" + str( mask ) )
+    # scrub example
+    # def censor_dwi( dwi, bval, bvec, threshold = 0.20, imputeb0=False, mask=None, verbose=False ):
+    dwi_sc, bval_sc, bvec_sc = antspymm.censor_dwi( dwi, bvalr, bvecr, threshold=th, mask=mask, verbose=True )
+    ## this is the right answer for PEDS097_20130215_0021_DTI_1_1x0_30x1000
+    # censoring: [4, 5, 6, 28]
+antspymm.write_bvals_bvecs( bvals=bval_sc, bvecs=bvec_sc, prefix='/tmp/temp' )
+ee = antspymm.dipy_dti_recon( dwi_sc, '/tmp/temp.bval', '/tmp/temp.bvec', verbose=True )
+# impute example
+dwi_imp = antspymm.impute_dwi( dwi, threshold=th, mask=mask, verbose=True )
+ff = antspymm.dipy_dti_recon( dwi_imp, prefix + ".bval", prefix + ".bvec", verbose=True )
+ants.image_write( dd['FA'], '/tmp/temp0.nii.gz' )
+ants.image_write( ee['FA'], '/tmp/temp1.nii.gz' )
+ants.image_write( ff['FA'], '/tmp/temp2.nii.gz' )

antspymm-1.5.2/tests/dwi_run_ptbp_scrub.py

@@ -1,43 +0,0 @@
-import sys, os
-import unittest
-
-os.environ["TF_NUM_INTEROP_THREADS"] = "8"
-os.environ["TF_NUM_INTRAOP_THREADS"] = "8"
-os.environ["ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS"] = "8"
-
-import tempfile
-import shutil
-import tensorflow as tf
-import antspymm
-import antspyt1w
-import antspynet
-import ants
-from dipy.io.gradients import read_bvals_bvecs                                 
-
-testingClass = unittest.TestCase( )
-islocal = False
-downloaddir = os.path.expanduser( "~/data/PTBP/images/" )
-if not "prefix" in globals():
-    prefix = downloaddir + "PEDS097/20130215/DWI/PEDS097_20130215_0021_DTI_1_1x0_30x1000." # has problems
-    # prefix = downloaddir + "PEDS022/20131101/DWI/PEDS022_20131101_0015_DTI_1_1x0_30x1000." # "normal" quality
-    imgfn = prefix + "nii.gz"
-    dwi = ants.image_read( imgfn )
-    dwi = ants.motion_correction( dwi )['motion_corrected']
-    dd = antspymm.dipy_dti_recon( dwi, prefix + "bval", prefix + "bvec", verbose=True )
-
-bvalr, bvecr = read_bvals_bvecs( prefix + "bval", prefix + "bvec" )
-mask=None
-mask=dd['dwi_mask']
-th=0.20
-for mask in [None,dd['dwi_mask']]:
-    print("Mask is" + str( mask ) )
-    # scrub example
-    dwi_sc, bval_sc, bvec_sc = antspymm.scrub_dwi( dwi, bvalr, bvecr, threshold=th, mask=mask, verbose=True )
-antspymm.write_bvals_bvecs( bvals=bval_sc, bvecs=bvec_sc, prefix='/tmp/temp' )
-ee = antspymm.dipy_dti_recon( dwi_sc, '/tmp/temp.bval', '/tmp/temp.bvec', verbose=True )
-# impute example
-dwi_imp = antspymm.impute_dwi( dwi, threshold=th, mask=mask, verbose=True )
-ff = antspymm.dipy_dti_recon( dwi_imp, prefix + "bval", prefix + "bvec", verbose=True )
-ants.image_write( dd['FA'], '/tmp/temp0.nii.gz' )
-ants.image_write( ee['FA'], '/tmp/temp1.nii.gz' )
-ants.image_write( ff['FA'], '/tmp/temp2.nii.gz' )