Fixed get_lib_fun when upgrading ANTs; added quick SyN to norma…

…lization

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rpyANTs
 Title: An Alternative Advanced Normalization Tools ('ANTs')
-Version: 0.0.3.9006
+Version: 0.0.3.9007
 Authors@R: 
     person("Zhengjia", "Wang", email = "[email protected]", 
             role = c("aut", "cre"))

inst/rpyants/requirements-dev.txt

@@ -3,3 +3,4 @@ mkdocs==1.5.2
 mkdocs-material==9.2.3
 mkdocstrings==0.22.0
 mkdocstrings-python==1.5.2
+nibabel>=5.0.1

inst/rpyants/requirements.txt

@@ -1 +1,2 @@
 antspyx>=0.3.8
+nibabel>=5.0.1

inst/rpyants/rpyants/registration/halpern.py

@@ -6,6 +6,7 @@
 
 import ants
 from ..utils.paths import normalize_path
+from ..utils.internals import get_lib_fn, ants_process_arguments
 
 def halpern_coregister_ct_mri(fixed_path, moving_path, outprefix, verbose=True):
   '''
@@ -17,8 +18,7 @@ def halpern_coregister_ct_mri(fixed_path, moving_path, outprefix, verbose=True):
   moving_path = normalize_path(moving_path, sep="/")
   outprefix = normalize_path(outprefix, sep="/")
   verbose = "1" if verbose else "0"
-  from ants import utils
-  libfn = utils.get_lib_fn("antsRegistration")
+  libfn = get_lib_fn("antsRegistration")
   # Build arguments, see https://github.com/ANTsX/ANTsPy/blob/78dad33ca4e12ae605e80d8d990ec73a52abe273/ants/registration/interface.py
   # The difference is we fit coreg twice
   args = [
@@ -42,7 +42,7 @@ def halpern_coregister_ct_mri(fixed_path, moving_path, outprefix, verbose=True):
     "-v", verbose
   ]
   # Clean args
-  processed_args = utils._int_antsProcessArguments(args)
+  processed_args = ants_process_arguments(args)
   reg_exit = libfn(processed_args)
   if verbose == "1":
     print("---- Call arguments --------------------------------")

inst/rpyants/rpyants/registration/normalization.py

@@ -0,0 +1,93 @@
+#########################################################
+# Custom Normalization scripts
+#########################################################
+
+import ants
+from ..utils.paths import normalize_path
+from ..utils.internals import get_lib_fn, ants_process_arguments
+
+# from rpyants.registration.normalization import normalize_to_template_syn
+# fixed_path="/Users/dipterix/rave_data/raw_dir/PAV044/rave-imaging/normalization/anat/MNI152NLin2009bAsym_orig.nii.gz"
+# moving_path="/Users/dipterix/rave_data/raw_dir/Precision001/rave-imaging/inputs/MRI/MRI_RAW.nii"
+# outprefix="/Users/dipterix/rave_data/raw_dir/Precision001/rave-imaging/mornalize_mni152b_"
+# normalize_to_template_syn(fixed_path, moving_path, outprefix, verbose=True)
+
+def normalize_to_template_syn(fixed_path, moving_path, outprefix, verbose=True):
+  '''
+  Ridig-body coregistration for CT and MRI for Casey Halpern's lab.
+  '''
+  # use forward slash to avoid escaping issues on windows
+  # Do not use memory pointers!!!
+  fixed_path = normalize_path(fixed_path, sep="/")
+  moving_path = normalize_path(moving_path, sep="/")
+  outprefix = normalize_path(outprefix, sep="/")
+  verbose = "1" if verbose else "0"
+  libfn = get_lib_fn("antsRegistration")
+  # Build arguments, see https://github.com/ANTsX/ANTsPy/blob/78dad33ca4e12ae605e80d8d990ec73a52abe273/ants/registration/interface.py
+  args = [
+    "--dimensionality", "3",
+    "--float", "1",
+    "-o", "[%s,%s,%s]" % (outprefix, outprefix + "Warped.nii.gz", outprefix + "InverseWarped.nii.gz"),
+    "--interpolation", "Linear",
+    "--use-histogram-matching", "1",
+
+    # Rigid Transformation
+    #     --transform Rigid[0.1] \
+    #     --metric MI[fixedImage, movingImage, 1, 32, Random, 0.25] \
+    #     --convergence [1000x500x250x0,1e-7,10] \
+    #     --shrink-factors 12x8x4x1 \
+    #     --smoothing-sigmas 5x4x3x1vox \
+    "--transform", "Rigid[2.0]",
+    "--metric", "MI[%s,%s,1,32,Random,0.25]" % (fixed_path, moving_path),
+    "--convergence", "[1000x500x250x0,1e-7,10]",
+    "--shrink-factors", "12x8x4x1",
+    "--smoothing-sigmas", "5x4x3x1vox",
+
+    # Affine Transformation
+    #   --transform Affine[0.1] \
+    #   --metric MI[/path/to/MNI152b.nii.gz,/path/to/subject_T1w.nii.gz,1,32,Random,0.25] \
+    #   --convergence [1000x500x250x0,1e-7,10] \
+    #   --shrink-factors 12x8x4x1 \
+    #   --smoothing-sigmas 5x4x3x1vox \
+    "--transform", "Affine[0.1]",
+    "--metric", "MI[%s,%s,1,32,Random,0.25]" % (fixed_path, moving_path),
+    "--convergence", "[1000x500x250x0,1e-7,10]",
+    "--shrink-factors", "12x8x4x1",
+    "--smoothing-sigmas", "5x4x3x1vox",
+
+    # SyN Transformation
+    #   --transform SyN[0.3,4,3] \
+    #   --metric MI[/path/to/MNI152b.nii.gz,/path/to/subject_T1w.nii.gz,1,32,Random,0.25] \
+    #   --convergence [1000x500x500x0,1e-7,7] \
+    #   --shrink-factors 8x4x4x1 \
+    #   --smoothing-sigmas 4x3x1x1vox
+    "--transform", "SyN[0.3,4.0,3.0]",
+    "--metric", "MI[%s,%s,1,32,Random,0.25]" % (fixed_path, moving_path),
+    "--convergence", "[1000x500x500x0,1e-7,7]",
+    "--shrink-factors", "8x4x4x1",
+    "--smoothing-sigmas", "4x3x1x1vox",
+
+    # subcortical refine stage
+    "--transform", "SyN[0.3,4,3]",
+    "--metric", "MI[%s,%s,1,32,Random,0.25]" % (fixed_path, moving_path),
+    "--convergence", "[200x50x10x0,1e-6,7]",
+    "--shrink-factors", "4x4x2x1",
+    "--smoothing-sigmas", "2x2x1x1vox",
+
+    "-v", verbose
+  ]
+  # Clean args
+  processed_args = ants_process_arguments(args)
+  reg_exit = libfn(processed_args)
+  if verbose == "1":
+    print("---- Call arguments --------------------------------")
+    print("antsRegistration %s" % " ".join(processed_args))
+  if not reg_exit == 0:
+    raise RuntimeError(f"Registration failed with error code {reg_exit}")
+  return {
+    "outprefix"    : outprefix,
+    "warpedmovout" : outprefix + "Warped.nii.gz",
+    "warpedfixout" : outprefix + "InverseWarped.nii.gz",
+    "transforms"   : [outprefix + "0GenericAffine.mat"]
+  }
+

inst/rpyants/rpyants/registration/yael.py

@@ -25,7 +25,7 @@ class YAELPreprocess():
     def work_path(self):
         return self._work_path
 
-    def __init__(self, subject_code : str, work_path : str):
+    def __init__(self, subject_code : str, work_path : str, image_types : list | tuple = ["CT", "T1w", "T2w", "FLAIR", "preopCT", "T1wContrast", "fGATIR", "DWI"] ):
         '''
         Initialize a YAELPreprocess object.
         
@@ -35,6 +35,9 @@ def __init__(self, subject_code : str, work_path : str):
         @param work_path: The path to the working directory, for example, `rave-imaging/`.
         @type work_path: str
 
+        @param image_types: Image types allowed to query
+        @type image_types: list or tuple
+
         '''
 
         # List of allowed image types
@@ -45,7 +48,7 @@ def __init__(self, subject_code : str, work_path : str):
         # preopCT: preop CT (for showing blood vessels)
         # T1wContrast: preop T1w MRI with contrast (for showing blood vessels)
         # fGATIR: preop fast Gray Matter Acquisition T1 Inversion Recovery
-        self.allowed_image_types = ["CT", "T1w", "T2w", "FLAIR", "preopCT", "T1wContrast", "fGATIR"]
+        self.allowed_image_types = [ *image_types ]
         # Each item is a dictionary returned by `parse_bids_filename`
         self._images = {}
 
@@ -65,7 +68,12 @@ def _fix_image_path(self, parsed : dict, name = None) -> dict:
         if parsed['ext'] == "nii":
             parsed['ext'] = "nii.gz"
         if parsed['components'].get('ses', None) is None:
-            if parsed['type'] in self.allowed_image_types:
+            image_type = parsed['type']
+            if image_type.startswith("preop"):
+                parsed['components']['ses'] = 'preop'
+            elif image_type.startswith("preop"):
+                parsed['components']['ses'] = 'postop'
+            elif image_type in self.allowed_image_types:
                 if parsed['type'] == "CT":
                     parsed['components']['ses'] = 'postop'
                 else:
@@ -191,10 +199,11 @@ def set_image(self, type : str, path : str, **kwargs):
             * overwrite : If True, overwrite the existing image. Otherwise throw an error if image exists.
             * Other argument keys are BIDS components (e.g., `sub`, `ses`, `space`, `rec`, `desc`)
         '''
-        if type not in self.allowed_image_types:
-            raise ValueError(f"Invalid image type: {type}. Must be one of {self.allowed_image_types}")
         if not os.path.exists(path):
             raise FileNotFoundError(f"Invalid image path: {path}")
+        if type not in self.allowed_image_types:
+            # raise ValueError(f"Invalid image type: {type}. Must be one of {self.allowed_image_types}")
+            self.allowed_image_types.append(type)
         overwrite = kwargs.get('overwrite', False)
         existing_path = self.input_image_path(type)
         if not overwrite and existing_path is not None:
@@ -431,11 +440,19 @@ def map_to_template(self,
             native_mask = ants.image_read(native_mask_path)
         else:
             native_mask = None
-        affine_reg = ants.registration(fixed = fix_img, moving = mov_img, 
+        affine_reg = ants.registration(
+            fixed = fix_img, moving = mov_img, 
             mask = template_mask, moving_mask = native_mask,
-            outprefix = file_path(ants_outputdir, "affine_"), type_of_transform = "antsRegistrationSyN[a]", 
-            aff_metric = "CC", syn_metric = "CC", write_composite_transform = False, 
-            aff_sampling = 2, syn_sampling = 2, verbose = verbose)
+            outprefix = file_path(ants_outputdir, "affine_"), 
+            type_of_transform = "antsRegistrationSyN[a]", 
+            write_composite_transform = False, 
+            aff_metric = "mattes",  
+            aff_random_sampling_rate=0.25,
+            aff_iterations=(1000, 500, 250, 0),
+            aff_shrink_factors=(12, 8, 4, 1),
+            aff_smoothing_sigmas=(5, 4, 3, 1),
+            verbose = verbose
+        )
         # save the registration result
         transform_from_template_prefix = to_bids_prefix({ 'sub': self._subject_code, 'from': template_name, 'to': native_type, 'desc': 'affine+SyN', })
         transform_to_template_prefix = to_bids_prefix({ 'sub': self._subject_code, 'from': native_type, 'to': template_name, 'desc': 'affine+SyN', })
@@ -453,9 +470,18 @@ def map_to_template(self,
         deformable_reg = ants.registration(
             fixed = fix_img, moving = affine_reg['warpedmovout'],
             mask = template_mask, moving_mask = native_mask,
-            outprefix = file_path(ants_outputdir, "deformable_"), type_of_transform = "antsRegistrationSyN[b]",
-            aff_metric = "CC", syn_metric = "CC", write_composite_transform = False,
-            aff_sampling = 2, syn_sampling = 2, verbose = verbose)
+            outprefix = file_path(ants_outputdir, "deformable_"), 
+            type_of_transform = "antsRegistrationSyNQuick[s]",
+            write_composite_transform = False,
+            aff_metric = "mattes", 
+            aff_random_sampling_rate=0.25,
+            aff_iterations=(1000, 500, 250, 0),
+            aff_shrink_factors=(12, 8, 4, 1),
+            aff_smoothing_sigmas=(5, 4, 3, 1),
+            syn_metric="mattes", 
+            reg_iterations=(1000, 500, 500, 0),
+            verbose = verbose
+        )
         # save forward (mov -> fix) transforms
         # simple experiment to check the composition of the transforms: the following two are the same
         # np.matmul(ants_AffineTransform_to_m44(affine_1), ants_AffineTransform_to_m44(affine_0))

inst/rpyants/rpyants/utils/internals.py

@@ -0,0 +1,19 @@
+
+def get_lib_fn(fn):
+  try:
+    from ants import utils
+    libfn = utils.get_lib_fn(fn)
+  except:
+    from ants.internal import get_lib_fn
+    libfn = get_lib_fn(fn)
+  return libfn
+
+
+def ants_process_arguments(args):
+  try:
+    from ants import utils
+    ret = utils._int_antsProcessArguments(args)
+  except:
+    from ants.internal import process_arguments
+    ret = process_arguments(args)
+  return ret