fixed bug in volinterp.py and volalign.py where the final set of tfm files was not defined in chunk_info

Author: tfunck

README.md

@@ -25,6 +25,13 @@ python3 -m pip install requirements.txt
 python3 -m pip install -e .
 ```
 
+4) Install Morphint submodule
+```
+cd morphint 
+python3 -m pip install -e .
+```
+
+
 ## Useage
 
 ```python3

brainbuilder/interp/volinterp.py

@@ -518,14 +518,16 @@ def apply_interpolated_volumes_to_stx(
             .values[0]
         )
 
-        if not os.path.exists(interp_stx_fin) or clobber:
-            cmd = f"antsApplyTransforms -d 3 -n {interpolation} -i {interp_nat_fin} -o {interp_stx_fin} -r {ref_vol_rsl_fn} -t {nl_3d_tfm_fn} --float 1"
-
-            print(cmd)
 
-            run(cmd, shell=True)
+        utils.simple_ants_apply_transforms(
+            interp_nat_fin,
+            interp_stx_fin,
+            ref_vol_rsl_fn,
+            nl_3d_tfm_fn,
+            interpolation=interpolation,
+            clobber=clobber,
+        )
 
-            assert nib.load(interp_stx_fin).get_fdata().sum() > 0, "Error: Empty Output"
 
     return curr_chunk_info
 

brainbuilder/utils/validate_inputs.py

@@ -2,15 +2,15 @@
 import os
 from typing import Union
 
-import nibabel as nib
 import numpy as np
 import pandas as pd
 from joblib import Parallel, cpu_count, delayed
-from PIL import Image
 
 import brainbuilder.utils.utils as utils
 from brainbuilder.utils.mesh_io import load_mesh_ext
 from brainbuilder.utils.utils import get_logger
+import nibabel as nib
+from PIL import Image
 
 global chunk_info_required_columns
 global sect_info_required_columns
@@ -82,9 +82,9 @@ def val_func(x: Union[int, float, str]) -> bool:
 sub = Column("sub", None)
 hemisphere = Column("hemisphere", None)
 chunk = Column("chunk", None)
-# direction = Column("direction", None) #DEPRECIATED
-# pixel_size_0 = Column("pixel_size_0", float) #DEPRECIATED
-# pixel_size_1 = Column("pixel_size_1", float) #DEPRECIATED
+#direction = Column("direction", None) #DEPRECIATED
+#pixel_size_0 = Column("pixel_size_0", float) #DEPRECIATED
+#pixel_size_1 = Column("pixel_size_1", float) #DEPRECIATED
 section_thickness = Column("section_thickness", float)
 acquisition = Column("acquisition", None)
 sample = Column("sample", int)
@@ -94,13 +94,12 @@ def val_func(x: Union[int, float, str]) -> bool:
 struct_ref_vol = Column("struct_ref_vol", "volume")
 
 # Surfaces
-# gm_surf = Column("gm_surf", "surface", False) #DEPRECIATED
-# wm_surf = Column("wm_surf", "surface", False) #DEPRECIATED
+#gm_surf = Column("gm_surf", "surface", False) #DEPRECIATED
+#wm_surf = Column("wm_surf", "surface", False) #DEPRECIATED
 
-
-chunk_info_required_columns = [sub, hemisphere, chunk, section_thickness]
-sect_info_required_columns = [acquisition, sub, hemisphere, chunk, raw, sample]
-hemi_info_required_columns = [sub, hemisphere, struct_ref_vol]
+chunk_info_required_columns = [sub, hemisphere, chunk, section_thickness ]
+sect_info_required_columns = [acquisition, sub, hemisphere, chunk, raw, sample ]
+hemi_info_required_columns = [sub, hemisphere, struct_ref_vol ] 
 
 
 def validate_dataframe(
@@ -212,7 +211,6 @@ def _can_open_volume(path: str) -> bool:
         logger.critical(last_exc)
     return False
 
-
 def validate_volume(fn: str, check_not_empty: bool = False) -> bool:
     """Validate that a volume exists and that it is not empty.
 
@@ -227,13 +225,13 @@ def validate_volume(fn: str, check_not_empty: bool = False) -> bool:
         valid_inputs = False
     else:
         try:
-            if check_not_empty:
+            if check_not_empty :
                 vol = utils.load_image(fn)
 
                 if np.sum(np.abs(vol)) == 0:
                     valid_inputs = False
                     logger.info(f"\tMissing input: empty template file {fn}")
-            else:
+            else :
                 valid_inputs = _can_open_volume(fn)
 
         except Exception as e:

brainbuilder/volalign.py

@@ -462,6 +462,9 @@ def alignment_iteration(
 
     chunk_info_out = paths.to_dataframe()
 
+    # set the nl_3d_tfm_fn column in chunk_info_out to the list of 3D transforms used for the current chunk and resolution
+    chunk_info_out["nl_3d_tfm_fn"] = vol_tfm_list
+
     sect_info_curr_resolution_csv = f"{output_dir}/sub-{sub}_hemi-{hemisphere}_chunk-{chunk}_{resolution}mm_sect_info.csv"
 
     sect_info.to_csv(sect_info_curr_resolution_csv, index=False)
@@ -514,11 +517,6 @@ def align_chunk(
     qc_dir = f"{output_dir}/qc/"
     os.makedirs(qc_dir, exist_ok=True)
 
-    chunk_pass_df = pd.DataFrame()
-    sect_pass_df = pd.DataFrame()
-    chunk_pass_last_df = pd.DataFrame()
-    sect_pass_last_df = pd.DataFrame()
-
     sect_info_out = sect_info
     chunk_info_out = chunk_info_row
 
@@ -604,15 +602,7 @@ def align_chunk(
                 landmark_dir=landmark_dir,
                 clobber=clobber,
             )
-            chunk_info_out["pass"] = pass_step
-            sect_info_out["pass"] = pass_step
-
-            chunk_pass_df = pd.concat([chunk_pass_df, chunk_info_out])
-            sect_pass_df = pd.concat([sect_pass_df, sect_info_out])
 
-            if pass_step == n_passes - 1 and resolution == resolution_list[-1]:
-                chunk_pass_last_df = pd.concat([chunk_pass_last_df, chunk_info_out])
-                sect_pass_last_df = pd.concat([sect_pass_last_df, sect_info_out])
 
     # un a final alignment
 
@@ -660,6 +650,7 @@ def align_chunk(
         landmark_dir=landmark_dir,
         clobber=clobber,
     )
+    chunk_info_out['pass'] = pass_step
     logger.info("Finished final alignment iteration at highest resolution")
 
-    return chunk_pass_last_df, sect_pass_last_df
+    return chunk_info_out, sect_info_out