reorienting all files before rpool initialization

CPAC/pipeline/engine.py

@@ -68,7 +68,7 @@
     read_json,
     write_output_json,
 )
-
+from nibabel.orientations import OrientationError
 
 class ResourcePool:
     def __init__(self, rpool=None, name=None, cfg=None, pipe_list=None):
@@ -2414,7 +2414,7 @@ def ingress_pipeconfig_paths(cfg, rpool, unique_id, creds_path=None):
 
     import pandas as pd
     import pkg_resources as p
-    from nibabel.orientations import OrientationError
+
 
     template_csv = p.resource_filename("CPAC", "resources/cpac_templates.csv")
     template_df = pd.read_csv(template_csv, keep_default_na=False)
@@ -2523,7 +2523,7 @@ def ingress_pipeconfig_paths(cfg, rpool, unique_id, creds_path=None):
         if val.endswith(".nii.gz"):
             templates.append([key, val])
 
-    table = check_all_orientations(templates, desired_orientation)
+    table = check_all_orientations(templates, desired_orientation, reorient=True)
     df = pd.DataFrame(table, columns=["Resource", "Path", "Orientation"])
 
     # check if any of the values in Orientation column are not RPI
@@ -2660,8 +2660,33 @@ def initiate_rpool(wf, cfg, data_paths=None, part_id=None):
         creds_path = None
 
     rpool = ResourcePool(name=unique_id, cfg=cfg)
+
+    desired_orientation = cfg.pipeline_setup["desired_orientation"]
 
     if data_paths:
+        # check all data_paths and convert it to the desired_orientations
+        #Convert all anat to desired_orientation
+        if "anat" in data_paths:
+            anat = []
+            for key in data_paths["anat"]:
+                anat.append([key, data_paths["anat"][key]])
+            if anat:
+                try:
+                    orientation = check_all_orientations(anat, desired_orientation, reorient=True)
+                except OrientationError as e:
+                    raise e("Anatomical data is not in the desired orientation")
+
+        #Convert all func to desired_orientation    
+        if "func" in data_paths:
+            func = []
+            for key in data_paths["func"]:
+                func.append([key, data_paths["func"][key]["scan"]])
+            if func:
+                try:
+                    orientation = check_all_orientations(func, desired_orientation, reorient=True)
+                except :
+                    raise OrientationError("Functional data is not in the desired orientation")
+
         # ingress outdir
         try:
             if (
@@ -2691,11 +2716,7 @@ def initiate_rpool(wf, cfg, data_paths=None, part_id=None):
     rpool = ingress_pipeconfig_paths(cfg, rpool, unique_id, creds_path)
 
     # output files with 4 different scans
-    for x in rpool.get_entire_pool().keys():
-        print(x)
-    import sys
 
-    sys.exit()
     return (wf, rpool)
 
 

CPAC/pipeline/utils.py

@@ -49,8 +49,48 @@ def find_orientation(input_file):
         .upper()
     )
 
+def reorient_image(input_file, orientation):
+    """Reorient the input image to the desired orientation. Replaces the original input_file with the reoriented image.
 
-def check_all_orientations(input_images: list, desired_orientation: str = "RPI"):
+    Parameters
+    ----------
+    input_file : str
+        Input image file path
+    orientation : str
+        Desired orientation of the input image
+
+    """
+    import os
+    import subprocess
+
+    output_file = os.path.join(
+        os.path.dirname(input_file),
+        f"reoriented_{os.path.basename(input_file)}",
+    )
+    cmd_3drefit = ["3drefit", "-deoblique", input_file]
+    cmd_3dresample = [
+        "3dresample",
+        "-orient",
+        orientation,
+        "-prefix",
+        output_file,
+        "-inset",
+        input_file,
+    ]
+    cmd_mv = ["mv", output_file, input_file]
+    print(f"""+++
+Reorienting : {input_file} 
+to : {orientation}
++++""")
+    subprocess.run(cmd_3drefit, check=True)
+    subprocess.run(cmd_3dresample, check=True)
+    print(f"""+++Replacing {input_file} with reoriented image
+          """)
+    subprocess.run(cmd_mv, check=True)
+    return
+
+
+def check_all_orientations(input_images: list, desired_orientation: str = "RPI", reorient=True):
     """Check the orientation of all input images.
 
     Parameters
@@ -80,6 +120,8 @@ def check_all_orientations(input_images: list, desired_orientation: str = "RPI")
     for key, image in input_images:
         find_orient.inputs.input_file = image
         orientation = find_orient.run().outputs.orientation
+        if reorient and orientation != desired_orientation:
+            reorient_image(image, desired_orientation)
         orientations.append([key, image, orientation])
     return orientations