A python script to wrap image read and write for Nifti Images.

WrapImage/nifti_wrapper.py

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+import argparse
+import json
+import os
+import nibabel as nib
+import numpy as np
+
+def read_nifti_4d(input_file):
+    """
+    For reading the 4d nifti image
+    """
+    nifti_img = nib.load(input_file)
+    return nifti_img.get_fdata()
+
+def read_json_file(json_file):
+    """
+    For reading the json file
+    """
+
+    if not os.path.exists(json_file):
+        raise FileNotFoundError(f"File '{json_file}' not found.")
+
+    with open(json_file, "r") as f:
+        try:
+            json_data = json.load(f)
+        except json.JSONDecodeError as e:
+            raise ValueError(f"Error decoding JSON in file '{json_file}': {e}")
+
+    return json_data
+
+def save_nifti_3d(data, output_file):
+    """
+    For saving the 3d nifti images of the output of the algorithm
+    """
+    output_img = nib.Nifti1Image(data, np.eye(4))
+    nib.save(output_img, output_file)
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Read a 4D NIfTI phantom file along with BIDS JSON, b-vector, and b-value files.")
+    parser.add_argument("input_file", type=str, help="Path to the input 4D NIfTI file.")
+    parser.add_argument("bids_dir", type=str, help="Path to the BIDS directory.")
+    parser.add_argument("--algorithm", type=str, choices=["algorithm1", "algorithm2"], default="algorithm1", help="Select the algorithm to use.")
+    parser.add_argument("algorithm_args", nargs=argparse.REMAINDER, help="Additional arguments for the algorithm.")
+
+    args = parser.parse_args()
+
+    try:
+        # Read the 4D NIfTI file
+        data = read_nifti_4d(args.input_file)
+
+        # Construct the full paths for the JSON, b-vector, and b-value files
+        json_file = os.path.join(args.bids_dir, "dataset_description.json")
+        bvec_file = os.path.join(args.bids_dir, "bvecs.json")
+        bval_file = os.path.join(args.bids_dir, "bvals.json")
+
+        # Read the JSON, b-vector, and b-value files
+        json_data = read_json_file(json_file)
+        bvecs = read_json_file(bvec_file)
+        bvals = read_json_file(bval_file)
+
+        # Pass additional arguments to the algorithm
+        # Passing the values to the selectect algorithm and saving it
+
+    except Exception as e:
+        print(f"Error: {e}")