commit before migration to habrok

code/utils_quintin.py

@@ -0,0 +1,82 @@
+import yaml
+from typing import List
+from collections import deque
+from pathlib import Path
+import numpy as np
+import SimpleITK as sitk
+
+def print_p(text, end="\n"):
+    """ Print function for on Peregrine. It needs a flush before printing. """
+    print(text, flush=True, end=end)
+
+def list_from_file(path: str) -> List:
+    """ Returns a list of all items on each line of the text file referenced in
+        the given path
+    
+    Parameters:
+    `path (str)`: path to the text file
+    """
+    print_p(path)
+    return [line.strip() for line in open(path, "r")]
+
+
+def dump_dict_to_yaml(
+    data: dict,
+    target_dir: str,
+    filename: str = "settings",
+    verbose: bool = True) -> None:
+    """ Writes the given dictionary as a yaml to the target directory.
+    
+    Parameters:
+    `data (dict)`: dictionary of data.
+    `target_dir (str)`: directory where the yaml will be saved.
+    `` filename (str)`: name of the file without extension
+    """
+    if verbose:
+        print("\nParameters")
+        for pair in data.items():
+            print(f"\t{pair}")
+        print()
+
+    path = f"{target_dir}/{filename}.yml"
+    print_p(f"Wrote yaml to: {path}")
+    with open(path, 'w') as outfile:
+        yaml.dump(data, outfile, default_flow_style=False)
+
+
+def read_yaml_to_dict(path: str) -> dict:
+    with open(path, 'r') as stream:
+        try:
+            parsed_yaml=yaml.safe_load(stream)
+            # print(parsed_yaml)
+            return parsed_yaml
+        except yaml.YAMLError as exc:
+            print(exc)
+
+
+def create_dirs_if_not_exists(dirs: List[str]) -> None:
+    """ Creates the list of supplied directories if they don't exist yet.
+    
+    Parameters:
+    `dirs (List[str]) or str`: list of strings representing the directories that
+    need to be created
+    """
+    
+    if isinstance(dirs, str):
+        dirs = [dirs]
+
+    for folder in dirs:
+        Path(folder).mkdir(parents=True, exist_ok=True)
+        print_p(f"Created directory {folder} or it already existed.")
+
+
+def save_np_to_nifti(data_np: np.ndarray,
+                    target_dir: str,
+                    fname: str,
+                    target_space: List[float] = [0.5, 0.5, 3.0]):
+
+    img_s = sitk.GetImageFromArray(data_np.T)
+    img_s.SetSpacing(target_space)
+    path = f"{target_dir}/{fname}.nii.gz"
+    sitk.WriteImage(img_s, path)
+    print_p(f"Saved numpy array to nifti: {path}")