Development robert

TPTBox/core/dicom/dicom2nii_utils.py

@@ -11,6 +11,7 @@
 from tqdm import tqdm
 
 from TPTBox import BIDS_FILE, NII, BIDS_Global_info, Print_Logger
+from TPTBox.core.internal.nii_help import save_json as secure_save_json
 
 # source_folder = Path("/DATA/NAS/datasets_source/epi/NAKO/NAKO-732_Nachlieferung_20_25/")
 source_folder = Path("/DATA/NAS/datasets_source/epi/NAKO/NAKO_2D_issue/")
@@ -309,21 +310,12 @@ def save_json(json_ob: dict, file: str | Path, check_exist: bool = False, overri
         FileExistsError: When *check_exist* is ``True`` and the existing file
             contains different content.
     """
-
-    def convert(obj):
-        if isinstance(obj, np.integer):
-            return int(obj)
-        if isinstance(obj, np.floating):
-            return float(obj)
-        raise TypeError(type(obj))
-
     if check_exist and test_name_conflict(json_ob, file):
         raise FileExistsError(file)
     if Path(file).exists() and not override:
         return True
     Print_Logger().on_save("save json with grid info", file)
-    with open(file, "w") as file_handel:
-        json.dump(json_ob, file_handel, indent=4, default=convert)
+    secure_save_json(file, json_ob, indent=4)
     return False
 
 

TPTBox/core/dicom/dicom_extract.py

@@ -28,26 +28,51 @@
 
 sys.path.append(str(Path(__file__).parent))
 
+import string
+
 from TPTBox.core.dicom.dicom2nii_utils import get_json_from_dicom, load_json, save_json, test_name_conflict
 
 logger = Print_Logger()
 
 
-def _inc_key(keys: dict, inc: int = 1) -> None:
-    """Increment the sequence key inside *keys* by *inc*."""
-    k = "sequ"
+def _next_letter_suffix(s: str, inc: int = 1) -> str:
+    """Increment a letter suffix: a -> b, z -> aa, aa -> ab."""
+    alphabet = string.ascii_lowercase
+    # Convert to a number (base 26, 1-indexed)
+    n = 0
+    for c in s:
+        n = n * 26 + (ord(c) - ord("a") + 1)
+    n += inc
+    # Convert back to letters
+    result = []
+    while n > 0:
+        n -= 1
+        result.append(alphabet[n % 26])
+        n //= 26
+    return "".join(reversed(result))
+
+
+def _inc_key(keys: dict, inc: int = 1, k="sequ") -> None:
+    """Increment the sequence key inside *keys* by appending letter suffixes."""
     if k not in keys:
-        keys[k] = 0
+        keys[k] = "0"
+    value = str(keys[k])
     try:
-        v = int(keys[k])
-        keys[k] = str(v + int(inc))
-    except Exception:
-        try:
-            a, b = str(keys[k]).rsplit("-", maxsplit=2)
-        except Exception:
-            a = keys[k]
-            b = 0
-        keys[k] = a + "-" + str(int(b) + int(inc))
+        # Pure number: 100 -> 100-a
+        int(value)
+        keys[k] = f"{value}-a"
+        return  # noqa: TRY300
+    except ValueError:
+        pass
+
+    try:
+        base, suffix = value.rsplit("-", maxsplit=1)
+        if suffix.isalpha():
+            keys[k] = f"{base}-{_next_letter_suffix(suffix, inc)}"
+        else:
+            keys[k] = f"{base}-a"
+    except ValueError:
+        keys[k] = f"{value}-a"
 
 
 def _generate_bids_path(

TPTBox/core/internal/elastic_deform.py

@@ -1,6 +1,7 @@
 import time
 
-import elasticdeform
+# pip install elasticdeform
+import elasticdeform  # See https://github.com/gvtulder/elasticdeform/issues/24 to install this for >2.x
 import numpy as np
 from numpy.typing import NDArray
 
@@ -49,19 +50,23 @@ def deformed_nii(
         deformed_data = deformed_NII(arr_dic, sigma=sigma, points=points)
     """
     if sigma is None or points is None:
+        np.random.seed(None)
         sigma, points = get_random_deform_parameter(deform_factor=deform_factor)
-
     print("deformation parameter sigma = ", round(sigma, 4), "; n_points = ", points)
     t = time.time()
-    values = list(nii_dic.values())
+
     # Deform
+    max_v = None
     if joint_normalize:
         max_v = max([img.max() for img in nii_dic.values() if not img.seg])
         nii_dic = {k: img if img.seg else img.set_dtype(np.float32) / max_v for k, img in nii_dic.items()}
     elif normalize:
-        nii_dic = {k: img if img.seg else img.set_dtype(np.float32).normalize() for k, img in nii_dic.items()}
+        max_v = {k: None if img.seg else (float(max(img.max() - img.min(), 1)), float(img.min())) for k, img in nii_dic.items()}
+        nii_dic = {k: img if img.seg else (img.set_dtype(np.float32) - max_v[k][1]) / max_v[k][0] for k, img in nii_dic.items()}
     else:
         nii_dic = {k: img if img.seg else img.set_dtype(np.float32) for k, img in nii_dic.items()}
+
+    values = list(nii_dic.values())
     assert sigma is not None
     p = deform_padding
     out: list[NDArray] = elasticdeform.deform_random_grid(
@@ -74,6 +79,10 @@ def deformed_nii(
     for (k, nii), arr in zip(nii_dic.items(), out, strict=True):
         out2[k] = nii.set_array(arr[p:-p, p:-p, p:-p])
     print("Deformation took", round(time.time() - t, 1), "Seconds")
+    if joint_normalize:
+        out2 = {k: img if img.seg else img.set_dtype(np.float32) * max_v for k, img in out2.items()}
+    elif normalize:
+        out2 = {k: img if img.seg else ((img.set_dtype(np.float32) * max_v[k][0]) + max_v[k][1]) for k, img in out2.items()}
     return out2
 
 

TPTBox/core/internal/nii_help.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import json
 import shutil
 from collections.abc import Callable
 from functools import wraps
@@ -14,10 +15,11 @@
 if TYPE_CHECKING:
     from TPTBox.core.nii_poi_abstract import Has_Grid
     from TPTBox.core.nii_wrapper import NII
+
 from TPTBox.core.vert_constants import AFFINE, MODES, SHAPE, ZOOMS, Sentinel, _supported_img_files
 
 
-def secure_save(func) -> Callable:
+def secure_save(func, *, file_types=tuple(_supported_img_files)) -> Callable:
     """Decorator that writes to a `.backup` file first and restores it if saving fails.
 
     Steps: (1) back up existing file, (2) call the wrapped save function, (3) delete backup on
@@ -48,7 +50,7 @@ def save_to_file(self, file: Path, data: Any):
     @wraps(func)
     def wrapper(self, file: str | Path | bids_files.BIDS_FILE, *args, **kwargs):
         if isinstance(file, bids_files.BIDS_FILE):
-            for file_type in _supported_img_files:
+            for file_type in file_types:
                 if file_type in file.file:
                     file = file.file[file_type]
                     break
@@ -81,6 +83,84 @@ def wrapper(self, file: str | Path | bids_files.BIDS_FILE, *args, **kwargs):
     return wrapper
 
 
+def _convert(obj):
+    if isinstance(obj, np.integer):
+        return int(obj)
+    if isinstance(obj, np.floating):
+        return float(obj)
+    if isinstance(obj, np.ndarray):
+        return obj.tolist()
+    if isinstance(obj, Path):
+        return str(obj.absolute())
+    raise TypeError(type(obj))
+
+
+def _save_json(data, filepath: str | Path | bids_files.BIDS_FILE, indent=4, convert=_convert):
+
+    if isinstance(filepath, bids_files.BIDS_FILE):
+        if "json" in filepath.file:
+            filepath = filepath.file["json"]
+        else:
+            nf = filepath.get_nii_file()
+            if nf is not None:
+                filepath = (nf.parent) / (nf.name.split(".")[0] + ".json")
+            else:
+                nf = next(iter(filepath.file.values()))
+                filepath = (nf.parent) / (nf.name.rsplit(".", maxsplit=1)[0] + ".json")
+    # print(markups[-1].get("display"))
+    with open(filepath, "w") as f:
+        json.dump(data, f, indent=indent, default=convert)
+
+
+def save_json(filepath: str | Path | bids_files.BIDS_FILE, data, indent=4, convert=_convert) -> None:
+    """Safely save a Python object as a JSON file with automatic backup protection.
+
+    This function writes JSON data to disk using a safe save mechanism:
+    if the target file already exists, it is first moved to a `.backup`
+    file. If writing succeeds, the backup is removed. If writing fails,
+    the original file is restored.
+
+    The function supports flexible input types for the target path:
+        - str or Path: written directly to disk
+        - bids_files.BIDS_FILE: resolved to an appropriate `.json` path
+
+    Non-JSON-serializable types are handled via a custom converter
+    that supports:
+        - numpy integers → int
+        - numpy floats → float
+        - numpy arrays → list
+        - pathlib.Path → absolute string path
+
+    Args:
+        filepath (str | Path | bids_files.BIDS_FILE):
+            Target file path or BIDS file container.
+        data (Any):
+            Python object to serialize into JSON.
+        indent (int, optional):
+            Pretty-print indentation level. Default is 4.
+        convert (callable, optional):
+            Custom serialization function for unsupported types.
+            Defaults to `_convert`.
+
+    Returns:
+        None
+
+    Notes:
+        - Uses `secure_save` to ensure atomic write semantics with backup/restore.
+        - If `filepath` is a `BIDS_FILE`, the `.json` path is inferred from:
+            1. explicit "json" entry in the file map
+            2. associated NIfTI file path
+            3. fallback to any available file in the container
+        - This function is intended for structured metadata and annotation storage.
+
+    Raises:
+        Exception:
+            Propagates any error raised during serialization or file writing,
+            after attempting automatic recovery of the original file.
+    """
+    return secure_save(_save_json, file_types=["json"])(data, filepath, indent=indent, convert=convert)
+
+
 def _resample_from_to(
     from_img: NII,
     to_img: tuple[SHAPE, AFFINE, ZOOMS] | Has_Grid,