🔀 Merge branch 'datetime-none' into 'organism'

Author: shnizzedy

CPAC/distortion_correction/distortion_correction.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
-# Copyright (C) 2017-2022  C-PAC Developers
+# Copyright (C) 2017-2025  C-PAC Developers
 
 # This file is part of C-PAC.
 
@@ -16,6 +16,8 @@
 
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
+"""Distortion correction in C-PAC."""
+
 import os
 import subprocess
 
@@ -663,7 +665,7 @@ def distcor_blip_fsl_topup(wf, cfg, strat_pool, pipe_num, opt=None):
         "import os",
         "import subprocess",
         "import numpy as np",
-        "import nibabel",
+        "import nibabel as nib",
         "import sys",
     ]
     phase_encoding = pe.Node(

CPAC/distortion_correction/utils.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2021-2023  C-PAC Developers
+# Copyright (C) 2021-2025  C-PAC Developers
 
 # This file is part of C-PAC.
 
@@ -14,6 +14,8 @@
 
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
+"""Distortion correction utilities."""
+
 import os
 import subprocess
 import sys

CPAC/utils/monitoring/monitoring.py

@@ -23,7 +23,7 @@
 import os
 import socketserver
 import threading
-from typing import Optional, TypeAlias
+from typing import Any, Optional, TypeAlias
 
 import networkx as nx
 from traits.trait_base import Undefined
@@ -124,6 +124,23 @@ def __str__(self) -> str:
         return super().__str__()
 
 
+class DatetimeJSONEncoder(json.JSONEncoder):
+    """JSON encoder that handles DatetimeWithSafeNone instances."""
+
+    def default(self, o: Any) -> str:
+        """Convert datetime objects to ISO format."""
+        if isinstance(o, datetime):
+            return o.isoformat()
+        if o is None or o is NoTime:
+            return ""
+        return super().default(o)
+
+
+def json_dumps(obj: Any, **kwargs) -> str:
+    """Convert an object to a JSON string."""
+    return json.dumps(obj, cls=DatetimeJSONEncoder, **kwargs)
+
+
 OptionalDatetime: TypeAlias = Optional[datetime | str | DatetimeWithSafeNone | _NoTime]
 """Type alias for a datetime, ISO-format string or None."""
 
@@ -144,7 +161,7 @@ def recurse_nodes(workflow, prefix=""):
 def log_nodes_initial(workflow):
     logger = getLogger("callback")
     for node in recurse_nodes(workflow):
-        logger.debug(json.dumps(node))
+        logger.debug(json_dumps(node))
 
 
 def log_nodes_cb(node, status):
@@ -242,7 +259,7 @@ def log_nodes_cb(node, status):
     ):
         status_dict["error"] = True
 
-    logger.debug(json.dumps(status_dict))
+    logger.debug(json_dumps(status_dict))
 
 
 log_nodes_cb.__doc__ = f"""{_nipype_log_nodes_cb.__doc__}
@@ -299,7 +316,7 @@ def handle(self):
                 tree = {s: t for s, t in tree.items() if t}
 
         headers = "HTTP/1.1 200 OK\nConnection: close\n\n"
-        self.request.sendall(headers + json.dumps(tree) + "\n")
+        self.request.sendall(headers + json_dumps(tree) + "\n")
 
 
 class LoggingHTTPServer(socketserver.ThreadingTCPServer, object):