brainprep/decorators: add and apply signature hook.

Author: AGrigis

brainprep/cli.py

@@ -150,6 +150,7 @@ def main():
         "subject-level-fmriprep": wf.brainprep_fmriprep,
         "group-level-fmriprep": wf.brainprep_group_fmriprep,
         "subject-level-sulcirec": wf.brainprep_sulcirec,
+        "group-level-sulcirec": wf.brainprep_group_sulcirec,
     }
     for key, fn in commands.items():
         commands[key] = make_wrapped(fn, is_vbm=key.endswith("vbm"))

brainprep/decorators.py

@@ -15,6 +15,7 @@
 import json
 import platform
 import subprocess
+import time
 from collections.abc import Callable, Iterable
 from pathlib import Path
 from typing import (
@@ -41,6 +42,7 @@
     coerce_to_list,
     coerce_to_path,
     parse_bids_keys,
+    print_call,
     print_command,
     print_title,
 )
@@ -706,8 +708,8 @@ class LogRuntimeHook(Hook):
     Log runtime metadata and input/output details of a function call.
 
     This hook uses an ``RSTReport`` instance to record metadata about the
-    execution of the decorated function. It captures the follwoing
-    informations:
+    execution of the decorated function. It captures the following
+    information:
 
     - the function's name, module, and docstring
     - the input arguments passed to the function
@@ -1048,3 +1050,69 @@ def step(
     for plug in hooks:
         outputs = plug.after_call(outputs)
     return outputs
+
+
+class SignatureHook(Hook):
+    """
+    Decorator that prints which function is called, its arguments and
+    execution time.
+
+    Examples
+    --------
+    >>> from brainprep.decorators import step, SignatureHook
+
+    >>> @step(
+    ...     hooks=[SignatureHook()]
+    ... )
+    ... def add(a, b):
+    ...     '''Adds two numbers.'''
+    ...     return a + b
+
+    >>> result = add(3, 5) # doctest: +SKIP
+    """
+
+    def before_call(
+            self,
+            func: Callable,
+            inputs: dict[str, Any],
+        ) -> dict[str, Any]:
+        """
+        Display start information.
+
+        Parameters
+        ----------
+        func : Callable
+            The function to be decorated.
+        inputs : dict[str, Any]
+            Positional and keyword arguments passed to `func`.
+
+        Returns
+        -------
+        inputs : dict[str, Any]
+            Unchanged positional and keyword arguments passed to `func`.
+        """
+        self._start = time.perf_counter()
+        if inputs:
+            args_lines = ",\n".join(
+                f"    {k}={v!r}" for k, v in inputs.items()
+            )
+            signature = f"{func.__qualname__}(\n{args_lines},\n)"
+        else:
+            signature = f"{func.__qualname__}()"
+
+        print_call("_" * 80)
+        print_call(f"[call] {signature}")
+        return inputs
+
+    def after_call(
+            self,
+            outputs: Any,
+        ) -> Any:
+        """
+        Display end information.
+        """
+        end = time.perf_counter()
+        duration = end - self._start
+        msg = f"{duration:.2f}s, {duration / 60:.2f}min"
+        print_call("_" * max(0, 80 - len(msg)) + msg)
+        return outputs

brainprep/interfaces/ants.py

@@ -16,6 +16,7 @@
     CommandLineWrapperHook,
     LogRuntimeHook,
     OutputdirHook,
+    SignatureHook,
     step,
 )
 from ..typing import (
@@ -32,6 +33,7 @@
             bunched=False
         ),
         CommandLineWrapperHook(),
+        SignatureHook(),
     ]
 )
 def biasfield(

brainprep/interfaces/cat12.py

@@ -27,6 +27,7 @@
     LogRuntimeHook,
     OutputdirHook,
     PythonWrapperHook,
+    SignatureHook,
     step,
 )
 from ..typing import (
@@ -50,6 +51,7 @@
             bunched=False
         ),
         CommandLineWrapperHook(),
+        SignatureHook(),
     ]
 )
 def cat12vbm_wf(
@@ -95,7 +97,8 @@ def cat12vbm_wf(
         for im_file, trg_dir in zip(t1_files, output_dirs, strict=True)
     ]
     qc_files = [
-        trg_dir / "report" / f"catreport_{im_file.name.replace('.gz', '')}"
+        trg_dir / "report" /
+        f"catreport_{im_file.name.replace('nii.gz', 'pdf')}"
         for im_file, trg_dir in zip(t1_files, output_dirs, strict=True)
     ]
 
@@ -117,6 +120,7 @@ def cat12vbm_wf(
             bunched=False
         ),
         PythonWrapperHook(),
+        SignatureHook(),
     ]
 )
 def write_catbatch(
@@ -224,6 +228,7 @@ def write_catbatch(
             bunched=False
         ),
         PythonWrapperHook(),
+        SignatureHook(),
     ]
 )
 def cat12vbm_morphometry(

brainprep/interfaces/fmriprep.py

@@ -33,6 +33,7 @@
     LogRuntimeHook,
     OutputdirHook,
     PythonWrapperHook,
+    SignatureHook,
     step,
 )
 from ..typing import (
@@ -53,6 +54,7 @@
             bunched=False
         ),
         CommandLineWrapperHook(),
+        SignatureHook(),
     ]
 )
 def fmriprep_wf(
@@ -225,6 +227,7 @@ def fmriprep_wf(
             bunched=False
         ),
         PythonWrapperHook(),
+        SignatureHook(),
     ]
 )
 def func_vol_connectivity(

brainprep/interfaces/freesurfer.py

@@ -26,6 +26,7 @@
     LogRuntimeHook,
     OutputdirHook,
     PythonWrapperHook,
+    SignatureHook,
     step,
 )
 from ..typing import (
@@ -47,6 +48,7 @@
             bunched=False
         ),
         CommandLineWrapperHook(),
+        SignatureHook(),
     ]
 )
 def brainmask(
@@ -105,6 +107,7 @@ def brainmask(
             bunched=False
         ),
         CommandLineWrapperHook(),
+        SignatureHook(),
     ]
 )
 def reconall(
@@ -188,6 +191,7 @@ def reconall(
             bunched=False
         ),
         CommandLineWrapperHook(),
+        SignatureHook(),
     ]
 )
 def reconall_longitudinal(
@@ -309,6 +313,7 @@ def reconall_longitudinal(
             bunched=False
         ),
         PythonWrapperHook(),
+        SignatureHook(),
     ]
 )
 def freesurfer_command_status(
@@ -389,6 +394,7 @@ def freesurfer_command_status(
             bunched=False
         ),
         CommandLineWrapperHook(),
+        SignatureHook(),
     ]
 )
 def localgi(
@@ -443,6 +449,7 @@ def localgi(
             bunched=False
         ),
         CommandLineWrapperHook(),
+        SignatureHook(),
     ]
 )
 def surfreg(
@@ -519,6 +526,7 @@ def surfreg(
             bunched=False
         ),
         CommandLineWrapperHook(),
+        SignatureHook(),
     ]
 )
 def xhemireg(
@@ -564,6 +572,7 @@ def xhemireg(
         LogRuntimeHook(
             bunched=False
         ),
+        SignatureHook(),
     ]
 )
 def fsaveragesym_surfreg(
@@ -638,6 +647,7 @@ def fsaveragesym_surfreg(
             bunched=False
         ),
         CommandLineWrapperHook(),
+        SignatureHook(),
     ]
 )
 def mris_apply_reg(
@@ -687,6 +697,7 @@ def mris_apply_reg(
             bunched=False
         ),
         PythonWrapperHook(),
+        SignatureHook(),
     ]
 )
 def fsaveragesym_projection(
@@ -786,6 +797,7 @@ def fsaveragesym_projection(
             bunched=False
         ),
         CommandLineWrapperHook(),
+        SignatureHook(),
     ]
 )
 def mri_convert(
@@ -831,6 +843,7 @@ def mri_convert(
         LogRuntimeHook(
             bunched=False
         ),
+        SignatureHook(),
     ]
 )
 def mgz_to_nii(
@@ -895,6 +908,7 @@ def mgz_to_nii(
             bunched=False
         ),
         CommandLineWrapperHook(),
+        SignatureHook(),
     ]
 )
 def aparcstats2table(
@@ -972,6 +986,7 @@ def aparcstats2table(
             bunched=False
         ),
         CommandLineWrapperHook(),
+        SignatureHook(),
     ]
 )
 def asegstats2table(
@@ -1022,6 +1037,7 @@ def asegstats2table(
         LogRuntimeHook(
             bunched=False
         ),
+        SignatureHook(),
     ]
 )
 def freesurfer_features_summary(
@@ -1124,19 +1140,16 @@ def freesurfer_features_summary(
         )
         summary_files.append(volume_stat_file)
 
-    # sort by participant_id
-    output_files = output_dir.glob('*')
-    for file in output_files:
-        if file.suffix == ".csv":
-            sep = ','
-        elif file.suffix == ".tsv":
-            sep = '\t'
-        else:
+    output_files = output_dir.glob("*")
+    seps = {".csv": ",", ".tsv": "\t"}
+    for table_file in output_files:
+        if table_file.suffix not in seps:
             continue
-        df = pd.read_csv(file, sep=sep)
+        sep = seps[table_file.suffix]
+        df = pd.read_csv(table_file, sep=sep)
         first_col = df.columns[0]
         df = df.sort_values(by=first_col)
-        df.to_csv(file, sep=sep, index=False)
+        df.to_csv(table_file, sep=sep, index=False)
 
     return summary_files
 
@@ -1149,6 +1162,7 @@ def freesurfer_features_summary(
             bunched=False
         ),
         PythonWrapperHook(),
+        SignatureHook(),
     ]
 )
 def freesurfer_tissues(
@@ -1305,6 +1319,7 @@ def freesurfer_tissues(
             bunched=False
         ),
         CommandLineWrapperHook(),
+        SignatureHook(),
     ]
 )
 def nextbrain(