Merge pull request #993 from nipreps/fix/965

ENH: Deprecate ``--start-idx`` / ``--stop-idx``

mriqc/cli/parser.py

@@ -29,7 +29,8 @@
 def _build_parser():
     """Build parser object."""
     import sys
-    from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser
+    import warnings
+    from argparse import Action, ArgumentDefaultsHelpFormatter, ArgumentParser
     from functools import partial
     from pathlib import Path
     from shutil import which
@@ -38,6 +39,11 @@ def _build_parser():
 
     from .version import check_latest, is_flagged
 
+    class DeprecateAction(Action):
+        def __call__(self, parser, namespace, values, option_string=None):
+            warnings.warn(f"Argument {option_string} is deprecated and is *ignored*.")
+            delattr(namespace, self.dest)
+
     def _path_exists(path, parser):
         """Ensure a given path exists."""
         if path is None or not Path(path).exists():
@@ -379,16 +385,16 @@ def _bids_filter(value):
     )
     g_func.add_argument(
         "--start-idx",
-        action="store",
+        action=DeprecateAction,
         type=int,
-        help="Initial volume in functional timeseries that should be "
+        help="DEPRECATED Initial volume in functional timeseries that should be "
         "considered for preprocessing.",
     )
     g_func.add_argument(
         "--stop-idx",
-        action="store",
+        action=DeprecateAction,
         type=int,
-        help="Final volume in functional timeseries that should be "
+        help="DEPRECATED Final volume in functional timeseries that should be "
         "considered for preprocessing.",
     )
     g_func.add_argument(

mriqc/config.py

@@ -507,10 +507,6 @@ class workflow(_Config):
     """Run ICA on the raw data and include the components in the individual reports."""
     inputs = None
     """List of files to be processed with MRIQC."""
-    start_idx = None
-    """Initial volume in functional timeseries that should be considered for preprocessing."""
-    stop_idx = None
-    """Final volume in functional timeseries that should be considered for preprocessing."""
     species = "human"
     """Subject species to choose most appropriate template"""
     template_id = "MNI152NLin2009cAsym"

mriqc/workflows/functional.py

@@ -676,43 +676,21 @@ def hmc(name="fMRI_HMC"):
 
     """
     from nipype.algorithms.confounds import FramewiseDisplacement
-    from nipype.interfaces.afni import Calc, Despike, Refit, TShift, Volreg
+    from nipype.interfaces.afni import Despike, Refit, TShift, Volreg
 
     mem_gb = config.workflow.biggest_file_gb
 
     workflow = pe.Workflow(name=name)
 
     inputnode = pe.Node(
-        niu.IdentityInterface(fields=["in_file", "fd_radius", "start_idx", "stop_idx"]),
+        niu.IdentityInterface(fields=["in_file", "fd_radius"]),
         name="inputnode",
     )
 
     outputnode = pe.Node(
         niu.IdentityInterface(fields=["out_file", "out_fd"]), name="outputnode"
     )
 
-    if any(
-        (
-            config.workflow.start_idx is not None,
-            config.workflow.stop_idx is not None,
-        )
-    ):
-        drop_trs = pe.Node(Calc(expr="a", outputtype="NIFTI_GZ"), name="drop_trs")
-        # fmt: off
-        workflow.connect([
-            (inputnode, drop_trs, [("in_file", "in_file_a"),
-                                   ("start_idx", "start_idx"),
-                                   ("stop_idx", "stop_idx")]),
-        ])
-        # fmt: on
-    else:
-        drop_trs = pe.Node(niu.IdentityInterface(fields=["out_file"]), name="drop_trs")
-        # fmt: off
-        workflow.connect([
-            (inputnode, drop_trs, [("in_file", "out_file")]),
-        ])
-        # fmt: on
-
     # calculate hmc parameters
     hmc = pe.Node(
         Volreg(args="-Fourier -twopass", zpad=4, outputtype="NIFTI_GZ"),
@@ -753,7 +731,7 @@ def hmc(name="fMRI_HMC"):
 
         # fmt: off
         workflow.connect([
-            (drop_trs, st_corr, [("out_file", "in_file")]),
+            (inputnode, st_corr, [("in_file", "in_file")]),
             (st_corr, despike_node, [("out_file", "in_file")]),
             (despike_node, deoblique_node, [("out_file", "in_file")]),
             (deoblique_node, hmc, [("out_file", "in_file")]),
@@ -762,52 +740,52 @@ def hmc(name="fMRI_HMC"):
     elif config.workflow.correct_slice_timing and config.workflow.despike:
         # fmt: off
         workflow.connect([
-            (drop_trs, st_corr, [("out_file", "in_file")]),
+            (inputnode, st_corr, [("in_file", "in_file")]),
             (st_corr, despike_node, [("out_file", "in_file")]),
             (despike_node, hmc, [("out_file", "in_file")]),
         ])
         # fmt: on
     elif config.workflow.correct_slice_timing and config.workflow.deoblique:
         # fmt: off
         workflow.connect([
-            (drop_trs, st_corr, [("out_file", "in_file")]),
+            (inputnode, st_corr, [("in_file", "in_file")]),
             (st_corr, deoblique_node, [("out_file", "in_file")]),
             (deoblique_node, hmc, [("out_file", "in_file")]),
         ])
         # fmt: on
     elif config.workflow.correct_slice_timing:
         # fmt: off
         workflow.connect([
-            (drop_trs, st_corr, [("out_file", "in_file")]),
+            (inputnode, st_corr, [("in_file", "in_file")]),
             (st_corr, hmc, [("out_file", "in_file")]),
         ])
         # fmt: on
     elif config.workflow.despike and config.workflow.deoblique:
         # fmt: off
         workflow.connect([
-            (drop_trs, despike_node, [("out_file", "in_file")]),
+            (inputnode, despike_node, [("in_file", "in_file")]),
             (despike_node, deoblique_node, [("out_file", "in_file")]),
             (deoblique_node, hmc, [("out_file", "in_file")]),
         ])
         # fmt: on
     elif config.workflow.despike:
         # fmt: off
         workflow.connect([
-            (drop_trs, despike_node, [("out_file", "in_file")]),
+            (inputnode, despike_node, [("in_file", "in_file")]),
             (despike_node, hmc, [("out_file", "in_file")]),
         ])
         # fmt: on
     elif config.workflow.deoblique:
         # fmt: off
         workflow.connect([
-            (drop_trs, deoblique_node, [("out_file", "in_file")]),
+            (inputnode, deoblique_node, [("in_file", "in_file")]),
             (deoblique_node, hmc, [("out_file", "in_file")]),
         ])
         # fmt: on
     else:
         # fmt: off
         workflow.connect([
-            (drop_trs, hmc, [("out_file", "in_file")]),
+            (inputnode, hmc, [("in_file", "in_file")]),
         ])
         # fmt: on
     return workflow

mriqc/workflows/utils.py

@@ -32,27 +32,6 @@ def _tofloat(inlist):
         return float(inlist)
 
 
-def fmri_getidx(in_file, start_idx, stop_idx):
-    """Heuristics to set the start and stop indices of fMRI series"""
-    from nibabel import load
-    from nipype.interfaces.base import isdefined
-
-    nvols = load(in_file).shape[3]
-    max_idx = nvols - 1
-
-    if (
-        start_idx is None
-        or not isdefined(start_idx)
-        or start_idx < 0
-        or start_idx > max_idx
-    ):
-        start_idx = 0
-
-    if stop_idx is None or not isdefined(stop_idx) or max_idx < stop_idx < start_idx:
-        stop_idx = max_idx
-    return start_idx, stop_idx
-
-
 def fwhm_dict(fwhm):
     """Convert a list of FWHM into a dictionary"""
     fwhm = [float(f) for f in fwhm]