DOC/RF: Improve graph intelligibility

effigies · Oct 16, 2023 · 617b2a1 · 617b2a1
1 parent 00fe8f5
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Showing 4 changed files with 9 additions and 22 deletions.
diff --git a/docs/api.rst b/docs/api.rst
@@ -14,13 +14,13 @@ you get started.
 Setting up your development environment
 ---------------------------------------
 We believe that *fMRIPrep* must be free to use, inspect, and critique.
-Correspondingly, you should be free to modify our software to improve it 
+Correspondingly, you should be free to modify our software to improve it
 or adapt it to new use cases and we especially welcome contributions to
 improve it or its documentation.
 
 We actively direct efforts into making the scrutiny and improvement processes
 as easy as possible.
-As part of such efforts, we maintain some 
+As part of such efforts, we maintain some
 `tips and guidelines for developers <https://www.nipreps.org/devs/devenv/>`__
 to help minimize your burden if you want to modify the software.
 
@@ -35,3 +35,4 @@ Workflows
 
 .. automodule:: fmriprep.workflows.base
 .. automodule:: fmriprep.workflows.bold
+.. automodule:: fmriprep.workflows.bold.fit
diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
@@ -24,8 +24,9 @@
 Orchestrating the BOLD-preprocessing workflow
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. autofunction:: init_func_preproc_wf
-.. autofunction:: init_func_derivatives_wf
+.. autofunction:: init_bold_wf
+.. autofunction:: init_bold_fit_wf
+.. autofunction:: init_bold_native_wf
 
 """
 import os

diff --git a/fmriprep/workflows/bold/fit.py b/fmriprep/workflows/bold/fit.py
@@ -20,14 +20,6 @@
 #
 #     https://www.nipreps.org/community/licensing/
 #
-"""
-Orchestrating the BOLD-preprocessing workflow
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. autofunction:: init_func_preproc_wf
-.. autofunction:: init_func_derivatives_wf
-
-"""
 import os
 import typing as ty
 
@@ -117,11 +109,11 @@ def init_bold_fit_wf(
 
             from fmriprep.workflows.tests import mock_config
             from fmriprep import config
-            from fmriprep.workflows.bold.fit import init_bold_fit
+            from fmriprep.workflows.bold.fit import init_bold_fit_wf
             with mock_config():
                 bold_file = config.execution.bids_dir / "sub-01" / "func" \
                     / "sub-01_task-mixedgamblestask_run-01_bold.nii.gz"
-                wf = init_bold_fit([str(bold_file)])
+                wf = init_bold_fit_wf(bold_series=[str(bold_file)])
 
     Parameters
     ----------
@@ -350,7 +342,6 @@ def init_bold_fit_wf(
         config.loggers.workflow.info("Stage 1: Adding HMC boldref workflow")
         hmc_boldref_wf = init_raw_boldref_wf(
             name="hmc_boldref_wf",
-            bold_file=bold_file,
             multiecho=multiecho,
         )
         hmc_boldref_wf.inputs.inputnode.dummy_scans = config.workflow.dummy_scans
@@ -365,6 +356,7 @@ def init_bold_fit_wf(
 
         # fmt:off
         workflow.connect([
+            (inputnode, hmc_boldref_wf, [('bold_file', 'inputnode.bold_file')]),
             (hmc_boldref_wf, hmcref_buffer, [
                 ("outputnode.bold_file", "bold_file"),
                 ("outputnode.boldref", "boldref"),

diff --git a/fmriprep/workflows/bold/reference.py b/fmriprep/workflows/bold/reference.py
@@ -30,7 +30,6 @@
 
 
 def init_raw_boldref_wf(
-    bold_file=None,
     multiecho=False,
     name="raw_boldref_wf",
 ):
@@ -53,8 +52,6 @@ def init_raw_boldref_wf(
 
     Parameters
     ----------
-    bold_file : :obj:`str`
-        BOLD series NIfTI file
     multiecho : :obj:`bool`
         If multiecho data was supplied, data from the first echo will be selected
     name : :obj:`str`
@@ -106,10 +103,6 @@ def init_raw_boldref_wf(
         name="outputnode",
     )
 
-    # Simplify manually setting input image
-    if bold_file is not None:
-        inputnode.inputs.bold_file = bold_file
-
     val_bold = pe.Node(
         ValidateImage(),
         name="val_bold",