From 4994a106525111f83f989a426e49e20f8bafddcc Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Sat, 4 May 2024 11:13:00 -0400
Subject: [PATCH] Keep working.

---
 src/fmripost_aroma/interfaces/resampler.py |  2 -
 src/fmripost_aroma/workflows/base.py       |  4 +-
 src/fmripost_aroma/workflows/resampling.py | 54 ++++++++++++++++++++++
 3 files changed, 57 insertions(+), 3 deletions(-)
 create mode 100644 src/fmripost_aroma/workflows/resampling.py

diff --git a/src/fmripost_aroma/interfaces/resampler.py b/src/fmripost_aroma/interfaces/resampler.py
index 7913064..61a30f8 100644
--- a/src/fmripost_aroma/interfaces/resampler.py
+++ b/src/fmripost_aroma/interfaces/resampler.py
@@ -3,10 +3,8 @@
 from nipype.interfaces.base import (
     BaseInterfaceInputSpec,
     File,
-    InputMultiObject,
     SimpleInterface,
     TraitedSpec,
-    isdefined,
     traits,
 )
 
diff --git a/src/fmripost_aroma/workflows/base.py b/src/fmripost_aroma/workflows/base.py
index 874200e..c6b228c 100644
--- a/src/fmripost_aroma/workflows/base.py
+++ b/src/fmripost_aroma/workflows/base.py
@@ -40,6 +40,7 @@
 from fmripost_aroma import config
 from fmripost_aroma.interfaces.bids import DerivativesDataSink
 from fmripost_aroma.interfaces.reportlets import AboutSummary, SubjectSummary
+from fmripost_aroma.workflows.resampling import init_resample_raw_wf
 
 
 def init_fmripost_aroma_wf():
@@ -256,7 +257,8 @@ def init_single_subject_wf(subject_id: str):
     )
 
     bids_info = pe.Node(
-        BIDSInfo(bids_dir=config.execution.bids_dir, bids_validate=False), name="bids_info"
+        BIDSInfo(bids_dir=config.execution.bids_dir, bids_validate=False),
+        name="bids_info",
     )
 
     summary = pe.Node(
diff --git a/src/fmripost_aroma/workflows/resampling.py b/src/fmripost_aroma/workflows/resampling.py
new file mode 100644
index 0000000..15d00ad
--- /dev/null
+++ b/src/fmripost_aroma/workflows/resampling.py
@@ -0,0 +1,54 @@
+"""Workflows to resample data."""
+
+from nipype.interfaces import utility as niu
+from nipype.pipeline import engine as pe
+
+
+def init_resample_raw_wf(bold_file, functional_cache):
+    """Resample raw BOLD data to MNI152NLin6Asym:res-2mm space."""
+    from fmriprep.workflows.bold.stc import init_bold_stc_wf
+    from niworkflows.engine.workflows import LiterateWorkflow as Workflow
+
+    from fmripost_aroma.interfaces.resampler import Resampler
+
+    workflow = Workflow(name="resample_raw_wf")
+
+    inputnode = pe.Node(
+        niu.IdentityInterface(fields=["bold_file", "mask_file"]),
+        name="inputnode",
+    )
+    inputnode.inputs.bold_file = bold_file
+    inputnode.inputs.mask_file = functional_cache["bold_mask"]
+
+    outputnode = pe.Node(
+        niu.IdentityInterface(fields=["bold_std", "bold_mask_std"]),
+        name="outputnode",
+    )
+
+    stc_wf = init_bold_stc_wf(name="resample_stc_wf")
+    workflow.connect([
+        (inputnode, stc_wf, [
+            ('bold_file', 'inputnode.bold_file'),
+            ('mask_file', 'inputnode.mask_file'),
+        ]),
+    ])  # fmt:skip
+
+    resample_bold = pe.Node(
+        Resampler(space="MNI152NLin6Asym", resolution="2"),
+        name="resample_bold",
+    )
+    workflow.connect([
+        (stc_wf, resample_bold, [('outputnode.bold_file', 'bold_file')]),
+        (resample_bold, outputnode, [('output_file', 'bold_std')]),
+    ])  # fmt:skip
+
+    resample_bold_mask = pe.Node(
+        Resampler(space="MNI152NLin6Asym", resolution="2"),
+        name="resample_bold_mask",
+    )
+    workflow.connect([
+        (inputnode, resample_bold_mask, [('mask_file', 'bold_file')]),
+        (resample_bold_mask, outputnode, [('output_file', 'bold_mask_std')]),
+    ])  # fmt:skip
+
+    return workflow