From d2b983cbdfce30d5c744e989124185ba817edf52 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Fri, 20 Nov 2020 18:59:42 +0100
Subject: [PATCH] wip: drafting base workflow leveraging new objects

---
 sdcflows/conftest.py       |   1 +
 sdcflows/workflows/base.py | 105 +++++++++++++++++++++++++++++++++++++
 2 files changed, 106 insertions(+)
 create mode 100644 sdcflows/workflows/base.py

diff --git a/sdcflows/conftest.py b/sdcflows/conftest.py
index 99aa3ebebc..bffaaf275b 100644
--- a/sdcflows/conftest.py
+++ b/sdcflows/conftest.py
@@ -29,6 +29,7 @@ def add_np(doctest_namespace):
     doctest_namespace['nb'] = nibabel
     doctest_namespace['os'] = os
     doctest_namespace['Path'] = Path
+    doctest_namespace['layouts'] = layouts
     for key, val in list(layouts.items()):
         doctest_namespace[key] = Path(val.root)
 
diff --git a/sdcflows/workflows/base.py b/sdcflows/workflows/base.py
new file mode 100644
index 0000000000..540eb2e7b4
--- /dev/null
+++ b/sdcflows/workflows/base.py
@@ -0,0 +1,105 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""Estimate fieldmaps for :abbr:`SDC (susceptibility distortion correction)`."""
+from nipype.pipeline import engine as pe
+from nipype.interfaces import utility as niu
+from nipype import logging
+
+from niworkflows.engine.workflows import LiterateWorkflow as Workflow
+
+
+LOGGER = logging.getLogger('nipype.workflow')
+DEFAULT_MEMORY_MIN_GB = 0.01
+
+
+def init_fmap_preproc_wf(
+    *,
+    layout,
+    omp_nthreads,
+    output_dir,
+    subject,
+    debug=False,
+    name='fmap_preproc_wf',
+):
+    """
+    Stage the fieldmap data preprocessing steps of *SDCFlows*.
+
+    Parameters
+    ----------
+    layout : :obj:`bids.layout.BIDSLayout`
+        An initialized PyBIDS layout.
+    omp_nthreads : :obj:`int`
+        Maximum number of threads an individual process may use
+    output_dir : :obj:`str`
+        Directory in which to save derivatives
+    subject : :obj:`str`
+        Participant label for this single-subject workflow.
+    debug : :obj:`bool`
+        Enable debugging outputs
+    name : :obj:`str`, optional
+        Workflow name (default: ``"fmap_preproc_wf"``)
+
+    Examples
+    --------
+    >>> init_fmap_preproc_wf(
+    ...     layout=layouts['ds001600'],
+    ...     omp_nthreads=1,
+    ...     output_dir="/tmp",
+    ...     subject="1",
+    ... )
+    [FieldmapEstimation(sources=<4 files>, method=<EstimatorType.PHASEDIFF: 3>),
+     FieldmapEstimation(sources=<4 files>, method=<EstimatorType.PHASEDIFF: 3>),
+     FieldmapEstimation(sources=<3 files>, method=<EstimatorType.PHASEDIFF: 3>),
+     FieldmapEstimation(sources=<2 files>, method=<EstimatorType.PEPOLAR: 2>)]
+
+    >>> init_fmap_preproc_wf(
+    ...     layout=layouts['testdata'],
+    ...     omp_nthreads=1,
+    ...     output_dir="/tmp",
+    ...     subject="HCP101006",
+    ... )
+    [FieldmapEstimation(sources=<2 files>, method=<EstimatorType.PHASEDIFF: 3>),
+     FieldmapEstimation(sources=<2 files>, method=<EstimatorType.PEPOLAR: 2>)]
+
+    """
+    from ..fieldmaps import FieldmapEstimation, FieldmapFile
+
+    base_entities = {
+        "subject": subject,
+        "extension": [".nii", ".nii.gz"],
+        "space": None,  # Ensure derivatives are not captured
+    }
+
+    estimators = []
+
+    # Set up B0 fieldmap strategies:
+    for fmap in layout.get(
+        suffix=["fieldmap", "phasediff", "phase1"], **base_entities
+    ):
+        e = FieldmapEstimation(
+            FieldmapFile(fmap.path, metadata=fmap.get_metadata())
+        )
+        estimators.append(e)
+
+    # A bunch of heuristics to select EPI fieldmaps
+    sessions = layout.get_sessions() or [None]
+    for session in sessions:
+        dirs = layout.get_directions(
+            suffix="epi",
+            session=session,
+            **base_entities,
+        )
+        if len(dirs) > 1:
+            e = FieldmapEstimation([
+                FieldmapFile(fmap.path, metadata=fmap.get_metadata())
+                for fmap in layout.get(suffix="epi", session=session,
+                                       direction=dirs, **base_entities)
+            ])
+            estimators.append(e)
+
+    for e in estimators:
+        LOGGER.info(
+            f"{e.method}:: <{':'.join(s.path.name for s in e.sources)}>."
+        )
+
+    return estimators