From d7a59eec1945d59a3f0d85b6a3870acc0ab57433 Mon Sep 17 00:00:00 2001
From: Taylor Salo <salot@pennmedicine.upenn.edu>
Date: Wed, 23 Oct 2024 16:12:20 -0400
Subject: [PATCH] Fix?

---
 min-requirements.txt       |  1 +
 requirements.txt           |  1 +
 sdcflows/fieldmaps.py      | 38 ++++++++++++++++++++++++++++----------
 sdcflows/utils/wrangler.py | 37 +++++++++++++++++++++++--------------
 4 files changed, 53 insertions(+), 24 deletions(-)

diff --git a/min-requirements.txt b/min-requirements.txt
index c18a3e04ea..817a3b3ec4 100644
--- a/min-requirements.txt
+++ b/min-requirements.txt
@@ -12,3 +12,4 @@ scikit-image==0.18
 scipy==1.8.1
 templateflow
 toml
+warpkit==0.1.1
diff --git a/requirements.txt b/requirements.txt
index 898616b40d..da9e6638c6 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -12,3 +12,4 @@ scikit-image>=0.18
 scipy>=1.8.1
 templateflow
 toml
+warpkit==0.1.1
diff --git a/sdcflows/fieldmaps.py b/sdcflows/fieldmaps.py
index d1c9b26bf0..9ce0ea97ad 100644
--- a/sdcflows/fieldmaps.py
+++ b/sdcflows/fieldmaps.py
@@ -321,19 +321,37 @@ def __attrs_post_init__(self):
             raise TypeError(f"Incompatible suffixes found: <{','.join(fmap_types)}>.")
 
         # Check for MEDIC
-        mag_bold, phase_bold, me_bold = 0, 0, 0
+        # They must have a bold suffix, multiple echoes, and both mag and phase data
+        echos = []
         for f in self.sources:
-            if f.suffix == "bold" and ("part-mag" in f.path.name):
-                mag_bold += 1
+            echo = re.search(r"(?<=_echo-)\d+", f.path.name)
+            if echo:
+                echos.append(int(echo.group()))
+
+        echos = sorted(list(set(echos)))
+        if len(echos) > 1:
+            for echo in echos:
+                has_mag, has_phase = False, False
+                for f in self.sources:
+                    if (
+                        f.suffix == "bold"
+                        and (f"echo-{echo}_" in f.path.name)
+                        and ("part-mag" in f.path.name)
+                    ):
+                        has_mag = True
+
+                    if (
+                        f.suffix == "bold"
+                        and (f"echo-{echo}_" in f.path.name)
+                        and ("part-phase" in f.path.name)
+                    ):
+                        has_phase = True
+
+                if not (has_mag and has_phase):
+                    break
 
-            if f.suffix == "bold" and ("part-phase" in f.path.name):
-                phase_bold += 1
-
-            if f.suffix == "bold" and ("echo-" in f.path.name):
-                me_bold += 1
-
-        if (mag_bold > 1) and (phase_bold > 1) and (me_bold > 2) and (mag_bold == phase_bold):
             self.method = EstimatorType.MEDIC
+            fmap_types = {}
 
         if fmap_types:
             sources = sorted(
diff --git a/sdcflows/utils/wrangler.py b/sdcflows/utils/wrangler.py
index 214d90ba82..e89996003e 100644
--- a/sdcflows/utils/wrangler.py
+++ b/sdcflows/utils/wrangler.py
@@ -483,22 +483,31 @@ def find_estimators(
                 str(item.path) for sublist in current_sources for item in sublist
             ]
             if complex_imgs[0].path in current_sources:
-                print("Skipping fieldmap %s (already in use)" % complex_imgs[0].relpath)
+                logger.debug("Skipping fieldmap %s (already in use)", complex_imgs[0].relpath)
                 continue
 
-            if current_sources:
-                raise Exception(complex_imgs[0].path, current_sources)
-
-            e = fm.FieldmapEstimation(
-                [
-                    fm.FieldmapFile(img.path, metadata=img.get_metadata())
-                    for img in complex_imgs
-                ]
-            )
-
-            _log_debug_estimation(logger, e, layout.root)
-            estimators.append(e)
-            continue
+            try:
+                e = fm.FieldmapEstimation(
+                    [
+                        fm.FieldmapFile(
+                            img.path,
+                            metadata=_filter_metadata(img.get_metadata(), subject),
+                        )
+                        for img in complex_imgs
+                    ]
+                )
+            except (ValueError, TypeError) as err:
+                _log_debug_estimator_fail(
+                    logger,
+                    "unnamed MEDIC",
+                    [],
+                    layout.root,
+                    str(err),
+                )
+            else:
+                _log_debug_estimation(logger, e, layout.root)
+                estimators.append(e)
+                continue
 
         # At this point, only single-PE _epi files WITH ``IntendedFor`` can
         # be automatically processed.