DNM: Draft pre-tedana echo-wise denoising workflow

pyproject.toml

@@ -76,6 +76,7 @@ all = ["tedana[dev,doc,tests]"]
 ica_reclassify = "tedana.workflows.ica_reclassify:_main"
 t2smap = "tedana.workflows.t2smap:_main"
 tedana = "tedana.workflows.tedana:_main"
+denoise_echoes = "tedana.workflows.denoise_echoes:_main"
 
 #
 # Hatch configurations

tedana/metrics/collect.py

@@ -82,6 +82,9 @@ def generate_metrics(
             "match."
         )
 
+    if isinstance(label, list):
+        assert len(label) == mixing.shape[1]
+
     # Derive mask from thresholded adaptive mask
     mask = adaptive_mask >= 3
 
@@ -109,10 +112,13 @@ def generate_metrics(
     # throughout this function
     n_components = mixing.shape[1]
     comptable = pd.DataFrame(index=np.arange(n_components, dtype=int))
-    comptable["Component"] = [
-        io.add_decomp_prefix(comp, prefix=label, max_value=comptable.shape[0])
-        for comp in comptable.index.values
-    ]
+    if isinstance(label, str):
+        comptable["Component"] = [
+            io.add_decomp_prefix(comp, prefix=label, max_value=comptable.shape[0])
+            for comp in comptable.index.values
+        ]
+    else:
+        comptable["Component"] = label
 
     # Metric maps
     # Maps will be stored as arrays in an easily-indexable dictionary

tedana/resources/config/outputs.json

@@ -121,15 +121,15 @@
     },
     "high kappa ts split img": {
         "orig": "hik_ts_e{echo}",
-        "bidsv1.5.0": "echo-{echo}_desc-Accepted_bold"
+        "bidsv1.5.0": "echo-{echo}_desc-accepted_bold"
     },
     "low kappa ts split img": {
         "orig": "lowk_ts_e{echo}",
-        "bidsv1.5.0": "echo-{echo}_desc-Rejected_bold"
+        "bidsv1.5.0": "echo-{echo}_desc-rejected_bold"
     },
     "denoised ts split img": {
         "orig": "dn_ts_e{echo}",
-        "bidsv1.5.0": "echo-{echo}_desc-Denoised_bold"
+        "bidsv1.5.0": "echo-{echo}_desc-denoised_bold"
     },
     "gs img": {
         "orig": "T1gs",

tedana/workflows/__init__.py

@@ -1,8 +1,14 @@
 # emacs: -*- mode: python-mode; py-indent-offset: 4; tab-width: 4; indent-tabs-mode: nil -*-
 # ex: set sts=4 ts=4 sw=4 et:
 """Command line interfaces and workflows."""
+from tedana.workflows.denoise_echoes import denoise_echoes_workflow
 from tedana.workflows.ica_reclassify import ica_reclassify_workflow
 from tedana.workflows.t2smap import t2smap_workflow
 from tedana.workflows.tedana import tedana_workflow
 
-__all__ = ["tedana_workflow", "t2smap_workflow", "ica_reclassify_workflow"]
+__all__ = [
+    "tedana_workflow",
+    "t2smap_workflow",
+    "ica_reclassify_workflow",
+    "denoise_echoes_workflow",
+]