[ENH] rudimentary support for nimads

examples/01_datasets/05_plot_nimads.py

@@ -0,0 +1,60 @@
+"""
+
+.. _nimads_object:
+
+========================
+Using NIMADS with NiMARE
+========================
+
+How to use the NeuroImaging Meta-Analysis Data Structure
+`(NIMADS) <https://neurostuff.github.io/NIMADS/>`_ with NiMARE.
+"""
+from requests import request
+
+from nimare.io import convert_nimads_to_dataset
+from nimare.nimads import Studyset
+
+###############################################################################
+# Download Data from NeuroStore
+# -----------------------------------------------------------------------------
+
+
+def download_file(url):
+    """Download a file from NeuroStore."""
+    response = request("GET", url)
+    return response.json()
+
+
+nimads_studyset = download_file(
+    "https://neurostore.org/api/studysets/Cv2LLUqG76W9?nested=true"
+)
+nimads_annotation = download_file(
+    "https://neurostore.org/api/annotations/76PyNqoTNEsE"
+)
+
+
+###############################################################################
+# Load Data
+# -----------------------------------------------------------------------------
+# Load the json files into a NiMADS Studyset object.
+
+studyset = Studyset(nimads_studyset, nimads_annotation)
+
+
+###############################################################################
+# Convert to NiMARE Dataset
+# -----------------------------------------------------------------------------
+# Convert the NiMADS Studyset object to a NiMARE Dataset object.
+# Then you can run NiMARE analyses on the Dataset object.
+
+nimare_dset = studyset.to_dataset()
+nimare_dset.coordinates.head()
+
+###############################################################################
+# Directly to NiMARE Dataset
+# -----------------------------------------------------------------------------
+# Alternatively, you can convert the NiMADS json files directly to a NiMARE Dataset object
+# if you wish to skip using the nimads studyset object directly.
+
+nimare_dset_2 = convert_nimads_to_dataset(nimads_studyset, nimads_annotation)
+nimare_dset_2.coordinates.head()

nimare/io.py

@@ -14,6 +14,7 @@
 
 from nimare.dataset import Dataset
 from nimare.extract.utils import _get_dataset_dir
+from nimare.utils import _create_name, load_nimads
 
 LGR = logging.getLogger(__name__)
 
@@ -26,6 +27,47 @@
 }
 
 
+def convert_nimads_to_dataset(studyset, annotation=None):
+    """Convert nimads studyset to a dataset."""
+
+    def _analysis_to_dict(study, analysis):
+        result = {
+            "metadata": {
+                "authors": study.name,
+                "journal": study.publication,
+                "title": study.name,
+                "sample_sizes": [study.metadata.get("sample_size")],
+            },
+            "coords": {
+                "space": analysis.points[0].space,
+                "x": [p.x for p in analysis.points],
+                "y": [p.y for p in analysis.points],
+                "z": [p.z for p in analysis.points],
+            },
+        }
+
+        if analysis.annotations:
+            result["labels"] = {}
+            for annotation in analysis.annotations.values():
+                result["labels"].update(annotation)
+
+        return result
+
+    def _study_to_dict(study):
+        return {
+            "metadata": {
+                "authors": study.authors,
+                "journal": study.publication,
+                "title": study.name,
+            },
+            "contrasts": {_create_name(a): _analysis_to_dict(study, a) for a in study.analyses},
+        }
+
+    # load nimads studyset
+    studyset = load_nimads(studyset, annotation)
+    return Dataset({_create_name(s): _study_to_dict(s) for s in list(studyset.studies)})
+
+
 def convert_neurosynth_to_dict(
     coordinates_file,
     metadata_file,