Add DoF map to IBMA report (#854)

* Add DoF Map to IBMA report * Update figures.py * Update test_reports.py * Update test_reports.py
neurostuff · Jan 9, 2024 · 6315367 · 6315367
1 parent efae75e
commit 6315367
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Showing 4 changed files with 65 additions and 16 deletions.
diff --git a/nimare/reports/base.py b/nimare/reports/base.py
@@ -32,6 +32,7 @@
 
 from nimare.meta.cbma.base import CBMAEstimator, PairwiseCBMAEstimator
 from nimare.reports.figures import (
+    _plot_dof_map,
     _plot_relcov_map,
     _plot_ridgeplot,
     gen_table,
@@ -478,12 +479,19 @@ def __init__(
                 ids_ = self.results.estimator.inputs_["id"]
                 x_label = "Z" if key_maps == "z_maps" else "Beta"
 
-                _plot_relcov_map(
-                    maps_arr,
-                    self.results.estimator.masker,
-                    self.results.estimator.inputs_["aggressive_mask"],
-                    self.fig_dir / f"preliminary_dset-{dset_i+1}_figure-relcov.png",
-                )
+                if self.results.estimator.aggressive_mask:
+                    _plot_relcov_map(
+                        maps_arr,
+                        self.results.estimator.masker,
+                        self.results.estimator.inputs_["aggressive_mask"],
+                        self.fig_dir / f"preliminary_dset-{dset_i+1}_figure-relcov.png",
+                    )
+                else:
+                    dof_map = self.results.get_map("dof")
+                    _plot_dof_map(
+                        dof_map,
+                        self.fig_dir / f"preliminary_dset-{dset_i+1}_figure-dof.png",
+                    )
 
                 _plot_ridgeplot(
                     maps_arr,

diff --git a/nimare/reports/default.yml b/nimare/reports/default.yml
@@ -53,6 +53,8 @@ sections:
     iframe: True
   - bids: {value: preliminary, dset: 1, suffix: figure-relcov}
     title: Relative Coverage Map
+  - bids: {value: preliminary, dset: 1, suffix: figure-dof}
+    title: DoF Map
   - bids: {value: preliminary, dset: 1, suffix: figure-ridgeplot}
     title: Ridge Plot
   - bids: {value: preliminary, dset: 1, suffix: figure-similarity}

diff --git a/nimare/reports/figures.py b/nimare/reports/figures.py
@@ -488,3 +488,31 @@ def _plot_relcov_map(maps_arr, masker, aggressive_mask, out_filename):
     )
     fig.savefig(out_filename, dpi=300)
     fig.close()
+
+
+def _plot_dof_map(dof_map, out_filename):
+    """Plot DoF map.
+
+    .. versionadded:: 0.2.1
+
+    """
+    _check_extention(out_filename, [".png", ".pdf", ".svg"])
+
+    epsilon = 1e-05
+
+    # Plot coverage map
+    template = datasets.load_mni152_template(resolution=1)
+    fig = plot_img(
+        dof_map,
+        bg_img=template,
+        black_bg=False,
+        draw_cross=False,
+        threshold=epsilon,
+        alpha=0.7,
+        colorbar=True,
+        cmap="YlOrRd",
+        vmin=0,
+        display_mode="mosaic",
+    )
+    fig.savefig(out_filename, dpi=300)
+    fig.close()
diff --git a/nimare/tests/test_reports.py b/nimare/tests/test_reports.py
@@ -6,6 +6,7 @@
 from nimare.correct import FWECorrector
 from nimare.diagnostics import FocusCounter, Jackknife
 from nimare.meta.cbma import ALESubtraction
+from nimare.meta.ibma import Stouffers
 from nimare.reports.base import run_reports
 from nimare.workflows import CBMAWorkflow, IBMAWorkflow, PairwiseCBMAWorkflow
 
@@ -27,13 +28,11 @@
             FocusCounter(voxel_thresh=0.01, display_second_group=True),
             "pairwise_cbma",
         ),
-        ("stouffers", "fdr", "jackknife", "ibma"),
     ],
 )
 def test_reports_function_smoke(
     tmp_path_factory,
     testdata_cbma_full,
-    testdata_ibma,
     estimator,
     corrector,
     diagnostics,
@@ -63,14 +62,26 @@ def test_reports_function_smoke(
         )
         results = workflow.fit(dset1, dset2)
 
-    elif meta_type == "ibma":
-        workflow = IBMAWorkflow(
-            estimator=estimator,
-            corrector=corrector,
-            diagnostics=diagnostics,
-            output_dir=tmpdir,
-        )
-        results = workflow.fit(testdata_ibma)
+    run_reports(results, tmpdir)
+
+    filename = "report.html"
+    outpath = op.join(tmpdir, filename)
+    assert op.isfile(outpath)
+
+
+@pytest.mark.parametrize("aggressive_mask", [True, False], ids=["aggressive", "liberal"])
+def test_reports_ibma_smoke(tmp_path_factory, testdata_ibma, aggressive_mask):
+    """Smoke test for IBMA reports."""
+    tmpdir = tmp_path_factory.mktemp("test_reports_ibma_smoke")
+
+    workflow = IBMAWorkflow(
+        estimator=Stouffers(aggressive_mask=aggressive_mask),
+        corrector="fdr",
+        diagnostics="jackknife",
+        voxel_thresh=3.2,
+        output_dir=tmpdir,
+    )
+    results = workflow.fit(testdata_ibma)
 
     run_reports(results, tmpdir)