Merge pull request #168 from oesteban/fix/fieldmap-reportlet

FIX: Cleanup annoying isolated dots in reportlets + new tests

.dockerignore

@@ -39,6 +39,7 @@ out/**/*
 out/
 tools/**/*
 tools
+.DS_Store
 
 # CI, etc.
 .circleci/**/*
@@ -49,4 +50,5 @@ tools
 .readthedocs.yml
 .travis.yml
 .zenodo.json
-CONTRIBUTING.md
+CONTRIBUTING.md
+

.gitignore

@@ -107,3 +107,6 @@ venv.bak/
 
 # mypy
 .mypy_cache/
+
+# Mac OSX
+.DS_Store

sdcflows/interfaces/reportlets.py

@@ -68,7 +68,7 @@ def _generate_report(self):
                     break
 
         if isdefined(self.inputs.moving):
-            movnii = load_img(self.inputs.moving)
+            movnii = rotate_affine(load_img(self.inputs.moving), rot=canonical_r)
 
         contour_nii = mask_nii = None
         if isdefined(self.inputs.mask):

sdcflows/interfaces/tests/test_reportlets.py

@@ -0,0 +1,30 @@
+"""Test the fieldmap reportlets."""
+from pathlib import Path
+import pytest
+from ..reportlets import FieldmapReportlet
+from ...utils.epimanip import epi_mask
+
+
+@pytest.mark.parametrize("mask", [True, False])
+@pytest.mark.parametrize("apply_mask", [True, False])
+def test_FieldmapReportlet(tmpdir, outdir, testdata_dir, mask, apply_mask):
+    """Generate one reportlet."""
+    tmpdir.chdir()
+
+    if not outdir:
+        outdir = Path.cwd()
+
+    report = FieldmapReportlet(
+        reference=str(testdata_dir / "epi.nii.gz"),
+        moving=str(testdata_dir / "epi.nii.gz"),
+        fieldmap=str(testdata_dir / "topup-field.nii.gz"),
+        out_report=str(
+            outdir / f"test-fieldmap{'-masked' * mask}{'-zeroed' * apply_mask}.svg"
+        ),
+        apply_mask=apply_mask,
+    )
+
+    if mask:
+        report.inputs.mask = epi_mask(str(testdata_dir / "epi.nii.gz"))
+
+    report.run()

sdcflows/interfaces/tests/test_utils.py

@@ -51,7 +51,6 @@ def test_ConvertWarp(tmpdir, shape):
 )
 def test_Xeoblique(tmpdir, angles, oblique):
     """Exercise De/Reoblique interfaces."""
-
     tmpdir.chdir()
 
     affine = nb.affines.from_matvec(nb.eulerangles.euler2mat(*angles))

sdcflows/utils/tests/test_misc.py

@@ -9,6 +9,7 @@
 @pytest.mark.parametrize("retval", [None, 10])
 def test_get_free_mem(monkeypatch, retval):
     """Test the get_free_mem utility."""
+
     def mock_func():
         if retval is None:
             raise ImportError

sdcflows/viz/utils.py

@@ -95,8 +95,9 @@ def coolwarm_transparent(max_alpha=0.7, opaque_perc=30, transparent_perc=8):
     midpoint = cmap.N // 2 + 1
     _10perc = (cmap.N * transparent_perc) // 100
     # Set alpha
-    alpha = np.ones(cmap.N) * max_alpha
-    alpha[midpoint - _10perc : midpoint + _10perc] = 0
+    alpha = np.zeros(cmap.N)
+    alpha[:_20perc] = max_alpha
+    alpha[-_20perc:] = max_alpha
     alpha[_20perc : midpoint - _10perc - 1] = np.linspace(
         max_alpha, 0, len(alpha[_20perc : midpoint - _10perc - 1])
     )