fix: dwi spikes iqm test

mriqc/qc/diffusion.py

@@ -302,4 +302,4 @@ def spike_percentage(
         for axis in range(data.ndim)
     ]
 
-    return {'spike_perc_global': spike_perc_global, 'spike_perc_slice': spike_perc_slice}
+    return {'global': spike_perc_global, 'slice': spike_perc_slice}

mriqc/qc/tests/test_diffusion.py

@@ -21,95 +21,18 @@
 #     https://www.nipreps.org/community/licensing/
 #
 
-import os.path as op
-
-import nibabel as nib
 import numpy as np
-import pytest
-from dipy.core.gradients import gradient_table, round_bvals
-from dipy.data.fetcher import fetch_sherbrooke_3shell
-
-from ..diffusion import (
-    cc_snr,
-    get_global_spike_percentage,
-    get_slice_spike_percentage,
-    get_spike_mask,
-    noise_func,
-    noise_func_for_shelled_data,
-)
-
-
-class DiffusionData:
-    def get_data(self):
-        """
-        Generate test data
-        """
-        _, path = fetch_sherbrooke_3shell()
-        fnifti = op.join(path, 'HARDI193.nii.gz')
-        fnifti, bval, bvec = (op.join(path, f'HARDI193.{ext}') for
-                              ext in ['nii.gz', 'bval', 'bvec'])
-        img = nib.load(fnifti)
-        data = img.get_fdata()
-        gtab = gradient_table(bval, bvec)
-        return data, gtab
-
-    def shelled_data(self):
-        data, gtab = self.get_data()
-        rounded_bvals = round_bvals(gtab.bvals)
-        unique_rounded_bvals = np.unique(rounded_bvals)
-
-        out_data = []
-        for u_bv in unique_rounded_bvals:
-            this = data[..., np.where(rounded_bvals == u_bv)]
-            out_data.append(this)
-        return out_data, gtab
-
-
-@pytest.fixture()
-def ddata():
-    return DiffusionData()
-
-
-def test_noise_function(ddata):
-    img, gtab = ddata.get_fdata()
-    noise_func(img, gtab)
-
-
-def test_get_spike_mask(ddata):
-    img, gtab = ddata.get_fdata()
-    spike_mask = get_spike_mask(img, 2)
-
-    assert np.min(np.ravel(spike_mask)) == 0
-    assert np.max(np.ravel(spike_mask)) == 1
-    assert spike_mask.shape == img.shape
-
-
-def test_get_slice_spike_percentage(ddata):
-    img, gtab = ddata.get_fdata()
-    slice_spike_percentage = get_slice_spike_percentage(img, 2, .2)
-
-    assert np.min(slice_spike_percentage) >= 0
-    assert np.max(slice_spike_percentage) <= 1
-    assert len(slice_spike_percentage) == img.ndim
-
-
-def test_get_global_spike_percentage(ddata):
-    img, gtab = ddata.get_fdata()
-    global_spike_percentage = get_global_spike_percentage(img, 2)
-
-    assert global_spike_percentage >= 0
-    assert global_spike_percentage <= 1
 
+from mriqc.qc.diffusion import spike_percentage
 
-def test_with_shelled_data(ddata):
-    shelled_data, gtab = ddata.shelled_data()
-    noise_func_for_shelled_data(shelled_data, gtab)
 
+def test_spike_percentage():
+    img = np.random.normal(loc=10, scale=1.0, size=(76, 76, 64, 124))
+    msk = np.random.randint(0, high=2, size=(76, 76, 64, 124), dtype=bool)
+    val = spike_percentage(img, msk, .5)
 
-def test_cc_snr(ddata):
-    img, gtab = ddata.get_fdata()
-    cc_snr_worst, cc_snr_best = cc_snr(img, gtab)
+    assert np.isclose(val['global'], 0.5, rtol=1, atol=1)
 
-    assert cc_snr_best.shape == gtab.bvals.shape
-    assert cc_snr_worst.shape == gtab.bvals.shape
-    assert np.min(cc_snr_best - cc_snr_worst) >= 0
+    assert np.min(val['slice']) >= 0
+    assert np.max(val['slice']) == 1
+    assert len(val['slice']) == img.ndim