Add edges vs nodes plotting, improve plotting in general

nigsp/operations/timeseries.py

@@ -51,6 +51,38 @@ def normalise_ts(timeseries):
     return z
 
 
+def spc_ts(timeseries):
+    """
+    Express timeseries in signal percentage change.
+
+    It is assumed that time is encoded in the second dimension (axis 1),
+    e.g. for 90 voxels and 300 timepoints, shape is [90, 300].
+
+    Parameters
+    ----------
+    timeseries : numpy.ndarray
+        The input timeseries. It is assumed that the second dimension is time.
+
+    Returns
+    -------
+    numpy.ndarray
+        The timeseries in SPC if timeseries is not a 1D array.
+        If timeseries is a 1D array, it is returned as is.
+    """
+    if timeseries.ndim < 2 or (timeseries.ndim == 2 and timeseries.shape[1] == 1):
+        LGR.warning(
+            "Given timeseries seems to be a single timepoint. " "Returning it as is."
+        )
+        return timeseries
+
+    scp = (timeseries - timeseries.mean(axis=1)[:, np.newaxis, ...]) / timeseries.mean(
+        axis=1
+    )[:, np.newaxis, ...]
+    scp[np.isnan(scp)] = timeseries[np.isnan(scp)]
+
+    return scp
+
+
 def graph_fourier_transform(timeseries, eigenvec, energy=False, mean=False):
     """
     Projet a graph decomposition onto the timeseries.

nigsp/tests/test_integration.py

@@ -52,9 +52,9 @@ def test_integration(timeseries, sc_mtx, atlas, mean_fc, sdi, testdir):
     assert isfile(join(testdir, "testfile_fc.png"))
     assert isfile(join(testdir, "testfile_fc_low.png"))
     assert isfile(join(testdir, "testfile_fc_high.png"))
-    assert isfile(join(testdir, "testfile_grayplot.png"))
-    assert isfile(join(testdir, "testfile_grayplot_low.png"))
-    assert isfile(join(testdir, "testfile_grayplot_high.png"))
+    assert isfile(join(testdir, "testfile_greyplot.png"))
+    assert isfile(join(testdir, "testfile_greyplot_low.png"))
+    assert isfile(join(testdir, "testfile_greyplot_high.png"))
     assert isfile(join(testdir, "testfile_sdi.png"))
     assert isfile(join(testdir, "testfile_mkd_sdi.png"))
 

nigsp/tests/test_viz.py

@@ -27,8 +27,8 @@ def test_plot_connectivity(mtx):
 
 
 @mark.parametrize("timeseries", [(rand(3, 50)), (rand(3, 50, 3)), (rand(3, 50, 4, 1))])
-def test_plot_grayplot(timeseries):
-    viz.plot_grayplot(timeseries, "troy.png", closeplot=True)
+def test_plot_greyplot(timeseries):
+    viz.plot_greyplot(timeseries, "troy.png", closeplot=True)
 
     assert isfile("troy.png")
     matplotlib.pyplot.close()
@@ -46,31 +46,48 @@ def test_plot_nodes(sdi, atlas):
     remove(atlas)
 
 
+def test_plot_edges(atlas):
+    mtx = rand(360, 360)
+    mtx = mtx - mtx.min() + 0.3
+    viz.plot_edges(mtx, atlas, "britta.png", thr="95%", closeplot=True)
+
+    assert isfile("britta.png")
+    matplotlib.pyplot.close()
+    remove("britta.png")
+    remove(atlas)
+
+
 # ### Break tests
 def test_break_plot_connectivity():
     sys.modules["matplotlib"] = None
     with raises(ImportError) as errorinfo:
         viz.plot_connectivity(rand(3, 3), "craig.png")
-    assert "is required" in str(errorinfo.value)
+    assert "are required" in str(errorinfo.value)
     sys.modules["matplotlib"] = matplotlib
 
+    sys.modules["nilearn.plotting"] = None
+    with raises(ImportError) as errorinfo:
+        viz.plot_connectivity(rand(3, 3), "craig.png")
+    assert "are required" in str(errorinfo.value)
+    sys.modules["nilearn.plotting"] = nilearn.plotting
+
     with raises(ValueError) as errorinfo:
         viz.plot_connectivity(rand(3, 3, 3, 4), "craig.png")
     assert "plot connectivity" in str(errorinfo.value)
 
     matplotlib.pyplot.close()
 
 
-def test_break_plot_grayplot():
+def test_break_plot_greyplot():
     sys.modules["matplotlib"] = None
     with raises(ImportError) as errorinfo:
-        viz.plot_grayplot(rand(3, 3), "dan.png")
+        viz.plot_greyplot(rand(3, 3), "dan.png")
     assert "is required" in str(errorinfo.value)
     sys.modules["matplotlib"] = matplotlib
 
     with raises(ValueError) as errorinfo:
-        viz.plot_grayplot(rand(3, 3, 3, 4), "dan.png")
-    assert "plot grayplots" in str(errorinfo.value)
+        viz.plot_greyplot(rand(3, 3, 3, 4), "dan.png")
+    assert "plot greyplots" in str(errorinfo.value)
 
     matplotlib.pyplot.close()
 
@@ -105,3 +122,38 @@ def test_break_plot_nodes(atlas):
 
     matplotlib.pyplot.close()
     remove(atlas)
+
+
+def test_break_plot_edges(atlas):
+    sys.modules["matplotlib"] = None
+    with raises(ImportError) as errorinfo:
+        viz.plot_edges(rand(3), rand(3, 3))
+    assert "are required" in str(errorinfo.value)
+    sys.modules["matplotlib"] = matplotlib
+
+    sys.modules["nilearn.plotting"] = None
+    with raises(ImportError) as errorinfo:
+        viz.plot_edges(rand(3), rand(3, 3))
+    assert "are required" in str(errorinfo.value)
+    sys.modules["nilearn.plotting"] = nilearn.plotting
+
+    with raises(ValueError) as errorinfo:
+        viz.plot_edges(rand(3, 3, 4, 5), rand(3, 3))
+    assert "plot node values" in str(errorinfo.value)
+
+    with raises(NotImplementedError) as errorinfo:
+        viz.plot_edges(rand(3), rand(3, 3, 2))
+    assert "atlases in nifti" in str(errorinfo.value)
+    with raises(NotImplementedError) as errorinfo:
+        viz.plot_edges(rand(3), rand(3, 4))
+    assert "atlases in nifti" in str(errorinfo.value)
+
+    with raises(ValueError) as errorinfo:
+        viz.plot_edges(rand(3), rand(4, 3))
+    assert "different length" in str(errorinfo.value)
+
+    matplotlib.pyplot.close()
+    remove(atlas)
+
+
+# ..and a movie!!!