Plots improvements

.gitattributes

@@ -1,4 +1,4 @@
-phys2bids/_version.py export-subst
+nigsp/_version.py export-subst
 
 *.py eol=lf
 *.rst eol=lf

nigsp/blocks.py

@@ -99,7 +99,7 @@ def export_metric(scgraph, outext, outprefix):
     return 0
 
 
-def plot_metric(scgraph, outprefix, atlas=None, thr=None):
+def plot_metric(scgraph, outprefix, atlas=None, title=None, thr=None):
     """
     If possible, plot metrics as markerplot.
 
@@ -109,10 +109,10 @@ def plot_metric(scgraph, outprefix, atlas=None, thr=None):
         The internal object containing all data.
     outprefix : str
         The prefix of the png file to export
-    img : 3DNiftiImage or None, optional
-        The nifti image of the atlas
     atlas : 3D Nifti1Image, numpy.ndarray, or None, optional
         Either a nifti image containing a valid atlas or a set of parcel coordinates.
+    title : None or str, optional
+        Add a title to the graph
     thr : float or None, optional
         The threshold to use in plotting the nodes.
     """
@@ -135,14 +135,19 @@ def plot_metric(scgraph, outprefix, atlas=None, thr=None):
     if atlas_plot is not None:
         if scgraph.sdi is not None:
             viz.plot_nodes(
-                scgraph.sdi, atlas_plot, filename=f"{outprefix}sdi.png", thr=thr
+                scgraph.sdi,
+                atlas_plot,
+                filename=f"{outprefix}sdi.png",
+                title=title,
+                thr=thr,
             )
         elif scgraph.gsdi is not None:
             for k in scgraph.gsdi.keys():
                 viz.plot_nodes(
                     scgraph.gsdi[k],
                     atlas_plot,
                     filename=f"{outprefix}gsdi_{k}.png",
+                    title=title,
                     thr=thr,
                 )
 

nigsp/objects.py

@@ -130,7 +130,7 @@ def compute_graph_energy(self, mean=False):  # pragma: no cover
         )
         return self
 
-    def split_graph(self, index=None, keys=["low", "high"]):
+    def split_graph(self, index=None, keys=["low-pass", "high-pass"]):
         """Implement timeseries.median_cutoff_frequency_idx as class method."""
         if index is None:
             index = self.index

nigsp/operations/timeseries.py

@@ -205,7 +205,7 @@ def resize_ts(timeseries, resize=None, globally=False):
         if resize == "spc":  # pragma: no cover
             LGR.info("Expressing timeseries in signal percentage change")
             timeseries = spc_ts(timeseries, globally=globally)
-        elif resize == "norm":  # pragma: no cover
+        elif resize in ["norm", "zscore"]:  # pragma: no cover
             LGR.info("Normalise timeseries")
             timeseries = normalise_ts(timeseries, globally=globally)
         elif resize == "demean":  # pragma: no cover
@@ -338,13 +338,13 @@ def median_cutoff_frequency_idx(energy):
     return freq_idx
 
 
-def graph_filter(timeseries, eigenvec, freq_idx, keys=["low", "high"]):
+def graph_filter(timeseries, eigenvec, freq_idx, keys=["low-pass", "high-pass"]):
     """
     Filter a graph decomposition into two parts based on freq_idx.
 
     Return the two eigenvector lists (high freq and low freq) that are equal
-    to the original eigenvector list, but "low" is zero-ed for all frequencies
-    >= of the given index, and "high" is zero-ed for all frequencies < to the
+    to the original eigenvector list, but "low-pass" is zero-ed for all frequencies
+    >= of the given index, and "high-pass" is zero-ed for all frequencies < to the
     given index.
     Also return their projection onto a timeseries.
 
@@ -357,7 +357,7 @@ def graph_filter(timeseries, eigenvec, freq_idx, keys=["low", "high"]):
     freq_idx : int or list
         The index of the frequency that splits the spectral power into two
         (more or less) equal parts - i.e. the index of the first frequency in
-        the "high" component.
+        the "high-pass" component.
     keys : list, optional
         The keys to call the split parts with
 
@@ -371,8 +371,8 @@ def graph_filter(timeseries, eigenvec, freq_idx, keys=["low", "high"]):
     Raises
     ------
     IndexError
-        If the given index is 0 (all "high"), the last possible index (all "low"),
-        or higher than the last possible index (not applicable).
+        If the given index is 0 (all "high-pass"), the last possible index
+        (all "low-pass"), or higher than the last possible index (not applicable).
     """
     # #!# Find better name
     # #!# Implement an index splitter

nigsp/tests/test_integration.py

@@ -34,27 +34,27 @@ def test_integration(timeseries, sc_mtx, atlas, mean_fc, sdi, testdir):
     # Check that files were created
     assert isdir(testdir)
     assert isdir(join(testdir, "logs"))
-    assert isdir(join(testdir, "testfile_timeseries_low"))
-    assert isdir(join(testdir, "testfile_timeseries_high"))
-    assert isfile(join(testdir, "testfile_timeseries_low", "000.tsv"))
-    assert isfile(join(testdir, "testfile_timeseries_high", "000.tsv"))
+    assert isdir(join(testdir, "testfile_timeseries_low-pass"))
+    assert isdir(join(testdir, "testfile_timeseries_high-pass"))
+    assert isfile(join(testdir, "testfile_timeseries_low-pass", "000.tsv"))
+    assert isfile(join(testdir, "testfile_timeseries_high-pass", "000.tsv"))
     assert isfile(join(testdir, "testfile_fc.tsv"))
-    assert isfile(join(testdir, "testfile_fc_low.tsv"))
-    assert isfile(join(testdir, "testfile_fc_high.tsv"))
+    assert isfile(join(testdir, "testfile_fc_low-pass.tsv"))
+    assert isfile(join(testdir, "testfile_fc_high-pass.tsv"))
     assert isfile(join(testdir, "testfile_eigenval.tsv"))
     assert isfile(join(testdir, "testfile_eigenvec.tsv"))
-    assert isfile(join(testdir, "testfile_eigenvec_low.tsv"))
-    assert isfile(join(testdir, "testfile_eigenvec_high.tsv"))
+    assert isfile(join(testdir, "testfile_eigenvec_low-pass.tsv"))
+    assert isfile(join(testdir, "testfile_eigenvec_high-pass.tsv"))
     assert isfile(join(testdir, "testfile_sdi.tsv"))
     assert isfile(join(testdir, "testfile_mkd_sdi.tsv"))
     assert isfile(join(testdir, "testfile_laplacian.png"))
     assert isfile(join(testdir, "testfile_sc.png"))
     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_fc_low-pass.png"))
+    assert isfile(join(testdir, "testfile_fc_high-pass.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_greyplot_low-pass.png"))
+    assert isfile(join(testdir, "testfile_greyplot_high-pass.png"))
     assert isfile(join(testdir, "testfile_sdi.png"))
     assert isfile(join(testdir, "testfile_mkd_sdi.png"))
 

nigsp/tests/test_metrics.py

@@ -16,11 +16,11 @@ def test_sdi():
     ts3 = np.arange(5, 7)[..., np.newaxis]
     sdi_in = np.log2(np.arange(3.0, 1.0, -1.0))
 
-    ts = {"low": ts1, "high": ts2}
+    ts = {"low-pass": ts1, "high-pass": ts2}
     sdi_out = metrics.sdi(ts)
     assert (sdi_out == sdi_in).all()
 
-    ts = {"HIGH": ts2, "LOW": ts1}
+    ts = {"HIGH-PASS": ts2, "LOW-PASS": ts1}
     sdi_out = metrics.sdi(ts)
     assert (sdi_out == sdi_in).all()
 
@@ -29,8 +29,8 @@ def test_sdi():
     assert (sdi_out == sdi_in).all()
 
     ts = {
-        "low": np.repeat(np.repeat(ts1[..., np.newaxis], 3, axis=1), 3, axis=2),
-        "high": np.repeat(np.repeat(ts2[..., np.newaxis], 3, axis=1), 3, axis=2),
+        "low-pass": np.repeat(np.repeat(ts1[..., np.newaxis], 3, axis=1), 3, axis=2),
+        "high-pass": np.repeat(np.repeat(ts2[..., np.newaxis], 3, axis=1), 3, axis=2),
     }
     sdi_out = metrics.sdi(ts, mean=True)
     sdi_out = np.around(sdi_out, decimals=15)
@@ -80,7 +80,7 @@ def test_break_sdi():
     ts = {"alpha": ts1, "beta": ts2, "gamma": ts3}
 
     with raises(ValueError) as errorinfo:
-        metrics.sdi(ts, keys=["high", "low"])
+        metrics.sdi(ts, keys=["high-pass", "low-pass"])
     assert "provided keys" in str(errorinfo.value)
 
     with raises(ValueError) as errorinfo:

nigsp/viz.py

@@ -26,12 +26,12 @@
 
 LGR = logging.getLogger(__name__)
 SET_DPI = 100
-FIGSIZE = (18, 10)
+FIGSIZE = (12, 7)
 FIGSIZE_SQUARE = (6, 5)
-FIGSIZE_LONG = (10, 5)
+FIGSIZE_LONG = (12, 4)
 
 
-def plot_connectivity(mtx, filename=None, closeplot=False):
+def plot_connectivity(mtx, filename=None, title=None, crange=None, closeplot=False):
     """
     Create a connectivity matrix plot.
 
@@ -43,6 +43,10 @@ def plot_connectivity(mtx, filename=None, closeplot=False):
         A (square) array with connectivity information inside.
     filename : None, str, or os.PathLike, optional
         The path to save the plot on disk.
+    title : None or str, optional
+        Add a title to the graph
+    range : None or list, optional
+        Set vmin and vmax
     closeplot : bool, optional
         Whether to close plots after saving or not. Mainly used for debug
         or use with live python/ipython instances.
@@ -85,11 +89,31 @@ def plot_connectivity(mtx, filename=None, closeplot=False):
         LGR.warning("Given matrix is not a square matrix!")
 
     LGR.info("Creating connectivity plot.")
-    plt.figure(figsize=FIGSIZE_SQUARE)
-    plot_matrix(mtx)
+    fig = plt.figure(figsize=FIGSIZE_SQUARE)
+    ax = fig.subplots()
+
+    pc_args = {"mat": mtx, "axes": ax}
+    if crange is not None:
+        if type(crange) in [list, tuple]:
+            pc_args["vmin"] = crange[0]
+            pc_args["vmax"] = crange[1]
+        else:
+            vmax = np.nanpercentile(mtx, 98)  # mtx.max()
+            vmin = np.abs(np.nanpercentile(mtx, 2))  # mtx.min()
+            if crange == "auto-symm" and mtx.min() < 0 and vmax > 0:
+                pc_args["vmax"] = vmax if vmax > vmin else vmin
+                pc_args["vmin"] = -vmin if vmin > vmax else -vmax
+            elif crange == "auto-zero" or mtx.min() > 0 or vmax < 0:
+                pass
+            else:
+                raise NotImplementedError(f"{crange} option not implemented.")
+
+    plot_matrix(**pc_args)
+    if title is not None:
+        fig.suptitle(title)
 
     if filename is not None:
-        plt.savefig(filename, dpi=SET_DPI)
+        plt.savefig(filename, dpi=SET_DPI, bbox_inches="tight")
         closeplot = True
 
     if closeplot:
@@ -162,17 +186,18 @@ def plot_greyplot(timeseries, filename=None, title=None, resize=None, closeplot=
     timeseries = resize_ts(timeseries, resize)
 
     LGR.info("Creating greyplot.")
-    plt.figure(figsize=FIGSIZE_LONG)
-    if title is not None:
-        plt.title(title)
     vmax = np.percentile(timeseries, 99)
     vmin = np.percentile(timeseries, 1)
-    plt.imshow(timeseries, cmap="gray", vmin=vmin, vmax=vmax)
-    plt.colorbar()
+    fig = plt.figure(figsize=FIGSIZE_LONG)
+    ax = fig.subplots()
+    im = ax.imshow(timeseries, cmap="gray", vmin=vmin, vmax=vmax)
+    plt.colorbar(im, ax=ax)
+    if title is not None:
+        fig.suptitle(title)
     plt.tight_layout()
 
     if filename is not None:
-        plt.savefig(filename, dpi=SET_DPI)
+        plt.savefig(filename, dpi=SET_DPI, bbox_inches="tight")
         closeplot = True
 
     if closeplot:
@@ -183,7 +208,9 @@ def plot_greyplot(timeseries, filename=None, title=None, resize=None, closeplot=
     return 0
 
 
-def plot_nodes(ns, atlas, filename=None, thr=None, closeplot=False):
+def plot_nodes(
+    ns, atlas, filename=None, title=None, thr=None, cmap=None, closeplot=False
+):
     """
     Create a marker plot in the MNI space.
 
@@ -198,8 +225,12 @@ def plot_nodes(ns, atlas, filename=None, thr=None, closeplot=False):
         or a list of coordinates of the center of mass of parcels.
     filename : None, str, or os.PathLike, optional
         The path to save the plot on disk.
+    title : None or str, optional
+        Add a title to the graph
     thr : float or None, optional
         The threshold to use in plotting the nodes.
+    cmap : None or matplotlib.pyplot.cm colormap object, optional.
+        The colormap to adopt in plotting nodes. Defaults to reverse viridis.
     closeplot : bool, optional
         Whether to close plots after saving or not. Mainly used for debug
         or use with live python/ipython instances.
@@ -252,11 +283,17 @@ def plot_nodes(ns, atlas, filename=None, thr=None, closeplot=False):
         raise ValueError("Node array and coordinates array have different length.")
 
     LGR.info("Creating markerplot.")
-    plt.figure(figsize=FIGSIZE)
-    plot_markers(ns, coord, node_threshold=thr)
+    fig = plt.figure(figsize=FIGSIZE)
+    ax = fig.subplots()
 
+    cmap = plt.cm.viridis_r if cmap is None else cmap
+    plot_markers(ns, coord, axes=ax, node_threshold=thr, node_cmap=cmap)
+    if title is not None:
+        fig.suptitle(title)
+
+    plt.tight_layout()
     if filename is not None:
-        plt.savefig(filename, dpi=SET_DPI)
+        plt.savefig(filename, dpi=SET_DPI, bbox_inches="tight")
         closeplot = True
 
     if closeplot:
@@ -265,7 +302,9 @@ def plot_nodes(ns, atlas, filename=None, thr=None, closeplot=False):
     return 0
 
 
-def plot_edges(mtx, atlas, filename=None, thr=None, closeplot=False):
+def plot_edges(
+    mtx, atlas, filename=None, title=None, thr=None, cmap=None, closeplot=False
+):
     """
     Create a connectivity plot in the MNI space.
 
@@ -280,9 +319,13 @@ def plot_edges(mtx, atlas, filename=None, thr=None, closeplot=False):
         or a list of coordinates of the center of mass of parcels.
     filename : None, str, or os.PathLike, optional
         The path to save the plot on disk.
+    title : None or str, optional
+        Add a title to the graph
     thr : float, str or None, optional
         The threshold to use in plotting the nodes.
         If `str`, needs to express a percentage.
+    cmap : None or matplotlib.pyplot.cm colormap object, optional.
+        The colormap to adopt in plotting nodes. Defaults to reverse viridis.
     closeplot : bool, optional
         Whether to close plots after saving or not. Mainly used for debug
         or use with live python/ipython instances.
@@ -335,26 +378,34 @@ def plot_edges(mtx, atlas, filename=None, thr=None, closeplot=False):
         raise ValueError("Matrix axis and coordinates array have different length.")
 
     LGR.info("Creating connectome-like plot.")
-    plt.figure(figsize=FIGSIZE)
+    fig = plt.figure(figsize=FIGSIZE)
+    ax = fig.subplots()
 
     pc_args = {
         "adjacency_matrix": mtx,
         "node_coords": coord,
         "node_color": "black",
         "node_size": 5,
         "edge_threshold": thr,
+        "edge_cmap": plt.cm.bwr,
         "colorbar": True,
+        "axes": ax,
     }
 
     if mtx.min() >= 0:
         pc_args["edge_vmin"] = 0
         pc_args["edge_vmax"] = mtx.max()
         pc_args["edge_cmap"] = cm.red_transparent_full_alpha_range
 
+    pc_args["edge_cmap"] = pc_args["edge_cmap"] if cmap is None else cmap
     plot_connectome(**pc_args)
 
+    if title is not None:
+        fig.suptitle(title)
+
+    plt.tight_layout()
     if filename is not None:
-        plt.savefig(filename, dpi=SET_DPI)
+        plt.savefig(filename, dpi=SET_DPI, bbox_inches="tight")
         closeplot = True
 
     if closeplot: