Merge pull request #2891 from samuelgarcia/mpl_cmap

Fix the new way of handling cmap in matpltolib. This fix the matplotib 3.9 problem related to this.

pyproject.toml

@@ -95,7 +95,7 @@ full = [
     "scikit-learn",
     "networkx",
     "distinctipy",
-    "matplotlib<3.9",  # See https://github.com/SpikeInterface/spikeinterface/issues/2863
+    "matplotlib>=3.6", # matplotlib.colormaps
     "cuda-python; platform_system != 'Darwin'",
     "numba",
 ]

src/spikeinterface/sortingcomponents/benchmark/benchmark_motion_estimation.py

@@ -728,7 +728,7 @@ def plot_summary_errors(self, case_keys=None, show_legend=True, colors=None, fig
 
 #         n = self.motion.shape[1]
 #         step = int(np.ceil(max(1, n / show_only)))
-#         colors = plt.cm.get_cmap("jet", n)
+#         colors = plt.colormaps["jet"].resampled(n)
 #         for i in range(0, n, step):
 #             ax = axs[0]
 #             ax.plot(self.temporal_bins, self.gt_motion[:, i], lw=1.5, ls="--", color=colors(i))

src/spikeinterface/sortingcomponents/benchmark/benchmark_peak_selection.py

@@ -382,7 +382,7 @@ def create_benchmark(self, key):
 
 #         import matplotlib
 
-#         my_cmap = plt.get_cmap(cmap)
+#         my_cmap = plt.colormaps[cmap]
 #         cNorm = matplotlib.colors.Normalize(vmin=clim[0], vmax=clim[1])
 #         scalarMap = plt.cm.ScalarMappable(norm=cNorm, cmap=my_cmap)
 

src/spikeinterface/sortingcomponents/clustering/clustering_tools.py

@@ -62,7 +62,7 @@ def _split_waveforms(
         local_feature_plot = local_feature
 
         unique_lab = np.unique(local_labels_with_noise)
-        cmap = plt.get_cmap("jet", unique_lab.size)
+        cmap = plt.colormaps["jet"].resampled(unique_lab.size)
         cmap = {k: cmap(l) for l, k in enumerate(unique_lab)}
         cmap[-1] = "k"
         active_ind = np.arange(local_feature.shape[0])
@@ -145,7 +145,7 @@ def _split_waveforms_nested(
             local_feature_plot = reducer.fit_transform(local_feature)
 
             unique_lab = np.unique(active_labels_with_noise)
-            cmap = plt.get_cmap("jet", unique_lab.size)
+            cmap = plt.colormaps["jet"].resampled(unique_lab.size)
             cmap = {k: cmap(l) for l, k in enumerate(unique_lab)}
             cmap[-1] = "k"
             cmap[-2] = "b"
@@ -276,7 +276,7 @@ def auto_split_clustering(
 
             fig, ax = plt.subplots()
             plot_labels_set = np.unique(local_labels_with_noise)
-            cmap = plt.get_cmap("jet", plot_labels_set.size)
+            cmap = plt.colormaps["jet"].resampled(plot_labels_set.size)
             cmap = {k: cmap(l) for l, k in enumerate(plot_labels_set)}
             cmap[-1] = "k"
             cmap[-2] = "b"

src/spikeinterface/sortingcomponents/clustering/sliding_hdbscan.py

@@ -349,7 +349,7 @@ def _find_clusters(cls, recording, peaks, wfs_arrays, sparsity_mask, noise, d):
                 wfs_no_noise = wfs[: -noise.shape[0]]
 
                 fig, axs = plt.subplots(ncols=3)
-                cmap = plt.get_cmap("jet", np.unique(local_labels).size)
+                cmap = plt.colormaps["jet"].resampled(np.unique(local_labels).size)
                 cmap = {label: cmap(l) for l, label in enumerate(local_labels_set)}
                 cmap[-1] = "k"
                 for label in local_labels_set:

src/spikeinterface/sortingcomponents/clustering/split.py

@@ -254,7 +254,7 @@ def split(
             import matplotlib.pyplot as plt
 
             labels_set = np.setdiff1d(possible_labels, [-1])
-            colors = plt.get_cmap("tab10", len(labels_set))
+            colors = plt.colormaps["tab10"].resampled(len(labels_set))
             colors = {k: colors(i) for i, k in enumerate(labels_set)}
             colors[-1] = "k"
             fix, axs = plt.subplots(nrows=2)

src/spikeinterface/widgets/collision.py

@@ -136,7 +136,7 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
 
             ax1.set_xlabel("lag (ms)")
         elif dp.mode == "lines":
-            my_cmap = plt.get_cmap(dp.cmap)
+            my_cmap = plt.colormaps[dp.cmap]
             cNorm = matplotlib.colors.Normalize(vmin=dp.similarity_bins.min(), vmax=dp.similarity_bins.max())
             scalarMap = plt.cm.ScalarMappable(norm=cNorm, cmap=my_cmap)
 
@@ -245,7 +245,7 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
 
         study = dp.study
 
-        my_cmap = plt.get_cmap(dp.cmap)
+        my_cmap = plt.colormaps[dp.cmap]
         cNorm = matplotlib.colors.Normalize(vmin=dp.similarity_bins.min(), vmax=dp.similarity_bins.max())
         scalarMap = plt.cm.ScalarMappable(norm=cNorm, cmap=my_cmap)
         study.precompute_scores_by_similarities(

src/spikeinterface/widgets/motion.py

@@ -128,7 +128,7 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
             if dp.scatter_decimate is not None:
                 amps = amps[:: dp.scatter_decimate]
                 amps_abs = amps_abs[:: dp.scatter_decimate]
-            cmap = plt.get_cmap(dp.amplitude_cmap)
+            cmap = plt.colormaps[dp.amplitude_cmap]
             if dp.amplitude_clim is None:
                 amps = amps_abs
                 amps /= q_95

src/spikeinterface/widgets/multicomparison.py

@@ -87,7 +87,7 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
             nodelist=sorted(g.nodes),
             edge_color=edge_col,
             alpha=dp.alpha_edges,
-            edge_cmap=plt.cm.get_cmap(dp.edge_cmap),
+            edge_cmap=plt.colormaps[dp.edge_cmap],
             edge_vmin=mcmp.match_score,
             edge_vmax=1,
             ax=self.ax,
@@ -106,7 +106,7 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
             import matplotlib.pyplot as plt
 
             norm = mpl_colors.Normalize(vmin=mcmp.match_score, vmax=1)
-            cmap = plt.cm.get_cmap(dp.edge_cmap)
+            cmap = plt.colormaps[dp.edge_cmap]
             m = plt.cm.ScalarMappable(norm=norm, cmap=cmap)
             self.figure.colorbar(m)
 
@@ -159,7 +159,7 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
         self.figure, self.axes, self.ax = make_mpl_figure(**backend_kwargs)
 
         mcmp = dp.multi_comparison
-        cmap = plt.get_cmap(dp.cmap)
+        cmap = plt.colormaps[dp.cmap]
         colors = np.array([cmap(i) for i in np.linspace(0.1, 0.8, len(mcmp.name_list))])
         sg_names, sg_units = mcmp.compute_subgraphs()
         # fraction of units with agreement > threshold
@@ -242,7 +242,7 @@ def plot_matplotlib(self, data_plot, **backend_kwargs):
         backend_kwargs["ncols"] = len(name_list)
         self.figure, self.axes, self.ax = make_mpl_figure(**backend_kwargs)
 
-        cmap = plt.get_cmap(dp.cmap)
+        cmap = plt.colormaps[dp.cmap]
         colors = np.array([cmap(i) for i in np.linspace(0.1, 0.8, len(mcmp.name_list))])
         sg_names, sg_units = mcmp.compute_subgraphs()
         # fraction of units with agreement > threshold

src/spikeinterface/widgets/utils.py

@@ -76,7 +76,8 @@ def get_some_colors(keys, color_engine="auto", map_name="gist_ncar", format="RGB
     elif color_engine == "matplotlib":
         # some map have black or white at border so +10
         margin = max(4, int(N * 0.08))
-        cmap = plt.get_cmap(map_name, N + 2 * margin)
+        cmap = plt.colormaps[map_name].resampled(N + 2 * margin)
+
         colors = [cmap(i + margin) for i, key in enumerate(keys)]
 
     elif color_engine == "colorsys":
@@ -160,7 +161,7 @@ def array_to_image(
     num_channels = data.shape[1]
     spacing = int(num_channels * spatial_zoom[1] * row_spacing)
 
-    cmap = plt.get_cmap(colormap)
+    cmap = plt.colormaps[colormap]
     zoomed_data = zoom(data, spatial_zoom)
     num_timepoints_after_scaling, num_channels_after_scaling = zoomed_data.shape
     num_timepoints_per_row_after_scaling = int(np.min([num_timepoints_per_row, num_timepoints]) * spatial_zoom[0])