Merge pull request #9 from int-brain-lab/fix_cmap

Fix cmap

CHANGELOG.md

@@ -1,3 +1,7 @@
+## [0.5.2]
+### Modified
+- `iblatlas.plots` uses colors.get_cmap instead of deprecated cm.get_cmap
+
 ## [0.5.1]
 ### Modified
 - `iblatlas.genomics.merfish.load` does not return an error when dask is installed but

iblatlas/__init__.py

@@ -194,4 +194,4 @@
 .. [10] Allen Mouse Common Coordinate Framework Technical White Paper (October 2017 v3)
    http://help.brain-map.org/download/attachments/8323525/Mouse_Common_Coordinate_Framework.pdf
 """
-__version__ = '0.5.1'
+__version__ = '0.5.2'

iblatlas/plots.py

@@ -302,7 +302,7 @@ def _plot_slice_vector(coords, slice, values, mapping, empty_color='silver', cle
     else:
         fig = ax.get_figure()
 
-    colormap = cm.get_cmap(cmap)
+    colormap = colors.get_cmap(cmap)
     norm = colors.Normalize(vmin=clevels[0], vmax=clevels[1])
     nan_vals = np.isnan(values)
     rgba_color = np.full((values.size, 4), fill_value=np.nan)
@@ -521,7 +521,7 @@ def plot_scalar_on_flatmap(regions, values, depth=0, flatmap='dorsal_cortex', ma
     d_idx = int(np.round(depth / ba.res_um))  # need to find nearest to 25
 
     if background == 'boundary':
-        cmap_bound = cm.get_cmap("bone_r").copy()
+        cmap_bound = colors.get_cmap("bone_r").copy()
         cmap_bound.set_under([1, 1, 1], 0)
 
     if ax:
@@ -893,7 +893,7 @@ def plot_swanson_vector(acronyms=None, values=None, ax=None, hemisphere=None, br
 
     if acronyms is not None:
         ibr, vals = br.propagate_down(acronyms, values)
-        colormap = cm.get_cmap(cmap)
+        colormap = colors.get_cmap(cmap)
         vmin = vmin or np.nanmin(vals)
         vmax = vmax or np.nanmax(vals)
         norm = colors.Normalize(vmin=vmin, vmax=vmax)