add support for single-channel plotting with selected colormaps; bump version to 0.3.5

Author: mbstadler

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ez_zarr"
-version = "0.3.4"
+version = "0.3.5"
 description = "Give easy, high-level access to ome-zarr filesets."
 readme = { file = "README.md", content-type = "text/markdown" }
 authors = [

src/ez_zarr/__init__.py

@@ -1,2 +1,2 @@
-__version__ = '0.3.4'
+__version__ = '0.3.5'
 __author__ = 'Silvia Barbiero, Michael Stadler, Charlotte Soneson'

src/ez_zarr/ome_zarr.py

@@ -9,7 +9,7 @@
 
 __all__ = ['Image', 'ImageList', 'create_name_row_col', 
            'create_name_plate_A01', 'import_plate']
-__version__ = '0.3.4'
+__version__ = '0.3.5'
 __author__ = 'Silvia Barbiero, Michael Stadler, Charlotte Soneson'
 
 

src/ez_zarr/plotting.py

@@ -276,12 +276,17 @@ def plot_image(im: np.ndarray,
                 in points (e.g. `12.5`) or a relative size (e.g. `'xx-large'`).
             channels (list[int]): The image channel(s) to be plotted. For example,
                 to plot the first and third channel of a 4-channel image with
-                shape (4,1,500,600), you can use `channels=[0, 2]`.
+                shape (4,1,500,600), you can use `channels=[0, 2]`. If several
+                channels are given, they will be mapped to colors using
+                `channel_colors`. In the case of a single channel, `channel_colors`
+                can also be the name of a supported colormap.
             channel_colors (list[str]): A list with python color strings
                 (e.g. 'red') defining the color for each channel in `channels`.
                 For example, to map the selected `channels=[0, 2]` to
                 cyan and magenta, respectively, you can use
-                `channel_colors=['cyan', 'magenta']`.
+                `channel_colors=['cyan', 'magenta']`. If a single channel is
+                given (e.g. `channels=[0]`), this can also be one of the following
+                colormaps: 'viridis', 'plasma', 'inferno', 'magma', 'cividis'.
             channel_ranges (list[list[float]]): A list of 2-element lists
                 (e.g. [0.01, 0.95]) giving the the value ranges that should
                 be mapped to colors for each channel. If the given numerical
@@ -361,6 +366,10 @@ def plot_image(im: np.ndarray,
         assert all([ch <= nch for ch in channels]), (
             f"Invalid `channels` parameter, must be less or equal to {nch}"
         )
+        assert len(channels) == len(channel_colors), (
+            f"`channels` and `channel_colors` must have the same length, "
+            f"but are {len(channels)} and {len(channel_colors)}"
+        )
         assert axis_style != 'micrometer' or spacing_yx != None, (
             f"For `axis_style='micrometer', the parameter `spacing_yx` needs to be provided."
         )
@@ -410,14 +419,22 @@ def plot_image(im: np.ndarray,
         if not image_transform is None:
             im = image_transform(im)
 
-        # convert (ch,y,x) to rgb (y,x,3) and plot
-        im_rgb = convert_to_rgb(im=im[channels],
-                                channel_colors=channel_colors,
-                                channel_ranges=channel_ranges)
+        # convert (ch,y,x) to rgb (y,x,3)
+        if len(channels) == 1 and channel_colors[0] in ['viridis', 'plasma', 'inferno',
+                                                        'magma', 'cividis']:
+            # map to colormap
+            im_rgb = np.squeeze(im[channels], axis=0)
+            cmap = channel_colors[0]
+        else:
+            # map to rgb
+            im_rgb = convert_to_rgb(im=im[channels],
+                                    channel_colors=channel_colors,
+                                    channel_ranges=channel_ranges)
+            cmap = None
 
         # define nested function with main plotting code
         def _do_plot():
-            plt.imshow(im_rgb)
+            plt.imshow(im_rgb, cmap=cmap)
             if not msk is None and np.max(msk) > 0:
                 plt.imshow(msk,
                            interpolation='none',

tests/test_plotting.py

@@ -102,6 +102,20 @@ def test_plot_image(npa4d: np.ndarray, npa3d: np.ndarray, tmpdir: str):
                    scalebar_pixel=100,
                    scalebar_position='error')
 
+    with pytest.raises(Exception) as e_info:
+        plot_image(im=npa4d, msk=None,
+                   channels=[0, 1],
+                   channel_colors=['white'],
+                   channel_ranges=[[0.01, 0.99]],
+                   title='test')
+
+    with pytest.raises(Exception) as e_info:
+        plot_image(im=npa4d, msk=None,
+                   channels=[0, 1],
+                   channel_colors=['viridis', 'inferno'],
+                   channel_ranges=[[0.01, 0.99]],
+                   title='test')
+
     with pytest.raises(Exception) as e_info:
         plot_image(im=npa4d, msk=None,
                    channels=[1],
@@ -133,6 +147,12 @@ def test_plot_image(npa4d: np.ndarray, npa3d: np.ndarray, tmpdir: str):
                        image_transform=np.log1p,
                        axis_style=st,
                        spacing_yx=[0.325, 0.325])
+        # single channel with colormap
+        plot_image(im=npa4d, msk=None,
+                    channels=[1],
+                    channel_colors=['inferno'],
+                    channel_ranges=[[0.01, 0.99]],
+                    title='test', call_show=False)
         # image with masks
         plot_image(im=npa4d, msk=npa3d,
                    channels=[1],