From 16a73dc32cd41c9e893536c61fd62c58aa766ce8 Mon Sep 17 00:00:00 2001
From: David Young <david@textflex.com>
Date: Sun, 26 Jan 2020 22:41:58 +0800
Subject: [PATCH] Fix errors from missing labels image when opacity is set to 0

- Rather than always skipping images that are invisible, provide an option for whether to create the `AxesImage` object or not
- Create these images for Atlas Editor plots since they need to be available if the opacity is increased
---
 magmap/gui/roi_editor.py    |  3 ++-
 magmap/io/export_stack.py   |  3 ++-
 magmap/plot/plot_support.py | 12 ++++++++----
 3 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/magmap/gui/roi_editor.py b/magmap/gui/roi_editor.py
index 7fb4416e7..4934aad5d 100644
--- a/magmap/gui/roi_editor.py
+++ b/magmap/gui/roi_editor.py
@@ -601,7 +601,8 @@ def show_overview(ax_ov, lev, imgs, cmaps, vmins, vmaxs):
                 show.setdefault("vmaxs", []).append(vmax)
             show["alphas"] = libmag.pad_seq(
                 config.alphas, len(show["imgs2d"]), 0.9)
-            plot_support.overlay_images(ax_ov, aspect, origin, **show)
+            plot_support.overlay_images(
+                ax_ov, aspect, origin, ignore_invis=True, **show)
             ax_ov.add_patch(patches.Rectangle(
                 np.divide(patch_offset, downsample),
                 *np.divide(roi_size[0:2], downsample),
diff --git a/magmap/io/export_stack.py b/magmap/io/export_stack.py
index dbea348d7..693b00af0 100644
--- a/magmap/io/export_stack.py
+++ b/magmap/io/export_stack.py
@@ -170,7 +170,8 @@ def _build_stack(ax, images, process_fnc, rescale=1, aspect=None,
         # a nested list containing a list for each image, which in turn 
         # contains a list of artists for each channel
         ax_imgs = plot_support.overlay_images(
-            ax, aspect, origin, imgs, None, cmaps_all, alphas)
+            ax, aspect, origin, imgs, None, cmaps_all, alphas,
+            ignore_invis=True)
         if colorbar and len(ax_imgs) > 0 and len(ax_imgs[0]) > 0:
             # add colorbar with scientific notation if outside limits
             cbar = ax.figure.colorbar(ax_imgs[0][0], ax=ax, shrink=0.7)
diff --git a/magmap/plot/plot_support.py b/magmap/plot/plot_support.py
index 6c64e81c7..ec15dd52c 100644
--- a/magmap/plot/plot_support.py
+++ b/magmap/plot/plot_support.py
@@ -26,7 +26,7 @@
 
 def imshow_multichannel(ax, img2d, channel, cmaps, aspect, alpha, vmin=None,
                         vmax=None, origin=None, interpolation=None,
-                        norms=None, nan_color=None):
+                        norms=None, nan_color=None, ignore_invis=False):
     """Show multichannel 2D image with channels overlaid over one another.
 
     Applies :attr:`config.transform` with :obj:`config.Transforms.ROTATE`
@@ -55,6 +55,8 @@ def imshow_multichannel(ax, img2d, channel, cmaps, aspect, alpha, vmin=None,
         norms: List of normalizations, which should correspond to ``cmaps``.
         nan_color (str): String of color to use for NaN values; defaults to
             None to use "black".
+        ignore_invis (bool): True to give None instead of an ``AxesImage``
+            object that would be invisible; defaults to False.
     
     Returns:
         List of ``AxesImage`` objects.
@@ -102,7 +104,7 @@ def imshow_multichannel(ax, img2d, channel, cmaps, aspect, alpha, vmin=None,
         if is_alpha_seq:
             alpha_plane = alpha[chl]
         img_chl = None
-        if alpha_plane > 0:
+        if not ignore_invis or alpha_plane > 0:
             # skip display if alpha is 0 to avoid outputting a hidden image 
             # that may show up in other renderers (eg PDF viewers)
             img_chl = ax.imshow(
@@ -127,7 +129,7 @@ def imshow_multichannel(ax, img2d, channel, cmaps, aspect, alpha, vmin=None,
 
 
 def overlay_images(ax, aspect, origin, imgs2d, channels, cmaps, alphas, 
-                   vmins=None, vmaxs=None):
+                   vmins=None, vmaxs=None, ignore_invis=False):
     """Show multiple, overlaid images.
     
     Wrapper function calling :meth:`imshow_multichannel` for multiple 
@@ -157,6 +159,8 @@ def overlay_images(ax, aspect, origin, imgs2d, channels, cmaps, alphas,
         vmaxs: A list of vmaxs for each image; defaults to None to use 
             :attr:``config.vmax_overview`` for the first image and None 
             for all others.
+        ignore_invis (bool): True to avoid creating ``AxesImage`` objects
+            for images that would be invisible; defaults to False.
     
     Returns:
         Nested list containing a list of ``AxesImage`` objects 
@@ -219,7 +223,7 @@ def fill(fill_with, chls, filled=None, pad=None):
         ax_img = imshow_multichannel(
             ax, img, channels[i], cmap, aspect, alphas[i], vmin=vmins[i], 
             vmax=vmaxs[i], origin=origin, interpolation="none",
-            norms=norm, nan_color=nan_color)
+            norms=norm, nan_color=nan_color, ignore_invis=ignore_invis)
         ax_imgs.append(ax_img)
     return ax_imgs