From a9f204268d5047578a368dad8b7b436e537cdefa Mon Sep 17 00:00:00 2001
From: Martin Chase <outofculture@gmail.com>
Date: Tue, 24 Sep 2024 11:00:42 -0700
Subject: [PATCH] add ctrl-c/v to copy the selected mask into the current layer

---
 cellpose/gui/gui3d.py                    | 24 ++++++++++++++++++++++++
 cellpose/gui/guihelpwindowtext.html      | 10 +++++++++-
 cellpose/gui/guitrainhelpwindowtext.html |  6 +++---
 3 files changed, 36 insertions(+), 4 deletions(-)

diff --git a/cellpose/gui/gui3d.py b/cellpose/gui/gui3d.py
index 8a3f9eea..ecb94751 100644
--- a/cellpose/gui/gui3d.py
+++ b/cellpose/gui/gui3d.py
@@ -1,6 +1,7 @@
 """
 Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
+from itertools import zip_longest
 
 import sys, os, pathlib, warnings, datetime, time
 
@@ -629,6 +630,29 @@ def keyPressEvent(self, event):
         if event.key() == QtCore.Qt.Key_Minus or event.key() == QtCore.Qt.Key_Equal:
             self.p0.keyPressEvent(event)
 
+        if event.modifiers() & QtCore.Qt.ControlModifier and self.selected > 0:
+            if event.key() == QtCore.Qt.Key_V:
+                self._copySelectedMaskIntoLayer(previous=False)
+            elif event.key() == QtCore.Qt.Key_C:
+                self._copySelectedMaskIntoLayer(previous=True)
+
+            self.update_plot()
+            self.draw_layer()
+            self.update_layer()
+
+    def _copySelectedMaskIntoLayer(self, previous: bool):
+        first = tuple(range(self.currentZ + 1, self.NZ))
+        second = tuple(range(self.currentZ - 1, -1, -1))
+        if previous:
+            first, second = second, first
+        zipped = zip_longest(first, second, fillvalue=None)
+        search = [item for sublist in zipped for item in sublist if item is not None]
+        for z in search:
+            selected = self.cellpix[z] == self.selected
+            if np.any(selected):
+                self.cellpix[self.currentZ][selected] = self.selected
+                break
+
     def update_ztext(self):
         zpos = self.currentZ
         try:
diff --git a/cellpose/gui/guihelpwindowtext.html b/cellpose/gui/guihelpwindowtext.html
index 4ca5d209..e5550efd 100644
--- a/cellpose/gui/guihelpwindowtext.html
+++ b/cellpose/gui/guihelpwindowtext.html
@@ -63,6 +63,14 @@
             <td>CTRL+Z</td>
             <td>undo previously drawn mask/stroke</td>
         </tr>
+        <tr>
+            <td>CTRL+C</td>
+            <td>(3D only) Copy the selected mask into the current layer, using the nearest containing layer
+                (preferring previous layers to later)</td>
+        </tr>
+        <tr>
+            <td>CTRL+V</td>
+            <td>(3D only) As CTRL+C, but preferring subsequent layers to previous ones.</td>
         <tr>
             <td>CTRL+Y</td>
             <td>undo remove mask</td>
@@ -105,7 +113,7 @@
         </tr>
         <tr>
             <td>A/D or LEFT/RIGHT</td>
-            <td>cycle through images in current directory</td>
+            <td>cycle through images in current directory/Z-stack</td>
         </tr>
         <tr>
             <td>W/S or UP/DOWN</td>
diff --git a/cellpose/gui/guitrainhelpwindowtext.html b/cellpose/gui/guitrainhelpwindowtext.html
index f1983591..5359a978 100644
--- a/cellpose/gui/guitrainhelpwindowtext.html
+++ b/cellpose/gui/guitrainhelpwindowtext.html
@@ -5,9 +5,9 @@
         <li>Run the built-in models on one of the images using the "model zoo" and find the one that works best for your
             data. Make sure that if you have a nuclear channel you have selected it for CHAN2.
         </li>
-        <li>Fix the labelling by drawing new ROIs (right-click) and deleting incorrect ones (CTRL+click). The GUI
-            autosaves any manual changes (but does not autosave after running the model, for that click CTRL+S). The
-            segmentation is saved in a "_seg.npy" file.
+        <li>Fix the labelling by drawing new ROIs (right-click) and deleting incorrect ones (CTRL+click). See general
+            GUI Help page for more keybindings. The GUI autosaves any manual changes (but does not autosave after
+            running the model, for that click CTRL+S). The segmentation is saved in a "_seg.npy" file.
         </li>
         <li> Go to the "Models" menu in the File bar at the top and click "Train new model..." or use shortcut CTRL+T.
         </li>