add the ability to insert a tile post-stitching

this is ... mostly successful. the patch-up tiles have to have
"roughly" the same 0,0 coordinate for anything to work, but it
seems to have worked on at least a couple of cases

schema.py

@@ -160,7 +160,13 @@ def add_tile(self, fpath, max_x = None, max_y = None):
         self.schema['tiles'][str(self.auto_index)] = tile
         self.log_to_undo('add', self.auto_index, {})
         self.auto_index += 1
-        self.coords_mm += [(metadata['x'], metadata['y'])]
+
+        if type(self.coords_mm) == np.ndarray:
+            # handle case that the coords_mm variable has been transformed into a numpy array, which
+            # overloads `+` to mean "add these numbers to every offset of the array" versus "append"
+            self.coords_mm = np.concatenate((self.coords_mm, [[metadata['x'], metadata['y']]]))
+        else:
+            self.coords_mm += [(metadata['x'], metadata['y'])]
 
     def contains_layer(self, layer):
         return self.schema['tiles'].get(str(layer)) is not None
@@ -238,6 +244,8 @@ def finalize(self):
         if x_res * THUMB_SCALE < THUMB_THRESHOLD_PX \
         or y_res * THUMB_SCALE < THUMB_THRESHOLD_PX:
             THUMB_SCALE = 1.0
+        # ensure auto-add index doesn't overwrite an existing tile.
+        self.auto_index = int(max(self.schema['tiles'].keys())) + 1
 
     def closest_tile_to_coord_mm(self, coord_um):
         offset_coords_mm = []
@@ -274,8 +282,7 @@ def remove_tile(self, layer):
         assert len(new_coords_mm) == len(self.coords_mm) - 1, "Did not remove exactly one element from coords_mm"
         self.coords_mm = new_coords_mm
         # regenerate convenience lists
-        self.x_list = np.unique(np.rot90(self.coords_mm)[1])
-        self.y_list = np.unique(np.rot90(self.coords_mm)[0])
+        self.finalize()
 
     def get_tile_by_coordinate(self, coord):
         for (layer, t) in self.schema['tiles'].items():

stitch.py

@@ -2,16 +2,17 @@
 
 import argparse
 from pathlib import Path
+from shutil import copyfile
 import logging
 import sys
 import threading
 
 from PyQt5.QtCore import QTimer, Qt
 from PyQt5.QtGui import QMouseEvent
-from PyQt5.QtWidgets import (QLabel, QApplication, QWidget, QDesktopWidget,
-                             QCheckBox, QMessageBox, QMainWindow, QPushButton,
+from PyQt5.QtWidgets import (QLabel, QApplication, QWidget, QFileDialog,
+                             QCheckBox, QMainWindow, QPushButton,
                              QComboBox, QSlider, QGroupBox, QGridLayout, QBoxLayout,
-                             QHBoxLayout, QVBoxLayout, QMenu, QAction, QFrame,
+                             QHBoxLayout, QVBoxLayout,
                              QSizePolicy, QFormLayout, QLineEdit, QSpinBox)
 
 from schema import Schema
@@ -171,6 +172,8 @@ def __init__(self):
         self.status_mse_visualize_button.clicked.connect(self.on_mse_visualize)
         self.status_remove_tile_button = QPushButton("Remove Selected")
         self.status_remove_tile_button.clicked.connect(self.on_remove_selected)
+        self.status_patch_tile_button = QPushButton("Add Tile")
+        self.status_patch_tile_button.clicked.connect(self.on_patch_tile)
         self.status_undo_button = QPushButton("Undo")
         self.status_undo_button.clicked.connect(self.on_undo_button)
         status_overall_layout.addWidget(self.status_redraw_button)
@@ -184,6 +187,7 @@ def __init__(self):
         status_overall_layout.addWidget(self.status_restitch_selection_button)
         status_overall_layout.addWidget(self.status_flag_manual_review_button)
         status_overall_layout.addWidget(self.status_remove_tile_button)
+        status_overall_layout.addWidget(self.status_patch_tile_button)
         status_overall_layout.addWidget(self.status_undo_button)
         status_overall_layout.addStretch()
         status_overall_layout.addWidget(self.status_save_button)
@@ -281,11 +285,26 @@ def on_flag_manual_review(self):
     def on_remove_selected(self):
         self.schema.set_undo_checkpoint()
         (layer, _tile) = self.schema.get_tile_by_coordinate(self.selected_image_centroid)
+        self.selected_image_centroid = None
         self.schema.remove_tile(layer)
         self.redraw_overview()
         if self.zoom_window_opened:
             self.update_zoom_window()
 
+    def on_patch_tile(self):
+        file_name = QFileDialog.getOpenFileName(self,
+            "Open Image", str(self.schema.path), "Image Files (*.png *.jpg *.bmp)")[0]
+        p = Path(file_name)
+        self.schema.add_tile(p)
+        if p.parent != self.schema.path.resolve():
+            copyfile(p, self.schema.path / p.name)
+        thumbnail_kernel(self.args, self.schema.path / p.name)
+        self.schema.finalize()
+        self.schema.set_undo_checkpoint()
+        self.redraw_overview()
+        if self.zoom_window_opened:
+            self.update_zoom_window()
+
     def on_redraw_button(self):
         self.redraw_overview()
         if self.zoom_window_opened:
@@ -479,6 +498,7 @@ def main():
 
     app = QApplication(sys.argv)
     w = MainWindow()
+    w.args = args
     w.setGeometry(200, 200, 2000, 2400)
 
     w.schema = Schema(use_cache=not args.no_caching)

template_stitch.py

@@ -1284,6 +1284,16 @@ def stitch_auto_template_linear(self, stitch_list=None, mse_cleanup=False):
     logging.info("Auto-stitch pass done")
     return restart
 
+def check_and_add_layer(layer, t, ref_layers):
+    if layer is not None:
+        if t['auto_error'] != 'false':
+            logging.warning(f"Skipping candidate layer {layer} because it has a bad stitch")
+        else:
+            ref_layers += [layer]
+        return True
+    else:
+        return False
+
 def restitch_one(self, moving_layer, mse_cleanup=False):
     self.schema.set_undo_checkpoint()
     # search for nearby tiles that have large overlaps and make them reference layers
@@ -1308,27 +1318,42 @@ def restitch_one(self, moving_layer, mse_cleanup=False):
     # katty corner back
     if next_lower_y_mm is not None and next_lower_x_mm is not None:
         (layer, t) = self.schema.get_tile_by_coordinate((next_lower_x_mm, next_lower_y_mm))
-        if layer is not None:
-            if t['auto_error'] != 'false':
-                logging.warning(f"Skipping candidate layer {layer} because it has a bad stitch")
-            else:
-                ref_layers += [layer]
+        if not check_and_add_layer(layer, t, ref_layers):
+            # this is likely a "patch" image that was taken in a different run; add a bunch of guesses nearby
+            if y_i > 1:
+                (layer, t) = self.schema.get_tile_by_coordinate((next_lower_x_mm, sorted_y[y_i - 2]))
+                check_and_add_layer(layer, t, ref_layers)
+            if y_i > 1 and x_i + 1 < len(sorted_x):
+                (layer, t) = self.schema.get_tile_by_coordinate((sorted_x[x_i + 1], sorted_y[y_i - 2]))
+                check_and_add_layer(layer, t, ref_layers)
+            if y_i + 2 < len(sorted_y):
+                (layer, t) = self.schema.get_tile_by_coordinate((next_lower_x_mm, sorted_y[y_i + 2]))
+                check_and_add_layer(layer, t, ref_layers)
+            if y_i + 2 < len(sorted_y) and x_i + 1 < len(sorted_x):
+                (layer, t) = self.schema.get_tile_by_coordinate((sorted_x[x_i + 1], sorted_y[y_i + 2]))
+                check_and_add_layer(layer, t, ref_layers)
     # up
     if next_lower_y_mm is not None:
         (layer, t) = self.schema.get_tile_by_coordinate((moving_x_mm, next_lower_y_mm))
-        if layer is not None:
-            if t['auto_error'] != 'false':
-                logging.warning(f"Skipping candidate layer {layer} because it has a bad stitch")
-            else:
-                ref_layers += [layer]
+        if not check_and_add_layer(layer, t, ref_layers):
+            # this is likely a "patch" image that was taken in a different run; add a bunch of guesses nearby
+            if x_i + 1 < len(sorted_x):
+                (layer, t) = self.schema.get_tile_by_coordinate((sorted_x[x_i + 1], next_lower_y_mm))
+                check_and_add_layer(layer, t, ref_layers)
+            if x_i - 1 > 0:
+                (layer, t) = self.schema.get_tile_by_coordinate((sorted_x[x_i - 1], next_lower_y_mm))
+                check_and_add_layer(layer, t, ref_layers)
     # left
     if next_lower_x_mm is not None:
         (layer, t) = self.schema.get_tile_by_coordinate((next_lower_x_mm, moving_y_mm))
-        if layer is not None:
-            if t['auto_error'] != 'false':
-                logging.warning(f"Skipping candidate layer {layer} because it has a bad stitch")
-            else:
-                ref_layers += [layer]
+        if not check_and_add_layer(layer, t, ref_layers):
+            # this is likely a "patch" image that was taken in a different run; add a bunch of guesses nearby
+            if y_i + 1 < len(sorted_y):
+                (layer, t) = self.schema.get_tile_by_coordinate((next_lower_x_mm, sorted_y[y_i + 1]))
+                check_and_add_layer(layer, t, ref_layers)
+            if y_i - 1 < 0:
+                (layer, t) = self.schema.get_tile_by_coordinate((next_lower_x_mm, sorted_y[y_i - 1]))
+                check_and_add_layer(layer, t, ref_layers)
 
     self.stitch_one_template(
         self.schema,