45 Move the view of the viewbox to a given position

cellpose/gui/gui.py

@@ -366,6 +366,48 @@ def minimap_closed(self):
         if hasattr(self, 'minimap'):
             del self.minimap
 
+    def center_view_on_position(self, normalized_x, normalized_y):
+        """
+        Centers the view on the given normalized coordinates (x, y).
+        This will be used to navigate using the minimap window.
+        The zoom level will be maintained.
+
+        Args:
+            normalized_x (float): Normalized x-coordinate (0.0 to 1.0).
+            normalized_y (float): Normalized y-coordinate (0.0 to 1.0).
+        """
+        # Get the size of the image
+        img_height = self.img.image.shape[0]
+        img_width = self.img.image.shape[1]
+
+        # Calculate the actual pixel coordinates
+        target_x = normalized_x * img_width
+        target_y = normalized_y * img_height
+
+        # Get the current view range of the viewbox.
+        # This tells us which part of the image is currently displayed.
+        view_range = self.p0.viewRange()
+
+        # Extract the x and y ranges
+        x_range = view_range[0]
+        y_range = view_range[1]
+
+        # Calculate the current zoom level
+        zoom_x = (x_range[1] - x_range[0]) / img_width
+        zoom_y = (y_range[1] - y_range[0]) / img_height
+
+        # Calculate the width and height of the view range based on the zoom level
+        view_width = img_width * zoom_x
+        view_height = img_height * zoom_y
+
+        # Calculate the new view range, centered on the target position
+        new_x_range = [target_x - view_width / 2, target_x + view_width / 2]
+        new_y_range = [target_y - view_height / 2, target_y + view_height / 2]
+
+        # Set the new view range to the ViewBox
+        self.p0.setXRange(*new_x_range, padding=0)
+        self.p0.setYRange(*new_y_range, padding=0)
+
 
     def make_buttons(self):
         self.boldfont = QtGui.QFont("Arial", 11, QtGui.QFont.Bold)
@@ -1833,7 +1875,7 @@ def update_plot(self):
 
         self.win.show()
         self.show()
-        
+
 
     def update_layer(self):
         if self.masksOn or self.outlinesOn:

cellpose/gui/io.py

@@ -10,7 +10,7 @@
 import logging
 import fastremap
 
-from ..io import imread, imsave, outlines_to_text, add_model, remove_model, save_rois
+from ..io import imread, imsave, outlines_to_text, add_model, remove_model, save_rois, save_settings
 from ..models import normalize_default, MODEL_DIR, MODEL_LIST_PATH, get_user_models
 from ..utils import masks_to_outlines, outlines_list
 from . import guiparts, gui
@@ -619,6 +619,15 @@ def _save_outlines(parent):
     else:
         print("ERROR: cannot save 3D outlines")
 
+def _save_settings(parent):
+    """ save settings to json file"""
+    filename = parent.filename
+    base = os.path.splitext(filename)[0]
+    if parent.NZ == 1:
+        print("GUI_INFO: saving Settings to json file")
+        save_settings(parent.filename)
+    else:
+        print("ERROR: cannot save settings")
 
 def _save_sets_with_check(parent):
     """ Save masks and update *_seg.npy file. Use this function when saving should be optional

cellpose/gui/menus.py

@@ -78,7 +78,13 @@ def mainmenu(parent):
     parent.minimapWindow.setChecked(False)
     parent.minimapWindow.triggered.connect(parent.minimap_window)
     file_menu.addAction(parent.minimapWindow)
-
+
+    parent.saveSettings = QAction("Save Settings as .&json", parent)
+    parent.saveSettings.setShortcut("Ctrl+J")
+    parent.saveSettings.triggered.connect(lambda: io._save_settings(parent))
+    file_menu.addAction(parent.saveSettings)
+    parent.saveSettings.setEnabled(True)
+
 def editmenu(parent):
     main_menu = parent.menuBar()
     edit_menu = main_menu.addMenu("&Edit")
@@ -155,5 +161,3 @@ def helpmenu(parent):
     openTrainHelp = QAction("Training instructions", parent)
     openTrainHelp.triggered.connect(parent.train_help_window)
     help_menu.addAction(openTrainHelp)
-
-

cellpose/io.py

@@ -1,7 +1,7 @@
 """
 Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
-
+import json
 import os, datetime, gc, warnings, glob, shutil
 from natsort import natsorted
 import numpy as np
@@ -590,7 +590,20 @@ def save_rois(masks, file_name):
 
     roiwrite(file_name, rois)
 
+def save_settings(file_name):
+    """ save settings to .json file and remove if it already exists
+
+    Args:
+        file_name (str): name to save the .json file to
 
+    Returns:
+        None
+    """
+    file_name = os.path.splitext(file_name)[0] + "_cp_settings.json"
+    if os.path.exists(file_name):
+        os.remove(file_name)
+    with open(file_name, 'w') as f:
+        json.dump({}, f)
 
 def save_masks(images, masks, flows, file_names, png=True, tif=False, channels=[0, 0],
                suffix="", save_flows=False, save_outlines=False,