Merge branch '30_new_export_option_.csv'

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, save_settings
+from ..io import imread, imsave, outlines_to_text, add_model, remove_model, save_rois, save_settings, save_features_csv
 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
@@ -570,6 +570,27 @@ def _masks_to_gui(parent, masks, outlines=None, colors=None):
     else:
         parent.ViewDropDown.setCurrentIndex(0)
 
+def _save_features_csv(parent):
+    """
+    Saves features to CSV if dataset is 2D.
+
+    Args:
+        parent: GUI object with filename and NZ attributes.
+    """
+
+    # check if a file is loaded, if not, print an error message and return
+    if not parent.filename:
+        print("ERROR: No file loaded. Please load a file before attempting to save features.")
+        return
+
+    filename = parent.filename
+    base = os.path.splitext(filename)[0] + "_features.csv"
+    # check if the dataset is 2D (NZ == 1 implies a single z-layer)
+    if parent.NZ == 1:
+        print("GUI_INFO: saving features to CSV file")
+        save_features_csv(parent.filename)
+    else:
+        print("ERROR: cannot save features")
 
 def _save_png(parent):
     """ save masks to png or tiff (if 3D) """

cellpose/gui/menus.py

@@ -77,6 +77,17 @@ def mainmenu(parent):
     file_menu.addAction(parent.saveSettings)
     parent.saveSettings.setEnabled(True)
 
+    """
+    This adds a new menu item for saving features as a .csv file. 
+    The user can activate this function to export specific data directly from the GUI.
+    The function `_save_features_as_csv` from the `io` module is called when the user clicks on the menu item.
+    """
+    parent.saveFeaturesCsv = QAction("Save Features as .&csv", parent)
+    parent.saveFeaturesCsv.setShortcut("Ctrl+Shift+C")
+    parent.saveFeaturesCsv.triggered.connect(lambda: io._save_features_csv(parent))
+    file_menu.addAction(parent.saveFeaturesCsv)
+    parent.saveFeaturesCsv.setEnabled(True)
+
     """
     This creates a new menu item for the minimap that the user can activate.
     It is deactivated by default and has to be checked.

cellpose/io.py

@@ -13,6 +13,7 @@
 import re
 from . import version_str
 from roifile import ImagejRoi, roiwrite
+import csv
 
 try:
     from qtpy import QtGui, QtCore, Qt, QtWidgets
@@ -560,6 +561,22 @@ def masks_flows_to_seg(images, masks, flows, file_names, diams=30., channels=Non
 
     np.save(base + "_seg.npy", dat)
 
+def save_features_csv(file_name):
+    """
+    Save features to .csv file and remove if it already exists
+    Args:
+        file_name (str): Target CSV file name
+
+    Returns:
+        None
+    """
+    file_name = os.path.splitext(file_name)[0] + "_cp_features.csv"
+    if os.path.exists(file_name):
+        os.remove(file_name)
+    with open(file_name, mode='w', newline='') as f:
+        # creating an empty csv file or clearing the existing one
+        pass
+
 def save_to_png(images, masks, flows, file_names):
     """ deprecated (runs io.save_masks with png=True)