Merge pull request #1431 from MouseLand/imagedraw_fixes

Imagedraw fixes & update logging

Author: carsen-stringer

cellpose/__init__.py

@@ -1 +1,5 @@
 from cellpose.version import version, version_str
+import logging
+
+# set base `cellpose` logger
+logging.getLogger(__name__).addHandler(logging.NullHandler())

cellpose/gui/gui.py

@@ -2,6 +2,7 @@
 Copyright © 2025 Howard Hughes Medical Institute, Authored by Carsen Stringer, Michael Rariden and Marius Pachitariu.
 """
 
+import logging
 import sys, os, pathlib, warnings, datetime, time, copy
 
 from qtpy import QtGui, QtCore
@@ -138,7 +139,7 @@ def make_cmap(cm=0):
 
 def run(image=None):
     from ..io import logger_setup
-    logger, log_file = logger_setup()
+    logger_setup()
     # Always start by initializing Qt (only once per application)
     warnings.filterwarnings("ignore")
     app = QApplication(sys.argv)
@@ -166,7 +167,7 @@ def run(image=None):
     app.setWindowIcon(app_icon)
     app.setStyle("Fusion")
     app.setPalette(guiparts.DarkPalette())
-    MainW(image=image, logger=logger)
+    MainW(image=image, logger=logging.getLogger(__name__))
     ret = app.exec_()
     sys.exit(ret)
 
@@ -1242,7 +1243,7 @@ def remove_single_cell(self, idx):
         self.ismanual = np.delete(self.ismanual, idx - 1)
         self.cellcolors = np.delete(self.cellcolors, [idx], axis=0)
         del self.zdraw[idx - 1]
-        print("GUI_INFO: removed cell %d" % (idx - 1))
+        self.logger.info(f'removed cell {idx-1}')
 
     def remove_region_cells(self):
         if self.removing_cells_list:

cellpose/gui/guiparts.py

@@ -8,6 +8,8 @@
 import numpy as np
 import pathlib, os
 
+from cellpose.gui.io import _save_sets
+
 
 def stylesheet():
     return """
@@ -628,8 +630,11 @@ def __init__(self, image=None, viewbox=None, parent=None, **kargs):
         self.parent.in_stroke = False
 
     def mouseClickEvent(self, ev):
-        if (self.parent.masksOn or
-                self.parent.outlinesOn) and not self.parent.removing_region:
+        if not (self.parent.masksOn or
+                self.parent.outlinesOn) and self.parent.removing_region:
+            return
+
+        try:
             is_right_click = ev.button() == QtCore.Qt.RightButton
             if self.parent.loaded \
                     and (is_right_click or ev.modifiers() & QtCore.Qt.ShiftModifier and not ev.double())\
@@ -665,9 +670,12 @@ def mouseClickEvent(self, ev):
                                 else:
                                     self.parent.select_cell_multi(idx)
                                     self.parent.removing_cells_list.append(idx)
-
                         elif self.parent.masksOn and not self.parent.deleting_multiple:
                             self.parent.unselect_cell()
+        except Exception as err:
+            print('Error encountered while drawing. Saving masks and exiting...')
+            _save_sets(self.parent)
+            raise(err)
 
     def mouseDragEvent(self, ev):
         ev.ignore()
@@ -713,7 +721,9 @@ def is_at_start(self, pos):
                 return False
 
     def end_stroke(self):
-        self.parent.p0.removeItem(self.scatter)
+        if hasattr(self, 'scatter') and self.scatter is not None:
+            if self.scatter.scene() == self.parent.layer.scene():
+                self.parent.p0.removeItem(self.scatter)
         if not self.parent.stroke_appended:
             self.parent.strokes.append(self.parent.current_stroke)
             self.parent.stroke_appended = True

cellpose/gui/io.py

@@ -170,7 +170,7 @@ def _initialize_images(parent, image, load_3D=False):
     load_3D = parent.load_3D if load_3D is False else load_3D
 
     parent.stack = image
-    print(f"GUI_INFO: image shape: {image.shape}")
+    parent.logger.info(f" : image shape: {image.shape}")
     if load_3D:
         parent.NZ = len(parent.stack)
         parent.scroll.setMaximum(parent.NZ - 1)
@@ -187,7 +187,7 @@ def _initialize_images(parent, image, load_3D=False):
     parent.stack *= 255
 
     if load_3D:
-        print("GUI_INFO: converted to float and normalized values to 0.0->255.0")
+        parent.logger.info(": converted to float and normalized values to 0.0->255.0")
 
     del image
     gc.collect()
@@ -205,13 +205,15 @@ def _initialize_images(parent, image, load_3D=False):
         parent.Lyr, parent.Lxr = parent.Ly, parent.Lx
     parent.clear_all()
 
+    if not hasattr(parent, "stack_filtered") and parent.restore:
+        parent.logger.info(": no 'img_restore' found, applying current settings")
+        parent.compute_restore()
+
     if parent.autobtn.isChecked():
         if parent.restore is None or parent.restore != "filter":
-            print(
-                "GUI_INFO: normalization checked: computing saturation levels (and optionally filtered image)"
-            )
+            parent.logger.info(": normalization checked: computing saturation levels (and optionally filtered image)")
             parent.compute_saturation()
-
+    
     parent.compute_scale()
     parent.track_changes = []
 
@@ -312,7 +314,7 @@ def _load_seg(parent, filename=None, image=None, image_file=None, load_3D=False)
 
         if "manual_changes" in dat:
             parent.track_changes = dat["manual_changes"]
-            print("GUI_INFO: loaded in previous changes")
+            parent.logger.info("loaded in previous changes")
         if "zdraw" in dat:
             parent.zdraw = dat["zdraw"]
         else:
@@ -398,7 +400,7 @@ def _masks_to_gui(parent, masks, outlines=None, colors=None):
     # get unique values
     shape = masks.shape
     if len(fastremap.unique(masks)) != masks.max() + 1:
-        print("GUI_INFO: renumbering masks")
+        parent.logger.info("renumbering masks")
         fastremap.renumber(masks, in_place=True)
         outlines = None
         masks = masks.reshape(shape)
@@ -423,7 +425,7 @@ def _masks_to_gui(parent, masks, outlines=None, colors=None):
             if parent.cellpix_orig.ndim == 2:
                 parent.cellpix_orig = parent.cellpix_orig[np.newaxis, :, :]
 
-    print(f"GUI_INFO: {masks.max()} masks found")
+    parent.logger.info(f"{masks.max()} masks found")
 
     # get outlines
     if outlines is None:  # parent.outlinesOn
@@ -437,7 +439,7 @@ def _masks_to_gui(parent, masks, outlines=None, colors=None):
                 outlines = masks_to_outlines(parent.cellpix_orig[z])
                 parent.outpix_orig[z] = outlines * parent.cellpix_orig[z]
             if z % 50 == 0 and parent.NZ > 1:
-                print("GUI_INFO: plane %d outlines processed" % z)
+                parent.logger.info("plane %d outlines processed" % z)
         if parent.restore and "upsample" in parent.restore:
             parent.outpix_resize = parent.outpix.copy()
     else:
@@ -449,7 +451,7 @@ def _masks_to_gui(parent, masks, outlines=None, colors=None):
                 outlines = masks_to_outlines(parent.cellpix_orig[z])
                 parent.outpix_orig[z] = outlines * parent.cellpix_orig[z]
                 if z % 50 == 0 and parent.NZ > 1:
-                    print("GUI_INFO: plane %d outlines processed" % z)
+                    parent.logger.info("plane %d outlines processed" % z)
 
     if parent.outpix.ndim == 2:
         parent.outpix = parent.outpix[np.newaxis, :, :]
@@ -461,7 +463,7 @@ def _masks_to_gui(parent, masks, outlines=None, colors=None):
 
     parent.ncells.set(parent.cellpix.max())
     colors = parent.colormap[:parent.ncells.get(), :3] if colors is None else colors
-    print("GUI_INFO: creating cellcolors and drawing masks")
+    parent.logger.info("creating cellcolors and drawing masks")
     parent.cellcolors = np.concatenate((np.array([[255, 255, 255]]), colors),
                                        axis=0).astype(np.uint8)
     if parent.ncells > 0:
@@ -483,28 +485,28 @@ def _save_png(parent):
     base = os.path.splitext(filename)[0]
     if parent.NZ == 1:
         if parent.cellpix[0].max() > 65534:
-            print("GUI_INFO: saving 2D masks to tif (too many masks for PNG)")
+            parent.logger.info("saving 2D masks to tif (too many masks for PNG)")
             imsave(base + "_cp_masks.tif", parent.cellpix[0])
         else:
-            print("GUI_INFO: saving 2D masks to png")
+            parent.logger.info("saving 2D masks to png")
             imsave(base + "_cp_masks.png", parent.cellpix[0].astype(np.uint16))
     else:
-        print("GUI_INFO: saving 3D masks to tiff")
+        parent.logger.info("saving 3D masks to tiff")
         imsave(base + "_cp_masks.tif", parent.cellpix)
 
 
 def _save_flows(parent):
     """ save flows and cellprob to tiff """
     filename = parent.filename
     base = os.path.splitext(filename)[0]
-    print("GUI_INFO: saving flows and cellprob to tiff")
+    parent.logger.info("saving flows and cellprob to tiff")
     if len(parent.flows) > 0:
         imsave(base + "_cp_cellprob.tif", parent.flows[1])
         for i in range(3):
             imsave(base + f"_cp_flows_{i}.tif", parent.flows[0][..., i])
         if len(parent.flows) > 2:
             imsave(base + "_cp_flows.tif", parent.flows[2])
-        print("GUI_INFO: saved flows and cellprob")
+        parent.logger.info("saved flows and cellprob")
     else:
         print("ERROR: no flows or cellprob found")
 
@@ -620,7 +622,7 @@ def _save_sets(parent):
             dat["img_restore"] = parent.stack_filtered
     try:
         np.save(base + "_seg.npy", dat)
-        print("GUI_INFO: %d ROIs saved to %s" % (parent.ncells.get(), base + "_seg.npy"))
+        parent.logger.info("%d ROIs saved to %s" % (parent.ncells.get(), base + "_seg.npy"))
     except Exception as e:
         print(f"ERROR: {e}")
     del dat

cellpose/io.py

@@ -81,18 +81,30 @@ def logger_setup(cp_path=".cellpose", logfile_name="run.log", stdout_file_replac
         log_file.unlink()
     except:
         print('creating new log file')
-    handlers = [logging.FileHandler(log_file),]
+    logfile_fh = logging.FileHandler(log_file)
     if stdout_file_replacement is not None:
-        handlers.append(logging.FileHandler(stdout_file_replacement))
+        stdout_fh = logging.FileHandler(stdout_file_replacement)
     else:
-        handlers.append(logging.StreamHandler(sys.stdout))
-    logging.basicConfig(
-                    level=logging.INFO,
-                    format="%(asctime)s [%(levelname)s] %(message)s",
-                    handlers=handlers,
-                    force=True
-    )
-    logger = logging.getLogger(__name__)
+        stdout_fh = logging.StreamHandler(sys.stdout)
+
+    formatter = logging.Formatter("%(asctime)s [%(module)s %(levelname)s] %(message)s")
+    debug_formatter = logging.Formatter("%(asctime)s %(levelname)s [%(filename)s:%(lineno)d - %(funcName)20s()] %(message)s")
+    logger = logging.getLogger('cellpose')
+    logger.setLevel(logging.INFO)
+    logger.handlers.clear()
+
+    logfile_fh.setFormatter(debug_formatter)
+    logfile_fh.setLevel(logging.DEBUG)
+    logger.addHandler(logfile_fh)
+
+    stdout_fh.setFormatter(formatter)
+    stdout_fh.setLevel(logging.INFO)
+    logger.addHandler(stdout_fh)
+
+    logger.propagate = False
+
+    print(f"[GUI INFO] : WRITING LOG OUTPUT TO {log_file}")
+    print(version_str)
     logger.info(f"WRITING LOG OUTPUT TO {log_file}")
     logger.info(version_str)