Merge branch 'main' of https://github.com/AdaptiveMotorControlLab/CellSeg3d into v0.0.1rc3

Author: MMathisLab

napari_cellseg3d/interface.py

@@ -2,6 +2,7 @@
 from typing import Union
 from typing import List
 
+
 from qtpy.QtCore import Qt
 from qtpy.QtCore import QUrl
 from qtpy.QtGui import QDesktopServices

napari_cellseg3d/log_utility.py

@@ -1,5 +1,7 @@
 import threading
+import warnings
 
+from qtpy import QtCore
 from qtpy.QtGui import QTextCursor
 from qtpy.QtWidgets import QTextEdit
 
@@ -22,23 +24,66 @@ def __init__(self, parent):
 
     # def receive_log(self, text):
     #     self.print_and_log(text)
+    def write(self, message):
+        self.lock.acquire()
+        try:
+            if not hasattr(self, "flag"):
+                self.flag = False
+            message = message.replace("\r", "").rstrip()
+            if message:
+                method = "replace_last_line" if self.flag else "append"
+                QtCore.QMetaObject.invokeMethod(
+                    self,
+                    method,
+                    QtCore.Qt.QueuedConnection,
+                    QtCore.Q_ARG(str, message),
+                )
+                self.flag = True
+            else:
+                self.flag = False
+
+        finally:
+            self.lock.release()
 
-    def print_and_log(self, text):
+    @QtCore.Slot(str)
+    def replace_last_line(self, text):
+        self.lock.acquire()
+        try:
+            cursor = self.textCursor()
+            cursor.movePosition(QTextCursor.End)
+            cursor.select(QTextCursor.BlockUnderCursor)
+            cursor.removeSelectedText()
+            cursor.insertBlock()
+            self.setTextCursor(cursor)
+            self.insertPlainText(text)
+        finally:
+            self.lock.release()
+
+    def print_and_log(self, text, printing=True):
         """Utility used to both print to terminal and log text to a QTextEdit
          item in a thread-safe manner. Use only for important user info.
 
         Args:
             text (str): Text to be printed and logged
+            printing (bool): Whether to print the message as well or not using print(). Defaults to True.
 
         """
         self.lock.acquire()
         try:
-            print(text)
-            # causes issue if you clik on terminal (tied to CMD QuickEdit mode)
+            if printing:
+                print(text)
+            # causes issue if you clik on terminal (tied to CMD QuickEdit mode on Windows)
             self.moveCursor(QTextCursor.End)
             self.insertPlainText(f"\n{text}")
             self.verticalScrollBar().setValue(
                 self.verticalScrollBar().maximum()
             )
         finally:
             self.lock.release()
+
+    def warn(self, warning):
+        self.lock.acquire()
+        try:
+            warnings.warn(warning)
+        finally:
+            self.lock.release()

napari_cellseg3d/model_framework.py

@@ -15,7 +15,7 @@
 from napari_cellseg3d.models import model_SegResNet as SegResNet
 from napari_cellseg3d.models import model_TRAILMAP as TRAILMAP
 from napari_cellseg3d.models import model_VNet as VNet
-from napari_cellseg3d.models import TRAILMAP_MS as TMAP
+from napari_cellseg3d.models import model_TRAILMAP_MS as TRAILMAP_MS
 from napari_cellseg3d.plugin_base import BasePluginFolder
 
 warnings.formatwarning = utils.format_Warning
@@ -62,8 +62,8 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
         self.models_dict = {
             "VNet": VNet,
             "SegResNet": SegResNet,
-            "TRAILMAP pre-trained": TRAILMAP,
-            "TRAILMAP_MS": TMAP,
+            "TRAILMAP": TRAILMAP,
+            "TRAILMAP_MS": TRAILMAP_MS,
         }
         """dict: dictionary of available models, with string for widget display as key