nettracer3d 1.1.0__tar.gz → 1.1.1__tar.gz

{nettracer3d-1.1.0/src/nettracer3d.egg-info → nettracer3d-1.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 1.1.0
+Version: 1.1.1
 Summary: Scripts for intializing and analyzing networks from segmentations of three dimensional images.
 Author-email: Liam McLaughlin <liamm@wustl.edu>
 Project-URL: Documentation, https://nettracer3d.readthedocs.io/en/latest/
@@ -110,6 +110,6 @@ McLaughlin, L., Zhang, B., Sharma, S. et al. Three dimensional multiscalar neuro
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 1.1.0 Updates --
+-- Version 1.1.1 Updates --
 
-	* Bug Fix
+	* Can now intermittently downsample while making the network and id overlays now to make their relevant elements larger in the actual rendered output.

{nettracer3d-1.1.0 → nettracer3d-1.1.1}/README.md

@@ -65,6 +65,6 @@ McLaughlin, L., Zhang, B., Sharma, S. et al. Three dimensional multiscalar neuro
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 1.1.0 Updates --
+-- Version 1.1.1 Updates --
 
-	* Bug Fix
+	* Can now intermittently downsample while making the network and id overlays now to make their relevant elements larger in the actual rendered output.

{nettracer3d-1.1.0 → nettracer3d-1.1.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "1.1.0"
+version = "1.1.1"
 authors = [
   { name="Liam McLaughlin", email="liamm@wustl.edu" },
 ]

{nettracer3d-1.1.0 → nettracer3d-1.1.1}/src/nettracer3d/nettracer_gui.py

@@ -4876,8 +4876,11 @@ class ImageViewerWindow(QMainWindow):
             self.cellpose_launcher.launch_cellpose_gui(use_3d = use_3d)
 
         except:
-            import traceback
-            print(traceback.format_exc())
+            QMessageBox.critical(
+                self,
+                "Error",
+                f"Error starting cellpose: {str(e)}\nNote: You may need to install cellpose with corresponding torch first - in your environment, please call 'pip install cellpose'. Please see: 'https://pytorch.org/get-started/locally/' to see what torch install command corresponds to your NVIDIA GPU"
+            )
             pass
 
 
@@ -8673,6 +8676,11 @@ class Show3dDialog(QDialog):
             self.accept()
 
         except Exception as e:
+            QMessageBox.critical(
+                self,
+                "Error",
+                f"Error showing 3D: {str(e)}\nNote: You may need to install napari first - in your environment, please call 'pip install napari'"
+            )
             print(f"Error: {e}")
             import traceback
             print(traceback.format_exc())
@@ -8688,6 +8696,9 @@ class NetOverlayDialog(QDialog):
 
         layout = QFormLayout(self)
 
+        self.downsample = QLineEdit("")
+        layout.addRow("Downsample Factor While Drawing? (Int - Makes the outputted lines larger):", self.downsample)
+
         # Add Run button
         run_button = QPushButton("Generate (Will go to Overlay 1)")
         run_button.clicked.connect(self.netoverlay)
@@ -8704,7 +8715,16 @@ class NetOverlayDialog(QDialog):
             if my_network.node_centroids is None:
                 return
 
-            my_network.network_overlay = my_network.draw_network()
+            try:
+                downsample = float(self.downsample.text()) if self.downsample.text() else None
+            except ValueError:
+                downsample = None
+
+            my_network.network_overlay = my_network.draw_network(down_factor = downsample)
+
+            if downsample is not None: 
+                my_network.network_overlay = n3d.upsample_with_padding(my_network.network_overlay, original_shape = self.parent().shape)
+
 
             self.parent().load_channel(2, channel_data = my_network.network_overlay, data = True, preserve_zoom = (self.parent().ax.get_xlim(), self.parent().ax.get_ylim()))
 
@@ -8731,6 +8751,9 @@ class IdOverlayDialog(QDialog):
         self.mode_selector.setCurrentIndex(0)  # Default to Mode 1
         layout.addRow("Execution Mode:", self.mode_selector)
 
+        self.downsample = QLineEdit("")
+        layout.addRow("Downsample Factor While Drawing? (Int - Makes the outputted numbers larger):", self.downsample)
+
         # Add Run button
         run_button = QPushButton("Generate (Will go to Overlay 2)")
         run_button.clicked.connect(self.idoverlay)
@@ -8740,6 +8763,11 @@ class IdOverlayDialog(QDialog):
 
         accepted_mode = self.mode_selector.currentIndex()
 
+        try:
+            downsample = float(self.downsample.text()) if self.downsample.text() else None
+        except ValueError:
+            downsample = None
+
         if accepted_mode == 0:
 
             if my_network.node_centroids is None:
@@ -8760,12 +8788,14 @@ class IdOverlayDialog(QDialog):
 
         if accepted_mode == 0:
 
-            my_network.id_overlay = my_network.draw_node_indices()
+            my_network.id_overlay = my_network.draw_node_indices(down_factor = downsample)
 
         elif accepted_mode == 1:
 
-            my_network.id_overlay = my_network.draw_edge_indices()
+            my_network.id_overlay = my_network.draw_edge_indices(down_factor = downsample)
 
+        if downsample is not None:
+            my_network.id_overlay = n3d.upsample_with_padding(my_network.id_overlay, original_shape = self.parent().shape)
 
         self.parent().load_channel(3, channel_data = my_network.id_overlay, data = True, preserve_zoom = (self.parent().ax.get_xlim(), self.parent().ax.get_ylim()))
 
@@ -8791,7 +8821,7 @@ class ColorOverlayDialog(QDialog):
         layout.addRow("Execution Mode:", self.mode_selector)
 
         self.down_factor = QLineEdit("")
-        layout.addRow("down_factor (for speeding up overlay generation - optional):", self.down_factor)
+        layout.addRow("down_factor (int - for speeding up overlay generation - optional):", self.down_factor)
 
         # Add Run button
         run_button = QPushButton("Generate (Will go to Overlay 2)")
@@ -14848,7 +14878,7 @@ class CalcAllDialog(QDialog):
         
         self.down_factor = QLineEdit(self.prev_down_factor)
         self.down_factor.setPlaceholderText("Leave empty for None")
-        speedup_layout.addRow("Downsample for Centroids (int):", self.down_factor)
+        speedup_layout.addRow("Downsample for Centroids/Overlays (int):", self.down_factor)
         
         self.GPU_downsample = QLineEdit(self.prev_GPU_downsample)
         self.GPU_downsample.setPlaceholderText("Leave empty for None")
@@ -15006,8 +15036,12 @@ class CalcAllDialog(QDialog):
                     directory = 'my_network'
                 
                 # Generate and update overlays
-                my_network.network_overlay = my_network.draw_network(directory=directory)
-                my_network.id_overlay = my_network.draw_node_indices(directory=directory)
+                my_network.network_overlay = my_network.draw_network(directory=directory, down_factor = down_factor)
+                my_network.id_overlay = my_network.draw_node_indices(directory=directory, down_factor = down_factor)
+
+                if down_factor is not None:
+                    my_network.id_overlay = n3d.upsample_with_padding(my_network.id_overlay, original_shape = self.parent().shape)
+                    my_network.network_overlay = n3d.upsample_with_padding(my_network.network_overlay, original_shape = self.parent().shape)
                 
                 # Update channel data
                 self.parent().load_channel(2, my_network.network_overlay, True)
@@ -15128,6 +15162,9 @@ class ProxDialog(QDialog):
         self.overlays.setCheckable(True)
         self.overlays.setChecked(True)
         output_layout.addRow("Generate Overlays:", self.overlays)
+
+        self.downsample = QLineEdit()
+        output_layout.addRow("(If above): Downsample factor for drawing overlays (Int - Makes Overlay Elements Larger):", self.downsample)
         
         self.populate = QPushButton("Populate Nodes from Centroids?")
         self.populate.setCheckable(True)
@@ -15199,6 +15236,12 @@ class ProxDialog(QDialog):
             except:
                 max_neighbors = None
 
+
+            try:
+                downsample = int(self.downsample.text()) if self.downsample.text() else None
+            except:
+                downsample = None
+
             overlays = self.overlays.isChecked()  
             fastdil = self.fastdil.isChecked()
 
@@ -15254,8 +15297,12 @@ class ProxDialog(QDialog):
                         directory = 'my_network'
                     
                     # Generate and update overlays
-                    my_network.network_overlay = my_network.draw_network(directory=directory)
-                    my_network.id_overlay = my_network.draw_node_indices(directory=directory)
+                    my_network.network_overlay = my_network.draw_network(directory=directory, down_factor = downsample)
+                    my_network.id_overlay = my_network.draw_node_indices(directory=directory, down_factor = downsample)
+
+                    if downsample is not None:
+                        my_network.id_overlay = n3d.upsample_with_padding(my_network.id_overlay, original_shape = self.parent().shape)
+                        my_network.network_overlay = n3d.upsample_with_padding(my_network.network_overlay, original_shape = self.parent().shape)
                     
                     # Update channel data
                     self.parent().load_channel(2, channel_data = my_network.network_overlay, data = True)

{nettracer3d-1.1.0 → nettracer3d-1.1.1/src/nettracer3d.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 1.1.0
+Version: 1.1.1
 Summary: Scripts for intializing and analyzing networks from segmentations of three dimensional images.
 Author-email: Liam McLaughlin <liamm@wustl.edu>
 Project-URL: Documentation, https://nettracer3d.readthedocs.io/en/latest/
@@ -110,6 +110,6 @@ McLaughlin, L., Zhang, B., Sharma, S. et al. Three dimensional multiscalar neuro
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 1.1.0 Updates --
+-- Version 1.1.1 Updates --
 
-	* Bug Fix
+	* Can now intermittently downsample while making the network and id overlays now to make their relevant elements larger in the actual rendered output.