nettracer3d 1.0.9__tar.gz → 1.1.1__tar.gz

{nettracer3d-1.0.9/src/nettracer3d.egg-info → nettracer3d-1.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 1.0.9
+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/
@@ -110,9 +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 1.0.9 Updates --
+-- Version 1.1.1 Updates --
 
-	* Some bug fixes
-	* Added ability to load a full sized highlight overlay from the file menu (in case you need it for a picture - on big images the highlight overlay is computed by slice so if you reload the channel its trying to highlight, it will alter the highlight overlay, but loading in the entire highlight overlay directly will stop this behavior until a new highlight is generated).
-	* For the 'calculate edge < > node interaction' method - now can compute the length of nearby edges as an alternative option to just the volumes.
-	* Added ability to select all nodes/edges participating in the network.
+	* Can now intermittently downsample while making the network and id overlays now to make their relevant elements larger in the actual rendered output.

{nettracer3d-1.0.9 → nettracer3d-1.1.1}/README.md

@@ -65,9 +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 1.0.9 Updates --
+-- Version 1.1.1 Updates --
 
-	* Some bug fixes
-	* Added ability to load a full sized highlight overlay from the file menu (in case you need it for a picture - on big images the highlight overlay is computed by slice so if you reload the channel its trying to highlight, it will alter the highlight overlay, but loading in the entire highlight overlay directly will stop this behavior until a new highlight is generated).
-	* For the 'calculate edge < > node interaction' method - now can compute the length of nearby edges as an alternative option to just the volumes.
-	* Added ability to select all nodes/edges participating in the network.
+	* Can now intermittently downsample while making the network and id overlays now to make their relevant elements larger in the actual rendered output.

{nettracer3d-1.0.9 → nettracer3d-1.1.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "1.0.9"
+version = "1.1.1"
 authors = [
   { name="Liam McLaughlin", email="liamm@wustl.edu" },
 ]

{nettracer3d-1.0.9 → nettracer3d-1.1.1}/src/nettracer3d/nettracer.py

@@ -3143,13 +3143,14 @@ class Network_3D:
         Can be called on a Network_3D object to save the nodes property to hard mem as a tif. It will save to the active directory if none is specified.
         :param directory: (Optional - Val = None; String). The path to an indended directory to save the nodes to.
         """
-        imagej_metadata = {
-            'spacing': self.z_scale,
-            'slices': self._nodes.shape[0],
-            'channels': 1,
-            'axes': 'ZYX'
-        }
-        resolution_value = 1.0 / self.xy_scale if self.xy_scale != 0 else 1
+        if self._nodes is not None:
+            imagej_metadata = {
+                'spacing': self.z_scale,
+                'slices': self._nodes.shape[0],
+                'channels': 1,
+                'axes': 'ZYX'
+            }
+            resolution_value = 1.0 / self.xy_scale if self.xy_scale != 0 else 1
 
         if filename is None:
             filename = "labelled_nodes.tif"
@@ -3184,14 +3185,15 @@ class Network_3D:
         :param directory: (Optional - Val = None; String). The path to an indended directory to save the edges to.
         """
 
-        imagej_metadata = {
-            'spacing': self.z_scale,
-            'slices': self._edges.shape[0],
-            'channels': 1,
-            'axes': 'ZYX'
-        }
+        if self._edges is not None:
+            imagej_metadata = {
+                'spacing': self.z_scale,
+                'slices': self._edges.shape[0],
+                'channels': 1,
+                'axes': 'ZYX'
+            }
 
-        resolution_value = 1.0 / self.xy_scale if self.xy_scale != 0 else 1
+            resolution_value = 1.0 / self.xy_scale if self.xy_scale != 0 else 1
 
         if filename is None:
             filename = "labelled_edges.tif"
@@ -3360,13 +3362,14 @@ class Network_3D:
 
     def save_network_overlay(self, directory = None, filename = None):
 
-        imagej_metadata = {
-            'spacing': self.z_scale,
-            'slices': self._network_overlay.shape[0],
-            'channels': 1,
-            'axes': 'ZYX'
-        }
-        resolution_value = 1.0 / self.xy_scale if self.xy_scale != 0 else 1
+        if self._network_overlay is not None:
+            imagej_metadata = {
+                'spacing': self.z_scale,
+                'slices': self._network_overlay.shape[0],
+                'channels': 1,
+                'axes': 'ZYX'
+            }
+            resolution_value = 1.0 / self.xy_scale if self.xy_scale != 0 else 1
 
         if filename is None:
             filename = "overlay_1.tif"
@@ -3390,13 +3393,14 @@ class Network_3D:
 
     def save_id_overlay(self, directory = None, filename = None):
 
-        imagej_metadata = {
-            'spacing': self.z_scale,
-            'slices': self._id_overlay.shape[0],
-            'channels': 1,
-            'axes': 'ZYX'
-        }
-        resolution_value = 1.0 / self.xy_scale if self.xy_scale != 0 else 1
+        if self._id_overlay is not None:
+            imagej_metadata = {
+                'spacing': self.z_scale,
+                'slices': self._id_overlay.shape[0],
+                'channels': 1,
+                'axes': 'ZYX'
+            }
+            resolution_value = 1.0 / self.xy_scale if self.xy_scale != 0 else 1
 
         if filename is None:
             filename = "overlay_2.tif"

{nettracer3d-1.0.9 → 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-1.0.9 → nettracer3d-1.1.1/src/nettracer3d.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 1.0.9
+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/
@@ -110,9 +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 1.0.9 Updates --
+-- Version 1.1.1 Updates --
 
-	* Some bug fixes
-	* Added ability to load a full sized highlight overlay from the file menu (in case you need it for a picture - on big images the highlight overlay is computed by slice so if you reload the channel its trying to highlight, it will alter the highlight overlay, but loading in the entire highlight overlay directly will stop this behavior until a new highlight is generated).
-	* For the 'calculate edge < > node interaction' method - now can compute the length of nearby edges as an alternative option to just the volumes.
-	* Added ability to select all nodes/edges participating in the network.
+	* Can now intermittently downsample while making the network and id overlays now to make their relevant elements larger in the actual rendered output.