nettracer3d 1.0.6__tar.gz → 1.0.7__tar.gz

{nettracer3d-1.0.6/src/nettracer3d.egg-info → nettracer3d-1.0.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 1.0.6
+Version: 1.0.7
 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 +110,7 @@ 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 1.0.5 Updates --
+-- Version 1.0.7 Updates --
 
 	* Bug fix
+	* Added handling if the user tries to load in a multichannel 3dimensional image (note this will not detect if you have a multi-channel image of 2d planes, it will think those are 3d. For now those can be split up with other software, or you can use the crop function to just isolate the channel you want as if it were a z-plane).

{nettracer3d-1.0.6 → nettracer3d-1.0.7}/README.md

@@ -65,6 +65,7 @@ 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 1.0.5 Updates --
+-- Version 1.0.7 Updates --
 
-	* Bug fix
+	* Bug fix
+	* Added handling if the user tries to load in a multichannel 3dimensional image (note this will not detect if you have a multi-channel image of 2d planes, it will think those are 3d. For now those can be split up with other software, or you can use the crop function to just isolate the channel you want as if it were a z-plane).

{nettracer3d-1.0.6 → nettracer3d-1.0.7}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "1.0.6"
+version = "1.0.7"
 authors = [
   { name="Liam McLaughlin", email="liamm@wustl.edu" },
 ]

{nettracer3d-1.0.6 → nettracer3d-1.0.7}/src/nettracer3d/nettracer_gui.py

@@ -5060,6 +5060,10 @@ class ImageViewerWindow(QMainWindow):
             dialog = MergeNodeIdDialog(self)
             dialog.exec()
 
+    def show_multichan_dialog(self, data):
+        dialog = MultiChanDialog(self, data)
+        dialog.show()
+
     def show_gray_water_dialog(self):
         """Show the gray watershed parameter dialog."""
         dialog = GrayWaterDialog(self)
@@ -5162,7 +5166,7 @@ class ImageViewerWindow(QMainWindow):
 
             my_network.edges = (my_network.nodes == 0) * my_network.edges
 
-            my_network.calculate_all(my_network.nodes, my_network.edges, xy_scale = my_network.xy_scale, z_scale = my_network.z_scale, search = None, diledge = None, inners = False, hash_inners = False, remove_trunk = 0, ignore_search_region = True, other_nodes = None, label_nodes = True, directory = None, GPU = False, fast_dil = False, skeletonize = False, GPU_downsample = None)
+            my_network.calculate_all(my_network.nodes, my_network.edges, xy_scale = my_network.xy_scale, z_scale = my_network.z_scale, search = None, diledge = None, inners = False, remove_trunk = 0, ignore_search_region = True, other_nodes = None, label_nodes = True, directory = None, GPU = False, fast_dil = False, skeletonize = False, GPU_downsample = None)
 
             self.load_channel(1, my_network.edges, data = True)
             self.load_channel(0, my_network.nodes, data = True)
@@ -5916,6 +5920,16 @@ class ImageViewerWindow(QMainWindow):
         msg.setStandardButtons(QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No)
         return msg.exec() == QMessageBox.StandardButton.Yes
 
+    def confirm_multichan_dialog(self):
+        """Shows a dialog asking user to confirm if image is multichan"""
+        msg = QMessageBox()
+        msg.setIcon(QMessageBox.Icon.Question)
+        msg.setText("Image Format Alert")
+        msg.setInformativeText("Is this a Multi-Channel (4D) image?")
+        msg.setWindowTitle("Confirm Image Format")
+        msg.setStandardButtons(QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No)
+        return msg.exec() == QMessageBox.StandardButton.Yes
+
     def confirm_resize_dialog(self):
         """Shows a dialog asking user to resize image"""
         msg = QMessageBox()
@@ -5999,7 +6013,7 @@ class ImageViewerWindow(QMainWindow):
             try:
                 if len(self.channel_data[channel_index].shape) == 3:  # potentially 2D RGB
                     if self.channel_data[channel_index].shape[-1] in (3, 4):  # last dim is 3 or 4
-                        if not data and self.shape is None:
+                        if not data:
                             if self.confirm_rgb_dialog():
                                 # User confirmed it's 2D RGB, expand to 4D
                                 self.channel_data[channel_index] = np.expand_dims(self.channel_data[channel_index], axis=0)
@@ -6009,12 +6023,18 @@ class ImageViewerWindow(QMainWindow):
             except:
                 pass
 
-            if not color:
-                try:
-                    if len(self.channel_data[channel_index].shape) == 4 and (channel_index == 0 or channel_index == 1):
+            if len(self.channel_data[channel_index].shape) == 4:
+                if not self.channel_data[channel_index].shape[-1] in (3, 4):
+                    if self.confirm_multichan_dialog(): # User is trying to load 4D channel stack:
+                        my_data = copy.deepcopy(self.channel_data[channel_index])
+                        self.channel_data[channel_index] = None 
+                        self.show_multichan_dialog(data = my_data)
+                        return
+                elif not color and (channel_index == 0 or channel_index == 1):
+                    try:
                         self.channel_data[channel_index] = self.reduce_rgb_dimension(self.channel_data[channel_index], 'weight')
-                except:
-                    pass
+                    except:
+                        pass
 
             reset_resize = False
 
@@ -8431,6 +8451,89 @@ class MergeNodeIdDialog(QDialog):
             print(traceback.format_exc())
             #print(f"Error: {e}")
 
+class MultiChanDialog(QDialog):
+
+    def __init__(self, parent=None, data = None):
+
+        super().__init__(parent)
+        self.setWindowTitle("Channel Loading")
+        self.setModal(False)
+        
+        layout = QFormLayout(self)
+
+        self.data = data
+
+        self.nodes = QComboBox()
+        self.edges = QComboBox()
+        self.overlay1 = QComboBox()
+        self.overlay2 = QComboBox()
+        options = ["None"]
+        for i in range(self.data.shape[0]):
+            options.append(str(i))
+        self.nodes.addItems(options)
+        self.edges.addItems(options)
+        self.overlay1.addItems(options)
+        self.overlay2.addItems(options)
+        self.nodes.setCurrentIndex(0)
+        self.edges.setCurrentIndex(0)
+        self.overlay1.setCurrentIndex(0)
+        self.overlay2.setCurrentIndex(0)
+        layout.addRow("Load this channel into nodes?", self.nodes)
+        layout.addRow("Load this channel into edges?", self.edges)
+        layout.addRow("Load this channel into overlay1?", self.overlay1)
+        layout.addRow("Load this channel into overlay2?", self.overlay2)
+
+        run_button = QPushButton("Load Channels")
+        run_button.clicked.connect(self.run)
+        layout.addWidget(run_button)
+
+        run_button2 = QPushButton("Save Channels to Directory")
+        run_button2.clicked.connect(self.run2)
+        layout.addWidget(run_button2)
+
+
+    def run(self):
+
+        try:
+            node_chan = int(self.nodes.currentText())
+            self.parent().load_channel(0, self.data[node_chan, :, :, :], data = True)
+        except:
+            pass
+        try:
+            edge_chan = int(self.edges.currentText())
+            self.parent().load_channel(1, self.data[edge_chan, :, :, :], data = True)
+        except:
+            pass
+        try:
+            overlay1_chan = int(self.overlay1.currentText())
+            self.parent().load_channel(2, self.data[overlay1_chan, :, :, :], data = True)
+        except:
+            pass
+        try:
+            overlay2_chan = int(self.overlay2.currentText())
+            self.parent().load_channel(3, self.data[overlay2_chan, :, :, :], data = True)
+        except:
+            pass
+
+    def run2(self):
+
+        try:
+            # First let user select parent directory
+            parent_dir = QFileDialog.getExistingDirectory(
+                self,
+                "Select Location to Save Channels",
+                "",
+                QFileDialog.Option.ShowDirsOnly
+            )
+
+            for i in range(self.data.shape[0]):
+                try:
+                    tifffile.imwrite(f'{parent_dir}/C{i}.tif', self.data[i, :, :, :])
+                except:
+                    continue
+        except:
+            pass
+
 
 class Show3dDialog(QDialog):
     def __init__(self, parent=None):

{nettracer3d-1.0.6 → nettracer3d-1.0.7/src/nettracer3d.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 1.0.6
+Version: 1.0.7
 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 +110,7 @@ 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 1.0.5 Updates --
+-- Version 1.0.7 Updates --
 
 	* Bug fix
+	* Added handling if the user tries to load in a multichannel 3dimensional image (note this will not detect if you have a multi-channel image of 2d planes, it will think those are 3d. For now those can be split up with other software, or you can use the crop function to just isolate the channel you want as if it were a z-plane).