Updated old code

Hjorthmedh · Nov 27, 2024 · be6bf01 · be6bf01
1 parent 80a9128
commit be6bf01
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Showing 4 changed files with 37 additions and 6 deletions.
diff --git a/snudda/neurons/neuron_morphology_extended.py b/snudda/neurons/neuron_morphology_extended.py
@@ -244,7 +244,14 @@ def get_section_coordinates(self, section_id, section_x):
         if "neuron" not in self.morphology_data or 3 not in self.morphology_data["neuron"].sections:
             raise ValueError(f"No dendrites loaded for neuron {self.swc_filename}")
 
-        section = self.morphology_data["neuron"].sections[3][section_id]
+        try:
+            section = self.morphology_data["neuron"].sections[3][section_id]
+        except:
+            import traceback
+            print(traceback.format_exc())
+            import pdb
+            pdb.set_trace()
+
         sec_x = section.section_x
         pos = section.position
 

diff --git a/snudda/plotting/plot_degeneration.py b/snudda/plotting/plot_degeneration.py
@@ -5,10 +5,30 @@
 
 class PlotDegeneration:
 
-    def __init__(self, original_network_path, degenerated_network_path):
+    def __init__(self, original_network_path, degenerated_network_path,
+                 original_input=None, degenerated_input=None,
+                 original_snudda_data=None, degenerated_snudda_data=None):
 
-        self.original_plot = SnuddaPlotInputLocations(network_path=original_network_path)
-        self.degenerated_plot = SnuddaPlotInputLocations(network_path=degenerated_network_path)
+        if os.path.isfile(original_network_path):
+            original_network_file = original_network_path
+            original_network_path = os.path.dirname(original_network_path)
+        else:
+            original_network_file = None
+
+        if os.path.isfile(degenerated_network_path):
+            degenerated_network_file = degenerated_network_path
+            degenerated_network_path = os.path.dirname(degenerated_network_path)
+        else:
+            degenerated_network_file = None
+
+        self.original_plot = SnuddaPlotInputLocations(network_path=original_network_path,
+                                                      network_file=original_network_file,
+                                                      input_file=original_input,
+                                                      snudda_data=original_snudda_data)
+        self.degenerated_plot = SnuddaPlotInputLocations(network_path=degenerated_network_path,
+                                                         network_file=degenerated_network_file,
+                                                         input_file=degenerated_input,
+                                                         snudda_data=degenerated_snudda_data)
 
         self.fig_path = os.path.join(degenerated_network_path, "figures")
         if not os.path.exists(self.fig_path):

diff --git a/snudda/plotting/plot_input_locations.py b/snudda/plotting/plot_input_locations.py
@@ -217,7 +217,7 @@ def get_input_soma_distance_summary(self, neuron_type, input_name):
 
     def load_input_config(self):
 
-        self.input_config = deepcopy(self.input_data["config"])
+        self.input_config = deepcopy(self.input_data["config"][()])
 
     def get_max_dendrite_distance(self, neuron_type):
 
@@ -359,6 +359,8 @@ def load_neuron(self, neuron_id):
         if neuron_id not in self.neuron_cache:
             neuron_info = self.snudda_load.data["neurons"][neuron_id]
 
+            # print(f"Loading: {snudda_parse_path(neuron_info['neuron_path'], self.snudda_data)}")
+
             prot = NeuronPrototype(neuron_path=neuron_info["neuron_path"], neuron_name=neuron_info["name"],
                                    snudda_data=self.snudda_data)
 
@@ -373,6 +375,8 @@ def load_neuron(self, neuron_id):
                             position=position, rotation=rotation)
             self.neuron_cache[neuron_id] = nm
 
+            print(f"Loading morphology: {nm.swc_filename}")
+
         return self.neuron_cache[neuron_id]
 
     def get_synapse_coords(self, neuron_id, pre_type=None):

diff --git a/snudda/utils/swap_to_degenerated_morphologies.py b/snudda/utils/swap_to_degenerated_morphologies.py
@@ -190,7 +190,7 @@ def filter_synapses(self, filter_axon=False):
 
         print(f"Keeping {self.new_hdf5['network/num_synapses'][()]} "
               f"out of {self.old_hdf5['network/num_synapses'][()]} synapses "
-              f"({self.new_hdf5['network/num_synapses'][()] / self.old_hdf5['network/num_synapses'][()]*100:.3f} %)")
+              f"({self.new_hdf5['network/num_synapses'][()] / np.max(1,self.old_hdf5['network/num_synapses'][()])*100:.3f} %)")
 
     def filter_gap_junctions(self):
         # First version, will keep all synapses in memory to write a more efficient file