diff --git a/src/deep_neurographs/intake.py b/src/deep_neurographs/intake.py index a02f635..9a8d575 100644 --- a/src/deep_neurographs/intake.py +++ b/src/deep_neurographs/intake.py @@ -16,7 +16,6 @@ from deep_neurographs.utils import graph_util as gutil from deep_neurographs.utils import img_util, swc_util, util - MIN_SIZE = 30 NODE_SPACING = 2 SMOOTH_BOOL = True @@ -125,7 +124,7 @@ def run(self, swc_pointer): # Graph size n_components = util.reformat_number(len(irreducibles)) print("\nGraph Overview...") - print("# connected components:", n_connected_components) + print("# connected components:", n_components) print("# nodes:", util.reformat_number(n_nodes)) print("# edges:", util.reformat_number(n_edges)) @@ -155,15 +154,17 @@ def get_irreducibles(self, swc_dicts): i += 1 # Store results + desc = "Extract Graphs" irreducibles = [] n_nodes, n_edges = 0, 0 - for process in tqdm(as_completed(processes), desc="Extract Graphs"): + for process in tqdm(as_completed(processes), desc=desc): irreducibles_i = process.result() irreducibles.extend(irreducibles_i) n_nodes += count_nodes(irreducibles_i) n_edges += count_edges(irreducibles_i) return irreducibles, n_nodes, n_edges + # --- utils --- def count_nodes(irreducibles): """ diff --git a/src/deep_neurographs/machine_learning/graph_datasets.py b/src/deep_neurographs/machine_learning/graph_datasets.py index b7737a9..2777eb9 100644 --- a/src/deep_neurographs/machine_learning/graph_datasets.py +++ b/src/deep_neurographs/machine_learning/graph_datasets.py @@ -15,7 +15,7 @@ import torch from torch_geometric.data import Data as GraphData -from deep_neurographs.machine_learning import feature_generation, datasets +from deep_neurographs.machine_learning import datasets, feature_generation from deep_neurographs.utils import gnn_util diff --git a/src/deep_neurographs/machine_learning/heterograph_datasets.py b/src/deep_neurographs/machine_learning/heterograph_datasets.py index 67499af..57acbea 100644 --- a/src/deep_neurographs/machine_learning/heterograph_datasets.py +++ b/src/deep_neurographs/machine_learning/heterograph_datasets.py @@ -17,7 +17,7 @@ import torch from torch_geometric.data import HeteroData as HeteroGraphData -from deep_neurographs.machine_learning import feature_generation, datasets +from deep_neurographs.machine_learning import datasets, feature_generation from deep_neurographs.utils import gnn_util DTYPE = torch.float32 diff --git a/src/deep_neurographs/neurograph.py b/src/deep_neurographs/neurograph.py index bbb66b1..8bc449c 100644 --- a/src/deep_neurographs/neurograph.py +++ b/src/deep_neurographs/neurograph.py @@ -19,7 +19,9 @@ from deep_neurographs import generate_proposals, geometry from deep_neurographs.geometry import dist as get_dist -from deep_neurographs.machine_learning.groundtruth_generation import init_targets +from deep_neurographs.machine_learning.groundtruth_generation import ( + init_targets, +) from deep_neurographs.utils import graph_util as gutil from deep_neurographs.utils import img_util, swc_util, util diff --git a/src/deep_neurographs/utils/ml_util.py b/src/deep_neurographs/utils/ml_util.py index b78bb65..8fc2270 100644 --- a/src/deep_neurographs/utils/ml_util.py +++ b/src/deep_neurographs/utils/ml_util.py @@ -16,8 +16,8 @@ from sklearn.ensemble import AdaBoostClassifier, RandomForestClassifier from deep_neurographs.machine_learning import ( - feature_generation, datasets, + feature_generation, graph_datasets, heterograph_datasets, ) diff --git a/src/deep_neurographs/utils/swc_util.py b/src/deep_neurographs/utils/swc_util.py index bdddc50..778c7d5 100644 --- a/src/deep_neurographs/utils/swc_util.py +++ b/src/deep_neurographs/utils/swc_util.py @@ -9,15 +9,20 @@ """ -from concurrent.futures import ProcessPoolExecutor, ThreadPoolExecutor, as_completed -from google.cloud import storage +import os +from concurrent.futures import ( + ProcessPoolExecutor, + ThreadPoolExecutor, + as_completed, +) from io import BytesIO from tqdm import tqdm from zipfile import ZipFile import networkx as nx import numpy as np -import os +from google.cloud import storage +from tqdm import tqdm from deep_neurographs.utils import util