From 0babccf464d1129aff3073bb3b9b420c184ea8f1 Mon Sep 17 00:00:00 2001
From: polarbean <harry.carey95@gmail.com>
Date: Mon, 17 Mar 2025 20:40:25 +0100
Subject: [PATCH] remove unused imports
---
PyNutil/io/propagation.py | 1 -
PyNutil/io/reconstruct_dzi.py | 1 -
PyNutil/main.py | 3 ---
PyNutil/processing/coordinate_extraction.py | 1 -
PyNutil/processing/counting_and_load.py | 1 -
PyNutil/processing/data_analysis.py | 2 +-
PyNutil/processing/generate_target_slice.py | 1 -
PyNutil/processing/transformations.py | 1 -
PyNutil/processing/utils.py | 2 --
PyNutil/processing/visualign_deformations.py | 2 --
demos/basic_example_custom_atlas.py | 2 --
11 files changed, 1 insertion(+), 16 deletions(-)
diff --git a/PyNutil/io/propagation.py b/PyNutil/io/propagation.py
index 600ad60..22a611f 100644
--- a/PyNutil/io/propagation.py
+++ b/PyNutil/io/propagation.py
@@ -1,6 +1,5 @@
import math, re
-
def propagate(arr):
arr = arr.copy()
for slice in arr:
diff --git a/PyNutil/io/reconstruct_dzi.py b/PyNutil/io/reconstruct_dzi.py
index bbdff40..862c2ec 100644
--- a/PyNutil/io/reconstruct_dzi.py
+++ b/PyNutil/io/reconstruct_dzi.py
@@ -4,7 +4,6 @@ import os
import zipfile
import xmltodict
-
def reconstruct_dzi(zip_file_path):
"""
Reconstructs a Deep Zoom Image (DZI) from a zip file containing the tiles.
diff --git a/PyNutil/main.py b/PyNutil/main.py
index c28a63c..8522cea 100644
--- a/PyNutil/main.py
+++ b/PyNutil/main.py
@@ -5,9 +5,6 @@ from .io.file_operations import save_analysis_output
from .io.read_and_write import open_custom_region_file
from .processing.coordinate_extraction import folder_to_atlas_space
-
-
-
class PyNutil:
"""
A class used to perform brain-wide quantification and spatial analysis of features in serial section images.
diff --git a/PyNutil/processing/coordinate_extraction.py b/PyNutil/processing/coordinate_extraction.py
index 210be15..ddf569e 100644
--- a/PyNutil/processing/coordinate_extraction.py
+++ b/PyNutil/processing/coordinate_extraction.py
@@ -3,7 +3,6 @@ import pandas as pd
from ..io.read_and_write import load_visualign_json
from .counting_and_load import flat_to_dataframe, rescale_image, load_image
from .visualign_deformations import triangulate
-from glob import glob
import cv2
from skimage import measure
import threading
diff --git a/PyNutil/processing/counting_and_load.py b/PyNutil/processing/counting_and_load.py
index c52c45a..da1fce6 100644
--- a/PyNutil/processing/counting_and_load.py
+++ b/PyNutil/processing/counting_and_load.py
@@ -5,7 +5,6 @@ import cv2
from .generate_target_slice import generate_target_slice
from .visualign_deformations import transform_vec
-
# related to counting and load
def label_points(points, label_volume, scale_factor=1):
"""
diff --git a/PyNutil/processing/data_analysis.py b/PyNutil/processing/data_analysis.py
index 70ab405..64cadce 100644
--- a/PyNutil/processing/data_analysis.py
+++ b/PyNutil/processing/data_analysis.py
@@ -1,5 +1,5 @@
import pandas as pd
-from .counting_and_load import pixel_count_per_region, label_points
+from .counting_and_load import pixel_count_per_region
import numpy as np
def map_to_custom_regions(custom_regions_dict, points_labels):
diff --git a/PyNutil/processing/generate_target_slice.py b/PyNutil/processing/generate_target_slice.py
index a8bc9c5..937d4d4 100644
--- a/PyNutil/processing/generate_target_slice.py
+++ b/PyNutil/processing/generate_target_slice.py
@@ -1,7 +1,6 @@
import numpy as np
import math
-
def generate_target_slice(ouv, atlas):
"""
Generates a target slice from the atlas using the given orientation and vectors.
diff --git a/PyNutil/processing/transformations.py b/PyNutil/processing/transformations.py
index 62b8ddb..671ea2d 100644
--- a/PyNutil/processing/transformations.py
+++ b/PyNutil/processing/transformations.py
@@ -1,7 +1,6 @@
import numpy as np
from .visualign_deformations import transform_vec
-
def transform_to_registration(seg_height, seg_width, reg_height, reg_width):
"""
Returns the scaling factors to transform the segmentation to the registration space.
diff --git a/PyNutil/processing/utils.py b/PyNutil/processing/utils.py
index 4f3e800..b09bc83 100644
--- a/PyNutil/processing/utils.py
+++ b/PyNutil/processing/utils.py
@@ -1,10 +1,8 @@
import numpy as np
import pandas as pd
import re
-import threading
from glob import glob
-
def number_sections(filenames, legacy=False):
"""
Returns the section numbers of filenames.
diff --git a/PyNutil/processing/visualign_deformations.py b/PyNutil/processing/visualign_deformations.py
index d030345..3b6e12f 100644
--- a/PyNutil/processing/visualign_deformations.py
+++ b/PyNutil/processing/visualign_deformations.py
@@ -1,8 +1,6 @@
"""This code was written by Gergely Csucs, Harry Carey and Rembrandt Bakker"""
-
import numpy as np
-
def triangulate(w, h, markers):
"""
Triangulates a set of markers.
diff --git a/demos/basic_example_custom_atlas.py b/demos/basic_example_custom_atlas.py
index d586e12..b2b9c18 100644
--- a/demos/basic_example_custom_atlas.py
+++ b/demos/basic_example_custom_atlas.py
@@ -1,6 +1,4 @@
import sys
-import os
-
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
from PyNutil import PyNutil
import os
--
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