diff --git a/PyNutil/io/propagation.py b/PyNutil/io/propagation.py index 600ad6033c5b296b17a6037a183ac15b14d160bb..22a611fe44b7ee85384cc70a56dcc942154ea5cd 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 bbdff4038d0577d2d0fba447d657af634627801f..862c2ec55078ed9e0ddbcdfc8f96f48a07ad476b 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 c28a63c54c679be458e581b2e7bc7cf1e20a2909..8522cea0c6d5d2e999c3d0c19676ab719d57ee26 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 210be15890bbb1ed3dcd08fa67956fb8ca5f6c69..ddf569eb565e14624d939792c89b9122ca43d878 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 c52c45abf25e26be800770216b3b45e9e33fd9d7..da1fce6f65091054f932022d4620b6c5ba45fe24 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 70ab405ee56294199e2cbc47a2fb54301e7bb451..64cadce6b9942512fdd0a3366b7e61719637532e 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 a8bc9c570d4d43b7d4db49e0f73c1cfd44bfb686..937d4d474047f7c8484744c2e50c9d11a47c58b1 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 62b8ddb4ebdc8b18ce4fb05c07b45fd65114f0e4..671ea2d5e9789bac7a6d2e5210a480e0a3096a1d 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 4f3e80065f575f7f115e3786bff4524ea9ea7d5e..b09bc8323834a577b6513e04af1a24e34b82fcbe 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 d0303452215f11f5fc399124621e02cf6cb91759..3b6e12ff5c88736aca1801d1dd167c6fef1c069c 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 d586e12e89840f7a75d53d71243ca5bbdbf715ad..b2b9c189f5e61108bd56a1c9037d2a3cc13ea78e 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