From 97fff9e0de697fcf2f89f216335e09f7f18d869e Mon Sep 17 00:00:00 2001
From: Harry Carey <38996929+PolarBean@users.noreply.github.com>
Date: Fri, 11 Aug 2023 16:26:11 +0200
Subject: [PATCH] Removed DeepSlice dependency and migrated function into
PyNutil codebase
---
PyNutil/coordinate_extraction.py | 30 +++++++++++++++++++++++++++++-
1 file changed, 29 insertions(+), 1 deletion(-)
diff --git a/PyNutil/coordinate_extraction.py b/PyNutil/coordinate_extraction.py
index db162ac..445aec0 100644
--- a/PyNutil/coordinate_extraction.py
+++ b/PyNutil/coordinate_extraction.py
@@ -1,6 +1,5 @@
import numpy as np
import pandas as pd
-from DeepSlice.coord_post_processing.spacing_and_indexing import number_sections
import json
from .read_and_write import load_visualign_json
from .counting_and_load import label_points, flat_to_dataframe
@@ -10,7 +9,36 @@ from tqdm import tqdm
import cv2
from skimage import measure
import threading
+import re
+def number_sections(filenames: List[str], legacy=False) -> List[int]:
+ """
+ returns the section numbers of filenames
+
+ :param filenames: list of filenames
+ :type filenames: list[str]
+ :return: list of section numbers
+ :rtype: list[int]
+ """
+ filenames = [filename.split("\\")[-1] for filename in filenames]
+ section_numbers = []
+ for filename in filenames:
+ if not legacy:
+ match = re.findall(r"\_s\d+", filename)
+ if len(match) == 0:
+ raise ValueError(f"No section number found in filename: {filename}")
+ if len(match) > 1:
+ raise ValueError(
+ "Multiple section numbers found in filename, ensure only one instance of _s### is present, where ### is the section number"
+ )
+ section_numbers.append(int(match[-1][2:]))
+ else:
+ match = re.sub("[^0-9]", "", filename)
+ ###this gets the three numbers closest to the end
+ section_numbers.append(match[-3:])
+ if len(section_numbers) == 0:
+ raise ValueError("No section numbers found in filenames")
+ return section_numbers
# related to coordinate_extraction
def get_centroids_and_area(segmentation, pixel_cut_off=0):
--
GitLab