From 08b8f7399c8ad20cf5316382c13cf56114c4dd93 Mon Sep 17 00:00:00 2001
From: polarbean <harry.carey95@gmail.com>
Date: Wed, 23 Oct 2024 21:44:53 +0200
Subject: [PATCH] removed redundant functions
---
PyNutil/coordinate_processing.py | 19 -------------------
PyNutil/data_analysis.py | 7 +++----
PyNutil/main.py | 5 +++--
3 files changed, 6 insertions(+), 25 deletions(-)
delete mode 100644 PyNutil/coordinate_processing.py
diff --git a/PyNutil/coordinate_processing.py b/PyNutil/coordinate_processing.py
deleted file mode 100644
index 6633273..0000000
--- a/PyNutil/coordinate_processing.py
+++ /dev/null
@@ -1,19 +0,0 @@
-from .coordinate_extraction import folder_to_atlas_space
-from .counting_and_load import label_points
-
-
-def extract_coordinates(segmentation_folder, alignment_json, atlas_labels, pixel_id, non_linear, object_cutoff, atlas_volume, use_flat):
- return folder_to_atlas_space(
- segmentation_folder,
- alignment_json,
- atlas_labels,
- pixel_id,
- non_linear,
- object_cutoff,
- atlas_volume,
- use_flat,
- )
-
-
-def label_points_group(points, atlas_volume):
- return label_points(points, atlas_volume, scale_factor=1)
diff --git a/PyNutil/data_analysis.py b/PyNutil/data_analysis.py
index ad5fd8d..ee8fff7 100644
--- a/PyNutil/data_analysis.py
+++ b/PyNutil/data_analysis.py
@@ -1,6 +1,5 @@
import pandas as pd
-from .counting_and_load import pixel_count_per_region
-from .coordinate_processing import label_points_group
+from .counting_and_load import pixel_count_per_region, label_points
def quantify_labeled_points(
@@ -12,8 +11,8 @@ def quantify_labeled_points(
atlas_labels,
atlas_volume
):
- labeled_points_centroids = label_points_group(centroids, atlas_volume)
- labeled_points = label_points_group(pixel_points, atlas_volume)
+ labeled_points_centroids = label_points(centroids, atlas_volume)
+ labeled_points = label_points(pixel_points, atlas_volume, scale_factor=1)
per_section_df = _quantify_per_section(
labeled_points,
diff --git a/PyNutil/main.py b/PyNutil/main.py
index b4cd489..3255d35 100644
--- a/PyNutil/main.py
+++ b/PyNutil/main.py
@@ -2,9 +2,10 @@ import json
import os
from .io.atlas_loader import load_atlas_data, load_custom_atlas
-from .coordinate_processing import extract_coordinates, label_points_group
from .data_analysis import quantify_labeled_points
from .io.file_operations import save_analysis_output
+from .coordinate_extraction import folder_to_atlas_space
+from .counting_and_load import label_points
class PyNutil:
@@ -64,7 +65,7 @@ class PyNutil:
self.points_len,
self.centroids_len,
self.segmentation_filenames,
- ) = extract_coordinates(
+ ) = folder_to_atlas_space(
self.segmentation_folder,
self.alignment_json,
self.atlas_labels,
--
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