From 1ff2a5a527917a77c1ff42db4acc63d5101d4be9 Mon Sep 17 00:00:00 2001
From: Harry Carey <harry.carey95@gmail.com>
Date: Wed, 13 Mar 2024 12:01:40 +0100
Subject: [PATCH] fixed several issues
---
PyNutil/__init__.py | 2 +-
PyNutil/coordinate_extraction.py | 29 ++++++++++++++++++-----------
PyNutil/counting_and_load.py | 3 ---
PyNutil/load_workflow.py | 3 ---
PyNutil/main.py | 19 ++++++++++---------
PyNutil/metadata/__init__.py | 2 +-
PyNutil/metadata/metadata_loader.py | 1 -
PyNutil/propagation.py | 3 ++-
PyNutil/read_and_write.py | 1 -
PyNutil/visualign_deformations.py | 1 -
10 files changed, 32 insertions(+), 32 deletions(-)
diff --git a/PyNutil/__init__.py b/PyNutil/__init__.py
index d06a307..5fa21b9 100644
--- a/PyNutil/__init__.py
+++ b/PyNutil/__init__.py
@@ -1 +1 @@
-from .main import PyNutil
+from .main import PyNutil
\ No newline at end of file
diff --git a/PyNutil/coordinate_extraction.py b/PyNutil/coordinate_extraction.py
index 157bdc6..3b9eddb 100644
--- a/PyNutil/coordinate_extraction.py
+++ b/PyNutil/coordinate_extraction.py
@@ -1,11 +1,9 @@
import numpy as np
import pandas as pd
-import json
from .read_and_write import load_visualign_json
-from .counting_and_load import label_points, flat_to_dataframe
+from .counting_and_load import flat_to_dataframe
from .visualign_deformations import triangulate, transform_vec
from glob import glob
-from tqdm import tqdm
import cv2
from skimage import measure
import threading
@@ -210,12 +208,23 @@ def folder_to_atlas_space(
[t.join() for t in threads]
# Flatten points_list
- points_len = [len(points) if points is not None else 0 for points in points_list]
+ points_len = [
+ len(points) if None not in points else 0 for points in points_list
+ ]
centroids_len = [
- len(centroids) if centroids is not None else 0 for centroids in centroids_list
- ]
- points = np.concatenate(points_list)
- centroids = np.concatenate(centroids_list)
+ len(centroids) if None not in centroids else 0 for centroids in centroids_list
+ ]
+ points_list = [points for points in points_list if None not in points]
+ centroids_list = [centroids for centroids in centroids_list if None not in centroids]
+ if len(points_list) == 0:
+ points = np.array([])
+ else:
+ points = np.concatenate(points_list)
+ if len(centroids_list) == 0:
+ centroids = np.array([])
+ else:
+ centroids = np.concatenate(centroids_list)
+
return (
np.array(points),
@@ -346,9 +355,7 @@ def segmentation_to_atlas_space(
else:
centroids = np.array([])
- print(
- f"Finished and points len is: {len(points)} and centroids len is: {len(centroids)}"
- )
+
points_list[index] = np.array(points)
centroids_list[index] = np.array(centroids)
region_areas_list[index] = region_areas
diff --git a/PyNutil/counting_and_load.py b/PyNutil/counting_and_load.py
index 9da941f..760e057 100644
--- a/PyNutil/counting_and_load.py
+++ b/PyNutil/counting_and_load.py
@@ -1,9 +1,6 @@
import numpy as np
import pandas as pd
import struct
-import matplotlib.pyplot as plt
-import os
-import nrrd
import cv2
from .generate_target_slice import generate_target_slice
diff --git a/PyNutil/load_workflow.py b/PyNutil/load_workflow.py
index 9675196..72ba0c3 100644
--- a/PyNutil/load_workflow.py
+++ b/PyNutil/load_workflow.py
@@ -1,10 +1,7 @@
"""Create workflow for calculating load based on atlas maps and segmentations"""
-import struct
-import matplotlib.pyplot as plt
import pandas as pd
import cv2
-import numpy as np
# from read_and_write import flat_to_array, label_to_array
from counting_and_load import flat_to_dataframe
diff --git a/PyNutil/main.py b/PyNutil/main.py
index 44ac2d4..a64249a 100644
--- a/PyNutil/main.py
+++ b/PyNutil/main.py
@@ -161,7 +161,7 @@ class PyNutil:
raise ValueError(
f"method {method} not recognised, valid methods are: per_pixel, per_object, or all"
)
- print("extracting coordinates")
+ print("extracting coordinates with method:", method)
(
pixel_points,
centroids,
@@ -188,6 +188,7 @@ class PyNutil:
self.centroids_len = centroids_len
self.segmentation_filenames = segmentation_filenames
self.region_areas_list = region_areas_list
+ self.method = method
def quantify_coordinates(self):
"""Quantifies the pixel coordinates by region.
@@ -205,11 +206,11 @@ class PyNutil:
print("quantifying coordinates")
labeled_points_centroids = None
labeled_points = None
- if hasattr(self, "centroids"):
+ if self.method == "per_object" or self.method == "all":
labeled_points_centroids = label_points(
self.centroids, self.atlas_volume, scale_factor=1
)
- if hasattr(self, "pixel_points"):
+ if self.method == "per_pixel" or self.method == "all":
labeled_points = label_points(
self.pixel_points, self.atlas_volume, scale_factor=1
)
@@ -224,9 +225,9 @@ class PyNutil:
for pl, cl, ra in zip(
self.points_len, self.centroids_len, self.region_areas_list
):
- if hasattr(self, "centroids"):
+ if self.method == "per_object" or self.method == "all":
current_centroids = labeled_points_centroids[prev_cl : prev_cl + cl]
- if hasattr(self, "pixel_points"):
+ if self.method == "per_pixel" or self.method == "all":
current_points = labeled_points[prev_pl : prev_pl + pl]
current_df = pixel_count_per_region(
current_points, current_centroids, self.atlas_labels
@@ -341,14 +342,14 @@ class PyNutil:
na_rep="",
index=False,
)
- if hasattr(self, "pixel_points"):
+ if self.method == "per_pixel" or self.method == "all":
write_points_to_meshview(
self.pixel_points[prev_pl : pl + prev_pl],
self.labeled_points[prev_pl : pl + prev_pl],
f"{output_folder}/per_section_meshview/{split_fn}_pixels.json",
self.atlas_labels,
)
- if hasattr(self, "centroids"):
+ if self.method == "per_object" or self.method == "all":
write_points_to_meshview(
self.centroids[prev_cl : cl + prev_cl],
self.labeled_points_centroids[prev_cl : cl + prev_cl],
@@ -358,14 +359,14 @@ class PyNutil:
prev_cl += cl
prev_pl += pl
- if hasattr(self, "pixel_points"):
+ if self.method == "per_pixel" or self.method == "all":
write_points_to_meshview(
self.pixel_points,
self.labeled_points,
f"{output_folder}/whole_series_meshview/pixels_meshview.json",
self.atlas_labels,
)
- if hasattr(self, "centroids"):
+ if self.method == "per_object" or self.method == "all":
write_points_to_meshview(
self.centroids,
self.labeled_points_centroids,
diff --git a/PyNutil/metadata/__init__.py b/PyNutil/metadata/__init__.py
index b6e690f..b974282 100644
--- a/PyNutil/metadata/__init__.py
+++ b/PyNutil/metadata/__init__.py
@@ -1 +1 @@
-from . import *
+from . import *
\ No newline at end of file
diff --git a/PyNutil/metadata/metadata_loader.py b/PyNutil/metadata/metadata_loader.py
index ae3361f..2763d55 100644
--- a/PyNutil/metadata/metadata_loader.py
+++ b/PyNutil/metadata/metadata_loader.py
@@ -1,6 +1,5 @@
import json
from pathlib import Path
-import os
def load_config() -> dict:
diff --git a/PyNutil/propagation.py b/PyNutil/propagation.py
index 1f3b643..d0ae3a6 100644
--- a/PyNutil/propagation.py
+++ b/PyNutil/propagation.py
@@ -2,6 +2,7 @@ import math, re
def propagate(arr):
+ arr = arr.copy()
for slice in arr:
if "nr" not in slice:
slice["nr"] = int(re.search(r"_s(\d+)", slice["filename"]).group(1))
@@ -12,7 +13,7 @@ def propagate(arr):
count = 0
for slice in arr:
if "anchoring" in slice:
- a = slice["anchoring"].copy()
+ a = slice["anchoring"]
for i in range(3):
a[i] += (a[i + 3] + a[i + 6]) / 2
a.extend(
diff --git a/PyNutil/read_and_write.py b/PyNutil/read_and_write.py
index 8be7f08..160e302 100644
--- a/PyNutil/read_and_write.py
+++ b/PyNutil/read_and_write.py
@@ -2,7 +2,6 @@ import json
import numpy as np
import struct
import pandas as pd
-import matplotlib.pyplot as plt
import os
import nrrd
import re
diff --git a/PyNutil/visualign_deformations.py b/PyNutil/visualign_deformations.py
index 2caef65..75f9fa2 100644
--- a/PyNutil/visualign_deformations.py
+++ b/PyNutil/visualign_deformations.py
@@ -1,6 +1,5 @@
"""This code was written by Gergely Csucs and Rembrandt Bakker"""
import numpy as np
-from scipy.spatial import Delaunay
def triangulate(w, h, markers):
--
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