From 11892cb65c3ecfcdc35b5013803f9611c7f21380 Mon Sep 17 00:00:00 2001
From: Harry Carey <harry.carey95@gmail.com>
Date: Wed, 24 May 2023 16:28:53 +0200
Subject: [PATCH] created function get_coordinates and added the ability to
provide settings json
---
PyNutil/coordinate_extraction.py | 10 +++---
PyNutil/main.py | 54 ++++++++++++++++++++++++++------
test/test1.json | 10 +++---
test/test4_2017.json | 12 +++----
testOOP.py | 11 ++-----
5 files changed, 62 insertions(+), 35 deletions(-)
diff --git a/PyNutil/coordinate_extraction.py b/PyNutil/coordinate_extraction.py
index 4f6c2b7..ff51c5e 100644
--- a/PyNutil/coordinate_extraction.py
+++ b/PyNutil/coordinate_extraction.py
@@ -2,9 +2,9 @@ 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 loadVisuAlignJson
-from counting_and_load import labelPoints
-from visualign_deformations import triangulate, transform_vec
+from .read_and_write import loadVisuAlignJson
+from .counting_and_load import labelPoints
+from .visualign_deformations import triangulate, transform_vec
from glob import glob
from tqdm import tqdm
import cv2
@@ -108,7 +108,7 @@ def SegmentationToAtlasSpace(slice, SegmentationPath, pixelID="auto", nonLinear=
triangulation = triangulate(RegWidth, RegHeight, slice["markers"])
newX, newY = transform_vec(triangulation, scaledX, scaledY)
else:
- print(f"no markers found for " + slice["filename"])
+ print(f"no markers found for {slice['filename']}, result for section will be linear")
newX, newY = scaledX, scaledY
else:
newX, newY = scaledX, scaledY
@@ -230,7 +230,7 @@ def SegmentationToAtlasSpaceMultiThreaded(
triangulation = triangulate(RegWidth, RegHeight, slice["markers"])
newX, newY = transform_vec(triangulation, scaledX, scaledY)
else:
- print(f"no markers found for " + slice["filename"])
+ print(f"no markers found for {slice['filename']}, result for section will be linear")
newX, newY = scaledX, scaledY
else:
newX, newY = scaledX, scaledY
diff --git a/PyNutil/main.py b/PyNutil/main.py
index 71fd2b3..f87b633 100644
--- a/PyNutil/main.py
+++ b/PyNutil/main.py
@@ -1,24 +1,44 @@
from .metadata import metadata_loader
from .read_and_write import readAtlasVolume
-
+from .coordinate_extraction import FolderToAtlasSpaceMultiThreaded
+import json
class PyNutil:
def __init__(
self,
- segmentation_folder,
- json_file,
- colour,
- atlas,
+ segmentation_folder=None,
+ alignment_json=None,
+ colour=None,
+ volume_path=None,
+ settings_file=None,
) -> None:
self.config, self.metadata_path = metadata_loader.load_config()
- if atlas not in self.config["annotation_volumes"]:
+ if settings_file is not None:
+ with open(settings_file, "r") as f:
+ settings = json.load(f)
+ try:
+ segmentation_folder = settings["segmentation_folder"]
+ alignment_json = settings["alignment_json"]
+ colour = settings["colour"]
+ volume_path = settings["volume_path"]
+ except KeyError as exc:
+ raise KeyError(
+ "settings file must contain segmentation_folder, alignment_json, colour, and volume_path"
+ ) from exc
+ # check if any values are None
+ if None in [segmentation_folder, alignment_json, colour, volume_path]:
+ raise ValueError(
+ "segmentation_folder, alignment_json, colour, and volume_path must all be specified and not be None"
+ )
+ if volume_path not in self.config["annotation_volumes"]:
raise ValueError(
- f"Atlas {atlas} not found in config file, valid atlases are: \n{' , '.join(list(self.config['annotation_volumes'].keys()))}"
+ f"Atlas {volume_path} not found in config file, valid atlases are: \n{' , '.join(list(self.config['annotation_volumes'].keys()))}"
)
+
self.segmentation_folder = segmentation_folder
- self.json_file = json_file
+ self.alignment_json = alignment_json
self.colour = colour
- self.atlas = atlas
+ self.atlas = volume_path
# load the metadata json as well as the path to stored data files
def build_quantifier(self):
@@ -27,7 +47,21 @@ class PyNutil:
current_atlas_path = self.config["annotation_volumes"][self.atlas]["volume"]
print("loading atlas volume")
self.atlas_volume = readAtlasVolume(atlas_root_path + current_atlas_path)
+ print("atlas volume loaded")
- def get_coordinates(self):
+ def get_coordinates(self, nonLinear=True, method="all"):
if not hasattr(self, "atlas_volume"):
raise ValueError("Please run build_quantifier before running get_coordinates")
+ if method not in ["per_pixel", "per_object", "all"]:
+ raise ValueError(f"method {method} not recognised, valid methods are: per_pixel, per_object, or all")
+ print("extracting coordinates")
+ points = FolderToAtlasSpaceMultiThreaded(
+ self.segmentation_folder,
+ self.alignment_json,
+ pixelID=self.colour,
+ nonLinear=nonLinear
+ )
+ self.points = points
+
+
+
diff --git a/test/test1.json b/test/test1.json
index c8f58ec..6ce2ef4 100644
--- a/test/test1.json
+++ b/test/test1.json
@@ -1,9 +1,9 @@
-{ "volume_path": "../annotation_volumes/annotation_10_reoriented_2017.nrrd",
+{ "volume_path": "allen2017",
"label_path": "../annotation_volumes/allen2017_colours.csv",
- "segmentation_folder": "../test_data/ttA_2877_NOP_segmentations",
- "alignment_json": "../test_data/ttA_2877_NOP_horizontal_final_2017.json",
+ "segmentation_folder": "test_data/ttA_2877_NOP_segmentations",
+ "alignment_json": "test_data/ttA_2877_NOP_horizontal_final_2017.json",
"nonlinear": true,
"colour": [0, 0, 255],
- "points_json_path": "../outputs/test1_points.json",
- "counts_per_label_name": "../outputs/test1_counts_per_allenID_2017.csv"
+ "points_json_path": "outputs/test1_points.json",
+ "counts_per_label_name": "outputs/test1_counts_per_allenID_2017.csv"
}
\ No newline at end of file
diff --git a/test/test4_2017.json b/test/test4_2017.json
index 9589000..bdb3959 100644
--- a/test/test4_2017.json
+++ b/test/test4_2017.json
@@ -1,9 +1,9 @@
-{ "volume_path": "../annotation_volumes/annotation_10_reoriented_2017.nrrd",
- "label_path": "../annotation_volumes/allen2017_colours.csv",
- "segmentation_folder": "../test_data/oneSection15",
- "alignment_json": "../test_data/C68_nonlinear_no_markers.json",
+{ "volume_path": "allen2017",
+ "label_path": "annotation_volumes/allen2017_colours.csv",
+ "segmentation_folder": "test_data/oneSection15",
+ "alignment_json": "test_data/C68_nonlinear_no_markers.json",
"nonlinear": true,
"colour": [255, 0, 255],
- "points_json_path": "../outputs/test4_points.json",
- "counts_per_label_name": "../outputs/test4_counts_per_allen2017.csv"
+ "points_json_path": "outputs/test4_points.json",
+ "counts_per_label_name": "outputs/test4_counts_per_allen2017.csv"
}
\ No newline at end of file
diff --git a/testOOP.py b/testOOP.py
index 2c6c0e3..92ee5f3 100644
--- a/testOOP.py
+++ b/testOOP.py
@@ -1,15 +1,8 @@
from PyNutil import PyNutil
-
-
-
-
pnt = PyNutil(
- 'test',
- 'test',
- [0,0,0],
- "allen2017")
-
+ settings_file=r"test/test4_2017.json"
+ )
pnt.build_quantifier()
pnt.get_coordinates()
--
GitLab