From 15d81c3973258ca86f20377278eefdf4f62cd927 Mon Sep 17 00:00:00 2001
From: sharoncy <s.c.yates@medisin.uio.no>
Date: Thu, 25 May 2023 11:05:25 +0200
Subject: [PATCH] Testing with Harry, clean up
---
PyNutil/folder_of_segmentations_to_meshview.py | 2 +-
PyNutil/main.py | 3 +--
PyNutil/metadata/config.json | 2 +-
PyNutil/oop_example.py | 14 ++++++++++++++
PyNutil/testing_openflatfile.py | 10 ++++++++--
test/test5_NOP_s037.json | 12 ++++++------
testOOP.py | 4 ++--
7 files changed, 33 insertions(+), 14 deletions(-)
create mode 100644 PyNutil/oop_example.py
diff --git a/PyNutil/folder_of_segmentations_to_meshview.py b/PyNutil/folder_of_segmentations_to_meshview.py
index 0fba9d9..2cfe10c 100644
--- a/PyNutil/folder_of_segmentations_to_meshview.py
+++ b/PyNutil/folder_of_segmentations_to_meshview.py
@@ -36,7 +36,7 @@ label_path = "../annotation_volumes//allen2022_colours.csv"
label_df = pd.read_csv(label_path)
# read the annotation volume, it also has a header but we don't need it
# now we can get the labels for each point
-labels = labelPoints(points, data, scale_factor=2.5)
+labels = labelPoints(points, data, scale_factor=1)
# save points to a meshview json
WritePointsToMeshview(points, labels, "../outputs/points.json", label_df)
diff --git a/PyNutil/main.py b/PyNutil/main.py
index 33927b6..1f14c29 100644
--- a/PyNutil/main.py
+++ b/PyNutil/main.py
@@ -6,7 +6,6 @@ import json
import pandas as pd
from datetime import datetime
-
class PyNutil:
def __init__(
self,
@@ -84,7 +83,7 @@ class PyNutil:
)
print("quantifying coordinates")
labeled_points = labelPoints(
- self.pixel_points, self.atlas_volume, scale_factor=2.5
+ self.pixel_points, self.atlas_volume, scale_factor=1
)
self.label_df = PixelCountPerRegion(labeled_points, self.atlas_labels)
self.labeled_points = labeled_points
diff --git a/PyNutil/metadata/config.json b/PyNutil/metadata/config.json
index 5cab460..064d131 100644
--- a/PyNutil/metadata/config.json
+++ b/PyNutil/metadata/config.json
@@ -5,7 +5,7 @@
},
"allen2017":{
"labels":"allen2017_colours.csv",
- "volume":"annotation_10_reoriented_2017.nrrd"
+ "volume":"annotation_25_reoriented_2017.nrrd"
},
"allen2022":{
"labels":"allen2022_colours.csv",
diff --git a/PyNutil/oop_example.py b/PyNutil/oop_example.py
new file mode 100644
index 0000000..4bdc2ee
--- /dev/null
+++ b/PyNutil/oop_example.py
@@ -0,0 +1,14 @@
+class Demo:
+ def __init__(self, test):
+ self.test = test
+
+ def print_test(self):
+ print(self.test)
+ self.output = 'success'
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/PyNutil/testing_openflatfile.py b/PyNutil/testing_openflatfile.py
index 2d7071c..e6e630e 100644
--- a/PyNutil/testing_openflatfile.py
+++ b/PyNutil/testing_openflatfile.py
@@ -3,9 +3,10 @@ import numpy as np
import struct
import pandas as pd
import matplotlib.pyplot as plt
+import cv2
"""read flat file and write into an np array"""
-
+np.set_printoptions(suppress=True)
with open(base, "rb") as f:
# i dont know what b is, w and h are the width and height that we get from the
# flat file header
@@ -27,12 +28,17 @@ with open(base, "rb") as f:
image[y, x] = imagedata[x + y * w]
image_arr = np.array(image)
+ print(image_arr.shape)
+ image_arr = cv2.resize(image_arr,(9848,12784),interpolation=cv2.INTER_NEAREST)
+ print(image_arr.shape)
+ val,count = np.unique(image_arr, return_counts=True)
+ print(list(zip(val,count)))
# show image with plt.imshow(image_arr)
"""assign label file values into image array"""
-labelfile = pd.read_csv(r"../annotation_volumes\allen2017_colours.csv")
+labelfile = pd.read_csv(r"../metadata/annotation_volumes\allen2017_colours.csv")
allen_id_image = np.zeros((h, w)) # create an empty image array
"""for ph in range(h):
diff --git a/test/test5_NOP_s037.json b/test/test5_NOP_s037.json
index f837711..d53d90f 100644
--- a/test/test5_NOP_s037.json
+++ b/test/test5_NOP_s037.json
@@ -1,10 +1,10 @@
-{ "volume_path": "../annotation_volumes/annotation_10_reoriented_2017.nrrd",
- "label_path": "../annotation_volumes/allen2017_colours.csv",
- "segmentation_folder": "../test_data/ttA_2877_NOP_s037_seg",
- "alignment_json": "../test_data/ttA_2877_NOP_horizontal_final_2017.json",
+{ "volume_path": "allen2017",
+ "label_path": "annotation_volumes/allen2017_colours.csv",
+ "segmentation_folder": "test_data/ttA_2877_NOP_s037_seg",
+ "alignment_json": "test_data/ttA_2877_NOP_horizontal_final_2017.json",
"nonlinear": false,
"colour": [0, 0, 255],
- "points_json_path": "../outputs/test5_points.json",
- "counts_per_label_name": "../outputs/test5_counts_per_allenID_2017_false.csv"
+ "points_json_path": "outputs/test5_points.json",
+ "counts_per_label_name": "outputs/test5_counts_per_allenID_2017_false.csv"
}
diff --git a/testOOP.py b/testOOP.py
index 617dcf7..235481d 100644
--- a/testOOP.py
+++ b/testOOP.py
@@ -1,10 +1,10 @@
from PyNutil import PyNutil
-pnt = PyNutil(settings_file=r"test/test4_2017.json")
+pnt = PyNutil(settings_file=r"test/test5_NOP_s037.json")
# pnt.build_quantifier()
pnt.get_coordinates()
pnt.quantify_coordinates()
-pnt.save_analysis("outputs/test4_2017")
+pnt.save_analysis("outputs/test5_NOP_25")
--
GitLab