From 83bc3fd222f0d05843bb87a5f8dc6bb7495f3a73 Mon Sep 17 00:00:00 2001
From: sharoncy <s.c.yates@medisin.uio.no>
Date: Tue, 23 May 2023 11:05:14 +0200
Subject: [PATCH] FilesinDirectory function
Create a list of flat file names
---
...segmentations_to_meshview_multithreaded.py | 15 +++++--
PyNutil/load_workflow.py | 13 +++++-
PyNutil/read_and_write.py | 15 +++++++
PyNutil/testing.py | 23 ----------
PyNutil/testing_sharon.py | 43 +++++++++++++++++++
5 files changed, 82 insertions(+), 27 deletions(-)
delete mode 100644 PyNutil/testing.py
create mode 100644 PyNutil/testing_sharon.py
diff --git a/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py b/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py
index b9ba254..9e5625d 100644
--- a/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py
+++ b/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py
@@ -16,7 +16,7 @@ with open('../test/test1.json', 'r') as f:
#import our function for converting a folder of segmentations to points
from coordinate_extraction import FolderToAtlasSpace, FolderToAtlasSpaceMultiThreaded
-from read_and_write import SaveDataframeasCSV, WritePointsToMeshview
+from read_and_write import SaveDataframeasCSV, WritePointsToMeshview, FilesinDirectory
from counting_and_load import PixelCountPerRegion, labelPoints
startTime = datetime.now()
@@ -36,7 +36,7 @@ data, header = nrrd.read(input["volume_path"])
#now we can get the labels for each point
labels = labelPoints(points, data, scale_factor=2.5)
-#save points to a meshview json
+#save points to a meshview jsonv
WritePointsToMeshview(points, labels, input["points_json_path"], label_df)
df_counts_per_label_name = PixelCountPerRegion(labels, input["label_path"])
@@ -50,4 +50,13 @@ print(f"overall time taken was: {time_taken}")
#get centroids and areas returns a list of objects and the center coordinate.
#we need to deform the center coordinate according to visualign deformations¨
#we need to then transform the coordinate into atlas space
-#and then save labels like before.
\ No newline at end of file
+#and then save labels like before.
+
+
+
+
+
+# Create a list of flat file names from a directory:
+
+#flatfiles = FilesinDirectory('../test_data/ttA_2877_NOP_atlasmaps')
+#print(flatfiles)
\ No newline at end of file
diff --git a/PyNutil/load_workflow.py b/PyNutil/load_workflow.py
index ccacb26..7960ac8 100644
--- a/PyNutil/load_workflow.py
+++ b/PyNutil/load_workflow.py
@@ -20,4 +20,15 @@ values = image_arr[coordsx, coordsy] # assign x,y coords from image_array into v
lbidx = labelfile['idx'].values
allen_id_image = lbidx[values.astype(int)] # assign allen IDs into image array
-plt.imshow(allen_id_image)
\ No newline at end of file
+plt.imshow(allen_id_image)
+
+
+# Count area per unique label
+# Scale up to size of corresponding segmentation
+# calculate segmentation value per slice
+# divide segmentation value per idx per slice by area per idx per slice
+# output reports
+# also do for whole brain
+
+#Also to do:
+# fix position of clear label in label files
diff --git a/PyNutil/read_and_write.py b/PyNutil/read_and_write.py
index 7d11ea1..a701ebf 100644
--- a/PyNutil/read_and_write.py
+++ b/PyNutil/read_and_write.py
@@ -3,6 +3,7 @@ import numpy as np
import struct
import pandas as pd
import matplotlib.pyplot as plt
+import os
#related to read and write
@@ -88,3 +89,17 @@ def LabeltoArray(label_path, image_array):
allen_id_image = lbidx[values.astype(int)] # assign allen IDs into image array
return allen_id_image
+
+def FilesinDirectory(directory):
+ """return list of flat file names in a directory"""
+ list_of_files = []
+ for file in os.scandir(directory):
+ if file.path.endswith(".flat") and file.is_file:
+ #print(filename.path)
+ #newfilename, file_ext = os.path.splitext(filename)
+ #print(newfilename)
+ filename = os.path.basename(file)
+ newfilename, file_ext = os.path.splitext(filename)
+ list_of_files.append(newfilename)
+ return list_of_files
+
diff --git a/PyNutil/testing.py b/PyNutil/testing.py
deleted file mode 100644
index e38dda5..0000000
--- a/PyNutil/testing.py
+++ /dev/null
@@ -1,23 +0,0 @@
-
-import subprocess
-import sys
-import os
-import glob
-
-directory = ('../test')
-
-"""
-for filename in os.scandir(directory):
- if filename.is_file:
- print(filename.path)
-"""
-
-directory = ('../test')
-
-for filename in os.scandir(directory):
- if filename.path.endswith(".json") and filename.is_file:
- print(filename.path)
-
-
-
-
diff --git a/PyNutil/testing_sharon.py b/PyNutil/testing_sharon.py
new file mode 100644
index 0000000..0a4b188
--- /dev/null
+++ b/PyNutil/testing_sharon.py
@@ -0,0 +1,43 @@
+
+import subprocess
+import sys
+import os
+import glob
+
+dir = ('../test_data/ttA_2877_NOP_atlasmaps')
+"""fetch file names in a directory"""
+
+def FilesinDirectory(directory):
+ for file in os.scandir(directory):
+ if file.path.endswith(".flat") and file.is_file:
+ #print(filename.path)
+ #newfilename, file_ext = os.path.splitext(filename)
+ #print(newfilename)
+ filename = os.path.basename(file)
+ newfilename, file_ext = os.path.splitext(filename)
+ return newfilename
+
+#Question: how to return multiple file names into a list?
+
+
+files = []
+newfiles = files.append(FilesinDirectory('../test_data/ttA_2877_NOP_atlasmaps'))
+print(files)
+
+
+
+
+
+import os
+
+# file name with extension
+file_name = os.path.basename('../test_data/ttA_2877_NOP_atlasmaps')
+
+print(file_name)
+
+# file name without extension
+print(os.path.splitext(file_name)[0])
+
+
+
+
--
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