From eb80e04c1e0b06b67628197f5b803ab557599bc7 Mon Sep 17 00:00:00 2001
From: sharoncy <s.c.yates@medisin.uio.no>
Date: Thu, 11 May 2023 12:47:34 +0200
Subject: [PATCH] Create SaveDataframeasCSV function
---
PyNutil/coordinate_extraction.py | 7 +++++--
.../folder_of_segmentations_to_meshview_multithreaded.py | 6 ++++--
PyNutil/read_and_write.py | 8 +++++++-
3 files changed, 16 insertions(+), 5 deletions(-)
diff --git a/PyNutil/coordinate_extraction.py b/PyNutil/coordinate_extraction.py
index fecb68f..1edb063 100644
--- a/PyNutil/coordinate_extraction.py
+++ b/PyNutil/coordinate_extraction.py
@@ -273,7 +273,7 @@ def labelPoints(points, label_volume, scale_factor=1):
# related to object_counting
# consider separating out writing to CSV in future
-def PixelCountPerRegion(labelsDict, label_colours, output_csv):
+def PixelCountPerRegion(labelsDict, label_colours):
"""Function for counting no. of pixels per region and writing to CSV based on
a dictionary with the region as the key and the points as the value, """
counted_labels, label_counts = np.unique(labelsDict, return_counts=True)
@@ -305,6 +305,9 @@ def PixelCountPerRegion(labelsDict, label_colours, output_csv):
new_rows.append(row)
df_counts_per_label_name = pd.DataFrame(new_rows)
+ return df_counts_per_label_name
- df_counts_per_label_name.to_csv(output_csv, sep=";", na_rep='', index= False)
+
+#def SaveDataframeasCSV(df_to_save):
+ #df_to_save.to_csv(output_csv, sep=";", na_rep='', index= False)
diff --git a/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py b/PyNutil/folder_of_segmentations_to_meshview_multithreaded.py
index 001cc7d..7c1d695 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/test2.json', 'r') as f:
#import our function for converting a folder of segmentations to points
from coordinate_extraction import FolderToAtlasSpace, labelPoints, WritePointsToMeshview, FolderToAtlasSpaceMultiThreaded, PixelCountPerRegion
-#from read_and_write import WritePointsToMeshview
+from read_and_write import SaveDataframeasCSV
startTime = datetime.now()
@@ -37,7 +37,9 @@ labels = labelPoints(points, data, scale_factor=2.5)
#save points to a meshview json
WritePointsToMeshview(points, labels, input["points_json_path"], label_df)
-PixelCountPerRegion(labels, input["allen_colours"], input["counts_per_label_name"])
+df_counts_per_label_name = PixelCountPerRegion(labels, input["allen_colours"])
+
+SaveDataframeasCSV(df_counts_per_label_name, input["counts_per_label_name"])
#while we havent added it here it would be good to next quantify the number of cells for each label.
diff --git a/PyNutil/read_and_write.py b/PyNutil/read_and_write.py
index 205de7a..e791c78 100644
--- a/PyNutil/read_and_write.py
+++ b/PyNutil/read_and_write.py
@@ -1,5 +1,6 @@
import json
+
#related to read and write: loadVisuAlignJson
def loadVisuAlignJson(filename):
with open(filename) as f:
@@ -34,4 +35,9 @@ def WritePoints(pointsDict, filename, infoFile):
def WritePointsToMeshview(points, pointNames, filename, infoFile):
"""this is the function you call more often as it combines the other functions for writing meshview"""
regionDict = createRegionDict(points, pointNames)
- WritePoints(regionDict, filename, infoFile)
\ No newline at end of file
+ WritePoints(regionDict, filename, infoFile)
+
+
+def SaveDataframeasCSV(df_to_save, output_csv):
+ """Function for saving a df as a CSV file"""
+ df_to_save.to_csv(output_csv, sep=";", na_rep='', index= False)
\ No newline at end of file
--
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