From 37b10118747e82b0a984308e841bb23c9da2bdde Mon Sep 17 00:00:00 2001
From: sharoncy <s.c.yates@medisin.uio.no>
Date: Mon, 22 May 2023 17:18:21 +0200
Subject: [PATCH] Flat to array fix
---
PyNutil/load_workflow.py | 5 +++--
PyNutil/read_and_write.py | 16 ++++++++++++++--
2 files changed, 17 insertions(+), 4 deletions(-)
diff --git a/PyNutil/load_workflow.py b/PyNutil/load_workflow.py
index 07c363e..ccacb26 100644
--- a/PyNutil/load_workflow.py
+++ b/PyNutil/load_workflow.py
@@ -3,16 +3,17 @@ import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
-from read_and_write import FlattoArray
+from read_and_write import FlattoArray, LabeltoArray
base= r"../test_data/ttA_2877_NOP_atlasmaps/2877_NOP_tTA_lacZ_Xgal_s037_nl.flat"
+label = r"../annotation_volumes\allen2017_colours.csv"
image_arr = FlattoArray(base)
plt.imshow(FlattoArray(base))
"""assign label file values into image array"""
-labelfile = pd.read_csv("../annotation_volumes/allen2017_colours.csv")
+labelfile = pd.read_csv(r"../annotation_volumes\allen2017_colours.csv")
allen_id_image = np.zeros((h,w)) # create an empty image array
coordsy, coordsx = np.meshgrid(list(range(w)), list(range(h)))
values = image_arr[coordsx, coordsy] # assign x,y coords from image_array into values
diff --git a/PyNutil/read_and_write.py b/PyNutil/read_and_write.py
index e474329..7d11ea1 100644
--- a/PyNutil/read_and_write.py
+++ b/PyNutil/read_and_write.py
@@ -56,7 +56,7 @@ def SaveDataframeasCSV(df_to_save, output_csv):
def FlattoArray(flatfile):
- """Read flat file and write into an np array"""
+ """Read flat file and write into an np array, return array"""
with open(flatfile,"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
@@ -75,4 +75,16 @@ def FlattoArray(flatfile):
image[y,x] = imagedata[x+y*w]
image_arr = np.array(image)
- return image_arr
\ No newline at end of file
+ return image_arr
+
+
+def LabeltoArray(label_path, image_array):
+ """assign label file values into image array, return array"""
+ labelfile = pd.read_csv(label_path)
+ allen_id_image = np.zeros((h,w)) # create an empty image array
+ coordsy, coordsx = np.meshgrid(list(range(w)), list(range(h)))
+ values = image_array[coordsx, coordsy] # assign x,y coords from image_array into values
+ lbidx = labelfile['idx'].values
+ allen_id_image = lbidx[values.astype(int)] # assign allen IDs into image array
+ return allen_id_image
+
--
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