Flat to array fix

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

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
+