snapshot...

modules/util/hdf5_conversion.py

 import h5py
 import numpy as np
 import pandas as pd
+import random
 
 
 def hdf5_to_npz_csv(hdf5_filename, output_file_prefix, chunk_size=10000):
@@ -14,6 +15,15 @@ def hdf5_to_npz_csv(hdf5_filename, output_file_prefix, chunk_size=10000):
     chunk_size (int): Size of chunks to process at once (default is 1000).
     """
 
+    # # New step: keep only 10 mask values == True
+    # mask_indices = list(np.nonzero(mask)[0])
+    # if len(mask_indices) > 10:
+    #     selected_indices = random.sample(mask_indices, 10)
+    #     new_mask = np.zeros(mask.size).astype(np.bool)
+    #     new_mask[selected_indices] = True
+    #     mask = new_mask
+    #     keep_array.append(data[mask])
+
     # Step 1: Open HDF5 file
     with h5py.File(hdf5_filename, "r") as file:
         fov_mask = np.asarray(file["FOV_mask"])