Fix error in cochlea rescaling

Author: constantinpape

scripts/resize_wrongly_scaled_cochleas.py

@@ -1,19 +1,24 @@
 import argparse
-import sys, os
+import os
 
 import multiprocessing as mp
 from concurrent import futures
 
 import imageio.v3 as imageio
-import numpy as np
 import nifty.tools as nt
 from tqdm import tqdm
 
 from elf.wrapper.resized_volume import ResizedVolume
 from elf.io import open_file
 
+
 def main(input_path, output_folder, scale, input_key, interpolation_order):
-    input_ = open_file(input_path, "r")[input_key]
+    if input_path.endswith(".tif"):
+        input_ = imageio.imread(input_path)
+        input_chunks = (128,) * 3
+    else:
+        input_ = open_file(input_path, "r")[input_key]
+        input_chunks = input_.chunks
 
     abs_path = os.path.abspath(input_path)
     basename = "".join(os.path.basename(abs_path).split(".")[:-1])
@@ -33,17 +38,20 @@ def main(input_path, output_folder, scale, input_key, interpolation_order):
     resized_volume = ResizedVolume(input_, new_shape, order=interpolation_order)
 
     output = open_file(output_path, mode="a")
-    dataset = output.create_dataset(input_key, shape=new_shape, dtype = input_.dtype, chunks=input_.chunks, compression="gzip")
-    blocking = nt.blocking([0] * ndim, new_shape, input_.chunks)
+    output_dataset = output.create_dataset(
+        input_key, shape=new_shape, dtype=input_.dtype,
+        chunks=input_chunks, compression="gzip"
+    )
+    blocking = nt.blocking([0] * ndim, new_shape, input_chunks)
 
     def copy_chunk(block_index):
-          block = blocking.getBlock(block_index)
-          volume_index = tuple(slice(begin, end) for (begin, end) in zip(block.begin, block.end))
-          data = resized_volume[volume_index]
-          output[volume_index] = data
+        block = blocking.getBlock(block_index)
+        volume_index = tuple(slice(begin, end) for (begin, end) in zip(block.begin, block.end))
+        data = resized_volume[volume_index]
+        output_dataset[volume_index] = data
 
     with futures.ThreadPoolExecutor(n_threads) as resize_pool:
-          list(tqdm(resize_pool.map(copy_chunk, range(blocking.numberOfBlocks)), total=blocking.numberOfBlocks))
+        list(tqdm(resize_pool.map(copy_chunk, range(blocking.numberOfBlocks)), total=blocking.numberOfBlocks))
 
 
 if __name__ == "__main__":
@@ -52,12 +60,14 @@ def copy_chunk(block_index):
         description="Script for resizing microscoopy data in n5 format.")
 
     parser.add_argument('input_file', type=str, help="Input file")
-    parser.add_argument('output_folder', type=str, help="Output folder. Default resized output is <basename>_resized.n5")
+    parser.add_argument(
+        'output_folder', type=str, help="Output folder. Default resized output is <basename>_resized.n5"
+    )
 
     parser.add_argument('-s', "--scale", type=float, default=0.38, help="Scale of input. Re-scaled to 1.")
     parser.add_argument('-k', "--input_key", type=str, default="setup0/timepoint0/s0", help="Input key for n5 file.")
     parser.add_argument('-i', "--interpolation_order", type=float, default=3, help="Interpolation order.")
 
     args = parser.parse_args()
 
-    main(args.input_file, args.output_folder, args.scale, args.input_key, args.interpolation_order)
+    main(args.input_file, args.output_folder, args.scale, args.input_key, args.interpolation_order)