Resize wrongly scaled cochleas

Author: schilling40

scripts/resize_wrongly_scaled_cochleas.py

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+import argparse
+import sys, 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]
+
+    abs_path = os.path.abspath(input_path)
+    basename = "".join(os.path.basename(abs_path).split(".")[:-1])
+    output_path = os.path.join(output_folder, basename + "_resized.n5")
+
+    shape = input_.shape
+    ndim = len(shape)
+
+    # Limit the number of cores for parallelization.
+    n_threads = min(16, mp.cpu_count())
+
+    shape = input_.shape
+    new_shape = tuple(
+        int(round(sh / scale)) for sh in shape
+    )
+
+    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)
+
+    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
+
+    with futures.ThreadPoolExecutor(n_threads) as resize_pool:
+          list(tqdm(resize_pool.map(copy_chunk, range(blocking.numberOfBlocks)), total=blocking.numberOfBlocks))
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser(
+        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('-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, args.output, args.scale, args.input_key, args.interpolation_order)