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assemble_data.py

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+import argparse
+import os
+from netCDF4 import Dataset
+
+
+def assemble_data(input_dir, output_file):
+ nc_files = [f for f in os.listdir(input_dir) if f.endswith(".nc")]
+ nc_files.sort()
+
+ samples = [0]
+ with Dataset(os.path.join(input_dir, nc_files[0]), "r") as first_nc:
+ samples.append(first_nc.dimensions["sample"].size)
+ num_times = first_nc.dimensions["time"].size
+ try:
+ num_channels = first_nc.dimensions["channel"].size
+ except:
+ num_channels = None
+ x_size = first_nc.dimensions["x"].size
+ y_size = first_nc.dimensions["y"].size
+ dtype = first_nc.variables[nc_files[0].split("_")[0]].dtype
+
+ for nc_file in nc_files[1:]:
+ with Dataset(os.path.join(input_dir, nc_file), "r") as nc:
+ samples.append(nc.dimensions["sample"].size)
+
+ num_samples = sum(samples)
+ for i in range(1, len(samples)):
+ samples[i] += samples[i - 1]
+ with Dataset(output_file, "w") as out_nc:
+ out_nc.createDimension("sample", num_samples)
+ out_nc.createDimension("time", num_times)
+ if num_channels is not None:
+ out_nc.createDimension("channel", num_channels)
+ out_nc.createDimension("x", x_size)
+ out_nc.createDimension("y", y_size)
+ if num_channels is not None:
+ out_nc.createVariable(
+ nc_files[0].split("_")[0], dtype, ("sample", "time", "channel", "x", "y")
+ )
+ else:
+ out_nc.createVariable(
+ nc_files[0].split("_")[0], dtype, ("sample", "time", "x", "y")
+ )
+
+ for i, nc_file in enumerate(nc_files):
+ with Dataset(os.path.join(input_dir, nc_file), "r") as nc:
+ print(f"Processing {os.path.join(input_dir, nc_file)}")
+ variable = nc.variables[nc_file.split("_")[0]]
+ out_nc[nc_file.split("_")[0]][samples[i] : samples[i + 1]] = variable[:]
+
+ print(f"Saved data to {output_file}")
+
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser()
+ parser.add_argument("--input_dir", type=str, required=True)
+ parser.add_argument("--output_file", type=str, required=True)
+ args = parser.parse_args()
+
+ assemble_data(args.input_dir, args.output_file)