Add script for merging dataset hdf5 files.

.gitattributes

@@ -58,3 +58,7 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
 bioscan_5m_dna_IndexFlatIP.index filter=lfs diff=lfs merge=lfs -text
 bioscan_5m_image_IndexFlatIP.index filter=lfs diff=lfs merge=lfs -text
+data/INSECT/* filter=lfs diff=lfs merge=lfs -text
+data/INSECT/** filter=lfs diff=lfs merge=lfs -text
+*.hdf5 filter=lfs diff=lfs merge=lfs -text
+data/** filter=lfs diff=lfs merge=lfs -text

merge_bioscan_1m.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python3
+import os
+import glob
+
+def merge_files(parts_dir, output_file, base_filename):
+    pattern = os.path.join(parts_dir, f"{base_filename}.part*")
+    parts = sorted(glob.glob(pattern))
+    if not parts:
+        print("No files found")
+        return
+
+    print(f"found {len(parts)} files, merge to {output_file} ...")
+    with open(output_file, 'wb') as outfile:
+        for part in parts:
+            print(f"Merging: {part} ...")
+            with open(part, 'rb') as infile:
+                while True:
+                    data = infile.read(1024 * 1024)
+                    if not data:
+                        break
+                    outfile.write(data)
+    print(f"Merged: {output_file}")
+
+if __name__ == '__main__':
+    parts_dir = "data/BIOSCAN_1M/split_data/splitted_files"
+    base_filename = "BioScan_data_in_splits.hdf5"
+    output_file = "data/BIOSCAN_1M/split_data/BioScan_data_in_splits.hdf5"
+    merge_files(parts_dir, output_file, base_filename)

merge_bioscan_5m.py

@@ -12,7 +12,7 @@ def merge_files(parts_dir, output_file, base_filename):
     print(f"found {len(parts)} files, merge to {output_file} ...")
     with open(output_file, 'wb') as outfile:
         for part in parts:
-            print(f"合并文件: {part} ...")
+            print(f"Merging: {part} ...")
             with open(part, 'rb') as infile:
                 while True:
                     data = infile.read(1024 * 1024)
@@ -22,7 +22,7 @@ def merge_files(parts_dir, output_file, base_filename):
     print(f"Merged: {output_file}")
 
 if __name__ == '__main__':
-    parts_dir = "data/BIOSCAN_1M/split_data/splitted_files"
-    base_filename = "BioScan_data_in_splits.hdf5"
-    output_file = "data/BIOSCAN_1M/split_data/BioScan_data_in_splits_merged.hdf5"
+    parts_dir = "data/BIOSCAN_5M/splitted_files"
+    base_filename = "BIOSCAN_5M.hdf5"
+    output_file = "data/BIOSCAN_5M/BIOSCAN_5M.hdf5"
     merge_files(parts_dir, output_file, base_filename)

split_bioscan_1m.py

@@ -0,0 +1,30 @@
+import os
+
+def split_file(input_file, output_dir, chunk_size):
+    if not os.path.exists(output_dir):
+        os.makedirs(output_dir)
+
+    file_size = os.path.getsize(input_file)
+    base_name = os.path.basename(input_file)
+    num_chunks = (file_size + chunk_size - 1) // chunk_size
+    print(f"Total size: {file_size} bytes, split to {num_chunks} files")
+
+    with open(input_file, 'rb') as f:
+        for i in range(num_chunks):
+            part_filename = os.path.join(output_dir, f"{base_name}.part{i + 1:03d}")
+            with open(part_filename, 'wb') as part_file:
+                bytes_written = 0
+                while bytes_written < chunk_size:
+                    buffer = f.read(min(1024 * 1024, chunk_size - bytes_written))
+                    if not buffer:
+                        break
+                    part_file.write(buffer)
+                    bytes_written += len(buffer)
+            print(f"Write to: {part_filename} Size: {bytes_written} bytes")
+
+
+if __name__ == '__main__':
+    input_file = "data/BIOSCAN_1M/split_data/BioScan_data_in_splits.hdf5"
+    output_dir = "data/BIOSCAN_1M/split_data/splitted_files"
+    chunk_size = 45 * (1024 ** 3)
+    split_file(input_file, output_dir, chunk_size)

split_bioscan_5m.py

@@ -24,7 +24,7 @@ def split_file(input_file, output_dir, chunk_size):
 
 
 if __name__ == '__main__':
-    input_file = "data/BIOSCAN_1M/split_data/BioScan_data_in_splits.hdf5"
-    output_dir = "data/BIOSCAN_1M/split_data/splitted_files"
+    input_file = "data/BIOSCAN_5M/BIOSCAN_5M.hdf5"
+    output_dir = "data/BIOSCAN_5M/splitted_files"
     chunk_size = 45 * (1024 ** 3)
     split_file(input_file, output_dir, chunk_size)