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Optimize reader #179

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9df1b0a
prevent duplicated reader object when writing in ndtiff dataset
LukasMicroscopy Mar 25, 2025
887520d
speed up random access reads with mmap in SingleNDTiffWriter
LukasMicroscopy Mar 25, 2025
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6 changes: 5 additions & 1 deletion python/ndstorage/ndtiff_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -258,7 +258,11 @@ def add_index_entry(self, data, new_image_updates=True):
self.index[frozenset(image_coordinates.items())] = index_entry

if index_entry.filename not in self._readers_by_filename:
new_reader = SingleNDTiffReader(os.path.join(self.path, index_entry.filename), file_io=self.file_io)
# prevent new reader object when writing:
if self._writable and self.current_writer.filename.split(os.sep)[-1] == index_entry.filename:
new_reader = self.current_writer.reader
else:
new_reader = SingleNDTiffReader(os.path.join(self.path, index_entry.filename), file_io=self.file_io)
self._readers_by_filename[index_entry.filename] = new_reader
# Should be the same on every file so resetting them is fine
self.major_version, self.minor_version = new_reader.major_version, new_reader.minor_version
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8 changes: 6 additions & 2 deletions python/ndstorage/ndtiff_file.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
import time
import struct
import warnings
import mmap
from collections import OrderedDict
from io import BytesIO
from .file_io import NDTiffFileIO, BUILTIN_FILE_IO
Expand Down Expand Up @@ -314,6 +315,8 @@ def __init__(self, tiff_path, file_io: NDTiffFileIO = BUILTIN_FILE_IO, summary_m
self.file_io = file_io
self.tiff_path = tiff_path
self.file = self.file_io.open(tiff_path, "rb")
# mmap speeds up random access
self.mmap_file = mmap.mmap(self.file.fileno(), 0, prot=mmap.PROT_READ)
if summary_md is None:
self.summary_md, self.first_ifd_offset = self._read_header()
else:
Expand All @@ -323,6 +326,7 @@ def __init__(self, tiff_path, file_io: NDTiffFileIO = BUILTIN_FILE_IO, summary_m

def close(self):
""" """
self.mmap_file.close()
self.file.close()

def _read_header(self):
Expand Down Expand Up @@ -364,8 +368,8 @@ def _read(self, start, end):
"""
convert to python ints
"""
self.file.seek(int(start), 0)
return self.file.read(end - start)
self.mmap_file.seek(int(start), 0)
return self.mmap_file.read(end - start)

def read_metadata(self, index):
return json.loads(
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