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change to relative paths #170

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Jul 26, 2024
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10 changes: 5 additions & 5 deletions python/ndstorage/_superclass.py
Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
import os
from ndstorage.ndtiff_dataset import NDTiffDataset
from ndstorage.ndtiff_pyramid_dataset import NDTiffPyramidDataset
from ndstorage.old_format_version_readers.nd_tiff_v2 import NDTiff_v2_0
from ndstorage.old_format_version_readers.ndtiff_v1 import NDTiff_v1
from .ndtiff_dataset import NDTiffDataset
from .ndtiff_pyramid_dataset import NDTiffPyramidDataset
from .old_format_version_readers.nd_tiff_v2 import NDTiff_v2_0
from .old_format_version_readers.ndtiff_v1 import NDTiff_v1
import numpy as np
from ndstorage.file_io import NDTiffFileIO, BUILTIN_FILE_IO
from .file_io import NDTiffFileIO, BUILTIN_FILE_IO

class Dataset:
"""
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2 changes: 1 addition & 1 deletion python/ndstorage/ndram_dataset.py
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
from typing import List, Dict, Union

import threading
from ndstorage.ndstorage_base import WritableNDStorageAPI, NDStorageBase
from .ndstorage_base import WritableNDStorageAPI, NDStorageBase


class NDRAMDataset(NDStorageBase, WritableNDStorageAPI):
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2 changes: 1 addition & 1 deletion python/ndstorage/ndstorage_base.py
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@
import dask.array as da
import threading

from ndstorage.ndtiff_file import _POSITION_AXIS, _ROW_AXIS, _COLUMN_AXIS, _Z_AXIS, _TIME_AXIS, _CHANNEL_AXIS
from .ndtiff_file import _POSITION_AXIS, _ROW_AXIS, _COLUMN_AXIS, _Z_AXIS, _TIME_AXIS, _CHANNEL_AXIS

# Standard order of axes when opening data. Data does not need to be acquired in this order -- this is just a convention
_AXIS_ORDER = {_ROW_AXIS: 7,
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12 changes: 6 additions & 6 deletions python/ndstorage/ndtiff_dataset.py
Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,14 @@
import warnings
import re

from ndstorage.file_io import NDTiffFileIO, BUILTIN_FILE_IO
from ndstorage.ndtiff_file import SingleNDTiffReader
from ndstorage.ndtiff_file import _CHANNEL_AXIS
from ndstorage.ndtiff_index import NDTiffIndexEntry, read_ndtiff_index
from .file_io import NDTiffFileIO, BUILTIN_FILE_IO
from .ndtiff_file import SingleNDTiffReader
from .ndtiff_file import _CHANNEL_AXIS
from .ndtiff_index import NDTiffIndexEntry, read_ndtiff_index

from ndstorage.ndtiff_file import SingleNDTiffWriter, MAJOR_VERSION, MINOR_VERSION
from .ndtiff_file import SingleNDTiffWriter, MAJOR_VERSION, MINOR_VERSION

from ndstorage.ndstorage_base import WritableNDStorageAPI, NDStorageBase
from .ndstorage_base import WritableNDStorageAPI, NDStorageBase

class NDTiffDataset(NDStorageBase, WritableNDStorageAPI):
"""
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4 changes: 2 additions & 2 deletions python/ndstorage/ndtiff_file.py
Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,8 @@
import warnings
from collections import OrderedDict
from io import BytesIO
from ndstorage.file_io import NDTiffFileIO, BUILTIN_FILE_IO
from ndstorage.ndtiff_index import NDTiffIndexEntry
from .file_io import NDTiffFileIO, BUILTIN_FILE_IO
from .ndtiff_index import NDTiffIndexEntry

from collections import deque
from concurrent.futures import ThreadPoolExecutor
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4 changes: 2 additions & 2 deletions python/ndstorage/ndtiff_pyramid_dataset.py
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
import os
import numpy as np
import threading
from ndstorage.file_io import NDTiffFileIO, BUILTIN_FILE_IO
from ndstorage.ndtiff_dataset import NDTiffDataset
from .file_io import NDTiffFileIO, BUILTIN_FILE_IO
from .ndtiff_dataset import NDTiffDataset

class NDTiffPyramidDataset:
"""Class that opens a single NDTiffStorage multi-resolution pyramid dataset"""
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2 changes: 1 addition & 1 deletion python/ndstorage/old_format_version_readers/nd_tiff_v2.py
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
import warnings
import struct
import threading
from ndstorage.file_io import NDTiffFileIO, BUILTIN_FILE_IO
from .file_io import NDTiffFileIO, BUILTIN_FILE_IO

_POSITION_AXIS = "position"
_ROW_AXIS = "row"
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2 changes: 1 addition & 1 deletion python/ndstorage/old_format_version_readers/ndtiff_v1.py
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
import dask.array as da
import warnings
import struct
from ndstorage.file_io import NDTiffFileIO, BUILTIN_FILE_IO
from .file_io import NDTiffFileIO, BUILTIN_FILE_IO

class _MultipageTiffReader:
# Class corresponsing to a single multipage tiff file in a Micro-Magellan dataset. Pass the full path of the TIFF to
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4 changes: 2 additions & 2 deletions python/ndstorage/test/write_speed_test.py
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
# import numpy as np
# import os
# import shutil
# from ndstorage.ndtiff_file import SingleNDTiffWriter, SingleNDTiffReader
# from ndstorage.ndtiff_dataset import NDTiffDataset
# from .ndtiff_file import SingleNDTiffWriter, SingleNDTiffReader
# from .ndtiff_dataset import NDTiffDataset
# import pytest
# import time
# from tqdm import tqdm
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6 changes: 3 additions & 3 deletions python/ndstorage/test/writing_test.py
Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
import numpy as np
import os
import shutil
from ndstorage.ndtiff_file import SingleNDTiffWriter, SingleNDTiffReader
from ndstorage.ndtiff_dataset import NDTiffDataset
from ndstorage.ndram_dataset import NDRAMDataset
from .ndtiff_file import SingleNDTiffWriter, SingleNDTiffReader
from .ndtiff_dataset import NDTiffDataset
from .ndram_dataset import NDRAMDataset
import pytest

@pytest.fixture(scope="function")
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