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WIP: Move all the TIFF metadata into datasets #437

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WIP: Move all the TIFF metadata into datasets #437

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25 changes: 18 additions & 7 deletions nanshe/io/xtiff.py
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Original file line number Diff line number Diff line change
Expand Up @@ -457,20 +457,30 @@ def convert_tiffs(new_tiff_filenames,
new_hdf5_dataset_dtype,
chunks=True
)
new_hdf5_dataset.attrs.create(
"filenames",
new_hdf5_dataset_filenames,
shape=new_hdf5_dataset_filenames.shape,
dtype=h5py.special_dtype(vlen=unicode)
)
new_hdf5_dataset.attrs["offsets"] = new_hdf5_dataset_offsets
# Workaround required due to this issue
# ( https://github.com/h5py/h5py/issues/289 ).
new_hdf5_filenames_dataset = new_hdf5_group.create_dataset(
"_".join([new_hdf5_dataset_name, "filenames"]),
shape=new_hdf5_dataset_filenames.shape[0:1],
dtype=h5py.special_dtype(vlen=unicode)
)
new_hdf5_offsets_dataset = new_hdf5_group.create_dataset(
"_".join([new_hdf5_dataset_name, "offsets"]),
data=new_hdf5_dataset_offsets
)
new_hdf5_descriptions_dataset = new_hdf5_group.create_dataset(
"_".join([new_hdf5_dataset_name, "descriptions"]),
shape=new_hdf5_dataset_shape[0:1],
dtype=h5py.special_dtype(vlen=unicode)
)
new_hdf5_dataset.attrs["filenames"] = (
new_hdf5_filenames_dataset.file.filename +
new_hdf5_filenames_dataset.name
)
new_hdf5_dataset.attrs["offsets"] = (
new_hdf5_offsets_dataset.file.filename +
new_hdf5_offsets_dataset.name
)
new_hdf5_dataset.attrs["descriptions"] = (
new_hdf5_descriptions_dataset.file.filename +
new_hdf5_descriptions_dataset.name
Expand Down Expand Up @@ -501,5 +511,6 @@ def convert_tiffs(new_tiff_filenames,
new_hdf5_dataset_axis_pos_next = new_hdf5_dataset_axis_pos + \
len(each_new_tiff_array)
new_hdf5_dataset[new_hdf5_dataset_axis_pos:new_hdf5_dataset_axis_pos_next] = each_new_tiff_array
new_hdf5_filenames_dataset[new_hdf5_dataset_axis_pos:new_hdf5_dataset_axis_pos_next] = each_new_tiff_filename
new_hdf5_descriptions_dataset[new_hdf5_dataset_axis_pos:new_hdf5_dataset_axis_pos_next] = each_new_tiff_description
new_hdf5_dataset_axis_pos = new_hdf5_dataset_axis_pos_next