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Small patch to html repr in #1100 #1201

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merged 4 commits into from
Nov 11, 2024
Merged

Small patch to html repr in #1100 #1201

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abc0efe
small patch to html repr
h-mayorquin Nov 6, 2024
1fc5879
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 6, 2024
b84008b
Merge branch 'dev' into patch_to_html_repr
stephprince Nov 8, 2024
35915d1
comment request
h-mayorquin Nov 9, 2024
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31 changes: 17 additions & 14 deletions src/hdmf/backends/hdf5/h5tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1609,22 +1609,25 @@
def generate_dataset_html(dataset):
"""Generates an html representation for a dataset for the HDF5IO class"""

# get info from hdf5 dataset
compressed_size = dataset.id.get_storage_size()
if hasattr(dataset, "nbytes"): # TODO: Remove this after h5py minimal version is larger than 3.0
uncompressed_size = dataset.nbytes
else:
uncompressed_size = dataset.size * dataset.dtype.itemsize
compression_ratio = uncompressed_size / compressed_size if compressed_size != 0 else "undefined"
array_info_dict = get_basic_array_info(dataset)
if isinstance(dataset, h5py.Dataset):

hdf5_info_dict = {"Chunk shape": dataset.chunks,
"Compression": dataset.compression,
"Compression opts": dataset.compression_opts,
"Compression ratio": compression_ratio}
# get info from hdf5 dataset
compressed_size = dataset.id.get_storage_size()
if hasattr(dataset, "nbytes"): # TODO: Remove this after h5py minimal version is larger than 3.0
uncompressed_size = dataset.nbytes
else:
uncompressed_size = dataset.size * dataset.dtype.itemsize

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compression_ratio = uncompressed_size / compressed_size if compressed_size != 0 else "undefined"

# get basic array info
array_info_dict = get_basic_array_info(dataset)
array_info_dict.update(hdf5_info_dict)
hdf5_info_dict = {
"Chunk shape": dataset.chunks,
"Compression": dataset.compression,
"Compression opts": dataset.compression_opts,
"Compression ratio": compression_ratio,
}

array_info_dict.update(hdf5_info_dict)

# generate html repr
repr_html = generate_array_html_repr(array_info_dict, dataset, "HDF5 dataset")
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2 changes: 1 addition & 1 deletion src/hdmf/container.py
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Original file line number Diff line number Diff line change
Expand Up @@ -754,7 +754,7 @@ def _generate_array_html(self, array, level):
"""Generates HTML for array data"""

read_io = self.get_read_io() # if the Container was read from file, get IO object
if read_io is not None:
if read_io is not None: # Note that sometimes numpy array have a read_io attribute
repr_html = read_io.generate_dataset_html(array)
else:
array_info_dict = get_basic_array_info(array)
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