tomoscan.esrf.volume.hdf5volume.HDF5Volume#

class tomoscan.esrf.volume.hdf5volume.HDF5Volume(file_path=None, data_path=None, data=None, source_scan=None, metadata=None, data_url=None, metadata_url=None, overwrite=False)#

Bases: VolumeBase

Volume where both data and metadata are store in a HDF5 file but at a different location.

__init__(file_path=None, data_path=None, data=None, source_scan=None, metadata=None, data_url=None, metadata_url=None, overwrite=False)#

Methods

`__init__`([file_path, data_path, data, ...])
`browse_data_files`([url])	return a generator go through all the existings files associated to the data volume
`browse_data_urls`([url])	generator on data urls used.
`browse_metadata_files`([url])	return a generator go through all the existings files associated to the data volume
`browse_slices`([url])	generator of 2D numpy array representing a slice
`build_drac_metadata`()	build the drac (successor of icat) metadata dict from existing volume metadata.
`check_can_provide_identifier`()
`clear_cache`()	remove object stored in data and metadata
`data_file_saver_generator`(n_frames, ...[, mode])	Provide a helper class to dump data frame by frame.
`deduce_data_and_metadata_urls`(url)	compute data and metadata urls from 'parent url' :return: data_url: DataUrl \| None, metadata_url: DataUrl \| None
`example_defined_from_str_identifier`()	example as string to explain how users can defined identifiers from a string
`from_identifier`(identifier)	Return the Dataset from a identifier
`get_bounding_box`([axis])	Return the bounding box covered by the Tomo object axis is expected to be in (0, 1, 2) or (x==0, y==1, z==2)
`get_identifier`()	dataset unique identifier.
`get_min_max`()	compute min max of the volume.
`get_min_max_values`([url])	compute min max over 'data' if exists else browsing the volume slice by slice
`get_slice`([index, axis, xy, xz, yz, url])	read a single slice of the volume
`get_slices`(slices)	retrieve a couple of slices along any axis:
`get_volume_shape`([url])	return volume shape as a tuple
`load`()
`load_chunk`(chunk[, url])	Load a sub-volume.
`load_data`([url, store])	load volume data from disk
`load_metadata`([url, store])	load volume metadata from disk
`save`([url])	save volume data and metadata to disk
`save_data`([url, mode])	save data to the provided url or existing one if none is provided
`save_metadata`([url])	save metadata to the provided url or existing one if none is provided
`select`(volume[, xy, xz, yz, axis, index])	select a slice at 'index' along an axis (axis)
`select_slices`(volume, slices)

Attributes

`DATA_DATASET_NAME`
`EXTENSION`
`METADATA_GROUP_NAME`
`data`
`data_extension`
`data_path`
`data_url`
`extension`	rtype `str`
`file_path`
`metadata`
`metadata_extension`
`metadata_url`
`overwrite`	rtype `bool`
`pixel_size`
`position`	position are provided as a tuple using the same reference for axis as the volume data.
`source_scan`
`url`
`voxel_size`	voxel size as (axis 0 dim - aka z, axis 1 dim - aka y, axis 2 dim aka z)

browse_data_files(url=None)#: return a generator go through all the existings files associated to the data volume

browse_data_urls(url=None)#

generator on data urls used.

Parameters: url – data url to be used. If not provided will take self.data_url

browse_metadata_files(url=None)#: return a generator go through all the existings files associated to the data volume

browse_slices(url=None)#

generator of 2D numpy array representing a slice

Parameters: url – data url to be used. If not provided will browse self.data if exists else self.data_url
Warning: this will get the slice from the data on disk and never use data property. so before browsing slices you might want to check if data is already loaded

build_drac_metadata()#

build the drac (successor of icat) metadata dict from existing volume metadata.

Return type: dict

clear_cache()#: remove object stored in data and metadata

data_file_saver_generator(n_frames, data_url, overwrite, mode='a', **kwargs)#

Provide a helper class to dump data frame by frame. For know the only possible interaction is Helper[:] = frame

Parameters

n_frames – number of frame the final volume will contain
data_url (DataUrl) – url to dump data
overwrite (bool) – overwrite existing file ?

deduce_data_and_metadata_urls(url)#: compute data and metadata urls from ‘parent url’ :return: data_url: DataUrl | None, metadata_url: DataUrl | None

static example_defined_from_str_identifier()#

example as string to explain how users can defined identifiers from a string

Return type: str

static from_identifier(identifier)#: Return the Dataset from a identifier

get_bounding_box(axis=None)#: Return the bounding box covered by the Tomo object axis is expected to be in (0, 1, 2) or (x==0, y==1, z==2)

get_identifier()#

dataset unique identifier. Can be for example a hdf5 and en entry from which the dataset can be rebuild

Return type: HDF5VolumeIdentifier

get_min_max()#

compute min max of the volume. Can take some time but avoid to load the full volume in memory

Return type: tuple

get_min_max_values(url=None)#

compute min max over ‘data’ if exists else browsing the volume slice by slice

Parameters: url – data url to be used. If not provided will take self.data_url
Return type: tuple

get_slice(index=None, axis=None, xy=None, xz=None, yz=None, url=None)#: read a single slice of the volume

get_slices(slices)#

retrieve a couple of slices along any axis:

For example, if you want to retrieve slice number 2 of axis 0 and slice number 56 of axis 1:

slices = volume.get_slices(
    (0, 2),
    (1, 56),
)
for (axis, slice), data in slices:
    ...

get_volume_shape(url=None)#: return volume shape as a tuple

load_chunk(chunk, url=None)#

Load a sub-volume.

Parameters

chunk – tuple of slice objects indicating which chunk of the volume has to be loaded.
url – data url to be used. If not provided will take self.data_url

load_data(url=None, store=True)#: load volume data from disk

load_metadata(url=None, store=True)#: load volume metadata from disk

property position#: position are provided as a tuple using the same reference for axis as the volume data. position is returned as (axis_0_pos, axis_1_pos, axis_2_pos). Can also be see as (z_position, y_position, x_position)

save(url=None, **kwargs)#: save volume data and metadata to disk

save_data(url=None, mode='a', **kwargs)#: save data to the provided url or existing one if none is provided

save_metadata(url=None)#: save metadata to the provided url or existing one if none is provided

static select(volume, xy=None, xz=None, yz=None, axis=None, index=None)#: select a slice at ‘index’ along an axis (axis)

property voxel_size#: voxel size as (axis 0 dim - aka z, axis 1 dim - aka y, axis 2 dim aka z)