tomoscan.esrf.volume.edfvolume.EDFVolume#
- class tomoscan.esrf.volume.edfvolume.EDFVolume(folder=None, volume_basename=None, data=None, source_scan=None, metadata=None, data_url=None, metadata_url=None, overwrite=False, header=None, start_index=0, data_extension='edf', metadata_extension='txt')#
Bases:
TIFFLikeDiskAccessor
,VolumeSingleFrameBase
Save volume data to single frame edf and metadata to .txt files
- Warning
each file saved under {volume_basename}_{index_zfill6}.edf is considered to be a slice of the volume.
- __init__(folder=None, volume_basename=None, data=None, source_scan=None, metadata=None, data_url=None, metadata_url=None, overwrite=False, header=None, start_index=0, data_extension='edf', metadata_extension='txt')#
Methods
__init__
([folder, volume_basename, data, ...])browse_data_files
([url])- param url
data url. If not provided will take self.data_url
browse_data_urls
([url])generator on data urls used.
browse_metadata_files
([url])- param url
metadata url. If not provided will take self.metadata_url
browse_slices
([url])generator of 2D numpy array representing a slice
build the drac (successor of icat) metadata dict from existing volume metadata.
check_can_provide_identifier
()remove object stored in data and metadata
data_file_name_generator
(n_frames, data_url)browse output files for n_frames
data_file_saver_generator
(n_frames, ...)Provide a helper class to dump data frame by frame.
compute data and metadata urls from 'parent url' :return: data_url: DataUrl | None, metadata_url: DataUrl | None
example as string to explain how users can defined identifiers from a string
format_data_path_for_data
(data_path, index, ...)Return file path to save the frame at index of the current volume
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_data_path_pattern_for_data
(data_path, ...)Return file path pattern (and not full path) to load data.
dataset unique identifier.
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_basename
([url])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_frame
(file_name, scheme)Function dedicated for volume saving each frame on a single file
load_metadata
([url, store])load volume metadata from disk
read_file
(file_name)- rtype
tuple
read_n_columns_in_file
(file_name, column_indices)- rtype
tuple
read_n_lines_in_file
(file_name, line_indices)- rtype
tuple
remove_existing_data_files
([url])Clean any existing files (if overwrite and rights) that must be used for saving
save
([url])save volume data and metadata to disk
save_data
([url])save data to the provided url or existing one if none is provided
save_frame
(frame, file_name, scheme)Function dedicated for volune saving each frame on a single file
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
DEFAULT_DATA_EXTENSION
DEFAULT_DATA_PATH_PATTERN
DEFAULT_DATA_SCHEME
DEFAULT_METADATA_EXTENSION
DEFAULT_METADATA_PATH_PATTERN
DEFAULT_METADATA_SCHEME
EXTENSION
data
data_extension
data_url
extension
- rtype
str
possible header for the edf files
metadata
metadata_extension
metadata_url
overwrite
- rtype
bool
pixel_size
position are provided as a tuple using the same reference for axis as the volume data.
The loading of the volume for single frame base is done by loading all the file contained in a folder data_url.file_path().
source_scan
start_index
- rtype
int
url
voxel size as (axis 0 dim - aka z, axis 1 dim - aka y, axis 2 dim aka z)
- browse_data_files(url=None)#
- Parameters
url – data url. If not provided will take self.data_url
return a generator go through all the existing 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)#
- Parameters
url – metadata url. If not provided will take self.metadata_url
return a generator go through all the existing 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_name_generator(n_frames, data_url)#
browse output files for n_frames
- data_file_saver_generator(n_frames, data_url, overwrite)#
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
- format_data_path_for_data(data_path, index, volume_basename)#
Return file path to save the frame at index of the current volume
- 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_data_path_pattern_for_data(data_path, volume_basename)#
Return file path pattern (and not full path) to load data. For example in edf it can return ‘myacquisition_*.edf’ in order to be handled by
- Return type
str
- get_identifier()#
dataset unique identifier. Can be for example a hdf5 and en entry from which the dataset can be rebuild
- Return type
- 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
- property header: dict | None#
possible header for the edf files
- 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_frame(file_name, scheme)#
Function dedicated for volume saving each frame on a single file
- Parameters
file_name – path to store the data
scheme – scheme to save the data
- load_metadata(url=None, store=True)#
load volume metadata from disk
- property position: tuple | None#
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)
- remove_existing_data_files(url=None)#
Clean any existing files (if overwrite and rights) that must be used for saving
- save(url=None, **kwargs)#
save volume data and metadata to disk
- save_data(url=None)#
save data to the provided url or existing one if none is provided
- save_frame(frame, file_name, scheme)#
Function dedicated for volune saving each frame on a single file
- Parameters
frame – frame to be save
file_name – path to store the data
scheme – scheme to save the data
- 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 skip_existing_data_files_removal: bool#
The loading of the volume for single frame base is done by loading all the file contained in a folder data_url.file_path(). When saving the data we make sure there is no ‘remaining’ of any previous saving by using the file pattern. But when we want to save a volume from several thread (one thread save the n first frame, second the n next frame …) this could be a limitation. So in this case we can use the ‘ignore_existing_files’ that will avoid calling ‘_remove_existing_data_files’
- Return type
bool
- property voxel_size: tuple | None#
voxel size as (axis 0 dim - aka z, axis 1 dim - aka y, axis 2 dim aka z)