dxchange.reader
¶
Module for importing data files.
Functions:
read_edf (fname[, slc]) |
Read data from edf file. |
read_hdf5 (fname, dataset[, slc, dtype, shared]) |
Read data from hdf5 file from a specific group. |
read_netcdf4 (fname, group[, slc]) |
Read data from netcdf4 file from a specific group. |
read_npy (fname[, slc]) |
Read binary data from a .npy file. |
read_spe (fname[, slc]) |
Read data from spe file. |
read_fits (fname[, fixdtype]) |
Read data from fits file. |
read_tiff (fname[, slc]) |
Read data from tiff file. |
read_tiff_stack (fname, ind[, digit, slc]) |
Read data from stack of tiff files in a folder. |
read_hdf5_stack (h5group, dname, ind[, ...]) |
Read data from stacked datasets in a hdf5 file |
read_xrm (fname[, slice_range]) |
Read data from xrm file. |
read_xrm_stack (fname, ind[, slc]) |
Read data from stack of xrm files in a folder. |
read_txrm (file_name[, slice_range]) |
Read data from a .txrm file, a compilation of .xrm files. |
-
dxchange.reader.
read_edf
(fname, slc=None)[source]¶ Read data from edf file.
Parameters: - fname (str) – String defining the path of file or file name.
- slc (sequence of tuples, optional) – Range of values for slicing data in each axis. ((start_1, end_1, step_1), ... , (start_N, end_N, step_N)) defines slicing parameters for each axis of the data matrix.
Returns: ndarray – Data.
-
dxchange.reader.
read_hdf5
(fname, dataset, slc=None, dtype=None, shared=False)[source]¶ Read data from hdf5 file from a specific group.
Parameters: - fname (str) – String defining the path of file or file name.
- dataset (str) – Path to the dataset inside hdf5 file where data is located.
- slc (sequence of tuples, optional) – Range of values for slicing data in each axis. ((start_1, end_1, step_1), ... , (start_N, end_N, step_N)) defines slicing parameters for each axis of the data matrix.
- dtype (numpy datatype (optional)) – Convert data to this datatype on read if specified.
- shared (bool (optional)) – If True, read data into shared memory location. Defaults to True.
Returns: ndarray – Data.
-
dxchange.reader.
read_netcdf4
(fname, group, slc=None)[source]¶ Read data from netcdf4 file from a specific group.
Parameters: - fname (str) – String defining the path of file or file name.
- group (str) – Variable name where data is stored.
- slc (sequence of tuples, optional) – Range of values for slicing data in each axis. ((start_1, end_1, step_1), ... , (start_N, end_N, step_N)) defines slicing parameters for each axis of the data matrix.
Returns: ndarray – Data.
-
dxchange.reader.
read_npy
(fname, slc=None)[source]¶ Read binary data from a
.npy
file.Parameters: - fname (str) – String defining the path of file or file name.
- slc (sequence of tuples, optional) – Range of values for slicing data in each axis. ((start_1, end_1, step_1), ... , (start_N, end_N, step_N)) defines slicing parameters for each axis of the data matrix.
Returns: ndarray – Data.
-
dxchange.reader.
read_spe
(fname, slc=None)[source]¶ Read data from spe file.
Parameters: - fname (str) – String defining the path of file or file name.
- slc (sequence of tuples, optional) – Range of values for slicing data in each axis. ((start_1, end_1, step_1), ... , (start_N, end_N, step_N)) defines slicing parameters for each axis of the data matrix.
Returns: ndarray – Data.
-
dxchange.reader.
read_fits
(fname, fixdtype=True)[source]¶ Read data from fits file.
Parameters: fname (str) – String defining the path of file or file name. Returns: ndarray – Data.
-
dxchange.reader.
read_tiff
(fname, slc=None)[source]¶ Read data from tiff file.
Parameters: - fname (str) – String defining the path of file or file name.
- slc (sequence of tuples, optional) – Range of values for slicing data in each axis. ((start_1, end_1, step_1), ... , (start_N, end_N, step_N)) defines slicing parameters for each axis of the data matrix.
Returns: ndarray – Output 2D image.
-
dxchange.reader.
read_tiff_stack
(fname, ind, digit=None, slc=None)[source]¶ Read data from stack of tiff files in a folder.
Parameters: - fname (str) – One of the file names in the tiff stack.
- ind (list of int) – Indices of the files to read.
- digit (int) – (Deprecated) Number of digits used in indexing stacked files.
- slc (sequence of tuples, optional) – Range of values for slicing data in each axis. ((start_1, end_1, step_1), ... , (start_N, end_N, step_N)) defines slicing parameters for each axis of the data matrix.
Returns: ndarray – Output 3D image.
-
dxchange.reader.
read_xrm
(fname, slice_range=None)[source]¶ Read data from xrm file.
Parameters: - fname (str) – String defining the path of file or file name.
- slice_range (sequence of tuples, optional) – Range of values for slicing data in each axis. ((start_1, end_1, step_1), ... , (start_N, end_N, step_N)) defines slicing parameters for each axis of the data matrix.
Returns: ndarray – Output 2D image.
-
dxchange.reader.
read_xrm_stack
(fname, ind, slc=None)[source]¶ Read data from stack of xrm files in a folder.
Parameters: - fname (str) – One of the file names in the tiff stack.
- ind (list of int) – Indices of the files to read.
- slc (sequence of tuples, optional) – Range of values for slicing data in each axis. ((start_1, end_1, step_1), ... , (start_N, end_N, step_N)) defines slicing parameters for each axis of the data matrix.
Returns: ndarray – Output 3D image.
-
dxchange.reader.
read_txrm
(file_name, slice_range=None)[source]¶ Read data from a .txrm file, a compilation of .xrm files.
Parameters: - file_name (str) – String defining the path of file or file name.
- slice_range (sequence of tuples, optional) – Range of values for slicing data in each axis. ((start_1, end_1, step_1), ... , (start_N, end_N, step_N)) defines slicing parameters for each axis of the data matrix.
Returns: - ndarray – Array of 2D images.
- dictionary – Dictionary of metadata.
-
dxchange.reader.
read_hdf5_stack
(h5group, dname, ind, digit=4, slc=None, out_ind=None)[source]¶ Read data from stacked datasets in a hdf5 file
Parameters: - fname (str) – One of the dataset names in the dataset stack
- ind (list of int) – Indices of the datasets to be read
- digit (int) – (Deprecated) Number of digits indexing the stacked datasets
- slc ({sequence, int}) – Range of values for slicing data. ((start_1, end_1, step_1), ... , (start_N, end_N, step_N)) defines slicing parameters for each axis of the data matrix
- out_ind (list of int, optional) – Outer level indices for files with two levels of indexing. i.e. [name_000_000.tif, name_000_001.tif, ..., name_000_lmn.tif, name_001_lmn.tif, ..., ..., name_fgh_lmn.tif]