florin.io

I/O functions for loading and saving data in a variety of formats.

Functions

load
Load image(s) from a file.
load_hdf5
Load data from an HDF5 file.
load_image
Load an image file.
load_images
Load a directory of image files.
load_npy
Load data from a numpy array file.
load_tiff
Load a TIFF stack.
save
Save image(s) in a variety of formats.
save_hdf5
Save an image to HDF5 format.
save_image
Save an image.
save_images
Save a sequence of images.
save_npy
Save an image to a numpy array file.
save_tiff
Save an image to TIFF format.

Functions

load(path, \*\*kwargs) Load images from a file.
load_hdf5(path[, key]) Load data from an HDF5 file.
load_image(path) Load an image file.
load_images(path[, ext]) Load a directory of image files.
load_npy(path) Load data from a numpy array file.
load_tiff(path) Load a TIFF stack.
save(img, path, \*\*kwargs) Save image(s) in a variety of formats.
save_hdf5(img, path[, key]) Save an image to HDF5 format.
save_image(img, path) Save an image.
save_images(img, path[, ext]) Save a sequence of images.
save_npy(img, path) Save an image to a numpy array file.
save_tiff(img, path) Save an image to TIFF format.
florin.io.load(path, **kwargs)[source]

Load images from a file.

Generic loader function that uses the file extension to determine how to load the data.

Parameters:path (str) – Path to the image file(s) to load.
Other Parameters:
 key – Key to load data from when working with key/value stores (e.g. HDF5, npz, etc.)
Returns:data
Return type:numpy.ndarray
florin.io.load_hdf5(path, key='stack')[source]

Load data from an HDF5 file.

Parameters:
  • path (str) – Path to the HDF5 file to load.
  • key – Key to load data from.
Returns:

data
Return type:

h5py.Dataset
florin.io.load_image(path)[source]

Load an image file.

Parameters:path (str) – Path to the image file to load.
Returns:data
Return type:numpy.ndarray
florin.io.load_images(path, ext='png')[source]

Load a directory of image files.

Parameters:
  • path (str) – Path to the image file(s) to load.
  • ext (str) – The file extension to match. Only files with this extension will be loaded. Default: ‘png’
Returns:

data
Return type:

numpy.ndarray
florin.io.load_npy(path)[source]

Load data from a numpy array file.

Parameters:path (str) – Path to the array file to load.
Returns:data
Return type:numpy.ndarray
florin.io.load_tiff(path)[source]

Load a TIFF stack.

Parameters:path (str) – Path to the TIFF stack to load.
Returns:data
Return type:numpy.ndarray
florin.io.save(img, path, **kwargs)[source]

Save image(s) in a variety of formats.

Parameters:
  • img (array_like) – The image/volume to save.
  • path (str) – The filepath to save the data to. This path determines which format the data will be saved as.
Returns:

The unaltered image/volume.
Return type:

img
Other Parameters:
 
  • See ``save_hdf5``, ``save_image``, ``save_images``, ``save_npy``, and
  • ``save_tiff`` for filetype-specific arguments.

Notes

The filetype passed as path will determine the format of the saved file. If no extension is found, 3D arrays will automatically be saved as numbered PNG files in a directory created at path and 2D arrays will be saved to path directly as a PNG.

florin.io.save_hdf5(img, path, key='stack')[source]

Save an image to HDF5 format.

Parameters:
  • img (array_like) – The image/volume to save.
  • path (str) – The filepath to save the data to.
florin.io.save_image(img, path)[source]

Save an image.

Parameters:
  • img (array_like) – The image/volume to save.
  • path (str) – The filepath to save the data to.
florin.io.save_images(img, path, ext='png')[source]

Save a sequence of images.

Parameters:
  • img (array_like) – The image/volume to save.
  • path (str) – The filepath to save the data to.
  • ext (str) – The file extension to save each image with.
florin.io.save_npy(img, path)[source]

Save an image to a numpy array file.

Parameters:
  • img (array_like) – The image/volume to save.
  • path (str) – The filepath to save the data to.
florin.io.save_tiff(img, path)[source]

Save an image to TIFF format.

Parameters:
  • img (array_like) – The image/volume to save.
  • path (str) – The filepath to save the data to.