ptyrad.io.generic

ptyrad.io.generic#

Generic file handling (load/save) for raw, npy, and tif formats

Functions

load_npy(file_path)

Loads an array from a binary NumPy .npy file.

load_raw(file_path, shape[, dtype, offset, gap])

Loads a raw binary file containing interleaved image data and gaps.

load_tif(file_path)

Loads an image array from a TIFF file.

write_npy(file_path, data)

Saves a NumPy array to a binary .npy file.

write_tif(file_path, data)

Saves a NumPy array as a TIFF file.
ptyrad.io.generic.load_raw(file_path, shape, dtype=<class 'numpy.float32'>, offset=0, gap=1024)[source]#

Loads a raw binary file containing interleaved image data and gaps.

This implementation uses a custom numpy.dtype with np.fromfile for fast I/O performance, extracting only the valid data regions and skipping the specified byte gaps between frames. Note that custom processed raw data might have a gap of 0.

Parameters:

  • file_path (str) – The path to the raw binary file.

  • shape (tuple of int) – The expected shape of the data in the format (N, height, width), where N is the number of frames.

  • dtype (data-type, optional) – The NumPy data type of the image pixels. Defaults to np.float32.

  • offset (int, optional) – The number of bytes to skip at the beginning of the file. Defaults to 0.

  • gap (int, optional) – The number of gap bytes to skip between each image frame. Defaults to 1024.

Returns:

An array of the extracted data with the specified shape and dtype.

Return type:

numpy.ndarray

Raises:

ValueError – If the actual file size does not match the expected size calculated from the inputs.

ptyrad.io.generic.load_tif(file_path)[source]#

Loads an image array from a TIFF file.

Parameters:

file_path (str) – The path to the TIFF file.

Returns:

The loaded image data.

Return type:

numpy.ndarray

Raises:

FileNotFoundError – If the specified file does not exist.

ptyrad.io.generic.load_npy(file_path)[source]#

Loads an array from a binary NumPy .npy file.

Parameters:

file_path (str) – The path to the .npy file.

Returns:

The loaded array data.

Return type:

numpy.ndarray

Raises:

FileNotFoundError – If the specified file does not exist.

ptyrad.io.generic.write_tif(file_path, data)[source]#

Saves a NumPy array as a TIFF file.

The file is saved with ImageJ compatibility enabled to ensure proper handling of hyperstacks and metadata in common microscopy viewers.

Parameters:

  • file_path (str) – The destination path for the TIFF file.

  • data (numpy.ndarray) – The array data to save.

ptyrad.io.generic.write_npy(file_path, data)[source]#

Saves a NumPy array to a binary .npy file.

Parameters:

  • file_path (str) – The destination path for the .npy file.

  • data (numpy.ndarray) – The array data to save.

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