aicsimageio.writers package

Submodules

aicsimageio.writers.ome_tiff_writer module

class aicsimageio.writers.ome_tiff_writer.OmeTiffWriter(file_path, overwrite_file=None)

Bases: object

This class can take arrays of pixel values and do the necessary metadata creation to write them properly in OME xml format.

Parameters

• file_path – Path to image output location

• overwrite_file – Flag to overwrite image or pass over image if it already exists. None: (default) throw IOError if file exists True: overwrite existing file if file exists False: silently perform no write actions if file exists

Example

>>> image = numpy.ndarray([1, 10, 3, 1024, 2048])
... writer = ome_tiff_writer.OmeTiffWriter("file.ome.tif")
... writer.save(image)

Using the context manager to close the write once done.

>>> image2 = numpy.ndarray([5, 486, 210])
... with ome_tiff_writer.OmeTiffWriter("file2.ome.tif") as writer2:
...     writer2.save(image2)

Convert a CZI file into OME-Tiff

>>> reader = cziReader.CziReader("file3.czi")
... with ome_tiff_writer.OmeTiffWriter("file3.ome.tif") as writer3:
...     writer.save(reader.load())

close()

save(data, ome_xml=None, channel_names=None, image_name='IMAGE0', pixels_physical_size=None, channel_colors=None, dimension_order='STZCYX')

Save an image with the proper OME XML metadata.

Parameters

• data (An array of 3, 4, or 5 dimensions to be written out to a file.)

• ome_xml (A premade omexml.OMEXML object to use for metadata.)

• channel_names (The names for each channel to be put into the OME metadata)

• image_name (The name of the image to be put into the OME metadata)

• pixels_physical_size (The physical size of each pixel in the image)

• channel_colors (The channel colors to be put into the OME metadata)

• dimension_order (The dimension ordering in the data array. Will be assumed)

• STZCYX if not specified

save_slice(data, z=0, c=0, t=0)

this doesn’t do the necessary functionality at this point

TODO:

• make this insert a YX slice in between two other slices inside a full image

• data should be a 5 dim array

Parameters

• data –

• z –

• c –

• t –

Returns

set_metadata(ome_metadata)

size_c()

size_t()

size_x()

size_y()

size_z()

aicsimageio.writers.png_writer module

class aicsimageio.writers.png_writer.PngWriter(file_path, overwrite_file=None)

Bases: object

This class can take 3D arrays of CYX pixel values and writes them to a PNG.

Parameters

• file_path – Path to image output location

• overwrite_file – Flag to overwrite image or pass over image if it already exists. None : (default) throw IOError if file exists. True : overwrite existing file if file exists. False: silently perform no write actions if file exists.

Examples

Construct and use as object

>>> image = numpy.ndarray([3, 1024, 2048])
... writer = png_writer.PngWriter("file.png")
... writer.save(image)

Construct within a context manager

>>> image2 = numpy.ndarray([3, 1024, 2048])
... with png_writer.PngWriter("file2.png") as writer2:
...     writer2.save(image2)

close()

save(data)

Takes in an array of CYX pixel values and writes them to a PNG.

Parameters

data – A CYX or YX array with C being the rgb channels for each pixel value.

save_slice(data, z=0, c=0, t=0)

Exactly the same functionality as save() but allows the interface to be the same as OmeTiffWriter.

Parameters

• data – A CYX or YX array with C being the rgb channels for each pixel value.

• z – An arbitrary Z index that does nothing.

• c – An arbitrary C index that does nothing.

• t – An arbitrary T index that does nothing.

aicsimageio.writers.writer module

class aicsimageio.writers.writer.Writer(file_path: Union[str, pathlib.Path])

Bases: abc.ABC

Write STCZYX data arrays to file, with accompanying metadata Will overwrite existing files of same name.

Parameters

file_path (types.PathLike) – Path to image output location

Examples

Construct and use as object

>>> image = numpy.ndarray([1, 10, 3, 1024, 2048])
... writer = DerivedWriter("file.ome.tif")
... writer.save(image)
... writer.close()

Construct with a context manager

>>> image2 = numpy.ndarray([5, 486, 210])
... with DerivedWriter("file2.ome.tif") as writer2:
...     writer2.set_metadata(myMetaData)
...     writer2.save(image2)

abstract close() → None

Close file objects

abstract save(data, dims='STCZYX', **kwargs) → None

Write to open file

Module contents