jicbioimage.core.io
¶
Module for reading and writing images.
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class
jicbioimage.core.io.
AutoName
[source]¶ Class for generating output file names automatically.
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directory
= None¶ Output directory to save images to.
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namespace
= ''¶ Image file namespace.
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prefix_format
= '{:d}_'¶ Image file prefix format.
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class
jicbioimage.core.io.
AutoWrite
[source]¶ Class for writing images automatically.
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on
= True¶ Whether or not auto writing of images is enabled.
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class
jicbioimage.core.io.
BFConvertWrapper
(backend)[source]¶ Class for unpacking microscopy files using bfconvert.
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already_converted
(fpath)[source]¶ Return true if the file already has a manifest file in the backend.
Parameters: fpath – potential path to the manifest file Returns: bool
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manifest
(entry)[source]¶ Returns manifest as a list.
Parameters: entry – jicbioimage.core.io.FileBackend.Entry
Returns: jicbioimage.core.io.Manifest
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metadata_from_fname
(fname, md5_hexdigest)[source]¶ Return meta data extracted from file name.
Parameters: fname – metadata file name Returns: dictionary with meta data required by
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class
jicbioimage.core.io.
DataManager
(backend=None)[source]¶ Manage
jicbioimage.core.image.ImageCollection
instances.
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class
jicbioimage.core.io.
FileBackend
(directory)[source]¶ Class for storing image files.
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class
Entry
(base_dir, fpath)[source]¶ Class representing a backend entry.
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directory
¶ Where the images are stored.
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FileBackend.
directory
¶ Where the entries are stored.
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class
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class
jicbioimage.core.io.
Manifest
[source]¶ Class for generating backend entry manifest files.
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add
(filename, **kwargs)[source]¶ Add an entry to the manifest.
Parameters: - filename – relative path to image
- kwargs – custom parameters, e.g. series, channel, zslice
Returns: the added entry
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json
¶ Return json representation.
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