jicbioimage.core.image
¶
Module for managing and accessing images.
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class
jicbioimage.core.image.
History
(creation=None)[source]¶ Class for storing the provenance of an image.
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class
jicbioimage.core.image.
Image
(shape, dtype=<type 'numpy.uint8'>, buffer=None, offset=0, strides=None, order=None, name=None, log_in_history=True)[source]¶ Image class.
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classmethod
from_file
(fpath, name=None, log_in_history=True)[source]¶ Return
jicbioimage.core.image.Image
instance from a file.Parameters: - fpath – path to the image file
- name – name of the image
- log_in_history – whether or not to log the creation event in the image’s history
Returns:
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classmethod
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class
jicbioimage.core.image.
Image3D
(shape, dtype=<type 'numpy.uint8'>, buffer=None, offset=0, strides=None, order=None, name=None, log_in_history=True)[source]¶ Image3D class; in other words a 3D stack.
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classmethod
from_directory
(directory)[source]¶ Return
jicbioimage.core.image.Image3D
from directory.Parameters: directory – name of input directory Returns: jicbioimage.core.image.Image3D
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classmethod
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class
jicbioimage.core.image.
ImageCollection
(fpath=None)[source]¶ Class for storing related images.
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image
(index=0)[source]¶ Return image as a
jicbioimage.core.image.Image
.Parameters: index – list index Returns: jicbioimage.core.image.Image
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parse_manifest
(fpath)[source]¶ Parse manifest file to build up the collection of images.
Parameters: fpath – path to the manifest file Raises: RuntimeError
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proxy_image
(index=0)[source]¶ Return a
jicbioimage.core.image.ProxyImage
instance.Parameters: index – list index Returns: jicbioimage.core.image.ProxyImage
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class
jicbioimage.core.image.
MicroscopyCollection
(fpath=None)[source]¶ Collection of
jicbioimage.core.image.MicroscopyImage
instances.-
channels
(s=0)[source]¶ Return list of channels in the collection.
Parameters: s – series Returns: list of channel identifiers
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image
(s=0, c=0, z=0, t=0)[source]¶ Return image as a
jicbioimage.core.image.Image
.Parameters: - s – series
- c – channel
- z – zslice
- t – timepoint
Returns:
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proxy_image
(s=0, c=0, z=0, t=0)[source]¶ Return a
jicbioimage.core.image.MicroscopyImage
instance.Parameters: - s – series
- c – channel
- z – zslice
- t – timepoint
Returns:
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series
¶ Return list of series in the collection.
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timepoints
(s=0)[source]¶ Return list of time points in the collection.
Parameters: s – series Returns: list of time point identifiers
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zslices
(s=0)[source]¶ Return list of z-slices in the collection.
Parameters: s – series Returns: list of zslice identifiers
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zstack
(s=0, c=0, t=0)[source]¶ Return zstack as a
jicbioimage.core.image.Image3D
.Parameters: - s – series
- c – channel
- t – timepoint
Returns: zstack as a
jicbioimage.core.image.Image3D
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zstack_array
(s=0, c=0, t=0)[source]¶ Return zstack as a
numpy.ndarray
.Parameters: - s – series
- c – channel
- t – timepoint
Returns: zstack as a
numpy.ndarray
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zstack_proxy_iterator
(s=0, c=0, t=0)[source]¶ Return zstack
jicbioimage.core.image.ProxyImage
iterator.Parameters: - s – series
- c – channel
- t – timepoint
Returns: zstack as a
jicbioimage.core.image.ProxyImage
iterator
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class
jicbioimage.core.image.
MicroscopyImage
(fpath, metadata={})[source]¶ Lightweight image class with microscopy meta data.
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class
jicbioimage.core.image.
ProxyImage
(fpath, metadata={})[source]¶ Lightweight image class.
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image
¶ Underlying
jicbioimage.core.image.Image
instance.
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