506b449f4d
- pytest - use pathlib - series as part of the path: path/PosN - summary only shows some available metadata - allow dict in Imread[dict(c=c, z=z, t=t)] - bfread in different process so the user can start another jvm - deal with multiple images (series/positions) in czi files - use jpype instead of javabridge/bioformats - poetry for install
76 lines
2.5 KiB
Markdown
76 lines
2.5 KiB
Markdown
# ndbioimage - Work in progress
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Exposes (bio) images as a numpy ndarray-like-object, but without loading the whole
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image into memory, reading from the file only when needed. Some metadata is read and
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and stored in an ome structure. Additionally, it can automatically calculate an affine
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transform that corrects for chromatic abberrations etc. and apply it on the fly to the image.
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Currently supports imagej tif files, czi files, micromanager tif sequences and anything
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bioformats can handle.
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## Installation
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pip install ndbioimage@git+https://github.com/wimpomp/ndbioimage.git
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Optionally:
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https://downloads.openmicroscopy.org/bio-formats/latest/artifacts/bioformats_package.jar
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## Usage
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- Reading an image file and plotting the frame at channel=2, time=1
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import matplotlib.pyplot as plt
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from ndbioimage import Imread
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with Imread('image_file.tif', axes='ctxy', dtype=int) as im:
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plt.imshow(im[2, 1])
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- Showing some image metadata
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from ndbioimage import Imread
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from pprint import pprint
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with Imread('image_file.tif') as im:
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pprint(im)
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- Slicing the image without loading the image into memory
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from ndbioimage import Imread
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with Imread('image_file.tif', axes='cztxy') as im:
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sliced_im = im[1, :, :, 100:200, 100:200]
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sliced_im is an instance of Imread which will load any image data from file only when needed
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- Converting (part) of the image to a numpy ndarray
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from ndbioimage import Imread
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import numpy as np
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with Imread('image_file.tif', axes='cztxy') as im:
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array = np.asarray(im[0, 0])
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## Adding more formats
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Readers for image formats subclass Imread. When an image reader is imported, Imread will
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automatically recognize it and use it to open the appropriate file format. Image readers
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subclass Imread and are required to implement the following methods:
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- staticmethod _can_open(path): return True if path can be opened by this reader
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- property ome: reads metadata from file and adds them to an OME object imported
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from the ome-types library
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- \_\_frame__(self, c, z, t): return the frame at channel=c, z-slice=z, time=t from the file
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Optional methods:
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- open(self): maybe open some file
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- close(self): close any file handles
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Optional fields:
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- priority (int): Imread will try readers with a lower number first, default: 99
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- do_not_pickle (strings): any attributes that should not be included when the object is pickled,
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for example: any file handles
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# TODO
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- more image formats
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- re-implement transforms
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