imsegm.utilities.data_samples module¶
Sandbox with some sample images
Some images are taken from following sources:
[ANHIR challenge](https://anhir.grand-challenge.org)
[PhD Thesis](https://www.researchgate.net/publication/323120618)
Copyright (C) 2015-2018 Jiri Borovec <jiri.borovec@fel.cvut.cz>
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imsegm.utilities.data_samples.
get_image_path
(name_img, path_base='/home/docs/checkouts/readthedocs.org/user_builds/pyimsegm/checkouts/v0.1.8/data-images')[source]¶ merge default image path and sample image
>>> p = get_image_path(IMAGE_LENNA) >>> os.path.isfile(p) True >>> os.path.basename(p) 'lena.png'
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imsegm.utilities.data_samples.
load_sample_image
(name_img='others/lena.png')[source]¶ load sample image
- Parameters
name_img (str) –
- Return ndarray
>>> img = load_sample_image(IMAGE_LENNA) >>> img.shape (512, 512, 3)
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imsegm.utilities.data_samples.
sample_color_image_rand_segment
(im_size=(150, 100), nb_classes=3, rand_seed=None)[source]¶ create samoe image and segmentation
>>> im, seg = sample_color_image_rand_segment((5, 6), 2, rand_seed=0) >>> im.shape (5, 6, 3) >>> seg array([[1, 1, 0, 0, 1, 0], [0, 1, 1, 0, 1, 0], [0, 1, 0, 0, 0, 1], [1, 0, 1, 0, 0, 0], [0, 0, 1, 0, 1, 0]])
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imsegm.utilities.data_samples.
sample_segment_vertical_2d
(seg_size=(20, 10), nb_labels=3)[source]¶ create sample segmentation with vertical stripes
>>> sample_segment_vertical_2d((7, 5), 2) array([[0, 0, 0, 1, 1, 1], [0, 0, 0, 1, 1, 1], [0, 0, 0, 1, 1, 1], [0, 0, 0, 1, 1, 1], [0, 0, 0, 1, 1, 1]])
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imsegm.utilities.data_samples.
sample_segment_vertical_3d
(seg_size=(10, 5, 6), nb_labels=3, levels=2)[source]¶ create sample regular 3D segmentation
- Parameters
- Return ndarray
>>> im = sample_segment_vertical_3d((10, 5, 6), 3) >>> im[:, :, 3] array([[1, 1, 1, 1, 1], [1, 1, 1, 1, 1], [1, 1, 1, 1, 1], [4, 4, 4, 4, 4], [4, 4, 4, 4, 4], [4, 4, 4, 4, 4]])
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imsegm.utilities.data_samples.
ANNOT_DROSOPHILA_DISC
= 'drosophila_disc/annot/img_6.png'[source]¶ three class tissue annotation of microscopy image of Drosophila imaginal disc
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imsegm.utilities.data_samples.
ANNOT_DROSOPHILA_OVARY_2D
= 'drosophila_ovary_slice/annot_struct/insitu7545.png'[source]¶ four class tissue annotation of microscopy image of Drosophila ovary
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imsegm.utilities.data_samples.
IMAGE_3CLS
= 'synthetic/texture_rgb_3cls.jpg'[source]¶ sample image with three different textures
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imsegm.utilities.data_samples.
IMAGE_DROSOPHILA_DISC
= 'drosophila_disc/image/img_6.jpg'[source]¶ sample microscopy image of Drosophila imaginal disc
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imsegm.utilities.data_samples.
IMAGE_DROSOPHILA_OVARY_2D
= 'drosophila_ovary_slice/image/insitu7545.jpg'[source]¶ sample microscopy image of Drosophila ovary
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imsegm.utilities.data_samples.
IMAGE_DROSOPHILA_OVARY_3D
= 'drosophila_ovary_3D/AU10-13_f0011.tif'[source]¶ sample 3D microscopy image of Drosophila ovary
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imsegm.utilities.data_samples.
IMAGE_HISTOL_CIMA
= 'histology_CIMA/29-041-Izd2-w35-CD31-3-les1.jpg'[source]¶ sample image of histology tissue from CIMA dataset - ANHIR challenge
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imsegm.utilities.data_samples.
IMAGE_HISTOL_FLAGSHIP
= 'histology_Flagship/Case001_Cytokeratin.jpg'[source]¶ sample image of histology tissue
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imsegm.utilities.data_samples.
IMAGE_LANGER_ISLET
= 'langerhans_islets/image/gtExoIsl_21.jpg'[source]¶ sample microscopy image of Langernat islets
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imsegm.utilities.data_samples.
IMAGE_OBJECTS
= 'synthetic/reference.jpg'[source]¶ sample image with three color objects of different shape
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imsegm.utilities.data_samples.
IMAGE_STAR
= 'others/sea_starfish-2.jpg'[source]¶ sample image of sea starfish
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imsegm.utilities.data_samples.
LIST_ALL_IMAGES
= ['others/lena.png', 'synthetic/texture_rgb_3cls.jpg', 'synthetic/reference.jpg', 'others/sea_starfish-2.jpg', 'histology_CIMA/29-041-Izd2-w35-CD31-3-les1.jpg', 'histology_Flagship/Case001_Cytokeratin.jpg', 'langerhans_islets/image/gtExoIsl_21.jpg', 'drosophila_disc/image/img_6.jpg', 'drosophila_disc/annot/img_6.png', 'drosophila_ovary_slice/image/insitu7545.jpg', 'drosophila_ovary_slice/annot_struct/insitu7545.png', 'drosophila_ovary_3D/AU10-13_f0011.tif'][source]¶ list of all default images
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imsegm.utilities.data_samples.
PATH_IMAGES
= '/home/docs/checkouts/readthedocs.org/user_builds/pyimsegm/checkouts/v0.1.8/data-images'[source]¶ path to the folder with all sample image/data
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imsegm.utilities.data_samples.
SAMPLE_SEG_SIZE_2D_NORM
= (150, 100)[source]¶ image size for normal 2D sample image