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)

imsegm.utilities.data_samples.get_image_path(name_img, path_base='/home/docs/checkouts/readthedocs.org/user_builds/pyimsegm/checkouts/latest/data-images')[source]¶

merge default image path and sample image

Parameters

name_img (str) –
path_base (str) –

Return str

>>> p = get_image_path(IMAGE_LENNA)
>>> os.path.isfile(p)
True
>>> os.path.basename(p)
'lena.png'

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)

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

Parameters

im_size (tuple(int,int)) –
nb_classes (int) –
rand_seed –

Returns

>>> 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]])

imsegm.utilities.data_samples.sample_segment_vertical_2d(seg_size=(20, 10), nb_labels=3)[source]¶

create sample segmentation with vertical stripes

Parameters

seg_size (tuple(int,int)) –
nb_labels (int) –

Return ndarray

>>> 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]])

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

seg_size (tuple(int,int)|tuple(int,int,int)) –
nb_labels (int) –
levels (int) –

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]])

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

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

imsegm.utilities.data_samples.IMAGE_3CLS = 'synthetic/texture_rgb_3cls.jpg'[source]¶: sample image with three different textures

imsegm.utilities.data_samples.IMAGE_DROSOPHILA_DISC = 'drosophila_disc/image/img_6.jpg'[source]¶: sample microscopy image of Drosophila imaginal disc

imsegm.utilities.data_samples.IMAGE_DROSOPHILA_OVARY_2D = 'drosophila_ovary_slice/image/insitu7545.jpg'[source]¶: sample microscopy image of Drosophila ovary

imsegm.utilities.data_samples.IMAGE_DROSOPHILA_OVARY_3D = 'drosophila_ovary_3D/AU10-13_f0011.tif'[source]¶: sample 3D microscopy image of Drosophila ovary

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

imsegm.utilities.data_samples.IMAGE_HISTOL_FLAGSHIP = 'histology_Flagship/Case001_Cytokeratin.jpg'[source]¶: sample image of histology tissue

imsegm.utilities.data_samples.IMAGE_LANGER_ISLET = 'langerhans_islets/image/gtExoIsl_21.jpg'[source]¶: sample microscopy image of Langernat islets

imsegm.utilities.data_samples.IMAGE_LENNA = 'others/lena.png'[source]¶: sample Lenna image

imsegm.utilities.data_samples.IMAGE_OBJECTS = 'synthetic/reference.jpg'[source]¶: sample image with three color objects of different shape

imsegm.utilities.data_samples.IMAGE_STAR = 'others/sea_starfish-2.jpg'[source]¶: sample image of sea starfish

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

imsegm.utilities.data_samples.PATH_IMAGES = '/home/docs/checkouts/readthedocs.org/user_builds/pyimsegm/checkouts/latest/data-images'[source]¶: path to the folder with all sample image/data

imsegm.utilities.data_samples.SAMPLE_SEG_NB_CLASSES = 3[source]¶: number of classes for segmentation

imsegm.utilities.data_samples.SAMPLE_SEG_SIZE_2D_NORM = (150, 100)[source]¶: image size for normal 2D sample image

imsegm.utilities.data_samples.SAMPLE_SEG_SIZE_2D_SMALL = (20, 10)[source]¶: image size for small 2D sample image

imsegm.utilities.data_samples.SAMPLE_SEG_SIZE_3D_SMALL = (10, 5, 6)[source]¶: image size for small 3D sample image