using for loop to install conda package

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ton
2023-04-16 11:03:27 +07:00
parent 49da9f29c1
commit 0c2b34d6f8
12168 changed files with 2656238 additions and 1 deletions

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This directory contains sample data from scikit-image.
By default, it only contains a small subset of the entire dataset.
The full detaset can be downloaded by using the following commands from
a python console.
>>> from skimage.data import download_all
>>> download_all()

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import lazy_loader as lazy
__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

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__all__ = [
'astronaut',
'binary_blobs',
'brain',
'brick',
'camera',
'cat',
'cell',
'cells3d',
'checkerboard',
'chelsea',
'clock',
'coffee',
'coins',
'colorwheel',
'create_image_fetcher',
'data_dir',
'download_all',
'eagle',
'file_hash',
'grass',
'gravel',
'horse',
'hubble_deep_field',
'human_mitosis',
'image_fetcher',
'immunohistochemistry',
'kidney',
'lbp_frontal_face_cascade_filename',
'lfw_subset',
'lily',
'logo',
'microaneurysms',
'moon',
'nickel_solidification',
'page',
'protein_transport',
'retina',
'rocket',
'shepp_logan_phantom',
'skin',
'stereo_motorcycle',
'text',
'vortex',
]
from ._binary_blobs import binary_blobs
from ._fetchers import (
astronaut,
brain,
brick,
camera,
cat,
cell,
cells3d,
checkerboard,
chelsea,
clock,
coffee,
coins,
colorwheel,
create_image_fetcher,
data_dir,
download_all,
eagle,
file_hash,
grass,
gravel,
horse,
hubble_deep_field,
human_mitosis,
image_fetcher,
immunohistochemistry,
kidney,
lbp_frontal_face_cascade_filename,
lfw_subset,
lily,
logo,
microaneurysms,
moon,
nickel_solidification,
page,
protein_transport,
retina,
rocket,
shepp_logan_phantom,
skin,
stereo_motorcycle,
text,
vortex,
)

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import numpy as np
from .._shared.filters import gaussian
def binary_blobs(length=512, blob_size_fraction=0.1, n_dim=2,
volume_fraction=0.5, seed=None):
"""
Generate synthetic binary image with several rounded blob-like objects.
Parameters
----------
length : int, optional
Linear size of output image.
blob_size_fraction : float, optional
Typical linear size of blob, as a fraction of ``length``, should be
smaller than 1.
n_dim : int, optional
Number of dimensions of output image.
volume_fraction : float, default 0.5
Fraction of image pixels covered by the blobs (where the output is 1).
Should be in [0, 1].
seed : {None, int, `numpy.random.Generator`}, optional
If `seed` is None the `numpy.random.Generator` singleton is used.
If `seed` is an int, a new ``Generator`` instance is used,
seeded with `seed`.
If `seed` is already a ``Generator`` instance then that instance is
used.
Returns
-------
blobs : ndarray of bools
Output binary image
Examples
--------
>>> from skimage import data
>>> data.binary_blobs(length=5, blob_size_fraction=0.2) # doctest: +SKIP
array([[ True, False, True, True, True],
[ True, True, True, False, True],
[False, True, False, True, True],
[ True, False, False, True, True],
[ True, False, False, False, True]])
>>> blobs = data.binary_blobs(length=256, blob_size_fraction=0.1)
>>> # Finer structures
>>> blobs = data.binary_blobs(length=256, blob_size_fraction=0.05)
>>> # Blobs cover a smaller volume fraction of the image
>>> blobs = data.binary_blobs(length=256, volume_fraction=0.3)
"""
# filters is quite an expensive import since it imports all of scipy.signal
# We lazy import here
rs = np.random.default_rng(seed)
shape = tuple([length] * n_dim)
mask = np.zeros(shape)
n_pts = max(int(1. / blob_size_fraction) ** n_dim, 1)
points = (length * rs.random((n_dim, n_pts))).astype(int)
mask[tuple(indices for indices in points)] = 1
mask = gaussian(mask, sigma=0.25 * length * blob_size_fraction,
preserve_range=False)
threshold = np.percentile(mask, 100 * (1 - volume_fraction))
return np.logical_not(mask < threshold)

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# flake8: noqa
# This minimal dataset was available as part of
# scikit-image 0.15 and will be retained until
# further notice.
# Testing data and additional datasets should only
# be made available by pooch
legacy_datasets = [
'astronaut.png',
'brick.png',
'camera.png',
'chessboard_GRAY.png',
'chessboard_RGB.png',
'chelsea.png',
'clock_motion.png',
'coffee.png',
'coins.png',
'color.png',
'cell.png',
'grass.png',
'gravel.png',
'horse.png',
'hubble_deep_field.jpg',
'ihc.png',
'lbpcascade_frontalface_opencv.xml',
'lfw_subset.npy',
'logo.png',
'microaneurysms.png',
'moon.png',
'page.png',
'text.png',
'retina.jpg',
'rocket.jpg',
'phantom.png',
'motorcycle_disp.npz',
'motorcycle_left.png',
'motorcycle_right.png',
]
# Registry of datafiles that can be downloaded along with their SHA256 hashes
# To generate the SHA256 hash, use the command
# openssl sha256 filename
registry = {
"color/tests/data/lab_array_a_10.npy": "a3ef76f1530e374f9121020f1f220bc89767dc866f4bbd1b1f47e5b84891a38c",
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"color/tests/data/lab_array_c_10.npy": "88b4ff2a2d2c4f48e7bb265609221d4b9ef439a4e2d8a86989696bfdb47790e6",
"color/tests/data/lab_array_c_2.npy": "e1b8acfdc7284ab9cd339de66948134304073b6f734ecf9ad42f8297b83d3405",
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"data/brick.png": "7966caf324f6ba843118d98f7a07746d22f6a343430add0233eca5f6eaaa8fcf",
"data/cell.png": "8d23a7fb81f7cc877cd09f330357fc7f595651306e84e17252f6e0a1b3f61515",
"data/camera.png": "b0793d2adda0fa6ae899c03989482bff9a42d3d5690fc7e3648f2795d730c23a",
"data/chessboard_GRAY.png": "3e51870774515af4d07d820bd8827364c70839bf9b573c746e485095e893df90",
"data/chessboard_RGB.png": "1ac01eff2d4e50f4eda55a2ddecdc28a6576623a58d7a7ef84513c5cc19a0331",
"data/chelsea.png": "596aa1e7cb875eb79f437e310381d26b338a81c2da23439704a73c4651e8c4bb",
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"registration/tests/data/TransformedX130Y130.png": "bb10c6ae3f91a313b0ac543efdb7ca69c4b95e55674c65a88472a6c4f4692a25",
"registration/tests/data/TransformedX75Y75.png": "a1e9ead5f8e4a0f604271e1f9c50e89baf53f068f1d19fab2876af4938e695ea",
"data/brain.tiff": "bcdbaf424fbad7b1fb0f855f608c68e5a838f35affc323ff04ea17f678eef5c6",
"data/cells3d.tif": "afc7c7d80d38bfde09788b4064ac1e64ec14e88454ab785ebdc8dbba5ca3b222",
"data/kidney.tif": "80c0799bc58b08cf6eaa53ecd202305eb42fd7bc73746cb6c5064dbeae7e8476",
"data/lily.tif": "395c2f0194c25b9824a8cd79266920362a0816bc9e906dd392adce2d8309af03",
"data/mitosis.tif": "2751ba667c4067c5d30817cff004aa06f6f6287f1cdbb5b8c9c6a500308cb456",
"data/skin.jpg": "8759fe080509712163453f4b17106582b8513e73b0788d80160abf840e272075",
"data/pivchallenge-B-B001_1.tif": "e95e09abbcecba723df283ac7d361766328abd943701a2ec2f345d4a2014da2a",
"data/pivchallenge-B-B001_2.tif": "4ceb5407e4e333476a0f264c14b7a3f6c0e753fcdc99ee1c4b8196e5f823805e",
"data/protein_transport.tif": "a8e24e8d187f33e92ee28508d5615286c850ca75374af7e74e527d290e8b06ea",
"data/solidification.tif": "50ef9a52c621b7c0c506ad1fe1b8ee8a158a4d7c8e50ddfce1e273a422dca3f9",
}
registry_urls = {
"data/brain.tiff": "https://gitlab.com/scikit-image/data/-/raw/2cdc5ce89b334d28f06a58c9f0ca21aa6992a5ba/brain.tiff",
"data/cells3d.tif": "https://gitlab.com/scikit-image/data/-/raw/2cdc5ce89b334d28f06a58c9f0ca21aa6992a5ba/cells3d.tif",
"data/eagle.png": "https://gitlab.com/scikit-image/data/-/raw/2cdc5ce89b334d28f06a58c9f0ca21aa6992a5ba/eagle.png",
"data/kidney.tif": "https://gitlab.com/scikit-image/data/-/raw/2cdc5ce89b334d28f06a58c9f0ca21aa6992a5ba/kidney-tissue-fluorescence.tif",
"data/lily.tif": "https://gitlab.com/scikit-image/data/-/raw/2cdc5ce89b334d28f06a58c9f0ca21aa6992a5ba/lily-of-the-valley-fluorescence.tif",
"data/mitosis.tif": "https://gitlab.com/scikit-image/data/-/raw/2cdc5ce89b334d28f06a58c9f0ca21aa6992a5ba/AS_09125_050116030001_D03f00d0.tif",
"data/rank_filters_tests_3d.npz": "https://gitlab.com/scikit-image/data/-/raw/2cdc5ce89b334d28f06a58c9f0ca21aa6992a5ba/Tests_besides_Equalize_Otsu/add18_entropy/rank_filters_tests_3d.npz",
"data/skin.jpg": "https://gitlab.com/scikit-image/data/-/raw/2cdc5ce89b334d28f06a58c9f0ca21aa6992a5ba/Normal_Epidermis_and_Dermis_with_Intradermal_Nevus_10x.JPG",
"data/pivchallenge-B-B001_1.tif": "https://gitlab.com/scikit-image/data/-/raw/2cdc5ce89b334d28f06a58c9f0ca21aa6992a5ba/pivchallenge/B/B001_1.tif",
"data/pivchallenge-B-B001_2.tif": "https://gitlab.com/scikit-image/data/-/raw/2cdc5ce89b334d28f06a58c9f0ca21aa6992a5ba/pivchallenge/B/B001_2.tif",
"data/protein_transport.tif": "https://gitlab.com/scikit-image/data/-/raw/2cdc5ce89b334d28f06a58c9f0ca21aa6992a5ba/NPCsingleNucleus.tif",
"data/solidification.tif": "https://gitlab.com/scikit-image/data/-/raw/2cdc5ce89b334d28f06a58c9f0ca21aa6992a5ba/nickel_solidification.tif",
"restoration/tests/astronaut_rl.npy": "https://gitlab.com/scikit-image/data/-/raw/2cdc5ce89b334d28f06a58c9f0ca21aa6992a5ba/astronaut_rl.npy",
}
legacy_registry = {
('data/' + filename): registry['data/' + filename]
for filename in legacy_datasets
}

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import numpy as np
import skimage.data as data
from skimage.data._fetchers import image_fetcher
from skimage import io
from skimage._shared.testing import assert_equal, assert_almost_equal, fetch
import os
import pytest
def test_data_dir():
# data_dir should be a directory people can use as a standard directory
# https://github.com/scikit-image/scikit-image/pull/3945#issuecomment-498141893
data_dir = data.data_dir
assert 'astronaut.png' in os.listdir(data_dir)
def test_download_all_with_pooch():
# jni first wrote this test with the intention of
# fully deleting the files in the data_dir,
# then ensure that the data gets downloaded accordingly.
# hmaarrfk raised the concern that this test wouldn't
# play well with parallel testing since we
# may be breaking the global state that certain other
# tests require, especially in parallel testing
# The second concern is that this test essentially uses
# a lot of bandwidth, which is not fun for developers on
# lower speed connections.
# https://github.com/scikit-image/scikit-image/pull/4666/files/26d5138b25b958da6e97ebf979e9bc36f32c3568#r422604863
data_dir = data.data_dir
if image_fetcher is not None:
data.download_all()
assert len(os.listdir(data_dir)) > 50
else:
with pytest.raises(ModuleNotFoundError):
data.download_all()
def test_astronaut():
""" Test that "astronaut" image can be loaded. """
astronaut = data.astronaut()
assert_equal(astronaut.shape, (512, 512, 3))
def test_camera():
""" Test that "camera" image can be loaded. """
cameraman = data.camera()
assert_equal(cameraman.ndim, 2)
def test_checkerboard():
""" Test that "checkerboard" image can be loaded. """
data.checkerboard()
def test_chelsea():
""" Test that "chelsea" image can be loaded. """
data.chelsea()
def test_clock():
""" Test that "clock" image can be loaded. """
data.clock()
def test_coffee():
""" Test that "coffee" image can be loaded. """
data.coffee()
def test_eagle():
""" Test that "eagle" image can be loaded. """
# Fetching the data through the testing module will
# cause the test to skip if pooch isn't installed.
fetch('data/eagle.png')
eagle = data.eagle()
assert_equal(eagle.ndim, 2)
assert_equal(eagle.dtype, np.dtype('uint8'))
def test_horse():
""" Test that "horse" image can be loaded. """
horse = data.horse()
assert_equal(horse.ndim, 2)
assert_equal(horse.dtype, np.dtype('bool'))
def test_hubble():
""" Test that "Hubble" image can be loaded. """
data.hubble_deep_field()
def test_immunohistochemistry():
""" Test that "immunohistochemistry" image can be loaded. """
data.immunohistochemistry()
def test_logo():
""" Test that "logo" image can be loaded. """
logo = data.logo()
assert_equal(logo.ndim, 3)
assert_equal(logo.shape[2], 4)
def test_moon():
""" Test that "moon" image can be loaded. """
data.moon()
def test_page():
""" Test that "page" image can be loaded. """
data.page()
def test_rocket():
""" Test that "rocket" image can be loaded. """
data.rocket()
def test_text():
""" Test that "text" image can be loaded. """
data.text()
def test_stereo_motorcycle():
""" Test that "stereo_motorcycle" image can be loaded. """
data.stereo_motorcycle()
def test_binary_blobs():
blobs = data.binary_blobs(length=128)
assert_almost_equal(blobs.mean(), 0.5, decimal=1)
blobs = data.binary_blobs(length=128, volume_fraction=0.25)
assert_almost_equal(blobs.mean(), 0.25, decimal=1)
blobs = data.binary_blobs(length=32, volume_fraction=0.25, n_dim=3)
assert_almost_equal(blobs.mean(), 0.25, decimal=1)
other_realization = data.binary_blobs(length=32, volume_fraction=0.25,
n_dim=3)
assert not np.all(blobs == other_realization)
def test_lfw_subset():
""" Test that "lfw_subset" can be loaded."""
data.lfw_subset()
def test_skin():
"""Test that "skin" image can be loaded.
Needs internet connection.
"""
skin = data.skin()
assert skin.ndim == 3
def test_cell():
""" Test that "cell" image can be loaded."""
data.cell()
def test_cells3d():
"""Needs internet connection."""
path = fetch('data/cells3d.tif')
image = io.imread(path)
assert image.shape == (60, 2, 256, 256)
def test_brain_3d():
"""Needs internet connection."""
path = fetch('data/brain.tiff')
image = io.imread(path)
assert image.shape == (10, 256, 256)
def test_kidney_3d_multichannel():
"""Test that 3D multichannel image of kidney tissue can be loaded.
Needs internet connection.
"""
fetch('data/kidney.tif')
kidney = data.kidney()
assert kidney.shape == (16, 512, 512, 3)
def test_lily_multichannel():
"""Test that microscopy image of lily of the valley can be loaded.
Needs internet connection.
"""
fetch('data/lily.tif')
lily = data.lily()
assert lily.shape == (922, 922, 4)
def test_vortex():
fetch('data/pivchallenge-B-B001_1.tif')
fetch('data/pivchallenge-B-B001_2.tif')
image0, image1 = data.vortex()
for image in [image0, image1]:
assert image.shape == (512, 512)
@pytest.mark.parametrize(
'function_name', ['create_image_fetcher', 'file_hash', 'image_fetcher']
)
def test_fetchers_are_public(function_name):
# Check that the following functions that are only used indirectly in the
# above tests are public.
assert hasattr(data, function_name)

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