repo stringlengths 2 99 | file stringlengths 13 225 | code stringlengths 0 18.3M | file_length int64 0 18.3M | avg_line_length float64 0 1.36M | max_line_length int64 0 4.26M | extension_type stringclasses 1
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gunpowder | gunpowder-master/gunpowder/nodes/hdf5like_write_base.py | from .batch_filter import BatchFilter
from gunpowder.batch_request import BatchRequest
from gunpowder.coordinate import Coordinate
from gunpowder.roi import Roi
import logging
import os
import warnings
logger = logging.getLogger(__name__)
class Hdf5LikeWrite(BatchFilter):
"""Assemble arrays of passing batches in... | 8,112 | 35.21875 | 88 | py |
gunpowder | gunpowder-master/gunpowder/nodes/zarr_source.py | from gunpowder.ext import ZarrFile
from gunpowder.batch import Batch
from gunpowder.coordinate import Coordinate
from gunpowder.profiling import Timing
from gunpowder.roi import Roi
from gunpowder.array import Array
from gunpowder.array_spec import ArraySpec
from .batch_provider import BatchProvider
from zarr._storage... | 8,175 | 33.066667 | 88 | py |
gunpowder | gunpowder-master/gunpowder/nodes/balance_labels.py | from .batch_filter import BatchFilter
from gunpowder.array import Array
from gunpowder.batch_request import BatchRequest
from gunpowder.batch import Batch
from collections.abc import Iterable
import itertools
import logging
import numpy as np
logger = logging.getLogger(__name__)
class BalanceLabels(BatchFilter):
... | 5,890 | 31.016304 | 88 | py |
gunpowder | gunpowder-master/gunpowder/nodes/generic_train.py | import glob
import logging
import multiprocessing
import re
import time
from gunpowder.nodes.batch_filter import BatchFilter
from gunpowder.producer_pool import ProducerPool, WorkersDied, NoResult
from gunpowder.array import ArrayKey
from gunpowder.array_spec import ArraySpec
from gunpowder.batch_request import BatchR... | 7,446 | 31.662281 | 82 | py |
gunpowder | gunpowder-master/gunpowder/nodes/graph_source.py | import logging
import networkx as nx
import numpy as np
from gunpowder.batch import Batch
from gunpowder.graph import Graph
from gunpowder.graph_spec import GraphSpec
from gunpowder.nodes.batch_provider import BatchProvider
from gunpowder.profiling import Timing
logger = logging.getLogger(__name__)
class GraphSourc... | 4,059 | 34.929204 | 81 | py |
gunpowder | gunpowder-master/gunpowder/nodes/random_provider.py | import copy
import numpy as np
from gunpowder.array import Array
from gunpowder.array_spec import ArraySpec
from .batch_provider import BatchProvider
class RandomProvider(BatchProvider):
"""Randomly selects one of the upstream providers::
(a + b + c) + RandomProvider()
will create a provider that ... | 3,171 | 34.244444 | 83 | py |
gunpowder | gunpowder-master/gunpowder/nodes/random_location.py | import math
import logging
from random import random, randint, choices, seed
import itertools
import numpy as np
from scipy.spatial import cKDTree
from skimage.transform import integral_image, integrate
from gunpowder.batch_request import BatchRequest
from gunpowder.coordinate import Coordinate
from gunpowder.roi impo... | 17,580 | 36.486141 | 95 | py |
gunpowder | gunpowder-master/gunpowder/nodes/defect_augment.py | import logging
import random
import numpy as np
# imports for deformed slice
from skimage.draw import line
from scipy.ndimage.measurements import label
from scipy.ndimage.interpolation import map_coordinates
from scipy.ndimage.morphology import binary_dilation
from gunpowder.batch_request import BatchRequest
from gun... | 13,030 | 38.36858 | 88 | py |
gunpowder | gunpowder-master/gunpowder/nodes/hdf5like_source_base.py | from gunpowder.batch import Batch
from gunpowder.coordinate import Coordinate
from gunpowder.profiling import Timing
from gunpowder.roi import Roi
from gunpowder.array import Array
from gunpowder.array_spec import ArraySpec
from .batch_provider import BatchProvider
import logging
import numpy as np
import warnings
lo... | 7,296 | 33.747619 | 88 | py |
gunpowder | gunpowder-master/gunpowder/nodes/zarr_write.py | from collections.abc import MutableMapping
from typing import Union
from zarr._storage.store import BaseStore
from zarr import N5FSStore, N5Store
from .batch_filter import BatchFilter
from gunpowder.batch_request import BatchRequest
from gunpowder.coordinate import Coordinate
from gunpowder.roi import Roi
from gunpow... | 8,757 | 35.798319 | 88 | py |
gunpowder | gunpowder-master/gunpowder/nodes/specified_location.py | from random import randrange
from random import choice, seed
import logging
import numpy as np
from gunpowder.coordinate import Coordinate
from gunpowder.batch_request import BatchRequest
from .batch_filter import BatchFilter
logger = logging.getLogger(__name__)
class SpecifiedLocation(BatchFilter):
"""Choses ... | 6,145 | 35.802395 | 88 | py |
gunpowder | gunpowder-master/gunpowder/nodes/__init__.py | from __future__ import absolute_import
from .add_affinities import AddAffinities
from .astype import AsType
from .balance_labels import BalanceLabels
from .batch_filter import BatchFilter
from .batch_provider import BatchProvider
from .crop import Crop
from .csv_points_source import CsvPointsSource
from .daisy_request... | 1,808 | 36.6875 | 70 | py |
gunpowder | gunpowder-master/gunpowder/nodes/stack.py | from .batch_filter import BatchFilter
from gunpowder.array import Array
from gunpowder.batch import Batch
from gunpowder.profiling import Timing
import numpy as np
class Stack(BatchFilter):
"""Request several batches and stack them together, introducing a new
dimension for each array. This is useful to create... | 1,519 | 28.803922 | 79 | py |
gunpowder | gunpowder-master/gunpowder/nodes/intensity_scale_shift.py | from .batch_filter import BatchFilter
class IntensityScaleShift(BatchFilter):
"""Scales the intensities of a batch by ``scale``, then adds ``shift``.
Args:
array (:class:`ArrayKey`):
The key of the array to modify.
scale (``float``):
shift (``float``):
The ... | 690 | 22.033333 | 75 | py |
gunpowder | gunpowder-master/gunpowder/nodes/hdf5_write.py | from .hdf5like_write_base import Hdf5LikeWrite
from gunpowder.ext import h5py
import os
class Hdf5Write(Hdf5LikeWrite):
"""Assemble arrays of passing batches in one HDF5 file. This is useful to
store chunks produced by :class:`Scan` on disk without keeping the larger
array in memory. The ROIs of the passi... | 1,607 | 33.212766 | 79 | py |
gunpowder | gunpowder-master/gunpowder/nodes/batch_filter.py | import copy
import logging
from .batch_provider import BatchProvider
from gunpowder.batch_request import BatchRequest
from gunpowder.profiling import Timing
logger = logging.getLogger(__name__)
class BatchFilterError(Exception):
def __init__(self, batch_filter, msg):
self.batch_filter = batch_filter
... | 8,452 | 32.677291 | 91 | py |
gunpowder | gunpowder-master/gunpowder/nodes/downsample.py | from .batch_filter import BatchFilter
from gunpowder.array import ArrayKey, Array
from gunpowder.batch_request import BatchRequest
from gunpowder.batch import Batch
import logging
import numbers
from funlib.geometry import Coordinate
logger = logging.getLogger(__name__)
class DownSample(BatchFilter):
"""Downsamp... | 2,387 | 28.481481 | 83 | py |
gunpowder | gunpowder-master/gunpowder/nodes/hdf5_source.py | from gunpowder.ext import h5py
from .hdf5like_source_base import Hdf5LikeSource
class Hdf5Source(Hdf5LikeSource):
"""An HDF5 data source.
Provides arrays from HDF5 datasets. If the attribute ``resolution`` is set
in a HDF5 dataset, it will be used as the array's ``voxel_size``. If the
attribute ``off... | 1,631 | 37.857143 | 82 | py |
gunpowder | gunpowder-master/gunpowder/nodes/upsample.py | from .batch_filter import BatchFilter
from gunpowder.coordinate import Coordinate
from gunpowder.array import ArrayKey, Array
from gunpowder.array_spec import ArraySpec
from gunpowder.batch_request import BatchRequest
from gunpowder.batch import Batch
import logging
import numbers
import numpy as np
logger = logging.g... | 2,967 | 27.266667 | 74 | py |
gunpowder | gunpowder-master/gunpowder/nodes/normalize.py | import logging
import copy
import numpy as np
from gunpowder.batch_request import BatchRequest
from .batch_filter import BatchFilter
logger = logging.getLogger(__name__)
class Normalize(BatchFilter):
"""Normalize the values of an array to be floats between 0 and 1, based on
the type of the array.
Args... | 2,525 | 28.717647 | 79 | py |
gunpowder | gunpowder-master/gunpowder/nodes/pad.py | import logging
import numpy as np
from .batch_filter import BatchFilter
from gunpowder.array import ArrayKey
from gunpowder.roi import Roi
from gunpowder.coordinate import Coordinate
from gunpowder.batch_request import BatchRequest
logger = logging.getLogger(__name__)
class Pad(BatchFilter):
"""Add a constant i... | 4,216 | 29.781022 | 87 | py |
gunpowder | gunpowder-master/gunpowder/nodes/precache.py | import copy
import logging
import multiprocessing
import time
import random
from .batch_filter import BatchFilter
from gunpowder.profiling import Timing
from gunpowder.producer_pool import ProducerPool
from collections import deque
logger = logging.getLogger(__name__)
class WorkersDiedException(Exception):
pas... | 4,336 | 30.889706 | 96 | py |
gunpowder | gunpowder-master/gunpowder/nodes/print_profiling_stats.py | import logging
from .batch_filter import BatchFilter
from gunpowder.profiling import Timing, TimingSummary, ProfilingStats
logger = logging.getLogger(__name__)
class PrintProfilingStats(BatchFilter):
"""Print profiling information about nodes upstream of this node in the DAG.
The output also includes a ``T... | 3,948 | 33.043103 | 87 | py |
gunpowder | gunpowder-master/gunpowder/nodes/shift_augment.py | from __future__ import print_function, division
import logging
import numpy as np
import random
from gunpowder.roi import Roi
from gunpowder.coordinate import Coordinate
from gunpowder.batch_request import BatchRequest
from .batch_filter import BatchFilter
logger = logging.getLogger(__name__)
class ShiftAugment(Bat... | 11,372 | 39.187279 | 115 | py |
gunpowder | gunpowder-master/gunpowder/contrib/__init__.py | from __future__ import absolute_import
from .nodes import *
| 61 | 14.5 | 38 | py |
gunpowder | gunpowder-master/gunpowder/contrib/nodes/add_vector_map.py | import copy
import logging
import numpy as np
from scipy.spatial import KDTree
from gunpowder.array import Array
from gunpowder.array_spec import ArraySpec
from gunpowder.batch_request import BatchRequest
from gunpowder.coordinate import Coordinate
from gunpowder.morphology import enlarge_binary_map
from gunpowder.nod... | 16,212 | 48.279635 | 122 | py |
gunpowder | gunpowder-master/gunpowder/contrib/nodes/add_gt_mask_exclusive_zone.py | import copy
import logging
import numpy as np
from scipy import ndimage
from gunpowder.nodes.batch_filter import BatchFilter
from gunpowder.array import Array, ArrayKeys
from gunpowder.nodes.rasterize_graph import RasterizationSettings
from gunpowder.morphology import enlarge_binary_map
logger = logging.getLogger(__n... | 5,113 | 38.953125 | 106 | py |
gunpowder | gunpowder-master/gunpowder/contrib/nodes/add_blobs_from_points.py | import logging
import itertools
import numpy as np
from gunpowder.array import Array
from gunpowder.nodes.batch_filter import BatchFilter
logger = logging.getLogger(__name__)
class AddBlobsFromPoints(BatchFilter):
"""Add an array with blobs at locations given by a specified points
collection. The blobs are ... | 11,060 | 38.503571 | 98 | py |
gunpowder | gunpowder-master/gunpowder/contrib/nodes/zero_out_const_sections.py | from gunpowder.nodes.batch_filter import BatchFilter
class ZeroOutConstSections(BatchFilter):
"""Every z-section that has constant values only will be set to 0.
This is to handle blank (missing) sections in a less invasive way: Instead
of leaving them at -1 (which is "black", the lowest possible input to... | 940 | 32.607143 | 84 | py |
gunpowder | gunpowder-master/gunpowder/contrib/nodes/add_boundary_distance_gradients.py | import logging
import numpy as np
from gunpowder.array import Array
from gunpowder.batch_request import BatchRequest
from gunpowder.nodes.batch_filter import BatchFilter
from numpy.lib.stride_tricks import as_strided
from scipy.ndimage.morphology import distance_transform_edt
logger = logging.getLogger(__name__)
cl... | 7,250 | 34.544118 | 86 | py |
gunpowder | gunpowder-master/gunpowder/contrib/nodes/add_nonsymmetric_affinities.py | import copy
import logging
import numpy as np
import pdb
from gunpowder.array import Array
from gunpowder.nodes.batch_filter import BatchFilter
logger = logging.getLogger(__name__)
class AddNonsymmetricAffinities(BatchFilter):
def __init__(
self,
affinity_vectors,
array_key_1,
ar... | 5,551 | 34.139241 | 85 | py |
gunpowder | gunpowder-master/gunpowder/contrib/nodes/hdf5_points_source.py | import copy
import logging
import numpy as np
from gunpowder.batch import Batch
from gunpowder.coordinate import Coordinate
from gunpowder.ext import h5py
from gunpowder.graph import GraphKey, Graph
from gunpowder.graph_spec import GraphSpec
from gunpowder.profiling import Timing
from gunpowder.roi import Roi
from gun... | 6,123 | 36.570552 | 88 | py |
gunpowder | gunpowder-master/gunpowder/contrib/nodes/prepare_malis.py | import copy
import logging
import numpy as np
from gunpowder.array import Array
from gunpowder.batch_request import BatchRequest
from gunpowder.nodes.batch_filter import BatchFilter
logger = logging.getLogger(__name__)
class PrepareMalis(BatchFilter):
"""Creates a component label array needed for two-phase mali... | 2,699 | 33.177215 | 87 | py |
gunpowder | gunpowder-master/gunpowder/contrib/nodes/__init__.py | from __future__ import absolute_import
from .add_blobs_from_points import AddBlobsFromPoints
from .add_boundary_distance_gradients import AddBoundaryDistanceGradients
from .add_gt_mask_exclusive_zone import AddGtMaskExclusiveZone
from .add_nonsymmetric_affinities import AddNonsymmetricAffinities
from .add_vector_map i... | 558 | 45.583333 | 73 | py |
gunpowder | gunpowder-master/gunpowder/contrib/nodes/dvid_partner_annotation_source.py | import distutils.util
import numpy as np
import logging
import requests
from copy import deepcopy
from gunpowder.batch import Batch
from gunpowder.nodes.batch_provider import BatchProvider
from gunpowder.graph import GraphKey, Graph
from gunpowder.graph_spec import GraphSpec
from gunpowder.profiling import Timing
fro... | 9,773 | 37.031128 | 141 | py |
gunpowder | gunpowder-master/gunpowder/ext/zarr_file.py | from collections.abc import MutableMapping
from typing import Union
import zarr
from zarr._storage.store import BaseStore
class ZarrFile:
"""To be used as a context manager, similar to h5py.File."""
def __init__(self, store: Union[BaseStore, MutableMapping, str], mode="a"):
self.store = store
... | 463 | 22.2 | 79 | py |
gunpowder | gunpowder-master/gunpowder/ext/__init__.py | from __future__ import print_function
import logging
import traceback
import sys
logger = logging.getLogger(__name__)
class NoSuchModule(object):
def __init__(self, name):
self.__name = name
self.__traceback_str = traceback.format_tb(sys.exc_info()[2])
errtype, value = sys.exc_info()[:2]... | 1,676 | 17.228261 | 69 | py |
gunpowder | gunpowder-master/gunpowder/tensorflow/local_server.py | import logging
import multiprocessing
import ctypes
from gunpowder.ext import tensorflow as tf
from gunpowder.freezable import Freezable
logger = logging.getLogger(__name__)
class LocalServer(Freezable):
"""Wrapper around ``tf.train.Server`` to create a local server on-demand.
This class is necessary becaus... | 1,711 | 33.938776 | 77 | py |
gunpowder | gunpowder-master/gunpowder/tensorflow/__init__.py | from __future__ import absolute_import
from .nodes import *
from .local_server import LocalServer
| 99 | 19 | 38 | py |
gunpowder | gunpowder-master/gunpowder/tensorflow/nodes/__init__.py | from __future__ import absolute_import
from .train import Train
from .predict import Predict
| 94 | 18 | 38 | py |
gunpowder | gunpowder-master/gunpowder/tensorflow/nodes/predict.py | import ctypes
import logging
import multiprocessing as mp
import numpy as np
from functools import reduce
from gunpowder.array import ArrayKey, Array
from gunpowder.ext import tensorflow as tf
from gunpowder.nodes.generic_predict import GenericPredict
from gunpowder.tensorflow.local_server import LocalServer
from oper... | 12,847 | 33.818428 | 88 | py |
gunpowder | gunpowder-master/gunpowder/tensorflow/nodes/train.py | import logging
import os
import numpy as np
from gunpowder.array import ArrayKey, Array
from gunpowder.ext import tensorflow as tf
from gunpowder.nodes.generic_train import GenericTrain
from gunpowder.tensorflow.local_server import LocalServer
logger = logging.getLogger(__name__)
class Train(GenericTrain):
"""T... | 12,704 | 35.93314 | 87 | py |
gunpowder | gunpowder-master/examples/cremi/mknet.py | from gunpowder.zoo.tensorflow import unet, conv_pass
import tensorflow as tf
import json
def create_network(input_shape, name):
tf.reset_default_graph()
# create a placeholder for the 3D raw input tensor
raw = tf.placeholder(tf.float32, shape=input_shape)
# create a U-Net
raw_batched = tf.reshap... | 2,432 | 29.797468 | 77 | py |
gunpowder | gunpowder-master/examples/cremi/predict.py | from __future__ import print_function
import gunpowder as gp
import json
def predict(iteration):
##################
# DECLARE ARRAYS #
##################
# raw intensities
raw = gp.ArrayKey('RAW')
# the predicted affinities
pred_affs = gp.ArrayKey('PRED_AFFS')
####################
... | 2,863 | 28.22449 | 77 | py |
gunpowder | gunpowder-master/examples/cremi/train.py | from __future__ import print_function
import gunpowder as gp
import json
import math
import logging
logging.basicConfig(level=logging.INFO)
def train(iterations):
##################
# DECLARE ARRAYS #
##################
# raw intensities
raw = gp.ArrayKey('RAW')
# objects labelled with uniq... | 5,395 | 28.167568 | 79 | py |
gunpowder | gunpowder-master/tests/conftest.py | import pytest
import multiprocessing as mp
# cannot parametrize unittest.TestCase. We should test both
# fork and spawn but I'm not sure how to.
# @pytest.fixture(params=["fork", "spawn"], autouse=True)
@pytest.fixture(autouse=True)
def context(monkeypatch):
ctx = mp.get_context("spawn")
monkeypatch.setattr(... | 492 | 29.8125 | 59 | py |
gunpowder | gunpowder-master/tests/__init__.py | 0 | 0 | 0 | py | |
gunpowder | gunpowder-master/tests/cases/add_vector_map.py | import unittest
from .provider_test import ProviderTest
from gunpowder import (
ArrayKeys,
ArraySpec,
GraphSpec,
Roi,
Array,
GraphKeys,
GraphKey,
Batch,
BatchProvider,
Graph,
Node,
Coordinate,
ArrayKey,
BatchRequest,
build,
)
from gunpowder.contrib import AddV... | 15,651 | 40.298153 | 92 | py |
gunpowder | gunpowder-master/tests/cases/unsqueeze.py | import copy
import numpy as np
import gunpowder as gp
from .provider_test import ProviderTest
class ExampleSourceUnsqueeze(gp.BatchProvider):
def __init__(self, voxel_size):
self.voxel_size = gp.Coordinate(voxel_size)
self.roi = gp.Roi((0, 0, 0), (10, 10, 10)) * self.voxel_size
self.raw ... | 2,965 | 29.57732 | 88 | py |
gunpowder | gunpowder-master/tests/cases/squeeze.py | import copy
import numpy as np
import gunpowder as gp
from .provider_test import ProviderTest
class ExampleSourceSqueeze(gp.BatchProvider):
def __init__(self, voxel_size):
self.voxel_size = gp.Coordinate(voxel_size)
self.roi = gp.Roi((0, 0, 0), (10, 10, 10)) * self.voxel_size
self.raw = ... | 3,211 | 29.884615 | 88 | py |
gunpowder | gunpowder-master/tests/cases/elastic_augment_points.py | import unittest
from gunpowder import (
BatchProvider,
Batch,
BatchRequest,
GraphSpec,
GraphKeys,
GraphKey,
Graph,
Node,
ArraySpec,
ArrayKeys,
ArrayKey,
Array,
Roi,
Coordinate,
ElasticAugment,
RasterizeGraph,
RasterizationSettings,
Snapshot,
bu... | 15,464 | 34.470183 | 98 | py |
gunpowder | gunpowder-master/tests/cases/intensity_augment.py | from .provider_test import ProviderTest
from gunpowder import IntensityAugment, ArrayKeys, build, Normalize
import numpy as np
class TestIntensityAugment(ProviderTest):
def test_shift(self):
pipeline = (
self.test_source
+ Normalize(ArrayKeys.RAW)
+ IntensityAugment(
... | 709 | 28.583333 | 85 | py |
gunpowder | gunpowder-master/tests/cases/elastic_augment.py | from gunpowder import (
BatchProvider,
GraphSpec,
Roi,
Coordinate,
ArrayKeys,
ArraySpec,
Batch,
Array,
ArrayKey,
GraphKey,
BatchRequest,
RasterizationSettings,
RasterizeGraph,
Snapshot,
ElasticAugment,
build,
)
from gunpowder.graph import GraphKeys, Graph,... | 4,944 | 31.966667 | 81 | py |
gunpowder | gunpowder-master/tests/cases/astype.py | from .provider_test import ProviderTest
from gunpowder import *
import numpy as np
class AsTypeTestSource(BatchProvider):
def setup(self):
self.provides(
ArrayKeys.RAW,
ArraySpec(roi=Roi((0, 0, 0), (1000, 1000, 1000)), voxel_size=(4, 4, 4)),
)
self.provides(
... | 3,700 | 36.01 | 105 | py |
gunpowder | gunpowder-master/tests/cases/graph_keys.py | from __future__ import print_function
from gunpowder import GraphKey, GraphKeys
import unittest
class TestGraphKeys(unittest.TestCase):
def test_register(self):
GraphKey("TEST_GRAPH")
self.assertTrue(GraphKeys.TEST_GRAPH)
self.assertRaises(AttributeError, getattr, GraphKeys, "TEST_GRAPH_2... | 323 | 26 | 77 | py |
gunpowder | gunpowder-master/tests/cases/resample.py | from .helper_sources import ArraySource
from gunpowder import (
ArrayKey,
ArraySpec,
Roi,
Coordinate,
Batch,
BatchRequest,
Array,
MergeProvider,
Resample,
build,
)
import numpy as np
def test_up_and_downsample():
meshgrids = np.meshgrid(range(0, 250), range(0, 250), range(... | 3,703 | 35.313725 | 230 | py |
gunpowder | gunpowder-master/tests/cases/noise_augment.py | from .provider_test import ProviderTest
from gunpowder import IntensityAugment, ArrayKeys, build, Normalize, NoiseAugment
import numpy as np
class TestIntensityAugment(ProviderTest):
def test_shift(self):
pipeline = (
self.test_source
+ Normalize(ArrayKeys.RAW)
+ Inten... | 826 | 29.62963 | 85 | py |
gunpowder | gunpowder-master/tests/cases/zarr_read_write.py | from .helper_sources import ArraySource
from gunpowder import *
from gunpowder.ext import zarr, ZarrFile, NoSuchModule
import pytest
import numpy as np
@pytest.mark.skipif(isinstance(zarr, NoSuchModule), reason="zarr is not installed")
@pytest.mark.parametrize(
"zarr_store_func",
[
"tmp_path / 'zarr... | 3,343 | 33.122449 | 88 | py |
gunpowder | gunpowder-master/tests/cases/placeholder_requests.py | from gunpowder import (
PipelineRequestError,
BatchProvider,
BatchRequest,
Batch,
Roi,
Coordinate,
GraphSpec,
GraphKey,
ArrayKeys,
ArrayKey,
ArraySpec,
Array,
ElasticAugment,
RandomLocation,
Snapshot,
build,
)
from gunpowder.graph import Graph, GraphKeys, ... | 5,273 | 31.355828 | 81 | py |
gunpowder | gunpowder-master/tests/cases/iterate_locations.py | from .provider_test import ProviderTest
from gunpowder import (
ArrayKey,
ArrayKeys,
ArraySpec,
BatchRequest,
Node,
Edge,
GraphSpec,
GraphKey,
GraphKeys,
GraphSource,
IterateLocations,
build,
Roi,
Coordinate,
)
import numpy as np
import networkx as nx
class Dum... | 3,300 | 30.740385 | 87 | py |
gunpowder | gunpowder-master/tests/cases/crop.py | from .provider_test import ProviderTest
from gunpowder import (
BatchProvider,
ArrayKeys,
ArraySpec,
Roi,
GraphKey,
GraphKeys,
GraphSpec,
Crop,
build,
)
import logging
logger = logging.getLogger(__name__)
class ExampleSourceCrop(BatchProvider):
def setup(self):
self.pr... | 1,648 | 26.032787 | 87 | py |
gunpowder | gunpowder-master/tests/cases/node_dependencies.py | from .provider_test import ProviderTest
from gunpowder import (
BatchProvider,
BatchFilter,
BatchRequest,
Batch,
ArrayKeys,
ArraySpec,
ArrayKey,
Array,
Roi,
build,
)
import numpy as np
class NodeDependenciesTestSource(BatchProvider):
def setup(self):
self.provides(
... | 4,593 | 27.184049 | 84 | py |
gunpowder | gunpowder-master/tests/cases/scan.py | from gunpowder import (
BatchProvider,
BatchRequest,
Batch,
ArrayKeys,
ArrayKey,
ArraySpec,
Array,
GraphKey,
GraphKeys,
GraphSpec,
Graph,
Node,
Roi,
Coordinate,
Scan,
build,
)
import numpy as np
import itertools
def coordinate_to_id(i, j, k):
i, j, k... | 4,999 | 30.446541 | 88 | py |
gunpowder | gunpowder-master/tests/cases/update_with.py | import numpy as np
from gunpowder import (
BatchProvider,
BatchFilter,
Array,
ArraySpec,
ArrayKey,
Graph,
GraphSpec,
GraphKey,
Batch,
BatchRequest,
Roi,
PipelineRequestError,
build,
)
import pytest
class ArrayTestSource(BatchProvider):
def __init__(self, key, s... | 4,517 | 27.2375 | 88 | py |
gunpowder | gunpowder-master/tests/cases/rasterize_points.py | from .provider_test import ProviderTest
from gunpowder import (
BatchProvider,
BatchRequest,
Batch,
Roi,
Coordinate,
GraphSpec,
Array,
ArrayKey,
ArrayKeys,
ArraySpec,
RasterizeGraph,
RasterizationSettings,
build,
)
from gunpowder.graph import GraphKeys, GraphKey, Grap... | 9,698 | 32.794425 | 87 | py |
gunpowder | gunpowder-master/tests/cases/dvid_source.py | from .provider_test import ProviderTest
from unittest import skipIf
from gunpowder import *
from gunpowder.ext import dvision, NoSuchModule
import numpy as np
import socket
import logging
logger = logging.getLogger(__name__)
DVID_SERVER = "slowpoke1"
def is_dvid_unavailable(server):
if isinstance(dvision, NoSu... | 2,158 | 31.223881 | 88 | py |
gunpowder | gunpowder-master/tests/cases/merge_provider.py | import unittest
from gunpowder import (
GraphSpec,
GraphKey,
Roi,
Coordinate,
Batch,
BatchProvider,
ArrayKeys,
ArrayKey,
ArraySpec,
Array,
BatchRequest,
MergeProvider,
RandomLocation,
build,
)
from gunpowder.graph import GraphKeys, Graph
from gunpowder.pipeline im... | 2,949 | 31.777778 | 88 | py |
gunpowder | gunpowder-master/tests/cases/add_affinities.py | from .provider_test import ProviderTest
from gunpowder import *
from itertools import product
from unittest import skipIf
import itertools
import numpy as np
import logging
class ExampleSource(BatchProvider):
def setup(self):
self.provides(
ArrayKeys.GT_LABELS,
ArraySpec(
... | 4,197 | 31.796875 | 87 | py |
gunpowder | gunpowder-master/tests/cases/random_location_points.py | from .provider_test import ProviderTest
from gunpowder import (
BatchProvider,
BatchRequest,
Batch,
Node,
Graph,
GraphSpec,
GraphKey,
GraphKeys,
RandomLocation,
build,
Roi,
Coordinate,
)
import numpy as np
import pytest
import unittest
class ExampleSourceRandomLocatio... | 6,872 | 32.857143 | 90 | py |
gunpowder | gunpowder-master/tests/cases/add_boundary_distance_gradients.py | from .provider_test import ProviderTest
from gunpowder import *
from gunpowder.contrib import AddBoundaryDistanceGradients
import numpy as np
class ExampleSource(BatchProvider):
def setup(self):
self.provides(
ArrayKeys.GT_LABELS,
ArraySpec(
roi=Roi((-40, -40, -40),... | 2,932 | 33.505882 | 83 | py |
gunpowder | gunpowder-master/tests/cases/batch.py | import logging
import numpy as np
from gunpowder import (
Array,
ArrayKey,
ArraySpec,
Batch,
Coordinate,
Roi,
)
logger = logging.getLogger(__name__)
def test_get_total_roi_nonspatial_array():
raw = ArrayKey("RAW")
nonspatial = ArrayKey("NONSPATIAL")
voxel_size = Coordinate((1, 2... | 666 | 20.516129 | 74 | py |
gunpowder | gunpowder-master/tests/cases/deform_augment.py | from gunpowder import (
BatchProvider,
GraphSpec,
Roi,
Coordinate,
ArraySpec,
Batch,
Array,
ArrayKey,
GraphKey,
BatchRequest,
DeformAugment,
build,
)
from gunpowder.graph import Graph, Node
from scipy.ndimage import center_of_mass
import pytest
import numpy as np
class... | 5,826 | 31.920904 | 88 | py |
gunpowder | gunpowder-master/tests/cases/snapshot.py | from gunpowder import (
GraphKey,
GraphKeys,
GraphSpec,
Graph,
ArrayKey,
ArrayKeys,
ArraySpec,
Array,
RasterizeGraph,
Snapshot,
BatchProvider,
BatchRequest,
Batch,
Coordinate,
Roi,
build,
)
import numpy as np
import unittest
import tempfile
import shutil
... | 3,115 | 26.821429 | 88 | py |
gunpowder | gunpowder-master/tests/cases/simple_augment.py | from gunpowder import (
Batch,
BatchProvider,
BatchRequest,
Array,
ArrayKey,
ArraySpec,
Graph,
GraphKey,
GraphSpec,
Node,
Coordinate,
Roi,
SimpleAugment,
MergeProvider,
build,
)
import numpy as np
from .helper_sources import GraphSource, ArraySource
def te... | 8,524 | 31.788462 | 91 | py |
gunpowder | gunpowder-master/tests/cases/profiling.py | from .provider_test import ProviderTest
from gunpowder import *
import time
class DelayNode(BatchFilter):
def __init__(self, time_prepare, time_process):
self.time_prepare = time_prepare
self.time_process = time_process
def prepare(self, request):
time.sleep(self.time_prepare)
... | 1,619 | 29 | 76 | py |
gunpowder | gunpowder-master/tests/cases/graph.py | from .provider_test import ProviderTest
from gunpowder import (
BatchProvider,
BatchRequest,
BatchFilter,
Batch,
Node,
Edge,
Graph,
GraphSpec,
GraphKey,
GraphKeys,
build,
Roi,
Coordinate,
)
import numpy as np
class ExampleGraphSource(BatchProvider):
def __init_... | 6,554 | 30.97561 | 87 | py |
gunpowder | gunpowder-master/tests/cases/balance_labels.py | from .provider_test import ProviderTest
from gunpowder import *
import numpy as np
class ExampleSource(BatchProvider):
def setup(self):
for identifier in [
ArrayKeys.GT_AFFINITIES,
ArrayKeys.GT_AFFINITIES_MASK,
ArrayKeys.GT_IGNORE,
]:
self.provides(
... | 5,703 | 37.281879 | 87 | py |
gunpowder | gunpowder-master/tests/cases/jax_train.py | from .provider_test import ProviderTest
from gunpowder import (
BatchProvider,
BatchRequest,
ArraySpec,
Roi,
Coordinate,
ArrayKeys,
ArrayKey,
Array,
Batch,
Scan,
PreCache,
build,
)
from gunpowder.ext import jax, haiku, optax, NoSuchModule
from gunpowder.jax import Train, ... | 8,810 | 31.274725 | 84 | py |
gunpowder | gunpowder-master/tests/cases/prepare_malis.py | from gunpowder import *
from gunpowder.contrib import PrepareMalis
import numpy as np
from .provider_test import ProviderTest
class ExampleSourcePrepareMalis(BatchProvider):
def setup(self):
self.provides(
ArrayKeys.GT_LABELS,
ArraySpec(
roi=Roi((0, 0, 0), (90, 90, ... | 6,991 | 33.44335 | 104 | py |
gunpowder | gunpowder-master/tests/cases/graph_source.py | from .provider_test import ProviderTest
from gunpowder import (
BatchRequest,
Node,
Edge,
GraphSpec,
GraphKey,
GraphKeys,
GraphSource,
build,
Roi,
Coordinate,
)
import numpy as np
import networkx as nx
class DummyDaisyGraphProvider:
"""Dummy graph provider mimicing daisy.S... | 3,874 | 32.119658 | 87 | py |
gunpowder | gunpowder-master/tests/cases/random_location_graph.py | from .provider_test import ProviderTest
from gunpowder import (
BatchProvider,
Graph,
Node,
GraphSpec,
GraphKey,
GraphKeys,
Roi,
Batch,
BatchRequest,
RandomLocation,
build,
BatchFilter,
)
import numpy as np
import logging
logger = logging.getLogger(__name__)
class Batc... | 4,869 | 29.248447 | 88 | py |
gunpowder | gunpowder-master/tests/cases/random_provider.py | from gunpowder import (
RandomProvider,
Roi,
ArrayKey,
ArraySpec,
Array,
Roi,
BatchRequest,
build,
)
import numpy as np
from .helper_sources import ArraySource
def test_output():
a = ArrayKey("A")
source_a = ArraySource(
a,
Array(
np.zeros((5, 15, 2... | 1,597 | 24.365079 | 87 | py |
gunpowder | gunpowder-master/tests/cases/random_location.py | from gunpowder import (
RandomLocation,
BatchProvider,
Roi,
Coordinate,
ArrayKeys,
ArrayKey,
ArraySpec,
Array,
Roi,
Coordinate,
Batch,
BatchRequest,
BatchProvider,
RandomLocation,
MergeProvider,
build,
)
import numpy as np
from gunpowder.pipeline import Pi... | 6,278 | 30.552764 | 86 | py |
gunpowder | gunpowder-master/tests/cases/helper_sources.py | from gunpowder import BatchProvider, GraphKey, Graph, ArrayKey, Array, Batch
import copy
class ArraySource(BatchProvider):
def __init__(self, key: ArrayKey, array: Array):
self.key = key
self.array = array
def setup(self):
self.provides(self.key, self.array.spec.copy())
def prov... | 895 | 25.352941 | 81 | py |
gunpowder | gunpowder-master/tests/cases/torch_train.py | from .provider_test import ProviderTest
from gunpowder import (
BatchProvider,
BatchRequest,
ArraySpec,
Roi,
Coordinate,
ArrayKeys,
ArrayKey,
Array,
Batch,
Scan,
PreCache,
build,
)
from gunpowder.ext import torch, NoSuchModule
from gunpowder.torch import Train, Predict
fr... | 9,228 | 29.259016 | 81 | py |
gunpowder | gunpowder-master/tests/cases/specified_location.py | # from .provider_test import ProviderTest, ExampleSource
from gunpowder import (
BatchProvider,
ArrayKeys,
ArraySpec,
Roi,
Batch,
Coordinate,
SpecifiedLocation,
build,
BatchRequest,
Array,
ArrayKey,
)
import numpy as np
import unittest
class ExampleSourceSpecifiedLocation(B... | 3,726 | 32.276786 | 80 | py |
gunpowder | gunpowder-master/tests/cases/__init__.py | 0 | 0 | 0 | py | |
gunpowder | gunpowder-master/tests/cases/tensorflow_train.py | from .provider_test import ProviderTest
from gunpowder import (
ArraySpec,
ArrayKeys,
ArrayKey,
Array,
Roi,
BatchProvider,
Batch,
BatchRequest,
build,
)
from gunpowder.ext import tensorflow, NoSuchModule
from gunpowder.tensorflow import Train, Predict, LocalServer
import multiprocess... | 5,108 | 28.362069 | 76 | py |
gunpowder | gunpowder-master/tests/cases/expected_failures.py | import gunpowder as gp
from gunpowder.nodes.batch_provider import BatchRequestError
from .helper_sources import ArraySource
from funlib.geometry import Roi, Coordinate
import numpy as np
import pytest
@pytest.mark.xfail()
def test_request_too_large():
raw_key = gp.ArrayKey("RAW")
data = np.ones((10, 10))
... | 970 | 24.552632 | 80 | py |
gunpowder | gunpowder-master/tests/cases/intensity_scale_shift.py | from .helper_sources import ArraySource
from gunpowder import (
IntensityScaleShift,
ArrayKey,
build,
Normalize,
Array,
ArraySpec,
Roi,
Coordinate,
BatchRequest,
)
import numpy as np
def test_shift():
raw_key = ArrayKey("RAW")
array = Array(
np.ones((10, 10), dtype... | 776 | 20.583333 | 61 | py |
gunpowder | gunpowder-master/tests/cases/hdf5_write.py | from .provider_test import ProviderTest
from gunpowder import *
import numpy as np
from gunpowder.ext import h5py
class Hdf5WriteTestSource(BatchProvider):
def setup(self):
self.provides(
ArrayKeys.RAW,
ArraySpec(
roi=Roi((20000, 2000, 2000), (2000, 200, 200)), voxe... | 2,939 | 31.307692 | 86 | py |
gunpowder | gunpowder-master/tests/cases/provider_test.py | from gunpowder import *
import shutil
import os
import copy
from warnings import warn
import unittest
from datetime import datetime
from tempfile import mkdtemp
import numpy as np
class ExampleSource(BatchProvider):
def setup(self):
self.provides(
ArrayKeys.RAW,
ArraySpec(
... | 4,330 | 31.810606 | 121 | py |
gunpowder | gunpowder-master/tests/cases/downsample.py | from .helper_sources import ArraySource
from gunpowder import *
import numpy as np
def test_output():
raw = ArrayKey("RAW")
raw_downsampled = ArrayKey("RAW_DOWNSAMPLED")
gt = ArrayKey("GT")
gt_downsampled = ArrayKey("GT_LABELS_DOWNSAMPLED")
request = BatchRequest()
request.add(raw, (200, 200... | 2,324 | 29.592105 | 87 | py |
gunpowder | gunpowder-master/tests/cases/hdf5_source.py | from unittest import skipIf
from .provider_test import ProviderTest
from gunpowder import *
import numpy as np
from gunpowder.ext import h5py, zarr, ZarrFile, NoSuchModule
class Hdf5LikeSourceTestMixin(object):
"""This class is to be used as a mixin for ProviderTest classes testing HDF5, N5 and Zarr
batch pr... | 4,152 | 34.194915 | 93 | py |
gunpowder | gunpowder-master/tests/cases/upsample.py | from .helper_sources import ArraySource
from gunpowder import *
import numpy as np
def test_output():
raw = ArrayKey("RAW")
raw_upsampled = ArrayKey("RAW_UPSAMPLED")
gt = ArrayKey("GT")
gt_upsampled = ArrayKey("GT_LABELS_UPSAMPLED")
request = BatchRequest()
request.add(raw, (200, 200, 200))
... | 2,628 | 31.060976 | 84 | py |
gunpowder | gunpowder-master/tests/cases/normalize.py | from .provider_test import ProviderTest
from gunpowder import *
class TestNormalize(ProviderTest):
def test_output(self):
pipeline = self.test_source + Normalize(ArrayKeys.RAW)
with build(pipeline):
batch = pipeline.request_batch(self.test_request)
raw = batch.arrays[Arra... | 429 | 27.666667 | 62 | py |
gunpowder | gunpowder-master/tests/cases/pad.py | from .provider_test import ProviderTest
from gunpowder import (
BatchProvider,
BatchRequest,
Batch,
ArrayKeys,
ArraySpec,
Roi,
Coordinate,
GraphKey,
GraphKeys,
GraphSpec,
Array,
ArrayKey,
Pad,
build,
)
import numpy as np
class ExampleSourcePad(BatchProvider):
... | 1,877 | 25.083333 | 87 | py |
gunpowder | gunpowder-master/tests/cases/precache.py | from .helper_sources import ArraySource
from gunpowder import *
import pytest
import numpy as np
import time
class Delay(BatchFilter):
def __init__(self, delay: float = 1):
self.delay = delay
def prepare(self, request):
time.sleep(self.delay)
return request
def process(self, ba... | 2,853 | 29.688172 | 88 | py |
gunpowder | gunpowder-master/tests/cases/shift_augment.py | import unittest
import numpy as np
import random
import h5py
import logging
import sys
import os
from gunpowder import (
ArrayKey,
ArraySpec,
GraphKey,
GraphSpec,
Graph,
Node,
RandomLocation,
Coordinate,
Roi,
BatchRequest,
Hdf5Source,
ShiftAugment,
CsvPointsSource,
... | 20,702 | 35.642478 | 95 | py |
gunpowder | gunpowder-master/docker/test_environment.py | import gunpowder
if __name__ == "__main__":
print("Successfully set up gunpowder")
| 88 | 16.8 | 42 | py |
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