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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rank-based-evaluation | rank-based-evaluation-main/src/kgm/training/matching.py | # coding=utf-8
"""Training loops for KG matching models."""
import logging
from abc import abstractmethod
from typing import Any, Iterable, List, Mapping, Optional, Tuple, Type
import torch
from torch.optim import Optimizer
from torch.utils import data
from .base import BaseTrainer
from ..data import KnowledgeGraphAl... | 8,475 | 30.509294 | 114 | py |
rank-based-evaluation | rank-based-evaluation-main/src/kgm/training/__init__.py | # coding=utf-8
"""Training Loops."""
| 37 | 11.666667 | 21 | py |
rank-based-evaluation | rank-based-evaluation-main/src/kgm/eval/matching.py | # coding=utf-8
"""Entity Alignment evaluation methods."""
from typing import Collection, Dict, Mapping, Optional, Tuple, TypeVar, Union
import torch
from .common import aggregate_ranks, get_rank
from ..data import MatchSideEnum, SIDES
from ..models import KGMatchingModel
from ..modules import Similarity
from ..utils.... | 6,525 | 31.63 | 110 | py |
rank-based-evaluation | rank-based-evaluation-main/src/kgm/eval/common.py | """Common utility methods for evaluation."""
import logging
from typing import Collection, Mapping, Optional
import torch
logger = logging.getLogger(name=__name__)
# Small constant for floating point comparison
EPSILON = 1.0e-08
def get_rank(sim: torch.FloatTensor, true: torch.LongTensor) -> torch.FloatTensor:
... | 4,478 | 36.957627 | 118 | py |
rank-based-evaluation | rank-based-evaluation-main/src/kgm/eval/__init__.py | # coding=utf-8
"""Evaluation methods."""
from .common import compute_ranks
from .matching import evaluate_alignment, evaluate_matching_model
__all__ = [
'compute_ranks',
'evaluate_alignment',
'evaluate_matching_model',
]
| 234 | 20.363636 | 65 | py |
rank-based-evaluation | rank-based-evaluation-main/src/kgm/models/__init__.py | # coding=utf-8
"""Entity Alignment Models."""
from .matching import GCNAlign, GraphBasedKGMatchingModel, KGMatchingModel, PureEmbeddingModel, get_matching_model_by_name
__all__ = [
'GraphBasedKGMatchingModel',
'GCNAlign',
'KGMatchingModel',
'PureEmbeddingModel',
'get_matching_model_by_name',
]
| 316 | 25.416667 | 122 | py |
rank-based-evaluation | rank-based-evaluation-main/src/kgm/models/matching/base.py | # coding=utf-8
"""API for models for knowledge graph matching."""
import logging
from abc import ABC, abstractmethod
from collections import defaultdict
from typing import Any, Callable, Mapping, Optional, Type
import torch
from frozendict import frozendict
from torch import nn
from ...data import KnowledgeGraphAlign... | 9,382 | 32.996377 | 130 | py |
rank-based-evaluation | rank-based-evaluation-main/src/kgm/models/matching/gcn_align.py | # coding=utf-8
"""
Implementation of GCN-Align.
The paper introducing the model can be found at https://www.aclweb.org/anthology/D18-1032.pdf.
The authors' implementation can be found at https://github.com/1049451037/GCN-Align and they also refer to
https://github.com/1049451037/HIN-Align for an improved implementati... | 6,089 | 37.789809 | 137 | py |
rank-based-evaluation | rank-based-evaluation-main/src/kgm/models/matching/__init__.py | # coding=utf-8
"""Models for (knowledge) graph matching."""
from .base import GraphBasedKGMatchingModel, KGMatchingModel, PureEmbeddingModel, get_matching_model_by_name
from .gcn_align import GCNAlign
__all__ = [
'GraphBasedKGMatchingModel',
'GCNAlign',
'KGMatchingModel',
'PureEmbeddingModel',
'get... | 348 | 25.846154 | 108 | py |
rank-based-evaluation | rank-based-evaluation-main/src/kgm/utils/mlflow_utils.py | # coding=utf-8
"""Utility methods for MLFlow."""
import hashlib
import itertools
import logging
import os
import platform
from typing import Any, Callable, Collection, Dict, List, Mapping, Optional, Tuple, Union
import mlflow
import mlflow.entities
import pandas
import tqdm
from .common import to_dot
logger = loggin... | 9,803 | 31.463576 | 170 | py |
rank-based-evaluation | rank-based-evaluation-main/src/kgm/utils/data_utils.py | """Utilities for retrieving and checking data files."""
import hashlib
import logging
import pathlib
from typing import Optional
import humanize
import requests
import tqdm
logger = logging.getLogger(name=__name__)
def resolve_google_drive_file_url(
id_: str,
session: requests.Session,
) -> requests.Respons... | 5,600 | 29.606557 | 141 | py |
rank-based-evaluation | rank-based-evaluation-main/src/kgm/utils/types.py | """Type annotation aliases."""
import torch
#: A (n, 3) tensor of IDs.
Triples = torch.LongTensor
#: A (n,) tensor of IDs.
EntityIDs = torch.LongTensor
#: A (n,) tensor of IDs.
RelationIDs = torch.LongTensor
#: A (n,) tensor of IDs.
NodeIDs = torch.LongTensor
#: A (2, n) tensor of IDs.
IDAlignment = torch.LongTens... | 381 | 17.190476 | 30 | py |
rank-based-evaluation | rank-based-evaluation-main/src/kgm/utils/torch_utils.py | """Utility methods using pytorch."""
import itertools
import logging
from abc import ABC
from collections import defaultdict
from operator import itemgetter
from typing import Any, Callable, MutableMapping, Optional, Sequence, Tuple, Type, TypeVar, Union
import numpy
import torch
from torch import nn, optim
from .com... | 21,537 | 32.86478 | 172 | py |
rank-based-evaluation | rank-based-evaluation-main/src/kgm/utils/common.py | """General utility methods."""
import hashlib
import inspect
import logging
import pickle
import random
import string
from collections import deque
from enum import Enum
from typing import Any, Callable, Collection, Dict, Iterable, List, Mapping, Optional, Sequence, Set, Type, TypeVar, Union
T = TypeVar('T')
logger =... | 9,553 | 29.234177 | 210 | py |
rank-based-evaluation | rank-based-evaluation-main/src/kgm/utils/__init__.py | # coding=utf-8
"""A collection of utility methods."""
| 54 | 17.333333 | 38 | py |
rank-based-evaluation | rank-based-evaluation-main/src/kgm/data/reduction.py | """Reduction strategies from Knowledge Graph to (weighted) uni-relational graphs."""
import enum
import logging
from typing import Callable, Optional
import torch
from .knowledge_graph import KnowledgeGraph
from ..utils.torch_utils import ExtendedModule, SparseCOOMatrix
logger = logging.getLogger(name=__name__)
# ... | 7,812 | 32.246809 | 155 | py |
rank-based-evaluation | rank-based-evaluation-main/src/kgm/data/loaders.py | """Data loading for Entity Alignment datasets."""
import abc
import io
import json
import logging
import lzma
import pathlib
import tarfile
import zipfile
from typing import Collection, Generic, Mapping, Optional, Tuple, Type, TypeVar, Union
import pandas
import requests
import torch
from .knowledge_graph import Enti... | 38,530 | 35.942474 | 184 | py |
rank-based-evaluation | rank-based-evaluation-main/src/kgm/data/knowledge_graph.py | # coding=utf-8
"""Various knowledge graph related data structures."""
import enum
import json
import logging
import lzma
import pathlib
from dataclasses import dataclass
from typing import Mapping, Optional, Tuple, Union
import torch
from ..utils.torch_utils import split_tensor
from ..utils.types import EntityIDs, ID... | 25,646 | 33.287433 | 215 | py |
rank-based-evaluation | rank-based-evaluation-main/src/kgm/data/__init__.py | # coding=utf-8
"""Data loading and representation."""
from .knowledge_graph import (
EntityAlignment,
KnowledgeGraph,
KnowledgeGraphAlignmentDataset,
MatchSideEnum,
SIDES,
exact_self_alignment,
get_erdos_renyi,
get_other_side,
get_synthetic_math_graph,
sub_graph_alignment,
va... | 802 | 22.617647 | 88 | py |
rank-based-evaluation | rank-based-evaluation-main/executables/adjusted_ranking_experiments.py | # coding=utf-8
"""Evaluation of different training and test sizes."""
import argparse
import logging
import random
import mlflow
import numpy
import torch
import tqdm
from kgm.data import get_dataset_by_name
from kgm.eval.matching import evaluate_matching_model
from kgm.models import GCNAlign
from kgm.modules import ... | 4,618 | 30.855172 | 87 | py |
rank-based-evaluation | rank-based-evaluation-main/executables/summarize.py | """Script to generate the plot #test alignments vs. #train alignments."""
import argparse
import logging
import mlflow
import pandas
import seaborn
from matplotlib import pyplot as plt
def main():
logging.basicConfig(level=logging.INFO)
parser = argparse.ArgumentParser()
parser.add_argument('--tracking_u... | 2,006 | 26.875 | 95 | py |
rank-based-evaluation | rank-based-evaluation-main/executables/degree_investigation.py | """Script to generate the evaluation for degree inductive bias."""
import numpy
import torch
from matplotlib import pyplot as plt
from scipy.stats import pearsonr, spearmanr
from kgm.data import SIDES, get_dataset_by_name
from kgm.models import GCNAlign, PureEmbeddingModel
def degree_vs_norm(
dataset
):
# ca... | 2,854 | 27.55 | 96 | py |
pydot | pydot-master/setup.py | #!/usr/bin/env python
"""Installation script."""
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
import ast
import codecs
import os
import re
CURRENT_DIR = os.path.dirname(__file__)
def get_long_description():
readme_path = os.path.join(CURRENT_DIR, "README.md")
... | 2,466 | 30.628205 | 78 | py |
pydot | pydot-master/src/pydot/core.py | """An interface to GraphViz."""
import copy
import io
import errno
import os
import re
import subprocess
import sys
import tempfile
import warnings
import pydot
try:
from pydot import dot_parser
except Exception as e:
warnings.warn(
"`pydot` could not import `dot_parser`, "
"so `pydot` will be... | 54,064 | 28.837196 | 79 | py |
pydot | pydot-master/src/pydot/exceptions.py | """Exception classes for pydot."""
class PydotException(Exception):
"""Base class for exceptions in Pydot.
This base class will not be raised directly.
Catch this base class to catch all derived exceptions, though be
aware that pydot may raise Python built-in exceptions or pyparsing
exceptions a... | 516 | 21.478261 | 70 | py |
pydot | pydot-master/src/pydot/__init__.py | """An interface to GraphViz."""
__author__ = "Ero Carrera"
__version__ = "2.0.0.dev0"
__license__ = "MIT"
from pydot.exceptions import *
from pydot.core import *
| 164 | 17.333333 | 31 | py |
pydot | pydot-master/src/pydot/dot_parser.py | """Graphviz's dot language parser.
The dotparser parses GraphViz files in
dot and dot files and transforms them
into a class representation defined by `pydot`.
Author: Michael Krause <[email protected]>
Fixes by: Ero Carrera <[email protected]>
"""
from pyparsing import (
nestedExpr,
Literal,
... | 15,074 | 25.871658 | 78 | py |
pydot | pydot-master/test/pydot_unittest.py | # coding=utf-8
"""Unit testing of `pydot`."""
# TODO:
# -test graph generation APIs (from adjacency, etc..)
# -test del_node, del_edge methods
# -test Common.set method
import argparse
from hashlib import sha256
import io
import os
import pickle
import string
import sys
import warnings
import chardet
import pydot
impo... | 14,517 | 33.484561 | 79 | py |
OPM | OPM-master/napari_opm_pymmcoreplus.py | '''
Initial work on napari interface to OPM using pymmcore-plus, magic-gui, and magic-class
Relevant hardware:
NI DAQ
Hamamatsu Fusion-BT
Coherent OBIS LaserBoxxx
This will work with any setup that can setup the camera as master, lasers can driven ON/OFF during camera readout time using digital input,
galvo can be m... | 30,110 | 44.970992 | 192 | py |
OPM | OPM-master/napari-control/opm_iterative_control.py | #!/usr/bin/python
'''
----------------------------------------------------------------------------------------
ASU OPM with iterative fluidics control via Napari, magic-class, and magic-gui
----------------------------------------------------------------------------------------
Peter Brown
Franky Djutanta
Douglas Sheph... | 2,756 | 37.291667 | 111 | py |
OPM | OPM-master/napari-control/opm_timelapse_reconstruction.py | import napari
from src.OPMMirrorReconstruction import OPMMirrorReconstruction
def main():
# setup OPM GUI and Napari viewer
reconstruction_widget = OPMMirrorReconstruction()
viewer = napari.Viewer()
# these methods have to be private to not show using magic-class. Maybe a better solution is available... | 634 | 27.863636 | 107 | py |
OPM | OPM-master/napari-control/opm_timelapse_control.py | #!/usr/bin/python
'''
----------------------------------------------------------------------------------------
ASU OPM timelapse via pymmcore-plus, napari, magic-class, and magic-gui
----------------------------------------------------------------------------------------
Peter Brown
Franky Djutanta
Douglas Shepherd
12/... | 2,809 | 39.142857 | 107 | py |
OPM | OPM-master/napari-control/src/OPMMirrorReconstruction.py | '''
Napari interface to process OPM timelapse data
TO DO: - Change to OME-Zarr output
- Add OME-tiff resave option
- Add ability to load old data
- Add option for number of iterations & TV setting for clij2-fft
Last update: 12/2022; Update to use clij2-fft, remove flatfield (due to Powell lens), ... | 12,061 | 37.292063 | 154 | py |
OPM | OPM-master/napari-control/src/OPM_main.py | #!/usr/bin/python
from magicgui import magicgui
from magicclass import magicclass, set_design
from pathlib import Path
@magicclass(labels=False)
@set_design(text="Stage monitor")
class OPMmain():
def __init__(self):
self.path_to_fluidics_flush_program = Path('C:/Users/qi2lab/Documents/GitHub/common_fluid... | 3,264 | 37.411765 | 138 | py |
OPM | OPM-master/napari-control/src/OPMMirrorScan.py | from pymmcore_plus import CMMCorePlus
from magicclass import magicclass, MagicTemplate
from magicgui import magicgui
from magicgui.tqdm import trange
from napari.qt.threading import thread_worker
#from superqt.utils import ensure_main_thread
from pathlib import Path
import numpy as np
import time
import zarr
from src... | 37,618 | 42.540509 | 252 | py |
OPM | OPM-master/napari-control/src/OPMStageMonitor.py | # napari imports
from magicclass import magicclass, set_design
from magicgui import magicgui, widgets
#general python imports
from pymmcore_plus import RemoteMMCore
# Stage monitor class
@magicclass(labels=False)
class OPMStageMonitor:
def __init__(self):
pass
x_stage_pos = widgets.LineEdit(label='x... | 1,018 | 29.878788 | 81 | py |
OPM | OPM-master/napari-control/src/OPMStageScan.py | # napari imports
from re import T
from magicclass import magicclass, set_design
from magicgui import magicgui
from magicgui.tqdm import trange
from napari.qt.threading import thread_worker
#general python imports
from pathlib import Path
import numpy as np
from datetime import datetime
import time
# data i/o imports
... | 56,334 | 45.21411 | 192 | py |
OPM | OPM-master/napari-control/src/OPMIterative.py | # napari imports
from magicclass import magicclass, set_design, MagicTemplate
from magicgui import magicgui, widgets
from napari.qt.threading import thread_worker
#general python imports
from pathlib import Path
from pymmcore_plus import RemoteMMCore
import numpy as np
from distutils.util import strtobool
# ASU OPM i... | 20,141 | 51.181347 | 141 | py |
OPM | OPM-master/napari-control/src/hardware/PicardShutter.py | #!/usr/bin/python
# ----------------------------------------------------------------------------------------
# The basic I/O class for Picard USB Shutter
# ----------------------------------------------------------------------------------------
# Doug Shepherd
# 11/2022
# [email protected]
# --------------------... | 3,585 | 38.844444 | 108 | py |
OPM | OPM-master/napari-control/src/hardware/HamiltonMVP.py | #!/usr/bin/python
# ----------------------------------------------------------------------------------------
# A basic class for serial interface with a series of daisy chained Hamilton MVP devices
# ----------------------------------------------------------------------------------------
# Jeff Moffitt
# 12/17/13
# jef... | 21,387 | 45.495652 | 125 | py |
OPM | OPM-master/napari-control/src/hardware/AbstractValve.py | #!/usr/bin/python
'''
Abstract class for controlling a hardware valve. Function names were derived from original valveChain and hamilton classes.
George Emanuel
2/16/2018
'''
from abc import ABC, abstractmethod
class AbstractValve(ABC):
@abstractmethod
def changePort(self, valve_ID, port_ID, direction = 0):... | 820 | 18.093023 | 123 | py |
OPM | OPM-master/napari-control/src/hardware/ASI.py |
#!/usr/bin/python
'''
----------------------------------------------------------------------------------------
OPM ASI Tiger functions
----------------------------------------------------------------------------------------
Douglas Shepherd
12/11/2021
[email protected]
------------------------------------------... | 5,987 | 30.851064 | 90 | py |
OPM | OPM-master/napari-control/src/hardware/APump.py | #!/usr/bin/python
# ----------------------------------------------------------------------------------------
# The basic I/O class for a Gibson peristaltic pump
# ----------------------------------------------------------------------------------------
# George Emanuel with modifications by Jeff Moffitt
# 11/16/15
# jef... | 5,237 | 33.460526 | 90 | py |
OPM | OPM-master/napari-control/src/hardware/OPMNIDAQ.py |
#!/usr/bin/python
'''
----------------------------------------------------------------------------------------
Basic class to run NIDAQ with camera as master for OPM using PyDAQMx
----------------------------------------------------------------------------------------
Peter Brown
Franky Djutanta
Douglas Shepherd
12/1... | 8,624 | 43.921875 | 164 | py |
OPM | OPM-master/napari-control/src/utils/autofocus_remote_unit.py | #!/usr/bin/env python
'''
Optimize O2-O3 coupling by capturing images of collimated 532 alignment laser injected into system
using the back of pentaband dichroic with O3 at different positions along the (tilted) optical axis.
Shepherd 11/2022
'''
import numpy as np
from scipy import ndimage
from pymmcore_plus import... | 7,440 | 37.35567 | 239 | py |
OPM | OPM-master/napari-control/src/utils/opm_psf.py | import psfmodels as psfm
import numpy as np
import matplotlib.pyplot as plt
from scipy.interpolate import interp2d
# ROI tools
def get_skewed_roi_size(sizes, theta, dc, dstep, ensure_odd=True):
"""
Get ROI size in OPM matrix that includes sufficient xy and z points
:param sizes: [z-size, y-size, x-size] in... | 5,177 | 32.623377 | 105 | py |
OPM | OPM-master/napari-control/src/utils/image_post_processing.py | '''
QI2lab OPM suite
Reconstruction tools
Image processing tools for OPM reconstruction
Last updated: Shepherd 01/22 - changes to include map_blocks based dexp deconvolution and recent other changes.
'''
#!/usr/bin/env python
import sys
import numpy as np
from pathlib import Path
#from tifffile import tifffile
from ... | 9,889 | 32.299663 | 133 | py |
OPM | OPM-master/napari-control/src/utils/data_io.py |
#!/usr/bin/python
'''
----------------------------------------------------------------------------------------
OPM I/O functions
----------------------------------------------------------------------------------------
Peter Brown
Douglas Shepherd
12/11/2021
[email protected]
------------------------------------... | 5,574 | 27.88601 | 125 | py |
OPM | OPM-master/napari-control/src/utils/flat_field.py | #!/usr/bin/env python
'''
Python and cupy implementation of BaSiC flat-field correction (doi: 10.1038/ncomms14836)
Adapted from code found at: https://github.com/peng-lab/PyBasicCellprofilerPlugin
TO DO: Tons of otpimization opportunities with cupy, numba, and cucim. Maybe need to write our own DCT operator for use o... | 14,832 | 34.570743 | 155 | py |
OPM | OPM-master/napari-control/src/utils/fluidics_control.py |
#!/usr/bin/python
'''
----------------------------------------------------------------------------------------
OPM fluidics controller functions
----------------------------------------------------------------------------------------
Douglas Shepherd
12/11/2021
[email protected]
--------------------------------... | 5,342 | 39.78626 | 143 | py |
OPM | OPM-master/control/run_opm_iterative_stagescan_GUI.py | #!/usr/bin/env python
'''
OPM stage control with iterative fluidics.
Shepherd 08/21 - refactor for easier reading, O2-O3 autofocus, and managing file transfer in seperate Python process
Shepherd 07/21 - switch to interleaved excitation during stage scan and initial work on O2-O3 autofocusing
Shepherd 06/21 - clean up... | 37,175 | 49.648501 | 196 | py |
OPM | OPM-master/reconstruction/recon_opm_stagescan.py | #!/usr/bin/env python
'''
Stage scanning OPM post-processing using numpy, numba, skimage, pyimagej, and npy2bdv.
Places all tiles in actual stage positions and places iterative rounds into the time axis of BDV H5 for alignment
Orthgonal interpolation method adapted from Vincent Maioli (http://doi.org/10.25560/68022)
... | 14,548 | 47.016502 | 167 | py |
OPM | OPM-master/reconstruction/run_opm_stagescan.py | #!/usr/bin/env python
'''
OPM stage control without fluidics.
Shepherd 04/21 - large-scale changes for new metadata and on-the-fly uploading to server for simultaneous reconstruction
'''
# imports
from pycromanager import Bridge, Acquisition
from pathlib import Path
import numpy as np
import time
import sys
import m... | 26,737 | 44.318644 | 177 | py |
OPM | OPM-master/reconstruction/run_opm_galvoscan.py | #!/usr/bin/env python
'''
OPM galvo scan using Pycromanager.
D. Shepherd 09/21 - bring metadata in line with new reconstruction code. Attempt timelapse with pause using event structure.
D. Shepherd 04/21 - streamline code for fast acquisition and immediate upload to server
P. Brown 03/21 - multiline digital and analo... | 15,693 | 42.715877 | 144 | py |
OPM | OPM-master/reconstruction/image_post_processing.py | '''
QI2lab OPM suite
Reconstruction tools
Image processing tools for OPM reconstruction
Last updated: Shepherd 01/22 - changes to include dexp deconvolution and recent other changes.
'''
#!/usr/bin/env python
import sys
import numpy as np
from pathlib import Path
from tifffile import tifffile
from numba import njit,... | 10,957 | 32.716923 | 190 | py |
OPM | OPM-master/reconstruction/data_io.py | #!/usr/bin/env python
'''
QI2lab OPM suite
Reconstruction tools
Read and write metadata; read raw data; read pre-generated OPM psfs
'''
import re
from npy2bdv.npy2bdv import BdvEditor
import pandas as pd
import numpy as np
from pathlib import Path
from tifffile import tifffile
def read_metadata(fname):
"""
R... | 5,989 | 27.388626 | 125 | py |
OPM | OPM-master/reconstruction/flat_field.py | #!/usr/bin/env python
'''
Python and cupy implementation of BaSiC flat-field correction (doi: 10.1038/ncomms14836)
Adapted from code found at: https://github.com/peng-lab/PyBasicCellprofilerPlugin
TO DO: Tons of otpimization opportunities with cupy, numba, and cucim. Maybe need to write our own DCT operator for use o... | 14,796 | 34.569712 | 155 | py |
OPM | OPM-master/reconstruction/recon_opm_galvoscan.py | #!/usr/bin/env python
'''
Galvo scanning OPM post-processing using numpy, numba, skimage, pyimagej, and npy2bdv.
Orthgonal interpolation method adapted from original description by Vincent Maioli (http://doi.org/10.25560/68022)
Last updated: Shepherd 06/21
'''
# imports
import numpy as np
from pathlib import Path
fr... | 13,051 | 44.006897 | 151 | py |
OPM | OPM-master/reconstruction/localize_gui.py | """
Localize skewed data with GUI for setting different parameters
"""
import os
import time
import numpy as np
import localize
import localize_skewed
import image_post_processing as ipp
import pycromanager
import napari
from napari.qt.threading import thread_worker
from magicgui import magicgui
root_dir = r"C:\Users\... | 17,910 | 42.055288 | 142 | py |
OPM | OPM-master/reconstruction/localize_skewed.py | """
Code for localization in native OPM frame
This file stores tools specific to the OPM skewed geometry. Most localization functions are found in localize.py
"""
import os
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.path import Path
import warnings
import time
import joblib
import fit_psf
impo... | 51,449 | 38.668466 | 152 | py |
OPM | OPM-master/pycromanager-control/run_opm_stagescan.py | #!/usr/bin/env python
'''
OPM stage control without fluidics.
Shepherd 04/21 - large-scale changes for new metadata and on-the-fly uploading to server for simultaneous reconstruction
'''
# imports
from pycromanager import Bridge, Acquisition
from pathlib import Path
import numpy as np
import time
import sys
import m... | 26,737 | 44.318644 | 177 | py |
OPM | OPM-master/pycromanager-control/run_opm_galvoscan.py | #!/usr/bin/env python
'''
OPM galvo scan using Pycromanager.
D. Shepherd 09/21 - bring metadata in line with new reconstruction code. Attempt timelapse with pause using event structure.
D. Shepherd 04/21 - streamline code for fast acquisition and immediate upload to server
P. Brown 03/21 - multiline digital and analo... | 15,693 | 42.715877 | 144 | py |
OPM | OPM-master/pycromanager-control/data_io.py | #!/usr/bin/env python
import re
from npy2bdv import BdvEditor
import pandas as pd
import numpy as np
def read_metadata(fname):
"""
Read data from csv file consisting of one line giving titles, and the other giving values. Return as dictionary
:param fname:
:return metadata:
"""
scan_data_raw_... | 4,729 | 29.915033 | 125 | py |
Max-value-Entropy-Search | Max-value-Entropy-Search-master/test_functions/python_related/generate_simudata3.py | #!/usr/bin/env python
# Copyright (c) 2017 Zi Wang
from push_world import *
import sys
if __name__ == '__main__':
rx = float(sys.argv[1])
ry = float(sys.argv[2])
gx = float(sys.argv[4])
gy = float(sys.argv[5])
simu_steps = int(float(sys.argv[3]) * 10)
# set it to False if no gui needed
... | 839 | 35.521739 | 128 | py |
Max-value-Entropy-Search | Max-value-Entropy-Search-master/test_functions/python_related/generate_simudata4.py | #!/usr/bin/env python
# Copyright (c) 2017 Zi Wang
from push_world import *
import sys
# difference to generate_simudata is an input that control angle of push
if __name__ == '__main__':
rx = float(sys.argv[1])
ry = float(sys.argv[2])
gx = float(sys.argv[4])
gy = float(sys.argv[5])
init_angle = flo... | 1,054 | 39.576923 | 128 | py |
Max-value-Entropy-Search | Max-value-Entropy-Search-master/test_functions/python_related/generate_simudata_2robot2thing.py | #!/usr/bin/env python
# Copyright (c) 2017 Zi Wang
from push_world import *
import sys
# difference to generate_simudata is an input that control angle of push
if __name__ == '__main__':
rx = float(sys.argv[1])
ry = float(sys.argv[2])
xvel = float(sys.argv[3])
yvel = float(sys.argv[4])
simu_steps =... | 1,823 | 42.428571 | 148 | py |
Max-value-Entropy-Search | Max-value-Entropy-Search-master/test_functions/python_related/push_world.py | #!/usr/bin/env python
# Author: Ari Anders and Zi Wang
from Box2D import *
from Box2D.b2 import *
import numpy as np
import pygame
import scipy.io
from numpy import linalg as LA
# this just makes pygame show what's going on
class guiWorld:
def __init__(self, fps):
self.SCREEN_WIDTH, self.SCREEN_HEIGHT ... | 10,238 | 36.097826 | 146 | py |
CIF-HieraDist | CIF-HieraDist-main/setup.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import os
import subprocess
import sys
from setuptools import setup, find_packages, Extension
from setuptools import E... | 8,435 | 28.291667 | 92 | py |
CIF-HieraDist | CIF-HieraDist-main/hubconf.py | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
"""isort:skip_file"""
import functools
import importlib
dependencies = [
"dataclasses",
"hydra",
"numpy",
"omegaconf",
"... | 2,099 | 27.378378 | 82 | py |
CIF-HieraDist | CIF-HieraDist-main/train.py | #!/usr/bin/env python3 -u
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
"""
Legacy entry point. Use fairseq_cli/train.py or fairseq-train instead.
"""
from fairseq_cli.train import cli_mai... | 366 | 23.466667 | 70 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/__init__.py | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from fairseq.version import __version__ # noqa
| 226 | 31.428571 | 65 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_to_text/prep_covost_data.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import argparse
import logging
from pathlib import Path
import shutil
from tempfile import NamedTemporaryFile
from typi... | 8,898 | 30.782143 | 86 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_to_text/prep_mtedx_data.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import argparse
import logging
import os
from pathlib import Path
import shutil
from itertools import groupby
from temp... | 10,404 | 34.03367 | 87 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_to_text/prep_aishell2_data.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import os
import argparse
import logging
from pathlib import Path
import shutil
from tempfile import NamedTemporaryFile... | 9,428 | 31.513793 | 95 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_to_text/prep_librispeech_data.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import argparse
import logging
from pathlib import Path
import shutil
from tempfile import NamedTemporaryFile
import p... | 3,811 | 29.253968 | 87 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_to_text/data_utils.py | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import csv
from pathlib import Path
import zipfile
from functools import reduce
from multiprocessing import cpu_count
from typing import Any, ... | 12,224 | 30.670984 | 88 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_to_text/prep_mustc_data.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import argparse
import logging
import os
from pathlib import Path
import shutil
from itertools import groupby
from temp... | 11,015 | 36.726027 | 87 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_to_text/prep_aishell1_data.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import os
import argparse
import logging
from pathlib import Path
import shutil
from tempfile import NamedTemporaryFile... | 11,501 | 31.038997 | 98 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_to_text/prep_ljspeech_data.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import argparse
import logging
from pathlib import Path
import shutil
from tempfile import NamedTemporaryFile
import p... | 3,352 | 26.483607 | 77 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_to_text/seg_mustc_data.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import argparse
import logging
from pathlib import Path
import soundfile as sf
from examples.speech_to_text.prep_mustc_... | 1,622 | 30.823529 | 81 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_to_text/gen_librispeech_vocab.py | # @Time : 2022/3/2
# @Author : Minglun Han
# @File : gen_vocab.py
import argparse
import logging
from pathlib import Path
import shutil
from tempfile import NamedTemporaryFile
import pandas as pd
from examples.speech_to_text.data_utils import (
create_zip,
extract_fbank_features,
gen_config_yaml,
... | 1,514 | 24.25 | 88 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_to_text/gen_vocab.py | # @Time : 2022/3/2
# @Author : Minglun Han
# @File : gen_vocab.py
import argparse
import logging
from pathlib import Path
import shutil
from tempfile import NamedTemporaryFile
import pandas as pd
from examples.speech_to_text.data_utils import (
create_zip,
extract_fbank_features,
gen_config_yaml,
... | 1,515 | 24.266667 | 63 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_to_text/bert_feat_extract/extract_bert_feats.py | # @Time : 2022/8/15
# @Author : Minglun Han
# @File : extract_bert_feats.py
import os
import sys
import argparse
import random
import string
import json
import numpy as np
import torch
from transformers import BertTokenizer, BertModel
"""
Description:
This program is used to extract the features from pret... | 6,843 | 32.54902 | 129 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_to_text/simultaneous_translation/agents/fairseq_simul_st_agent.py | import math
import os
import json
import numpy as np
import torch
import torchaudio.compliance.kaldi as kaldi
import yaml
from fairseq import checkpoint_utils, tasks
from fairseq.file_io import PathManager
try:
from simuleval import READ_ACTION, WRITE_ACTION, DEFAULT_EOS
from simuleval.agents import SpeechAgen... | 12,271 | 32.347826 | 105 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_recognition/ctc_decoder.py | # @Time : 2021/7/26
# @Author : Minglun Han
# @File : ctc_decoder.py
import os
import sys
import torch
import random
import logging
import torch.nn.functional as F
import numpy as np
import itertools as it
# Control print options
torch.set_printoptions(profile="full")
torch.set_printoptions(profile="default")
... | 5,750 | 35.169811 | 88 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_recognition/__init__.py | from . import criterions, models, tasks # noqa
| 48 | 23.5 | 47 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_recognition/infer.py | #!/usr/bin/env python3 -u
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
"""
Run inference for pre-processed data with a trained model.
"""
import ast
import logging
import math
import os
... | 18,560 | 32.203936 | 115 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_recognition/w2l_decoder.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
"""
Flashlight decoders.
"""
import gc
import itertools as it
import os.path as osp
from typing import List
import wa... | 17,561 | 34.336016 | 171 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_recognition/cif_decoder.py | # @Time : 2021/7/14
# @Author : Minglun Han
# @File : cif_decoder.py
"""""
Update:
By 2022/06/19
1. support LM decoding with language model by shallow fusion;
""" ""
import os
import sys
import torch
import logging
import numpy as np
import itertools as it
from torch import Tensor
import torch.... | 40,532 | 43.057609 | 116 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_recognition/criterions/cross_entropy_acc.py | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from __future__ import absolute_import, division, print_function, unicode_literals
import logging
import math
import torch
import torch.nn.f... | 5,372 | 40.015267 | 85 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_recognition/criterions/ASG_loss.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import torch
from examples.speech_recognition.data.replabels import pack_replabels
from fairseq import utils
from fair... | 5,870 | 33.333333 | 85 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_recognition/criterions/__init__.py | import importlib
import os
# ASG loss requires flashlight bindings
files_to_skip = set()
try:
import flashlight.lib.sequence.criterion
except ImportError:
files_to_skip.add("ASG_loss.py")
for file in sorted(os.listdir(os.path.dirname(__file__))):
if file.endswith(".py") and not file.startswith("_") and f... | 510 | 27.388889 | 87 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_recognition/models/vggtransformer.py | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import argparse
import math
from collections.abc import Iterable
import torch
import torch.nn as nn
from examples.speech_recognition.data.dat... | 37,258 | 35.564279 | 88 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_recognition/models/w2l_conv_glu_enc.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import math
import torch
import torch.nn as nn
import torch.nn.functional as F
from fairseq.models import (
Fairs... | 6,077 | 33.338983 | 87 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_recognition/models/__init__.py | import importlib
import os
for file in sorted(os.listdir(os.path.dirname(__file__))):
if file.endswith(".py") and not file.startswith("_"):
model_name = file[: file.find(".py")]
importlib.import_module("examples.speech_recognition.models." + model_name)
| 276 | 29.777778 | 83 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_recognition/datasets/asr_prep_json.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from __future__ import absolute_import, division, print_function, unicode_literals
import argparse
import concurrent.f... | 3,775 | 28.968254 | 84 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_recognition/new/__init__.py | 0 | 0 | 0 | py | |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_recognition/new/infer.py | #!/usr/bin/env python -u
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import ast
import hashlib
import logging
import os
import shutil
import sys
from dataclasses import dataclass, field,... | 16,498 | 33.955508 | 103 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_recognition/new/decoders/decoder_config.py | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import math
from dataclasses import dataclass, field
from typing import Optional
from fairseq.dataclass.configs import FairseqDataclass
from ... | 2,004 | 27.239437 | 69 | py |
CIF-HieraDist | CIF-HieraDist-main/examples/speech_recognition/new/decoders/decoder.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from typing import Union
from fairseq.data.dictionary import Dictionary
from .decoder_config import DecoderConfig, F... | 943 | 28.5 | 76 | py |
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