text stringlengths 185 73.3k | repo stringlengths 7 100 | path stringlengths 4 146 | language stringclasses 7
values | hash stringlengths 16 16 | score float64 7 8.5 | stars int64 0 237k |
|---|---|---|---|---|---|---|
'''
Defining the design matrix
'''
from __future__ import print_function
import numpy as np
import logging
import sys
def getsimpledesignmat(n):
'''
For a two smaple case, get a design matrix
'''
x1=np.identity(n)
x2=np.zeros(n)
x3=np.ones(n)
c1=np.column_stack((x1,x2))
c2=np.column_stack((x1,x3))
c... | morphic-bio/gRNA-Enrichment | workflows/mageck_count/widgets/mageck_count/MAGeCK_count/Dockerfiles/mageck-0.5.9.5/mageck/mledesignmat.py | .py | 2cf40a177cf4daf3 | 7 | 0 |
'''
Defining the core EM MLE approach
'''
from __future__ import print_function
import re
import sys
import scipy
from scipy.stats import nbinom
from scipy.stats import norm
import random
import math
import numpy as np
import numpy.linalg as linalg
import copy
from mleclassdef import *
from mledesi... | morphic-bio/gRNA-Enrichment | workflows/mageck_count/widgets/mageck_count/MAGeCK_count/Dockerfiles/mageck-0.5.9.5/mageck/mleem_bayes.py | .py | 60f789e84296db5b | 7 | 0 |
'''
Reading and writing instances
'''
from __future__ import print_function
import sys
import numpy as np
from mageck.mleclassdef import *
import logging
def read_gene_from_file(filename,includesamples=None):
'''
Reading gene models
Parameters
----------
filename
file name of the read count table
i... | morphic-bio/gRNA-Enrichment | workflows/mageck_count/widgets/mageck_count/MAGeCK_count/Dockerfiles/mageck-0.5.9.5/mageck/mleinstanceio.py | .py | f5680f3ce447d51c | 7 | 0 |
'''
Modeling mean and variance
'''
from __future__ import print_function
import re
import sys
import scipy
from scipy.stats import nbinom
from scipy.stats import linregress
from scipy.optimize import curve_fit
import random
import math
import numpy as np
import numpy.linalg as linalg
import logging
# debug
try:
f... | morphic-bio/gRNA-Enrichment | workflows/mageck_count/widgets/mageck_count/MAGeCK_count/Dockerfiles/mageck-0.5.9.5/mageck/mlemeanvar.py | .py | a87779de32c42dc6 | 7 | 0 |
'''
MAGeCK MLE multiprocessing
'''
from __future__ import print_function
import re
import sys
import logging
import multiprocessing
import copy
import numpy as np
import signal
from mageck.mleem import iteratenbem
# debug
try:
from IPython.core.debugger import Tracer
except:
pass
def thread_p_func(dinst,args,it... | morphic-bio/gRNA-Enrichment | workflows/mageck_count/widgets/mageck_count/MAGeCK_count/Dockerfiles/mageck-0.5.9.5/mageck/mlemultiprocessing.py | .py | 905ade268766ef79 | 7 | 0 |
'''
sgRNA efficiency related functions
'''
from __future__ import print_function
import sys
import numpy as np
from mageck.mleclassdef import *
import logging
def read_sgrna_eff(args):
'''
Read sgRNA efficiency score from file, and convert to initial prediction
'''
if args.sgrna_efficiency != None:
# e... | morphic-bio/gRNA-Enrichment | workflows/mageck_count/widgets/mageck_count/MAGeCK_count/Dockerfiles/mageck-0.5.9.5/mageck/mlesgeff.py | .py | cb9193b8c2118f7d | 7 | 0 |
#!/usr/bin/env python
"""MAGeCK pathway analysis module
Copyright (c) 2014 Wei Li, Han Xu, Xiaole Liu lab
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file COPYING included with
the distribution).
@status: experimental
@version: $Revision$
@author: W... | morphic-bio/gRNA-Enrichment | workflows/mageck_count/widgets/mageck_count/MAGeCK_count/Dockerfiles/mageck-0.5.9.5/mageck/pathwayFunc.py | .py | c0f73654ef5953d4 | 7 | 0 |
#
#
from __future__ import print_function
import sys
import re
import os
import logging
from mageck.fileOps import *
from mageck.mageckCount import *
class VisualRValue:
'''
Class for R visualization
'''
outprefix='sample1'
original_prefix='sample1' # used to record the original prefix
genesummaryfile=''... | morphic-bio/gRNA-Enrichment | workflows/mageck_count/widgets/mageck_count/MAGeCK_count/Dockerfiles/mageck-0.5.9.5/mageck/testVisual.py | .py | 332c6416d6c49ab3 | 7.5 | 0 |
#
#
from __future__ import print_function
import sys
import re
import os
import logging
from mageck.fileOps import *
from mageck.mageckCount import *
class VisualRCount:
'''
Class for generating reports of count command
'''
outprefix='sample1'
original_prefix='sample1' # used to record the original prefix... | morphic-bio/gRNA-Enrichment | workflows/mageck_count/widgets/mageck_count/MAGeCK_count/Dockerfiles/mageck-0.5.9.5/mageck/testVisualCount.py | .py | 1c81affb5668e282 | 7.5 | 0 |
"""Runtime configuration: every path comes from the environment, read at call time.
Tests point these at tmp dirs, docker-compose points them at /library and
/data — the real database can never be reached by accident.
"""
import os
from pathlib import Path
def library_dir() -> Path:
"""Root of the media library... | panjacek/library_of_mess | src/library_of_mess/config.py | .py | 68df70e4cf7e3b1f | 7 | 0 |
"""Parquet database: load, save, filter and merge edits."""
from pathlib import Path, PurePosixPath
import pandas as pd
from library_of_mess.config import library_dir
from library_of_mess.scanner import DB_COLUMNS, DB_COLUMNS_RO
def resolve_media_path(path_str: str | Path) -> Path:
"""Resolve a stored (library... | panjacek/library_of_mess | src/library_of_mess/database.py | .py | 9c655f99c09ae642 | 7 | 0 |
"""Embedding store + cosine search for semantic video lookup.
Pure array-in/array-out logic — no streamlit, no model runtime here. Encoders
are injected as plain callables so tests use fake vectors and a future model
backend stays swappable (research plan: docs/plans/2026-08-25_plan_embedding_research.md).
"""
import... | panjacek/library_of_mess | src/library_of_mess/embeddings.py | .py | 06a107dc66b5ecde | 7 | 0 |
"""Thumbnail generation via ffmpeg."""
from collections.abc import Callable, Iterable
from concurrent.futures import ThreadPoolExecutor, as_completed
from pathlib import Path
import ffmpeg
import pandas as pd
from streamlit.logger import get_logger
from library_of_mess.config import thumbnails_dir, thumbnail_workers... | panjacek/library_of_mess | src/library_of_mess/thumbnails.py | .py | 4680dd85d3ab0838 | 7 | 0 |
"""Streamlit glue: session-state DB loading and widgets shared across pages."""
from pathlib import Path
import pandas as pd
import streamlit as st
from streamlit.logger import get_logger
from library_of_mess import config, database
from library_of_mess import thumbnails as thumbs
logger = get_logger(__name__)
# s... | panjacek/library_of_mess | src/library_of_mess/ui/helpers.py | .py | 6af02b5718de4857 | 7 | 0 |
"""Based on example from https://gist.github.com/treuille/2ce0acb6697f205e44e3e0f576e810b7"""
import itertools
from collections.abc import Iterable, Iterator
from typing import Any
import streamlit as st
def page_format_func(i: int) -> str:
return f"Page {i}"
def paginator(
label: str, items: Iterable[Any... | panjacek/library_of_mess | src/library_of_mess/ui/paginator.py | .py | 5c6d43c3bb62e4ba | 7 | 0 |
"""Test fixtures.
Isolation guarantee: an autouse fixture chdirs into tmp_path and points every
config env var there, so the real library.parquet can never be touched.
"""
import datetime
import subprocess
import shutil
from collections.abc import Iterator
from pathlib import Path
import pandas as pd
import pytest
... | panjacek/library_of_mess | tests/conftest.py | .py | 235df13335bbea77 | 7.5 | 0 |
"""Helpers for calling the Auth0 Management API."""
import requests
class Auth0ManagementAPIClient:
"""Talk to Auth0 Management API.
Do *not* instantiate directly. Use `get_auth0_management_client` instead so
we don't end up requesting too many tokens and using up our quota.
Needs the client ID and... | catalyst-cooperative/eel-hole | eel_hole/auth0_management.py | .py | cd5a25d4bd8b1f56 | 7 | 0 |
"""Shared loading/validation for dashboard gallery configuration."""
from pathlib import Path
import yaml
from pydantic import BaseModel, ConfigDict, Field, TypeAdapter
class DashboardConfig(BaseModel):
"""Configuration for a single hosted dashboard in the gallery.
slug: short name for the dashboard URL in... | catalyst-cooperative/eel-hole | eel_hole/dashboards_config.py | .py | c61baa31366a5170 | 7 | 0 |
"""Generate DuckDB queries."""
import itertools
from dataclasses import dataclass
from pydantic import BaseModel
def _camelize(string: str) -> str:
"""snake_case to camelCase."""
words = string.split("_")
return words[0] + "".join(word.capitalize() for word in words[1:])
class Filter(BaseModel):
"... | catalyst-cooperative/eel-hole | eel_hole/duckdb_query.py | .py | d56b8b1bb696d85f | 7 | 0 |
"""Helper functions for using feature flags."""
from dataclasses import dataclass
from flask import abort, current_app, request, session
@dataclass
class FeatureVariants:
default: str
variants: set[str]
def __post_init__(self):
assert self.default in self.variants
def is_valid(self, varian... | catalyst-cooperative/eel-hole | eel_hole/feature_variants.py | .py | 6eca591e18434796 | 7 | 0 |
"""DB model definitions."""
from flask_login import UserMixin
from flask_sqlalchemy import SQLAlchemy
from sqlalchemy.orm import Mapped, mapped_column
from sqlalchemy.sql import false
db = SQLAlchemy()
class User(UserMixin, db.Model):
"""It's the user.
The auth0_id is a unique ID that comes from auth0. Thi... | catalyst-cooperative/eel-hole | eel_hole/models.py | .py | 6e5e83386d6adf62 | 7 | 0 |
"""Interact with the document search."""
import dataclasses
import re
import shutil
from collections.abc import Callable
from pathlib import Path
import requests
from frictionless import Package
from pydantic import BaseModel, ConfigDict
from rapidfuzz import fuzz
# TODO 2025-01-15: think about switching this over t... | catalyst-cooperative/eel-hole | eel_hole/search.py | .py | 297223ab2c054b2c | 7 | 0 |
"""Useful helper functions."""
import html
import re
from dataclasses import dataclass, field
from urllib.parse import urljoin
import structlog
from docutils.core import publish_parts
from frictionless import Resource
from markupsafe import Markup, escape
log = structlog.get_logger(__name__)
SPHINX_TAGS = re.compi... | catalyst-cooperative/eel-hole | eel_hole/utils.py | .py | 8fb8100f6429afa5 | 7 | 0 |
import logging
from logging.config import fileConfig
from alembic import context
from flask import current_app
# this is the Alembic Config object, which provides
# access to the values within the .ini file in use.
config = context.config
# Interpret the config file for Python logging.
# This line sets up loggers ba... | catalyst-cooperative/eel-hole | migrations/env.py | .py | 1b7e7a47f5d7fad6 | 7 | 0 |
"""add email verification flag
Revision ID: 0203498a6957
Revises: 745f26f7b81f
Create Date: 2026-03-19 16:31:01.640622
"""
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision = "0203498a6957"
down_revision = "745f26f7b81f"
branch_labels = None
depends_on = None
def upg... | catalyst-cooperative/eel-hole | migrations/versions/0203498a6957_add_email_verification_flag.py | .py | 30b3cf265591cdb3 | 7 | 0 |
"""Make username non-unique
Revision ID: 0309db1e86c0
Revises: fc78dcef5f42
Create Date: 2025-01-15 16:16:19.431269
"""
from alembic import op
# revision identifiers, used by Alembic.
revision = "0309db1e86c0"
down_revision = "fc78dcef5f42"
branch_labels = None
depends_on = None
def upgrade():
# ### commands ... | catalyst-cooperative/eel-hole | migrations/versions/0309db1e86c0_make_username_non_unique.py | .py | 4c09aab39614792a | 7 | 0 |
"""Initial user model
Revision ID: de00b5a84172
Revises:
Create Date: 2025-01-06 12:55:32.141492
"""
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision = "de00b5a84172"
down_revision = None
branch_labels = None
depends_on = None
def upgrade():
# ### commands auto ... | catalyst-cooperative/eel-hole | migrations/versions/de00b5a84172_initial_user_model.py | .py | 51ba222221965e9a | 7 | 0 |
"""Add auth0 id
Revision ID: fc78dcef5f42
Revises: de00b5a84172
Create Date: 2025-01-06 14:44:42.412604
"""
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision = "fc78dcef5f42"
down_revision = "de00b5a84172"
branch_labels = None
depends_on = None
def upgrade():
# #... | catalyst-cooperative/eel-hole | migrations/versions/fc78dcef5f42_add_auth0_id.py | .py | 20aeca6a38716931 | 7 | 0 |
"""Pytest hooks for relevancy reporting."""
from pathlib import Path
from tests.relevancy.reporting import render_variant_report
def pytest_configure(config):
"""Initialize an in-memory collector for relevancy report blocks."""
config._relevancy_reports = {}
config._sweep_results = []
def pytest_addop... | catalyst-cooperative/eel-hole | tests/relevancy/conftest.py | .py | e80952e916ae86d0 | 7.5 | 0 |
"""Formatting helpers for relevancy diagnostics output."""
import yaml
def _format_results(results, relevant_names):
"""Serialize top results with rank, relevance marker, and score.
The report output is designed for quick visual inspection in terminal logs,
so this function emits compact, aligned string... | catalyst-cooperative/eel-hole | tests/relevancy/reporting.py | .py | 1a2bff58ce25d8bd | 7.5 | 0 |
"""Shared loading/validation for parameter sweep configuration."""
from pathlib import Path
import yaml
from pydantic import BaseModel, ConfigDict, Field
class SweepConfig(BaseModel):
"""Configuration for a parameter sweep for a single search variant."""
model_config = ConfigDict(extra="forbid")
class... | catalyst-cooperative/eel-hole | tests/relevancy/sweep_config.py | .py | be7317b431be4279 | 7.5 | 0 |
import re
from collections import namedtuple
from itertools import product
from pathlib import Path
import pytest
import requests
import yaml
from eel_hole.search import search_variants
from tests.relevancy.sweep_config import load_sweep_config
def query_search_api(query: str, variant: str, config: str) -> dict:
... | catalyst-cooperative/eel-hole | tests/relevancy/test_relevancy.py | .py | 1e5c1f0ae5b1b2c8 | 7.5 | 0 |
"""class Solution:
def searchRange(self, nums: List[int], target: int) -> List[int]:
left = 0
right = len(nums) - 1
while left <= right:
mid = (left + right) // 2
if nums[mid] < target:
left = mid + 1
elif nums[mid] > target:
... | AlexKalll/LeetCode-Problems-Solution | 0034-find-first-and-last-position-of-element-in-sorted-array/0034-find-first-and-last-position-of-element-in-sorted-array.py | .py | 97ba8a474058e237 | 7 | 0 |
class Solution:
def rotate(self, matrix: List[List[int]]) -> None:
"""
Do not return anything, modify matrix in-place instead.
"""
n = len(matrix)
for i in range(n//2):
for j in range(n):
# Swap the top and bottom elements in the column
... | AlexKalll/LeetCode-Problems-Solution | 0048-rotate-image/0048-rotate-image.py | .py | 4394e73dc59370c1 | 7 | 0 |
class Solution:
def setZeroes(self, mat: List[List[int]]) -> None:
"""
Do not return anything, modify matrix in-place instead.
"""
m=len(mat)
n=len(mat[0])
row=[0]*m
col=[0]*n
for i in range(m):
for j in range(n):
if mat[i][... | AlexKalll/LeetCode-Problems-Solution | 0073-set-matrix-zeroes/0073-set-matrix-zeroes.py | .py | 5df6457dbd8fec8c | 7 | 0 |
class Solution:
def sortColors(self, nums: List[int]) -> None:
"""
Do not return anything, modify nums in-place instead.
"""
# this is gonna be done in bubble sort
n = len(nums)
for i in range(n-1):
swapped = False
for j in range(n - i - 1):
... | AlexKalll/LeetCode-Problems-Solution | 0075-sort-colors/0075-sort-colors.py | .py | fb3a470dcdea287d | 7 | 0 |
# Definition for a binary tree node.
# class TreeNode:
# def __init__(self, val=0, left=None, right=None):
# self.val = val
# self.left = left
# self.right = right
class Solution:
def recoverTree(self, root: Optional[TreeNode]) -> None:
"""
Do not return anything, modify root in-place i... | AlexKalll/LeetCode-Problems-Solution | 0099-recover-binary-search-tree/0099-recover-binary-search-tree.py | .py | 91aec1f855bf808e | 7 | 0 |
# Definition for a binary tree node.
# class TreeNode:
# def __init__(self, val=0, left=None, right=None):
# self.val = val
# self.left = left
# self.right = right
"""
class Solution:
def maxDepth(self, root: Optional[TreeNode]) -> int:
if not root:
return 0
... | AlexKalll/LeetCode-Problems-Solution | 0104-maximum-depth-of-binary-tree/0104-maximum-depth-of-binary-tree.py | .py | 58b0f871ed4d8b3e | 7 | 0 |
#!/usr/bin/env python3
# Copyright (c) 2026 Eclipse Oniro for OpenHarmony contributors.
# SPDX-License-Identifier: Apache-2.0
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://ww... | eclipse-oniro4openharmony/vendor_oniro | hybris_generic/custom_conf/telephony/convert_apns.py | .py | 967e0c6d90d4ed55 | 7 | 0 |
from typing import Any, Callable
from ..classes import UnaryFn
__all__ = [
'to',
'apply',
'partial',
'identity',
]
def to(T: type) -> UnaryFn:
"""Return a unary function that casts its argument to `T`"""
return UnaryFn(T)
def apply(fn: Callable[[Any], Any]) -> UnaryFn:
"""Return a unary ... | MetGang/advent | src/advent/modules/functions.py | .py | e6b23092ecacfdb7 | 7.15 | 1 |
import builtins
import itertools
from pathlib import Path
from typing import Any
from ..classes import NullaryFn
__all__ = [
'iterate',
'range',
'irange',
'infinite_range',
'read_input',
'read_file',
'read_file_lines',
]
def iterate(iterable: Any) -> NullaryFn:
"""Return iterator for ... | MetGang/advent | src/advent/modules/generators.py | .py | b9c7be62a0f56b40 | 7.15 | 1 |
import re
from typing import Any
from ..classes import UnaryFn
__all__ = [
'split',
'replace',
'find_all',
'find_first',
'find_last',
]
def split(pattern: str | re.Pattern[str], limit: int = 0) -> UnaryFn:
"""Return list of substrings split by occurrences matching `pattern`"""
def __inner... | MetGang/advent | src/advent/modules/regex.py | .py | 988553083c1ff450 | 7.15 | 1 |
import builtins
import collections
import functools
import itertools
import operator
from collections import defaultdict
from collections.abc import Iterable, Mapping, Reversible, Sequence
from functools import cmp_to_key
from typing import Any, Callable, Sized
from ..classes import UnaryFn
__all__ = [
'map',
... | MetGang/advent | src/advent/modules/sequences.py | .py | fbc6fec637063dfd | 7.15 | 1 |
from collections.abc import Iterable
from ..classes import UnaryFn
__all__ = [
'join',
'trim',
'trim_left',
'trim_right',
'split',
'split_by',
'replace',
'substring',
'contains',
'starts_with',
'ends_with',
'is_space',
'is_alnum',
'is_alpha',
'is_upper',
... | MetGang/advent | src/advent/modules/textual.py | .py | 3fb9f39cc482dd62 | 7.15 | 1 |
#!/usr/bin/env python3
"""Tdarr AV1 quality gate.
Polls Tdarr's FileJSONDB for successful h264 → AV1 transcodes that
haven't been validated yet, runs a 3-window libvmaf check on each, and
on pass replaces the source with the AV1 output. On fail, leaves both
files in place and logs the failure for manual review.
Runs ... | agonbar/agonbar-kubernetes | tdarr/validator/validator.py | .py | fc92f10a3ed13c33 | 7 | 0 |
"""mkdocs hook: (re)generate the API reference pages under docs/reference/.
Runs automatically on `mkdocs build`/`mkdocs serve` (module-level code below
executes as soon as mkdocs loads this config) -- no third-party plugin needed.
"""
import shutil
from pathlib import Path
DOCS_DIR = Path(__file__).parent
ROOT = DO... | ondrejstranik/plim | docs/hooks.py | .py | 003c9941763b390b | 7 | 0 |
'''
script to create desktop shortcuts for all run scripts in plim.main
'''
import sys
from pathlib import Path
from pyshortcuts import make_shortcut
SCRIPTS = {
'runRealIFC': 'Real IFC',
'runVirtualIFC': 'Virtual IFC',
'runRealMSC': 'Real MSC',
'runSImageAnalyser': 'Spectral Image Analyser',
'run... | ondrejstranik/plim | plim/_install/createShortcut.py | .py | b92e866b65a549a4 | 7 | 0 |
"""
FileData - class for unified saving/loading data generated in plim experiment
Created on Mon Nov 15 12:08:51 2021
@author: ostranik
"""
#%%
#TODO: correct time loading !!!!!!!!!!!!
import os
import time
import logging
import numpy as np
import pickle
from pathlib import Path
from plim.algorithm.plasmonFit impo... | ondrejstranik/plim | plim/algorithm/fileData.py | .py | b47d63b5b6e43777 | 7 | 0 |
'''
class for calculating spot spectra from 3D spectral cube
'''
#%%
import numpy as np
import time
class FlowData:
''' class for processing flow data from pump '''
DEFAULT = {}
def __init__(self,signal=None,time=None,**kwarg):
''' initialization of the parameters '''
self.signal = None... | ondrejstranik/plim | plim/algorithm/flowData.py | .py | 62c3de728d65f4ab | 7 | 0 |
''' class to preprocess kinetic data for fit'''
from plim.algorithm.spotData import SpotData
from plim.algorithm.fileData import FileData
from spectralCamera.algorithm.gridSuperPixel import GridSuperPixel
import pyqtgraph as pg
import napari
import numpy as np
import matplotlib.pyplot as plt
class PreprocessSignal... | ondrejstranik/plim | plim/algorithm/preprocessSignal.py | .py | e5d35cf61428fc75 | 7 | 0 |
'''
class for processing signal from spots
'''
#%%
import numpy as np
import time
import pickle
import csv
import re
class SpotData:
''' class for processing signal from spots '''
DEFAULT = {}
def __init__(self,signal=None,time=None, **kwarg):
''' initialization of the parameters '''
#TOD... | ondrejstranik/plim | plim/algorithm/spotData.py | .py | bc6ac2c02950ea37 | 7 | 0 |
#%%
'''
class for identification of plasmonic spots
'''
from skimage.filters import threshold_otsu, threshold_local, gaussian, rank
from skimage.morphology import binary_closing, square, disk
from skimage.segmentation import clear_border
from skimage.measure import label, regionprops_table
import skimage as ski
impor... | ondrejstranik/plim | plim/algorithm/spotIdentification.py | .py | 25bddf7a85c43289 | 7 | 0 |
'''
class for pushing a delta-signal image layer into the offline signal analyser
'''
#%%
from qtpy.QtWidgets import QWidget, QVBoxLayout, QPushButton
from viscope.gui.baseGUI import BaseGUI
from plim.gui.deltaSignalGUI import DeltaSignalGUI
class DeltaSignal2GUI(DeltaSignalGUI):
''' offline counterpart of Delta... | ondrejstranik/plim | plim/gui/deltaSignal2GUI.py | .py | dda5b559d6daec92 | 7 | 0 |
'''
class for pushing a delta-signal image layer into a live spectral viewer
'''
#%%
import numpy as np
from qtpy.QtWidgets import QWidget, QVBoxLayout, QPushButton, QCheckBox
from viscope.gui.baseGUI import BaseGUI
class DeltaSignalGUI(BaseGUI):
''' dockable panel with 'new Image'/'live Image' buttons that pain... | ondrejstranik/plim | plim/gui/deltaSignalGUI.py | .py | 1ccd85261326a816 | 7 | 0 |
'''
class for live viewing spectral images
'''
#%%
#from spectralCamera.gui.xywViewerGUI import XYWViewerGui
from viscope.gui.baseGUI import BaseGUI
from plim.gui.spectralViewer.plasmonViewer import PlasmonViewer
from qtpy.QtCore import Signal
class PlasmonViewerGUI(BaseGUI):
''' main class to show plasmonViewer... | ondrejstranik/plim | plim/gui/plasmonViewerGUI.py | .py | d69fe24324882320 | 7 | 0 |
'''
class for tracking of plasmon peaks
'''
#%%
from viscope.gui.baseGUI import BaseGUI
from plim.gui.signalViewer.signalWidget import SignalWidget
from plim.gui.signalViewer.flowRateWidget import FlowRateWidget
from plim.gui.signalViewer.injectionWidget import InjectionWidget
from plim.gui.signalViewer.infoWidget i... | ondrejstranik/plim | plim/gui/positionTrackGUI.py | .py | 076157188756e732 | 7 | 0 |
'''
Load/Save/Export panel for the offline signal analyser, paired with a FileDataProcessor device
'''
#%%
from pathlib import Path
import logging
from qtpy.QtWidgets import QFileDialog, QWidget, QVBoxLayout, QLabel, QPushButton
import pyqtgraph.exporters
from viscope.gui.baseGUI import BaseGUI
logger = logging.getL... | ondrejstranik/plim | plim/gui/signalAnalyser/fileDataProcessorGUI.py | .py | b4dbe4fe394138f5 | 7 | 0 |
'''
thin wrapper GUI for FitWidget - kinetic fitting of a completed signal curve
'''
#%%
from viscope.gui.baseGUI import BaseGUI
from plim.gui.signalViewer.fitWidget import FitWidget
class FitGUI(BaseGUI):
''' GUI wrapping FitWidget for the offline signal analyser. offline-analysis-only
(kinetic fitting on a ... | ondrejstranik/plim | plim/gui/signalAnalyser/fitGUI.py | .py | f8e281c3e921215f | 7 | 0 |
'''
lightweight, read-only napari viewer for the offline signal analyser
'''
#%%
import numpy as np
import logging
from qtpy.QtCore import Signal
from viscope.gui.napariGUI import NapariGUI
logger = logging.getLogger(__name__)
class SpotViewerGUI(NapariGUI):
''' shows the overview image and spot positions of a l... | ondrejstranik/plim | plim/gui/signalAnalyser/spotViewerGUI.py | .py | 6d0291122df44936 | 7 | 0 |
'''
class for viewing signals from spots' plasmon resonance
'''
import napari
import pyqtgraph as pg
from PyQt5.QtGui import QColor, QPen
from qtpy.QtWidgets import QLabel, QSizePolicy,QWidget, QApplication, QVBoxLayout
from qtpy import QtCore
from qtpy.QtCore import Qt, Signal
from magicgui import magicgui
import nu... | ondrejstranik/plim | plim/gui/signalViewer/flowRateWidget.py | .py | 97b2290b5ff1af35 | 7 | 0 |
'''
class for viewing info from spots' plasmon resonance
'''
import logging
from qtpy.QtGui import QColor
from qtpy.QtWidgets import QWidget,QVBoxLayout,QTableWidget,QTableWidgetItem,QAbstractItemView
from qtpy.QtCore import Signal, Qt, QItemSelectionModel
import numpy as np
from plim.algorithm.spotData import SpotDa... | ondrejstranik/plim | plim/gui/signalViewer/infoWidget.py | .py | d63569bb927fd642 | 7 | 0 |
'''
class for viewing info about injection of solutions in the sensor
'''
import time
from qtpy.QtWidgets import QWidget,QVBoxLayout,QHBoxLayout,QTextEdit, QPushButton, QLineEdit
from qtpy.QtCore import Signal
from plim.algorithm.injectionData import InjectionData
class InjectionWidget(QWidget):
''' main class... | ondrejstranik/plim | plim/gui/signalViewer/injectionWidget.py | .py | 7286a67f101185af | 7 | 0 |
'''
class for viewing spots's plasmon resonance
'''
from spectralCamera.gui.spectralViewer.xywViewer import XYWViewer
import napari
import time
import pyqtgraph as pg
from PyQt5.QtGui import QColor, QPen
from qtpy.QtWidgets import QLabel, QSizePolicy
from qtpy.QtCore import Qt
from magicgui import magicgui
from enum ... | ondrejstranik/plim | plim/gui/spectralViewer/transmissionViewer.py | .py | 3a3e8b2ec37d7c51 | 7.5 | 0 |
'''
class for live viewing spectral images
'''
#%%
from viscope.gui.baseGUI import BaseGUI
from plim.gui.spectralViewer.spotSpectraViewer import SpotSpectraViewer
class STViewerGUI(BaseGUI):
''' main class to show spot transmission Viewer (called spotSpectraViewer)
calculation of the spectra are done in the m... | ondrejstranik/plim | plim/gui/stViewerGUI.py | .py | a717b8842ee37469 | 7 | 0 |
'''
class for live viewing spectral images
'''
#%%
from spectralCamera.gui.xywViewerGUI import XYWViewerGui
from plim.gui.spectralViewer.transmissionViewer import TransmissionViewer
class TViewerGui(XYWViewerGui):
''' main class to show transmissionViewer'''
DEFAULT = {'nameGUI': 'tViewer'}
def __init__(... | ondrejstranik/plim | plim/gui/tViewerGUI.py | .py | ff2fc72477772c4b | 7 | 0 |
"""
file data processor - "device" wrapping a saved dataset for offline review
@author: ostranik
"""
#%%
from viscope.instrument.base.baseProcessor import BaseProcessor
from plim.algorithm.fileData import FileData
class FileDataProcessor(BaseProcessor):
''' "device" for the offline signal analyser: wraps a File... | ondrejstranik/plim | plim/instrument/fileDataProcessor.py | .py | 3b9705ece26764ba | 7 | 0 |
"""
plasmon processor - process the spectral images
Created on Mon Nov 15 12:08:51 2021
@author: ostranik
"""
#%%
import os
import time
import logging
import numpy as np
from viscope.instrument.base.baseProcessor import BaseProcessor
from plim.algorithm.plasmonFit import PlasmonFit
from plim.algorithm.spotSpectra im... | ondrejstranik/plim | plim/instrument/plasmonProcessor.py | .py | 440d15d9aa5a5cbf | 7 | 0 |
"""
容器类，用于储存文件、文件夹，支持 list 的操作，同时支持许多方法方便操作元素
元素类型为 namedtuple，至少拥有 name id 两个属性才能放入容器
"""
__all__ = ['FileList', 'FolderList']
class ItemList:
"""具有 name, id 属性对象的列表"""
def __init__(self):
self._items = []
def __len__(self):
return len(self._items)
def __getitem__(self, index):
... | farfarfun/funlanzou | lanzou/api/models.py | .py | 31a1469a1c96b87c | 7 | 0 |
"""
重新封装的控件
"""
import os
from PyQt6.QtCore import Qt, pyqtSignal, QTimer, QSize
from PyQt6.QtGui import QTextDocument, QAbstractTextDocumentLayout, QPalette, QFontMetrics, QIcon, QStandardItem
from PyQt6.QtWidgets import (QApplication, QAbstractItemView, QStyle, QListView, QLineEdit, QTableView,
... | farfarfun/funlanzou | lanzou/gui/others.py | .py | 73573b9ebd5660f2 | 7 | 0 |
# src/gui/data_loading_tab.py
import logging
from pathlib import Path
import h5py
import matplotlib.pyplot as plt
import yaml
from matplotlib.backends.backend_qtagg import FigureCanvasQTAgg as FigureCanvas
from PyQt6.QtCore import QTimer
from PyQt6.QtGui import QTextCursor, QTextOption # Import QTextOption for word ... | BAMresearch/McSAS3GUI | src/mcsas3gui/gui/data_loading_tab.py | .py | 2650dff39fd26d35 | 7.24 | 2 |
# src/gui/file_line_selection_widget.py
import logging
from pathlib import Path
from PyQt6.QtCore import Qt, pyqtSignal # , QDragEnterEvent, QDropEvent, Qt
from PyQt6.QtWidgets import QFileDialog, QHBoxLayout, QLineEdit, QPushButton, QWidget
logger = logging.getLogger("McSAS3")
class FilePathLineEdit(QLineEdit):
... | BAMresearch/McSAS3GUI | src/mcsas3gui/gui/file_line_selection_widget.py | .py | 8ffacb301c84fbf8 | 7.24 | 2 |
import logging
from collections.abc import Callable
from pathlib import Path
from typing import Protocol
from PyQt6.QtWidgets import QMessageBox, QWidget
logger = logging.getLogger("McSAS3")
class FilePathSelector(Protocol):
def set_file_path(self, file_path: str) -> None: ...
def load_existing_selector_file(... | BAMresearch/McSAS3GUI | src/mcsas3gui/gui/file_selection_helpers.py | .py | fa55f58b8b91e7f3 | 7.24 | 2 |
import logging
from pathlib import Path
from PyQt6.QtCore import Qt
from PyQt6.QtWidgets import (
QFileDialog,
QHBoxLayout,
QHeaderView,
QLabel,
QPushButton,
QTableWidget,
QTableWidgetItem,
QVBoxLayout,
QWidget,
)
logger = logging.getLogger("McSAS3")
class FileSelectionWidget(QWi... | BAMresearch/McSAS3GUI | src/mcsas3gui/gui/file_selection_widget.py | .py | 5dec74077fae686f | 7.24 | 2 |
import logging
from pathlib import Path
import yaml
from PyQt6.QtCore import QTimer
from PyQt6.QtWidgets import QComboBox, QLabel, QTextBrowser, QVBoxLayout, QWidget
from mcsas3gui.utils.file_utils import get_default_config_files, get_main_path
from mcsas3gui.utils.yaml_utils import load_yaml_file
from .yaml_editor_... | BAMresearch/McSAS3GUI | src/mcsas3gui/gui/getting_started_tab.py | .py | 0dc2954ac09111eb | 7.24 | 2 |
import logging
from pathlib import Path
from PyQt6.QtWidgets import QMessageBox, QProgressBar, QPushButton, QVBoxLayout, QWidget
from ..utils.file_utils import make_out_path
from ..utils.mcsas3_cli import histogram_subprocess_spec
from ..utils.task_runner_mixin import TaskRunnerMixin
from .file_line_selection_widget ... | BAMresearch/McSAS3GUI | src/mcsas3gui/gui/hist_run_tab.py | .py | a70850acfb97f792 | 7.24 | 2 |
import logging
import os
import subprocess
from pathlib import Path
from sys import platform
from tempfile import gettempdir
import yaml
from PyQt6.QtWidgets import (
QComboBox,
QLabel,
QMessageBox,
QPushButton,
QTextEdit,
QVBoxLayout,
QWidget,
)
from ..utils.file_utils import get_default_... | BAMresearch/McSAS3GUI | src/mcsas3gui/gui/hist_settings_tab.py | .py | dbd465403e409816 | 7.24 | 2 |
# main_window.py
# import inspect
from pathlib import Path
from PyQt6.QtWidgets import QMainWindow, QTabWidget
from .data_loading_tab import DataLoadingTab
from .getting_started_tab import GettingStartedTab
from .hist_run_tab import HistRunTab
from .hist_settings_tab import HistogramSettingsTab
from .optimization_ta... | BAMresearch/McSAS3GUI | src/mcsas3gui/gui/main_window.py | .py | eba170f9200e9a85 | 7.24 | 2 |
from __future__ import annotations
from dataclasses import dataclass
from pathlib import Path, PurePosixPath
from typing import Any, Mapping
import numpy as np
import pandas as pd
from mcsas3.data_adapters import (
STAGE_BINNED,
STAGE_CLIPPED,
STAGE_RAW,
fit_arrays_from_bundle,
frame_from_bundle,
... | BAMresearch/McSAS3GUI | src/mcsas3gui/gui/mcsas3_bridge.py | .py | 12c57d6d98260388 | 7.24 | 2 |
import logging
from pathlib import Path
from PyQt6.QtWidgets import QMessageBox, QProgressBar, QPushButton, QVBoxLayout, QWidget
from ..utils.file_utils import make_out_path
from ..utils.task_runner_mixin import TaskRunnerMixin
from .file_line_selection_widget import FileLineSelectionWidget
from .file_selection_helpe... | BAMresearch/McSAS3GUI | src/mcsas3gui/gui/optimization_tab.py | .py | ebab9b4f3445ee70 | 7.24 | 2 |
from __future__ import annotations
import logging
from collections.abc import Callable, Mapping
from pathlib import Path
from typing import Any
import yaml
from PyQt6.QtCore import QThread, pyqtSignal
from mcsas3gui._bootstrap import ensure_compatible_mcsas3
ensure_compatible_mcsas3()
logger = logging.getLogger("M... | BAMresearch/McSAS3GUI | src/mcsas3gui/gui/optimization_worker.py | .py | 52b452fb6531d6ff | 7.24 | 2 |
from typing import Protocol
RUNNING_BUTTON_TEXT = "Running... Click to abort."
RUNNING_BUTTON_STYLE = "QPushButton { background-color: #c65a3a; color: white; font-weight: bold; }"
class AbortableButton(Protocol):
"""Minimal button interface needed for shared run/abort state handling."""
def setText(self, te... | BAMresearch/McSAS3GUI | src/mcsas3gui/gui/run_control_helpers.py | .py | a0236b1de509bbe4 | 7.24 | 2 |
from __future__ import annotations
import math
import re
from collections.abc import Mapping
from pathlib import Path
from typing import Any
RunConfiguration = dict[str, Any]
_PROGRESS_PATTERN = re.compile(r"chiSqr:\s*(.+?),\s*N accepted:\s*([0-9]+)\s*/\s*([0-9]+)")
_FINAL_PROGRESS_PATTERN = re.compile(r"Final chiSqr... | BAMresearch/McSAS3GUI | src/mcsas3gui/gui/run_settings_helpers.py | .py | 2c437da4ff03638f | 7.24 | 2 |
import logging
import re
from pathlib import Path
from typing import Sequence
from matplotlib import pyplot as plt
from matplotlib.backends.backend_qtagg import FigureCanvasQTAgg as FigureCanvas
from PyQt6.QtCore import QTimer
from PyQt6.QtWidgets import QComboBox, QDialog, QLabel, QPushButton, QTextEdit, QVBoxLayout,... | BAMresearch/McSAS3GUI | src/mcsas3gui/gui/run_settings_tab.py | .py | d76570cbf1ead9cb | 7.24 | 2 |
# src/gui/yaml_editor_widget.py
import logging
import re
import yaml
from PyQt6.QtCore import QEvent, QRegularExpression, pyqtSignal
from PyQt6.QtGui import QColor, QFont, QSyntaxHighlighter, QTextCharFormat
from PyQt6.QtWidgets import (
QFileDialog,
QHBoxLayout,
QPushButton,
QTextEdit,
QToolTip,
... | BAMresearch/McSAS3GUI | src/mcsas3gui/gui/yaml_editor_widget.py | .py | 2f4ad06aea5e42e8 | 7.24 | 2 |
import logging
import subprocess
from collections.abc import Callable, Mapping
from pathlib import Path
from typing import Any
from PyQt6.QtCore import QThread, pyqtSignal
from .mcsas3_cli import SubprocessSpec
logger = logging.getLogger("McSAS3")
CommandBuilder = Callable[[Path, Path, Mapping[str, Any]], list[str] ... | BAMresearch/McSAS3GUI | src/mcsas3gui/utils/base_worker.py | .py | 10dde24c065d4a5b | 7.24 | 2 |
from importlib.resources import files
from pathlib import Path
def get_default_config_files(directory: Path) -> list[str]:
"""Get a list of YAML configuration files in the specified directory."""
config_dir = Path(directory)
if not config_dir.exists():
config_dir.mkdir(parents=True) # Create dire... | BAMresearch/McSAS3GUI | src/mcsas3gui/utils/file_utils.py | .py | a987e2ac04e83a67 | 7.24 | 2 |
from __future__ import annotations
import os
import sys
from dataclasses import dataclass
from pathlib import Path
from shutil import which
from .. import _bootstrap
@dataclass(frozen=True)
class SubprocessSpec:
"""Subprocess argument list plus optional environment overrides."""
args: list[str]
env_ove... | BAMresearch/McSAS3GUI | src/mcsas3gui/utils/mcsas3_cli.py | .py | 3362a18d91b7c805 | 7.24 | 2 |
from __future__ import annotations
from collections.abc import Mapping
from typing import Any
from PyQt6.QtWidgets import QMessageBox
from .base_worker import BaseWorker, CommandBuilder, FileMap
class TaskRunnerMixin:
"""Shared worker/progress wiring for file-oriented GUI task tabs."""
task_dialog_title =... | BAMresearch/McSAS3GUI | src/mcsas3gui/utils/task_runner_mixin.py | .py | 51c48093e00e35ce | 7.24 | 2 |
#!/usr/bin/env python3
"""Sign a PyInstaller macOS app bundle with a stable, minimal strategy."""
from __future__ import annotations
import argparse
import json
import os
import shutil
import subprocess
import sys
from pathlib import Path
def _run(cmd: list[str], quiet: bool = False) -> None:
if not quiet:
... | BAMresearch/McSAS3GUI | tools/sign_macos_bundle.py | .py | 9cf7ae3a0c6b2b89 | 7.24 | 2 |
import re
import urllib.parse
import urllib.request
import base64
def fetch_subscription(url):
"""从订阅 URL 获取节点文本内容（支持 Base64 订阅）"""
try:
req = urllib.request.Request(
url,
headers={"User-Agent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64)"},
)
with urllib.request... | ForkFF/Freedom | update_config.py | .py | 91dba12326cd0595 | 7 | 0 |
"""
# -*- coding: utf-8 -*-
@Project: picture
@File: archivist
@Author: zander
@Date: 2024/11/9 11:02
@Software: PyCharm
@Description: 文件归档 - 写入 SQLite 数据库、写入 MarkDown 文件展示
"""
import os
from lxml import etree
from src.utils import DataBase, FileUtils, DateUtils
class ArchivistUtil:
def __init__(self):
d... | Zander-Hwang/picture | src/archivist.py | .py | 7402a45188cfe769 | 7 | 0 |
"""
# -*- coding: utf-8 -*-
@Project: picture
@File: remote
@Author: zander
@Date: 2024/11/6 22:55
@Software: PyCharm
@Description: 远程图片 -- 爬虫
"""
from src.utils import DateUtils
from src.utils import FetchUtils
from src.archivist import ArchivistUtil
class RemoteReq:
def __init__(self):
self.get_bing_wa... | Zander-Hwang/picture | src/remote.py | .py | df50e72d533eb2e9 | 7 | 0 |
"""
# -*- coding: utf-8 -*-
@File: dateutils
@Author: zander
@Date: 2024/10/21 14:12
@Software: PyCharm
@Description: 时间处理工具类
"""
import time
class DateUtils:
@staticmethod
def sleep(secs):
time.sleep(secs)
@staticmethod
def time():
return time.time()
@staticmethod
def loca... | Zander-Hwang/picture | src/utils/dateutils.py | .py | 656504ea057f9a74 | 7 | 0 |
"""
# -*- coding: utf-8 -*-
@File: fetchutils
@Author: zander
@Date: 2024/11/3 22:54
@Software: PyCharm
@Description: 请求方法封装
"""
import os
import requests
from .useragent import UserAgent
from .dateutils import DateUtils
class FetchUtils:
def __init__(self, method, url, **args):
self.request(method=metho... | Zander-Hwang/picture | src/utils/fetchutils.py | .py | ccc79d8fbcc8718c | 7 | 0 |
"""
# -*- coding: utf-8 -*-
@File: readfile
@Author: zander
@Date: 2024/10/20 12:03
@Software: PyCharm
@Description: 文件读取方法类
"""
import json
import os
TYPE_LIST = {
'3c68313ee689abe68f8f': 'html',
'504B0304140006000800': 'xlsx',
'504b0304140008080800': 'docx',
"d0cf11e0a1b11ae10000": 'doc/xls/vsd',
... | Zander-Hwang/picture | src/utils/fileutils.py | .py | 2c6b49143c85dcb4 | 7 | 0 |
"""
# -*- coding: utf-8 -*-
@File: urlparse
@Author: zander
@Date: 2024/10/20 11:16
@Software: PyCharm
@Description: 解析URL字符返回对应组成部分
"""
from urllib.parse import urlparse
class ParseUrl:
url_dict = {}
def __init__(self, url):
self.url_dict = self.get_url_parts(url)
@staticmethod
def get_url_... | Zander-Hwang/picture | src/utils/parseurl.py | .py | 5ab8df67902851b7 | 7 | 0 |
"""
# -*- coding: utf-8 -*-
@File: useragent
@Author: zander
@Date: 2024/11/4 15:17
@Software: PyCharm
@Description: 获取userAgent列表
"""
import glob
from lxml import etree
import requests
from .dateutils import DateUtils
import os
import random
class UserAgent:
fileAbsPath = os.path.dirname(__file__)
url = 'ht... | Zander-Hwang/picture | src/utils/useragent.py | .py | 625686af4f522c44 | 7 | 0 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
from typing import cast, Tuple, List
import logging
import torch
from torch import nn
from torch import Tensor
import gymnasium as gym
from stable_baselines3.common.torch_layers import FlattenExtractor, create_mlp
from stable_baselines3.common.distributions import make_pr... | mphe/upside-down-reinforcement-learning | UDRL/behavior.py | .py | 02ed460b5bec9166 | 7.39 | 5 |
# Note: initially copied from https://github.com/florimondmanca/httpx-sse/blob/master/src/httpx_sse/_decoders.py
from __future__ import annotations
import json
import inspect
from types import TracebackType
from typing import TYPE_CHECKING, Any, Generic, TypeVar, Iterator, Optional, AsyncIterator, cast
from typing_ext... | Metronome-Industries/metronome-python | src/metronome/_streaming.py | .py | 3956199a190c2427 | 7.35 | 4 |
from __future__ import annotations
from os import PathLike
from typing import (
IO,
TYPE_CHECKING,
Any,
Dict,
List,
Type,
Tuple,
Union,
Mapping,
TypeVar,
Callable,
Iterable,
Iterator,
Optional,
Sequence,
AsyncIterable,
)
from typing_extensions import (
... | Metronome-Industries/metronome-python | src/metronome/_types.py | .py | 9334bdf07ea37c02 | 7.35 | 4 |
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