From d46b276c9c5127deeb4d3bbb400f870ff3fd541b Mon Sep 17 00:00:00 2001 From: PaulSharp <44529197+DrPaulSharp@users.noreply.github.com> Date: Thu, 23 Oct 2025 12:10:05 +0100 Subject: [PATCH 1/4] Upgrades minimum python version to 3.12 --- .github/workflows/test.yml | 3 ++- .gitignore | 8 +++++--- .pre-commit-config.yaml | 10 ++++++++++ conftest.py | 11 +++++++++++ pyproject.toml | 27 ++++++++++++++++++++++++++- requirements.txt | 13 +++++++++++++ 6 files changed, 67 insertions(+), 5 deletions(-) create mode 100644 .pre-commit-config.yaml create mode 100644 conftest.py diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 343fed71..e4d11c39 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -15,6 +15,7 @@ jobs: - uses: actions/checkout@v4 - uses: astral-sh/ruff-action@v3 with: + version: "latest" args: "check --fix-only --exit-non-zero-on-fix" - uses: pre-commit-ci/lite-action@v1.1.0 if: always() @@ -27,7 +28,7 @@ jobs: strategy: matrix: os: [macos-latest, ubuntu-latest, windows-latest] - python-version: ['3.10', '3.11', '3.12'] + python-version: ['3.12'] fail-fast: false env: diff --git a/.gitignore b/.gitignore index d19967b4..26302d4d 100644 --- a/.gitignore +++ b/.gitignore @@ -25,6 +25,11 @@ /dist .mplconfig +# INSTALL.md recommends a venv that should not be committed +venv +.venv +uv.lock + # doc build /docs/sphinx-docs/build @@ -42,6 +47,3 @@ tests.log /installers/dist *.exe sasdata/_version.py - -# Local pre-commit hooks -.pre-commit-config.yaml diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 00000000..e75be384 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,10 @@ +default_install_hook_types: [pre-commit, pre-push] + +repos: + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.14.1 + hooks: + # Run the linter, applying any available fixes + - id: ruff-check + stages: [ pre-commit, pre-push ] + args: [ --fix-only ] diff --git a/conftest.py b/conftest.py new file mode 100644 index 00000000..2206968d --- /dev/null +++ b/conftest.py @@ -0,0 +1,11 @@ +import pytest + + +def pytest_addoption(parser): + parser.addoption( + "--show_plots", action="store_true", default=False, help="Display diagnostic plots during tests" + ) + +@pytest.fixture +def show_plots(request): + return request.config.getoption("--show_plots") diff --git a/pyproject.toml b/pyproject.toml index 402e4cd5..71b1b2cf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,7 +20,7 @@ dynamic = [ ] description = "Sas Data Loader application" readme = "README.md" -requires-python = ">=3.9" +requires-python = ">=3.12" license = { text = "BSD-3-Clause" } authors = [ {name = "SasView Team", email = "developers@sasview.org"}, @@ -118,3 +118,28 @@ testpaths = [ norecursedirs = [ "sasdata", ] + +[tool.ruff] +line-length = 120 + +[tool.ruff.lint] +# The ruff rules are available at: https://docs.astral.sh/ruff/rules/ +select = ["E", # pycodestyle errors + "F", # pyflakes + "I", # isort + "UP", # pyupgrade + "W", # pycodestyle warnings + "SIM118", # Use `key in dict` instead of `key in dict.keys()` + "SIM300"] # Yoda condition detected + + +ignore = ["E501", # line too long (leave to formatter) + "UP008", # Use `super()` instead of `super(__class__, self)` + "UP031"] # Use format specifiers instead of percent format + +[tool.ruff.lint.isort.sections] +# Group all SasView and SasModels imports into a separate section. +"sas" = ["sas", "sasmodels"] + +[tool.ruff.lint.isort] +section-order = ["future", "standard-library", "third-party", "sas", "first-party", "local-folder"] diff --git a/requirements.txt b/requirements.txt index 337e5f04..463703b1 100644 --- a/requirements.txt +++ b/requirements.txt @@ -4,3 +4,16 @@ lxml # Calculation numpy +scipy + +# Unit testing +pytest +unittest-xml-reporting + +# Documentation (future) +sphinx +html5lib + +# Other stuff +matplotlib +pre-commit From 4df4d2a9aaee257b6a99ef875b5fc3d4194d6136 Mon Sep 17 00:00:00 2001 From: PaulSharp <44529197+DrPaulSharp@users.noreply.github.com> Date: Thu, 23 Oct 2025 12:18:31 +0100 Subject: [PATCH 2/4] Applies automatic ruff fixes --- sasdata/data_util/formatnum.py | 12 +- sasdata/data_util/loader_exceptions.py | 9 +- sasdata/data_util/manipulations.py | 8 +- sasdata/data_util/nxsunit.py | 31 +-- sasdata/data_util/registry.py | 18 +- sasdata/data_util/uncertainty.py | 2 +- sasdata/data_util/util.py | 4 +- sasdata/dataloader/__init__.py | 2 +- sasdata/dataloader/data_info.py | 37 ++-- sasdata/dataloader/filereader.py | 26 ++- sasdata/dataloader/loader.py | 25 +-- sasdata/dataloader/readers/__init__.py | 2 +- sasdata/dataloader/readers/abs_reader.py | 2 +- .../readers/anton_paar_saxs_reader.py | 19 +- sasdata/dataloader/readers/ascii_reader.py | 15 +- sasdata/dataloader/readers/associations.py | 20 +- sasdata/dataloader/readers/cansas_reader.py | 65 +++--- .../dataloader/readers/cansas_reader_HDF5.py | 205 +++++++++--------- sasdata/dataloader/readers/csv_reader.py | 1 + sasdata/dataloader/readers/danse_reader.py | 19 +- sasdata/dataloader/readers/red2d_reader.py | 5 +- sasdata/dataloader/readers/sesans_reader.py | 4 +- sasdata/dataloader/readers/tiff_reader.py | 6 +- sasdata/dataloader/readers/xml_reader.py | 3 +- .../file_converter/FileConverterUtilities.py | 13 +- sasdata/file_converter/ascii2d_loader.py | 31 ++- sasdata/file_converter/bsl_loader.py | 8 +- sasdata/file_converter/cansas_writer.py | 2 +- sasdata/file_converter/nxcansas_writer.py | 19 +- sasdata/file_converter/otoko_loader.py | 2 +- sasdata/file_converter/red2d_writer.py | 1 + test/fileconverter/utest_bsl_loader.py | 2 +- test/fileconverter/utest_nxcansas_writer.py | 6 +- test/run_one.py | 10 +- test/sasdataloader/error_conditions.py | 5 +- test/sasdataloader/utest_abs_reader.py | 4 +- test/sasdataloader/utest_ascii.py | 12 +- test/sasdataloader/utest_averaging.py | 15 +- test/sasdataloader/utest_cansas.py | 12 +- .../sasdataloader/utest_extension_registry.py | 5 +- .../utest_generic_file_reader_class.py | 7 +- test/sasdataloader/utest_red2d_reader.py | 6 +- test/sasdataloader/utest_sesans.py | 3 +- test/sasmanipulations/utest_manipulations.py | 2 +- test/utest_sasdata.py | 8 +- 45 files changed, 381 insertions(+), 332 deletions(-) diff --git a/sasdata/data_util/formatnum.py b/sasdata/data_util/formatnum.py index f3c5566b..e706880b 100644 --- a/sasdata/data_util/formatnum.py +++ b/sasdata/data_util/formatnum.py @@ -37,7 +37,9 @@ formatter.compact flag. """ import math + import numpy as np + __all__ = ['format_uncertainty', 'format_uncertainty_pm', 'format_uncertainty_compact'] @@ -85,7 +87,7 @@ class UncertaintyFormatter: True or False. The default is True. """ compact = True - + def __call__(self, value, uncertainty): """ Given *value* and *uncertainty*, return a string representation. @@ -140,7 +142,7 @@ def _format_uncertainty(value, uncertainty, compact): # Extreme cases: zeros before value or after error # The value is ###.###(##)e#, ##.####(##)e# or #.#####(##)e# pass - + # Force engineering notation, with exponent a multiple of 3 val_place = int(math.floor(val_place / 3.)) * 3 @@ -279,7 +281,7 @@ def test_compact(): assert value_str(-np.inf,None) == "-inf" assert value_str(np.inf,None) == "inf" assert value_str(np.nan,None) == "NaN" - + # bad or missing uncertainty assert value_str(-1.23567,np.nan) == "-1.23567" assert value_str(-1.23567,-np.inf) == "-1.23567" @@ -410,7 +412,7 @@ def test_pm(): assert value_str(-np.inf,None) == "-inf" assert value_str(np.inf,None) == "inf" assert value_str(np.nan,None) == "NaN" - + # bad or missing uncertainty assert value_str(-1.23567,np.nan) == "-1.23567" assert value_str(-1.23567,-np.inf) == "-1.23567" @@ -432,7 +434,7 @@ def main(): test_compact() test_pm() test_default() - + import doctest doctest.testmod() diff --git a/sasdata/data_util/loader_exceptions.py b/sasdata/data_util/loader_exceptions.py index c9a19a27..7075687a 100644 --- a/sasdata/data_util/loader_exceptions.py +++ b/sasdata/data_util/loader_exceptions.py @@ -2,7 +2,6 @@ Exceptions specific to loading data. """ -from typing import Optional class NoKnownLoaderException(Exception): @@ -11,7 +10,7 @@ class NoKnownLoaderException(Exception): extension of the loaded file. This exception should only be thrown by loader.py. """ - def __init__(self, e: Optional[str] = None): + def __init__(self, e: str | None = None): self.message = e @@ -20,7 +19,7 @@ class DefaultReaderException(Exception): Exception for files with no associated reader. This should be thrown by default readers only to tell Loader to try the next reader. """ - def __init__(self, e: Optional[str] = None): + def __init__(self, e: str | None = None): self.message = e @@ -29,7 +28,7 @@ class FileContentsException(Exception): Exception for files with an associated reader, but with no loadable data. This is useful for catching loader or file format issues. """ - def __init__(self, e: Optional[str] = None): + def __init__(self, e: str | None = None): self.message = e @@ -39,5 +38,5 @@ class DataReaderException(Exception): along the way. Any exceptions of this type should be put into the datainfo.errors """ - def __init__(self, e: Optional[str] = None): + def __init__(self, e: str | None = None): self.message = e diff --git a/sasdata/data_util/manipulations.py b/sasdata/data_util/manipulations.py index 65be6532..c470d3fb 100644 --- a/sasdata/data_util/manipulations.py +++ b/sasdata/data_util/manipulations.py @@ -20,8 +20,8 @@ # TODO: copy the meta data from the 2D object to the resulting 1D object import math + import numpy as np -from typing import Optional, Union from sasdata.dataloader.data_info import Data1D, Data2D @@ -41,7 +41,7 @@ def position_and_wavelength_to_q(dx: float, dy: float, detector_distance: float, return (4.0 * math.pi / wavelength) * math.sin(theta) -def get_q_compo(dx: float, dy: float, detector_distance: float, wavelength: float, compo: Optional[str] = None) -> float: +def get_q_compo(dx: float, dy: float, detector_distance: float, wavelength: float, compo: str | None = None) -> float: """ This reduces tiny error at very large q. Implementation of this func is not started yet.<--ToDo @@ -102,7 +102,7 @@ def get_pixel_fraction_square(x: float, x_min: float, x_max: float) -> float: return 1.0 -def get_intercept(q: float, q_0: float, q_1: float) -> Union[float, None]: +def get_intercept(q: float, q_0: float, q_1: float) -> float | None: """ Returns the fraction of the side at which the q-value intercept the pixel, None otherwise. @@ -235,7 +235,7 @@ def get_dq_data(data2d: Data2D) -> np.array: ################################################################################ -def reader2D_converter(data2d: Optional[Data2D] = None) -> Data2D: +def reader2D_converter(data2d: Data2D | None = None) -> Data2D: """ convert old 2d format opened by IhorReader or danse_reader to new Data2D format diff --git a/sasdata/data_util/nxsunit.py b/sasdata/data_util/nxsunit.py index 19d611b3..2e3d948c 100644 --- a/sasdata/data_util/nxsunit.py +++ b/sasdata/data_util/nxsunit.py @@ -45,11 +45,12 @@ import math import re -from typing import Dict, Union, TypeVar, Tuple, Sequence, Optional, List +from collections.abc import Sequence +from typing import TypeVar, Union __all__ = ['Converter', 'standardize_units'] T = TypeVar('T') -ConversionType = Union[float, Tuple[float, float]] +ConversionType = Union[float, tuple[float, float]] DIMENSIONS = {} # type: Dict[str, Dict[str, ConversionType]] AMBIGUITIES = {} # type: Dict[str, str] PREFIX = dict(peta=1e15, tera=1e12, giga=1e9, mega=1e6, kilo=1e3, deci=1e-1, centi=1e-2, milli=1e-3, mili=1e-3, @@ -60,7 +61,7 @@ # Limited form of units for returning objects of a specific type. # Maybe want to do full units handling with e.g., pyre's # unit class. For now lets keep it simple. Note that -def _build_metric_units(unit: str, abbr: str) -> Dict[str, float]: +def _build_metric_units(unit: str, abbr: str) -> dict[str, float]: """ Construct standard SI names for the given unit. Builds e.g., @@ -89,7 +90,7 @@ def _build_metric_units(unit: str, abbr: str) -> Dict[str, float]: return units -def _build_plural_units(**kw: Dict[str, ConversionType]) -> Dict[str, ConversionType]: +def _build_plural_units(**kw: dict[str, ConversionType]) -> dict[str, ConversionType]: """ Construct names for the given units. Builds singular and plural form. """ @@ -99,7 +100,7 @@ def _build_plural_units(**kw: Dict[str, ConversionType]) -> Dict[str, Conversion return units -def _build_degree_units(name: str, symbol: str, conversion: ConversionType) -> Dict[str, ConversionType]: +def _build_degree_units(name: str, symbol: str, conversion: ConversionType) -> dict[str, ConversionType]: """ Builds variations on the temperature unit name, including the degree symbol or the word degree. @@ -118,7 +119,7 @@ def _build_degree_units(name: str, symbol: str, conversion: ConversionType) -> D def _build_inv_n_units(names: Sequence[str], conversion: ConversionType, - n: int = 2) -> Dict[str, ConversionType]: + n: int = 2) -> dict[str, ConversionType]: """ Builds variations on inverse x to the nth power units, including 1/x^n, invx^n, x^-n and x^{-n}. """ @@ -132,7 +133,7 @@ def _build_inv_n_units(names: Sequence[str], conversion: ConversionType, return units -def _build_inv_n_metric_units(unit: str, abbr: str, n: int = 2) -> Dict[str, ConversionType]: +def _build_inv_n_metric_units(unit: str, abbr: str, n: int = 2) -> dict[str, ConversionType]: """ Using the return from _build_metric_units, build inverse to the nth power variations on all units (1/x^n, invx^n, x^{-n} and x^-n) @@ -265,7 +266,7 @@ def _build_all_units(): DIMENSIONS['dimensionless'] = unknown -def standardize_units(unit: Union[str, None]) -> List[str]: +def standardize_units(unit: str | None) -> list[str]: """ Convert supplied units to a standard format for maintainability :param unit: Raw unit as supplied @@ -301,7 +302,7 @@ def standardize_units(unit: Union[str, None]) -> List[str]: return _format_unit_structure(unit) -def _format_unit_structure(unit: Optional[str] = None) -> List[str]: +def _format_unit_structure(unit: str | None = None) -> list[str]: """ Format units a common way :param unit: Unit string to be formatted @@ -373,7 +374,7 @@ def units(self) -> str: def units(self, unit: str): self._units = standardize_units(unit) - def __init__(self, units: Optional[str] = None, dimension: Optional[List[str]] = None): + def __init__(self, units: str | None = None, dimension: list[str] | None = None): self.units = units if units is not None else 'a.u.' # type: str # Lookup dimension if not given @@ -398,20 +399,20 @@ def __init__(self, units: Optional[str] = None, dimension: Optional[List[str]] = self.scalebase = base[0] self.scaleoffset = base[1] - def scale(self, units: str = "", value: T = None) -> Union[List[float], T]: + def scale(self, units: str = "", value: T = None) -> list[float] | T: """Scale the given value using the units string supplied""" units = standardize_units(units) if units is not None else [''] base = self._get_scale_for_units(units) value = self._scale_with_offset(value, base) return value - def _scale_with_offset(self, value: float, scale_base: Tuple[float, float]) -> float: + def _scale_with_offset(self, value: float, scale_base: tuple[float, float]) -> float: """Scale the given value and add the offset using the units string supplied""" inscale, inoffset = self.scalebase, self.scaleoffset outscale, outoffset = scale_base return (value + outoffset) * inscale / outscale - inoffset - def _get_scale_for_units(self, units: List[str]): + def _get_scale_for_units(self, units: list[str]): """Protected method to get scale factor and scale offset as a combined value""" base = (1.0, 0.0) for scalemap, unit in zip(self.scalemap, units): @@ -423,7 +424,7 @@ def _get_scale_for_units(self, units: List[str]): base = (base[0] * unit_scale[0], base[1] + unit_scale[1]) return base - def get_compatible_units(self) -> List[str]: + def get_compatible_units(self) -> list[str]: """Return a list of compatible units for the current Convertor object""" unique_units = [] conv_list = [] @@ -436,7 +437,7 @@ def get_compatible_units(self) -> List[str]: unique_units = [x for _, x in sorted(zip(conv_list, unique_units))] return unique_units - def __call__(self, value: T, units: Optional[str] = "") -> Union[List[float], T]: + def __call__(self, value: T, units: str | None = "") -> list[float] | T: # Note: calculating a*1 rather than simply returning a would produce # an unnecessary copy of the array, which in the case of the raw # counts array would be bad. Sometimes copying and other times diff --git a/sasdata/data_util/registry.py b/sasdata/data_util/registry.py index 7812dcfa..a5d2ec50 100644 --- a/sasdata/data_util/registry.py +++ b/sasdata/data_util/registry.py @@ -5,11 +5,11 @@ and registers the built-in file extensions. """ import os -from urllib.request import urlopen -from io import BytesIO -from typing import Optional, List, Union, TYPE_CHECKING from collections import defaultdict +from io import BytesIO from pathlib import Path +from typing import TYPE_CHECKING, Union +from urllib.request import urlopen from sasdata.data_util.loader_exceptions import NoKnownLoaderException from sasdata.data_util.util import unique_preserve_order @@ -25,7 +25,7 @@ "was made, but, should it be successful, SasView cannot guarantee the accuracy of the data.") -def create_empty_data_with_errors(path: Union[str, Path], errors: List[Exception]): +def create_empty_data_with_errors(path: str | Path, errors: list[Exception]): """Create a Data1D instance that only holds errors and a filepath. This allows all file paths to return a common data type, regardless if the data loading was successful or a failure.""" from sasdata.dataloader.data_info import Data1D @@ -121,13 +121,13 @@ def __init__(self): def __setitem__(self, ext: str, loader): self.readers[ext].insert(0, loader) - def __getitem__(self, ext: str) -> List: + def __getitem__(self, ext: str) -> list: return self.readers[ext] def __contains__(self, ext: str) -> bool: return ext in self.readers - def formats(self) -> List[str]: + def formats(self) -> list[str]: """ Return a sorted list of the registered formats. """ @@ -135,7 +135,7 @@ def formats(self) -> List[str]: names.sort() return names - def extensions(self) -> List[str]: + def extensions(self) -> list[str]: """ Return a sorted list of registered extensions. """ @@ -143,7 +143,7 @@ def extensions(self) -> List[str]: exts.sort() return exts - def lookup(self, path: str) -> List[callable]: + def lookup(self, path: str) -> list[callable]: """ Return the loader associated with the file type of path. @@ -162,7 +162,7 @@ def lookup(self, path: str) -> List[callable]: # Ensure the list of readers only includes unique values and the order is maintained return unique_preserve_order(readers) - def load(self, path: str, ext: Optional[str] = None) -> List[Union["Data1D", "Data2D"]]: + def load(self, path: str, ext: str | None = None) -> list[Union["Data1D", "Data2D"]]: """ Call the loader for a single file. diff --git a/sasdata/data_util/uncertainty.py b/sasdata/data_util/uncertainty.py index 3aa24eff..c57f713c 100644 --- a/sasdata/data_util/uncertainty.py +++ b/sasdata/data_util/uncertainty.py @@ -23,7 +23,7 @@ # TODO: rename to Measurement and add support for units? # TODO: C implementation of *,/,**? -class Uncertainty(object): +class Uncertainty: # Make standard deviation available def _getdx(self): return np.sqrt(self.variance) def _setdx(self,dx): diff --git a/sasdata/data_util/util.py b/sasdata/data_util/util.py index 6323fb28..5923735f 100644 --- a/sasdata/data_util/util.py +++ b/sasdata/data_util/util.py @@ -1,7 +1,7 @@ -from typing import List, Any +from typing import Any -def unique_preserve_order(seq: List[Any]) -> List[Any]: +def unique_preserve_order(seq: list[Any]) -> list[Any]: """ Remove duplicates from list preserving order Fastest according to benchmarks at https://www.peterbe.com/plog/uniqifiers-benchmark """ diff --git a/sasdata/dataloader/__init__.py b/sasdata/dataloader/__init__.py index a1f73470..a59e1705 100644 --- a/sasdata/dataloader/__init__.py +++ b/sasdata/dataloader/__init__.py @@ -1,3 +1,3 @@ -from sasdata.dataloader.data_info import * from sasdata.data_util.manipulations import * +from sasdata.dataloader.data_info import * from sasdata.dataloader.readers import * diff --git a/sasdata/dataloader/data_info.py b/sasdata/dataloader/data_info.py index 21359282..b5c23bd4 100644 --- a/sasdata/dataloader/data_info.py +++ b/sasdata/dataloader/data_info.py @@ -19,16 +19,16 @@ # TODO: This module should be independent of plottables. We should write # an adapter class for plottables when needed. +import copy import math from math import fabs -import copy import numpy as np from sasdata.data_util.uncertainty import Uncertainty -class plottable_1D(object): +class plottable_1D: """ Data1D is a place holder for 1D plottables. """ @@ -84,7 +84,7 @@ def yaxis(self, label, unit): self._yunit = unit -class plottable_2D(object): +class plottable_2D: """ Data2D is a place holder for 2D plottables. """ @@ -164,7 +164,7 @@ def zaxis(self, label, unit): self._zunit = unit -class Vector(object): +class Vector: """ Vector class to hold multi-dimensional objects """ @@ -193,7 +193,7 @@ def __str__(self): return msg -class Detector(object): +class Detector: """ Class to hold detector information """ @@ -248,7 +248,7 @@ def __str__(self): return _str -class Aperture(object): +class Aperture: # Name name = None # Type @@ -266,7 +266,7 @@ def __init__(self): self.size = Vector() -class Collimation(object): +class Collimation: """ Class to hold collimation information """ @@ -293,7 +293,7 @@ def __str__(self): return _str -class Source(object): +class Source: """ Class to hold source information """ @@ -358,7 +358,7 @@ def __str__(self): ELECTRON = 'electron' -class Sample(object): +class Sample: """ Class to hold the sample description """ @@ -411,7 +411,7 @@ def __str__(self): return _str -class Process(object): +class Process: """ Class that holds information about the processes performed on the data. @@ -452,7 +452,7 @@ def __str__(self): return _str -class TransmissionSpectrum(object): +class TransmissionSpectrum: """ Class that holds information about transmission spectrum for white beams and spallation sources. @@ -476,19 +476,18 @@ def __init__(self): def __str__(self): _str = "Transmission Spectrum:\n" - _str += " Name: \t{0}\n".format(self.name) - _str += " Timestamp: \t{0}\n".format(self.timestamp) - _str += " Wavelength unit: \t{0}\n".format(self.wavelength_unit) - _str += " Transmission unit:\t{0}\n".format(self.transmission_unit) - _str += " Trans. Dev. unit: \t{0}\n".format( - self.transmission_deviation_unit) + _str += f" Name: \t{self.name}\n" + _str += f" Timestamp: \t{self.timestamp}\n" + _str += f" Wavelength unit: \t{self.wavelength_unit}\n" + _str += f" Transmission unit:\t{self.transmission_unit}\n" + _str += f" Trans. Dev. unit: \t{self.transmission_deviation_unit}\n" length_list = [len(self.wavelength), len(self.transmission), len(self.transmission_deviation)] - _str += " Number of Pts: \t{0}\n".format(max(length_list)) + _str += f" Number of Pts: \t{max(length_list)}\n" return _str -class DataInfo(object): +class DataInfo: """ Class to hold the data read from a file. It includes four blocks of data for the diff --git a/sasdata/dataloader/filereader.py b/sasdata/dataloader/filereader.py index 4ca5bce8..aa6c6edb 100644 --- a/sasdata/dataloader/filereader.py +++ b/sasdata/dataloader/filereader.py @@ -8,14 +8,20 @@ import logging from abc import abstractmethod from pathlib import Path -from typing import List, Union, Optional import numpy as np + from sasdata.data_util.loader_exceptions import NoKnownLoaderException -from sasdata.dataloader.data_info import Data1D, Data2D, DataInfo, plottable_1D, plottable_2D,\ - combine_data_info_with_plottable from sasdata.data_util.nxsunit import Converter from sasdata.data_util.registry import CustomFileOpen +from sasdata.dataloader.data_info import ( + Data1D, + Data2D, + DataInfo, + combine_data_info_with_plottable, + plottable_1D, + plottable_2D, +) logger = logging.getLogger(__name__) @@ -73,8 +79,8 @@ def __init__(self): # Open file handle self.f_open = None - def read(self, filepath: Union[str, Path], file_handler: Optional[CustomFileOpen] = None, - f_pos: Optional[int] = 0) -> List[Union[Data1D, Data2D]]: + def read(self, filepath: str | Path, file_handler: CustomFileOpen | None = None, + f_pos: int | None = 0) -> list[Data1D | Data2D]: """ Basic file reader @@ -92,7 +98,7 @@ def read(self, filepath: Union[str, Path], file_handler: Optional[CustomFileOpen return self._read(file_handler) return self._read(file_handler) - def _read(self, file_handler: CustomFileOpen) -> List[Union[Data1D, Data2D]]: + def _read(self, file_handler: CustomFileOpen) -> list[Data1D | Data2D]: """ Private method to handle file loading @@ -274,7 +280,7 @@ def _reorder_1d_array(array: np.array, ind: int) -> np.array: return array[ind] @staticmethod - def _remove_nans_in_data(data: Union[Data1D, Data2D]) -> Union[Data1D, Data2D]: + def _remove_nans_in_data(data: Data1D | Data2D) -> Data1D | Data2D: """ Remove data points where nan is loaded :param data: 1D or 2D data object @@ -301,7 +307,7 @@ def _remove_nans_in_data(data: Union[Data1D, Data2D]) -> Union[Data1D, Data2D]: return data @staticmethod - def set_default_1d_units(data: Union[Data1D, Data2D]) -> Union[Data1D, Data2D]: + def set_default_1d_units(data: Data1D | Data2D) -> Data1D | Data2D: """ Set the x and y axes to the default 1D units :param data: 1D data set @@ -312,7 +318,7 @@ def set_default_1d_units(data: Union[Data1D, Data2D]) -> Union[Data1D, Data2D]: return data @staticmethod - def set_default_2d_units(data: Union[Data1D, Data2D]) -> Union[Data1D, Data2D]: + def set_default_2d_units(data: Data1D | Data2D) -> Data1D | Data2D: """ Set the x and y axes to the default 2D units :param data: 2D data set @@ -494,7 +500,7 @@ def reset_data_list(self, no_lines: int = 0): self.current_dataset = plottable_1D(x, y, dx, dy) @staticmethod - def splitline(line: str) -> List[str]: + def splitline(line: str) -> list[str]: """ Splits a line into pieces based on common delimiters :param line: A single line of text diff --git a/sasdata/dataloader/loader.py b/sasdata/dataloader/loader.py index 91d1470b..e005a969 100644 --- a/sasdata/dataloader/loader.py +++ b/sasdata/dataloader/loader.py @@ -17,16 +17,15 @@ # copyright 2008, University of Tennessee ###################################################################### +import logging import os import sys -import logging import time -from zipfile import ZipFile from collections import defaultdict -from types import ModuleType -from typing import Optional, Union, List from itertools import zip_longest from pathlib import Path +from types import ModuleType +from zipfile import ZipFile from sasdata.data_util.registry import ExtensionRegistry from sasdata.data_util.util import unique_preserve_order @@ -59,10 +58,10 @@ def __init__(self): # Register default readers readers.read_associations(self) - def load(self, file_path_list: Union[List[Union[str, Path]], str, Path], - ext: Optional[Union[List[str], str]] = None, - debug: Optional[bool] = False, - use_defaults: Optional[bool] = True): + def load(self, file_path_list: list[str | Path] | str | Path, + ext: list[str] | str | None = None, + debug: bool | None = False, + use_defaults: bool | None = True): """ Call the loader for the file type of path. @@ -294,7 +293,7 @@ def lookup_writers(self, path): # All done return writers - def save(self, path: str, data, format: Optional[str] = None): + def save(self, path: str, data, format: str | None = None): """ Call the writer for the file type of path. Raises ValueError if no writer is available. @@ -337,9 +336,9 @@ def associate_file_reader(self, ext: str, loader) -> bool: """ return self.__registry.associate_file_reader(ext, loader) - def load(self, file_path_list: Union[List[Union[str, Path]], str, Path], - format: Optional[Union[List[str], str]] = None - ) -> List[Union[Data1D, Data2D]]: + def load(self, file_path_list: list[str | Path] | str | Path, + format: list[str] | str | None = None + ) -> list[Data1D | Data2D]: """ Load a file or series of files :param file_path_list: String representations of any number of file paths. This can either be a list or a string @@ -377,7 +376,7 @@ def get_wildcards(self): """ return self.__registry.wildcards - def __call__(self, file_path_list: List[str]) -> List[Union[Data1D, Data2D]]: + def __call__(self, file_path_list: list[str]) -> list[Data1D | Data2D]: """Allow direct calls to the loader system for transient file loader systems. :param file_path_list: A list of string representations of file paths. Each item can either be a local file path or a URI. diff --git a/sasdata/dataloader/readers/__init__.py b/sasdata/dataloader/readers/__init__.py index 66eff6ad..c41fc078 100644 --- a/sasdata/dataloader/readers/__init__.py +++ b/sasdata/dataloader/readers/__init__.py @@ -1,2 +1,2 @@ # Method to associate extensions to default readers -from .associations import read_associations, get_fallback_readers +from .associations import get_fallback_readers, read_associations diff --git a/sasdata/dataloader/readers/abs_reader.py b/sasdata/dataloader/readers/abs_reader.py index d4462c9e..72c01bf6 100644 --- a/sasdata/dataloader/readers/abs_reader.py +++ b/sasdata/dataloader/readers/abs_reader.py @@ -14,8 +14,8 @@ import numpy as np from sasdata.data_util.nxsunit import Converter -from sasdata.dataloader.filereader import FileReader from sasdata.dataloader.data_info import DataInfo, Detector +from sasdata.dataloader.filereader import FileReader logger = logging.getLogger(__name__) diff --git a/sasdata/dataloader/readers/anton_paar_saxs_reader.py b/sasdata/dataloader/readers/anton_paar_saxs_reader.py index 28509f64..f5468c85 100644 --- a/sasdata/dataloader/readers/anton_paar_saxs_reader.py +++ b/sasdata/dataloader/readers/anton_paar_saxs_reader.py @@ -2,14 +2,23 @@ CanSAS 2D data reader for reading HDF5 formatted CanSAS files. """ + import numpy as np -from typing import Optional from lxml.etree import Element +from sasdata.data_util.loader_exceptions import DataReaderException, FileContentsException +from sasdata.dataloader.data_info import ( + Aperture, + Collimation, + DataInfo, + Detector, + Process, + Sample, + Source, + TransmissionSpectrum, + plottable_1D, +) from sasdata.dataloader.readers.xml_reader import XMLreader -from sasdata.dataloader.data_info import plottable_1D, DataInfo, Sample, Source -from sasdata.dataloader.data_info import Process, Aperture, Collimation, TransmissionSpectrum, Detector -from sasdata.data_util.loader_exceptions import FileContentsException, DataReaderException class Reader(XMLreader): @@ -127,7 +136,7 @@ def read_data(self): if not correctly_loaded: raise DataReaderException(error_message) - def _parse_child(self, dom: Element, parent: Optional[str] = ''): + def _parse_child(self, dom: Element, parent: str | None = ''): """ Recursive method for stepping through the embedded XML :param dom: XML node with or without children diff --git a/sasdata/dataloader/readers/ascii_reader.py b/sasdata/dataloader/readers/ascii_reader.py index 2659c671..2cbd02ee 100644 --- a/sasdata/dataloader/readers/ascii_reader.py +++ b/sasdata/dataloader/readers/ascii_reader.py @@ -13,11 +13,10 @@ ############################################################################# import logging -from typing import Optional -from sasdata.dataloader.filereader import FileReader +from sasdata.data_util.loader_exceptions import DefaultReaderException, FileContentsException from sasdata.dataloader.data_info import DataInfo, plottable_1D -from sasdata.data_util.loader_exceptions import FileContentsException, DefaultReaderException +from sasdata.dataloader.filereader import FileReader logger = logging.getLogger(__name__) @@ -135,23 +134,23 @@ def get_file_contents(self): self.set_all_to_none() if self.extension in self.ext: msg = "ASCII Reader error: Fewer than five Q data points found " - msg += "in {}.".format(filename) + msg += f"in {filename}." raise FileContentsException(msg) else: - msg = "ASCII Reader could not load the file {}".format(filename) + msg = f"ASCII Reader could not load the file {filename}" raise DefaultReaderException(msg) # Sanity check if has_error_dy and not len(self.current_dataset.y) == \ len(self.current_dataset.dy): msg = "ASCII Reader error: Number of I and dI data points are" - msg += " different in {}.".format(filename) + msg += f" different in {filename}." # TODO: Add error to self.current_datainfo.errors instead? self.set_all_to_none() raise FileContentsException(msg) if has_error_dx and not len(self.current_dataset.x) == \ len(self.current_dataset.dx): msg = "ASCII Reader error: Number of Q and dQ data points are" - msg += " different in {}.".format(filename) + msg += f" different in {filename}." # TODO: Add error to self.current_datainfo.errors instead? self.set_all_to_none() raise FileContentsException(msg) @@ -163,7 +162,7 @@ def get_file_contents(self): self.current_datainfo.meta_data['loader'] = self.type_name self.send_to_output() - def write(self, filename: str, dataset: plottable_1D, sep: Optional[str] = " "): + def write(self, filename: str, dataset: plottable_1D, sep: str | None = " "): """ Output data in ascii or similar format, depending on the separator provided diff --git a/sasdata/dataloader/readers/associations.py b/sasdata/dataloader/readers/associations.py index fc171fef..0f4316fb 100644 --- a/sasdata/dataloader/readers/associations.py +++ b/sasdata/dataloader/readers/associations.py @@ -15,15 +15,17 @@ ############################################################################# import logging -from . import abs_reader -from . import anton_paar_saxs_reader -from . import ascii_reader -from . import cansas_reader -from . import cansas_reader_HDF5 -from . import csv_reader -from . import danse_reader -from . import red2d_reader -from . import sesans_reader +from . import ( + abs_reader, + anton_paar_saxs_reader, + ascii_reader, + cansas_reader, + cansas_reader_HDF5, + csv_reader, + danse_reader, + red2d_reader, + sesans_reader, +) logger = logging.getLogger(__name__) diff --git a/sasdata/dataloader/readers/cansas_reader.py b/sasdata/dataloader/readers/cansas_reader.py index f2fdfed2..be1baf60 100644 --- a/sasdata/dataloader/readers/cansas_reader.py +++ b/sasdata/dataloader/readers/cansas_reader.py @@ -1,24 +1,33 @@ -import logging -import os import datetime import inspect +import logging +import os from inspect import FrameInfo -from typing import Optional, Union +from xml.dom.minidom import parseString import numpy as np -from xml.dom.minidom import parseString from lxml import etree from lxml.etree import ElementTree +import sasdata.dataloader.readers.xml_reader as xml_reader +from sasdata.data_util.loader_exceptions import DefaultReaderException, FileContentsException from sasdata.data_util.nxsunit import Converter # For saving individual sections of data -from sasdata.dataloader.data_info import Data1D, Data2D, DataInfo, plottable_1D, plottable_2D, \ - Collimation, TransmissionSpectrum, Detector, Process, Aperture -from sasdata.data_util.loader_exceptions import FileContentsException, DefaultReaderException -import sasdata.dataloader.readers.xml_reader as xml_reader -from sasdata.dataloader.readers.xml_reader import XMLreader +from sasdata.dataloader.data_info import ( + Aperture, + Collimation, + Data1D, + Data2D, + DataInfo, + Detector, + Process, + TransmissionSpectrum, + plottable_1D, + plottable_2D, +) from sasdata.dataloader.readers.cansas_constants import CansasConstants +from sasdata.dataloader.readers.xml_reader import XMLreader logger = logging.getLogger(__name__) @@ -85,7 +94,7 @@ def get_file_contents(self): # Raises FileContentsException is_valid_cansas = self.load_file_and_schema(xml_file, '') except FileContentsException: - msg = "CanSAS Reader could not load {}".format(xml_file) + msg = f"CanSAS Reader could not load {xml_file}" if self.extension not in self.ext: # If the file has no associated loader raise DefaultReaderException(msg) @@ -119,7 +128,7 @@ def get_file_contents(self): # Convert all other exceptions to FileContentsExceptions raise FileContentsException(str(e)) - def load_file_and_schema(self, xml_file: str, schema_path: Optional[str] = "") -> bool: + def load_file_and_schema(self, xml_file: str, schema_path: str | None = "") -> bool: # Try and parse the XML file try: self.set_xml(xml_file) @@ -134,7 +143,7 @@ def load_file_and_schema(self, xml_file: str, schema_path: Optional[str] = "") - self.set_default_schema() return self.is_cansas(self.extension) - def is_cansas(self, ext: Optional[str] = "xml"): + def is_cansas(self, ext: str | None = "xml"): """ Checks to see if the XML file is a CanSAS file @@ -173,7 +182,7 @@ def set_default_schema(self): ) self.set_schema(schema_path) - def _parse_entry(self, dom: ElementTree, recurse: Optional[bool] = False) -> (Data1D, None): + def _parse_entry(self, dom: ElementTree, recurse: bool | None = False) -> (Data1D, None): if not self._is_call_local() and not recurse: self.reset_state() if not recurse: @@ -738,7 +747,7 @@ def _unit_conversion(self, node: ElementTree, tagname: str, node_value: float) - err_msg = "CanSAS reader: unexpected " err_msg += "\"{0}\" unit [{1}]; " err_msg = err_msg.format(tagname, local_unit) - err_msg += "expecting [{0}]".format(default_unit) + err_msg += f"expecting [{default_unit}]" value_unit = local_unit except Exception: err_msg = "CanSAS reader: unknown error converting " @@ -762,7 +771,7 @@ def _initialize_new_data_set(self, node=None): self.current_dataset = plottable_1D(np.array(0), np.array(0)) # Writing Methods - def write(self, filename: str, datainfo: Union[Data1D, Data2D]): + def write(self, filename: str, datainfo: Data1D | Data2D): """ Write the content of a Data1D as a CanSAS XML file @@ -779,7 +788,7 @@ def write(self, filename: str, datainfo: Union[Data1D, Data2D]): pretty_print=True, xml_declaration=True) file_ref.close() - def _to_xml_doc(self, datainfo: Union[Data1D, Data2D]): + def _to_xml_doc(self, datainfo: Data1D | Data2D): """ Create an XML document to contain the content of a Data1D @@ -835,7 +844,7 @@ def _to_xml_doc(self, datainfo: Union[Data1D, Data2D]): doc, entry_node = self._check_origin(entry_node, doc) return doc, entry_node - def write_node(self, parent: ElementTree, name: str, value: Union[float, str], attr: Optional[dict] = None) -> bool: + def write_node(self, parent: ElementTree, name: str, value: float | str, attr: dict | None = None) -> bool: """ :param doc: document DOM :param parent: parent node @@ -880,7 +889,7 @@ def _create_main_node(self) -> ElementTree: attrib=attrib, nsmap=nsmap) return main_node - def _write_run_names(self, datainfo: Union[Data1D, Data2D], entry_node: ElementTree): + def _write_run_names(self, datainfo: Data1D | Data2D, entry_node: ElementTree): """ Writes the run names to the XML file @@ -897,7 +906,7 @@ def _write_run_names(self, datainfo: Union[Data1D, Data2D], entry_node: ElementT runname = {'name': datainfo.run_name[item]} self.write_node(entry_node, "Run", item, runname) - def _write_data(self, datainfo: Union[Data1D, Data2D], entry_node: ElementTree): + def _write_data(self, datainfo: Data1D | Data2D, entry_node: ElementTree): """ Writes 1D I and Q data to the XML file @@ -940,7 +949,7 @@ def _write_data(self, datainfo: Union[Data1D, Data2D], entry_node: ElementTree): self.write_node(entry_node, "zacceptance", datainfo.sample.zacceptance[0], {'unit': datainfo.sample.zacceptance[1]}) - def _write_data_2d(self, datainfo: Union[Data1D, Data2D], entry_node: ElementTree): + def _write_data_2d(self, datainfo: Data1D | Data2D, entry_node: ElementTree): """ Writes 2D data to the XML file @@ -982,7 +991,7 @@ def _write_data_2d(self, datainfo: Union[Data1D, Data2D], entry_node: ElementTre mask = ','.join("1" if v else "0" for v in datainfo.mask) self.write_node(point, "Mask", mask) - def _write_trans_spectrum(self, datainfo: Union[Data1D, Data2D], entry_node: ElementTree): + def _write_trans_spectrum(self, datainfo: Data1D | Data2D, entry_node: ElementTree): """ Writes the transmission spectrum data to the XML file @@ -1010,7 +1019,7 @@ def _write_trans_spectrum(self, datainfo: Union[Data1D, Data2D], entry_node: Ele point, "Tdev", spectrum.transmission_deviation[i], {'unit': spectrum.transmission_deviation_unit}) - def _write_sample_info(self, datainfo: Union[Data1D, Data2D], entry_node: ElementTree): + def _write_sample_info(self, datainfo: Data1D | Data2D, entry_node: ElementTree): """ Writes the sample information to the XML file @@ -1059,7 +1068,7 @@ def _write_sample_info(self, datainfo: Union[Data1D, Data2D], entry_node: Elemen for item in datainfo.sample.details: self.write_node(sample, "details", item) - def _write_instrument(self, datainfo: Union[Data1D, Data2D], entry_node: ElementTree): + def _write_instrument(self, datainfo: Data1D | Data2D, entry_node: ElementTree): """ Writes the instrumental information to the XML file @@ -1071,7 +1080,7 @@ def _write_instrument(self, datainfo: Union[Data1D, Data2D], entry_node: Element self.write_node(instr, "name", datainfo.instrument) return instr - def _write_source(self, datainfo: Union[Data1D, Data2D], instr: ElementTree): + def _write_source(self, datainfo: Data1D | Data2D, instr: ElementTree): """ Writes the source information to the XML file @@ -1117,7 +1126,7 @@ def _write_source(self, datainfo: Union[Data1D, Data2D], instr: ElementTree): datainfo.source.wavelength_spread, {"unit": datainfo.source.wavelength_spread_unit}) - def _write_collimation(self, datainfo: Union[Data1D, Data2D], instr: ElementTree): + def _write_collimation(self, datainfo: Data1D | Data2D, instr: ElementTree): """ Writes the collimation information to the XML file @@ -1162,7 +1171,7 @@ def _write_collimation(self, datainfo: Union[Data1D, Data2D], instr: ElementTree self.write_node(apert, "distance", aperture.distance, {"unit": aperture.distance_unit}) - def _write_detectors(self, datainfo: Union[Data1D, Data2D], instr: ElementTree): + def _write_detectors(self, datainfo: Data1D | Data2D, instr: ElementTree): """ Writes the detector information to the XML file @@ -1228,7 +1237,7 @@ def _write_detectors(self, datainfo: Union[Data1D, Data2D], instr: ElementTree): self.write_node(det, "slit_length", item.slit_length, {"unit": item.slit_length_unit}) - def _write_process_notes(self, datainfo: Union[Data1D, Data2D], entry_node: ElementTree): + def _write_process_notes(self, datainfo: Data1D | Data2D, entry_node: ElementTree): """ Writes the process notes to the XML file @@ -1257,7 +1266,7 @@ def _write_process_notes(self, datainfo: Union[Data1D, Data2D], entry_node: Elem if len(item.notes) == 0: self.write_node(node, "SASprocessnote", "") - def _write_notes(self, datainfo: Union[Data1D, Data2D], entry_node: ElementTree): + def _write_notes(self, datainfo: Data1D | Data2D, entry_node: ElementTree): """ Writes the notes to the XML file and creates an empty note if none exist diff --git a/sasdata/dataloader/readers/cansas_reader_HDF5.py b/sasdata/dataloader/readers/cansas_reader_HDF5.py index dab5876b..3896cb6f 100644 --- a/sasdata/dataloader/readers/cansas_reader_HDF5.py +++ b/sasdata/dataloader/readers/cansas_reader_HDF5.py @@ -3,15 +3,26 @@ """ import logging -import h5py -import numpy as np import re import traceback -from typing import Any, Union, Optional +from typing import Any + +import h5py +import numpy as np -from sasdata.dataloader.data_info import plottable_1D, plottable_2D, Data1D, Data2D, DataInfo, Process, Aperture,\ - Collimation, TransmissionSpectrum, Detector from sasdata.data_util.loader_exceptions import FileContentsException +from sasdata.dataloader.data_info import ( + Aperture, + Collimation, + Data1D, + Data2D, + DataInfo, + Detector, + Process, + TransmissionSpectrum, + plottable_1D, + plottable_2D, +) from sasdata.dataloader.filereader import FileReader, decode logger = logging.getLogger(__name__) @@ -93,13 +104,13 @@ def reset_state(self): self.errors = [] self.logging = [] self.q_names = [] - self.mask_name = u'' - self.i_name = u'' - self.i_node = u'' - self.i_uncertainties_name = u'' + self.mask_name = '' + self.i_name = '' + self.i_node = '' + self.i_uncertainties_name = '' self.q_uncertainty_names = [] self.q_resolution_names = [] - self.parent_class = u'' + self.parent_class = '' self.detector = Detector() self.collimation = Collimation() self.aperture = Aperture() @@ -115,14 +126,14 @@ def read_children(self, data: dict, parent_list: list): """ # Loop through each element of the parent and process accordingly - for key in data.keys(): + for key in data: # Get all information for the current key value = data.get(key) - class_name = h5attr(value, u'canSAS_class') + class_name = h5attr(value, 'canSAS_class') if isinstance(class_name, (list, tuple, np.ndarray)): class_name = class_name[0] if class_name is None: - class_name = h5attr(value, u'NX_class') + class_name = h5attr(value, 'NX_class') if class_name is not None: class_prog = re.compile(class_name) else: @@ -135,9 +146,9 @@ def read_children(self, data: dict, parent_list: list): parent_list.append(key) # If a new sasentry, store the current data sets and create # a fresh Data1D/2D object - if class_prog.match(u'SASentry'): + if class_prog.match('SASentry'): self.add_data_set() - elif class_prog.match(u'SASdata'): + elif class_prog.match('SASdata'): self._find_data_attributes(value) self._initialize_new_data_set(value) # Recursion step to access data within the group @@ -166,7 +177,7 @@ def read_children(self, data: dict, parent_list: list): else: data_point = decode(data_point) # Top Level Meta Data - if key == u'definition': + if key == 'definition': if isinstance(data_set, str): self.current_datainfo.meta_data['reader'] = data_set break @@ -174,7 +185,7 @@ def read_children(self, data: dict, parent_list: list): self.current_datainfo.meta_data[ 'reader'] = data_point # Run - elif key == u'run': + elif key == 'run': try: run_name = h5attr(value, 'name', default='name') run_dict = {data_point: run_name} @@ -187,47 +198,47 @@ def read_children(self, data: dict, parent_list: list): else: self.current_datainfo.run.append(data_point) # Title - elif key == u'title': + elif key == 'title': if isinstance(data_set, str): self.current_datainfo.title = data_set break else: self.current_datainfo.title = data_point # Note - elif key == u'SASnote': + elif key == 'SASnote': self.current_datainfo.notes.append(data_set) break # Sample Information - elif self.parent_class == u'SASsample': + elif self.parent_class == 'SASsample': self.process_sample(data_point, key) # Instrumental Information - elif (key == u'name' - and self.parent_class == u'SASinstrument'): + elif (key == 'name' + and self.parent_class == 'SASinstrument'): self.current_datainfo.instrument = data_point # Detector - elif self.parent_class == u'SASdetector': + elif self.parent_class == 'SASdetector': self.process_detector(data_point, key, unit) # Collimation - elif self.parent_class == u'SAScollimation': + elif self.parent_class == 'SAScollimation': self.process_collimation(data_point, key, unit) # Aperture - elif self.parent_class == u'SASaperture': + elif self.parent_class == 'SASaperture': self.process_aperture(data_point, key) # Process Information - elif self.parent_class == u'SASprocess': # CanSAS 2.0 + elif self.parent_class == 'SASprocess': # CanSAS 2.0 self.process_process(data_point, key) # Source - elif self.parent_class == u'SASsource': + elif self.parent_class == 'SASsource': self.process_source(data_point, key, unit) # Everything else goes in meta_data - elif self.parent_class == u'SASdata': + elif self.parent_class == 'SASdata': if isinstance(self.current_dataset, plottable_2D): self.process_2d_data_object(data_set, key, unit) else: self.process_1d_data_object(data_set, key, unit) break - elif self.parent_class == u'SAStransmission_spectrum': + elif self.parent_class == 'SAStransmission_spectrum': self.process_trans_spectrum(data_set, key) break else: @@ -281,7 +292,7 @@ def process_1d_data_object(self, data_set: np.array, key: str, unit: str): self.current_dataset.dx = data_set.flatten() elif key == self.mask_name: self.current_dataset.mask = data_set.flatten() - elif key == u'wavelength': + elif key == 'wavelength': self.current_datainfo.source.wavelength = data_set[0] self.current_datainfo.source.wavelength_unit = unit @@ -324,15 +335,15 @@ def process_2d_data_object(self, data_set: np.array, key: str, unit: str): self.current_dataset.dqy_data = data_set.flatten() elif key == self.mask_name: self.current_dataset.mask = data_set.flatten() - elif key == u'Qy': + elif key == 'Qy': self.current_dataset.yaxis("Q_y", unit) self.current_dataset.qy_data = data_set.flatten() - elif key == u'Qydev': + elif key == 'Qydev': self.current_dataset.dqy_data = data_set.flatten() - elif key == u'Qx': + elif key == 'Qx': self.current_dataset.xaxis("Q_x", unit) self.current_dataset.qx_data = data_set.flatten() - elif key == u'Qxdev': + elif key == 'Qxdev': self.current_dataset.dqx_data = data_set.flatten() def process_trans_spectrum(self, data_set: np.array, key: str): @@ -341,11 +352,11 @@ def process_trans_spectrum(self, data_set: np.array, key: str): :param data_set: data from HDF5 file :param key: canSAS_class attribute """ - if key == u'T': + if key == 'T': self.trans_spectrum.transmission = data_set.flatten() - elif key == u'Tdev': + elif key == 'Tdev': self.trans_spectrum.transmission_deviation = data_set.flatten() - elif key == u'lambda': + elif key == 'lambda': self.trans_spectrum.wavelength = data_set.flatten() def process_sample(self, data_point: Any, key: str): @@ -354,29 +365,29 @@ def process_sample(self, data_point: Any, key: str): :param data_point: Single point from an HDF5 data file :param key: class name data_point was taken from """ - if key == u'Title': + if key == 'Title': self.current_datainfo.sample.name = data_point - elif key == u'name': + elif key == 'name': self.current_datainfo.sample.name = data_point - elif key == u'ID': + elif key == 'ID': self.current_datainfo.sample.name = data_point - elif key == u'thickness': + elif key == 'thickness': self.current_datainfo.sample.thickness = data_point - elif key == u'temperature': + elif key == 'temperature': self.current_datainfo.sample.temperature = data_point - elif key == u'transmission': + elif key == 'transmission': self.current_datainfo.sample.transmission = data_point - elif key == u'x_position': + elif key == 'x_position': self.current_datainfo.sample.position.x = data_point - elif key == u'y_position': + elif key == 'y_position': self.current_datainfo.sample.position.y = data_point - elif key == u'pitch': + elif key == 'pitch': self.current_datainfo.sample.orientation.x = data_point - elif key == u'yaw': + elif key == 'yaw': self.current_datainfo.sample.orientation.y = data_point - elif key == u'roll': + elif key == 'roll': self.current_datainfo.sample.orientation.z = data_point - elif key == u'details': + elif key == 'details': self.current_datainfo.sample.details.append(data_point) def process_detector(self, data_point: Any, key: str, unit: str): @@ -386,39 +397,39 @@ def process_detector(self, data_point: Any, key: str, unit: str): :param key: class name data_point was taken from :param unit: unit attribute from data set """ - if key == u'name': + if key == 'name': self.detector.name = data_point - elif key == u'SDD': + elif key == 'SDD': self.detector.distance = float(data_point) self.detector.distance_unit = unit - elif key == u'slit_length': + elif key == 'slit_length': self.detector.slit_length = float(data_point) self.detector.slit_length_unit = unit - elif key == u'x_position': + elif key == 'x_position': self.detector.offset.x = float(data_point) self.detector.offset_unit = unit - elif key == u'y_position': + elif key == 'y_position': self.detector.offset.y = float(data_point) self.detector.offset_unit = unit - elif key == u'pitch': + elif key == 'pitch': self.detector.orientation.x = float(data_point) self.detector.orientation_unit = unit - elif key == u'roll': + elif key == 'roll': self.detector.orientation.z = float(data_point) self.detector.orientation_unit = unit - elif key == u'yaw': + elif key == 'yaw': self.detector.orientation.y = float(data_point) self.detector.orientation_unit = unit - elif key == u'beam_center_x': + elif key == 'beam_center_x': self.detector.beam_center.x = float(data_point) self.detector.beam_center_unit = unit - elif key == u'beam_center_y': + elif key == 'beam_center_y': self.detector.beam_center.y = float(data_point) self.detector.beam_center_unit = unit - elif key == u'x_pixel_size': + elif key == 'x_pixel_size': self.detector.pixel_size.x = float(data_point) self.detector.pixel_size_unit = unit - elif key == u'y_pixel_size': + elif key == 'y_pixel_size': self.detector.pixel_size.y = float(data_point) self.detector.pixel_size_unit = unit @@ -429,10 +440,10 @@ def process_collimation(self, data_point: Any, key: str, unit: str): :param key: class name data_point was taken from :param unit: unit attribute from data set """ - if key == u'distance': + if key == 'distance': self.collimation.length = data_point self.collimation.length_unit = unit - elif key == u'name': + elif key == 'name': self.collimation.name = data_point def process_aperture(self, data_point: Any, key: str): @@ -441,11 +452,11 @@ def process_aperture(self, data_point: Any, key: str): :param data_point: Single point from an HDF5 data file :param key: class name data_point was taken from """ - if key == u'shape': + if key == 'shape': self.aperture.shape = data_point - elif key == u'x_gap': + elif key == 'x_gap': self.aperture.size.x = data_point - elif key == u'y_gap': + elif key == 'y_gap': self.aperture.size.y = data_point def process_source(self, data_point: Any, key: str, unit: str): @@ -455,31 +466,31 @@ def process_source(self, data_point: Any, key: str, unit: str): :param key: class name data_point was taken from :param unit: unit attribute from data set """ - if key == u'incident_wavelength': + if key == 'incident_wavelength': self.current_datainfo.source.wavelength = data_point self.current_datainfo.source.wavelength_unit = unit - elif key == u'wavelength_max': + elif key == 'wavelength_max': self.current_datainfo.source.wavelength_max = data_point self.current_datainfo.source.wavelength_max_unit = unit - elif key == u'wavelength_min': + elif key == 'wavelength_min': self.current_datainfo.source.wavelength_min = data_point self.current_datainfo.source.wavelength_min_unit = unit - elif key == u'incident_wavelength_spread': + elif key == 'incident_wavelength_spread': self.current_datainfo.source.wavelength_spread = data_point self.current_datainfo.source.wavelength_spread_unit = unit - elif key == u'beam_size_x': + elif key == 'beam_size_x': self.current_datainfo.source.beam_size.x = data_point self.current_datainfo.source.beam_size_unit = unit - elif key == u'beam_size_y': + elif key == 'beam_size_y': self.current_datainfo.source.beam_size.y = data_point self.current_datainfo.source.beam_size_unit = unit - elif key == u'beam_shape': + elif key == 'beam_shape': self.current_datainfo.source.beam_shape = data_point - elif key == u'radiation': + elif key == 'radiation': self.current_datainfo.source.radiation = data_point - elif key == u'type': + elif key == 'type': self.current_datainfo.source.type = data_point - elif key == u'probe': + elif key == 'probe': self.current_datainfo.source.probe = data_point def process_process(self, data_point: Any, key: str): @@ -488,14 +499,14 @@ def process_process(self, data_point: Any, key: str): :param data_point: Single point from an HDF5 data file :param key: class name data_point was taken from """ - term_match = re.compile(u'^term[0-9]+$') - if key == u'Title': # CanSAS 2.0 + term_match = re.compile('^term[0-9]+$') + if key == 'Title': # CanSAS 2.0 self.process.name = data_point - elif key == u'name': # NXcanSAS + elif key == 'name': # NXcanSAS self.process.name = data_point - elif key == u'description': + elif key == 'description': self.process.description = data_point - elif key == u'date': + elif key == 'date': self.process.date = data_point elif term_match.match(key): self.process.term.append(data_point) @@ -511,22 +522,22 @@ def add_intermediate(self): finished being processed """ - if self.parent_class == u'SASprocess': + if self.parent_class == 'SASprocess': self.current_datainfo.process.append(self.process) self.process = Process() - elif self.parent_class == u'SASdetector': + elif self.parent_class == 'SASdetector': self.current_datainfo.detector.append(self.detector) self.detector = Detector() - elif self.parent_class == u'SAStransmission_spectrum': + elif self.parent_class == 'SAStransmission_spectrum': self.current_datainfo.trans_spectrum.append(self.trans_spectrum) self.trans_spectrum = TransmissionSpectrum() - elif self.parent_class == u'SAScollimation': + elif self.parent_class == 'SAScollimation': self.current_datainfo.collimation.append(self.collimation) self.collimation = Collimation() - elif self.parent_class == u'SASaperture': + elif self.parent_class == 'SASaperture': self.collimation.aperture.append(self.aperture) self.aperture = Aperture() - elif self.parent_class == u'SASdata': + elif self.parent_class == 'SASdata': if isinstance(self.current_dataset, plottable_2D): self.data2d.append(self.current_dataset) elif isinstance(self.current_dataset, plottable_1D): @@ -626,7 +637,7 @@ def _initialize_new_data_set(self, value=None): self.current_datainfo.filename = self.filepath.name @staticmethod - def as_list_or_array(data: Any) -> Union[list, np.ndarray]: + def as_list_or_array(data: Any) -> list | np.ndarray: """ Return value as a list if not already a list or array. :param iterable: @@ -643,10 +654,10 @@ def _find_data_attributes(self, value): :param value: SASdata/NXdata HDF5 Group """ # Initialize values to base types - self.mask_name = u'' - self.i_name = u'' - self.i_node = u'' - self.i_uncertainties_name = u'' + self.mask_name = '' + self.i_name = '' + self.i_node = '' + self.i_uncertainties_name = '' self.q_names = [] self.q_uncertainty_names = [] self.q_resolution_names = [] @@ -700,7 +711,7 @@ def _is_2d_not_multi_frame(self, value, i_base="", q_base=""): return (i_vals is not None and len(i_vals.shape) != 1 and not self.multi_frame) - def _create_unique_key(self, dictionary: dict, name: str, numb: Optional[int] = 0) -> str: + def _create_unique_key(self, dictionary: dict, name: str, numb: int | None = 0) -> str: """ Create a unique key value for any dictionary to prevent overwriting Recurses until a unique key value is found. @@ -713,7 +724,7 @@ def _create_unique_key(self, dictionary: dict, name: str, numb: Optional[int] = if dictionary.get(name) is not None: numb += 1 name = name.split("_")[0] - name += "_{0}".format(numb) + name += f"_{numb}" name = self._create_unique_key(dictionary, name, numb) return name @@ -724,12 +735,12 @@ def _get_unit(self, value: h5py.Dataset) -> str: :param value: attribute dictionary for a particular value set :return: unit for the value passed to the method """ - unit = h5attr(value, u'units') + unit = h5attr(value, 'units') if unit is None: - unit = h5attr(value, u'unit') + unit = h5attr(value, 'unit') return unit - def write(self, filename: str, dataset: Union[Data1D, Data2D]): + def write(self, filename: str, dataset: Data1D | Data2D): """ Export data in NXcanSAS format diff --git a/sasdata/dataloader/readers/csv_reader.py b/sasdata/dataloader/readers/csv_reader.py index 27a3de94..339ed615 100644 --- a/sasdata/dataloader/readers/csv_reader.py +++ b/sasdata/dataloader/readers/csv_reader.py @@ -3,6 +3,7 @@ """ import logging + from sasdata.dataloader.readers.ascii_reader import Reader as ASCIIReader logger = logging.getLogger(__name__) diff --git a/sasdata/dataloader/readers/danse_reader.py b/sasdata/dataloader/readers/danse_reader.py index 0e2750ea..1c168aa9 100644 --- a/sasdata/dataloader/readers/danse_reader.py +++ b/sasdata/dataloader/readers/danse_reader.py @@ -11,14 +11,14 @@ #This work benefited from DANSE software developed under NSF award DMR-0520547. #copyright 2008, University of Tennessee ############################################################################# -import os import logging +import os import numpy as np -from sasdata.dataloader.data_info import plottable_2D, DataInfo, Detector +from sasdata.data_util.loader_exceptions import DataReaderException, FileContentsException +from sasdata.dataloader.data_info import DataInfo, Detector, plottable_2D from sasdata.dataloader.filereader import FileReader -from sasdata.data_util.loader_exceptions import FileContentsException, DataReaderException logger = logging.getLogger(__name__) @@ -101,14 +101,14 @@ def get_file_contents(self): elif toks[0] == "SIZE_Y": size_y = int(toks[1]) except ValueError: - error_message += "Unable to parse {}. Default value used.\n".format(toks[0]) + error_message += f"Unable to parse {toks[0]}. Default value used.\n" loaded_correctly = False # Read the data data = [] error = [] if not fversion >= 1.0: - msg = "danse_reader can't read this file {}".format(self.f_open.name) + msg = f"danse_reader can't read this file {self.f_open.name}" raise FileContentsException(msg) for line_num, data_str in enumerate(self.nextlines()): @@ -119,17 +119,16 @@ def get_file_contents(self): data.append(val) error.append(err) except ValueError: - msg = "Unable to parse line {}: {}".format(line_num + data_start_line, data_str.strip()) + msg = f"Unable to parse line {line_num + data_start_line}: {data_str.strip()}" raise FileContentsException(msg) num_pts = size_x * size_y if len(data) < num_pts: - msg = "Not enough data points provided. Expected {} but got {}".format( - size_x * size_y, len(data)) + msg = f"Not enough data points provided. Expected {size_x * size_y} but got {len(data)}" raise FileContentsException(msg) elif len(data) > num_pts: - error_message += ("Too many data points provided. Expected {0} but" - " got {1}. Only the first {0} will be used.\n").format(num_pts, len(data)) + error_message += (f"Too many data points provided. Expected {num_pts} but" + f" got {len(data)}. Only the first {num_pts} will be used.\n") loaded_correctly = False data = data[:num_pts] error = error[:num_pts] diff --git a/sasdata/dataloader/readers/red2d_reader.py b/sasdata/dataloader/readers/red2d_reader.py index 1c519ecc..81897b44 100644 --- a/sasdata/dataloader/readers/red2d_reader.py +++ b/sasdata/dataloader/readers/red2d_reader.py @@ -13,11 +13,10 @@ import numpy as np +from sasdata.data_util.loader_exceptions import FileContentsException from sasdata.data_util.nxsunit import Converter - -from sasdata.dataloader.data_info import plottable_2D, Data2D, DataInfo, Detector +from sasdata.dataloader.data_info import Data2D, DataInfo, Detector, plottable_2D from sasdata.dataloader.filereader import FileReader -from sasdata.data_util.loader_exceptions import FileContentsException def check_point(x_point: Any): diff --git a/sasdata/dataloader/readers/sesans_reader.py b/sasdata/dataloader/readers/sesans_reader.py index a7da80f6..06dd30e8 100644 --- a/sasdata/dataloader/readers/sesans_reader.py +++ b/sasdata/dataloader/readers/sesans_reader.py @@ -8,9 +8,9 @@ import numpy as np -from sasdata.dataloader.filereader import FileReader -from sasdata.dataloader.data_info import plottable_1D, DataInfo from sasdata.data_util.loader_exceptions import FileContentsException +from sasdata.dataloader.data_info import DataInfo, plottable_1D +from sasdata.dataloader.filereader import FileReader # Check whether we have a converter available has_converter = True diff --git a/sasdata/dataloader/readers/tiff_reader.py b/sasdata/dataloader/readers/tiff_reader.py index 23fdfc66..72ed533e 100644 --- a/sasdata/dataloader/readers/tiff_reader.py +++ b/sasdata/dataloader/readers/tiff_reader.py @@ -9,12 +9,14 @@ Image reader. Untested. """ # TODO: load and check data and orientation of the image (needs rendering) -import math import logging +import math import os + import numpy as np -from sasdata.dataloader.data_info import Data2D + from sasdata.data_util.manipulations import reader2D_converter +from sasdata.dataloader.data_info import Data2D logger = logging.getLogger(__name__) diff --git a/sasdata/dataloader/readers/xml_reader.py b/sasdata/dataloader/readers/xml_reader.py index f917114a..f0541c07 100644 --- a/sasdata/dataloader/readers/xml_reader.py +++ b/sasdata/dataloader/readers/xml_reader.py @@ -16,7 +16,6 @@ import logging import os - from urllib.parse import urlparse from lxml import etree @@ -249,7 +248,7 @@ def _create_unique_key(self, dictionary, name, numb=0): if dictionary.get(name) is not None: numb += 1 name = name.split("_")[0] - name += "_{0}".format(numb) + name += f"_{numb}" name = self._create_unique_key(dictionary, name, numb) return name diff --git a/sasdata/file_converter/FileConverterUtilities.py b/sasdata/file_converter/FileConverterUtilities.py index 4022e46c..b2ffa070 100644 --- a/sasdata/file_converter/FileConverterUtilities.py +++ b/sasdata/file_converter/FileConverterUtilities.py @@ -3,11 +3,12 @@ Module with file loader specific static utilities. """ import os + import numpy as np +from sasdata.file_converter.cansas_writer import CansasWriter from sasdata.file_converter.nxcansas_writer import NXcanSASWriter from sasdata.file_converter.otoko_loader import OTOKOLoader -from sasdata.file_converter.cansas_writer import CansasWriter def extract_ascii_data(filename): @@ -21,7 +22,7 @@ def extract_ascii_data(filename): data = np.loadtxt(filename, dtype=str) except: # Check if file is a BSL or OTOKO header file - f = open(filename, 'r') + f = open(filename) f.readline() f.readline() bsl_metadata = f.readline().strip().split() @@ -29,11 +30,11 @@ def extract_ascii_data(filename): if len(bsl_metadata) == 10: msg = ("Error parsing ASII data. {} looks like a BSL or OTOKO " "header file.") - raise IOError(msg.format(os.path.split(filename)[-1])) + raise OSError(msg.format(os.path.split(filename)[-1])) if len(data.shape) != 1: msg = "Error reading {}: Only one column of data is allowed" - raise IOError(msg.format(filename.split('\\')[-1])) + raise OSError(msg.format(filename.split('\\')[-1])) is_float = True try: @@ -49,7 +50,7 @@ def extract_ascii_data(filename): else: msg = ("Error reading {}: Lines must end with a digit, comma " "or semi-colon").format(filename.split('\\')[-1]) - raise IOError(msg) + raise OSError(msg) return np.array(data, dtype=np.float32) @@ -68,7 +69,7 @@ def extract_otoko_data(qfile, ifile): if len(qdata) > 1: msg = ("Q-Axis file has multiple frames. Only 1 frame is " "allowed for the Q-Axis") - raise IOError(msg) + raise OSError(msg) qdata = qdata[0] return qdata, iqdata diff --git a/sasdata/file_converter/ascii2d_loader.py b/sasdata/file_converter/ascii2d_loader.py index b2f19233..35939dad 100644 --- a/sasdata/file_converter/ascii2d_loader.py +++ b/sasdata/file_converter/ascii2d_loader.py @@ -1,9 +1,10 @@ """ ASCII 2D Loader """ -from sasdata.dataloader.data_info import Data2D import numpy as np +from sasdata.dataloader.data_info import Data2D + # ISIS 2D ASCII File Format # http://www.isis.stfc.ac.uk/instruments/loq/software/colette-ascii-file-format-descriptions9808.pdf # line: property @@ -35,7 +36,7 @@ def load(self): :raises ValueError: Raises a ValueError if the file is incorrectly formatted """ - with open(self.data_path, 'r') as file_handle: + with open(self.data_path) as file_handle: file_buffer = file_handle.read() all_lines = file_buffer.splitlines() @@ -70,11 +71,10 @@ def _load_points(lines, start_line, num_points): err_msg = "File incorrectly formatted.\n" if str(e).find('broadcast') != -1: err_msg += "Incorrect number of q data points provided. " - err_msg += "Expected {}.".format(num_qs) + err_msg += f"Expected {num_qs}." elif str(e).find('invalid literal') != -1: - err_msg += ("Expected integer on line {}. " - "Instead got '{}'").format(current_line + 1, - all_lines[current_line]) + err_msg += (f"Expected integer on line {current_line + 1}. " + f"Instead got '{all_lines[current_line]}'") else: err_msg += str(e) raise ValueError(err_msg) @@ -88,16 +88,15 @@ def _load_points(lines, start_line, num_points): height = int(dimensions[1]) except ValueError: err_msg = "File incorrectly formatted.\n" - err_msg += ("Expected line {} to be of the form: " - " .").format(current_line + 1) - err_msg += " Instead got '{}'.".format(all_lines[current_line]) + err_msg += (f"Expected line {current_line + 1} to be of the form: " + " .") + err_msg += f" Instead got '{all_lines[current_line]}'." raise ValueError(err_msg) if width > len(qx) or height > len(qy): err_msg = "File incorrectly formatted.\n" - err_msg += ("Line {} says to use {}x{} points. " - "Only {}x{} provided.").format(current_line + 1, width, - height, len(qx), len(qy)) + err_msg += (f"Line {current_line + 1} says to use {width}x{height} points. " + f"Only {len(qx)}x{len(qy)} provided.") raise ValueError(err_msg) # More qx and/or qy points can be provided than are actually used @@ -114,8 +113,8 @@ def _load_points(lines, start_line, num_points): except: err_msg = "File incorrectly formatted.\n" iflag = all_lines[current_line].strip()[0] - err_msg += ("Expected iflag on line {} to be 1, 2 or 3. " - "Instead got '{}'.").format(current_line+1, iflag) + err_msg += (f"Expected iflag on line {current_line+1} to be 1, 2 or 3. " + f"Instead got '{iflag}'.") raise ValueError(err_msg) current_line += 1 @@ -131,8 +130,8 @@ def _load_points(lines, start_line, num_points): except Exception as e: err_msg = "File incorrectly formatted.\n" if str(e).find("list index") != -1: - err_msg += ("Incorrect number of data points. Expected {}" - " intensity").format(width * height) + err_msg += (f"Incorrect number of data points. Expected {width * height}" + " intensity") if iflag == 3: err_msg += " and error" err_msg += " points." diff --git a/sasdata/file_converter/bsl_loader.py b/sasdata/file_converter/bsl_loader.py index 829bd995..86c42ab6 100644 --- a/sasdata/file_converter/bsl_loader.py +++ b/sasdata/file_converter/bsl_loader.py @@ -28,14 +28,14 @@ def __init__(self, filename): sasdata_filename = filename.replace('000.', '001.') if sasdata_filename == filename: - err_msg = ("Invalid header filename {}.\nShould be of the format " + err_msg = (f"Invalid header filename {filename}.\nShould be of the format " "Xnn000.XXX where X is any alphanumeric character and n is any" - " digit.").format(filename) + " digit.") raise BSLParsingError(err_msg) data_info = {} - with open(os.path.join(folder, filename), 'r') as header_file: + with open(os.path.join(folder, filename)) as header_file: data_info = self._parse_header(header_file, filename, sasdata_filename, folder) self.filename = data_info['filename'] @@ -61,7 +61,7 @@ def _parse_header(self, header_file, filename, sasdata_filename, folder): data_filename = header_file.readline().strip() if len(metadata) != 10: - err_msg = "Invalid header file: {}".format(filename) + err_msg = f"Invalid header file: {filename}" raise BSLParsingError(err_msg) if data_filename != sasdata_filename: diff --git a/sasdata/file_converter/cansas_writer.py b/sasdata/file_converter/cansas_writer.py index f987a4c6..d08dabf5 100644 --- a/sasdata/file_converter/cansas_writer.py +++ b/sasdata/file_converter/cansas_writer.py @@ -1,5 +1,5 @@ -from sasdata.dataloader.readers.cansas_reader import Reader as CansasReader from sasdata.dataloader.data_info import Data1D +from sasdata.dataloader.readers.cansas_reader import Reader as CansasReader class CansasWriter(CansasReader): diff --git a/sasdata/file_converter/nxcansas_writer.py b/sasdata/file_converter/nxcansas_writer.py index 9fb67984..c9665def 100644 --- a/sasdata/file_converter/nxcansas_writer.py +++ b/sasdata/file_converter/nxcansas_writer.py @@ -115,7 +115,7 @@ def _write_h5_vector(entry, vector, names=['x_position', 'y_position'], sasentry.attrs['version'] = '1.1' for i, data_obj in enumerate(dataset): - data_entry = sasentry.create_group("sasdata{0:0=2d}".format(i+1)) + data_entry = sasentry.create_group(f"sasdata{i+1:0=2d}") data_entry.attrs['canSAS_class'] = 'SASdata' if isinstance(data_obj, Data1D): self._write_1d_data(data_obj, data_entry) @@ -190,7 +190,7 @@ def _write_h5_vector(entry, vector, names=['x_position', 'y_position'], if len(data_info.collimation) > 0: for i, coll_info in enumerate(data_info.collimation): collimation_entry = instrument_entry.create_group( - 'sascollimation{0:0=2d}'.format(i + 1)) + f'sascollimation{i + 1:0=2d}') collimation_entry.attrs['canSAS_class'] = 'SAScollimation' if coll_info.length is not None: _write_h5_float(collimation_entry, coll_info.length, 'SDD') @@ -207,7 +207,7 @@ def _write_h5_vector(entry, vector, names=['x_position', 'y_position'], i = 1 for i, det_info in enumerate(data_info.detector): detector_entry = instrument_entry.create_group( - 'sasdetector{0:0=2d}'.format(i + 1)) + f'sasdetector{i + 1:0=2d}') detector_entry.attrs['canSAS_class'] = 'SASdetector' if det_info.distance is not None: _write_h5_float(detector_entry, det_info.distance, 'SDD') @@ -243,8 +243,7 @@ def _write_h5_vector(entry, vector, names=['x_position', 'y_position'], # Process meta data for i, process in enumerate(data_info.process): - process_entry = sasentry.create_group('sasprocess{0:0=2d}'.format( - i + 1)) + process_entry = sasentry.create_group(f'sasprocess{i + 1:0=2d}') process_entry.attrs['canSAS_class'] = 'SASprocess' if process.name: name = _h5_string(process.name) @@ -259,19 +258,17 @@ def _write_h5_vector(entry, vector, names=['x_position', 'y_position'], # Don't save empty terms if term: h5_term = _h5_string(term) - process_entry.create_dataset('term{0:0=2d}'.format( - j + 1), data=h5_term) + process_entry.create_dataset(f'term{j + 1:0=2d}', data=h5_term) for j, note in enumerate(process.notes): # Don't save empty notes if note: h5_note = _h5_string(note) - process_entry.create_dataset('note{0:0=2d}'.format( - j + 1), data=h5_note) + process_entry.create_dataset(f'note{j + 1:0=2d}', data=h5_note) # Transmission Spectrum for i, trans in enumerate(data_info.trans_spectrum): trans_entry = sasentry.create_group( - 'sastransmission_spectrum{0:0=2d}'.format(i + 1)) + f'sastransmission_spectrum{i + 1:0=2d}') trans_entry.attrs['canSAS_class'] = 'SAStransmission_spectrum' trans_entry.attrs['signal'] = 'T' trans_entry.attrs['T_axes'] = 'T' @@ -297,7 +294,7 @@ def _write_h5_vector(entry, vector, names=['x_position', 'y_position'], notes = [np.bytes_('')] if notes is not None: for i, note in enumerate(notes): - note_entry = sasentry.create_group('sasnote{0}'.format(i)) + note_entry = sasentry.create_group(f'sasnote{i}') note_entry.attrs['canSAS_class'] = 'SASnote' note_entry.create_dataset('SASnote', data=note) diff --git a/sasdata/file_converter/otoko_loader.py b/sasdata/file_converter/otoko_loader.py index 322b0403..84acbd3a 100644 --- a/sasdata/file_converter/otoko_loader.py +++ b/sasdata/file_converter/otoko_loader.py @@ -70,7 +70,7 @@ def _load_otoko_axis(self, header_path): total_frames = 0 header_dir = os.path.dirname(os.path.abspath(header_path)) - with open(header_path, "r") as header_file: + with open(header_path) as header_file: lines = header_file.readlines() if len(lines) < 4: raise OTOKOParsingError("Expected more lines in %s." % header_path) diff --git a/sasdata/file_converter/red2d_writer.py b/sasdata/file_converter/red2d_writer.py index d6341910..292472d4 100644 --- a/sasdata/file_converter/red2d_writer.py +++ b/sasdata/file_converter/red2d_writer.py @@ -1,5 +1,6 @@ import os import time + from sasdata.dataloader.readers.red2d_reader import Reader as Red2DReader diff --git a/test/fileconverter/utest_bsl_loader.py b/test/fileconverter/utest_bsl_loader.py index f3a54ec2..46448da6 100644 --- a/test/fileconverter/utest_bsl_loader.py +++ b/test/fileconverter/utest_bsl_loader.py @@ -1,8 +1,8 @@ import os import os.path import unittest - from xml.etree import ElementTree as ET + import numpy as np from sasdata.file_converter.bsl_loader import BSLLoader diff --git a/test/fileconverter/utest_nxcansas_writer.py b/test/fileconverter/utest_nxcansas_writer.py index 2527b653..ac878b66 100644 --- a/test/fileconverter/utest_nxcansas_writer.py +++ b/test/fileconverter/utest_nxcansas_writer.py @@ -1,11 +1,11 @@ -from sasdata.file_converter.nxcansas_writer import NXcanSASWriter -from sasdata.dataloader.loader import Loader - import os import os.path import unittest import warnings +from sasdata.dataloader.loader import Loader +from sasdata.file_converter.nxcansas_writer import NXcanSASWriter + warnings.simplefilter("ignore") diff --git a/test/run_one.py b/test/run_one.py index cbd5024d..edede747 100644 --- a/test/run_one.py +++ b/test/run_one.py @@ -1,12 +1,14 @@ #!/usr/bin/env python +import importlib.util +import logging import os import sys -import xmlrunner import unittest -import importlib.util -from os.path import abspath, split as splitpath +from os.path import abspath +from os.path import split as splitpath + +import xmlrunner -import logging logger = logging.getLogger(__name__) if not logger.root.handlers: import logging.config diff --git a/test/sasdataloader/error_conditions.py b/test/sasdataloader/error_conditions.py index b0799129..8c5a3b0b 100644 --- a/test/sasdataloader/error_conditions.py +++ b/test/sasdataloader/error_conditions.py @@ -1,6 +1,7 @@ -from sasdata.dataloader.loader import Loader import unittest +from sasdata.dataloader.loader import Loader + class testLoader(unittest.TestCase): def setUp(self): @@ -12,7 +13,7 @@ def test_load_unknown(self): should raise a ValueError exception (thrown by data_util.registry) """ self.assertRaises(ValueError, self.s.load, 'angles_flat.mat') - + def test_corrupt(self): """ Loading a corrupted file with a known extension diff --git a/test/sasdataloader/utest_abs_reader.py b/test/sasdataloader/utest_abs_reader.py index e195c6c3..b0122a99 100644 --- a/test/sasdataloader/utest_abs_reader.py +++ b/test/sasdataloader/utest_abs_reader.py @@ -1,13 +1,13 @@ """ Unit tests for data manipulations """ +import os.path import unittest + from sasdata.dataloader.loader import Loader from sasdata.dataloader.readers.abs_reader import Reader as AbsReader from sasdata.dataloader.readers.danse_reader import Reader as DANSEReader -import os.path - def find(filename): return os.path.join(os.path.dirname(__file__), 'data', filename) diff --git a/test/sasdataloader/utest_ascii.py b/test/sasdataloader/utest_ascii.py index 4c679b26..62a27bd8 100644 --- a/test/sasdataloader/utest_ascii.py +++ b/test/sasdataloader/utest_ascii.py @@ -2,13 +2,13 @@ Unit tests for the ascii (n-column) reader """ +import math import os.path +import unittest import warnings -import math -import unittest -from sasdata.dataloader.loader import Loader from sasdata.dataloader.data_info import Data2D +from sasdata.dataloader.loader import Loader warnings.simplefilter("ignore") @@ -18,7 +18,7 @@ def find(filename): class ABSReaderTests(unittest.TestCase): - + def setUp(self): self.loader = Loader() self.f1_list = self.loader.load(find("ascii_test_1.txt")) @@ -47,7 +47,7 @@ def test_checkdata(self): self.assertEqual(self.f1.x[9],0.0497) self.assertTrue(self.f1.x_unit == 'A^{-1}') self.assertTrue(self.f1.y_unit == 'cm^{-1}') - + self.assertEqual(self.f1.meta_data['loader'],"ASCII") def test_truncated_1(self): @@ -178,4 +178,4 @@ def test_save_ascii(self): if __name__ == '__main__': unittest.main() - + diff --git a/test/sasdataloader/utest_averaging.py b/test/sasdataloader/utest_averaging.py index 2d817931..c8eda2dd 100644 --- a/test/sasdataloader/utest_averaging.py +++ b/test/sasdataloader/utest_averaging.py @@ -1,12 +1,23 @@ import math import os import unittest + import numpy as np import sasdata.dataloader.data_info as data_info +from sasdata.data_util.manipulations import ( + Boxavg, + Boxsum, + CircularAverage, + Ring, + SectorPhi, + SectorQ, + SlabX, + SlabY, + position_and_wavelength_to_q, + reader2D_converter, +) from sasdata.dataloader.loader import Loader -from sasdata.data_util.manipulations import (Boxavg, Boxsum, CircularAverage, Ring, SectorPhi, SectorQ, SlabX, - SlabY, position_and_wavelength_to_q, reader2D_converter) def find(filename): diff --git a/test/sasdataloader/utest_cansas.py b/test/sasdataloader/utest_cansas.py index 02a468b0..44a8632a 100644 --- a/test/sasdataloader/utest_cansas.py +++ b/test/sasdataloader/utest_cansas.py @@ -1,22 +1,22 @@ """ Unit tests for the new recursive cansas reader """ +import logging import os import unittest -import logging import warnings from io import StringIO +from xml.dom import minidom from lxml import etree from lxml.etree import XMLSyntaxError -from xml.dom import minidom +from sasdata.dataloader.data_info import Data1D, Data2D from sasdata.dataloader.filereader import decode from sasdata.dataloader.loader import Loader -from sasdata.dataloader.data_info import Data1D, Data2D -from sasdata.dataloader.readers.xml_reader import XMLreader -from sasdata.dataloader.readers.cansas_reader import Reader from sasdata.dataloader.readers.cansas_constants import CansasConstants +from sasdata.dataloader.readers.cansas_reader import Reader +from sasdata.dataloader.readers.xml_reader import XMLreader logger = logging.getLogger(__name__) @@ -58,7 +58,7 @@ def get_number_of_entries(self, dictionary, name, i): if dictionary.get(name) is not None: i += 1 name = name.split("_")[0] - name += "_{0}".format(i) + name += f"_{i}" name = self.get_number_of_entries(dictionary, name, i) return name diff --git a/test/sasdataloader/utest_extension_registry.py b/test/sasdataloader/utest_extension_registry.py index 50624d2c..ae4b3cbb 100644 --- a/test/sasdataloader/utest_extension_registry.py +++ b/test/sasdataloader/utest_extension_registry.py @@ -3,13 +3,14 @@ """ import logging -import unittest import os import shutil +import unittest + import numpy as np -from sasdata.dataloader.loader import Registry as Loader from sasdata.dataloader.loader import Loader as LoaderMain +from sasdata.dataloader.loader import Registry as Loader logger = logging.getLogger(__name__) diff --git a/test/sasdataloader/utest_generic_file_reader_class.py b/test/sasdataloader/utest_generic_file_reader_class.py index 04bcbc28..2cbb325b 100644 --- a/test/sasdataloader/utest_generic_file_reader_class.py +++ b/test/sasdataloader/utest_generic_file_reader_class.py @@ -2,14 +2,15 @@ Unit tests for the generic file reader class """ +import logging import os import unittest -import logging + import numpy as np -from sasdata.dataloader.data_info import DataInfo, plottable_1D, Data1D -from sasdata.dataloader.loader import Loader +from sasdata.dataloader.data_info import Data1D, DataInfo, plottable_1D from sasdata.dataloader.filereader import FileReader +from sasdata.dataloader.loader import Loader logger = logging.getLogger(__name__) diff --git a/test/sasdataloader/utest_red2d_reader.py b/test/sasdataloader/utest_red2d_reader.py index bd9ca6ea..323dff6b 100644 --- a/test/sasdataloader/utest_red2d_reader.py +++ b/test/sasdataloader/utest_red2d_reader.py @@ -1,11 +1,9 @@ """ Unit tests for the red2d (3-7-column) reader """ -import warnings - -import unittest - import os.path +import unittest +import warnings from sasdata.dataloader.loader import Loader diff --git a/test/sasdataloader/utest_sesans.py b/test/sasdataloader/utest_sesans.py index f0038d2d..5f954bdc 100644 --- a/test/sasdataloader/utest_sesans.py +++ b/test/sasdataloader/utest_sesans.py @@ -4,9 +4,10 @@ import os.path import unittest + from sasdata.data_util.loader_exceptions import FileContentsException -from sasdata.dataloader.readers.sesans_reader import Reader from sasdata.dataloader.loader import Loader +from sasdata.dataloader.readers.sesans_reader import Reader def find(filename): diff --git a/test/sasmanipulations/utest_manipulations.py b/test/sasmanipulations/utest_manipulations.py index 0fc5ad8a..1762d463 100644 --- a/test/sasmanipulations/utest_manipulations.py +++ b/test/sasmanipulations/utest_manipulations.py @@ -9,8 +9,8 @@ import numpy as np from numpy.testing import assert_allclose -from sasdata.dataloader.loader import Loader from sasdata.dataloader.data_info import Data1D, Data2D +from sasdata.dataloader.loader import Loader RTOL = 1e-12 diff --git a/test/utest_sasdata.py b/test/utest_sasdata.py index 79045700..cebc748e 100644 --- a/test/utest_sasdata.py +++ b/test/utest_sasdata.py @@ -1,10 +1,10 @@ #!/usr/bin/env python\ +import logging.config import os -import subprocess import re +import subprocess import sys -import logging.config LOGGER_CONFIG_FILE = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'logging.ini') logging.config.fileConfig(LOGGER_CONFIG_FILE) logger = logging.getLogger(__name__) @@ -61,10 +61,10 @@ def run_tests(dirs=None, run_all=False): failure_text.append("== %s std err ==\n%s" % (module_name, std_out)) - m = re.search("FAILED \(.*errors=([0-9]+)", std_out) + m = re.search(r"FAILED \(.*errors=([0-9]+)", std_out) if m is not None: n_errors += int(m.group(1)) - m = re.search("FAILED \(.*failures=([0-9]+)", std_out) + m = re.search(r"FAILED \(.*failures=([0-9]+)", std_out) if m is not None: n_failures += int(m.group(1)) From 4ec7b88c610452334687680abb8aa761c0c0d0c7 Mon Sep 17 00:00:00 2001 From: PaulSharp <44529197+DrPaulSharp@users.noreply.github.com> Date: Thu, 23 Oct 2025 12:43:40 +0100 Subject: [PATCH 3/4] Fixes further linting errors --- sasdata/data_util/formatnum.py | 7 +-- sasdata/data_util/nxsunit.py | 4 +- sasdata/data_util/registry.py | 4 +- sasdata/data_util/uncertainty.py | 57 +++++++++++++--------- sasdata/dataloader/data_info.py | 2 +- sasdata/dataloader/filereader.py | 2 +- sasdata/dataloader/readers/__init__.py | 2 + sasdata/dataloader/readers/ascii_reader.py | 2 - sasdata/dataloader/readers/danse_reader.py | 4 +- sasdata/dataloader/readers/red2d_reader.py | 2 - sasdata/file_converter/ascii2d_loader.py | 6 ++- test/sasdataloader/error_conditions.py | 2 +- test/sasdataloader/utest_ascii.py | 6 +-- test/sasdataloader/utest_cansas.py | 1 - 14 files changed, 55 insertions(+), 46 deletions(-) diff --git a/sasdata/data_util/formatnum.py b/sasdata/data_util/formatnum.py index e706880b..2f888bf3 100644 --- a/sasdata/data_util/formatnum.py +++ b/sasdata/data_util/formatnum.py @@ -9,9 +9,9 @@ where the number in parenthesis is the uncertainty in the last two digits of v. :func:`format_uncertainty` uses the compact format by default, but this -can be changed to use the expanded +/- format by setting +can be changed to use the expanded +/- format by setting format_uncertainty.compact to False. - + The formatted string uses only the number of digits warranted by the uncertainty in the measurement. @@ -438,4 +438,5 @@ def main(): import doctest doctest.testmod() -if __name__ == "__main__": main() +if __name__ == "__main__": + main() diff --git a/sasdata/data_util/nxsunit.py b/sasdata/data_util/nxsunit.py index 2e3d948c..422d301b 100644 --- a/sasdata/data_util/nxsunit.py +++ b/sasdata/data_util/nxsunit.py @@ -46,11 +46,11 @@ import math import re from collections.abc import Sequence -from typing import TypeVar, Union +from typing import TypeVar __all__ = ['Converter', 'standardize_units'] T = TypeVar('T') -ConversionType = Union[float, tuple[float, float]] +ConversionType = float | tuple[float, float] DIMENSIONS = {} # type: Dict[str, Dict[str, ConversionType]] AMBIGUITIES = {} # type: Dict[str, str] PREFIX = dict(peta=1e15, tera=1e12, giga=1e9, mega=1e6, kilo=1e3, deci=1e-1, centi=1e-2, milli=1e-3, mili=1e-3, diff --git a/sasdata/data_util/registry.py b/sasdata/data_util/registry.py index a5d2ec50..b5ad4724 100644 --- a/sasdata/data_util/registry.py +++ b/sasdata/data_util/registry.py @@ -131,7 +131,7 @@ def formats(self) -> list[str]: """ Return a sorted list of the registered formats. """ - names = [a for a in self.readers.keys() if not a.startswith('.')] + names = [a for a in self.readers if not a.startswith('.')] names.sort() return names @@ -139,7 +139,7 @@ def extensions(self) -> list[str]: """ Return a sorted list of registered extensions. """ - exts = [a for a in self.readers.keys() if a.startswith('.')] + exts = [a for a in self.readers if a.startswith('.')] exts.sort() return exts diff --git a/sasdata/data_util/uncertainty.py b/sasdata/data_util/uncertainty.py index c57f713c..5362ae0b 100644 --- a/sasdata/data_util/uncertainty.py +++ b/sasdata/data_util/uncertainty.py @@ -158,7 +158,6 @@ def __repr__(self): def __floordiv__(self, other): return NotImplemented def __mod__(self, other): return NotImplemented def __divmod__(self, other): return NotImplemented - def __mod__(self, other): return NotImplemented def __lshift__(self, other): return NotImplemented def __rshift__(self, other): return NotImplemented def __and__(self, other): return NotImplemented @@ -168,7 +167,6 @@ def __or__(self, other): return NotImplemented def __rfloordiv__(self, other): return NotImplemented def __rmod__(self, other): return NotImplemented def __rdivmod__(self, other): return NotImplemented - def __rmod__(self, other): return NotImplemented def __rlshift__(self, other): return NotImplemented def __rrshift__(self, other): return NotImplemented def __rand__(self, other): return NotImplemented @@ -178,22 +176,21 @@ def __ror__(self, other): return NotImplemented def __ifloordiv__(self, other): return NotImplemented def __imod__(self, other): return NotImplemented def __idivmod__(self, other): return NotImplemented - def __imod__(self, other): return NotImplemented def __ilshift__(self, other): return NotImplemented def __irshift__(self, other): return NotImplemented def __iand__(self, other): return NotImplemented def __ixor__(self, other): return NotImplemented def __ior__(self, other): return NotImplemented - def __invert__(self): return NotImplmented # For ~x - def __complex__(self): return NotImplmented - def __int__(self): return NotImplmented - def __long__(self): return NotImplmented - def __float__(self): return NotImplmented - def __oct__(self): return NotImplmented - def __hex__(self): return NotImplmented - def __index__(self): return NotImplmented - def __coerce__(self): return NotImplmented + def __invert__(self): return NotImplemented # For ~x + def __complex__(self): return NotImplemented + def __int__(self): return NotImplemented + def __long__(self): return NotImplemented + def __float__(self): return NotImplemented + def __oct__(self): return NotImplemented + def __hex__(self): return NotImplemented + def __index__(self): return NotImplemented + def __coerce__(self): return NotImplemented def log(self): return Uncertainty(*err1d.log(self.x,self.variance)) @@ -201,8 +198,10 @@ def log(self): def exp(self): return Uncertainty(*err1d.exp(self.x,self.variance)) -def log(val): return self.log() -def exp(val): return self.exp() +def log(val): + return self.log() +def exp(val): + return self.exp() def test(): a = Uncertainty(5,3) @@ -250,35 +249,44 @@ def test(): # ===== Inplace operations ===== # Scalar operations - y = a+0; y += 4 + y = a+0 + y += 4 z = a+4 assert y.x == z.x and abs(y.variance-z.variance) < 1e-15 - y = a+0; y -= 4 + y = a+0 + y -= 4 z = a-4 assert y.x == z.x and abs(y.variance-z.variance) < 1e-15 - y = a+0; y *= 4 + y = a+0 + y *= 4 z = a*4 assert y.x == z.x and abs(y.variance-z.variance) < 1e-15 - y = a+0; y /= 4 + y = a+0 + y /= 4 z = a/4 assert y.x == z.x and abs(y.variance-z.variance) < 1e-15 # Power operations - y = a+0; y **= 4 + y = a+0 + y **= 4 z = a**4 assert y.x == z.x and abs(y.variance-z.variance) < 1e-15 # Binary operations - y = a+0; y += b + y = a+0 + y += b z = a+b assert y.x == z.x and abs(y.variance-z.variance) < 1e-15 - y = a+0; y -= b + y = a+0 + y -= b z = a-b assert y.x == z.x and abs(y.variance-z.variance) < 1e-15 - y = a+0; y *= b + y = a+0 + y *= b z = a*b assert y.x == z.x and abs(y.variance-z.variance) < 1e-15 - y = a+0; y /= b + y = a+0 + y /= b z = a/b assert y.x == z.x and abs(y.variance-z.variance) < 1e-15 @@ -312,4 +320,5 @@ def test(): assert str(Uncertainty(15,3)) == "15.0(17)" assert str(Uncertainty(151.23356,0.324185**2)) == "151.23(32)" -if __name__ == "__main__": test() +if __name__ == "__main__": + test() diff --git a/sasdata/dataloader/data_info.py b/sasdata/dataloader/data_info.py index b5c23bd4..16676a4b 100644 --- a/sasdata/dataloader/data_info.py +++ b/sasdata/dataloader/data_info.py @@ -768,7 +768,7 @@ def is_slit_smeared(self): :return: True is slit smearing info is present, False otherwise """ def _check(v): - return ((v.__class__ == list or v.__class__ == np.ndarray) + return (isinstance(v.__class__ == list | np.ndarray) and len(v) > 0 and min(v) > 0) return _check(self.dxl) or _check(self.dxw) diff --git a/sasdata/dataloader/filereader.py b/sasdata/dataloader/filereader.py index aa6c6edb..c43a52f2 100644 --- a/sasdata/dataloader/filereader.py +++ b/sasdata/dataloader/filereader.py @@ -110,7 +110,7 @@ def _read(self, file_handler: CustomFileOpen) -> list[Data1D | Data2D]: # Move to the desired initial file position in case of successive reads on the same handle self.f_open.seek(self.f_pos) - basename, extension = self.filepath.stem, self.filepath.suffix + _, extension = self.filepath.stem, self.filepath.suffix self.extension = extension.lower() if self.extension in self.ext or self.allow_all: try: diff --git a/sasdata/dataloader/readers/__init__.py b/sasdata/dataloader/readers/__init__.py index c41fc078..c68ce745 100644 --- a/sasdata/dataloader/readers/__init__.py +++ b/sasdata/dataloader/readers/__init__.py @@ -1,2 +1,4 @@ # Method to associate extensions to default readers from .associations import get_fallback_readers, read_associations + +__all__ = ["read_associations", "get_fallback_readers"] diff --git a/sasdata/dataloader/readers/ascii_reader.py b/sasdata/dataloader/readers/ascii_reader.py index 2cbd02ee..fed6b889 100644 --- a/sasdata/dataloader/readers/ascii_reader.py +++ b/sasdata/dataloader/readers/ascii_reader.py @@ -62,8 +62,6 @@ def get_file_contents(self): # More than "5" lines of data is considered as actual # To count # of current data candidate lines candidate_lines = 0 - # To count total # of previous data candidate lines - candidate_lines_previous = 0 # Current line number line_no = 0 # minimum required number of columns of data diff --git a/sasdata/dataloader/readers/danse_reader.py b/sasdata/dataloader/readers/danse_reader.py index 1c168aa9..d1851c77 100644 --- a/sasdata/dataloader/readers/danse_reader.py +++ b/sasdata/dataloader/readers/danse_reader.py @@ -26,7 +26,7 @@ has_converter = True try: from sasdata.data_util.nxsunit import Converter -except: +except ImportError: has_converter = False @@ -183,7 +183,7 @@ def get_file_contents(self): # Reshape data x_vals = np.tile(x_vals, (size_y, 1)).flatten() y_vals = np.tile(y_vals, (size_x, 1)).T.flatten() - if (np.all(self.current_dataset.err_data == None) + if (np.all(self.current_dataset.err_data is None) or np.any(self.current_dataset.err_data <= 0)): new_err_data = np.sqrt(np.abs(self.current_dataset.data)) else: diff --git a/sasdata/dataloader/readers/red2d_reader.py b/sasdata/dataloader/readers/red2d_reader.py index 81897b44..3d468911 100644 --- a/sasdata/dataloader/readers/red2d_reader.py +++ b/sasdata/dataloader/readers/red2d_reader.py @@ -79,8 +79,6 @@ def get_file_contents(self): # Defaults lines = buf.split('\n') - x = [] - y = [] wavelength = None distance = None diff --git a/sasdata/file_converter/ascii2d_loader.py b/sasdata/file_converter/ascii2d_loader.py index 35939dad..bf46b0b8 100644 --- a/sasdata/file_converter/ascii2d_loader.py +++ b/sasdata/file_converter/ascii2d_loader.py @@ -83,7 +83,8 @@ def _load_points(lines, start_line, num_points): try: dimensions = np.fromstring(all_lines[current_line], dtype=np.float32, sep=' ') - if len(dimensions) != 3: raise ValueError() + if len(dimensions) != 3: + raise ValueError() width = int(dimensions[0]) height = int(dimensions[1]) except ValueError: @@ -109,7 +110,8 @@ def _load_points(lines, start_line, num_points): # iflag = 3 => q axis, intensity and error data try: iflag = int(all_lines[current_line].strip()[0]) - if iflag <= 0 or iflag > 3: raise ValueError() + if iflag <= 0 or iflag > 3: + raise ValueError() except: err_msg = "File incorrectly formatted.\n" iflag = all_lines[current_line].strip()[0] diff --git a/test/sasdataloader/error_conditions.py b/test/sasdataloader/error_conditions.py index 8c5a3b0b..4661a765 100644 --- a/test/sasdataloader/error_conditions.py +++ b/test/sasdataloader/error_conditions.py @@ -18,7 +18,7 @@ def test_corrupt(self): """ Loading a corrupted file with a known extension should raise a runtime exception. - The error condition is similar to an unknown + The error condition is similar to an unknown type (file extension). When a reader is identified as knowing the file extension, it tries to load. If it raises an exception, the system should try to identify diff --git a/test/sasdataloader/utest_ascii.py b/test/sasdataloader/utest_ascii.py index 62a27bd8..87c785c6 100644 --- a/test/sasdataloader/utest_ascii.py +++ b/test/sasdataloader/utest_ascii.py @@ -52,7 +52,7 @@ def test_checkdata(self): def test_truncated_1(self): """ - Test an ascii file with header and a + Test an ascii file with header and a comment line in the middle of the data section. The business rule says that we should stop reading at the first comment once the data @@ -66,7 +66,7 @@ def test_truncated_1(self): def test_truncated_2(self): """ - Test a 6-col ascii file with header and a + Test a 6-col ascii file with header and a line with only 2 columns in the middle of the data section. The business rule says that we should stop reading at the first inconsitent line. @@ -78,7 +78,7 @@ def test_truncated_2(self): def test_truncated_3(self): """ - Test a 6-col ascii file with complex header and + Test a 6-col ascii file with complex header and many lines with 2 or 2 columns in the middle of the data section. The business rule says that we should stop reading at the last line of header. diff --git a/test/sasdataloader/utest_cansas.py b/test/sasdataloader/utest_cansas.py index 44a8632a..5114e181 100644 --- a/test/sasdataloader/utest_cansas.py +++ b/test/sasdataloader/utest_cansas.py @@ -230,7 +230,6 @@ def set_processing_instructions(self, minidom_object, dic): def get_processing_instructions(self, xml_reader_object): dict = {} pi = xml_reader_object.xmlroot.getprevious() - i = 0 while pi is not None: attr = {} pi_name = "" From c42c501d1f018732a76039219ede2f73a6fc3b8e Mon Sep 17 00:00:00 2001 From: PaulSharp <44529197+DrPaulSharp@users.noreply.github.com> Date: Thu, 23 Oct 2025 14:56:52 +0100 Subject: [PATCH 4/4] Adds uv.lock --- .gitignore | 1 - uv.lock | 1123 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 1123 insertions(+), 1 deletion(-) create mode 100644 uv.lock diff --git a/.gitignore b/.gitignore index 26302d4d..4485f2bc 100644 --- a/.gitignore +++ b/.gitignore 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