Changelog

This page contains a summary of changes between the official ASpecD releases. Only the biggest changes are listed here. A complete and detailed log of all changes is available through the GitHub Repository Browser.

Version 0.11.0

Released 2024-10-17

New features

• Plotting

  • aspecd.plotting.PatchProperties for properties of patches, as used for aspecd.annotation.VerticalSpan and aspecd.annotation.HorizontalSpan.

  • aspecd.plotting.AnnotationProperties and aspecd.plotting.AnnotationTextProperties for properties of text annotations with lines, as used for aspecd.annotation.TextWithLine.

  • aspecd.plotting.AxesProperties has new attributes frame_on, xlabelposition, and ylabelposition.

  • aspecd.plotting.Spines and aspecd.plotting.SpineProperties for controlling spine properties of axes.

  • aspecd.plotting.MarkerProperties for properties of markers, as used for aspecd.annotation.Marker.

• Plot annotations

  • aspecd.annotation.VerticalSpan for adding vertical spans (rectangles) to plot(ter)s

  • aspecd.annotation.HorizontalSpan for adding horizontal spans (rectangles) to plot(ter)s

  • aspecd.annotation.TextWithLine for adding text with additional lines

  • aspecd.annotation.Marker for adding markers to plot(ter)s

  • aspecd.annotation.FillBetween for colouring the surface below a curve.

• Analysis

  • aspecd.analysis.PeakFinding can return both, peak positions and intensities, as pairs, ready to be used in aspecd.annotation.TextWithLine annotations.

  • aspecd.analysis.CentreOfMass for calculating the centre of mass for ND datasets.

• IO

  • aspecd.io.TxtImporter has an additional parameter axis specifying which column to use for axis values when reading 2D data. (#6)

Changes

• Plotting: Default figure size in aspecd.plotting.FigureProperties set to None to allow setting from matplotlibrc to take effect.

  Without adjustments, this may change the size (and aspect ratio) of your figures from 6x4 inches to 6.4x4.8 inches.

Fixes

• CompositePlotter operates on copies of plotters.

• Plot task writes correct filename for each plotter if results is used.

• PlotannotationTask saves properties to recipe history.

• PlotannotationTask can be applied to plotter and stored for later use as result at the same time.

• Text plot annotation with scalar y position set to zero works.

Version 0.10.1

Released 2024-08-13

Fixes

• CompositePlotter shares axes correctly

Version 0.10.0

Released 2024-08-10

New features

• Plotting

  • Set individual properties for each of the lines of a aspecd.plotting.SinglePlotter2DStacked

  • Conveniently set identical properties for all lines of aspecd.plotting.SinglePlotter2DStacked and aspecd.plotting.MultiPlotter1D

  • aspecd.plotting.TextProperties

  • aspecd.plotting.DrawingProperties has attribute zorder.

  • aspecd.plotting.SubplotGridSpecs for properties of the subplot grid of a CompositePlotter.

  • aspecd.plotting.CompositePlotter allows to share x and y axes.

• Plot annotations

  • aspecd.annotations.Text for text annotations to plot(ter)s

• Tasks

  • aspecd.tasks.SingleplotTask allows to set as many results as datasets, to allow for adding an individual plotter (for one of the datasets) to a aspecd.tasks.CompositeplotTask. (#3)

• Models

  • aspecd.model.Voigtian for creating Voigt profiles frequently used in spectroscopy to describe line shapes.

Fixes

• Tasks

  • aspecd.tasks.MultiplotTask preserves order of datasets the task is applied to, regardless whether the datasets are originally imported or result from prior tasks (via result property). (#2)

  • aspecd.tasks.Recipe.get_datasets() preserves order of datasets, regardless whether the datasets are originally imported or result from prior tasks (via result property).

  • aspecd.tasks.Chef.cook() closes open figures.

• Plotting

  • CompositePlotter does not add additional drawings any more to the plotters used. (#5)

Version 0.9.3

Released 2024-07-22

Fixes

• Correct method for area normalization: take number of points into account.

• Adjust stacking in SinglePlotter2DStacked for data with larger minima than maxima.

• Templates for LaTeX dataset report: escape _ and # in dataset label.

• Axis labels can be removed by setting one or both of xlabel and ylabel to None (or null in YAML/recipe).

Version 0.9.2

Released 2024-03-24

Fixes

• Revert changes in aspecd.utils.ToDictMixin from version 0.9.1, as it caused problems with Matplotlib.

• Updates on contour plots to work with Matplotlib 3.8

• Updates to prevent deprecation warning for NumPy 1.25

• aspecd.processing.RangeExtraction extracts correct range for axis values.

Version 0.9.1

Released 2024-01-15

Fixes

• aspecd.utils.ToDictMixin does no longer modify the __dict__ or __odict__ property of a class directly, what may have resulted in unexpected behaviour, but operates on a (deep)copy.

Changes

• Use Black for automatic code formatting

Version 0.9.0

Released 2024-01-13

New features

• Processing steps

  • aspecd.processing.CommonRangeExtraction works for ND datasets with arbitrary dimension N

• Plotting

  • Legend title can be set from recipes

  • New attribute aspecd.plotting.AxesProperties.invert for inverting axes. Helpful, e.g., for plotting FTIR data without having to resort to explicitly provide descending axis limits.

  • Setting font size of axes labels via label_fontsize property.

  • Colorbar for 2D plotter

  • Annotations for plots

    For details, see the documentation of plot annotations and the aspecd.annotation module.

• Device data

  • New property aspecd.dataset.Dataset.device_data for storing additional/secondary (monitoring) data.

  • New class aspecd.dataset.DeviceData for device data.

  • New class aspecd.analysis.DeviceDataExtraction for extracting device data from a dataset as a separate dataset. This allows to proceed with the extracted datasets as with any other dataset.

  • New class aspecd.plotting.MultiDeviceDataPlotter1D for plotting multiple device data of a single dataset.

  • New parameter device_data in aspecd.plotting.Plotter for plotting device data rather than primary data of a dataset/datasets

• Logging

  • New function aspecd.utils.get_logger() to get a logger object for a given module with the logger within the hierarchy of the ASpecD root logger. Important for packages derived from the ASpecD framework in order to get their log messages being captured, e.g. during recipe-driven data analysis.

Changes

• Plotters can now handle device data instead of the primary data of a dataset (see above). This means, however, that instead of accessing self.dataset.data (or self.datasets[#].data), plotters need to access self.data.data (or self.data[#].data) instead.

  Authors of derived packages should update their plotters accordingly. See the hints for developers on device data in the plotting module.

• Serving recipes logs messages from all ASpecD modules, not only from the aspecd.tasks module.

• aspecd.io.DatasetImporterFactory logs warning if no concrete importer could be found for a given dataset, as this will usually result in (sometimes hard to detect) downstream problems.

• aspecd.io.DatasetExporter adds a history record to aspecd.dataset.Dataset.tasks.

• aspecd.plotting.SinglePlotter1D and aspecd.plotting.MultiPlotter1D issue warning with log plotters and negative values.

• aspecd.annotation.DatasetAnnotation has been renamed from Annotation to reflect the fact that there are now plot annotations as well.

Documentation

• New example: Plotting FTIR spectra normalised to spectral feature

• Section with general tips and tricks for styling plotters.

Fixes

• aspecd.utils.ToDictMixin.to_dict() does not traverse settings for properties to exclude and include.

• Workaround for matplotlib.figure.Figure.savefig() not correctly handling figure DPI settings.

Version 0.8.3

Released 2023-09-08

Fixes

• Exporter tasks (aspecd.tasks.ExportTask) automatically save datasets with default name if no target is provided.

• Correct setting of contour plot properties with newer versions of Matplotlib

Changes

• aspecd.processing.Interpolation changed interpolation method for 2D data from deprecated scipy.interpolate.interp2d to scipy.interpolate.RegularGridInterpolator

New features

• aspecd.processing.Interpolation works for ND datasets with arbitrary dimension N

• aspecd.tasks.Recipe with new setting autosave_datasets (default: True)

Version 0.8.2

Released 2023-08-24

Fixes

• Handling of too long filenames when saving plots: the filename is replaced by its MD5 hash.

New features

• New setting default_colormap in recipes.

• Property colormap in aspecd.plotting.SinglePlot2DProperties, allowing for consistently setting (default) colormaps for 2D surface plots within a recipe.

Version 0.8.1

Released 2023-08-11

Documentation

• New section on metadata during data acquisition

• New section with examples

• New section with data publications

Fixes

• Baseline correction in aspecd.processing.BaselineCorrection issues warning if more than 100% of the data are used and resets to 50% on each side.

• Recipe history contains importer parameters

Version 0.8.0

Released 2023-03-26

New features

• Plotting

  • MultiPlotter1D can use colormaps for coloring multiple lines

  • Number of columns can be set for legends of plots

• Processing steps

  • New class aspecd.processing.SliceRemoval for removing slices from a ND dataset with N>1.

  • New class aspecd.processing.RelativeAxis for converting an axis into a relative axis, centred about a (given) origin.

Fixes

• Interpolation in aspecd.processing.Interpolation works correctly if axis range is given and no corresponding axis point exists in the original dataset.

Version 0.7.1

Released 2022-06-12

New features

• Reference to publication in documentation and colophon of reports.

Version 0.7.0

Released 2022-01-30

New features

• aspecd.tasks.FigurereportTask for creating figure captions that can, e.g., be included in other documents

• Attributes labelspacing and fontsize in aspecd.plotting.LegendProperties

• Attribute output in aspecd.tasks.ModelTask controlling the type of output returned (dataset or model)

• Method aspecd.model.Model.evaluate() for fast evaluation of models without any checks (useful in context of fitting)

• Attribute dataset_type in aspecd.analysis.AnalysisStep to define type of calculated dataset that gets returned

• aspecd.plotting.MultiPlotter1D and aspecd.plotting.MultiPlotter1DStacked with parameter “tight” for tight axes and “switch_axes” for switching axes

• aspecd.plotting.SinglePlotter1D with parameter “switch_axes” for switching axes

• aspecd.plotting.AxesProperties: angles of the axes tick labels can be set using the xticklabelangle and yticklabelangle properties

Changes

• aspecd.processing.SliceExtraction sets dataset label to slice position

• aspecd.processing.Averaging sets dataset label to averaging range

Fixes

• Dataset importer does not override dataset label.

• AnalysisSteps assign data to _origdata attribute if result is dataset

• MultiprocessingTask correctly sets label of resulting datasets

Version 0.6.4

Released 2021-11-25

Changes

• New attribute comment in aspecd.tasks.Task, aspecd.report.Reporter, aspecd.plotting.Plotter, aspecd.io.DatasetExporter allowing for storing user-supplied comments

Fixes

• Warnings issued during cooking of a recipe are now log messages.

Version 0.6.3

Released 2021-11-24

Changes

• aspecd.report.Reporter adds template loader for package if aspecd.report.Reporter.package is provided, allowing to override templates from the ASpecD framework within derived packages.

• aspecd.tasks.ReportTask passes through the default package from the recipe to the reporter for overriding templates.

• aspecd.infofile.Infofile: Comment gets converted into a single string

• Dependency change: Jinja >= 3.0

• aspecd.io.TxtImporter handles decimal separator different than dot

Fixes

• aspecd.tasks.Task warns if key in dict (recipe) is no property of the task.

• aspecd.processing.DatasetAlgebra returns shape in error message if shapes differ.

• Processing and analysis tasks issue warning if result name is identical to dataset label

• Ensure window length for Savitzky-Golay filter in aspecd.processing.Filtering to always be odd

• aspecd.processing.CommonRangeExtraction ignores unit of last axis (i.e., intensity) when checking for identical units

• aspecd.utils.ToDictMixin: Added superclass call to preserve mro in dependent subclasses

• Tasks properly handle non-dataset results from recipe

• aspecd.plotting.MultiPlotter sets axis labels when units are empty

• aspecd.processing.Normalisation removes unit from last axis

• aspecd.processing.BaselineCorrection handles zero values in range properly

• aspecd.analysis.AggregateAnalysisStep no longer adds datasets and result to output of to_dict()

• aspecd.tasks.AggregatedAnalysisTask sets correct type in output of to_dict()

• aspecd.tasks.ReportTask does not add empty figure filenames to includes

• aspecd.Tasks.PlotTask preserves labels of drawings

• Recipe history does not contain path to current directory in dataset source

Version 0.6.2

Released 2021-11-16

Changes

• New parameter ytickcount for aspecd.plotting.SinglePlotter2DStacked to control maximum number of yticks

• New parameter tight_layout for aspecd.plotting.Plotter to prevent labels from getting clipped

Fixes

• Recipe containing a MultiplotTask does not contain datasets as dicts

• PlotTask with automatically generated filenames and >1 datasets writes correct filenames to figure record in recipe

• CompositePlotter sets plot style of plotters

• Grammar in dataset.tex template

• Colophon of report via ReportTask contains default package set in recipe

• CompositePlotter does not add plotters of subfigures to list of dataset representations and list of dataset tasks

• Escaping of “_” in LaTeX templates

Version 0.6.1

Released 2021-11-10

Fixes

• ReportTask works with output directory set in recipe

• LatexReporter finds templates with relative path

• Yaml handles numpy floats and ints

• ProcessingTask handles multiple datasets, SinglePlotTask automatically generated figure filenames with multiple datasets

• ProcessingTask no longer tries to deep-copy matplotlib objects

• Replacing dataset labels in recipes works with dataset ids/source

Version 0.6.0

Released 2021-11-05

New features

• Reports

  • Templates for reporting information contained in datasets come bundled with ASpecD.

  • Context contains templates_dir allowing to include sub-templates.

  • New class TxtReporter for plain text reports

• Tasks/Recipe-driven data analysis

  • YAML representation of recipe and tasks via aspecd.tasks.Recipe.to_yaml() and aspecd.tasks.Task.to_yaml()

  • Figure labels can be set in plotters; otherwise a default label will be set and can be accessed from within reports.

• Utils

  • change_working_dir() can be used as context manager to temporarily change the working directory.

• General

  • aspecd.utils.ToDictMixin.to_dict() can optionally remove keys with empty values.

  • to_dict() method in aspecd.processing.ProcessingStep, aspecd.analysis.AnalysisStep, aspecd.annotation.Annotation, aspecd.plotting.Plotter, aspecd.table.Table, aspecd.report.Reporter, aspecd.model.Model

• Models

  • Axes quantities and units can be explicitly set on model creation.

Changes

• Dataset labels do not contain source path.

• Recipe dataset_source and output directories are no longer converted to absolute paths.

• More complete recipe history for tasks, including more of their properties

• Recipe-driven data analysis: Figures get added to recipe with default label if no label is provided.

• aspecd.processing.Noise: explicit noise amplitude can be given.

• Model can add label to created dataset.

• ModelTask adds result label as id to result.

• Plotter: Default figure size changed to (6., 4.) inch

Fixes

• aspecd.tasks.Task.to_yaml() serialises numpy arrays

• Datasets from foreign packages are correctly listed in recipe history

• aspecd.utils.copy_keys_between_dicts() properly traverses

• aspecd.utils.Yaml handles numpy.double

• Recipe-driven data analysis: automatically generated figure filenames get added to recipe figure record

• Models work now correctly when based on a dataset

• aspecd.model.FamilyOfCurves sets correct values for additional axis

• aspecd.processing.Differentiation works correctly for 2D datasets

• aspecd.processing.Noise: normalisation works with >1D datasets

• aspecd.plotting.SinglePlotter2DStacked: ylabel is set to third axis if offset = 0

Version 0.5.0

Released 2021-10-12

New features

• Tasks/Recipe-driven data analysis

  • YAML representation of tasks and recipes using aspecd.tasks.Task.to_yaml() and aspecd.tasks.Recipe.to_yaml() - convenience methods for later use in guided recipe generation

  • aspecd.tasks.AggregatedanalysisTask for performing a SingleAnalysisStep on a series of datasets, aggregating the result in a CalculatedDataset

  • aspecd.tasks.TabulateTask for tabular representation of data of a dataset

• Datasets

  • New attribute aspecd.dataset.Axis.index (for individual labels for each data point, similar to pandas and for tabular data)

  • aspecd.dataset.Dataset.tabulate() to create tables from datasets

• Analysis steps

  • New class aspecd.analysis.AggregatedAnalysisStep for aggregating the results of a SingleAnalysisStep on multiple datasets in a CalculatedDataset

• Tabular representation of datasets

  • New module aspecd.table

  • Series of output formats for tables (including DokuWiki and LaTeX)

  • Tables can have captions that are output as well

• Utils

  • aspecd.utils.get_package_data() for obtaining package data (i.e., non-code files contained in distribution)

Changes

• aspecd.analysis.BasicCharacteristics always returns scalars or lists in its results and writes index (for compatibility with aspecd.analysis.AggregatedAnalysisStep and tabular output).

Version 0.4.0

Released 2021-10-08

Note: Starting with this release ASpecD requires Python >= 3.7.

New features

• Tasks/Recipe-driven data analysis

  • New attribute aspecd.tasks.PlotTask.target allows adding a plot to an already existing plot.

  • aspecd.tasks.Task.to_dict() adds (implicit) parameters of underlying task object

  • Classes from the ASpecD framework can be used without prefixing them with “aspecd” in recipes with “default_package” set to a package based on the ASpecD framework.

  • serve command outputs log messages for each task

  • Command-line options for serve setting the log level/verbosity

  • Catching of errors, excluding the stack trace and only showing the error message (but full stack trace in verbose mode)

  • Switch in recipe to suppress writing history (for development/debugging, issuing warning on the command line via logging)

  • New structure of recipes: Move default_package and autosave_plots to new dict settings; output_directory and datasets_source_directory to new dict directories

  • Add format dict to recipe with fields type and version

  • Automatically convert old recipe formats within aspecd.io.RecipeYamlImporter

  • Processing steps writing parameters during execution and applied to multiple datasetes are unpacked in the recipe history if these parameters change for each dataset

• References in processing and analysis steps and models (using bibrecord package)

Version 0.3.1

Released 2021-09-21

The following bugs have been fixed:

• Handling of lists as properties in recipes

• Improved handling of axes labels with xkcd style

• Offset in SinglePlotter2DStacked can be set to zero

Version 0.3.0

Released 2021-09-02

Note: This is the last ASpecD release with explicit support for Python 3.5.

New features

• Processing steps

  • Adding (coloured) noise to datasets (aspecd.processing.Noise)

  • Provide a new range of axis values for a dataset for correction (aspecd.processing.ChangeAxesValues)

• Analysis steps

  • Power spectral density of 1D dataset (aspecd.analysis.PowerDensitySpectrum), e.g., for analysing noise

  • Polynomial fit of 1D data (aspecd.analysis.PolynomialFit)

  • Linear regression of 1D data without fitting the intercept (aspecd.analysis.LinearRegressionWithFixedIntercept)

  • Additional methods in aspecd.analysis.BlindSNREstimation

• Class aspecd.model.Model

  • New attribute aspecd.model.Model.description

  • New non-public method _sanitise_parameters

• New models

  • aspecd.model.Polynomial for evaluating polynomials (e.g., as obtained using aspecd.analysis.PolynomialFit)

  • aspecd.model.Zeros

  • aspecd.model.Ones

  • aspecd.model.Gaussian

  • aspecd.model.NormalisedGaussian

  • aspecd.model.Lorentzian

  • aspecd.model.NormalisedLorentzian

  • aspecd.model.Sine

  • aspecd.model.Exponential

  • aspecd.model.CompositeModel for models consisting of a (weighted) sum of individual models

  • aspecd.model.FamilyOfCurves for inspecting systematic variations of one parameter of a given model

• Tasks

  • Comments can be added easily to processing and analysis steps using the top-level key comment of the respective task.

• Utils

  • aspecd.utils.not_zero() ensuring a float not to cause DivisionByZero errors

Changes

• aspecd.processing.Differentiation uses numpy.gradient() instead of numpy.diff()

• aspecd.processing.BaselineCorrection returns polynomial coefficients in unscaled data domain

Fixes

• Axis labels without “/” if no unit is present

• aspecd.metadata.Measurement handles dates imported from YAML (implicitly converted into datetime.date object)

Version 0.2.2

Released 2021-06-19

The following bugs have been fixed:

• Normalisation to minimum now divides by absolute value of minimum

• Normalisation raises ValueError in case of unknown kind

• Import with explicit importer when importer resides in (sub)package

• Recipe history shortens dataset source if dataset_source_directory has trailing slash

Version 0.2.1

Released 2021-06-03

The following bugs have been fixed:

• Report: template can have “..” in its path

• aspecd.utils.copy_values_between_dicts() cascades through source dict

• Add missing template files for sphinx multiversion

Additionally, the following new helper functions appeared:

• aspecd.utils.remove_empty_values_from_dict()

• aspecd.utils.convert_keys_to_variable_names()

Version 0.2.0

Released 2021-05-19

New features

• Singleplot and multiplot tasks automatically save results to generic file(s) when no filename is provided

• Importer and importer parameters can be set in recipe

• DatasetImporterFactory: importer can be set explicitly, parameters can be passed to importers

• DatasetImporter with parameters property

• Meaningful error messages for exceptions in ProcessingSteps, AnalysisSteps, Plotters

• Method create_dataset() in AnalysisStep

• PeakFinding (for 1D data)

• BlindSNREstimation (currently only with simplest method)

• BasicStatistics (mean, median, std, var)

• BasicCharacteristics (min, max, amplitude, area)

• ProcessingStep provides non-public method _set_defaults() for setting default parameters before sanitising parameters.

• Filtering (with uniform, Gaussian, and Savitzky-Golay filter)

• Interpolation (at least for 1D and 2D datasets)

• Normalisation:

  • Act on parts of the data of a dataset

  • Handle noise for ND data with N>1

• RangeExtraction: extract range of data from dataset (using slice notation)

• MultiprocessingTask (and SingleprocessingTask aliasing ProcessingTask)

• ScalarAxisAlgebra: perform scalar algebra on axis values

• DatasetAlgebra: add and subtract data of second dataset to/from dataset

• CommonRangeExtraction for 1D and 2D datasets

• SinglePlotter2D:

  • Filled contour plot with additional contour lines that can be styled

  • Lines of contour plot can be styled

• SliceExtraction now handles both, axis indices and axis values

Changes

• Removed parameter source from method _get_importer in DatasetImporterFactory, importer factories of derived packages now handle ASpecD-implemented importers by default.

• Dataset: method aspecd.dataset.append_history_record() made public

• SystemInfo: Packages contain now full list of dependencies with version numbers of currently installed packages

• SliceExtraction:

  • parameter “index” renamed to “position”

  • works for ND datasets with N>1

• ProcessingStep split into SingleProcessingStep and MultiProcessingStep

  All processing steps previously inheriting from aspecd.ProcessingStep need to inherit now from aspecd.SingleProcessingStep to continue working as expected.

• Plots throw “NotApplicableToDataset” exceptions rather than “PlotNotApplicableToDataset”

Fixes

• SingleanalysisTask assigns results of multiple (individual) datasets

• Exceptions print messages

New dependencies

• scipy (for interpolation in ExtractCommonRange and various analysis steps)

Version 0.1.1

Released 2021-05-03

The following bugs have been fixed:

• MetadataMapper: Fix sequence of mapping operations performed

• MetadataMapper: Mappings are automatically loaded from file if filename is given

• CompositePlotter: Legends for subplots work

• SliceExtraction: Remove correct axis from dataset

• MultiPlotter1D*: Fix problem in conjunction with CompositePlotter and assigning drawings

• SliceExtraction: fix problem extracting slice with index zero

• CompositePlotter: more intuitive axes_positions

• Fix bug with aspect ratio of 2D plots using imshow

• Update intersphinx mapping for matplotlib

Version 0.1.0

Released 2021-04-24

• First public release

• List of generally applicable concrete processing steps

• List of generally applicable concrete plotters

• Recipe-driven data analysis fully working with history

• Introduced ASpecD dataset format (ADF)

Version 0.1.0.dev280

Released 2019-06-14

• First public pre-release on PyPI