Version 0.12.0

Released 2024-12-22

Note: This version comes with a new version of the recipe format: 0.3. Existing recipes are updated automatically on import.

New features

• I/O

  • Importer logs warning if importing did not populate data array in dataset.

• Plotting

  • Attribute clim in :class:aspecd.plotting.SurfaceProperties
  • Parameter threshold for determining the levels of a contour plot in class :class:aspecd.plotting.SinglePlotter2D
  • Attributes number_of_colors and first_color in :class:aspecd.plotting.MultiPlot1DProperties: Fixed number of elements from colormap, to have same colour succession in plots with different number of curves if a colormap is specified, and potential offset in colormap if starting with white/a light colour.
  • Attributes norm and norm_parameters in :class:aspecd.plotting.SurfaceProperties.

• Plot annotations

  • Parameter units in :class:aspecd.annotation.Text, :class:aspecd.annotation.Marker, :class:aspecd.annotation.VerticalLine, :class:aspecd.annotation.HorizontalLine, :class:aspecd.annotation.VerticalSpan, and :class:aspecd.annotation.HorizontalSpan allowing to position using axes rather than data coordinates.

• Processing

  • :class:aspecd.processing.SliceRearrangement for rearranging slices of a dataset along one dimension.
  • :class:aspecd.processing.DatasetAlgebra operates on a list of datasets, allowing to add/subtract multiple datasets from a given dataset.
  • :class:aspecd.processing.Denoising1DSVD for denoising 1D datasets using singular value decomposition.

• Tasks

  • Functions add and multiply for properties of tasks in recipes.
  • New default setting number_of_colors on recipe level: Fixed number of elements from colormap, to have same colour succession in plots with different number of curves if a colormap is specified.
  • Tasks can be marked as to be skipped, using the skip keyword on the top level of the task definition in a recipe.

Changes

• Recipe structure changed slightly: The settings dictionary has a new sub-dictionary colors, and the default_colormap key moved there, together with the new keys number_of_colors and first_color.

  • New recipe format version: 0.3.
  • Existing recipes are updated automatically on import.

• Figure properties (see :class:aspecd.plotting.FigureProperties) are applied to the figure before the actual plotting is done, as some plotters need to know the (final) figure size or else.

• Axes properties (see :class:aspecd.plotting.AxesProperties) are applied to the axes before the actual plotting is done, as some plotters need to know the (final) axes limits or else.

Fixes

• Plotter with colorbar work with recipes (no longer recursion in to_dict())
• :class:aspecd.processing.SliceRemoval handles lists properly
• :class:aspecd.processing.SliceRemoval removes value(s) from corresponding axis
• :class:aspecd.processing.Averaging handles inverted axes (e.g., ppm scale) correctly regardless how ranges are given
• :class:aspecd.plotting.MultiPlot1DProperties handles explicit colours of individual drawings correctly.

Updated requirements

• bibrecord >= 0.2

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.TextProerties
  • 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 :class: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
• :class: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

• 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.