GrainSizeTools - Release v3.1.0

This is a major release. Main changes:

• The calc_shape method of the stereology module has been renamed to two_step.
• A new method, called calc_volume_fraction, has been added to the stereology module. It uses the lognormal parameters estimated by the two-step method to estimate a volume fraction occupied by any range of grain sizes.
• Several templates with different examples of grain size population analysis have been added. These include:
  • quantification of grain size distributions (grain_size_analysis_template.ipynb)
  • approximation of grain size distributions using stereological methods (stereology_analysis_template.ipynb),
  • paleopiezometry (paleopizometry_template.ipynb).
• Restructuring of the script organisation and refactoring code to improve readability.
• The script documentation has been completely rewritten for the new script organisation. It should now be easier for newcomers. See new documentation at https://github.com/marcoalopez/GrainSizeTools/wiki

Scientific Software - Peer-reviewed - Python
Published by marcoalopez almost 2 years ago

GrainSizeTools - Release v3.0.2

This is a minor release. This version corrects the issue #15 (a bug in the Van der Wal piezometer).

Scientific Software - Peer-reviewed - Python
Published by marcoalopez about 5 years ago

GrainSizeTools - Release v3.0.1

This is a minor release. This version corrects the issue #15 (a bug in the Van der Wal piezometer).

Scientific Software - Peer-reviewed - Python
Published by marcoalopez about 5 years ago

GrainSizeTools - Release v3.0RC

This is the GrainSizeTools script v3.0RC (release candidate). The script has been completely reorganized including new modules and features. Its use is no longer compatible with previous versions (v2.x). You can find the new documentation on the main page of the script. In addition, the script now has a folder with use-examples based on Jupyter notebooks. Enjoy it!

Scientific Software - Peer-reviewed - Python
Published by marcoalopez almost 6 years ago

GrainSizeTools - Release v3.0beta3

This is a major (beta3) release

The script has been completely reorganized with new modules and functions. Its functionality is not compatible with previous versions. You can find the new documentation (still in development) with usage examples here: https://github.com/marcoalopez/GrainSizeTools/blob/master/DOCS/getting_started.md

Scientific Software - Peer-reviewed - Python
Published by marcoalopez almost 6 years ago

GrainSizeTools - Release v2.0.4

This is a minor release fixing a bug

• Bug correction (issue#15)

Scientific Software - Peer-reviewed - Python
Published by marcoalopez almost 6 years ago

GrainSizeTools - Release v3.0beta2

This is a major (beta2) release

The script has been completely reorganized with new modules and functions. Its functionality is not compatible with previous versions. You can find the new documentation (still in development) with usage examples here: https://github.com/marcoalopez/GrainSizeTools/blob/master/DOCS/getting_started.md

Scientific Software - Peer-reviewed - Python
Published by marcoalopez almost 6 years ago

GrainSizeTools - Release v3.0beta1

This is a major (beta) release

The script has been completely reorganized with new modules and functions. Its functionality is not compatible with previous versions. You can find the new documentation (still in development) with usage examples here: https://github.com/marcoalopez/GrainSizeTools/blob/master/DOCS/getting_started.md

Scientific Software - Peer-reviewed - Python
Published by marcoalopez almost 6 years ago

GrainSizeTools - Release v2.0.3

This is a minor release with incremental improvements. The following features were added:

• Add new functions test_lognorm and qq_plot to test lognormality
• Bug correction (issue#13)
• Now the maximum precision of the kde estimator can be set manually
• Incremental improvements in the code (including some reorganization)
• Incremental improvements in the plots
• Requirements list update

Scientific Software - Peer-reviewed - Python
Published by marcoalopez almost 7 years ago

GrainSizeTools - Release v2.0.2

This is a minor release with incremental improvements made during the review of the script in the Journal of Open Source Software. The following features were added:

• Some tweaks in the plots to make them look better and avoid blank spaces when using Jupyter notebooks
• Improvements in the documentation of some functions.
• Use np.sum() instead of sum() throughout the script for consistency
• The calc_diffstress function indicates the valid names when the piezometer is misspelt

Scientific Software - Peer-reviewed - Python
Published by marcoalopez over 7 years ago

GrainSizeTools - Release v2.0.1

Release Notes

This is a minor release with incremental improvements. The following features were added: - The find_grain_size function now returns the geometric mean when using a linear scale. - The calc_diffstress function allows correcting paleostress estimates for plane stress using the correction factor proposed by Behr and Platt (2013).

Scientific Software - Peer-reviewed - Python
Published by marcoalopez over 7 years ago

GrainSizeTools - Release 2.0

Release Notes

This is a major release

• The code has been completely reorganized, some functions added, and most Python functions renamed. GrainSizeTools v2.0 is only compatible with Python 3.5 or higher.

Added: - New piezometric relations - Normalized grain size distribution (allowing to use the mean, median, or frequency peak as the normalized factor) - The two-step method now automatically finds the optimal number of classes to adjust the logarithmic function. - Other minor additions (see documentation)

Improved: - The script is now separated in different Python files to facilitate modifications, extension, and for easy bug tracking - Now the Saltykov and the two-step stereology methods are in separated functions

Scientific Software - Peer-reviewed - Python
Published by marcoalopez over 7 years ago

GrainSizeTools - Release v1.4.5

Release Notes

Fix a problem with labels in the plots - cosmetic improvements in the figures

Planned features: - Add more paleopiezometric relations for other phases: ice, salt, alloys, etc. - A new method to estimate optimal bandwidth and binsizes in multimodal populations

Scientific Software - Peer-reviewed - Python
Published by marcoalopez almost 8 years ago

GrainSizeTools - Release v1.4.4

Release Notes

This is a minor release with incremental improvements - added a new function to estimate reliable confidence intervals - cosmetic improvements in the figures

Planned features: - Add more paleopiezometric relations for other phases: ice, salt, alloys, etc. - A new method to estimate optimal bandwidth and binsizes in multimodal populations

Scientific Software - Peer-reviewed - Python
Published by marcoalopez almost 8 years ago

GrainSizeTools - Release v1.4.3

Release Notes

This is a minor release with incremental improvements (mostly cosmetic). - all matplotlib code is now in oop style - the script warns you if you are using a data set that is too small - cosmetic improvements in the figures

Planned features: - Add more paleopiezometric relations for other phases: ice, salt, alloys, etc. - A new method to estimate an optimal kde bandwidth in multimodal populations

Scientific Software - Peer-reviewed - Python
Published by marcoalopez almost 8 years ago

GrainSizeTools - Release v1.4.2

Release Notes

This is a minor release. The following changes were implemented: - Added new piezometric relations including: - Quartz: Stipp and Tullis (2003) and Holyoke and Kronenberg (2010) for BLG recrystallization - Olivine: Van der Wal et al. (1993) and Jung and Karato (2001) - Calcite: Rutter (1995) for GBM recrystallization - Albite: Post and Tullis (1999) - Improvements in the function specifications

Planned features: - Add more paleopiezometric relations for other phases: ice, salt, alloys, etc. - A new method to estimate an optimal kde bandwidth in m

Scientific Software - Peer-reviewed - Python
Published by marcoalopez about 8 years ago

GrainSizeTools - Release v1.4.1

Release Notes

This is a minor release. The following change was implemented: - Added a new function to estimate differential stress in calcite using the Rutter (1995) paleopiezometer

Planned features (v1.4): - Add more paleopiezometric relations for other phases: olivine, calcite, ice, alloys, etc. - A new method to estimate an optimal kde bandwidth in m

Scientific Software - Peer-reviewed - Python
Published by marcoalopez about 8 years ago

GrainSizeTools - Release v1.4

Release Notes

This is a major release. The following changes were implemented: - Added a new function to estimate differential stress in quartz via paleopiezometric relations

Planned features (v1.4): - Add paleopiezometric relations for other phases: olivine, calcite, ice, alloys, etc. - A new method to estimate an optimal kde bandwidth in multimodal population

Scientific Software - Peer-reviewed - Python
Published by marcoalopez over 8 years ago

GrainSizeTools - Release v1.3.4

Release Notes

This is a minor release. The following changes were implemented: - The 'extract_areas' function now can open excel (.xlsx) files. - Improvements in the format of the function documentation strings.

Planned features (v1.4): - Estimate differential stress from grain size using different paleopizometric relations - A new method to estimate an optimal kde bandwidth in multimodal populations. - A new method to estimate a safe bin size (or number of classes) when using the Saltykov method.

Scientific Software - Peer-reviewed - Python
Published by marcoalopez over 8 years ago

GrainSizeTools - Release v1.3.3

Release Notes

This is a minor release. The following changes were implemented: - The 'derive3d' function now checks whether 'numbins' is an integer (as required by the function) - The function responsible for estimating the area weighted grain size distribution (calcareaweightedgrainsize) has been partially rewritten and optimized.

Fixed errors: - The previous version of the script (v1.3.2) raised an error when trying to define a specific bin size using a number-weighted approach.

Planned features (v1.4): - Estimate differential stress from grain size using different paleopizometric relations - A new method to estimate an optimal kde bandwidth in multimodal populations. - A new method to estimate a safe bin size (or number of classes) when using the Saltykov method.

Scientific Software - Peer-reviewed - Python
Published by marcoalopez over 8 years ago

GrainSizeTools - Release v1.3.2

Release Notes

This is a minor release. The following changes were implemented: - Now the plots are optimized for Matplotlib v2.0 or higher. - The findgrainsize function now returns the interquartile range - Improved functions output in the shell - Minor change in the calcareaweighted_grainsize function to prevent bad behavior when using Pandas data frame instead of Numpy arrays

Upcoming features (v1.4): - New method to estimate an optimal kde bandwidth in multimodal populations. - New method to estimate a safe bin size (or number of classes) when using the Saltykov method.

Scientific Software - Peer-reviewed - Python
Published by marcoalopez almost 9 years ago

GrainSizeTools - Release v1.3.1

Release Notes

This is a minor release. The following changes were implemented: - Now the extractareas function allows you to search and load the data through the file explorer of your operating system (i.e. you no longer have to define the file path manually). Also, it recognizes the type of file automatically. - Several changes to prepare the script to the Matplotlib v2.0 new features. - For consistency, the parameter 'addPerimeter' in the calcdiameters function was renamed as 'correct_diameter'.

Upcoming features: - New method to estimate an optimal kde bandwidth in multimodal populations

Scientific Software - Peer-reviewed - Python
Published by marcoalopez about 9 years ago

GrainSizeTools - Release v1.3

Release Notes

This is a major release. The following changes were implemented: - Now the script requires Numpy v1.11 or higher to work properly. The script will check your Numpy version once you run it. - The parameter type in the extract_areas function has been renamed as form to avoid the use of a Python keyword. - Taking advantage of the new features implemented in Numpy v1.11, the find_grain_size function implements new methods to estimate the bin size in the histograms including an automatic mode (the default) and the Freedman-Diaconis', Sturge's, Scott's, Doane's, Rice's, and square root rules. See more details in the script documentation or here. - The output showed in the shell after calling the find_grain_size function have been reorganized and improved for better clarity. - The derive3D function automatically generates a text (csv) file containing the midpoints, class frequencies and cumulative volume estimated. - The titles of the different plots have been renamed for better clarity. - The get_Scott_binsize and get_FD_binsize functions have been deprecated. - Improvements in the function specifications. - Minor changes to meet the Style Guide for Python Code

Upcoming features: - New method to estimate an optimal kde bandwidth in multimodal populations

Scientific Software - Peer-reviewed - Python
Published by marcoalopez about 9 years ago

GrainSizeTools - Release v1.2

Release Notes

This is a major release. It adds new features and plots in the function find_grain_size. For details see below: - Now the user can define in the extract_areas function other column names different to the default name 'Areas'. - The find_grain_size function allows estimating the logarithmic and square root grain sizes (including the generation of new plots). - For better consistency, several functions responsible for generating the plots have been renamed. - Minor cosmetic changes.

Upcoming features: - New methods to estimate optimal bin sizes and bandwidths in multimodal populations

Scientific Software - Peer-reviewed - Python
Published by marcoalopez over 9 years ago

GrainSizeTools - Release v1.1.1

Release Notes

This is a minor release. - Now the same script is compatible with Python 2.7.x and 3.x versions.

Scientific Software - Peer-reviewed - Python
Published by marcoalopez almost 10 years ago

GrainSizeTools - Release v1.1

Release Notes

This is a major release. It fixes a known bug in the previous version. For details see below: - This release fixes a problem when using the two-step method in Python 3. Now, there are two different versions of the same source code, one for Python 2.7.x and one for Python 3.x versions. I am currently working to have a single compatible script (i.e. Py2-3) in the next version. - The 'importdata' function has been renamed as 'extractareas'. - now it is indicated how to change the current directory when running the script. - There is a general reorganization of the source code to facilitate future implementations, this includes: i) a simplification of the 'derive3D' function; ii) the addition of a new function named 'genxgrid'; iii) the relocation of the functions responsible for generating the plots. - It is now possible to obtain the antispheres plot by changing a parameter in the 'Saltykov' function. - A number of minor changes to improve the source code following the Style Guide for Python Code and other language corrections in the specifications of the functions

Scientific Software - Peer-reviewed - Python
Published by marcoalopez almost 10 years ago

GrainSizeTools - Release v1.0

Release Notes

This is a major release. The script contains a large number of changes and new features. See below: - GrainSizeTools script is now licensed under the Apache License, Version 2.0. - The script now requires Pandas 0.16 or higher installed in the system. - The importdata function now automatically extracts the data corresponding to the areas of grain profiles from the tabular-like data generated by the ImageJ application. It is no longer necessary to make intermediate steps between the ImageJ output and the GrainSizeTools script input. - The organization of the script has changed significantly. All the code to generate the plots is now separated from the main functions. Specifically, each plot has their self-contained Python function. This facilitates to modify the parameters that control the aesthetics of the different plots. - The GrainSizeTools script shows the Python current working directory when running the script for the first time. - The Saltykov method implemented within the Saltykov function places the R parameter at the center of the classes (i.e. the midpoints) instead of at the upper edges of the bins (as in previous versions). - Now the rule used by default to estimate the bin size in the findgrainsize function is the Scott rule instead of the Freedman-Diaconis rule. - The derive3D function now includes several new features, including i) the ability to quantitatively estimate the volume occupied by a particular grain fraction defined by the user, ii) an experimental method to quantitatively estimating the actual 3D population of grain sizes when log-normal distributions are expected. See details in the documentation. - A number of cosmetic changes either in the results and the plots.

For previous versions see: https://sourceforge.net/projects/grainsizetools/files/?source=navbar

Scientific Software - Peer-reviewed - Python
Published by marcoalopez over 10 years ago