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NEWS
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Notes for updating IO Pages
----------------------------------
dep nifti-mrs -> from conda-forge for python311 env
Version 1.1.1rc1 - 11 Feb, 2024
------------------------------------------------------------------------------
New icon for Datasim, some updates for Python 3.9 and later, bugfix for Linux
shortcut creation.
Analysis
- New file parser format for Analysis to read Advanced (multi-frame) DICOM
files for eja_svs_mpress sequence data.
- bugfix in twix reader, saving plots to file
Pulse
- refactor algorithm for refocus gradient calculation.
Version 1.1.0 - 10 May, 2023
------------------------------------------------------------------------------
Some updates for XA software data formats on Siemens, bugfixes, and a couple
of new utility functions. Also updated manuals for citation of VESPA paper
in MRM journal.
Analysis
- Added a utility function to sort a directory of DICOM files into
subdirectories based on each Series name. The utility is launched in via:
Help->Utilities->DICOM_Series_Sort_and_Rename
A 'Select Directory' dialog pops up to select the directory with DICOM files
in it. Sub-directories are created at that level and DICOM files are moved
under respective Series subdirectories. NOTE - This command may take up to a
few minutes depending on the number/size of files being parsed. The only
indication of when it is finished is when the subdirectories appear, if you
have a file browser open.
- Updated I/O parsers for CMRR eja_xxx spectroscopy sequences, press/mpress due
to XA30 recompile. Also for dkd_slaser sequence.
- Updated GE I/O parser for software versions 27 and 28 thanks to a patch from
Alexander Richard Craig-Craven from University of Bergen.
- Can now open FIDSUM and NON-FIDSUM datasets into same notebook so long as
sw, frequency and npts are still the same. This was to allow users to open a
macromolecular basis spectrum for fitting FIDSUM sLASER data.
- Added functionality in View to create a Derived dataset tab from Plot C for
added/subtracted Plots A/B. This was needed to properly process MPRESS
datasets after Preprocess of ON and OFF data into SUB after all FIDs are
aligned, and NOT when the twix/DICOM FIDs are opened. At that point there
might be jitter in the ON/OFF that processing could better correct.
- Can also create a Derived dataset tab from the SVD sub-tab in Spectral Tab
Pulse
- minor bug fixes for refocusing profile display when xaxis in cm/kHz.
- default xaxis is now kHz rather than cm.
Version 1.0.2 - 23 July, 2021
------------------------------------------------------------------------------
This is mainly a bugfix release - thanks to our users for the feedback
Analysis
- Changed code so that the User Defined Parser file in AppData/Local/Vespa
expects the original name of analysis_import_menu_additions.ini rather than
analysis_import_menu_additions_py3.ini used as a hack during upgrade to Py3.
The default behavior was to create a file called 'analysis_import_menu_additions.ini'
on installation, so that (hopefully) won't mess users up too much.
Version 1.0.1 - 23 July, 2021
------------------------------------------------------------------------------
This is mainly a bugfix release - thanks to our users for the feedback
Analysis
- A few small whitespace tweaks in LCM style PDF file output
- Bugfix, Py2 to Py3 'if' logic for empty list or not-empty list in LM optimize
- Updated WBNAA parser to read Siemens twix VE data
REMINDER - See News for Version 1.0.0 for Python 3 and GitHub updates.
Version 1.0.0 - 14 April, 2021
------------------------------------------------------------------------------
!!! Backwards compatibility warning !!!
This is a Major udate to the Vespa package. The two most important changes are:
1) the Vespa code base has been updated to Python 3.
2) the Vespa code repository and docs have moved to GitHub and GitHub Pages
Due to a lot of free time during the COVID-19 pandemic, Vespa has been
rewritten, refactored, and redesigned to work under Python 3.x. Due to numerous
changes in the Vespa code, this version does NOT work in Python 2.7.x anymore.
But, the overall program is backwards compatible at the level of the Vespa
database and VIFF and other saved file formats. Ie. it should read in your old
*.xml results sets just fine.
We have bumped a major version number to 1.0.0 to reflect this change. There
may still be a few bugs under the hood from all the coding 'improvements' but
we are working diligently to squash them all as reported.
Note. To use Vespa 1.0.0 you MUST do a 'new' install into a Python 3.7
environment. If you have a previous Vespa installation, the new version should
find and make use of your existing Vespa database.
Analysis
--------------
- added algorithms to Preprocess tab for more Coil combination, Data Exclusion,
B0 and Phase Correction, and more ways to display and review results.
- added standard data parsers for Philips DICOM MRS files, Siemens Twix sLASER
files from CMRR, Siemens Twix svs_se and Twix svs_se_edit WIP529 files.
- moved wavelet filter baseline code into Python code
- moved HLSVDPro water removal into Python code
- HLSVDPro results from the Analysis 'Spectral' sub-tab can now be output for
use in other applications or user's projects.
- added LMFIT optimizaton to Analysis to allow users to set inequality constraints
on metabolite frequencies to better separate small peaks from larger ones to
which they are adjacent.
- there is a single and multi-page results output called 'LCM Layout' that can
be sent to PDF or PNG. This simulates a layout similar to LCModel.
Simulation
-------------
- slight change to default plot layouts in the Experiment-Visualize sub-tab.
Windows are set up at tabs on first plot. User can then move the tabs into
a more side-by-side layout if they desire.
- updated example Pulse Sequence and Experiments to Python 3
Pulse
-------------
- updated example Pulse Designs and Transform Kernels to Python 3
DataSim
-------------
- The previous 'Priorset' app has been renamed to 'DataSim' for better clarity
(otherwise known as a 'marketing decision' :)
- Separated the 'Baseline' tab into two separate tabs now called 'Baseline' and
'Macromolecules'. This allows users to create these two signal contributions
separately using either Gaussian or Lorentzian lineshapes.
- HSLVDPro fitting results from the Analysis 'Spectral' sub-tab can be read
in to the 'Macromolecules' tab and turned on/off to create a simulated MMol
signal contribution.
Vespa is now on GitHub!
---------------------------------------------
This is the first release from Vespa's new GitHub repository. Due to an
unfortunate (or fortuitous) server crash, the Vespa project and documentation
(installation, user manuals and development topics) have relocated to GitHub:
https://github.com/vespa-mrs/vespa (Vespa source repository)
https://vespa-mrs.github.io/vespa.io/ (Vespa Pages web site)
The Vespa repository remains primarily a resource for developers as the Vespa
package should still be installed from PyPI under the name of Vespa-Suite:
https://pypi.org/project/Vespa-Suite/
Please note that the PyGAMMA/GAMMA package, one of Vespa's dependencies, has
also been updated to Python 3.x and relocated to GitHub at:
https://github.com/pygamma-mrs/gamma/ (PyGAMMA/GAMMA source repository)
https://pygamma-mrs.github.io/gamma.io/ (PyGAMMA/GAMMA GitHub Pages web site)
Please note that both Pages sites are still in the process of being translated
from Trac, so there may be typos, broken links, poor formatting, etc. We
appreciate your patience during this process.