NITRC JIST: Java Image Science Toolkit Forum: open-discussion

one bracket too many?

Emma Sprooten — Fri, 25 Aug 2017 14:19:04 GMT

Dear Andrew Plassard et al,

I just installed py-jist (which has been a lifesaver!) on a new machine. I got the same message when running setup.py and JIST-run tests:

 [color=#808080]File "/Users/emmasprooten/Library/Python/2.7/lib/python/site-packages/PyJIST/PyJIST.py", line 155[/color]
[color=#808080] [/color]os.system(full_cmd))
[color=#808080] [/color]^
[color=#808080] [/color]SyntaxError: invalid syntax

 Based on this I removed the last bracket on line 155 in setup.py: os.system(full_cmd)[b])[/b]

Now it all runs fine. Not sure if this little bracket was added recently but I thought it's worth sharing my experience.

Emma

The layout file does not work.

Seongjin Choi — Thu, 25 Feb 2016 20:30:31 GMT

The layout included in the DTI tutorial does not work as described in the tutorial.
When the layout was called JIST console was idling without further activity.
It simply does not react. No error or warning message at all.
My system is CentOS 6.7 with Mipav (7.3) and a recent nightly version of JIST-CRUISE.

Announcement: PyJIST

Andrew Asman — Sun, 06 Apr 2014 20:28:32 GMT

We are pleased to announce the first release of PyJIST.

PyJIST is Python-based wrapper for accessing the JIST command line interface (CLI) without the hassle of constructing complicated classpaths and memorizing long module definitions.

It's pretty cool. You should try it. See the link below for the installation instructions and common use cases.

https://www.nitrc.org/plugins/mwiki/index.php/jist:PyJIST

JIST installed as JAR

Justin Senseney — Mon, 23 Dec 2013 15:24:10 GMT

Using a nightly build of MIPAV and JIST 3.0, you can install JIST by placing the JIST jar in the MIPAV plugin directory (this is the /mipav/plugins directory in your user folder). This speeds up the installation process of JIST.

-Justin

New JIST Modules: T1 mapping

dpolders — Wed, 03 Mar 2010 15:57:50 GMT

Hi all!

I'd like to introduce two new JIST modules, and a supporting algorithm:
-plugins.quantitative.UnshuffleT1MappingVolumes
-plugins.quantitative.T1Mapping_SliceShift
-algorithms.quantitative.T1Fitting

Although this slice-shift technique is rather specialized, the T1 fitting might appeal to a wider audience, so I thought to share it with all.

This set of modules allows for post-processing of a quantitative T1 sequence using the slice-shift technique. By 'sharing' a global inversion pulse a volume of ~50 slices are acquired at different times. Next repetition, the order in which these slices are acquired is shifted, and in ~25 repetitions all slices are measured at 25 different time points.
The result is a relatively quick method to acquire 20-30 time points to fit a T1 value to, which allows for high quality T1 fitting. The disadvantage of this slice-shifting is that the slices need to be re-ordered before fitting can be done.

These modules allow for automatic reordering of slices, based on our current implementation of the slice-shift technique (over the dynamics), and the slice-ordering of the sequence (interleaved/ascending/descending) (over one volume).

The second module, responsible for the actual T1 fitting, is an implementation of the Levenberg-Marquardt optimizer. The optimization was -drastically- sped up by using the analytical solutions for the 1st and 2nd derivatives of the function to be optimized (with thanks to Mathematica). Of course this wont work for all functions and applications, but it increased the processing speed from 455 to roughly 7500 voxels per minute. I am in no way a real programmer however, and I am sure there are many more steps that can be taken to optimize this code.

While I think I did a reasonable job at annotating the code and explaining the modules in the description fields, I will have a stab at writing a small manual for the Wiki. Not sure when that will be finished though.

I look forward to getting some feedback, or even -gasp- user questions!

kind regards,
Daniel

Welcome to Open-Discussion

Christian Haselgrove — Tue, 02 Jun 2009 23:13:02 GMT

Welcome to Open-Discussion