JTutils is a set of python scripts that enhance processing capabilites of Topspin.

Some scripts are specific to process data acquired with pulse sequences developped in Lille, France by Julien TREBOSC.

WARNING : use of these script WILL CORRUPT your Bruker data (in sense of GPL: Good Laboratory Practice):

• no MD5 signature of files is done
• no auditing is done

The script will modify in place fid, ser, acqu(123)(s), 1r, 2rr etc... files

The author decline any responsability for program or data loss that would result from the installation and use of these scripts.

JTutils sets of scripts comprise:

• JTutils/TSpy : contains the python scripts run under Topspin environment
• JTutils/CpyBin : contains C python scritps usually called from TSpy scripts (but then can be run as standalone scripts)
• JTutils/CpyLib : contains python library to read/write Bruker data

Developped with python 2.7 (ubuntu, macosx/topspin 4).

Updated for python 3 (ubuntu, topspin 4).

Requirements for running python program:

Scripts are designed to run with the lowest version number possible. But with time tests were run with more recent versions. So minimum version can depend upon script

• in CpyLib: brukerIO.py or brukerPARIO.py package will needs at least
  • python 2.5
  • numpy 1.0.1
• in CpyBin : same requirement as CpyLib + processing module for covariance script
• in TSpy : all scripts should work with topspin provided jython version except for those using argparse and subprocess.check_call which exist only in jython 2.7 which is provided within topspin >=3.5.

Other used standard modules :

• sys
• os
• math
• shutil
• re
• array
• subprocess

INSTALLATION

1. Install folder JTutils to a destination directory DESTDIR.

2. Install a working python + numpy environment (tested with anaconda/miniconda on Linux, MacOSX and windows).

   For miniconda installation:

   1. download miniconda (python 2 or 3) at https://docs.conda.io/en/latest/miniconda.html
   2. run the miniconda installer (100-200Mb). No need to ask for numpy: during the setup script (see step 4) you will be asked to create a specific conda environment named JTutils which will have numpy.

3. In Topspin preferences, set [DESTDIR]/JTutils/TSpy as scanned directory for python script then restart topspin.

4. run setup_JTutils in topspin : if report does not point out problem, everything should work!

Remarks

Old versions of topspin :

Old versions of topspin are using too old version of jython. This version can be updated by changing jython.jar file found in TOPSPIN_INSTALL_DIR/classes/lib/ with one more recent. Be aware that jython.jar files on jython website also depend on java version. For example, only jython version up to 2.5 can be installed on topspin 2.1 since higher versions of jython (2.7) require java 7 while topspin 2.1 only provides java 6.

Jython version < 2.7

For jython versions <2.7, argparse module is not provided as standard module. Scripts can run without but adding argparse is easy :

• simply copy argparse.py file found at https://github.com/ThomasWaldmann/argparse/ in <TOPSPIN_DIR>/jython/Lib/ directory.