pyport

Python port of siemens_to_ismrmrd.

Notes

The XProtocol parser (xprot_get_val) is a string-search based implementation, not an actual parser, so it’s really slow, but does get the job done very well. Next steps would be to figure out how to speed this up or rewrite the parser to work with everything. I was working on a parser but was stuck on how to handle some of Siemens’ very strange syntax.

There are several different XML libraries being used. xml.etree was my preference, so that’s what I started with. I needed to use xmltodict to convert between dictionaries and xml, because it’s quicker/easier to have a dictionary hold the config information as we move along. It turns out that schema verification is not supported by xml.etree, so that’s when I pulled in lxml.etree – so there’s some weirdness trying to get xml.etree and lxml.etree to play together nicely. The last one is pybx – a bizarrely complicated library that the ismrmrd python library uses. I hate the thing and think it’s overly complicated for what we need to use it for.

One of the ideas I had was to pull down the schema/parammaps from the interwebs so it would always be current. While this is a neat feature that probably no one will use, it would speed up the raw data conversion to use a local copy instead, even if that means pulling it down the first time and keeping it.

The script to read in an ismrmrd dset provided in ismrmrd-python-tools is great at illustrating how to do it, but is incredibly slow, especiailly if you want to remove oversampling in readout direction. Next steps are to figure out how to quickly read in and process these datasets. I’m kind of put off from using this data format because of how unweildy it is, but I suppose it’s better to be an open standards player…

The only datasets I have are cartesian VB17. So there’s currently little support for anything else.

Command-line interface has not been looked at in a long time, might not be working still.

mr_utils.load_data.pyport.pyport(version=False, list_embed=False, extract=None, user_stylesheet=None, file=None, pMapStyle=None, measNum=1, pMap=None, user_map=None, debug=False, header_only=False, output='output.h5', flash_pat_ref_scan=False, append_buffers=False, study_date_user_supplied='')[source]

Run the program with arguments.

Parameters:
  • version (bool, optional) – Prints converter version and ISMRMRD version
  • list_embed (bool, optional) – Print list embedded files
  • extract (bool, optional) – Extract embedded file
  • user_stylesheet (str, optional) – Provide a parameter stylesheet XSL file
  • file (str, optional) – SIEMENS dat file
  • pMapStyle (str, optional) – Parameter stylesheet XSL
  • measNum (int, optional) – Measurement number
  • pMap (str, optional) – Parameter map XML
  • user_map (str, optional) – Provide a parameter map XML file
  • debug (bool, optional) – Debug XML flag
  • header_only (bool, optional) – HEADER ONLY flag (create xml header only)
  • output (str, optional) – ISMRMRD output file
  • flash_pat_ref_scan (bool, optional) – FLASH PAT REF flag
  • append_buffers (bool, optional) – Append protocol buffers
  • study_date_user_supplied (str, optional) – User can supply study date, in the format of yyyy-mm-dd
Returns:

ismrmrd_dataset – Converted raw data
Return type:

ismrmrd.Dataset
Raises:
  • ValueError – When .dat file is not provided, when user-supplied parameter map XSL stylesheet AND embedded stylesheet are provided at the same time
  • IOError – When .dat file does not exist, when provided user_stylesheet does not exist, when pMapStyle does not exist
  • NotImplementedError – When VD raw data file is provided

Notes

Not all Raises are listed currently.