Patch to make adding fieldmap meta data more robust

Author: marcelzwiers

bidscoin/bidscoiner.py

@@ -258,9 +258,12 @@ def coin_data2bids(dataformat: str, session: Path, bidsmap: dict, bidsfolder: Pa
             acqlabel  = bids.get_bidsvalue(bidsname, 'acq')
             patterns  = (bidsname.replace('_run-1_',     '_run-[0-9]*_').
                                   replace('_magnitude1', '_magnitude*').
-                                  replace('_phase1',     '_phase*'),
+                                  replace('_magnitude2', '_magnitude*').
+                                  replace('_phase1',     '_phase*').
+                                  replace('_phase2',     '_phase*'),
                          bidsname.replace('_run-1_',     '_run-[0-9]*_').
-                                  replace('_magnitude1', '_phase*'))
+                                  replace('_magnitude1', '_phase*').
+                                  replace('_magnitude2', '_phase*'))
             for pattern in patterns:
                 jsonfiles.extend((bidsses/'fmap').glob(pattern  + '.json'))
                 if acqlabel:

docs/advanced.rst

@@ -12,7 +12,7 @@ Generally speaking, a bidsmap file contains a collection of key-value dictionari
 
    A snippet of a study bidsmap, showing a ``DICOM`` section with a few `run` items in the ``anat`` subsection
 
-A good start to create your own template is to have a look at the DCCN ``[path_to_bidscoin]/heuristics/bidsmap_dccn.yaml`` template and see if you can adapt that to your needs. If you open the template, there are a few things to take notice of (as shown in the template snippet below). First, you can see that the DCCN template makes use of YAML `anchors and aliases <https://blog.daemonl.com/2016/02/yaml.html>`__ (to make maintanance more sustainable). The second thing to notice is that, of the first run, all values of the attribute dictionary are empty. In that way, the subsequent runs that alias (``<<: *anatattributes_dicom``) this anchor (``&anatattributes_dicom``) will inherit only the keys and can inject their own values. The first run of each modality sub-section (like ``anat``) also serves as the default bidsmapping when users manually overrule / change the bids modality using the `bidsmapper <workflow.html#step-1a-running-the-bidsmapper>`__ GUI. Finally, it is important to take notice of the usage of `matching patterns <workflow.html#step-1b-running-the-bidseditor>`__ (see ``DICOM Attributes``).
+A good start to create your own template is to have a look at the DCCN ``[path_to_bidscoin]/heuristics/bidsmap_dccn.yaml`` template and see if you can adapt that to your needs. If you open the template, there are a few things to take notice of (as shown in the template snippet below). First, you can see that the DCCN template makes use of YAML `anchors and aliases <https://blog.daemonl.com/2016/02/yaml.html>`__ (to make maintanance more sustainable). The second thing to notice is that, of the first run, all values of the attribute dictionary are empty, meaning that it won't match any run. In that way, however, the subsequent runs that alias (``<<: *anatattributes_dicom``) this anchor (``&anatattributes_dicom``) will inherit only the keys and can inject their own values. The first run of each modality sub-section (like ``anat``) also serves as the default bidsmapping when users manually overrule / change the bids modality using the `bidsmapper <workflow.html#step-1a-running-the-bidsmapper>`__ GUI. Finally, it is important to take notice of the usage of `matching patterns <workflow.html#step-1b-running-the-bidseditor>`__ (see ``DICOM Attributes``).
 
 .. code-block:: yaml