Development¶
Development can concern one of the four aspects of this package. Either the GUI, the CLI, the loadable fileformats or the readouts allowed in the cachefile.
Developing Readouts¶
Currently implemented readouts can be found at ALL_RIOS, although not all recording protocols might be supported. Each readout comes with a definition of its TraceAttributes, i.e.
a specific set of keys for the MetaData of each Trace. All keys should be restricted to str. We recommend that each fields values are limited to str, int, float, or List[str], List[int], List[float]. They need to be stored in HDF5 which works best withs strings as keys and values. When annotations are being accessed, it sensible to decode() and encode() for safe parsing.
In general, it is the responsibility of the developer to add the respective list of valid keys for each readin / readout combination.
To allow for a clear organization, please put each protocol handlers in the input folder. There, each readin has its readout folder. In this lowest level, the handlers for the protocols are defined in their own modules, while the valid trace keys are defined in their __init__.py. See e.g. valid_keys. Be aware that at least the valid_trace_keys always need to be implemented during the prepare_annotation specific for this protocol. Please note also that across merged files the TraceAnnotation values for some keys must_be_identical_in_merged_file, while others can_vary_across_merged_files.
GUI test and development¶
Mock two xdf5 files using python tests/mock/cache.py fname1.hdf5 fname2.hdf5 from the project root. Merge these two files with offspect merge -f fname1.hdf5 fname2.hdf5 -t merged.hdf5. Peek into the merged file with offspect peek merged.hdf5. This should give you the following output:
-------------------------------------------------------------------------------
origin : template_R001.xdf
filedate : 1970-01-01 00:01:01
subject : VnNn
samplingrate : 1000
samples_pre_event : 100
samples_post_event : 100
channel_labels : ['EDC_L']
channel_of_interest : EDC_L
readout : cmep
readin : tms
global_comment : patient was tired
history :
version : 0.0.1
traces_count : 2
-------------------------------------------------------------------------------
origin : template_R002.xdf
filedate : 1970-01-01 23:59:59
subject : VnNn
samplingrate : 1000
samples_pre_event : 100
samples_post_event : 100
channel_labels : ['EDC_L']
channel_of_interest : EDC_L
readout : cmep
readin : tms
global_comment :
history :
version : 0.0.1
traces_count : 2
Start visual inspection using the GUI with this file with offspect gui -f merged.hdf5 or run offspect gui and select the desired cachefile using the menu. You can also set the gui resolution, see Command Line Interface for more information.