Add GE scanner physiological file functionality #424
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Additional details and impacted files@@ Coverage Diff @@
## master #424 +/- ##
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+ Coverage 94.77% 94.82% +0.04%
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Files 8 8
Lines 881 966 +85
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+ Hits 835 916 +81
- Misses 46 50 +4
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@nw-duncan once #430 is tested and merged, could you rebase this PR on the new master? I switched back CI to Circle CI, so we can exclude missed runs due to CI providers. |
…nner physiological file. If so, adds a .gep filename extension.
…nner physiological file. If so, adds a .gep filename extension. Do nothing if extension is already present.
…input for trigger_idx. Make this input optional with default of 0. If "None" is set as the input then it records this in the log
…s an optional input in their BlueprintInput calls (need to follow up with this so that it's truly optional? At the moment it's hardcoded that they all will actually have an input)
…as visualisation is based upon there being a trigger channel. Changed load_gep to insert a column of zeros for the trigger channel
…rches for other modalities based on the filename the user enters. Need to modify check_ge in io.py before proceeding
… files and adds the .gep extension to them too
… files and adds the .gep extension to them too
…les that might be produced if phys2bids is run without a heuristics file or no subject id. Also stopped it adding .gep to files that already end in that
…lename contains data that isn't consistent with GE physiological format. Catches strings and files with more than one column
…ta where the scan is running (i.e., from 30s into the data to the end)
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@nw-duncan if you agree, we merge this part in now, and we wait for documentation later? |
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Yes, let's do that. |
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🚀 PR was released in |
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Functionality to read and process GE scanner physiological recording files is added to the tool.
Users can enter a single scanner generated file (with the name given to it by the scanner). Note that these do not have any suffix. If there are other files corresponding to other measurement modalities (i.e., PPG, respiration belt, or EKG) then these will be found automatically and added.
Proposed Changes
Change Type
bugfix(+0.0.1)minor(+0.1.0)major(+1.0.0)refactoring(no version update)test(no version update)infrastructure(no version update)documentation(no version update)InternalTestingChecklist before review