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Clarify filenames in README.md (#46)
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Clarified filenames for write_NIRS and write_SNIRF functions calls.
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nidadu authored Mar 14, 2023
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10 changes: 5 additions & 5 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ data = LumoData(filename)
Convert the file to a SNIRF file:

```
data.write_SNIRF(filename);
data.write_SNIRF(snirf_filename);
```

Get information about channel 342 of your data:
Expand Down Expand Up @@ -336,7 +336,7 @@ Whilst SNIRF has some support for local indexing (similar to the canonical index
To construct a SNIRF structure and write a SNIRF file:

```
snirf = data.write_SNIRF(filename);
snirf = data.write_SNIRF(snirf_filename);
```

The returned structure represents the contents of the SNIRF output file as a nested MATLAB structure, where indexed groups are replaced with arrays of structures. This data structure can be used directly if a globally indexed spectroscopic representation is of use.
Expand Down Expand Up @@ -421,7 +421,7 @@ This package writes additional fields in the SNIRF metadata, as permitted by the
Additional extended metadata can also be written to the output file, however the resultant file is not compliant with the SNIRF specification. To enable writing the extended metadata:

```
snirf = data.write_SNIRF(filename, 'meta', 'extended');
snirf = data.write_SNIRF(snirf_filename, 'meta', 'extended');
```

This will result in the following fields being written under the `nirs(i)/metaDataTags/lumo/` group:
Expand Down Expand Up @@ -466,7 +466,7 @@ The NIRS file format is based upon MATLAB output files, and was originally used
To construct a NIRS structure and write a NIRS file:

```
nirs = data.write_NIRS(filename);
nirs = data.write_NIRS(nirs_filename);
```

The NIRS file contains an `SD` structure which describes the physical configuration of the sources and detectors of the system. In some references this layout is considered to be two-dimensional, though the specification provides for three-dimensional co-ordinates. The `write_NIRS` method provides an option which allows the `SD` structure to be written in two different formats to accommodate varying use cases:
Expand All @@ -477,7 +477,7 @@ The NIRS file contains an `SD` structure which describes the physical configurat
To select a scheme, pass the appropriate argument pair, e.g.:

```
data.write_NIRS(filename, 'sd_style', 'flat');
data.write_NIRS(nirs_filename, 'sd_style', 'flat');
```

*Note: The channel list in a NIRS file is re-indexed such that it is sorted by (wavelength, source index, detector index), as this is assumed in some analysis software.*
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