update docs for importv3

JaneliaSciComp · Feb 6, 2019 · 74a3144 · 74a3144
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diff --git a/docs/usage/index.rst b/docs/usage/index.rst
@@ -71,6 +71,8 @@ Documentation and help
 Pipeline commands
 ~~~~~~~~~~~~~~~~~
 
+-  ``jrc importv3 mysession_jrc.mat``: Import a JRCv3 ``_jrc.mat`` file to the new format.
+   **Does not overwrite your old results.**
 -  ``jrc bootstrap``: Create a :ref:`config file <bootstrapping>`.
 -  ``jrc detect myparams.prm``: Perform spike detection and feature extraction.
    (Replace ``myparams`` with a unique name of your choosing.)

diff --git a/docs/usage/migrating.rst b/docs/usage/migrating.rst
@@ -14,3 +14,13 @@ What's different
 - Logging and curation history are stored in the DensityPeakClustering object ``hClust``, instead of in a separate file where they might get out of sync.
 - You must specify your parameter file for every invocation of JRCLUST.
 - JRCLUST will overwrite old config files and save a backup copy to 'filename.prm.bak'.
+
+.. note::
+
+	Old sortings must be manually imported with ``jrc importv3 mysession_jrc.mat``.
+	This will output ':ref:`mysession_res.mat <io-res>`' and update your config file.
+	(A backup will be made of your config file at 'mysession.prm.bak'.)
+	Additionally, your '_spkraw.jrc', '_spkwav.jrc', and '_spkfet.jrc' will be renamed
+	to ':ref:`_raw.jrc <io-raw-traces>`', ':ref:`_filt.jrc <io-filt-traces>`', and
+	':ref:`_features.jrc <io-features>`', respectively.
+	Nothing will be altered except for this renaming.