From 4154688f5e91772f9a9c0d001316886b74686d9e Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Fri, 23 Apr 2021 16:11:22 +0200
Subject: Add documentation about ZMQ/MsgPack

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+==========================================
+Real-time data processing with indexamajig
+==========================================
+
+Instead of reading from files, indexamajig can get its data over a ZeroMQ
+socket.  Use ``--zmq-input`` instead of ``--input`` or ``-i``.  An error will
+be generated if you use ``--zmq-input`` and ``--input``  or ``-i``
+simultaneously.
+
+Indexamajig assumes that the socket is a *pub/sub* socket.  You will also need
+to specify which message prefixes to subscribe to.  Use ``--zmq-subscribe`` for
+this::
+
+  indexamajig --zmq-input=tcp://127.0.0.1:5002 \
+              --zmq-subscribe=ondaframedata \
+              -o output.stream -g Eiger.geom ...
+
+You can use ``--zmq-subscribe`` multiple times to subscribe to multiple message
+prefixes.
+
+The option ``--no-image-data`` will be honoured, if given.  This makes it
+possible to quickly check streaming data for "indexability".
+
+
+Data format
+===========
+
+In this version, CrystFEL makes the following assumptions about the data
+received via ZeroMQ:
+
+* The data is serialised using MessagePack
+* The data consists of either a single MsgPack 'map' object, or an array of
+  maps.
+  If there are multiple map objects in the array, only the first one will be
+  used.  The others will be ignored.
+* The image data is given as a two-dimensional array (i.e. no 3D arrays with
+  'panel number' as one of the dimensions).
+* The image data itself is given as a MsgPack 'map' object with "type"=>"<i4".
+
+Note that *all* of the above assumptions are 'open for negotiation' and will be
+relaxed in future CrystFEL versions, as new online data formats arise.  Anyone
+interested in streaming CBF files over ZeroMQ?
+
+You can specify which map objects to look at in the geometry file.  The
+following example will get the incident photon energy (in eV) and detector
+distance (in mm) by looking up the ``beam_energy`` and ``detector_distance``
+keys, respectively, in the MsgPack map object.  It will then look up
+``detector_data`` to find the image data itself.  See the next section for an
+explanation of ``peak_list``::
+
+  photon_energy = beam_energy eV
+  adu_per_photon = 1
+  clen = detector_distance mm
+  res = 5814.0
+  peak_list = peak_list
+  
+  thepanel/data = detector_data
+  thepanel/min_fs = 0
+  thepanel/max_fs = 2067
+  thepanel/min_ss = 0
+  thepanel/max_ss = 2161
+  thepanel/corner_x = -1034
+  thepanel/corner_y = -1081
+  thepanel/fs = x
+  thepanel/ss = y
+
+
+Peak lists
+==========
+
+You can use all of the usual peak search methods for streaming data.
+
+In addition, you can use ``--peaks=msgpack`` to get the peak locations from
+the MsgPack data.  In this case, the ``peak_list`` directive in the geometry
+file specifies the key for the peak information in the MsgPack map object.
+The peak information itself is expected to be a map object with three keys:
+``fs``, ``ss`` and ``intensity``.  Each of these keys should correspond to an
+array containing (respectively) the fast scan and slow scan coordinates of each
+peak, and their intensities.  Obviously, the three arrays must have equal sizes.
+
+Note that there is no way, in this structure, to communicate which detector
+panel contains a peak, in the case where different detector panels cover the
+same pixel ranges (in this case, the pixel data would from multiple data
+blocks).  In practice, this means that the ``data`` directives for all panels
+need to be the same when using ``--peaks=msgpack``.
-- 
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