formatting PixelatorControllerSettings

PixelatorControllerSettings.md

@@ -11,148 +11,150 @@ The file format is [JSON](http://www.json.org/)
 Every scan creates a hdf5 file. The directory they are stored in is:
 _base directory/YYYY-mm-dd/_
 
-**NeXusBaseDirectory**::
-- base directory to save scan files
+**NeXusBaseDirectory**::<BR>
+&emsp;base directory to save scan files
 
- **NeXusLocalBaseDirectory**::<BR>
-    base directory used when '''Save local''' is active
+**NeXusLocalBaseDirectory**::<BR>
+&emsp;base directory used when **Save local** is active
 
- **defaultSaveLocal**::<BR>
-    Save local setting on startup. <BR>
-    "yes": use '''NeXusLocalBaseDirectory''' directory <BR>
-    anything else: use '''NeXusBaseDirectory''' directory
+**defaultSaveLocal**::<BR>
+&emsp;Save local setting on startup. <BR>
+&emsp;"yes": use **NeXusLocalBaseDirectory** directory <BR>
+&emsp;anything else: use **NeXusBaseDirectory** directory
 
 Depending on the scan type, the files are archived or not.
 The archived ones are put in that date directory.
 The others in a discard sub directory of the date directory.
 
- NeXusDiscardSubDirectory::
-    sub directory for files not archived
+ **NeXusDiscardSubDirectory**::<BR>
+&emsp;sub directory for files not archived
 
-The '''''ScanType''_Archive_Default''' options define a default archive flag for each scan type.
-They are used when '''''ScanType''_Archive''' is missing.
+The **ScanType_Archive_Default** options define a default archive flag for each scan type.
+They are used when **ScanType_Archive** is missing.
 
- Sample_Archive_Default::
- Focus_Archive_Default::
- OSA_Archive_Default::
- OSA Focus_Archive_Default::
- Detector_Archive_Default::
- Motor_Archive_Default::
- Motor2D_Archive_Default::
-   "yes": files are archived \\
-   "no": files are put in the discard sub directory \\
-   "locked": as yes, but users cannot toggle the archive flag for this scan type \\
-   '''Default''': "locked"
+ **Sample_Archive_Default**::<BR>
+ **Focus_Archive_Default**::<BR>
+ **OSA_Archive_Default**::<BR>
+ **OSA Focus_Archive_Default**::<BR>
+ **Detector_Archive_Default**::<BR>
+ **Motor_Archive_Default**::<BR>
+ **Motor2D_Archive_Default**::<BR>
+&emsp;"yes": files are archived <BR>
+&emsp;"no": files are put in the discard sub directory <BR>
+&emsp;"locked": as yes, but users cannot toggle the archive flag for this scan type <BR>
+&emsp;**Default**: "locked"
 
 Users can toggle the archive flag for a scan type (unless locked).
-When they do so, '''''ScanType''_Archive''' is added or updated.
+When they do so, **ScanType_Archive** is added or updated.
 
- Sample_Archive::
- Focus_Archive::
- OSA_Archive::
- OSA Focus_Archive::
- Detector_Archive::
- Motor_Archive::
- Motor2D_Archive::
-   "yes": files are archived \\
-   "no": files are put in the discard sub directory \\
-   '''Default''': '''''ScanType''_Archive_Default'''
+ Sample_Archive::<BR>
+ Focus_Archive::<BR>
+ OSA_Archive::<BR>
+ OSA Focus_Archive::<BR>
+ Detector_Archive::<BR>
+ Motor_Archive::<BR>
+ Motor2D_Archive::<BR>
+&emsp;"yes": files are archived <BR>
+&emsp;"no": files are put in the discard sub directory <BR>
+&emsp;**Default**: **ScanType_Archive_Default**
 
 ### Scan Files
 The name of the file is:
-''ScanType''_''YYYY-mm-dd''_''ScanNumber''.hdf5
+_ScanType_YYYY-mm-dd_ScanNumber_.hdf5
 
 For Sample scans, the spatial type
-- _Point
-- _Line
-- _Image
-- _Stack
-is added after ''ScanType''.
+- _Point_
+- _Line_
+- _Image_
+- _Stack_
+
+is added after _ScanType_.
 
 ScanNumber is a three digit number, starting with 001 every day.
 
- NeXusScanNumber::
-   ScanNumber counter \\
-   Updated every time a new scan file is created (beginning of the scan). \\
-   '''Default''': 0
+**NeXusScanNumber**::<BR>
+&emsp;ScanNumber counter<BR>
+&emsp;Updated every time a new scan file is created (beginning of the scan).<BR>
+&emsp;**Default**: 0
 
- compression::
-   "LZW": Use LZW compression in hdf5 file \\
-   "NONE": No compression \\
-   '''Default''': "NONE"
+ **compression**::<BR>
+&emsp;"LZW": Use LZW compression in hdf5 file<BR>
+&emsp;"NONE": No compression<BR>
+&emsp;**Default**: "NONE"
 
- beamline::
-   String value that is written into the scan file at ''/entry*/collection/beamline''
+ **beamline**::<BR>
+&emsp;String value that is written into the scan file at _/entry*/collection/beamline_
 
 ### scripts
- changeUserScript::
-   name of the script that is run on startup and whenever the user is changed \\
-   '''Optional''': no script is run when this setting is missing
+ **changeUserScript**::<BR>
+&emsp;name of the script that is run on startup and whenever the user is changed<BR>
+&emsp;**Optional**: no script is run when this setting is missing
 
- defaultUsername::
-   username set on startup
+ **defaultUsername**::<BR>
+&emsp;username set on startup
 
- endOfScanScript::
-   name of the script that is run on the controller at the end of every scan \\
-   '''Optional''': no script is run when this setting is missing
+ **endOfScanScript**::<BR>
+&emsp;name of the script that is run on the controller at the end of every scan<BR>
+&emsp;**Optional**: no script is run when this setting is missing
 
 ### ZeroMQ Ports
- publisherPort::
-   TCP port used to publish messages
+ **publisherPort**::<BR>
+&emsp;TCP port used to publish messages
 
- requestPort::
-   TCP port used to listen for requests
+ **requestPort**::<BR>
+&emsp;TCP port used to listen for requests
 
 ### missing data check
 At the end of a point by point line, some data of asynchronous detectors may be missing.
 They are read until no more data is missing.
 
- missingDataCheckInterval::
-   interval (in seconds) at which missing data is read \\
-   '''Default''': 0.1 seconds
+ **missingDataCheckInterval**::<BR>
+&emsp;interval (in seconds) at which missing data is read<BR>
+&emsp;**Default**: 0.1 seconds
 
- missingDataCheckMaxChecks::
-   maximum number of times missing data is read
-   '''Default''': 5
+ **missingDataCheckMaxChecks**::<BR>
+&emsp;maximum number of times missing data is read<BR>
+&emsp;**Default**: 5
 
 ### settings files names
 The following settings define the name of additional settings files.
 Each of these settings files is described in a section below.
- axisConfigFileName::
-   [#Axis Axis]
 
- controllerConfigFileName::
-   [#Controller Controller]
+ **axisConfigFileName**::<BR>
+&emsp;[Axis](#Axis)
 
- detectorConfigFileName::
-   [#Detector Detector]
+ **controllerConfigFileName**::<BR>
+&emsp;[#Controller Controller]
 
- epicsConfigFileName::
-   [#Epics Epics]
+ **detectorConfigFileName**::<BR>
+&emsp;[Detector](#Detector)
 
- instrumentConfigFileName::
-   [#Instrument Instrument]
+ **epicsConfigFileName**::<BR>
+&emsp;[Epics](#Epics)
 
- log4cppPropertiesFileName::
-   [#Log4cppProperties Log4cpp Properties]
+ **instrumentConfigFileName**::<BR>
+&emsp;[Instrument](#Instrument)
 
- microscopeControlConfigFileName::
-   [#MicroscopeControl Microscope Control]
+ **log4cppPropertiesFileName**::<BR>
+&emsp;[Log4cpp Properties](#Log4cppProperties)
 
- pixelClockConfigFileName::
-   [#PixelClock Pixel Clock]
+ **microscopeControlConfigFileName**::<BR>
+&emsp;[Microscope Control](#MicroscopeControl)
 
- polarizationConfigFileName::
-   [#Polarization Polarization]
+ **pixelClockConfigFileName**::<BR>
+&emsp;[Pixel Clock](#PixelClock)
 
- positionerConfigFileName::
-   [#Positioner Positioner]
+ **polarizationConfigFileName**::<BR>
+&emsp;[Polarization](#Polarization)
 
- topupConfigFileName::
-   '''Optional''': no topup handling when this setting is missing or the file cannot be read. \\
-   [#Topup Topup]
+ **positionerConfigFileName**::<BR>
+&emsp;[Positioner](#Positioner)
 
- zonePlateConfigFileName::
+ **topupConfigFileName**::<BR>
+&emsp;'''Optional''': no topup handling when this setting is missing or the file cannot be read. <BR>
+&emsp;[Topup](#Topup)
+
+ **zonePlateConfigFileName**::
    [#ZonePlate Zone Plate]
 
 ## Axis