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<HTML>
<HEAD>
<TITLE>EPICS Support for Area Detectors</TITLE>
</HEAD>
<BODY>
<CENTER>
<H1>areaDetector: EPICS Area Detector Support</H1>
<H2> R1-2</H2>
<H2> May 16, 2008</H2>
<H2> Mark Rivers</H2>
<H2> University of Chicago</H2>
</CENTER>
<P>&nbsp;</P>
<CENTER><H2>Contents</H2></CENTER>
<UL>
<LI><A href="#Overview">
Overview</A>
<LI><A href="#Architecture">
Architecture</A>
<LI><A href="#asynParamBase">
asynParamBase</A>
<LI><A href="#NDArray">
NDArray</A>
<LI><A href="#asynNDArrayBase">
asynNDArrayBase</A>
<LI><A href="#ADDriverBase">
ADDriverBase</A>
<LI><A href="#simDetector">
simDetector</A>
<LI><A href="#Prosilica driver">
Prosilica driver</A>
<LI><A href="#NDPluginBase">
NDPluginBase</A>
<LI><A href="#NDPluginStdArrays">
NDPluginStdArrays</A>
<LI><A href="#NDPluginROI">
NDPluginROI</A>
<LI><A href="#NDPluginFile">
NDPluginFile</A>
<LI><A href="#EPICS records">
EPICS records</A>
<UL>
<LI><A href="#Acquisition related records">
Acquisition related records</A>
<LI><A href="#Detector related records">
Detector related records</A>
<LI><A href="#File name related records">
File name related records</A>
<LI><A href="#ROI related records">
ROI related records</A>
<LI><A href="#Image related records">
Image related records</A>
<LI><A href="#Bad pixel map related records">
Bad pixel map related records</A>
<LI><A href="#Flat field correction related records">
Flat field correction related records</A>
<LI><A href="#Communication related records">
Communication related records</A>
<LI><A href="#Scan related records">
Scan related records</A>
</UL>
<LI><A href="#EPICS startup script">
EPICS startup script</A>
<LI><A href="#MEDM screens">
MEDM Screens</A>
<LI><A href="#IDL Image Display Client">
IDL Image Display Client</A>
<LI><A href="#Performance measurements">
Performance measurements</A>
<LI><A href="#Hardware notes">
Hardware notes</A>
<LI><A href="#Restrictions">
Restrictions</A>
</UL>
<P>&nbsp;</P>
<CENTER><H2><A name=Overview>
Overview</A></H2></CENTER>
<P>
The areaDetector module provides a general-purpose interface for area (2-D) detectors in EPICS.
It is intended to be used with a wide variety of detectors and cameras, ranging from high frame rate
CCD and CMOS cameras, pixel-array detectors such as the Pilatus, and large format detectors like the
MAR-345 online imaging plate.</P>
The goals of this module are:
<UL>
<LI> Minimize the amount of code that needs to be written to implement a
new detector.
<LI> Provide a standard interface defining the functions and parameters that
a detector driver must support.
<LI> Provide a set of base EPICS records that will be present for every detector
using this module. This allows the use of generic EPICS clients for
displaying images and controlling cameras and detectors.
<LI> Allow easy extensibility to take advantage of detector-specific features
beyond the standard parameters.
<LI> Have high-performance. Applications can be written to get the detector
image data through EPICS, but an interface is also available to receive the detector
data at a lower-level for very high performance.
<LI> Provide an optional Region-Of-Interest (ROI) driver that performs computations
on regions within the image data. A basic ROI driver is included in the module,
and it is easy to add addtional ROI drivers for specific applications.
<LI> Provide detector drivers for commonly used detectors in synchrotron applications.
These include Prosilica GigE video cameras, MAR-CCD x-ray detectors, MAR-345 online
imaging plate detectors, the Pilatus pixel-array detector, and the Roper Scientific CCD
cameras.
</UL>
<P>&nbsp;</P>
<CENTER><H2><A name=Architecture>
Architecture</A></H2></CENTER>
<P>
The architecture of the areaDetector module is shown in Figure 1.
<CENTER><H3>Figure 1. Architecture of areaDetector module.</H3>
<IMG src="areaDetectorArchitecture.png"></CENTER>
From the bottom to the top this architecture consists of the following:</P>
<UL>
<LI>Layer 1. This is the layer that allows user written code to
communicate with the hardware.
It is usually provided by the detector vendor. It may consist of a library or DLL,
of a socket protocol to a driver, a Microsoft COM interface, etc.
<LI>Layer 2. This is the driver that is written for the area detector application to
control a particular detector. It is normally written in C++ and inherits from the
ADDriverBase class. It uses the standard asyn interfaces for control and status
information. Each time it receives a new data array it passes it as an NDArray object
to all Layer 3 clients that have registered for callbacks. This is the only code that
needs to be written to implement a new detector. Existing drivers range from
650 to 950 lines of code.
<LI>Layer 3. Code running at this level is called a "plug-in". This code registers with a
driver for a callback whenever there is a new data array. The existing plugins implement
file saving (NDPluginFile), region-of-interest (ROI) calculations (NDPluginROI),
and conversion of detector data to standard EPICS array types for use by
Channel Access clients (NDPluginStdArrays). Plugins are normally written in C++ and
inherit from NDPluginBase. Existing plugins range from 280 to 550 lines
of code.
<LI>Layer 4. This is standard asyn device support that comes with the EPICS asyn module.
<LI>Layer 5. These are standard EPICS records, and EPICS database (template) files that
define records to communicate with drivers at Layer 2 and plugins at Layer 3.
<LI>Layer 6. These are EPICS channel access clients, such as MEDM that communicate with
the records at Layer 5. There is a free IDL client that can display images using
EPICS waveform and other records communicating with the NDPluginStdArrays plugin
at Layer 3.
</UL>
The code in Layers 1-3 is essentially independent of EPICS. There are only 2 EPICS dependencies in this
code.
<OL>
<LI>libCom. libCom from EPICS base provides operating-system independent functions for
threads, mutexes, etc.
<LI>asyn. asyn is a module that provides interthread messaging services, including queueing
and callbacks.
</OL>
In particular it is possible to eliminates layers 4-6 in the architecture shown in Figure 1, providing
there is a programs such as the high-performance GUI shown in Layer 3. This means that it is not necessary
to run an EPICS IOC or to use EPICS Channel Access when using the drivers and plugins at Layers 2 and 3.
<P>
The plugin architecture is very powerful, because plugins can be reconfigured at run-time. For example
the NDPluginStdArrays can switch from getting its array data from a detector driver to an NDPluginROI
plugin. That way it will switch from displaying the entire detector to whatever sub-region the ROI
driver has selected. Any Channel Access clients connected to the NDPluginStdArrays driver
will automatically switch to displaying this subregion.
Similarly, the NDPluginFile plugin can be switched at run-time from saving the entire image to saving
a selected ROI, just by changing its input source.
<P>
The use of plugins is optional, and it is only plugins that require the driver to make the
image data available. If there are no plugins being used then EPICS can be used simply
to control the detector, without accessing the data itself. This is most useful when
the vendor API has the ability to save the data to a file.
<P>
What follows is a detailed description of the software, working from the bottom up.
Most of the code is object oriented, and written in C++. The parts of the code that depend
on anything from EPICS except libCom and asyn have been kept in in separate C files, so that
it is easy to build applications that do not run as part of an EPICS IOC.
<P>&nbsp;</P>
<CENTER><H2><A name=asynParamBase>
asynParamBase</A></H2></CENTER>
The areaDetector module depends heavily on asyn. It is the software that is used for interthread communication,
using the standard asyn interfaces (e.g. asynInt32, asynOctet, etc.), and callbacks. Detector drivers and plugins
are asyn port drivers, meaning that they implement one or more of the standard asyn interfaces. They register
themselves as interrupt sources, so that they do callbacks to registered asyn clients when values change.
asynParamBase handles all of the details of registering the port driver, registering the supported interfaces,
and registering the required interrupt sources.
<P>
Drivers and plugins each need to support a number of parameters that control their operation and provide
status information. Most of these can be treated as 32-bit integers, 64-bit floats, or strings.
When the new value of a parameter is sent to a driver, (e.g. detector binning in the X direction)
from an asyn client (e.g. an EPICS record),
then the driver will need to take some action. It may change some other parameters in response to this
new value (e.g. image size in the X direction). The sequence of operations in the driver can be summarized as
<OL>
<LI>New parameter value arrives, or new data arrives from detector.
<LI>Change values of one or more parameters.
<LI>For each parameter whose value changes set a flag noting that it changed.
<LI>When operation is complete, call the registered callbacks for each changed parameter.
</OL>
asynParamBase provides methods to simplify the above sequence, which must be
implemented for the many parameters that the driver supports. Each parameter is assigned
a number, which is the value in the pasynUser-&gt reason field that asyn clients pass to
the driver when reading or writing that parameter. asynParamBase maintains a table
of parameter values, associating each parameter number with a data type (integer, double, or string),
caching the current value, and maintaining a flag indicating if a value has changed.
Drivers use asynParamBase methods to read the current value
from the table, and to set new values in the table. There is a method to call all registered callbacks
for values that have changed since callbacks were last done.
<P>The following is the definition of the asynParamBase class:
<PRE>
class asynParamBase {
public:
asynParamBase(const char *portName, int maxAddr, int paramTableSize, int interfaceMask, int interruptMask);
virtual asynStatus getAddress(asynUser *pasynUser, const char *functionName, int *address);
virtual asynStatus findParam(asynParamString_t *paramTable, int numParams, const char *paramName, int *param);
virtual asynStatus readInt32(asynUser *pasynUser, epicsInt32 *value);
virtual asynStatus writeInt32(asynUser *pasynUser, epicsInt32 value);
virtual asynStatus getBounds(asynUser *pasynUser, epicsInt32 *low, epicsInt32 *high);
virtual asynStatus readFloat64(asynUser *pasynUser, epicsFloat64 *value);
virtual asynStatus writeFloat64(asynUser *pasynUser, epicsFloat64 value);
virtual asynStatus readOctet(asynUser *pasynUser, char *value, size_t maxChars,
size_t *nActual, int *eomReason);
virtual asynStatus writeOctet(asynUser *pasynUser, const char *value, size_t maxChars,
size_t *nActual);
virtual asynStatus readInt8Array(asynUser *pasynUser, epicsInt8 *value,
size_t nElements, size_t *nIn);
virtual asynStatus writeInt8Array(asynUser *pasynUser, epicsInt8 *value,
size_t nElements);
virtual asynStatus doCallbacksInt8Array(epicsInt8 *value,
size_t nElements, int reason, int addr);
virtual asynStatus readInt16Array(asynUser *pasynUser, epicsInt16 *value,
size_t nElements, size_t *nIn);
virtual asynStatus writeInt16Array(asynUser *pasynUser, epicsInt16 *value,
size_t nElements);
virtual asynStatus doCallbacksInt16Array(epicsInt16 *value,
size_t nElements, int reason, int addr);
virtual asynStatus readInt32Array(asynUser *pasynUser, epicsInt32 *value,
size_t nElements, size_t *nIn);
virtual asynStatus writeInt32Array(asynUser *pasynUser, epicsInt32 *value,
size_t nElements);
virtual asynStatus doCallbacksInt32Array(epicsInt32 *value,
size_t nElements, int reason, int addr);
virtual asynStatus readFloat32Array(asynUser *pasynUser, epicsFloat32 *value,
size_t nElements, size_t *nIn);
virtual asynStatus writeFloat32Array(asynUser *pasynUser, epicsFloat32 *value,
size_t nElements);
virtual asynStatus doCallbacksFloat32Array(epicsFloat32 *value,
size_t nElements, int reason, int addr);
virtual asynStatus readFloat64Array(asynUser *pasynUser, epicsFloat64 *value,
size_t nElements, size_t *nIn);
virtual asynStatus writeFloat64Array(asynUser *pasynUser, epicsFloat64 *value,
size_t nElements);
virtual asynStatus doCallbacksFloat64Array(epicsFloat64 *value,
size_t nElements, int reason, int addr);
virtual asynStatus readHandle(asynUser *pasynUser, void *handle);
virtual asynStatus writeHandle(asynUser *pasynUser, void *handle);
virtual asynStatus doCallbacksHandle(void *handle, int reason, int addr);
virtual asynStatus drvUserCreate(asynUser *pasynUser, const char *drvInfo,
const char **pptypeName, size_t *psize);
virtual asynStatus drvUserGetType(asynUser *pasynUser,
const char **pptypeName, size_t *psize);
virtual asynStatus drvUserDestroy(asynUser *pasynUser);
virtual void report(FILE *fp, int details);
virtual asynStatus connect(asynUser *pasynUser);
virtual asynStatus disconnect(asynUser *pasynUser);
virtual asynStatus setIntegerParam(int index, int value);
virtual asynStatus setIntegerParam(int list, int index, int value);
virtual asynStatus setDoubleParam(int index, double value);
virtual asynStatus setDoubleParam(int list, int index, double value);
virtual asynStatus setStringParam(int index, const char *value);
virtual asynStatus setStringParam(int list, int index, const char *value);
virtual asynStatus getIntegerParam(int index, int * value);
virtual asynStatus getIntegerParam(int list, int index, int * value);
virtual asynStatus getDoubleParam(int index, double * value);
virtual asynStatus getDoubleParam(int list, int index, double * value);
virtual asynStatus getStringParam(int index, int maxChars, char *value);
virtual asynStatus getStringParam(int list, int index, int maxChars, char *value);
virtual asynStatus callParamCallbacks();
virtual asynStatus callParamCallbacks(int list, int addr);
virtual void reportParams();
char *portName;
int maxAddr;
paramList **params;
epicsMutexId mutexId;
/* The asyn interfaces this driver implements */
asynStandardInterfaces asynStdInterfaces;
/* asynUser connected to ourselves for asynTrace */
asynUser *pasynUser;
};
</PRE>
A brief explanation of the methods and data in this class is provided here. Users should look at the
example driver (simDetector) and plugins provided with areaDetector for examples of how this
class is used.
<PRE>
asynParamBase(const char *portName, int maxAddr, int paramTableSize, int interfaceMask, int interruptMask);
</PRE>
This is the constructor for the class.
<UL>
<LI><CODE>portName</CODE> is the name of the asyn port for this driver or plugin.
<LI><CODE>maxAddr</CODE> is the maximum number of asyn addresses that this driver or plugin supports.
This number returned by the <CODE>pasynManager-&gt getAddr()</CODE> function. Typically it is 1, but some
plugins (e.g. NDPluginROI) support values &gt 1. This controls the number of parameter
tables that are created.
<LI><CODE>parmTableSize</CODE> is the maximum number of parameters that this driver or plugin supports.
This controls the size of the parameter tables.
<LI><CODE>interfaceMask</CODE> is a mask with each bit defining which asyn interfaces this driver
or plugin supports.
The bit mask values are defined in asynParamBase.h, e.g. <CODE>asynInt32Mask</CODE>.
<LI><CODE>interruptMask</CODE> is a mask with each bit defining which of the asyn interfaces this driver
or plugin supports can generate interrupts.
The bit mask values are defined in asynParamBase.h, e.g. <CODE>asynInt8ArrayMask</CODE>.
</UL>
<BR>
<PRE>
virtual asynStatus getAddress(asynUser *pasynUser, const char *functionName, int *address);
</PRE>
Returns the value from pasynManager-&gt getAddr(pasynUser,...).
Returns an error if the address is not valid, e.g. &gt= this-&gt maxAddr.
<PRE>
virtual asynStatus readInt32(asynUser *pasynUser, epicsInt32 *value);
virtual asynStatus readFloat64(asynUser *pasynUser, epicsFloat64 *value);
virtual asynStatus readOctet(asynUser *pasynUser, char *value, size_t maxChars,
size_t *nActual, int *eomReason);
</PRE>
These methods are called by asyn clients to return the current cached value for the
parameter indexed by pasynUser-&gt reason in the parameter table defined by <CODE>getAddress()</CODE>.
Derived classed typically do not need to implement these methods.
<BR>
<PRE>
virtual asynStatus writeInt32(asynUser *pasynUser, epicsInt32 value);
virtual asynStatus writeFloat64(asynUser *pasynUser, epicsFloat64 value);
virtual asynStatus writeOctet(asynUser *pasynUser, const char *value, size_t maxChars,
size_t *nActual);
</PRE>
These methods are called by asynClients to set the new value of a parameter. These
methods only have stub methods that return an error in asynParamBase, so they
must be implemented in the derived classes if the corresponding interface is
used. They are not pure virtual functions so that the derived class need not implement
the interface if it is not used.
<BR>
<PRE>
virtual asynStatus readXXXArray(asynUser *pasynUser, epicsInt8 *value,
size_t nElements, size_t *nIn);
virtual asynStatus writeXXXArray(asynUser *pasynUser, epicsInt8 *value,
size_t nElements);
virtual asynStatus doCallbacksXXXArray(epicsInt8 *value,
size_t nElements, int reason, int addr);
virtual asynStatus readHandle(asynUser *pasynUser, void *handle);
virtual asynStatus writeHandle(asynUser *pasynUser, void *handle);
virtual asynStatus doCallbacksHandle(void *handle, int reason, int addr);
</PRE>
where XXX=(Int8, Int16, Int32, Float32, or Float64).
The readXXX and writeXXX methods only have stub methods that return an error in asynParamBase, so they
must be implemented in the derived classes if the corresponding interface is
used. They are not pure virtual functions so that the derived class need not implement
the interface if it is not used. The doCallbacksXXX methods in asynParamBase
call any registered asyn clients on the corresponding interface if the <CODE>reason</CODE>
and <CODE>addr</CODE> values match. It typically does not need to be implemented in derived classes.
<BR>
<PRE>
virtual asynStatus findParam(asynParamString_t *paramTable, int numParams, const char *paramName, int *param);
virtual asynStatus drvUserCreate(asynUser *pasynUser, const char *drvInfo,
const char **pptypeName, size_t *psize);
virtual asynStatus drvUserGetType(asynUser *pasynUser,
const char **pptypeName, size_t *psize);
virtual asynStatus drvUserDestroy(asynUser *pasynUser);
</PRE>
drvUserCreate must be implemented in derived classes that use the parameter facilities of asynParamBase.
The <CODE>findParam</CODE> method is a convenience function that searches an array of {enum, string} structures
and returns the enum (parameter number) matching the string. This is typically used in the
implementation of <CODE>drvUserCreate</CODE> in derived classes. <CODE>drvUserGetType</CODE> and
<CODE>drvUserDestroy</CODE> typically do not need to be implemented in derived classes.
<BR>
<PRE>
virtual void report(FILE *fp, int details);
virtual asynStatus connect(asynUser *pasynUser);
virtual asynStatus disconnect(asynUser *pasynUser);
</PRE>
The <CODE>report</CODE> function prints information on registered interrupt clients if details &gt 0, and prints
parameter table information if details &gt 5. It is typically called by the implementation of
<CODE>report</CODE> in derived classes before or after
they print specific information about themselves. <CODE>connect</CODE> and <CODE>disconnect</CODE> call
<CODE>pasynManager-&gt exceptionConnect</CODE> and <CODE>pasynManager-&gt exceptionDisconnect</CODE> respectively.
Derived classes may or may not need to implement these functions.
<BR>
<PRE>
virtual asynStatus setIntegerParam(int index, int value);
virtual asynStatus setIntegerParam(int list, int index, int value);
virtual asynStatus setDoubleParam(int index, double value);
virtual asynStatus setDoubleParam(int list, int index, double value);
virtual asynStatus setStringParam(int index, const char *value);
virtual asynStatus setStringParam(int list, int index, const char *value);
virtual asynStatus getIntegerParam(int index, int * value);
virtual asynStatus getIntegerParam(int list, int index, int * value);
virtual asynStatus getDoubleParam(int index, double * value);
virtual asynStatus getDoubleParam(int list, int index, double * value);
virtual asynStatus getStringParam(int index, int maxChars, char *value);
virtual asynStatus getStringParam(int list, int index, int maxChars, char *value);
virtual asynStatus callParamCallbacks();
virtual asynStatus callParamCallbacks(int list, int addr);
</PRE>
The <CODE>setXXXParam</CODE> methods set the value of a parameter in the parameter table
in the object. If the value is different from the previous value of the parameter
they also set the flag indicating that the value has changed. The <CODE>getXXXParam</CODE>
methods return the current value of the parameter. There are two versions of the
<CODE>setXXXParam</CODE> and <CODE>getXXXParam</CODE> methods, one with a <CODE>list</CODE>
argument, and one without. The one without uses <CODE>list=0</CODE>, since there
is often only a single parameter list (i.e. if maxAddr=1). The <CODE>callParamCallbacks</CODE>
methods call back any registered clients for parameters that have changed since the last
time <CODE>callParamCallbacks</CODE> was called. The version of <CODE>callParamCallbacks</CODE>
with no arguments uses the first parameter list and matches asyn address=0. There is a
second version of <CODE>callParamCallbacks</CODE> that takes an argument specifying the parameter list
number, and the asyn address to match.
<CENTER><H2><A name=NDArray>
NDArray</A></H2></CENTER>
The NDArray (N-Dimensional array) is the class that is used for passing detector data from drivers
to plugins. The NDArray class is defined as follows:
<PRE>
#define ND_ARRAY_MAX_DIMS 10
typedef enum
{
NDInt8,
NDUInt8,
NDInt16,
NDUInt16,
NDInt32,
NDUInt32,
NDFloat32,
NDFloat64
} NDDataType_t;
typedef struct NDDimension {
int size;
int offset;
int binning;
int reverse;
} NDDimension_t;
typedef struct NDArrayInfo {
int nElements;
int bytesPerElement;
int totalBytes;
} NDArrayInfo_t;
class NDArray {
public:
/* Data: NOTE this must come first because ELLNODE must be first, i.e. same address as object */
/* The first 2 fields are used for the freelist */
ELLNODE node;
int referenceCount;
/* The NDArrayPool object that created this array */
void *owner;
int uniqueId;
double timeStamp;
int ndims;
NDDimension_t dims[ND_ARRAY_MAX_DIMS];
NDDataType_t dataType;
int dataSize;
void *pData;
/* Methods */
NDArray();
int initDimension (NDDimension_t *pDimension, int size);
int getInfo (NDArrayInfo_t *pInfo);
int convertDimension(NDArray *pOut,
void *pDataIn,
void *pDataOut,
int dim);
int copy (NDArray *pOut);
int reserve();
int release();
};
</PRE>
An NDArray is a general purpose class for handling array data. An NDArray object is self-describing,
meaning it contains enough information to describe the data itself. It is not intended to
contain meta-data describing how the data was collected, etc.
<P>
An NDArray can have up to ND_ARRAY_MAX_DIMS dimensions, currently 10. A fixed maximum
number of dimensions is used to significantly simplify the code compared to
unlimited number of dimensions. Each dimension of the array is described
by an NDDimension_t structure. The fields in NDDimension_t are as follows:
<UL>
<LI><CODE>size</CODE> is the number of elements in this dimension.
<LI><CODE>offset</CODE> is the starting element in this dimension
relative to the first element of the detector in unbinned units. If a selected
region of the detector is being read, then this value may be
&gt 0. The offset value is cumulative, so if a plugin such as NDPluginROI
further selects a subregion, the offset is relative
to the first element in the detector and not to the first element of
the region passed to NDPluginROI.
<LI><CODE>binning</CODE> is the binning (sumation of elements) in this
dimension. The offset value is cumulative, so if a plugin such as
NDPluginROI performs binning,
the binning is expressed relative
to the pixels in the detector and not to the possibly binned
pixels passed to NDPluginROI.
<LI><CODE>reverse</CODE> is 0 if the data are in their normal order
as read out from the detector in this dimension,
and 1 if they are in reverse order. This value is cumulative,
so if a plugin such as
NDPluginROI reverses the data, the value must reflect the
orientation relative to the original detector, and not to
the possibly reversed data passed to NDPluginROI.
</UL>
The first 3 data fields in the NDArray class, <CODE>(node, referenceCount, owner)</CODE> are used
by the NDArrayPool class discussed below.
The remaining data fields are as follows:
<UL>
<LI><CODE>uniqueId</CODE> This should be a number that uniquely identifies this array. Detector
drivers should assign this number to the NDArray before calling the plugins.
<LI><CODE>timeStamp</CODE> This should be a timestamp value in seconds recording when the frame
was collected. The time=0 reference is driver-dependent because of differences in vendor
libraries. If there is a choice, it is recommended to use timeStamp=0 for Epoch, (00:00:00 UTC,
January 1, 1970).
<LI><CODE>ndims</CODE> The number of dimensions in this array.
<LI><CODE>dims</CODE> Array of NDDimension_t structures. The array is of length ND_MAX_DIMS, but
only the first <CODE>ndims</CODE> values must contain valid information.
<LI><CODE>dataType</CODE> The data type of this array, one of the NDDataType_t enum values.
The data types supported are signed and unsigned 8, 16, and 32-bit integers, and 32 and 64-bit floats.
<LI><CODE>dataSize</CODE> The size of the memory buffer pointed to by <CODE>pData</CODE> in bytes. This may be
larger than the amount actually required to hold the data for this array.
<LI><CODE>pData</CODE> Pointer to the memory for this array. The data is assumed to be stored
in the order of <CODE>dims[0]</CODE> changing fastest, and <CODE>dims[ndims-1]</CODE> changing slowest.
</UL>
The methods of the NDArray class are:
<UL>
<LI><CODE>initDimension</CODE> This method ...
</UL>
<CENTER><H2><A name="EPICS records">
EPICS records</A></H2></CENTER>
<P>
The following EPICS records are used by pilatusROI. All records are prefixed by the macro
$(DET) which must be passed to the template file when the records are loaded.</P>
<H3><A name="Acquisition related records">
Acquisition related records</A></H3>
<UL>
<LI><CODE>AcquireMode</CODE> (mbbo)<BR>
This record controls the acquisition mode. The allowed values are:
<UL>
<LI>0 ("Internal") Internal exposure mode, external signal not used.
<LI>1 ("Ext. Enable") External enable mode. External signal controls acquire and readout.
<LI>2 ("Ext. Trigger") External trigger mode. External signal triggers an acquisition sequence.
<LI>3 ("Mult. Trigger") Multiple trigger mode. Each external trigger edge triggers a single acquisition
for the programmed exposure time.
<LI>4 ("Alignment") Alignment mode. Repetitively collects single images as quickly as possible.
The images are written to a temporary file.
The <CODE>MinImageUpdateTime</CODE> PV is ignorred in
this mode, so that all images are sent to EPICS for display.
It is similar to the <CODE>exposem</CODE> command in TVX.
</UL>
The first 4 acquisition modes correspond directly to the camserver commands <CODE>Exposure</CODE>,
<CODE>ExtEnable</CODE>, <CODE>ExtTrigger</CODE>, and <CODE>ExtMTrigger</CODE>respectively.
Alignment mode uses the <CODE>Exposure</CODE> command as well, but continuously takes images into
the same temporary file (<CODE>alignment.tif</CODE>).
<LI><CODE>ExposureTime</CODE> (ao)<BR>
This record controls the exposure time in seconds. In External Enable mode this value is not
used by camserver. However, it should be set larger than the maximum time exposure time from the
external source, so that pilatusROI.st can estimate how long
to wait for the data files to be created before timing out.
<LI><CODE>NImages</CODE> (longout)<BR>
This record controls the number of images to acquire. It applies in all acquisition modes except
Alignment.
<LI><CODE>ExposurePeriod</CODE> (ao)<BR>
This record controls the exposure period in seconds. It is only in Internal or External Trigger modes
when NImages>1.
<LI><CODE>NExposures (longout)</CODE><BR>
This record controls the number of exposures per image. It is only used in External Enable mode.
<LI><CODE>DelayTime</CODE> (ao)<BR>
This record controls the delay in seconds between the external trigger
and the start of image acquisition. It only applies in External Trigger mode.
<LI><CODE>Acquire</CODE> (busy)<BR>
This record controls the acquisition. Setting this record to 1 ("Busy") starts image acquisition.
The SNL program sets the record to 0 ("Done") when acquisition is complete. This means an entire
acquisition series if NImages>1. This record is an EPICS
"busy" record from the synApps sscan module. This record does not call recGblFwdLink until
acquisition is complete. It can thus be used with the sscan record as a detector trigger that
will wait for acquisition to complete before going to the next point in the scan. It can also
be used with EPICS caPutCallback to wait for acquisition to complete before the callback completes.
<LI><CODE>Armed</CODE> (bo)<BR>
This record signals when the Pilatus is ready to accept trigger pulses. It changes from 0 to 1
after camserver sends a response to an acquire start command indicating that the Pilatus is ready to
begin taking data. The SNL program sets the record to 0 when acquisition is complete.
This PV should be used by clients to indicate when it is OK to start sending trigger pulses
to the Pilatus. If pulses are send before Armed=1 then the Pilatus may miss them, leading to
DMA timeout errors from camserver.
<LI><CODE>Abort</CODE> (bo)<BR>
This record aborts an acquisition. Setting this record to 1 stops whatever acquisition is in progress.
If pilatusROI
was currently acquiring imges (Acquire=Busy) then this record will cause the "K" (Kill) command to
be sent to camserver. It will also set Acquire back to Done.
<LI><CODE>StatusMessage</CODE> (stringout)<BR>
This record contains a string that provides status information on the state of pilatusROI. It contains
strings like "Starting exposure", "Waiting for TIFF file", etc.
</UL>
<P>
<H3><A name="Detector related records">
Detector related records</A></H3>
<UL>
<LI><CODE>ThresholdEnergy</CODE> (ao)<BR>
This record controls the threshold energy in eV.
<LI><CODE>Gain</CODE> (mbbo)<BR>
This record controls the value of Vrf, which in determines the shaping time and gain of the
input amplifiers. The allowed values are:
<UL>
<LI>0 ("Fast/Low") Fastest shaping time (~125ns) and lowest gain.
<LI>1 ("Medium/Medium") Medium shaping time (~200 ns) and medium gain.
<LI>2 ("Slow/High") Slow shaping time (~400 ns) and high gain.
<LI>3 ("Slow/Ultrahigh") Slowest peaking time (? ns) and highest gain.
</UL>
</UL>
<P>
<H3><A name="File name related records">
File name related records</A></H3>
The FilePath, Filename, FileNumber, and FileFormat PVs are all used to create the final FullFilename.
<UL>
<LI><CODE>FilePath</CODE> (waveform, FTVL=UCHAR, NELM=256)<BR>
This record controls the path for saving images. It must be a valid path for camserver
<i>and</i> for the SNL program.
If camserver and the EPICS IOC are not running on the same machine then soft links
will typically be used to make the paths look identical.<P>
This record is an EPICS waveform record with FTVL=UCHAR and NELM=256.
This removes the 40 character
restriction on path name lengths that arise if an EPICS "string" PV is used. medm allows one to
edit and display such records correctly. EPICS clients will typically need to convert the path
name from a string to an integer or byte array before sending the path name to EPICS. This is easy
to do in clients like SPEC, Matlab, and IDL.
<LI><CODE>Filename</CODE> (stringout)<BR>
This record controls the base file name for saving images. It is limited to 40 characters.
<LI><CODE>FileNumber</CODE> (longout)<BR>
This record controls the number of the next file for saving images.
<LI><CODE>FileFormat</CODE> (stringout)<BR>
This record controls how the FilePath, Filename, and FileNumber are combined to form the final
file name. The format string is limited to 40 characters.
The final file name (which can be up to 256 characters) is created with the following code:
<PRE>
epicsSnprintf(FullFilename, sizeof(FullFilename), FileFormat,
FilePath, Filename, FileNumber);
</PRE>
FilePath, Filename, FileNumber are converted in that order with FileFormat.
The default file format is <CODE>"%s%s%4.4d.tif"</CODE>. The first %s converts the FilePath,
followed immediately by another %s for Filename.
FileNumber is formatted with %4.4d, which results in a
fixed field with of 4 digits, with leading zeros as required. Finally, the .tif extension
is added to the file name. This will make camserver save files in TIFF format with that extension.
<P>
This mechanism for creating file names is very flexible. Other characters, such as _ can be put
in Filename or FileFormat as desired. If one does not want to have FileNumber in the file name
at all, then just omit the %d format specifier from FileFormat.
<P>
Note that when saving multiple images (NImages>1) camserver has its own rules for creating the
names of the individual files. The rules are as follows:
<P>
The name constructed using the above algorithm is used as a basename.
The following examples show the interpretation of the basename.
<PRE>
Basename Files produced
test6.tif test6_00000.tif, test6_00001.tif, ...
test6_.tif test6_00000.tif, test6_00001.tif, ...
test6_000.tif test6_000.tif, test6_001.tif, ...
test6_014.tif test6_014.tif, test6_015.tif, ...
test6_0008.tif test6_0008.tif, test6_0009.tif, ...
test6_2_0035.tif test6_2_0035.tif, test6_2_0036.tif, ...
</PRE>
The numbers following the last '_' are taken as a format template,
and as a start value. The minimum format is 3; there is no maximum; the
default is 5. The format is also constrained by the requested number of images.
<LI><CODE>AutoIncrement</CODE> (bo)<BR>
This record controls whether FileNumber is automatically incremented by 1 each time an acquisition
completes. 0=No, 1=Yes.
<LI><CODE>FullFilename</CODE> (waveform, FTVL=UCHAR, NELM=256)<BR>
This is a read-only record that contains the full filename of the current file, after the above
code has been executed. Note that the FullFilename is not constructed until Acquire is set to 1.
</UL>
<H3><A name="ROI related records">
ROI related records</A></H3>
The SNL code supports up to 32 rectangular ROIs. Fewer ROIs can be used by loading the pilatusROI_N.template file
fewer than 32 times, and passing NROIS<32 to the SNL program when it is started. In the following
record names $(N) is a number from 1 to 32. ROIs can be any size from a single pixel to the entire
chip.
An ROI is considered invalid and ignorred by the SNL program if any of Xmin, Xmax, YMin, YMax is less than 0 or
greater than the size of the chip in that direction. The ROI is also invalid if Xmin>XMax or YMin>YMax.
<UL>
<LI><CODE>ROI$(N)XMin</CODE> (longout)<BR>
The minimum value of X for ROI N.
<LI><CODE>ROI$(N)XMax</CODE> (longout)<BR>
The maximum value of X for ROI N.
<LI><CODE>ROI$(N)YMin</CODE> (longout)<BR>
The minimum value of Y for ROI N.
<LI><CODE>ROI$(N)YMax</CODE> (longout)<BR>
The maximum value of Y for ROI N.
<LI><CODE>ROI$(N)BgdWidth</CODE> (longout)<BR>
The background width ROI N. ROI$(N)BgdWidth<=0 means no background subtraction is done, and
ROI$(N)NetCounts=ROI$(N)TotalCounts. The background region is defined as follows:
<UL>
<LI>If ROI$(N)BgdWidth=1 then the background is one pixel outside of the perimeter of the ROI,
i.e the single-pixel wide
rectangular box defined by ROI$(N)XMin-1, ROI$(N)XMax+1, ROI$(N)YMin-1, and ROI$(N)YMax+1.
However, if any of those locations would be outside of the chip then that dimension is changed
to be on the perimeter of the ROI. This ensures that
a valid background region can be defined even if the ROI touches the edge of the detector.
<LI>If ROI$(N)BgdWidth>1 then the background is a rectangular box of width ROI$(N)BgdWidth, moving
out from the ROI location defined above. However, if the background would go
beyond the edge of the detector, then it is clipped to the largest valid width in
that direction.
</UL>
<LI><CODE>ROI$(N)TotalCounts</CODE> (ao)<BR>
The total counts in ROI N.
<LI><CODE>ROI$(N)NetCounts</CODE> (ao)<BR>
The net counts in ROI N, i.e. the total counts minus the background counts. This is determined
by computing the average number of counts per pixel in the background, and subtracting this from
the counts in the ROI.
<LI><CODE>ROI$(N)MinCounts</CODE> (longout)<BR>
The minimum counts in any pixel in ROI N.
<LI><CODE>ROI$(N)MaxCounts</CODE> (longout)<BR>
The maximum counts in any pixel in ROI N. This can be useful to monitor to make sure that the 20-bit
limit of 1,048,575 is not being approached.
<LI><CODE>ROI$(N)Label</CODE> (stringout)<BR>
The string label for ROI N.
<LI><CODE>ROI$(N)WFTotalCounts</CODE> (waveform, FTVL=DOUBLE, NELM=$(NCHANS))<BR>
The total counts in ROI N in a waveform record. Valid when NImages>1.
<LI><CODE>ROI$(N)WFNetCounts</CODE> (waveform, FTVL=DOUBLE, NELM=$(NCHANS))<BR>
The net counts in ROI N in a waveform record. Valid when NImages>1.
<LI><CODE>MinWFUpdateTime</CODE> (ao)<BR>
This record controls the minimum time between posting the ROI$(N)WFTotalCounts and ROI$(N)WFNetCounts
arrays to EPICS.
This should normally be set to a value >0.1 second to reduce the network bandwidth use. The SNL
program always posts the arrays when acquisition completes, so that the final ROI data for the
series is sent to EPICS.
</UL>
The ROI$(N)TotalCounts and ROI$(N)NetCounts are computed as each TIFF file is read, regardless of the
value of NImages. The ROI$(N)WFTotalCounts and ROI$(N)WFNetCounts arrays are computed and posted to
EPICS when acquiring data with NImages>1. The first element in each array is the for the first image
in the series, etc.
<H3><A name="Image related records">
Image related records</A></H3>
<UL>
<LI><CODE>ImageData</CODE> (waveform, FTVL=LONG, NELM=$(NPIXELS))<BR>
The detector image data as an EPICS waveform record. In order for EPICS clients
to receive this data they must be built with EPICS R3.14 (not R3.13), and the environment variable
EPICS_CA_MAX_ARRAY_BYTES on both the EPICS IOC computer and EPICS client computer must be set to a value
at least as large as the image size in bytes, i.e. to 379860 or more.
<LI><CODE>NXPixels</CODE> (longout)<BR>
The number of pixels in the X direction on the detector. The SNL program needs to know this value.
EPICS clients can use this value to reformat ImageData from
a 1-D array to a 2-D array.
<LI><CODE>NYPixels</CODE> (longout)<BR>
The number of pixels in the Y direction on the detector. The SNL program needs to know this value.
EPICS clients can use this value to reformat ImageData from
a 1-D array to a 2-D array.
<LI><CODE>HighlightROIs</CODE> (bo)<BR>
This record controls the whether the SNL program highlights the ROI borders in the image before
sending the images to EPICS. If selected then the pixels on the ROI borders are replaced with the
value of the most intense pixel in the image, so they will always be visible in the display.
0=No, don't highlight, 1=Yes, highlight.
<LI><CODE>PostImages</CODE> (bo)<BR>
This record controls the whether the SNL program sends ImageData to EPICS.
0=No, don't send, 1=Yes, send. This can be set to 0 to reduce the network bandwidth use.
<LI><CODE>MinImageUpdateTime</CODE> (ao)<BR>
This record controls the minimum time between posting ImageData to EPICS.
This should normally be set to a value >0.5 second to reduce the network bandwidth use. This
means that not all images may be sent to EPICS. This value is ignorred when AcquireMode=Alignment.
</UL>
<H3><A name="Bad pixel map related records">
Bad pixel map related records</A></H3>
<UL>
<LI><CODE>BadPixelFile</CODE> (waveform, FTVL=UCHAR, NELM=256)<BR>
This record contains the name of a file to be used to replace bad pixels.
If this record does not point to a valid bad pixel file then no bad pixel mapping is performed.
See the notes on theFilePath regarding using waveform records for long strings.
The bad pixel map
is used before computing the ROIs and before sending ImageData to EPICS. It does not modify
the data in the files that camserver writes. This is a simple ASCII file with the following
format:
<PRE>
badX1,badY1 replacementX1,replacementY1
badX2,badY2 replacementX2,replacementY2
...
</PRE>
The X and Y coordinates range from 0 to NXPixels-1 and NYPixels-1. Up to 100 bad pixels can be defined.
The bad pixel mapping simply replaces the bad pixels with another pixel's value.
It does not do any averaging. It is felt that this is sufficient for the purpose for which
pilatusROI was written, namely fast on-line viewing of ROIs and ImageData. More sophisticated
algorithms can be used for offline analysis of the image files themselves.
The following is an example bad pixel file for the GSECARS detector:
<PRE>
263,3 262,3
264,3 266,3
263,3 266,3
300,85 299,85
300,86 299,86
471,129 472,129
</PRE>
<LI><CODE>NBadPixels</CODE> (longout)<BR>
The number of bad pixels defined in the bad pixel file.
Useful for seeing if the bad pixel file was read correctly.
</UL>
<H3><A name="Flat field correction related records">
Flat field correction related records</A></H3>
<UL>
<LI><CODE>FlatFieldFile</CODE> (waveform, FTVL=UCHAR, NELM=256)<BR>
This record contains the name of a file to be used to correct for the flat field.
If this record does not point to a valid flat field file then no flat field correction is performed.
See the notes on theFilePath regarding using waveform records for long strings.
The flat field file is simply a TIFF file collected by the Pilatus that is used to correct for
spatial non-uniformity in the response of the detector. It should be collected with a spatially uniform
intensity on the detector at roughly the same energy as the measurements being corrected.
When the flat field file is read, the average pixel value (averageFlatField) is computed
using all pixels with intensities > MinFlatField. All pixels with intensity < MinFlatField
in the flat field are replaced with averageFlatField.
When images are collected, before the ROIs are computed, and before the images
are sent to EPICS, the following per-pixel correction is applied:
<PRE>
ImageData[i] = (averageFlatField * ImageData[i])/flatField[i];
</PRE>
<LI><CODE>MinFlatField</CODE> (ao)<BR>
The mimimum valid intensity in the flat field. This value must be set > 0 to prevent divide by 0 errors.
If the flat field was collected with some pixels having very low intensity then this value can be used to
replace those pixels with the average response.
<LI><CODE>FlatFieldValid</CODE> (bo)<BR>
This record indicates if a valid flat field file has been read. 0=No, 1=Yes.
</UL>
<H3><A name="Communication related records">
Communication related records</A></H3>
<UL>
<LI><CODE>ReadTiffTimeout</CODE> (ao)<BR>
This record controls the timeout in seconds between when the SNL program thinks a TIFF file should be ready
to read, and when a timeout will occur. It should be set to several seconds, because there can be delays
for various reasons. One reason is that there is sometimes a delay between when an External Enable
acquisition is started and when the first external pulse occurs. Another is that it can take some time for
camserver processes to finish writing the files.
<LI><CODE>SendMessage</CODE> (waveform, FTVL=UCHAR, NELM=256)<BR>
This read-only record contains the most recent message sent from the SNL program to camserver.
<LI><CODE>ReplyMessage</CODE> (waveform, FTVL=UCHAR, NELM=256)<BR>
This read-only record contains the most recent reply message from camserver to the SNL program.
<LI><CODE>Connect</CODE> (bo)<BR>
Processing this record causes the drvAsynIPPort server to connect to camserver.
This normally happens once in the
startup script, and does not need to be processed again unless Disconnect is processed.
<LI><CODE>Disconnect</CODE> (bo)<BR>
Processing this record causes the drvAsynIPPort server to disconnect from camserver.
This can be used to allow another
program, such as TVX, to temporarily take control of camserver, without restarting the EPICS IOC. Use
the Connect record to reconnect the IOC to camserver.
</UL>
<H3><A name="Scan related records">
Scan related records</A></H3>
<UL>
<LI><CODE>scan1, scan2, scan3, scan4, scanH</CODE> (sscan)<BR>
The example IOC startup script loads the scan.sb database from the SSCAN module. This loads 5 sscan
records which can be used to perform up to 4-dimensional scans with any EPICS PV as positioners and
detectors. The scan records are very useful with the Pilatus for scanning the ThresholdEnergy PV
and plotting the counts in an ROI that includes the entire detector. This allows setting the energy
threshold to detect the x-rays of interest.
<P>&nbsp;</P>
<CENTER><H2><A name="EPICS startup script">
EPICS startup script</A></H2></CENTER>
<P>
pilatusROI.template is loaded with the following macro parameters:
<TABLE style="TEXT-ALIGN: left" cellSpacing=2 cellPadding=2 border=1>
<TBODY>
<TR>
<TH>Macro parameter</TH>
<TH>Description</TH>
</TR>
<TR>
<TD><CODE>$(DET)</CODE></TD>
<TD>PV name prefix. This identifies this Pilatus detector from others that may be
running on the same subnet.
</TD>
</TR>
<TR>
<TD><CODE>$(NXPIXELS)</CODE></TD>
<TD>The number of pixels in the X (fast index) direction on the detector. This is 487 for the Pilatus 100K.</TD>
</TR>
<TR>
<TD><CODE>$(NYPIXELS)</CODE></TD>
<TD>The number of pixels in the Y (slow index) direction on the detector. This is 195 for the Pilatus 100K.</TD>
</TR>
<TR>
<TD><CODE>$(NPIXELS)</CODE></TD>
<TD>The total number of pixels on the detector. This is NXPIXELS*NYPIXELS=94965 for the Pilatus 100K.</TD>
</TR>
<TR>
<TD><CODE>$(PORT)</CODE></TD>
<TD>The name of the asyn port connected to the Pilatus via a TCP/IP socket.</TD>
</TR>
</TBODY>
</TABLE>
<P>
pilatusROI_N.template is loaded for each ROI with the following macro parameters:
<TABLE style="TEXT-ALIGN: left" cellSpacing=2 cellPadding=2 border=1>
<TBODY>
<TR>
<TH>Macro parameter</TH>
<TH>Description</TH>
<TR>
<TD><CODE>$(DET)</CODE></TD>
<TD>PV name prefix. This identifies this Pilatus detector from others that may be
running on the same subnet.</TD>
</TR>
<TR>
<TD><CODE>$(N)</CODE></TD>
<TD>The number of this ROI. Starts with 1.</TD>
</TR>
<TR>
<TD><CODE>$(XMIN)</CODE></TD>
<TD>The minimum value of X for this ROI. Starts with 0.</TD>
</TR>
<TR>
<TD><CODE>$(XMAX)</CODE></TD>
<TD>The maximum value of X for this ROI. Starts with 0.</TD>
</TR>
<TR>
<TD><CODE>$(YMIN)</CODE></TD>
<TD>The minimum value of Y for this ROI. Starts with 0.</TD>
</TR>
<TR>
<TD><CODE>$(YMAX)</CODE></TD>
<TD>The maximum value of Y for this ROI. Starts with 0.</TD>
</TR>
<TR>
<TD><CODE>$(BGD_WIDTH)</CODE></TD>
<TD>The background width for this ROI.
If BGD_WIDTH <=0 then no background subtraction is done, and NetCounts=TotalCounts.</TD>
</TR>
<TR>
<TD><CODE>$(NCHANS)</CODE></TD>
<TD>The maximum number of elements in the WFTotalCounts and WFNetCounts waveform arrays.
This sets the maximum value of NImages for collecting ROI arrays.</TD>
</TR>
</TBODY>
</TABLE>
<P>
The pilatusROIs SNL program is started with the following macro parameters:
<TABLE style="TEXT-ALIGN: left" cellSpacing=2 cellPadding=2 border=1>
<TBODY>
<TR>
<TH>Macro parameter</TH>
<TH>Description</TH>
<TR>
<TD><CODE>DET</CODE></TD>
<TD>PV name prefix. This identifies this Pilatus detector from others that may be
running on the same subnet.</TD>
</TR>
<TR>
<TD><CODE>PORT</CODE></TD>
<TD>The name of the asyn port connected to the Pilatus via a TCP/IP socket.</TD>
</TR>
<TR>
<TD><CODE>NROIS</CODE></TD>
<TD>The number of ROIs loaded in the substitutions file with pilatusROI_N.template.
Maximum=32.</TD>
</TR>
</TBODY>
</TABLE>
<P>
The following is an example st.cmd startup script:
<PRE>
< envPaths
###
# Load the EPICS database file
dbLoadDatabase("$(PILATUS)/dbd/pilatus.dbd")
pilatus_registerRecordDeviceDriver(pdbbase)
###
# Create the asyn port to talk to the Pilatus on port 41234.
drvAsynIPPortConfigure("pilatus","gse-pilatus1:41234")
# Set the input and output terminators.
asynOctetSetInputEos("pilatus", 0, "\030")
asynOctetSetOutputEos("pilatus", 0, "\n")
# Define the environment variable pointing to stream protocol files.
epicsEnvSet("STREAM_PROTOCOL_PATH", "$(PILATUS)/pilatusApp/Db")
###
# Specify where save files should be
set_savefile_path(".", "autosave")
###
# Specify what save files should be restored. Note these files must be
# in the directory specified in set_savefile_path(), or, if that function
# has not been called, from the directory current when iocInit is invoked
set_pass0_restoreFile("auto_settings.sav")
set_pass1_restoreFile("auto_settings.sav")
###
# Specify directories in which to to search for included request files
set_requestfile_path("./")
set_requestfile_path("$(AUTOSAVE)", "asApp/Db")
set_requestfile_path("$(CALC)", "calcApp/Db")
set_requestfile_path("$(SSCAN)", "sscanApp/Db")
set_requestfile_path("$(PILATUS)", "pilatusApp/Db")
###
# Load the save/restore status PVs
dbLoadRecords("$(AUTOSAVE)/asApp/Db/save_restoreStatus.db", "P=PILATUS:")
###
# Load the substitutions for for this IOC
dbLoadTemplate("PILATUS_all.subs")
# Load an asyn record for debugging
dbLoadRecords("$(ASYN)/db/asynRecord.db", "P=PILATUS:,R=asyn1,PORT=pilatus,ADDR=0,IMAX=80,OMAX=80")
# Load sscan records for scanning
dbLoadRecords("$(SSCAN)/sscanApp/Db/scan.db", "P=PILATUS:,MAXPTS1=2000,MAXPTS2=200,MAXPTS3=20,MAXPTS4=10,MAXPTSH=2048")
###
# Set debugging flags if desired
#asynSetTraceIOMask("pilatus",0,2)
#asynSetTraceMask("pilatus",0,3)
###
# Start the IOC
iocInit
###
# Save settings every thirty seconds
create_monitor_set("auto_settings.req", 30, "P=PILATUS:")
###
# Start the SNL program
seq(pilatusROIs, "DET=PILATUS:, PORT=pilatus, NROIS=16")
</PRE>
The following is the substutitions file PILATUS_all.subs referenced above.
It creates 16 ROIS, and defines 5 valid ones: the entire chip, and the 4 quadrants of the chip:
<PRE>
ffile $(PILATUS)/db/pilatusROI.template {
pattern
{DET, NXPIXELS, NYPIXELS, NPIXELS, PORT}
{PILATUS:, 487, 195, 94965, pilatus}
}
file $(PILATUS)/db/pilatusROI_N.template {
pattern
{DET, N, XMIN, XMAX, YMIN, YMAX, BGD_WIDTH, NCHANS}
{PILATUS:, 1, 0, 486, 0, 194, 1, 2000}
{PILATUS:, 2, 0, 243, 0, 97, 1, 2000}
{PILATUS:, 3, 0, 243, 98, 194, 1, 2000}
{PILATUS:, 4, 244, 486, 0, 97, 1, 2000}
{PILATUS:, 5, 244, 486, 98, 194, 1, 2000}
{PILATUS:, 6, -1, -1, -1, -1, 1, 2000}
{PILATUS:, 7, -1, -1, -1, -1, 1, 2000}
{PILATUS:, 8, -1, -1, -1, -1, 1, 2000}
{PILATUS:, 9, -1, -1, -1, -1, 1, 2000}
{PILATUS:, 10, -1, -1, -1, -1, 1, 2000}
{PILATUS:, 11, -1, -1, -1, -1, 1, 2000}
{PILATUS:, 12, -1, -1, -1, -1, 1, 2000}
{PILATUS:, 13, -1, -1, -1, -1, 1, 2000}
{PILATUS:, 14, -1, -1, -1, -1, 1, 2000}
{PILATUS:, 15, -1, -1, -1, -1, 1, 2000}
{PILATUS:, 16, -1, -1, -1, -1, 1, 2000}
}
</PRE>
<P>&nbsp;</P>
<CENTER><H2><A name="MEDM screens">
MEDM screens</A></H2></CENTER>
<P>
The following show the MEDM screens that are used to control the pilatusROI software.</P>
<P>&nbsp;</P>
<CODE>pilatusROI.adl</CODE> is the main screen used to control the pilatusROI SNL
program. All records except those that are specific to each ROI are accessed through this
screen.
<CENTER><H3>pilatusROI.adl</H3>
<IMG src="pilatusROI.png"></CENTER>
<P>&nbsp;</P>
<CODE>pilatus8ROIs.adl</CODE> is used to define the ROIs, and to display the statistics for
each ROI. In this example there are 2 valid ROIs defined. ROI 1 is a small rectangle near the center
containing the Bragg diffraction peak from a crystal. ROI 2 is the entire chip.
<CENTER><H3>pilatus8ROIs.adl</H3>
<IMG src="pilatus8ROIs.png"></CENTER>
<P>&nbsp;</P>
<CODE>pilatusROI_waveform.adl</CODE> is used to plot the net or total counts in an ROI when
NImages>1. In this example the plot is the net counts in ROI 1 as the diffractometer chi was scanned
+- 1 degree with 1000 points at .02 seconds/point. This was done with the SPEC command
<PRE>
lup chi -1 1 1000 .02
</PRE>
using trajectory scanning on a Newport kappa diffractometer. This was a compound motor scan with the
Newport XPS putting out pulses every .02 seconds. These pulses triggered the Pilatus in External Enable mode.
The pilatusROI program read each TIFF file as it was created and updated this plot every 0.2 seconds.
The total time to collect this scan with 1000 images was 20 seconds.
<CENTER><H3>pilatusROI_waveform.adl</H3>
<IMG src="pilatusROI_waveform.png"></CENTER>
<P>&nbsp;</P>
<CODE>scan_more.adl</CODE> is used to define a scan. In this example the sscan record is set up
to scan the ThresholdEnergy PV and to collect the total counts in ROI2, which was defined to include
the entire detector.
<CENTER><H3>scan_more.adl</H3>
<IMG src="pilatusROI_scan_more.png"></CENTER>
<P>&nbsp;</P>
<CODE>scanDetPlot.adl</CODE> is used to plot the results of a scan after it is complete.
In this example the total counts in ROI 2 are plotted as a function of the ThresholdEnergy as it was
scanned from 3000 to 10000 eV in 250 eV steps. The source was Fe55, and the cut-off is at 6 keV, as
expected for the Mn Ka and Mn Kb x-rays that this source produces.
<CENTER><H3>scanDetPlot.adl</H3>
<IMG src="pilatusROI_scan_plot.png"></CENTER>
<P>&nbsp;</P>
<CODE>asynRecord.adl</CODE> is used to control the debugging information printed by the asyn TCP/IP driver
(asynTraceIODriver) and the SNL program (asynTraceIODevice).
<CENTER><H3>asynRecord.adl</H3>
<IMG src="pilatusAsynRecord.png"></CENTER>
<P>&nbsp;</P>
<CODE>asynOctet.adl</CODE> can be used to send any command to camserver and display the response. It can
be loaded from the More menu in asynRecord.adl above.
<CENTER><H3>asynOctet.adl</H3>
<IMG src="pilatusAsynOctet.png"></CENTER>
<P>&nbsp;</P>
<CENTER><H2><A name="IDL Image Display Client">
IDL Image Display Client</A></H2></CENTER>
There is an IDL program called <CODE>epics_image_display</CODE>
that can be used to display the ImageData PV that pilatusROI sends over EPICS. This IDL
client is available as source code (which requires an IDL license), and also as a pre-built IDL .sav
file that can be run for free under the IDL Virtual Machine. This IDL program can run on any machine that IDL
runs on, and that has the ezcaIDL shareable library built for it. This includes Windows, Linux, Solaris, and Mac.
<CODE>epics_image_display</CODE> is included in the
<A HREF="http://cars.uchicago.edu/software/IDL/imaging.html">CARS IDL imaging software.</A>
<P>
The control window for <CODE>epics_image_display</CODE> is shown below. It has fields to input the name of
the EPICS PV with the image data, which is $(DET)ImageData in the case of pilatusROI. It also has fields
for the number of pixels in the X and Y directions. This is needed because EPICS waveform records are
1-dimensional only, and so do not contain the information on the number of rows and columns in the image.
<CENTER><H3>Main window for IDL epics_image_display</H3>
<IMG src="pilatusROI_EPICS_ImageDisplay.png"></CENTER>
<P>&nbsp;</P>
<CODE>epics_image_display</CODE> uses the routine
<A HREF="http://cars.uchicago.edu/software/IDL/imaging_routines.html#IMAGE_DISPLAY">image_display.pro</A>
to display the images. This routine displays row and column profiles as the cursor is moved. It allows
changing the color lookup tables, and zooming in and out with the left and right mouse buttons. The following
is an example of <CODE>image_display</CODE> displaying a Pilatus image with an Fe55 source in front of the detector.
<CENTER><H3>IDL image_display with Fe55 radioactive source</H3>
<IMG src="pilatusROI_IDL_ImageDisplay.png"></CENTER>
<P>&nbsp;</P>
<CENTER><H2><A name="SPEC interface">
SPEC interface</A></H2></CENTER>
At the GSECARS beamlines (13-ID-C and 13-BM-C) at the APS we use SPEC to control our Newport diffractometers.
We have added and modified SPEC macros to use pilatusROI to treat the Pilatus detector as a SPEC
counter. This works in both traditional step-scanning mode, as well as in
<A href="http://cars.uchicago.edu/software/epics/trajectoryScan.html">trajectory scanning</A> mode.
Here are some snippets from the SPEC macros for the Pilatus. We can supply the source files on request.
<PRE>
# need some more globals (kludge)
global PILATUS_ROI_PV
global PILATUS_IMGPATH_PV
global PILATUS_FNAME_PV
global PILATUS_FILENUMBER_PV
global PILATUS_FILEFORMAT_PV
global PILATUS_EXPSRTM_PV
global PILATUS_NFRAME_PV
global PILATUS_EXPPRD_PV
global PILATUS_NEXPFRM_PV
global PILATUS_ACQ_PV
global PILATUS_ACQMODE_PV
###############################################################
def _setup_img '{
local j, str
# PILATUS_PREFIX should be detector aquisition pv (GSE-PILATUS1:)
if ( PILATUS_PREFIX == "") PILATUS_PREFIX = "GSE-PILATUS1:"
PILATUS_PREFIX = getval("Enter PILATUS pv prefix",PILATUS_PREFIX)
# rois pvs
PILATUS_ROI_PV = PILATUS_PREFIX "ROI1NetCounts"
PILATUS_IMGPATH_PV = PILATUS_PREFIX "FilePath"
PILATUS_FNAME_PV = PILATUS_PREFIX "Filename"
PILATUS_FILENUMBER_PV = PILATUS_PREFIX "FileNumber"
PILATUS_FILEFORMAT_PV = PILATUS_PREFIX "FileFormat"
PILATUS_EXPSRTM_PV = PILATUS_PREFIX "ExposureTime"
PILATUS_NFRAME_PV = PILATUS_PREFIX "NImages"
PILATUS_EXPPRD_PV = PILATUS_PREFIX "ExposurePeriod"
PILATUS_NEXPFRM_PV = PILATUS_PREFIX "NExposures"
PILATUS_ACQ_PV = PILATUS_PREFIX "Acquire"
PILATUS_ACQMODE_PV = PILATUS_PREFIX "AcquireMode"
...
def epics_pilatus_count '{
...
# write to data base fields
# Need to convert path from string to byte array
# Note: we use the "wait" parameter in epics_put here (new to spec5.7.02) so that
# it uses ca_put_callback, to know that all PVs have been processed
# before we start counting. Use 1 second timeout, will actually be
# much faster than this unless something is wrong.
array _temp[256]
_temp = PILATUS_IMAGE_DIR
# Do not change path for now
#epics_put(PILATUS_IMGPATH_PV,_temp, 1)
epics_put(PILATUS_FNAME_PV,img_fname, 1)
epics_put(PILATUS_FILENUMBER_PV,NPTS, 1)
epics_put(PILATUS_FILEFORMAT_PV,_fileformat, 1)
epics_put(sc_prtm_pv,cnt_time_val, 1)
epics_put(PILATUS_EXPSRTM_PV,cnt_time_val, 1)
epics_put(PILATUS_ACQMODE_PV,0, 1) # Internal trigger
epics_put(PILATUS_NFRAME_PV, 1, 1)
epics_put(PILATUS_NEXPFRM_PV, 1, 1)
def user_getcounts '{
local pv_roi, j, pv
...
# using image_count routine
} else if ( EPICS_COUNT == 4 ) {
S[iroi] = 0
S[iroi] = epics_get(PILATUS_ROI_PV)
</PRE>
<P>&nbsp;</P>
<CENTER><H2><A name="Performance measurements">
Performance measurements</A></H2></CENTER>
The following measurements were done to demonstrate the performance that can be obtained with pilatusROI.
<OL>
<LI>AcquireMode=Internal, NImages=1000, ExposureTime=.005, ExposurePeriod=.01, NExposures=1.
The time to collect this series should be exactly 10.0 seconds.
The actual time was measured using the EPICS camonitor program. It printed the time when
acquisition was started (Acquire changed to Busy) and when acquisition was complete (Acquire changed to Done).
The time was 10.274 seconds. This includes the time for camserver to save all 1000 images to disk (366 MB),
and for pilatusROI to read each file, correct the bad pixels and flat field, compute the ROIs, and post the ROIs
to EPICS. It also posted the images to EPICS at 1Hz (10 images total). The total additional time was less
than 0.3 seconds for all 1000 images.
<LI>AcquireMode=Internal, NImages=1, ExposureTime=.01, NExposures=1.
An EPICS sscan record was used to collect 1000 points.
There were no positioner PVs (to eliminate motor overhead).
The only detector trigger was the pilatusROI Acquire PV. The only detector PV was ROI1TotalCounts.
In this mode camserver is being told to individually collect each file.
If there were no overhead then time to collect this series should be exactly 10.0 seconds.
The actual time measured using the EPICS camonitor program was 49.161 seconds.
The overhead is thus 39.161 seconds, or 39 ms per point.
In this single-frame mode pilatusROI is thus able to collect >20 images/second.
For comparison, another measurement was done using the same EPICS sscan record,
but using a Joerger VSC16 scaler as the detector
trigger and detector. The preset time was also .01 seconds. The elapsed time for a 1000 point scan was
16.068 seconds, so the overhead was 6.068 seconds, or 6 ms per point.
<LI>AcquireMode=Ext. Enable, NImages=1000, NExposures=1.
SPEC was used to collect 1000 points using
<A href="http://cars.uchicago.edu/software/epics/trajectoryScan.html">trajectory scanning</A> mode
with the Newport XPS motor controller. The following SPEC command was used:
<PRE>
lup chi -2 2 1000 .015
</PRE>
This tells SPEC to do a relative scan of the chi axis from -2 degrees to +2 degrees with 1000 points
at .015 seconds/point. On our kappa diffractometer this entails a coordinated motion of the phi, kappa
and omega axes. The EPICS trajectory scanning software downloads the non-linear trajectory that SPEC computes
into the XPS controller, which executes it. As the motors are moving the XPS outputs synchronization pulses
at the period of the collection time, .015 seconds in this case. These pulses are stretched
(see <A href="#Hardware notes">Hardware notes</A> below) and used as the external input to the Pilatus.
The time to execute this scan should be 15.0 seconds. The actual time was 16.3 seconds, measured
using camonitor on the Acquire PV. Again, this includes the time for camserver to save all 1000 images to disk
(366 MB), and for pilatusROI to read each file, correct the bad pixels and flat field, compute the ROIs, and post the ROIs
to EPICS. It also posted the images to EPICS at 1Hz (15 images total). The total additional time was less
than 1.3 seconds for all 1000 images. As soon as the acquisition was complete SPEC plotted the net counts in
the first ROI (containing the Bragg peak) as follows:
<CENTER><H3>1000 point SPEC scan with 15 ms per point collected in 16.3 seconds</H3>
<IMG src="pilatusROI_spec.png"></CENTER>
<P>
For comparison this identical scan was executed in traditional step-scanning mode, where the motors stopped
at each point in the scan. The Pilatus was run in Internal mode with NImages=1. The total time for the scan
was 870 seconds (more than 14 minutes), compared to 16.3 seconds in trajectory mode. Most of this overhead
is the settling time for the motors, with only a small fraction due to the Pilatus single-exposure mode. The
trajectory scanning mode is thus more than 50 times faster to execute the identical SPEC scan.
</OL>
<P>&nbsp;</P>
<CENTER><H2><A name="Hardware notes">
Hardware notes</A></H2></CENTER>
<H3>Trigger pulses</H3>
The Pilatus supports 3 types of external triggering. In External Trigger mode (the camserver ExtTrigger command)
the Pilatus uses the programmed values of ExposureTime, ExposurePeriod, NImages and NExposures. It waits for
a single external trigger, then waits for Delay seconds and then collects the entire sequence. It is very similar
to Internal mode with NImages>1, except that it waits for a trigger to begin collecting the sequence.
<P>In External Enable mode (the camserver ExtEnable command) the Pilatus uses the external signal to control acquisition.
Only NImages and NExposures are used, ExposureTime and ExposurePeriod are not used. When the signal
is high the detector counts, and on the transition to low it begins its readout.
<P>In External MultiTrigger Mode (the camserver ExtMTrigger command) the Pilatus uses the programmed ExposureTime,
in addition to NImages and NExposures. Each external trigger pulse causes the Pilatus to collect one image
at the programmed exposure time. This mode works well with a trigger source like the Newport motor controllers
or the SIS380x multichannel scaler,
that put out a short trigger pulse for each image. One only needs to take care that the time between external trigger
pulses is at least 4msec longer than the programmed exposure time, to allow time for the detector to read out before
the next trigger pulse arrives.
<P>When using the External Enable mode, we use an inexpensive analog pulse generator
to convert the trigger pulses from the MM4005 and XPS to a form suitable for External Enable mode
with the Pilatus. This is the solution we have developed that seems to be reliable:
<UL>
<LI>The synchonization pulses from the Newport MM4005 or XPS controller are input into the external next pulse
(channel advance, control signal 1) input of the SIS3801 multiscaler.
This is the normal configuration used for MCS counting
without the Pilatus in trajectory scanning mode.
<LI>The Copy In Progress (CIP) output of the SIS3801 (control signal 5) is connected to the Trigger Input of a
Tenma TGP110 10 MHz Pulse Generator. CIP will output a pulse whenever the SIS3801 does a channel advance,
either in external mode with the motor controller pulse input, or in internal timed channel advance mode.
The TGP100 Pulse Generator is configured as follows:
<UL>
<LI>Trigger Input connected to CIP output of SIS3801.
<LI>Triggered mode.
<LI>Complement output.
<LI>Pulse duration set with knobs to 3msec.
<LI>TTL Output connected to the External Input of the Pilatus.
</UL>
<LI>With this configuration the SIS3801 CIP output is normally at 5V, and outputs a 0V pulse 1 microsecond long.
The trailing (rising) edge of that pulse triggers the TGP110. The TGP110 TTL output is also normally at 5V,
and outputs a 0V pulse 3 milliseconds long each time the SIS3801 pulses. That output is connected to the
Pilatus External Input. In External Enable mode when Pilatus External Input is
high the Pilatus is counting. When the External Input is low the Pilatus reads out. The readout time is
set via the knobs on the pulse generator to be 3 ms, which is close to the minimum time allowed on the
Pilatus.
</UL>
The Tenma TGP110 seems to be currently called a Tenma 72-6860, and lists for about $350 new
at <A href="http://www.newark.com">Newark</A>.
<H3>Detector Voltage</H3>
When we were initially testing the Pilatus in the lab, we had many errors in External Enable mode, where it did
not seem to be seeing the external pulses. camserver would get DMA timeouts, and need to be restarted. Dectris
said these were happening because the cables on our detector are longer than normal, and the voltage
drop from the power supply to the detector was leading to marginal voltage values. They suggested shortening
the cables or increasing the supply voltage slightly. When moving the detector to the hutch these
problems initially went away. However, they then recurred, and we fixed the problem by increasing
the power supply voltage from 4.4 to 4.7 volts at the detector.
<P>
Dectris has since informed me that they have increased the power supply voltage on all new Pilatus systems,
so this should no longer be an issue.
<P>&nbsp;</P>
<CENTER><H2><A name="Restrictions">
Restrictions</A></H2></CENTER>
The following are some current restrictions of the pilatusROI SNL program:
<UL>
<LI>Limited to TIFF file format.
camserver can save files in other formats, but pilatusROI can currently only read TIFF files.
Furthermore, it
has a very simple TIFF reader. It does not read the TIFF tags at all, but simply assumes that there
is a 4096 byte header, followed by the 32-bit image data. The size of the image data is controlled
by the NXPixels and NYPixels PVs, which thus must be correctly set.
<LI>The EPICS IOC should be run on the same computer as camserver.
This is not strictly necessary, and places a small additional load on the CPU and network
on that computer. However, we have found that TIFF files are available to be read within 10ms after
camserver says they have been written if the IOC is running on the same machine as camserver. This is true
even if the files are being saved on a remote NFS or SMB file system. On the other hand, if the IOC and
camserver are running on separate machines, then the filesystem can wait up to 1 second after camserver
says the TIFF file has been written before the IOC can read it. This is true even if the files are being
written to the computer that the IOC is running on! This 1 second delay is often unacceptable for fast
single-exposure scans, i.e. with NImages=1.
<LI>pilatusROI keeps retrying to read each TIFF file until
the modification date of the TIFF file is <I>after</I> the time that the exposure command was issued.
If it did not
do this check then it could be reading and displaying old files that happen to have the same name as the
current files being collected. This check requires that the computer that is running the soft IOC must
have its clock well synchronized with the
clock on the computer on which the files are being written
(i.e. the computer generating the file modification time).
If the clocks are not synchronized then the files may appear to be stale when they are not,
and pilatusROI will time out. pilatusROI actually tolerates up to 10 second clock skew betweeen the computers
but any more than this may lead to problems.
<LI>The Abort PV does not always work because camserver does not reliably implement the "K" command to stop
an exposure sequence. In particular with NImages>1 camserver seems to often ignore
the K command completely, even with exposure times/periods as long as 10 seconds.
With NImages=1 it does kill the exposure after a few seconds.
<LI>The following items are hardcoded in the SNL program. They can be changed before compiling if necessary.
Some could be changed to be EPICS PVs, so they could be controlled at run-time, but others must be defined
at compile time because of limitations in the SNL semantics.
<UL>
<LI>MAX_MESSAGE_SIZE=256 The maximum size of message to/from camserver.
<LI>MAX_FILENAME_LEN=256 The maximum size of a complete file name including path and extension.
<LI>FILE_READ_DELAY=.01 seconds. The time between polling to see if the TIFF file exists
or if it is the expected size.
<LI>MAX_BAD_PIXELS=100 The maximum number of bad pixels.
<LI>MAX_ROIS=32 The maximum number of ROIs
<LI>MAX_CHANS=2000 The maximum number of points in the ROI waveform arrays.
<LI>MAX_PIXELS=94965 The maximum number of pixels in the ImageData array. Because of SNL semantics
limitations this value must be defined at compile time, and cannot be changed at run time.
<LI>MAX_READ_ERRORS=3 The maximum number of TIFF file read errors before the SNL gives up and aborts
acquisition.
</UL>
</UL>
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