Startup
This commit is contained in:
gac-x04sa
@@ -41,4 +41,4 @@ oa=ch.psi.pshell.epics.Motor|X04SA-ES3-XPS:OMEGAA|||true
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#sixch=ch.psi.pshell.device.MotorGroupBase|alpha delta gamma omegaH nu phi|||
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fourcv=ch.psi.pshell.device.MotorGroupBase|alpha delta gamma omegaV|||
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$energy=ch.psi.pshell.epics.Positioner|X04SA-DCM:E X04SA-DCM:E-READ|||true
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transm=ch.psi.pshell.epics.ControlledVariable|X04SA-ES2-FI:TRANSM-SET X04SA-ES2-FI:TRANSM|||
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transm=ch.psi.pshell.epics.ControlledVariable|X04SA-ES2-FI:TRANSM-SET X04SA-ES2-FI:TRANSM|||true
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@@ -0,0 +1,8 @@
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#Thu Oct 18 17:36:38 CEST 2018
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maxValue=1.0
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minValue=0.0
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offset=0.0
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precision=5
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resolution=NaN
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scale=1.0
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unit=
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@@ -0,0 +1,757 @@
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#==============================================================================
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# Macroname: image.mac
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# =========
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#+
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# $Date: 2008/03/20 13:36:14 $
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# $Author: schlepuetz $
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# $Source: /cvs/G/SPEC/local/X04SA/ES3/image.mac,v $
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# $Revision: 1.11 $
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# $Tag: $
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#
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# Description: This macro file provides a set of macro definitions which are
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# used to analyze images (taken by any sort of imaging device)
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# on-line during data acquisition and return a set of charac-
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# teristic values to SPEC.
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# It is thus possible to plot results of a scan (usually an
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# intensity value) during data acquisition with the imaging
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# device, just like one would with a point detector.
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# Furthermore, the image information can be used to automate
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# filter transmission and exposure time settings during a scan
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# (refer to auto.mac for more information on automated scans).
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#
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# Note: This macro is based on an earlier version by O. Bunk
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# and R. Herger
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#
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# Author: C. M. Schlepuetz (CS)
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# Co-author(s): R. Herger (RH), P. R. Willmott (PW)
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# Address: Surface Diffraction Station
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# Materials Science Beamline X04SA
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# Swiss Light Source (SLS)
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# Paul Scherrer Institute
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# CH - 5232 Villigen PSI
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# Created: 2005/07/12
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#
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#-
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# Chained macro definitions affected by this macro:
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# -------------------------------------------------
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# - user_getcounts
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#
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# Change Log:
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# -----------
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#
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# 2005/07/12 (CS):
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# - created first version of this file.
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#
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# 2005/12/10 (CS):
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# - fixed bug in imageGetInt: background region area was not correctly
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# calculated in the c-routine and consequently all intensities were wrong.
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# (also changed the c-routine, of course)
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#
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# 2005/12/11 (CS):
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# - attempt to generalize the image_get_int routine to images of different
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# sizes and color-depths, and possibly header lengths.
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# Introduced new globals variables:
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# IMAGE_INFO_FILENAME
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# IMAGE_HEADER_LENGTH (in bytes)
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# IMAGE_COLOR_DEPTH (in number of bits, e.g. 16 or 32)
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# - write an info-file with information about each image in imageUserGetcounts
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# which can be accessed by all external programs which want to look at the
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# images.
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# - Increase the number of threshold levels for image analysis to 4. That way,
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# the thresholds for adjusting the exposure time automatically (see also
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# auto.mac) and the filter transmission are independent of each other.
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# Introduced new global variables:
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# IMAGE_THRESH4
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# IMAGE_THRESH4_COUNT
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#
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# 2006/01/27 (CS):
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# - fixed typo in imageCheckRoi
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#
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# 2006/06/23 (CS):
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# - retrieve IMAGE_PATH from IMAGE_FILENAME with unix command DIRNAME.
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# - copy image information file into IMAGE_PATH such that it is accessible
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# to all applications which have access to the image path.
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#
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# 2006/08/09 (CS):
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# - input to 'imgeSetRoi' is now possible in several ways, including user
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# interaction.
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# - removed old commented out workarounds.
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#
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# 2006/09/21 (CS):
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# - added new functionality to the image_get_int.c routine for selectively
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# median filtering only those pixels where the measured intensity differs
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# from the mean of the surrounding pixels by more than N times the standard
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# deviation of these neighbours. N is presently set to 30 in imageGetInt.
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#
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# 2006/11/29 (CS):
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# - include wait loop in imageUserGetcounts to make sure the image file is
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# available an non-empty in order to do statistical analysis with
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# image_get_int.c.
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#
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# 2007/04/05 (CS):
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# - new error message if image file to be analyzed is not found.
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#
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# 2007/04/22 (CS):
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# - changed imageCheckROI to allow for ROIs of 1 pixel width/height (used to
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# be at least 2 pixels).
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#
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# 2008/03/19 (CS):
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# - removed quotation marks around argument variables $1,$2 in imageSetRoi,
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# allowing one to also pass the arguments via variables.
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# - added imageShowRoi.
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#
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#==============================================================================
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#
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global IMAGE_MAC
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#
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IMAGE_MAC = DOFILE # Save the name of this macro file.
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# (Used for the help function).
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#+
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#==============================================================================
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# This macro file contains the following commands:
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#-
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#
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#+
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#------------------------------------------------------------------------------
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# imagehelp - generates this help text. This is obtained by
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# displaying the file image.txt, which should sit in the
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# same directory as this macro file.
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#-
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# allow for misspelled help commands
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def helpimage 'imagehelp'
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def helpImage 'imagehelp'
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def imageHelp 'imagehelp'
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def imagehelp '{
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# =========
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unix (sprintf ("dirname %s", IMAGE_MAC), _1)
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ll = length (_1)
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if (substr (_1, ll, 1) == "\n") _1 = substr (_1, 1, (ll - 1))
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file = sprintf ("%s/image.txt", _1)
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if (file_info (file, "-e")) {
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unix (sprintf ("cat %s | less", file))
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} else {
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printf("\n Macros available in file image.mac ($Revision: 1.11 $):\n")
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printf( " ========="\n)
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printf("\n")
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printf(" imagehelp - creates this help text\n")
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printf(" imageOn - turn on image analysis functionality\n")
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printf(" imageOff - turn off image analysis functionality\n")
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printf(" imageShow - show current image analysis setup.\n")
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printf(" imageShowRoi - show current region of interest info.\n")
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printf(" imageSetRoi - define a signal and background region-\n")
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printf(" of-interest (ROI).")
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printf(" imageCheckRoi - checks whether ROI is valid and within\n")
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printf(" image bounds.
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printf(" imageGetInt - description\n")
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}
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}'
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#+
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#------------------------------------------------------------------------------
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# imageInit - initializes all global variables used by image.mac
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#-
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def imageInit '{
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# =========
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global IMAGE_DEVICE, IMAGE_IS_ON
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global IMAGE_FILENAME, IMAGE_PATH, IMAGE_FNUM, IMAGE_FBASE
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global IMAGE_INFO_FILENAME, IMAGE_HEADER_LENGTH
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global IMAGE_XDIM, IMAGE_YDIM, IMAGE_COLOR_DEPTH
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global IMAGE_I_SIG, IMAGE_I_BG, IMAGE_I_SUM
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global IMAGE_AREA_SIG, IMAGE_AREA_BG
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global IMAGE_THRESH1, IMAGE_THRESH2, IMAGE_THRESH3, IMAGE_THRESH4
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global IMAGE_THRESH1_COUNT, IMAGE_THRESH2_COUNT
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global IMAGE_THRESH3_COUNT, IMAGE_THRESH4_COUNT
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global IMAGE_SX1, IMAGE_SY1, IMAGE_SX2, IMAGE_SY2
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global IMAGE_BX1, IMAGE_BY1, IMAGE_BX2, IMAGE_BY2
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}'
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#+
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#------------------------------------------------------------------------------
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# imageOn - turn on macro functionality to analyze images acquired by
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# an area detector on-line and return the results to SPEC.
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#-
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def imageon 'imageOn'
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def imageOn '{
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# =======
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global IMAGE_DEVICE, IMAGE_IS_ON
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global IMAGE_FILENAME, IMAGE_PATH, IMAGE_FNUM, IMAGE_FBASE
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global IMAGE_INFO_FILENAME, IMAGE_HEADER_LENGTH
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global IMAGE_XDIM, IMAGE_YDIM, IMAGE_COLOR_DEPTH
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global IMAGE_I_SIG, IMAGE_I_BG, IMAGE_I_SUM
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global IMAGE_AREA_SIG, IMAGE_AREA_BG
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global IMAGE_THRESH1, IMAGE_THRESH2, IMAGE_THRESH3, IMAGE_THRESH4
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global IMAGE_THRESH1_COUNT, IMAGE_THRESH2_COUNT
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global IMAGE_THRESH3_COUNT, IMAGE_THRESH4_COUNT
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global IMAGE_SX1, IMAGE_SY1, IMAGE_SX2, IMAGE_SY2
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global IMAGE_BX1, IMAGE_BY1, IMAGE_BX2, IMAGE_BY2
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#--------------------------------------------
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# include necessary chained macro definitions
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#---------------------
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def imageUserGetcounts \'
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# ==================
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if (IMAGE_IS_ON) {
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# update IMAGE_PATH variable
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unix(sprintf("dirname %s",IMAGE_FILENAME), IMAGE_PATH)
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# write important image information to file so image_get_int.c and other
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# possible helper applications can read it.
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local ux_cmd
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ux_cmd = ""
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IMAGE_INFO_FILENAME = "/tmp/spec_image_info.dat"
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ux_cmd = sprintf("echo \"%s\" > %s",\\
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IMAGE_FILENAME, IMAGE_INFO_FILENAME)
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if (unix(ux_cmd) != 0) {
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eprint ">> Cannot store image information file <<"
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} else {
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ux_cmd = sprintf("echo \"%.6f\" >> %s",\\
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time(), IMAGE_INFO_FILENAME)
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if (unix(ux_cmd) != 0) {
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eprint ">> Cannot store image information file <<"
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}
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unix(sprintf("echo \"%d\" >> %s",\\
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IMAGE_HEADER_LENGTH,IMAGE_INFO_FILENAME))
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unix(sprintf("echo \"%d %d %d\" >> %s",\\
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IMAGE_XDIM, IMAGE_YDIM, IMAGE_COLOR_DEPTH,\\
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IMAGE_INFO_FILENAME))
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unix(sprintf("echo \"%d %d %d %d\" >> %s",\\
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IMAGE_SX1, IMAGE_SY1, IMAGE_SX2, IMAGE_SY2, \\
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IMAGE_INFO_FILENAME))
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unix(sprintf("echo \"%d %d %d %d\" >> %s",\\
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IMAGE_BX1, IMAGE_BY1, IMAGE_BX2, IMAGE_BY2, \\
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IMAGE_INFO_FILENAME))
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}
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# copy information file into image path
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unix(sprintf("cp -f %s %s", IMAGE_INFO_FILENAME, IMAGE_PATH))
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# get the AUTO_THRESH2 value if auto levels are enabled
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if ((whatis("AUTO_THRESH2") & 0x08000000) == 0) {
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IMAGE_THRESH2=AUTO_THRESH2
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}
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# check whether image file is ready to be read (size > 0 bytes)
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retry = 0
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_tmp_filename = IMAGE_FILENAME
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while((!(file_info(_tmp_filename,"-s"))) & (retry<3000)){
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printf("waiting for image file %s\n",IMAGE_FILENAME)
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printf("retry %d of 3000\n",retry)
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retry++
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if (retry%100 == 0) {
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unix(sprintf("head -n 1 %f", IMAGE_FILENAME))
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}
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sleep(0.01)
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}
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# get the integrated intensity in the intensity and background boxes
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imageGetInt IMAGE_THRESH1 IMAGE_THRESH2 IMAGE_THRESH3 IMAGE_THRESH4
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# update the auto-level threshold count values if auto-level support
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# is available
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if ((whatis("AUTO_THRESH1_COUNT") & 0x08000000) == 0) {
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AUTO_THRESH1_COUNT=IMAGE_THRESH1_COUNT
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AUTO_THRESH2_COUNT=IMAGE_THRESH2_COUNT
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AUTO_THRESH3_COUNT=IMAGE_THRESH3_COUNT
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AUTO_THRESH4_COUNT=IMAGE_THRESH4_COUNT
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}
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# return the background corrected intensity
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if (IMAGE_AREA_BG > 0){
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S[2] = (IMAGE_I_SUM - IMAGE_I_BG/IMAGE_AREA_BG*IMAGE_AREA_SIG)
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} else{
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S[2] = IMAGE_I_SUM
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}
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# correct for filter transmission and exposure time
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# p epics_get("X04SA-ES2-FI:TRANSM")
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S[3] = S[2] / COUNT_TIME / epics_get("X04SA-ES2-FI:TRANSM")
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# write plot information for Matlab
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local ux_cmd, comFile, tmpFile
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ux_cmd = ""
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tmpFile = "/tmp/spec_image_temp.dat"
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comFile = "/tmp/spec_matlab_image.dat"
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ux_cmd = sprintf("echo \"%s\" > %s",\\
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IMAGE_FILENAME, tmpFile)
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if (unix(ux_cmd) != 0) {
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eprint ">> Can not store Matlab plot information <<"
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} else {
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ux_cmd = sprintf("echo \"%.6f\" >> %s",\\
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time(), tmpFile)
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if (unix(ux_cmd) != 0) {
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eprint ">> Can not store Matlab plot information <<"
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}
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unix(sprintf("echo \"%d %d\" >> %s",\\
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IMAGE_XDIM, IMAGE_YDIM, tmpFile))
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unix(sprintf("echo \"%d %d %d %d\" >> %s",\\
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IMAGE_SX1, IMAGE_SY1, IMAGE_SX2, IMAGE_SY2, tmpFile))
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unix(sprintf("echo \"%d %d %d %d\" >> %s",\\
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IMAGE_BX1, IMAGE_BY1, IMAGE_BX2, IMAGE_BY2, tmpFile))
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# overwrite the last file
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unix(sprintf("mv -f %s %s",tmpFile,comFile))
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}
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}
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\'
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# add imageUserGetcounts to middle of user_getcounts
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cdef("user_getcounts","imageUserGetcounts; ","image_user_getcounts_key")
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#---------------------------------------------------
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# update the global variables for auto-level support
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if ((whatis("AUTO_THRESH1") & 0x08000000) == 0) {
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AUTO_THRESH1 = IMAGE_THRESH1
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AUTO_THRESH2 = IMAGE_THRESH2
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AUTO_THRESH3 = IMAGE_THRESH3
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AUTO_THRESH4 = IMAGE_THRESH4
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}
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IMAGE_IS_ON=1
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imageShow
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}'
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#+
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#------------------------------------------------------------------------------
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# imageOff - turn off macro functionality to analyze images acquired by
|
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# an area detector on-line and return the results to SPEC.
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#-
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def imageoff 'imageOff'
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def imageOff '{
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# ========
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global IMAGE_DEVICE, IMAGE_IS_ON
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global IMAGE_FILENAME, IMAGE_PATH, IMAGE_FNUM, IMAGE_FBASE
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global IMAGE_INFO_FILENAME, IMAGE_HEADER_LENGTH
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global IMAGE_XDIM, IMAGE_YDIM, IMAGE_COLOR_DEPTH
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global IMAGE_I_SIG, IMAGE_I_BG, IMAGE_I_SUM
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global IMAGE_AREA_SIG, IMAGE_AREA_BG
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global IMAGE_THRESH1, IMAGE_THRESH2, IMAGE_THRESH3, IMAGE_THRESH4
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global IMAGE_THRESH1_COUNT, IMAGE_THRESH2_COUNT
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global IMAGE_THRESH3_COUNT, IMAGE_THRESH4_COUNT
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global IMAGE_SX1, IMAGE_SY1, IMAGE_SX2, IMAGE_SY2
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global IMAGE_BX1, IMAGE_BY1, IMAGE_BX2, IMAGE_BY2
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#---------------------------------------------
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||||
# remove unnecessary chained macro definitions
|
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# remove imageUserGetcounts from user_getcounts
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cdef("user_getcounts","imageUserGetcounts; ","image_user_getcounts_key",\\
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"delete")
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IMAGE_IS_ON=0
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imageShow
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|
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}'
|
||||
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||||
#+
|
||||
#------------------------------------------------------------------------------
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||||
# imageShow - show whether image analysis is currently enabled and
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||||
# display the region-of-interest (ROI) settings.
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#-
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||||
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def imageshow 'imageShow'
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||||
def imageInfo 'imageShow'
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||||
def imageinfo 'imageShow'
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def imageShow '{
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# =========
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global IMAGE_DEVICE, IMAGE_IS_ON
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global IMAGE_FILENAME, IMAGE_PATH, IMAGE_FNUM, IMAGE_FBASE
|
||||
global IMAGE_INFO_FILENAME, IMAGE_HEADER_LENGTH
|
||||
global IMAGE_XDIM, IMAGE_YDIM, IMAGE_COLOR_DEPTH
|
||||
global IMAGE_I_SIG, IMAGE_I_BG, IMAGE_I_SUM
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||||
global IMAGE_AREA_SIG, IMAGE_AREA_BG
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||||
global IMAGE_THRESH1, IMAGE_THRESH2, IMAGE_THRESH3, IMAGE_THRESH4
|
||||
global IMAGE_THRESH1_COUNT, IMAGE_THRESH2_COUNT
|
||||
global IMAGE_THRESH3_COUNT, IMAGE_THRESH4_COUNT
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||||
global IMAGE_SX1, IMAGE_SY1, IMAGE_SX2, IMAGE_SY2
|
||||
global IMAGE_BX1, IMAGE_BY1, IMAGE_BX2, IMAGE_BY2
|
||||
|
||||
if(IMAGE_IS_ON==1){
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||||
printf("\nImage analysis is currently enabled.\n")
|
||||
printf("The active imaging device name is: %s\n", IMAGE_DEVICE)
|
||||
imageShowRoi
|
||||
} else{
|
||||
printf("Image analysis is disabled.\n")
|
||||
}
|
||||
|
||||
}'
|
||||
|
||||
#+
|
||||
#------------------------------------------------------------------------------
|
||||
# imageShowRoi - show information on the currently active region of interest
|
||||
#-
|
||||
|
||||
def imageshowroi 'imageShowRoi'
|
||||
def imageshowROI 'imageShowRoi'
|
||||
def imageShowROI 'imageShowRoi'
|
||||
|
||||
def imageShowRoi '{
|
||||
# ============
|
||||
|
||||
global IMAGE_DEVICE, IMAGE_IS_ON
|
||||
global IMAGE_FILENAME, IMAGE_PATH, IMAGE_FNUM, IMAGE_FBASE
|
||||
global IMAGE_INFO_FILENAME, IMAGE_HEADER_LENGTH
|
||||
global IMAGE_XDIM, IMAGE_YDIM, IMAGE_COLOR_DEPTH
|
||||
global IMAGE_I_SIG, IMAGE_I_BG, IMAGE_I_SUM
|
||||
global IMAGE_AREA_SIG, IMAGE_AREA_BG
|
||||
global IMAGE_THRESH1, IMAGE_THRESH2, IMAGE_THRESH3, IMAGE_THRESH4
|
||||
global IMAGE_THRESH1_COUNT, IMAGE_THRESH2_COUNT
|
||||
global IMAGE_THRESH3_COUNT, IMAGE_THRESH4_COUNT
|
||||
global IMAGE_SX1, IMAGE_SY1, IMAGE_SX2, IMAGE_SY2
|
||||
global IMAGE_BX1, IMAGE_BY1, IMAGE_BX2, IMAGE_BY2
|
||||
|
||||
imageCheckRoi
|
||||
|
||||
}'
|
||||
|
||||
|
||||
#+
|
||||
#------------------------------------------------------------------------------
|
||||
# imageSetRoi - set the region-of-interest for intensity and background
|
||||
# integration.
|
||||
#
|
||||
# Usage : imageSetRoi
|
||||
# prompts user for roi coordinates
|
||||
# or imageSetRoi <Sx1> <Sy1> <Sx2> <Sy2>
|
||||
# set signal roi to <Sx1> <Sy1> <Sx2> <Sy2> and use same
|
||||
# coordinates for background roi
|
||||
# (as a result, no background is subtracted)
|
||||
# or imageSetRoi <Sx1> <Sy1> <Sx2> <Sy2> <Bx1> <By1> <Bx2> <By2>
|
||||
# set signal roi to <Sx1> <Sy1> <Sx2> <Sy2> and background
|
||||
# roi to <Bx1> <By1> <Bx2> <By2>.
|
||||
#-
|
||||
|
||||
def imagesetroi 'imageSetRoi'
|
||||
def imageSetROI 'imageSetRoi'
|
||||
|
||||
def imageSetRoi '{
|
||||
# ===========
|
||||
|
||||
global IMAGE_DEVICE, IMAGE_IS_ON
|
||||
global IMAGE_FILENAME, IMAGE_PATH, IMAGE_FNUM, IMAGE_FBASE
|
||||
global IMAGE_INFO_FILENAME, IMAGE_HEADER_LENGTH
|
||||
global IMAGE_XDIM, IMAGE_YDIM, IMAGE_COLOR_DEPTH
|
||||
global IMAGE_I_SIG, IMAGE_I_BG, IMAGE_I_SUM
|
||||
global IMAGE_AREA_SIG, IMAGE_AREA_BG
|
||||
global IMAGE_THRESH1, IMAGE_THRESH2, IMAGE_THRESH3, IMAGE_THRESH4
|
||||
global IMAGE_THRESH1_COUNT, IMAGE_THRESH2_COUNT
|
||||
global IMAGE_THRESH3_COUNT, IMAGE_THRESH4_COUNT
|
||||
global IMAGE_SX1, IMAGE_SY1, IMAGE_SX2, IMAGE_SY2
|
||||
global IMAGE_BX1, IMAGE_BY1, IMAGE_BX2, IMAGE_BY2
|
||||
|
||||
if ($# == 8) {
|
||||
IMAGE_SX1 = $1
|
||||
IMAGE_SY1 = $2
|
||||
IMAGE_SX2 = $3
|
||||
IMAGE_SY2 = $4
|
||||
IMAGE_BX1 = $5
|
||||
IMAGE_BY1 = $6
|
||||
IMAGE_BX2 = $7
|
||||
IMAGE_BY2 = $8
|
||||
} else if($# == 4){
|
||||
IMAGE_SX1 = $1
|
||||
IMAGE_SY1 = $2
|
||||
IMAGE_SX2 = $3
|
||||
IMAGE_SY2 = $4
|
||||
IMAGE_BX1 = $1
|
||||
IMAGE_BY1 = $2
|
||||
IMAGE_BX2 = $3
|
||||
IMAGE_BY2 = $4
|
||||
} else if($# == 0){
|
||||
sig_roi = getval("Signal Roi (sx1 sy1 sx2 sy2):",sprintf("%d %d %d %d",\
|
||||
IMAGE_SX1,IMAGE_SY1,IMAGE_SX2,IMAGE_SY2))
|
||||
sscanf(sig_roi,"%d %d %d %d",IMAGE_SX1,IMAGE_SY1,IMAGE_SX2,IMAGE_SY2)
|
||||
bg_roi = getval("Background Roi (bx1 by1 bx2 by2):",sprintf("%d %d %d %d",\
|
||||
IMAGE_SX1,IMAGE_SY1,IMAGE_SX2,IMAGE_SY2))
|
||||
sscanf(bg_roi,"%d %d %d %d",IMAGE_BX1,IMAGE_BY1,IMAGE_BX2,IMAGE_BY2)
|
||||
} else{
|
||||
eprint "Wrong number of arguments in \'imageSetRoi\'"
|
||||
eprint "Usage:"
|
||||
eprint " imageSetRoi"
|
||||
eprint " prompts the user for input"
|
||||
eprint " imageSetRoi <sx1> <sy1> <sx2> <sy2>"
|
||||
eprint " set background roi = signal roi (no background subtraction)"
|
||||
eprint " imageSetRoi <sx1> <sy1> <sx2> <sy2> <bx1> <by1> <bx2> <by2>"
|
||||
eprint " sets signal and background roi individually"
|
||||
exit
|
||||
}
|
||||
|
||||
imageCheckRoi
|
||||
|
||||
}'
|
||||
|
||||
#+
|
||||
#------------------------------------------------------------------------------
|
||||
# imageCheckRoi - Check the region of interest for intensity and background
|
||||
# integration for consistency with the image dimensions, etc.
|
||||
#
|
||||
# Usage : imageCheckRoi # no arguments needed
|
||||
#-
|
||||
|
||||
def imageCheckRoi '{
|
||||
# =============
|
||||
|
||||
global IMAGE_DEVICE, IMAGE_IS_ON
|
||||
global IMAGE_FILENAME, IMAGE_PATH, IMAGE_FNUM, IMAGE_FBASE
|
||||
global IMAGE_INFO_FILENAME, IMAGE_HEADER_LENGTH
|
||||
global IMAGE_XDIM, IMAGE_YDIM, IMAGE_COLOR_DEPTH
|
||||
global IMAGE_I_SIG, IMAGE_I_BG, IMAGE_I_SUM
|
||||
global IMAGE_AREA_SIG, IMAGE_AREA_BG
|
||||
global IMAGE_THRESH1, IMAGE_THRESH2, IMAGE_THRESH3, IMAGE_THRESH4
|
||||
global IMAGE_THRESH1_COUNT, IMAGE_THRESH2_COUNT
|
||||
global IMAGE_THRESH3_COUNT, IMAGE_THRESH4_COUNT
|
||||
global IMAGE_SX1, IMAGE_SY1, IMAGE_SX2, IMAGE_SY2
|
||||
global IMAGE_BX1, IMAGE_BY1, IMAGE_BX2, IMAGE_BY2
|
||||
|
||||
local coordAdjusted
|
||||
|
||||
coordAdjusted = 0
|
||||
|
||||
#-----------------
|
||||
# check signal box
|
||||
|
||||
if (IMAGE_SX1 < 1) {
|
||||
IMAGE_SX1 = 1
|
||||
coordAdjusted = 1
|
||||
}
|
||||
if (IMAGE_SY1 < 1) {
|
||||
IMAGE_SY1 = 1
|
||||
coordAdjusted = 1
|
||||
}
|
||||
if (IMAGE_SX1 > IMAGE_XDIM-1) {
|
||||
IMAGE_SX1 = IMAGE_XDIM-1
|
||||
coordAdjusted = 1
|
||||
}
|
||||
if (IMAGE_SY1 > IMAGE_YDIM-1) {
|
||||
IMAGE_SY1 = IMAGE_YDIM-1
|
||||
coordAdjusted = 1
|
||||
}
|
||||
if (IMAGE_SX2 > IMAGE_XDIM-1) {
|
||||
IMAGE_SX2 = IMAGE_XDIM-1
|
||||
coordAdjusted = 1
|
||||
}
|
||||
if (IMAGE_SY2 > IMAGE_YDIM-1) {
|
||||
IMAGE_SY2 = IMAGE_YDIM-1
|
||||
coordAdjusted = 1
|
||||
}
|
||||
if (IMAGE_SX2 < IMAGE_SX1) {
|
||||
IMAGE_SX2 = IMAGE_SX1
|
||||
coordAdjusted = 1
|
||||
}
|
||||
if (IMAGE_SY2 < IMAGE_SY1) {
|
||||
IMAGE_SY2 = IMAGE_SY1
|
||||
coordAdjusted = 1
|
||||
}
|
||||
|
||||
#---------------------
|
||||
# check background box
|
||||
|
||||
if (IMAGE_BX1 < 1) {
|
||||
IMAGE_BX1 = 1
|
||||
coordAdjusted = 1
|
||||
}
|
||||
if (IMAGE_BY1 < 1) {
|
||||
IMAGE_BY1 = 1
|
||||
coordAdjusted = 1
|
||||
}
|
||||
if (IMAGE_BX1 > IMAGE_XDIM-1) {
|
||||
IMAGE_BX1 = IMAGE_XDIM-1
|
||||
coordAdjusted = 1
|
||||
}
|
||||
if (IMAGE_BY1 > IMAGE_YDIM-1) {
|
||||
IMAGE_BY1 = IMAGE_YDIM-1
|
||||
coordAdjusted = 1
|
||||
}
|
||||
if (IMAGE_BX2 > IMAGE_XDIM-1) {
|
||||
IMAGE_BX2 = IMAGE_XDIM-1
|
||||
coordAdjusted = 1
|
||||
}
|
||||
if (IMAGE_BY2 > IMAGE_YDIM-1) {
|
||||
IMAGE_BY2 = IMAGE_YDIM-1
|
||||
coordAdjusted = 1
|
||||
}
|
||||
if (IMAGE_BX2 < IMAGE_BX1) {
|
||||
IMAGE_BX2 = IMAGE_BX1
|
||||
coordAdjusted = 1
|
||||
}
|
||||
if (IMAGE_BY2 < IMAGE_BY1) {
|
||||
IMAGE_BY2 = IMAGE_BY1
|
||||
coordAdjusted = 1
|
||||
}
|
||||
|
||||
if (coordAdjusted != 0) {
|
||||
eprint">> Coordinates out of range - automatically adjusted. <<"
|
||||
}
|
||||
printf("signal region of interest : (%3d,%3d) (%3d,%3d)\n",\\
|
||||
IMAGE_SX1,IMAGE_SY1,IMAGE_SX2,IMAGE_SY2)
|
||||
printf("background region of interest: (%3d,%3d) (%3d,%3d)\n",\\
|
||||
IMAGE_BX1,IMAGE_BY1,IMAGE_BX2,IMAGE_BY2)
|
||||
printf("image dimensions (x*y) : %3d * %3d pixels\n",\\
|
||||
IMAGE_XDIM,IMAGE_YDIM)
|
||||
|
||||
}'
|
||||
|
||||
#+
|
||||
#------------------------------------------------------------------------------
|
||||
# imageGetInt - This macro analyzes the last image taken by the active area
|
||||
# detector. It checks the region-of-interest defined via
|
||||
# imageSetRoi and sets some global variables to the intensity
|
||||
# values determined. Calling parameters are the three threshold
|
||||
# values (no. of pixels with intensity above these values is
|
||||
# returned).
|
||||
#-
|
||||
|
||||
def imagegetint 'imageGetInt'
|
||||
|
||||
def imageGetInt '{
|
||||
# ===========
|
||||
|
||||
global IMAGE_DEVICE, IMAGE_IS_ON
|
||||
global IMAGE_FILENAME, IMAGE_PATH, IMAGE_FNUM, IMAGE_FBASE
|
||||
global IMAGE_INFO_FILENAME, IMAGE_HEADER_LENGTH
|
||||
global IMAGE_XDIM, IMAGE_YDIM, IMAGE_COLOR_DEPTH
|
||||
global IMAGE_I_SIG, IMAGE_I_BG, IMAGE_I_SUM
|
||||
global IMAGE_AREA_SIG, IMAGE_AREA_BG
|
||||
global IMAGE_THRESH1, IMAGE_THRESH2, IMAGE_THRESH3, IMAGE_THRESH4
|
||||
global IMAGE_THRESH1_COUNT, IMAGE_THRESH2_COUNT
|
||||
global IMAGE_THRESH3_COUNT, IMAGE_THRESH4_COUNT
|
||||
global IMAGE_SX1, IMAGE_SY1, IMAGE_SX2, IMAGE_SY2
|
||||
global IMAGE_BX1, IMAGE_BY1, IMAGE_BX2, IMAGE_BY2
|
||||
|
||||
local unixCommand, unixReturn
|
||||
|
||||
if ($# != 4) {
|
||||
eprint "Wrong number of arguments in \'imageGetInt\'"
|
||||
eprint "Usage:"
|
||||
eprint "imageGetInt <threshold1> <threshold2> <threshold3> <threshold4>"
|
||||
exit
|
||||
}
|
||||
|
||||
commandDir = ""
|
||||
unix(sprintf("dirname %s", IMAGE_MAC),commandDir)
|
||||
if(index(commandDir,"\n") != 0){
|
||||
commandDir = substr(commandDir,0,length(commandDir)-1)
|
||||
}
|
||||
|
||||
unixCommand = sprintf("%s%s %s %d %d %d %d -median 30",\\
|
||||
commandDir,\\
|
||||
"/bin/image_get_int.py",\\
|
||||
"/tmp/spec_image_info.dat",\\
|
||||
$1, $2, $3, $4)
|
||||
|
||||
if(IMAGE_DEBUG){
|
||||
printf("unix command: %s\n", unixCommand)
|
||||
}
|
||||
|
||||
unixReturn = ""
|
||||
unix(unixCommand,unixReturn)
|
||||
|
||||
if(IMAGE_DEBUG){
|
||||
printf("unix return: %s\n", unixReturn)
|
||||
}
|
||||
|
||||
IMAGE_I_SUM = ""
|
||||
IMAGE_AREA_SIG = ""
|
||||
IMAGE_THRESH1_COUNT = ""
|
||||
IMAGE_THRESH2_COUNT = ""
|
||||
IMAGE_THRESH3_COUNT = ""
|
||||
IMAGE_I_BG = ""
|
||||
IMAGE_AREA_BG = ""
|
||||
|
||||
if (sscanf(unixReturn,"I_sum %d area_I %d Threshold1 %d Threshold2 %d Threshold3 %d Threshold4 %d I_bgr %d area_bgr %d",\\
|
||||
IMAGE_I_SUM, IMAGE_AREA_SIG,\\
|
||||
IMAGE_THRESH1_COUNT, IMAGE_THRESH2_COUNT, IMAGE_THRESH3_COUNT,\\
|
||||
IMAGE_THRESH4_COUNT, IMAGE_I_BG, IMAGE_AREA_BG) != 8) {
|
||||
printf("Couldn\'t get intensity data\n")
|
||||
exit
|
||||
}
|
||||
if (IMAGE_AREA_BG > 0){
|
||||
IMAGE_I_SIG = IMAGE_I_SUM - ((IMAGE_I_BG / IMAGE_AREA_BG) * IMAGE_AREA_SIG)
|
||||
} else {
|
||||
IMAGE_I_SIG = IMAGE_I_SUM
|
||||
}
|
||||
|
||||
if (IMAGE_DEBUG){
|
||||
printf("I_sum: %d, area_I: %d\nthresh1: %d, thresh2: %d, thresh3: %d, thresh4: %d\n",\\
|
||||
IMAGE_I_SUM, IMAGE_AREA_SIG,\\
|
||||
IMAGE_THRESH1_COUNT, IMAGE_THRESH2_COUNT,\\
|
||||
IMAGE_THRESH3_COUNT, IMAGE_THRESH4_COUNT)
|
||||
printf("I_bgr: %d, area_bgr: %d\n",IMAGE_I_BG,IMAGE_AREA_BG)
|
||||
}
|
||||
|
||||
}'
|
||||
|
||||
#+
|
||||
#------------------------------------------------------------------------------
|
||||
#-
|
||||
#==============================================================================
|
||||
#
|
||||
#####################################################
|
||||
# emacs setup: force text mode to get no help with #
|
||||
# indentation and force use of spaces #
|
||||
# when tabbing. #
|
||||
# Local Variables: #
|
||||
# mode:text #
|
||||
# indent-tabs-mode:nil #
|
||||
# End: #
|
||||
#####################################################
|
||||
#
|
||||
# $Log: image.mac,v $
|
||||
# Revision 1.11 2008/03/20 13:36:14 schlepuetz
|
||||
# removed quotation marks around argument variables ,,... in imageSetRoi, added imageShowRoi.
|
||||
#
|
||||
# Revision 1.10 2007/04/22 15:42:11 schlepuetz
|
||||
# changed imageCheckROI to allow for ROIs of 1 pixel width/height.
|
||||
#
|
||||
# Revision 1.9 2007/04/05 09:57:21 schlepuetz
|
||||
# new error message if image file to be analyzed is not found
|
||||
#
|
||||
# Revision 1.8 2006/12/01 08:28:52 schlepuetz
|
||||
# include wait loop in imageUserGetcounts to make sure the image file is available and non-empty
|
||||
#
|
||||
# Revision 1.7 2006/09/21 11:49:43 schlepuetz
|
||||
# added new feature in imageGetInt to selectively median filter hot and dead pixels
|
||||
#
|
||||
# Revision 1.6 2006/08/09 13:44:38 schlepuetz
|
||||
# added more input options for imageSetRoi.
|
||||
#
|
||||
# Revision 1.5 2006/06/23 16:26:52 schlepuetz
|
||||
# missing bracket...
|
||||
#
|
||||
# Revision 1.4 2006/06/23 08:07:32 schlepuetz
|
||||
# copy image info file also into image directory for accessibility
|
||||
#
|
||||
# Revision 1.3 2006/03/01 13:02:47 maden
|
||||
# Check-in newer version from /work ...
|
||||
#
|
||||
# Revision 1.2 2005/12/10 16:32:57 schlepuetz
|
||||
# fixed bug in imageGetInt.
|
||||
#
|
||||
# Revision 1.1 2005/11/10 11:01:21 schlepuetz
|
||||
# first tested version of this file
|
||||
#
|
||||
#
|
||||
#============================= End of $RCSfile: image.mac,v $ ===
|
||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,427 @@
|
||||
#==============================================================================
|
||||
# Macroname: sdStartup.mac
|
||||
# =============
|
||||
#
|
||||
# $Date: 2009/05/28 10:09:21 $
|
||||
# $Header: /cvs/G/SPEC/local/X04SA/ES3/sdStartup.mac,v 1.10 2009/05/28 10:09:21 schlepuetz Exp $
|
||||
#+
|
||||
# $Source: /cvs/G/SPEC/local/X04SA/ES3/sdStartup.mac,v $
|
||||
# $Revision: 1.10 $
|
||||
#
|
||||
# Description: specialized startup macro for the surface diffraction station.
|
||||
# includes all setup routines required to use the pixel detector.
|
||||
#
|
||||
# Note:
|
||||
#
|
||||
# Author(s): C. M. Schlepuetz (CS)
|
||||
# Co-author(s): P. R. Willmott (PW)
|
||||
# Address: Surface Diffraction Station
|
||||
# Materials Science Beamline X04SA
|
||||
# Swiss Light Source (SLS)
|
||||
# Paul Scherrer Institut
|
||||
# CH - 5232 Villigen PSI
|
||||
# Created: 2005/06/10
|
||||
#
|
||||
#-
|
||||
# Chained macro definitions affected by this macro:
|
||||
# -------------------------------------------------
|
||||
# - none
|
||||
#
|
||||
# Change Log:
|
||||
# -----------
|
||||
#
|
||||
# 2005/06/10 (CS):
|
||||
# - created the first version of this macro.
|
||||
#
|
||||
# 2005/11/30 (CS):
|
||||
# - modified sdStartup to make sure that no previous experiment is still active
|
||||
# when starting a new one.
|
||||
#
|
||||
# 2006/04/24 (CS):
|
||||
# - changed call to 'setsample' (which was part of the hkl-workaround) to
|
||||
# 'startgeo'.
|
||||
#
|
||||
# 2006/08/08 (CS):
|
||||
# - avoid that a logfile is overwritten if sdStartup is called twice with the
|
||||
# same logfile name. Now, information is appended to an existing logfile.
|
||||
# - included call to scanlist.mac in sdStartup.
|
||||
#
|
||||
# 2008/02/20 (CS):
|
||||
# - removed links to 'specmacros' and 'scanlogs' in directory tree. This led to
|
||||
# confusion and sometimes the duplication of the data if links were not
|
||||
# followed correctly by backup software.
|
||||
#
|
||||
# 2008/02/21 (CS):
|
||||
# - removed 'archives' directory under 'pixel'
|
||||
# - renamed 'analyzed_data' to 'analysis_runtime'
|
||||
#
|
||||
# 2009/05/27 (CS):
|
||||
# - enable scanlists and scanlogs by default (remove user option to turn it on)
|
||||
# - force use of pixel detector (shortened setup routine)
|
||||
#
|
||||
# 2009/05/28 (CS):
|
||||
# - change permissions of pixel directory recursively by 'a+w' automatically
|
||||
# when created (chmod -R a+w pixel).
|
||||
#
|
||||
#==============================================================================
|
||||
#
|
||||
global SD_STARTUP_MAC
|
||||
#
|
||||
SD_STARTUP_MAC = DOFILE # Save the name of this macro file.
|
||||
_sav_geo_mot = 1 # spec's global variable used by setscans macro
|
||||
#+
|
||||
#==============================================================================
|
||||
# This macro file contains the following commands:
|
||||
#-
|
||||
#
|
||||
#+
|
||||
#------------------------------------------------------------------------------
|
||||
# sdStartuphelp - generates this help text. This is obtained by
|
||||
# displaying the file sd_startup.txt, which should sit in
|
||||
# the same directory as this file.
|
||||
#-
|
||||
|
||||
def helpSdStartup 'sdStartuphelp'
|
||||
def sdStartupHelp 'sdStartuphelp'
|
||||
def sdstartuphelp 'sdStartuphelp'
|
||||
|
||||
def sdStartuphelp '{
|
||||
# =============
|
||||
|
||||
unix (sprintf ("dirname %s", _MAC), _1)
|
||||
ll = length (_1)
|
||||
if (substr (_1, ll, 1) == "\n") _1 = substr (_1, 1, (ll - 1))
|
||||
file = sprintf ("%s/sms.txt", _1)
|
||||
if (file_info (file, "-e")) {
|
||||
unix (sprintf ("cat %s | less", file))
|
||||
} else {
|
||||
printf ("\n Macros available in file sd_startup.mac ($Revision: 1.10 $):\n")
|
||||
print " =============="
|
||||
print ""
|
||||
print " sdStartuphelp - creates this help text"
|
||||
print " sdStartup - startup routine for the surface diffraction"
|
||||
print " station. Sets all important parameters and"
|
||||
print " paths."
|
||||
print " sdShutdown - shutdown routine for the surface diffraction"
|
||||
print " station. Resets all paths and filenames to"
|
||||
print " standard values to prevent writing to"
|
||||
print " experiment-specific files."
|
||||
}
|
||||
}'
|
||||
|
||||
#+
|
||||
#------------------------------------------------------------------------------
|
||||
# sdStartup - startup procedure for the surface diffraction station.
|
||||
# It sets up important parameters and the data storage
|
||||
# environment for the experiment. Experimental data is
|
||||
# stored in the following directory structure:
|
||||
#
|
||||
# [<E-ACCOUNT>]
|
||||
# `-- <PROJECT_NAME>
|
||||
# |-- analysis_runtime # on-the-fly analysis during experiments
|
||||
# |-- archive # backup directory for experimental data (zip)
|
||||
# | |-- images # zip-files of images
|
||||
# | |-- imagelogs # zip-files of imagelogs
|
||||
# |-- fotos # fotos of experimental setup, etc.
|
||||
# |-- pixel # pixel detector related information
|
||||
# | |-- flatfield # flatfield data
|
||||
# | | |-- flatfield(1) # 1st flatfield data set
|
||||
# | | |-- flatfield(2) # 2nd flatfield data set
|
||||
# | | `-- ... # ...
|
||||
# | |-- imagelogs # logfiles for each individual pixel image
|
||||
# | |-- images # the pixel detector images themselves
|
||||
# |-- software # user made software (i.e. shell scripts, etc.)
|
||||
# | |-- matlab # matlab routines for data analysis
|
||||
# | |-- shell_scripts # shell scripts
|
||||
# `-- spec # SPEC related information
|
||||
# |-- logs # logfiles (.spec, .log, etc.)
|
||||
# |-- scanlogs # log files for each individual scan
|
||||
# `-- specmacros # working directory for user made SPEC macros
|
||||
#
|
||||
# <PROJECT_NAME> is set during the startup procedure. If the user is running
|
||||
# from an e-account, the above directory tree is created inside the e-account
|
||||
# directory <E-ACCOUNT> (i.e. e10003/<PROJECTNAME>/pixel/...)
|
||||
#-
|
||||
|
||||
def sdStartup '{
|
||||
# =========
|
||||
|
||||
global DATAFILE, LOGFILE, DO_DIR
|
||||
global TITLE, COUNT, UPDATE
|
||||
global SDSTARTUP_ON, SDSTARTUP_PROJECT
|
||||
|
||||
local dataBaseDir, expBaseDir, pixelBaseDir
|
||||
local eAccount, projectDirName, _dir
|
||||
local _append, _cont
|
||||
local specFile
|
||||
|
||||
dataBaseDir = "/sls/X04SA/data/"
|
||||
expBaseDir = "/sls/X04SA/data/x04sa/ES3/expdata/"
|
||||
pixelBaseDir = "/sls/X04SA/data/x04sa/ES3/pixel/"
|
||||
tmpLog = "/tmp/tmpLog.spec"
|
||||
|
||||
def sdStartupCleanupOnce \'
|
||||
tty_cntl("se")
|
||||
\'
|
||||
cdef("cleanup_once","sdStartupCleanupOnce;","sdStartup_cleanup_once_key")
|
||||
|
||||
|
||||
if(SDSTARTUP_ON){
|
||||
printf("Currently, the following experiment is still active:\n%s\n", \\
|
||||
SDSTARTUP_PROJECT)
|
||||
tty_cntl("so")
|
||||
if(yesno("Close the active experiment and start a new one?",0)){
|
||||
tty_cntl("se")
|
||||
close(DATAFILE)
|
||||
close(LOGFILE)
|
||||
} else{
|
||||
tty_cntl("se")
|
||||
printf("Startup routine aborted...\n")
|
||||
exit
|
||||
}
|
||||
}
|
||||
|
||||
# turn on logging to a temporary file (this will be moved to
|
||||
# the projects permanent log file later).
|
||||
on(tmpLog)
|
||||
|
||||
#-------------------------------
|
||||
# get information on the project
|
||||
tty_cntl("so")
|
||||
if(yesno("Are you using an e-account?",0) == 1){
|
||||
eAccount=getsval("Please enter your e-account name \(i.e. e10003\)")
|
||||
}
|
||||
else{
|
||||
eAccount=""
|
||||
}
|
||||
tty_cntl("se")
|
||||
|
||||
_cont=0
|
||||
while(_cont==0){
|
||||
printf("\nPlease enter a name for your project\'s data directory ending ")
|
||||
printf("with the current\ndate in the following format: _yyyymmdd")
|
||||
printf("\(e.g., Ni111_20050226\)\n")
|
||||
tty_cntl("so")
|
||||
projectDirName=getsval("Project name:","")
|
||||
tty_cntl("se")
|
||||
# set up the project directory
|
||||
if(eAccount != ""){
|
||||
_dir=sprintf("%s%s/%s/",dataBaseDir,eAccount,projectDirName)
|
||||
}
|
||||
else{
|
||||
_dir=sprintf("%s%s/",expBaseDir,projectDirName)
|
||||
}
|
||||
|
||||
printf("\nYour project directory name is:\n %s\n",projectDirName)
|
||||
tty_cntl("so")
|
||||
if(yesno("Is that o.k.?",1)){
|
||||
_cont=1
|
||||
}
|
||||
tty_cntl("se")
|
||||
if(file_info(_dir,"-d")== 1){
|
||||
printf("\nDirectory %s already exists!\n", _dir)
|
||||
printf("It contains the following items:\n")
|
||||
unix(sprintf("ls -g --color %s",_dir))
|
||||
tty_cntl("so")
|
||||
if(yesno("Change your project name?",1)==0){
|
||||
_cont=1
|
||||
_append=1
|
||||
} else{
|
||||
_cont=0
|
||||
}
|
||||
tty_cntl("se")
|
||||
}
|
||||
}
|
||||
printf("\nYour data will be stored in\n %s\n", _dir)
|
||||
SDSTARTUP_PROJECT = projectDirName
|
||||
|
||||
#----------------------------------
|
||||
# set up the project directory tree
|
||||
|
||||
cmd_file="/tmp/startup_cmd.sh"
|
||||
unix(sprintf("rm -f %s",cmd_file))
|
||||
open(cmd_file)
|
||||
fprintf(cmd_file,"mkdir %s\n", _dir)
|
||||
fprintf(cmd_file,"cd %s\n", _dir)
|
||||
fprintf(cmd_file,"mkdir spec pixel fotos software analysis_runtime ")
|
||||
fprintf(cmd_file,"archive \n")
|
||||
fprintf(cmd_file,"# create subdirs of archive\n")
|
||||
fprintf(cmd_file,"cd archive; mkdir images imagelogs; cd ..\n")
|
||||
fprintf(cmd_file,"# create subdirs of spec\n")
|
||||
fprintf(cmd_file,"cd spec; mkdir logs scanlogs specmacros; cd ..\n")
|
||||
fprintf(cmd_file,"# create subdirs of pixel\n")
|
||||
fprintf(cmd_file,"cd pixel; mkdir images imagelogs ")
|
||||
fprintf(cmd_file,"flatfield; cd ..\n")
|
||||
fprintf(cmd_file,"# create subdirs of software\n")
|
||||
fprintf(cmd_file,"cd software; mkdir matlab shell_scripts; cd ..\n")
|
||||
fprintf(cmd_file,"# change permissions on pixel directory\n")
|
||||
fprintf(cmd_file,"chmod -R a+w pixel\n")
|
||||
close(cmd_file)
|
||||
unix(sprintf("chmod 700 %s; %s",cmd_file,cmd_file))
|
||||
unix(sprintf("rm -f %s",cmd_file))
|
||||
|
||||
printf("directory structure:\n")
|
||||
unix(sprintf("tree %s",_dir),_tmp)
|
||||
print _tmp #this ensures that the tree appears in the log file
|
||||
|
||||
# set working directory
|
||||
chdir(sprintf("%s%s",_dir,"spec/specmacros"))
|
||||
DO_DIR=sprintf("%s%s",_dir,"spec/specmacros")
|
||||
|
||||
# open the spec file
|
||||
specFile=sprintf("%sspec/logs/%s.spec",_dir,projectDirName)
|
||||
eval(sprintf("newfile %s 0",specFile))
|
||||
|
||||
# turn on the log file and copy
|
||||
# contents of temporary log into it.
|
||||
LOGFILE=sprintf("%sspec/logs/%s.log",_dir,projectDirName)
|
||||
close(tmpLog)
|
||||
if(file_info(LOGFILE,"-e")){
|
||||
# if logfile already exists, append contents of temporary file to the end.
|
||||
open(LOGFILE)
|
||||
fprintf(LOGFILE,"\n\n-----------------------------------------------\n\n")
|
||||
close(LOGFILE)
|
||||
unix(sprintf("cat %s >> %s",tmpLog,LOGFILE))
|
||||
unix(sprintf("rm -f %s",tmpLog))
|
||||
} else{
|
||||
unix(sprintf("mv %s %s",tmpLog,LOGFILE))
|
||||
}
|
||||
on(LOGFILE)
|
||||
|
||||
tty_cntl("so")
|
||||
TITLE=getsval("\nTitle for scan headers (i.e. sample name)",TITLE)
|
||||
COUNT = getval("Default count time for ct and uct",COUNT)
|
||||
UPDATE = getval("Update interval for umv, uct, etc. in seconds",UPDATE)
|
||||
tty_cntl("se")
|
||||
|
||||
# set geometry parameters
|
||||
printf("\nSet the geometry parameters: \(startgeo\)\n")
|
||||
startgeo
|
||||
|
||||
# set scan options
|
||||
printf("\nSet some scan options: \(setscans\)\n")
|
||||
setscans
|
||||
|
||||
# enable scanlogs
|
||||
if (SCANLOG_MAC){
|
||||
eval(sprintf("scanlogSetPath %s%s", _dir,"spec/scanlogs/"))
|
||||
scanlogOn
|
||||
}
|
||||
|
||||
# enable scanlist
|
||||
if (SCANLIST_MAC){
|
||||
eval(sprintf("scanlistFilename %s%s",_dir,"spec/logs/scanlist.txt"))
|
||||
scanlistOn
|
||||
}
|
||||
|
||||
# set plot options
|
||||
printf("\nSet some plotting options: \(setplot\)\n")
|
||||
setplot
|
||||
|
||||
# set up the pixel detector as default detector
|
||||
printf("\nSet up the PILATUS Pixel detector\n")
|
||||
if(eAccount != ""){
|
||||
eprint "e-Accounts are not yet supported in conjunction with the pixel"
|
||||
eprint "detector. This is due to write permission errors and will be"
|
||||
eprint "resolved with the new generation of the pixel detector control"
|
||||
eprint "software. Please contact your user-supporter if you encounter"
|
||||
eprint "this problem here."
|
||||
exit
|
||||
} else{
|
||||
pixFilePath = sprintf("%s%s%s","../../expdata/",projectDirName,\\
|
||||
"/pixel/images/")
|
||||
eval(sprintf("pixsetup %s",pixFilePath)) # run the setup routine
|
||||
pixon # enable the pixel detector
|
||||
# turn on logging for each image taken to standard path:
|
||||
pixLogPath = sprintf("%s%s", _dir,"pixel/imagelogs/")
|
||||
eval(sprintf("pixlogon %s", pixLogPath))
|
||||
}
|
||||
|
||||
printf("\n%s\n%s\n%s\n",\\
|
||||
"Your experiment has been set up successfully. Please remember to",\\
|
||||
"run \'sdShutdown\' after completing your measurements to prevent",\\
|
||||
"other users from accidentally modifying your experimental data.")
|
||||
|
||||
SDSTARTUP_ON = 1
|
||||
cdef("cleanup_once","","sdStartup_cleanup_once_key","delete")
|
||||
|
||||
}'
|
||||
|
||||
#+
|
||||
#------------------------------------------------------------------------------
|
||||
# sdShutdown - Cleanup procedure to be executed after an experiment.
|
||||
# Experimental files are closed and logging is redirected
|
||||
# to some standard files. The entire experimenal environ-
|
||||
# ment used before is abandoned by SPEC.
|
||||
#-
|
||||
|
||||
def sdShutdown '{
|
||||
# ==========
|
||||
|
||||
global DATAFILE, LOGFILE, DO_DIR
|
||||
|
||||
# reset the current working directory to standard location
|
||||
chdir(sprintf("%s","~/specmacros"))
|
||||
|
||||
# close the SPEC data file and reopen the standard file.
|
||||
close(DATAFILE)
|
||||
eval(sprintf("newfile %s 0","/sls/X04SA/data/x04sa/ES3/tmp/dummy.spec"))
|
||||
|
||||
# close the SPEC log file and reset the global variable to the standard value
|
||||
close(LOGFILE)
|
||||
LOGFILE = "/sls/X04SA/data/x04sa/ES3/tmp/dummy.log"
|
||||
|
||||
# redirect pixel detector output to standard locations
|
||||
pixsetpath "tmp/"
|
||||
pixlogoff
|
||||
|
||||
SDSTARTUP_ON = 0
|
||||
|
||||
}'
|
||||
|
||||
#+
|
||||
#------------------------------------------------------------------------------
|
||||
#-
|
||||
#####################################################
|
||||
# emacs setup: force text mode to get no help with #
|
||||
# indentation and force use of spaces #
|
||||
# when tabbing. #
|
||||
# Local Variables: #
|
||||
# mode:text #
|
||||
# indent-tabs-mode:nil #
|
||||
# End: #
|
||||
#####################################################
|
||||
#
|
||||
# $Log: sdStartup.mac,v $
|
||||
# Revision 1.10 2009/05/28 10:09:21 schlepuetz
|
||||
# change permissions on pixel directory automatically by a+w
|
||||
#
|
||||
# Revision 1.9 2009/05/27 15:59:36 schlepuetz
|
||||
# shortened setup routine
|
||||
#
|
||||
# Revision 1.8 2008/02/21 09:59:25 schlepuetz
|
||||
# updated documentation
|
||||
#
|
||||
# Revision 1.7 2008/02/21 09:55:35 schlepuetz
|
||||
# removed archives directory under pixel, renamed analyzed_data to analysis_runtime
|
||||
#
|
||||
# Revision 1.6 2008/02/20 09:10:13 schlepuetz
|
||||
# removed links to specmacros and scanlogs in directory tree
|
||||
#
|
||||
# Revision 1.5 2006/08/11 10:34:10 schlepuetz
|
||||
# improved output formatting of sdStartup
|
||||
#
|
||||
# Revision 1.4 2006/08/08 14:07:38 schlepuetz
|
||||
# prevent overwrite of old log files, added enable/disble of scanlist
|
||||
#
|
||||
# Revision 1.3 2006/05/04 10:15:23 schlepuetz
|
||||
# call startgeo instead of setsample
|
||||
#
|
||||
# Revision 1.2 2005/11/30 15:33:11 schlepuetz
|
||||
# modified sdStartup to make sure that no previous experiment is still active when starting a new one.
|
||||
#
|
||||
# Revision 1.1 2005/11/10 11:24:07 schlepuetz
|
||||
# first tested version of this file
|
||||
#
|
||||
#
|
||||
#============================= End of $RCSfile: sdStartup.mac,v $ ===
|
||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,142 @@
|
||||
def count (count_time):
|
||||
waitmove
|
||||
count_em (count_time) # triggers the counting process
|
||||
waitcount # waits for counting to finish
|
||||
count_end # clean up after counting
|
||||
get_counts # retrieve the counts from detectors
|
||||
chk_xray # verify quality of xray
|
||||
chk_counts # verify quality of counts
|
||||
chk_beam # terminate this count loop
|
||||
if (S[sec] && MON >= 0)
|
||||
MON_RATE=S[MON]/S[sec]
|
||||
|
||||
|
||||
|
||||
|
||||
def count_em (count_time):
|
||||
# ========
|
||||
while (mythen.is_acquiring()):
|
||||
mythen.stop()
|
||||
time.sleep(0.25)
|
||||
|
||||
user_precount()
|
||||
|
||||
if (count_time != 0):
|
||||
if (count_time > 0):
|
||||
# MYTHEN
|
||||
mythen.set_acquire_time(count_time)
|
||||
mythen.set_acquire_mode("Single")
|
||||
mythen.start()
|
||||
else:
|
||||
print "Preset monitor counting is not supported\!"
|
||||
user_postcount()
|
||||
|
||||
|
||||
|
||||
# define new count_end, chk_counts, and chk_xray macros:
|
||||
def count_end 'user_count_end'
|
||||
def chk_counts 'user_chk_counts'
|
||||
def chk_xray 'user_chk_xray'
|
||||
# use the EPICS DCR508 scaler
|
||||
# initially, user_count_end, user_chk_counts, and user_chk_xray are empty:
|
||||
def user_count_end '' # if used, this should be a chained macro definition
|
||||
def user_chk_counts '' # if used, this should be a chained macro definition
|
||||
def user_chk_xray '' # if used, this should be a chained macro definition
|
||||
|
||||
#+
|
||||
#------------------------------------------------------------------------------
|
||||
# ct - second lowest level count command - for manual count.
|
||||
# This version is slightly expanded with respect to
|
||||
# the original definition in standard.mac:
|
||||
# count_end has been added to provide further
|
||||
# flexibility regarding the use of various detectors.
|
||||
#
|
||||
# Note: See also the description of the modified 'count' command for more
|
||||
# information.
|
||||
#-
|
||||
|
||||
def ct (count_time):
|
||||
# ==
|
||||
|
||||
cdef("cleanup_once", "onp; show_cnts; offp; user_ct", "ct")
|
||||
waitmove
|
||||
count_em (count_time) # triggers the counting process
|
||||
waitcount # waits for counting to finish
|
||||
count_end # clean up after counting
|
||||
cdef("cleanup_once", "", "ct", "delete")
|
||||
onp; show_cnts; offp
|
||||
user_ct
|
||||
|
||||
}'
|
||||
|
||||
#+
|
||||
#------------------------------------------------------------------------------
|
||||
# recount - allows to retake the last data point - useful when
|
||||
# files (images) need to be overwritten. Include
|
||||
# device-specific code in user_pre_recount and
|
||||
# user_post_recount.
|
||||
#
|
||||
# Note: This is essentially a modified version of count
|
||||
# without the check commands (chk_xray, chk_counts,
|
||||
# and chk_beam) at the end.
|
||||
#-
|
||||
|
||||
def recount '{
|
||||
# =======
|
||||
|
||||
waitmove
|
||||
user_pre_recount # should be a chained macro definition
|
||||
count_em $1 # triggers the counting process
|
||||
waitcount # waits for counting to finish
|
||||
count_end # clean up after counting
|
||||
get_counts # retrieve the counts from detectors
|
||||
user_post_recount # should be a chained macro definition
|
||||
}'
|
||||
|
||||
# initially, user_pre_recount and user_post_recount are empty.
|
||||
def user_pre_recount ''
|
||||
def user_post_recount ''
|
||||
|
||||
#+
|
||||
#------------------------------------------------------------------------------
|
||||
# waitcount - waits for counting to stop
|
||||
#-
|
||||
|
||||
def waitcount(count_time):
|
||||
user_waitcount()
|
||||
|
||||
i = 0
|
||||
while (mythen.is_acquiring()):
|
||||
sleep (0.05)
|
||||
i += 1
|
||||
if (i * 0.05 >= count_time * 2):
|
||||
print "MYTHEN Izero times out, status: " + str(mythen.get_status())
|
||||
break
|
||||
|
||||
#+
|
||||
#------------------------------------------------------------------------------
|
||||
# get_counts - lowest level counter reading macro.
|
||||
#-
|
||||
|
||||
def get_counts():
|
||||
# ==========
|
||||
|
||||
S[0] = mythen.get_acquire_time(readback=False)
|
||||
S[1] = mythen.get_total_counts()
|
||||
# S[2] is detector counts from image.mac
|
||||
S[3] = S[2] / COUNT_TIME / epics_get("X04SA-ES2-FI:TRANSM")
|
||||
|
||||
S[5] = epics_get ("X04SA-ES2-FI:TRANSM")
|
||||
|
||||
COUNT_ID++ # increment the exposure ID
|
||||
|
||||
# set threshold counts in case auto-level support is available
|
||||
if ((whatis("AUTO_THRESH1") & 0x08000000) == 0) {
|
||||
AUTO_THRESH1_COUNT = (S[2]>=AUTO_THRESH1)?S[2]:0
|
||||
AUTO_THRESH2_COUNT = (S[2]>=AUTO_THRESH2)?S[2]:0
|
||||
AUTO_THRESH3_COUNT = (S[2]>=AUTO_THRESH3)?S[2]:0
|
||||
AUTO_THRESH4_COUNT = (S[2]>=AUTO_THRESH4)?S[2]:0
|
||||
}
|
||||
|
||||
user_getcounts
|
||||
}'
|
||||
Reference in New Issue
Block a user