From 142be9dd8f811449a0efeb48cbb75fc0f0cf6af4 Mon Sep 17 00:00:00 2001 From: rivers Date: Tue, 4 Aug 2009 16:30:42 +0000 Subject: [PATCH] Added more documentation on ImageJ plugin git-svn-id: https://subversion.xor.aps.anl.gov/synApps/areaDetector/trunk@9165 dc6c5ff5-0b8b-c028-a01f-ffb33f00fc8b --- documentation/areaDetectorViewers.html | 474 +++++++++++++------------ 1 file changed, 252 insertions(+), 222 deletions(-) diff --git a/documentation/areaDetectorViewers.html b/documentation/areaDetectorViewers.html index 46c36ff..85ab053 100755 --- a/documentation/areaDetectorViewers.html +++ b/documentation/areaDetectorViewers.html @@ -1,223 +1,253 @@ - - - areaDetector Viewers - - - -
-

- areaDetector Viewers

-

- August 3, 2009

-

- Mark Rivers

-

- University of Chicago

-
-

- Contents

- -

- Overview -

-

- One of the advantages of areaDetector is that it enables the use of generic image - display clients that obtain their data via EPICS Channel Access and work with any - detector. There are currently two such generic clients provided with the areaDetector - distribution. The first is a plugin for the popular ImageJ Java-based image processing - program. The second is an IDL-based viewer which can be run without an IDL license - under the IDL Virtual Machine. Because ImageJ is free and more widely available - and used than IDL, future enhancements are more likely to be done on the ImageJ - plugin rather than the IDL viewer. -

-

- ImageJ Viewer

-

- This is a plugin for the popular ImageJ - program that can be used to display 2-dimensional array data that the - NDStdArrays plugin sends to EPICS. This plugin is contained in the areaDetector - distribution in the Viewers/ImageJ/EPICS_areaDetector directory. This plugin was - begun by Tim Madden from APS, and now includes support for all NDArray data types - and color modes, i.e. Mono, RGB1 (pixel interleave), RGB2 (row interleave) and RGB3 - (plane interleave). The plugin directory includes a plugin written elsewhere for - reading and writing netCDF files, so ImageJ can be used to display images and image - sequences (movies) saved with the NDFileNetCDF plugin. It also includes a dynamic - profile plugin written elsewhere for line profiles that update in real time as new - images are displayed or as the profile line segment is moved.

-

- To use this ImageJ plugin do the following:

- -

- The control window for EPICS_AD_Viewer is shown below. The PVPrefix - field is used to input the base name of the EPICS PVs with the image data. The array - dimensions and the number of frames - per second actually being displayed by ImageJ is shown. There is a status window that - shows whether the EPICS PVs are connected and the number of arrays received since the last - update, which is every 2 seconds. -

To capture a sequence of images into an ImageJ "stack" select "Capture To Stack". - The image sequence will be stored in the ImageJ buffer and a scroll bar will appear - to allow you to scroll through the images. The stack can be saved to disk in a large - number of formats, including AVI.

-

-
-

- ImageJ EPICS_AD_Viewer plugin control window

-

- EPICS_AD_Viewer.png

-
-

- This is the.

-
-

- ImageJ EPICS_AD_Viewer plugin display window

-

- EPICS_AD_Viewer_display.jpg

-
-

- IDL Viewer

-

- There is an IDL procedure called - epics_ad_display that can be used to display 2-dimensional array data that - the NDStdArrays plugin sends to 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. - epics_ad_display is included in the - CARS IDL imaging software. It is also available in the Viewers/IDL directory - in the areaDetector application. -

-

- The Viewers/IDL directory contains both the IDL source code and a standalone IDL - file, epics_ad_display.sav, for the epics_ad_display GUI to display images from - areaDetector detectors. This file can be run for free on any Linux or Windows system - under the IDL Virtual Machine, which can be downloaded free of charge from - ITT VIS. That directory also contains the shareable libraries used to call - EPICS Channel Access from IDL (ezcaIDL.dll for Windows and libezcaIDL.so for Linux). - Before using the IDL source code or .sav file it is necessary to define the environment - variable EZCA_IDL_SHARE to point to the complete path to ezcaIDL.dll or libezcaIDL.so. - For example on Linux:

- 
setenv EZCA_IDL_SHARE /home/epics/support/areaDetector/1-5/Viewers/IDL/libezcaIDL.so
-
-

- On Windows use -

- 
My Computer/Properties/Advanced/Environment Variables/ 
-
-

- to add a new environment variable EZCA_IDL_SHARE to point to the location of ezcaIDL.dll - on your system. To run the standalone IDL epics_ad_display.sav file without an IDL - license exectute the following on Linux:

- 
idl -32 -vm=epics_ad_display.sav 
-
-

- On Windows simply double-click on the icon for the epics_ad_display.sav file.

-

- When the GUI comes up type the base PV name for the NDStdArrays plugin for your - detector in the "Base PV" widget. For example with the simulation detector supplied - with the areaDetector application this is "13SIM1:image1:" (without the quotes). - Once the detector begins acquiring images they should be displayed in the IDL window. -

-

- To run the GUI from the IDL command line on a system with an IDL license type the - epics_ad_display command followed by the base PV name of the NDStdArrays plugin. - For example: -

- 
  IDL> epics_ad_display, '13SIM1:image1:'
-
-

- The control window for epics_ad_display is shown below. It has a field - to input the base name of the EPICS PVs with the image data. It also has fields - to enable/display the IDL display update, to change the display mode, to autoscale - the intensity, and to invert the image in the Y direction. If autoscale is set to - No then manual scaling can be entered in the Min and Max fields. The number of frames - per second actually being displayed by IDL is shown. There is a status window that - shows whether the EPICS PVs are connected and the time the last was array received, - updated once per second. -

-
-

- Main window for IDL epics_ad_display

-

- IDL_epics_ad_display.png

-
-

- epics_ad_display can use the simple IDL routine tv to - display the images. This is the fastest mode, and results in a non-scalable unadorned - window.

-
-

- IDL epics_ad_display using the IDL tv routine.

-

- IDL_epics_ad_display_tv.jpg

-
-

- epics_ad_display can also use the routine - image_display.pro 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 (right mouse click) and out (left mouse click). Note that image_display - is not currently capable of displaying color data i.e., RGB1, RGB2, or RGB3 NDArrays). - It can however, display Mono data in false color. The following is an example of - image_display displaying an image from the simulation detector.

-
-

- epics_ad_display using the image_display routine

-

- simDetector_image_display.png

-
-

- The Viewers/IDL directory also contains an IDL function to read the areaDetector - netCDF files. This is described in the NDPluginFile - netCDF documentation.

-

- Stephen Mudie at the Australian Synchrotron has written a very nice IDL client to - display the EPICS images from the Flea Firewire cameras. This client is being converted - to display the data from this areaDetector plugin, and will be provided in a future - release of areaDetector. -

- - + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> + + + areaDetector Viewers + + + +
+

+ areaDetector Viewers

+

+ August 3, 2009

+

+ Mark Rivers

+

+ University of Chicago

+
+

+ Contents

+ +

+ Overview +

+

+ One of the advantages of areaDetector is that it enables the use of generic image + display clients that obtain their data via EPICS Channel Access and work with any + detector. There are currently two such generic clients provided with the areaDetector + distribution. The first is a plugin for the popular ImageJ Java-based image processing + program. The second is an IDL-based viewer which can be run without an IDL license + under the IDL Virtual Machine. Because ImageJ is free and more widely available + and used than IDL, future enhancements are more likely to be done on the ImageJ + plugin rather than the IDL viewer. +

+

+ ImageJ Viewer

+

+ This is a plugin for the popular ImageJ + program that can be used to display 2-dimensional array data that the + NDStdArrays plugin sends to EPICS. This plugin is contained in the areaDetector + distribution in the Viewers/ImageJ/EPICS_areaDetector directory. This plugin was + begun by Tim Madden from APS, and now includes support for all NDArray data types + and color modes, i.e. Mono, RGB1 (pixel interleave), RGB2 (row interleave) and RGB3 + (plane interleave). The plugin directory includes a plugin written elsewhere for + reading and writing netCDF files, so ImageJ can be used to display images and image + sequences (movies) saved with the NDFileNetCDF plugin.

+

+ To use this ImageJ plugin do the following:

+ +

+ The control window for EPICS_AD_Viewer is shown below. The PVPrefix + field is used to input the base name of the EPICS PVs with the image data. The array + dimensions and the number of frames per second actually being displayed by ImageJ + is shown. There is a status window that shows whether the EPICS PVs are connected + and the number of arrays received since the last update, which is every 2 seconds.

+

+ Press the Snap button to make a copy of the current frame in a new window. ImageJ + can then be used to process, annotate, etc. that image.

+

+ To capture a sequence of images into an ImageJ "stack" select "Capture To Stack". + The image sequence will be stored in the ImageJ buffer and a scroll bar will appear + to allow you to scroll through the images. The stack can be saved to disk in a large + number of formats, including AVI.

+

+ The following is the main ImageJ window. +

+
+

+ ImageJ main window.

+

+ ImageJ_Main_Screen.png

+
+

+ The following is the EPICS_AD_Viewer plugin control, located in the ImageJ "Plugins/EPICS_areaDetector/EPICS + AD Viewer" menu.

+
+

+ ImageJ EPICS_AD_Viewer plugin control window

+

+ ImageJ_EPICS_AD_Viewer.png

+
+

+ The following is the EPICS_AD_Viewer image display window, which will appear when + the Start button is pressed in the EPICS_AD_Viewer control window.

+
+

+ ImageJ EPICS_AD_Viewer plugin display window with line selection

+

+ )mageJ_EPICS_AD_Viewer_display.jpg

+
+

+ Recent versions of ImageJ come with a Dynamic Line Profile tool in the Graphics + plugin menu. This tool can be used to plot a live line profile through an image + which updates as new images are displayed. It also updates when the line position + is changed. The version of this plugin that is supplied with the version of ImageJ + current as of this writing (1.42q) does not obey the "Fixed Y-axis scale" property + on the Edit/Options/Profile Plot Options menu in ImageJ. There is a newer version + of this plugin available on the Web and also in the EPICS_areaDetector plugin folder + that does obey the "Fixed Y-axis scale" property. Compile this version and replace + the Dynamic_Profiler.class file in the ImageJ Graphics/ plugin folder to use the + newer version.

+
+

+ ImageJ EPICS_AD_Viewer dynamic line profile of the above image

+

+ ImageJ_EPICS_AD_Viewer_DynamicProfile.png

+
+

+ IDL Viewer

+

+ There is an IDL procedure called + epics_ad_display that can be used to display 2-dimensional array data that + the NDStdArrays plugin sends to 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. + epics_ad_display is included in the + CARS IDL imaging software. It is also available in the Viewers/IDL directory + in the areaDetector application. +

+

+ The Viewers/IDL directory contains both the IDL source code and a standalone IDL + file, epics_ad_display.sav, for the epics_ad_display GUI to display images from + areaDetector detectors. This file can be run for free on any Linux or Windows system + under the IDL Virtual Machine, which can be downloaded free of charge from + ITT VIS. That directory also contains the shareable libraries used to call + EPICS Channel Access from IDL (ezcaIDL.dll for Windows and libezcaIDL.so for Linux). + Before using the IDL source code or .sav file it is necessary to define the environment + variable EZCA_IDL_SHARE to point to the complete path to ezcaIDL.dll or libezcaIDL.so. + For example on Linux:

+ 
setenv EZCA_IDL_SHARE /home/epics/support/areaDetector/1-5/Viewers/IDL/libezcaIDL.so
+
+

+ On Windows use +

+ 
My Computer/Properties/Advanced/Environment Variables/ 
+
+

+ to add a new environment variable EZCA_IDL_SHARE to point to the location of ezcaIDL.dll + on your system. To run the standalone IDL epics_ad_display.sav file without an IDL + license exectute the following on Linux:

+ 
idl -32 -vm=epics_ad_display.sav 
+
+

+ On Windows simply double-click on the icon for the epics_ad_display.sav file.

+

+ When the GUI comes up type the base PV name for the NDStdArrays plugin for your + detector in the "Base PV" widget. For example with the simulation detector supplied + with the areaDetector application this is "13SIM1:image1:" (without the quotes). + Once the detector begins acquiring images they should be displayed in the IDL window. +

+

+ To run the GUI from the IDL command line on a system with an IDL license type the + epics_ad_display command followed by the base PV name of the NDStdArrays plugin. + For example: +

+ 
  IDL> epics_ad_display, '13SIM1:image1:'
+
+

+ The control window for epics_ad_display is shown below. It has a field + to input the base name of the EPICS PVs with the image data. It also has fields + to enable/display the IDL display update, to change the display mode, to autoscale + the intensity, and to invert the image in the Y direction. If autoscale is set to + No then manual scaling can be entered in the Min and Max fields. The number of frames + per second actually being displayed by IDL is shown. There is a status window that + shows whether the EPICS PVs are connected and the time the last was array received, + updated once per second. +

+
+

+ Main window for IDL epics_ad_display

+

+ IDL_epics_ad_display.png

+
+

+ epics_ad_display can use the simple IDL routine tv to + display the images. This is the fastest mode, and results in a non-scalable unadorned + window.

+
+

+ IDL epics_ad_display using the IDL tv routine.

+

+ IDL_epics_ad_display_tv.jpg

+
+

+ epics_ad_display can also use the routine + image_display.pro 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 (right mouse click) and out (left mouse click). Note that image_display + is not currently capable of displaying color data i.e., RGB1, RGB2, or RGB3 NDArrays). + It can however, display Mono data in false color. The following is an example of + image_display displaying an image from the simulation detector.

+
+

+ epics_ad_display using the image_display routine

+

+ simDetector_image_display.png

+
+

+ The Viewers/IDL directory also contains an IDL function to read the areaDetector + netCDF files. This is described in the NDPluginFile + netCDF documentation.

+

+ Stephen Mudie at the Australian Synchrotron has written a very nice IDL client to + display the EPICS images from the Flea Firewire cameras. This client is being converted + to display the data from this areaDetector plugin, and will be provided in a future + release of areaDetector. +

+ +