Merge pull request #48 from nikitinvv/master

add plane rotation recon
xray-imaging · Nov 11, 2021 · 66408e3 · 66408e3
2 parents 6e5567d + eb2e73f
commit 66408e3
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diff --git a/iocBoot/iocTomoStream_32ID/Makefile b/iocBoot/iocTomoStream_32ID/Makefile
@@ -0,0 +1,6 @@
+TOP = ../..
+include $(TOP)/configure/CONFIG
+#ARCH = windows-x64-static
+ARCH = linux-x86_64
+TARGETS = envPaths dllPath.bat
+include $(TOP)/configure/RULES.ioc
diff --git a/iocBoot/iocTomoStream_32ID/auto_settings.req b/iocBoot/iocTomoStream_32ID/auto_settings.req
@@ -0,0 +1,2 @@
+file "tomoStream.req", P=$(P), R=$(R)
+file "tomoStream_settings.req", P=$(P), R=$(R)
diff --git a/iocBoot/iocTomoStream_32ID/autosave/README b/iocBoot/iocTomoStream_32ID/autosave/README
@@ -0,0 +1,3 @@
+This directory contains the save/restore files to retain settings between IOC reboots.
+The distribution directory does not contain a auto_settings.sav file, but this will
+be created the first time the IOC is run.
diff --git a/iocBoot/iocTomoStream_32ID/save_restore.cmd b/iocBoot/iocTomoStream_32ID/save_restore.cmd
@@ -0,0 +1,36 @@
+### save_restore setup
+#
+# The rest this file does not require modification for standard use, but...
+# If you want save_restore to manage its own NFS mount, specify the name and
+# IP address of the file server to which save files should be written.
+# This currently is supported only on vxWorks.
+#save_restoreSet_NFSHost("oxygen", "164.54.52.4")
+
+# Debug-output level
+save_restoreSet_Debug(0)
+
+# Ok to save/restore save sets with missing values (no CA connection to PV)?
+save_restoreSet_IncompleteSetsOk(1)
+# Save dated backup files?
+save_restoreSet_DatedBackupFiles(1)
+
+# Number of sequenced backup files to write
+save_restoreSet_NumSeqFiles(3)
+# Time interval between sequenced backups
+save_restoreSet_SeqPeriodInSeconds(300)
+
+# specify where save files should be
+set_savefile_path(".", "autosave")
+
+# specify what save files should be restored.  Note these files must be
+# in the directory specified in set_savefile_path(), or, if that function
+# has not been called, from the directory current when iocInit is invoked
+set_pass0_restoreFile("auto_settings.sav")
+set_pass1_restoreFile("auto_settings.sav")
+
+# specify directories in which to to search for included request files
+# Note cdCommands defines 'startup', but envPaths does not
+set_requestfile_path(".",  "")
+set_requestfile_path(".",  "autosave")
+set_requestfile_path($(AUTOSAVE), "db")
+set_requestfile_path($(TOP),      "db")
diff --git a/iocBoot/iocTomoStream_32ID/st.cmd b/iocBoot/iocTomoStream_32ID/st.cmd
@@ -0,0 +1,25 @@
+< envPaths
+
+epicsEnvSet("P", "32id:")
+epicsEnvSet("R", "TomoStream:")
+
+## Register all support components
+
+# Use these lines to run the locally built tomoStreamApp
+dbLoadDatabase "../../dbd/tomoStreamApp.dbd"
+tomoStreamApp_registerRecordDeviceDriver pdbbase
+
+# Use these lines to run the xxx application on APSshare.
+#dbLoadDatabase "/APSshare/epics/synApps_6_1/support/xxx-R6-1/dbd/iocxxxLinux.dbd"
+#iocxxxLinux_registerRecordDeviceDriver pdbbase
+
+
+dbLoadTemplate("tomoStream.substitutions")
+
+< save_restore.cmd
+save_restoreSet_status_prefix($(P))
+dbLoadRecords("$(AUTOSAVE)/asApp/Db/save_restoreStatus.db", "P=$(P)")
+
+iocInit
+
+create_monitor_set("auto_settings.req", 30, "P=$(P),R=$(R)")
diff --git a/iocBoot/iocTomoStream_32ID/start_IOC b/iocBoot/iocTomoStream_32ID/start_IOC
@@ -0,0 +1,6 @@
+# Use this line to run the locally built tomoStreamApp
+../../bin/linux-x86_64/tomoStreamApp st.cmd
+
+# Use this line to run the xxx application on /APSshare
+#/APSshare/epics/synApps_6_1/support/xxx-R6-1/bin/linux-x86_64/xxx st.cmd
+
diff --git a/iocBoot/iocTomoStream_32ID/start_medm b/iocBoot/iocTomoStream_32ID/start_medm
@@ -0,0 +1 @@
+medm -x -macro "P=32id:,R=TomoStream:" ../../tomoStreamApp/op/adl/tomoStream.adl &
diff --git a/iocBoot/iocTomoStream_32ID/start_tomostream.py b/iocBoot/iocTomoStream_32ID/start_tomostream.py
@@ -0,0 +1,6 @@
+# This script creates an object of type TomoStream for doing tomography streaming reconstruction
+# To run this script type the following:
+#     python -i start_tomostream.py
+# The -i is needed to keep Python running, otherwise it will create the object and exit
+from tomostream.tomostream import TomoStream
+ts = TomoStream(["../../db/tomoStream_settings.req","../../db/tomoStream_settings.req"], {"$(P)":"32id:", "$(R)":"TomoStream:"})
diff --git a/iocBoot/iocTomoStream_32ID/tomoStream.substitutions b/iocBoot/iocTomoStream_32ID/tomoStream.substitutions
@@ -0,0 +1,6 @@
+file "$(TOP)/db/tomoStream.template"
+{
+pattern
+{  P,      R, TOMO_SCAN, IMAGE_P, DARK_PVA, FLAT_PVA, THETA_PVA, RECON_PVA}
+{32id:, TomoStream:, 32id:TomoScanStream:, 32id:TomoScanStream:PvaPluginPVPrefix, 32id:TomoScanStream:StreamDarkFields, 32id:TomoScanStream:StreamFlatFields, 32id:TomoScanStream:StreamTheta, 32id:TomoStream:StreamRecon}
+}
diff --git a/readme.rst b/readme.rst
@@ -3,6 +3,10 @@
 .. _EPICS_NTNDA_Viewer: https://cars9.uchicago.edu/software/epics/areaDetectorViewers.html
 .. _ImageJ: https://imagej.nih.gov/ij/
 
+================
+TomoStream
+================
+
 **tomostream** is Python module for supporting streaming analysis of tomographic data where all pre-processing and reconstruction procedures are performed in real time while images are collected and the rotary stage is moving.  **tomostream** provides this main functionality:
 
 - Streaming reconstruction of 3 X-Y-Z ortho-slices through the sample
@@ -34,3 +38,109 @@ The output of **tomostream** is a live reconstruction diplaying in ImageJ using
     :align: center
 
 While the sample is rotating is possible to optimize instrument (alignment, focus, sample to detector distance etc.) and  beamline (energy etc.) conditions and monitor the effect live on the 3 orthogonal slices. It is also possible to automatically trigger data capturing based on events occurring in the sample and its environment as a result of segmentation or machine learning.
+
+================
+ Installation
+================
+
+.. _areadetector: https://cars9.uchicago.edu/software/epics/areaDetector.html
+
+The computer performing the tomographic reconstruction must have CUDA/GPU installed. **tomostream** consists of two modules
+TomoScanApp and tomostream tools.
+
+TomoScanApp
+===========
+
+Provides all the EPICS PVs needed by **tomostream**. To install TomoScanApp follow these steps:
+
+Build a minimal synApps
+-----------------------
+
+To build a minimal synApp::
+
+    $ mkdir ~/epics
+    $ cd epics
+
+
+- Download in ~/epics `assemble_synApps <https://github.com/EPICS-synApps/support/blob/master/assemble_synApps.sh>`_.sh
+- Edit the assemble_synApps.sh script as follows:
+    - Set FULL_CLONE=True
+    - Set EPICS_BASE to point to the location of EPICS base.  This could be on APSshare (the default), or a local version you built.
+    - For tomostream you only need BUSY and AUTOSAVE.  You can comment out all of the other modules (ALLENBRADLEY, ALIVE, etc.)
+
+- Run::
+
+    $ assemble_synApps.sh
+
+- This will create a synApps/ directory::
+
+    $ cd synApps/support/
+
+- Edit  busy-R1-7-2/configure/RELEASE to comment out this line::
+    
+    ASYN=$(SUPPORT)/asyn-4-32).
+
+- Clone the tomostream module into synApps/support::
+    
+    $ git clone https://github.com/tomography/tomostream.git
+
+- Edit tomostream/configure/RELEASE to comment out this line::
+    
+    ASYN=$(SUPPORT)/asyn-4-38
+
+- Edit tomostream/tomoStreamApp/src/Makefile to comment out this line::
+    
+    tomoStreamApp_LIBS += asyn
+
+- Edit configure/RELEASE add this line to the end::
+    
+    TOMOSTREAM=$(SUPPORT)/tomostream
+
+- Edit Makefile add this line to the end of the MODULE_LIST::
+    
+    MODULE_LIST += TOMOSTREAM
+
+- Run the following commands::
+
+    $ make release
+    $ make -sj
+
+Testing the installation
+------------------------
+
+- Edit /epics/synApps/support/tomostream/configure
+    - Set EPICS_BASE to point to the location of EPICS base:
+    - EPICS_BASE=/APSshare/epics/base-3.15.6
+
+- Start the epics ioc and associated medm screen with::
+
+    $ cd ~/epics/synApps/support/tomostream/iocBoot/iocTomoStream
+    $ start_IOC
+    $ start_medm
+
+
+tomostream python tools
+=======================
+
+::
+
+    $ cd ~/epics/synApps/support/tomostream/
+    $ python setup.py install
+
+Testing the installation
+------------------------
+
+::
+
+    $ cd ~/epics/synApps/support/tomostream/iocBoot/iocTomoStream
+    $ python -i start_tomostream.py
+
+
+
+
+================
+ Developers
+================
+Viktor Nikitin (vnikitin@anl.gov)
+
+Francesco De Carlo (decarlo@anl.gov)
diff --git a/tomoStreamApp/Db/tomoStream.template b/tomoStreamApp/Db/tomoStream.template
@@ -84,6 +84,21 @@ record(longout, "$(P)$(R)OrthoZ")
    field(HOPR, "2448")
 }
 
+record(ao, "$(P)$(R)RotX")
+{
+   field(PREC, "3")   
+}
+
+record(ao, "$(P)$(R)RotY")
+{
+   field(PREC, "3")   
+}
+
+record(ao, "$(P)$(R)RotZ")
+{
+   field(PREC, "3")   
+}
+
 ##################################
 # Stream status via Channel Access
 ##################################

diff --git a/tomoStreamApp/Db/tomoStream_settings.req b/tomoStreamApp/Db/tomoStream_settings.req
@@ -30,6 +30,9 @@ $(P)$(R)FilterType
 $(P)$(R)OrthoX
 $(P)$(R)OrthoY
 $(P)$(R)OrthoZ
+$(P)$(R)RotX
+$(P)$(R)RotY
+$(P)$(R)RotZ
 
 ##################################
 # Stream status via Channel Access