Merge pull request #50 from nikitinvv/master

merging latest from 7-BM and 2-BM

iocBoot/iocTomoStream3D_7BM/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

iocBoot/iocTomoStream3D_7BM/auto_settings.req

@@ -0,0 +1,2 @@
+file "tomoStream.req", P=$(P), R=$(R)
+file "tomoStream_settings.req", P=$(P), R=$(R)

iocBoot/iocTomoStream3D_7BM/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")

iocBoot/iocTomoStream3D_7BM/st.cmd

@@ -0,0 +1,25 @@
+< envPaths
+
+epicsEnvSet("P", "7bmtomo:")
+epicsEnvSet("R", "EncoderStream:")
+
+## 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)")

iocBoot/iocTomoStream3D_7BM/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
+

iocBoot/iocTomoStream3D_7BM/start_medm

@@ -0,0 +1 @@
+medm -x -macro "P=7bmtomo:,R=EncoderStream:" ../../tomoStreamApp/op/adl/tomoStream.adl &

iocBoot/iocTomoStream3D_7BM/start_tomostream3d.py

@@ -0,0 +1,68 @@
+# 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
+
+import sys
+sys.path.append('/home/beams/7BMB/solder_beamtime/solder_imaging')
+
+from tomostream3d import EncoderStream
+ts = EncoderStream(["../../db/tomoStream_settings.req","../../db/tomoStream_settings.req"], {"$(P)":"7bmtomo:", "$(R)":"EncoderStream:"})
+
+
+
+
+# import vedo
+# import matplotlib.pyplot as plt
+# from vedo.applications import IsosurfaceBrowser
+
+# clip_val = 0.3
+# from pdb import set_trace
+# from time import sleep
+
+
+# def run_vis(vol_vis):
+
+#     vol_vis = vol_vis < clip_val
+#     vol = vedo.Volume(vol_vis)
+#     plt = IsosurfaceBrowser(vol, c='gold') # Plotter instance
+#     plt.show(axes = 7, bg2 = 'lb').close()
+#     return
+
+
+# import threading, queue
+
+# q = queue.Queue(maxsize = 2)
+
+# def worker():
+#     while True:
+#         if q.qsize() > 2:
+#             continue
+#         vol_vis = ts.slv.rec_vol[::2,::2,::2].get()
+#         q.put(vol_vis)
+#         q.task_done()
+#         sleep(2.0)
+
+
+
+# sleep(30.0)
+
+# # turn-on the worker thread
+# threading.Thread(target=worker, daemon=True).start()
+
+
+
+# while True:
+#     vol_vis = q.get()
+#     run_vis(vol_vis)
+#     sleep(5.0)
+
+# # block until all tasks are done
+# q.join()
+# print('All work completed')
+
+
+
+
+
+

iocBoot/iocTomoStream3D_7BM/tomoStream.substitutions

@@ -0,0 +1,6 @@
+file "$(TOP)/db/tomoStream.template"
+{
+pattern
+{  P,      R, TOMO_SCAN, IMAGE_P, DARK_PVA, FLAT_PVA, RECON_PVA, THETA_PVA}
+{7bmtomo:, EncoderStream:, 7bmtomo:TomoScanStream:, 7bmtomo:TSS:PvaPluginPVPrefix, 7bmtomo:TSS:StreamDarkFields, 7bmtomo:TSS:StreamFlatFields, 7bmtomo:EncoderStream:StreamRecon, 7bmtomo:TSS:StreamTheta}
+}

iocBoot/iocTomoStream_2BM/tomoStream.substitutions

@@ -2,5 +2,5 @@ file "$(TOP)/db/tomoStream.template"
 {
 pattern
 {  P,      R, TOMO_SCAN, IMAGE_P, DARK_PVA, FLAT_PVA, RECON_PVA, THETA_PVA}
-{2bmb:, TomoStream:, 2bmb:TomoScanStream:, 2bmb:TomoScanStream:PvaPluginPVPrefix, 2bmb:TomoScanStream:StreamDarkFields, 2bmb:TomoScanStream:StreamFlatFields, 2bmb:TomoStream:StreamRecon, 2bmb:TomoStream:StreamTheta}
+{2bmb:, TomoStream:, 2bmb:TomoScanStream:, 2bmb:TomoScanStream:PvaPluginPVPrefix, 2bmb:TomoScanStream:StreamDarkFields, 2bmb:TomoScanStream:StreamFlatFields, 2bmb:TomoStream:StreamRecon, 2bmb:TomoScanStream:StreamTheta}
 }

iocBoot/iocTomoStream_7BM/auto_python.sh

@@ -0,0 +1,229 @@
+#!/bin/sh
+#
+# description: start/stop/restart an EPICS IOC in a screen session
+#
+
+# Manually set IOC_STARTUP_DIR if 7bm_dau3.sh will reside somewhere other than softioc
+IOC_STARTUP_DIR=/home/beams/7BMB/epics/synApps/support/tomostream/iocBoot/iocTomoStream_7BM
+IOC_BINARY="python -i"
+IOC_NAME=TomoStream_python
+# The name of the IOC binary isn't necessarily the same as the name of the IOC
+# Change YES to NO in the following line to disable screen-PID lookup 
+GET_SCREEN_PID=YES
+
+# Commands needed by this script
+ECHO=echo
+ID=id
+PGREP=pgrep
+SCREEN=screen
+KILL=kill
+BASENAME=basename
+DIRNAME=dirname
+READLINK=readlink
+PS=ps
+#####################################################################
+
+SNAME=${BASH_SOURCE:-$0}
+SELECTION=$1
+
+IOC_STARTUP_FILE="start_tomostream_7bm.py"
+
+if [ -z "$IOC_STARTUP_DIR" ] ; then
+    # If no startup dir is specified, use the script's directory
+    IOC_STARTUP_DIR=`dirname ${SNAME}`
+    IOC_CMD="${IOC_BINARY} ${IOC_STARTUP_FILE}"
+else
+    IOC_CMD="${IOC_BINARY} ${IOC_STARTUP_DIR}/${IOC_STARTUP_FILE}"
+fi
+
+#####################################################################
+
+screenpid() {
+    if [ -z ${SCREEN_PID} ] ; then
+        ${ECHO}
+    else
+        ${ECHO} " in a screen session (pid=${SCREEN_PID})"
+    fi
+}
+
+checkpid() {
+    MY_UID=`${ID} -u`
+    # The '\$' is needed in the pgrep pattern to select 7bmLinux, but not 7bmLinux.sh
+    IOC_PID=`${PGREP} ${IOC_BINARY}\$ -u ${MY_UID}`
+    #!${ECHO} "IOC_PID=${IOC_PID}"
+
+    if [ "${IOC_PID}" != "" ] ; then
+        # Assume the IOC is down until proven otherwise
+        IOC_DOWN=1
+
+        # At least one instance of the IOC binary is running; 
+        # Find the binary that is associated with this script/IOC
+        for pid in ${IOC_PID}; do
+            BIN_CWD=`${READLINK} /proc/${pid}/cwd`
+            IOC_CWD=`${READLINK} -f ${IOC_STARTUP_DIR}`
+
+                if [ "$BIN_CWD" = "$IOC_CWD" ] ; then
+                    # The IOC is running; the binary with PID=$pid is the IOC that was run from $IOC_STARTUP_DIR
+                    IOC_PID=${pid}
+                    IOC_DOWN=0
+
+                    SCREEN_PID=""
+
+                    if [ "${GET_SCREEN_PID}" = "YES" ] ; then
+                        # Get the PID of the parent of the IOC (shell or screen)
+                        P_PID=`${PS} -p ${IOC_PID} -o ppid=`
+
+                        # Get the PID of the grandparent of the IOC (sshd, screen, or ???)
+                        GP_PID=`${PS} -p ${P_PID} -o ppid=`
+
+                        #!${ECHO} "P_PID=${P_PID}, GP_PID=${GP_PID}"
+
+                        # Get the screen PIDs
+                        S_PIDS=`${PGREP} screen`
+
+                        for s_pid in ${S_PIDS} ; do
+                            #!${ECHO} ${s_pid}
+
+                            if [[ ${s_pid} -eq ${P_PID} ]] ; then
+                                SCREEN_PID=${s_pid}
+                                break
+                            fi
+
+                            if [[ ${s_pid} -eq ${GP_PID} ]] ; then
+                                SCREEN_PID=${s_pid}
+                                break
+                            fi
+
+                        done
+                    fi
+
+                    break
+                    #else
+                    #    ${ECHO} "PATHS are different"
+                    #    ${ECHO} ${BIN_CWD}
+                    #    ${ECHO} ${IOC_CWD}
+                fi
+        done
+    else
+        # IOC is not running
+        IOC_DOWN=1
+    fi
+
+    return ${IOC_DOWN}
+}
+
+start() {
+    if checkpid; then
+        ${ECHO} -n "${IOC_NAME} is already running (pid=${IOC_PID})"
+        screenpid
+    else
+        ${ECHO} "Starting ${IOC_NAME}"
+        cd ${IOC_STARTUP_DIR}
+        # Run 7bmLinux inside a screen session
+        ${SCREEN} -dm -S ${IOC_NAME} -h 5000 ${IOC_CMD}
+    fi
+}
+
+stop() {
+    if checkpid; then
+        ${ECHO} "Stopping ${IOC_NAME} (pid=${IOC_PID})"
+        ${KILL} ${IOC_PID}
+    else
+        ${ECHO} "${IOC_NAME} is not running"
+    fi
+}
+
+restart() {
+    stop
+    start
+}
+
+status() {
+    if checkpid; then
+        ${ECHO} -n "${IOC_NAME} is running (pid=${IOC_PID})"
+        screenpid
+    else
+        ${ECHO} "${IOC_NAME} is not running"
+    fi
+}
+
+console() {
+    if checkpid; then
+        ${ECHO} "Connecting to ${IOC_NAME}'s screen session"
+        # The -r flag will only connect if no one is attached to the session
+        #!${SCREEN} -r ${IOC_NAME}
+        # The -x flag will connect even if someone is attached to the session
+        ${SCREEN} -x ${IOC_NAME}
+    else
+        ${ECHO} "${IOC_NAME} is not running"
+    fi
+}
+
+run() {
+    if checkpid; then
+        ${ECHO} -n "${IOC_NAME} is already running (pid=${IOC_PID})"
+        screenpid
+    else
+        ${ECHO} "Starting ${IOC_NAME}"
+        cd ${IOC_STARTUP_DIR}
+        # Run 7bmLinux outside of a screen session, which is helpful for debugging
+        ${IOC_CMD}
+    fi
+}
+
+start_medm() {
+    ${IOC_STARTUP_DIR}/../../start_MEDM_7bmLinux
+}
+
+start_caqtdm() {
+    ${IOC_STARTUP_DIR}/../../start_caQtDM_7bmLinux
+}
+
+usage() {
+    ${ECHO} "Usage: $(${BASENAME} ${SNAME}) {start|stop|restart|status|console|run|medm|caqtdm}"
+}
+
+#####################################################################
+
+if [ ! -d ${IOC_STARTUP_DIR} ] ; then
+    ${ECHO} "Error: ${IOC_STARTUP_DIR} doesn't exist."
+    ${ECHO} "IOC_STARTUP_DIR in ${SNAME} needs to be corrected."
+else
+    case ${SELECTION} in
+        start)
+        start
+        ;;
+
+        stop | kill)
+        stop
+        ;;
+
+        restart)
+        restart
+        ;;
+
+        status)
+        status
+        ;;
+
+        console)
+            console
+        ;;
+
+        run)
+            run
+        ;;
+
+        medm)
+            start_medm
+        ;;
+
+        caqtdm)
+            start_caqtdm
+        ;;
+
+        *)
+        usage
+        ;;
+    esac
+fi