merged dev

.github/workflows/install-rocky.yml

@@ -20,11 +20,11 @@ jobs:
         with:
           path: /opt/MagAOX/
           key: rocky-9-dependencies-cache-v1-${{ hashFiles('setup/*', 'setup/**/*') }}
-      - run: 'bash -x setup/steps/install_rocky_9.2_packages.sh'
+      - run: 'bash -x setup/steps/install_rocky_9_packages.sh'
         name: Install OS dependencies
       - run: 'bash -lx setup/provision.sh'
         name: Auto-provision
       - run: 'bash -l setup/steps/install_MagAOX.sh'
         name: Install MagAO-X
-      # - run: 'make test'
-      #   name: Run tests
+      - run: 'make test'
+        name: Run tests

.github/workflows/install-ubuntu.yml

@@ -24,11 +24,11 @@ jobs:
         with:
           path: /opt/MagAOX/
           key: ubuntu-22.04-dependencies-cache-v1-${{ hashFiles('setup/*', 'setup/**/*') }}
-      - run: 'bash -x setup/steps/install_ubuntu_22.04_packages.sh'
+      - run: 'bash -x setup/steps/install_ubuntu_22_packages.sh'
         name: Install OS dependencies
       - run: 'bash -lx setup/provision.sh'
         name: Auto-provision
       - run: 'bash -l setup/steps/install_MagAOX.sh'
         name: Install MagAO-X
-      # - run: 'make test'
-      #   name: Run tests
+      - run: 'make test'
+        name: Run tests

.gitignore

@@ -97,6 +97,7 @@ INDI/xindidriver/xindidriver
 apps/indiTSAccumulator/indiTSAccumulator
 
 #k
+apps/kcubeCtrl/kcubeCtrl
 apps/kTracker/kTracker
 apps/koolanceCtrl/koolanceCtrl
 

Dockerfile.rocky

@@ -2,12 +2,12 @@ FROM rockylinux/rockylinux:9-ubi-init
 ENV MAGAOX_ROLE container
 RUN echo "MAGAOX_ROLE=${MAGAOX_ROLE}" > /etc/profile.d/magaox_role.sh
 ADD ./setup/_common.sh /setup/
-ADD ./setup/steps/install_rocky_9.2_packages.sh /setup/steps/
-RUN bash /setup/steps/install_rocky_9.2_packages.sh
+ADD ./setup/steps/install_rocky_9_packages.sh /setup/steps/
+RUN bash /setup/steps/install_rocky_9_packages.sh
 ADD ./setup/setup_users_and_groups.sh /setup/
 RUN bash /setup/setup_users_and_groups.sh
-ADD ./setup/steps/configure_rocky_9.2.sh /setup/steps/
-RUN bash /setup/steps/configure_rocky_9.2.sh
+ADD ./setup/steps/configure_rocky_9.sh /setup/steps/
+RUN bash /setup/steps/configure_rocky_9.sh
 ADD . /opt/MagAOX/source/MagAOX
 WORKDIR /opt/MagAOX/source/MagAOX/setup
 RUN bash -lx provision.sh

Dockerfile.ubuntu

@@ -8,10 +8,10 @@ RUN echo "MAGAOX_ROLE=${MAGAOX_ROLE}" > /etc/profile.d/magaox_role.sh
 ADD ./setup/_common.sh /setup/
 ADD ./setup/setup_users_and_groups.sh /setup/
 RUN bash /setup/setup_users_and_groups.sh
-ADD ./setup/steps/install_ubuntu_22.04_packages.sh /setup/steps/
-RUN bash /setup/steps/install_ubuntu_22.04_packages.sh
-ADD ./setup/steps/configure_ubuntu_22.04.sh /setup/steps/
-RUN bash /setup/steps/configure_ubuntu_22.04.sh
+ADD ./setup/steps/install_ubuntu_22_packages.sh /setup/steps/
+RUN bash /setup/steps/install_ubuntu_22_packages.sh
+ADD ./setup/steps/configure_ubuntu_22.sh /setup/steps/
+RUN bash /setup/steps/configure_ubuntu_22.sh
 ADD . /opt/MagAOX/source/MagAOX
 WORKDIR /opt/MagAOX/source/MagAOX/setup
 # RUN bash setup_users_and_groups.sh

INDI/libcommon/IndiConnection.cpp

@@ -83,6 +83,20 @@ const IndiConnection &IndiConnection::operator= ( const IndiConnection &idRhs )
 
 IndiConnection::~IndiConnection()
 {
+    try
+    {
+        deactivate();
+    }
+    catch(...)
+    {
+        //do nothing
+    }
+
+    if(m_fstreamOutput)
+    {
+        fclose(m_fstreamOutput);
+    }
+
 }
 
 ////////////////////////////////////////////////////////////////////////////////
@@ -104,7 +118,7 @@ void IndiConnection::construct( const string &szName,
 
   // These are the two descriptors we will use to talk to the outside world.
   m_fdInput = STDIN_FILENO;
-  m_fdOutput = STDOUT_FILENO;
+  setOutputFd(STDOUT_FILENO);
 
   // setup the signal handler.
   //::signal( SIGHUP, IndiConnection::handleSignal );
@@ -363,18 +377,14 @@ void IndiConnection::sendXml( const string &szXml ) const
 {
   MutexLock::AutoLock autoOut( &m_mutOutput );
 
-  //Convert to stream b/c dprintf will kill silently on a bad file descriptor
-  FILE * fdout = fdopen(m_fdOutput, "w+");
-
-  if(!fdout)
+  if(!m_fstreamOutput)
   {
     return;
   }
 
-  ::fprintf( fdout, "%s", szXml.c_str() );
-  fflush(fdout);
+  ::fprintf( m_fstreamOutput, "%s", szXml.c_str() );
+  fflush(m_fstreamOutput);
 
-  //dprintf(m_fdOutput, "%s", szXml.c_str());
 }
 
 ////////////////////////////////////////////////////////////////////////////////
@@ -415,6 +425,11 @@ void IndiConnection::setInputFd( const int &iFd )
 void IndiConnection::setOutputFd( const int &iFd )
 {
   m_fdOutput = iFd;
+  if(m_fstreamOutput)
+  {
+    fclose(m_fstreamOutput);
+  }
+  m_fstreamOutput = fdopen(m_fdOutput, "w+");
 }
 
 ////////////////////////////////////////////////////////////////////////////////

INDI/libcommon/IndiConnection.hpp

@@ -155,8 +155,13 @@ class IndiConnection : public pcf::Thread
     mutable pcf::MutexLock m_mutOutput;
     /// The file descriptor to read from.
     int m_fdInput;
+
     /// The file descriptor to write to.
     int m_fdOutput;
+
+    /// Stream for safer output
+    FILE * m_fstreamOutput {NULL};
+
     /// If the processing of INDI messages is put in a separate thread,
     /// this is the thread id of it.
     pthread_t m_idProcessThread;

Make/magAOX.mk

@@ -49,7 +49,11 @@ TARGETNAME = $(PATHNAME)$(notdir $(BASENAME))
 
 all:  pch magaox_git_version.h $(TARGETNAME)
 	rm $(SELF_DIR)/../magaox_git_version.h
-
+
+debug: CXXFLAGS += -g -O0
+debug: pch magaox_git_version.h $(TARGETNAME)
+	rm $(SELF_DIR)/../magaox_git_version.h
+
 pch:
 	cd $(SELF_DIR)/../libMagAOX; ${MAKE}
 

Makefile

@@ -13,30 +13,32 @@ apps_common = \
 	shmimIntegrator \
 	timeSeriesSimulator
 
-apps_rtcicc = alpaoCtrl \
-              cacaoInterface \
-			  userGainCtrl \
-			  zaberCtrl \
-	          zaberLowLevel \
-			  picoMotorCtrl
+apps_rtcicc = \
+	bmcCtrl \
+	rhusbMon \
+	alpaoCtrl \
+	cacaoInterface \
+	userGainCtrl \
+	zaberCtrl \
+	zaberLowLevel \
+	picoMotorCtrl
 
 apps_rtc = \
+	alpaoCtrl \
 	ocam2KCtrl \
-    andorCtrl \
+	andorCtrl \
 	siglentSDG \
 	ttmModulator \
-	bmcCtrl \
-    rhusbMon \
 	pi335Ctrl \
 	pupilFit \
 	t2wOffloader \
 	dmSpeckle \
-    w2tcsOffloader \
+	w2tcsOffloader \
 	pwfsSlopeCalc
 
 
 apps_icc = \
-   acronameUsbHub \
+	acronameUsbHub \
 	flipperCtrl \
 	filterWheelCtrl \
 	hsfwCtrl \
@@ -65,8 +67,7 @@ apps_tic = \
 	acronameUsbHub \
 	baslerCtrl \
 	bmcCtrl \
-	trippLitePDU 
-
+	trippLitePDU
 
 libs_to_build = libtelnet
 
@@ -85,13 +86,13 @@ else ifeq ($(MAGAOX_ROLE),TIC)
 endif
 
 all_guis = \
-   dmCtrlGUI \
+	dmCtrlGUI \
 	dmModeGUI \
 	offloadCtrlGUI \
 	pupilGuideGUI \
 	pwr \
 	coronAlignGUI \
-   loopCtrlGUI \
+	loopCtrlGUI \
 	roiGUI \
 	cameraGUI \
 	stageGUI
@@ -126,11 +127,12 @@ else
   rtimv_plugins_to_build = $(all_rtimv_plugins)
 endif
 
-utils_to_build = logdump \
-				 logstream \
-                 cursesINDI \
-				 xrif2shmim \
-				 xrif2fits
+utils_to_build = \
+	logdump \
+	logstream \
+	cursesINDI \
+	xrif2shmim \
+	xrif2fits
 
 scripts_to_install = magaox \
 	query_seeing \
@@ -202,7 +204,6 @@ lib_clean:
 	cd libMagAOX; ${MAKE} clean
 
 apps_all: libs_install flatlogs_all
-
 	for app in ${apps_to_build}; do \
 		(cd apps/$$app; ${MAKE} )|| exit 1; \
 	done
@@ -282,8 +283,11 @@ utils_clean:
 			(cd utils/$$app; ${MAKE} clean) || exit 1; \
 		done
 
+test: tests_clean
+	cd tests; ${MAKE} test || exit 1;
+
 tests_clean:
-	cd tests; ${MAKE} clean || exit1;
+	cd tests; ${MAKE} clean || exit 1;
 
 .PHONY: doc
 doc:

apps/alpaoCtrl/alpaoCtrl.hpp

@@ -468,7 +468,7 @@ int alpaoCtrl::releaseDM()
 
    if(m_dm == nullptr)
    {
-      return log<software_error, -1>({__FILE__, __LINE__, "dm is not initialized"});
+      return 0;
    }
 
    state(stateCodes::READY);
@@ -478,7 +478,7 @@ int alpaoCtrl::releaseDM()
       pthread_kill(m_smThread.native_handle(), SIGUSR1);
    }
 
-   sleep(1); ///\todo need to trigger shmimMonitor loop to pause it.
+   sleep(1);
 
    if(zeroDM() < 0)
    {

apps/andorCtrl/andorCtrl.hpp

@@ -663,7 +663,6 @@ void andorCtrl::loadConfig()
 
    if(writeConfig() < 0)
    {
-      std::cerr << "m_configFile: " << m_configFile << "\n";
       log<software_critical>({__FILE__,__LINE__});
       m_shutdown = true;
       return;
@@ -1050,7 +1049,7 @@ int andorCtrl::cameraSelect()
    log<text_log>(std::string("Decode: ") + std::to_string(Decode));
    log<text_log>(std::string("f/w: ") + std::to_string(CameraFirmwareVersion) + "." + std::to_string(CameraFirmwareBuild));
 
-#if 0
+#if 0 //We don't normally need to do this, but keep here in case we want to check in the future
    int em_speeds;
    error=GetNumberHSSpeeds(0,0, &em_speeds);
    if(error != DRV_SUCCESS)
@@ -1081,7 +1080,7 @@ int andorCtrl::cameraSelect()
       std::cerr << i << " " << speed << "\n";
    }
 #endif
-#if 0
+#if 0 //We don't normally need to do this, but keep here in case we want to check in the future
    int v_speeds;
    error=GetNumberVSSpeeds(&v_speeds);
    if(error != DRV_SUCCESS)
@@ -1103,7 +1102,7 @@ int andorCtrl::cameraSelect()
    int ss = 2;
    if(m_shutterState == 1) ss = 1;
    else m_shutterState = 0; //handles startup case
-   error = SetShutter(1,ss,50,50);
+   error = SetShutter(1,ss,500,500);
    if(error != DRV_SUCCESS)
    {
       log<software_critical>({__FILE__, __LINE__, "ANDOR SDK SetShutter failed: " + andorSDKErrorName(error)});
@@ -1460,15 +1459,25 @@ int andorCtrl::setShutter( unsigned os )
    recordCamera(true);
    AbortAcquisition();
    state(stateCodes::CONFIGURING);
-
+    
    if(os == 0) //Shut
    {
-      SetShutter(1,2,50,50);
+      int error = SetShutter(1,2,500,500);
+      if(error != DRV_SUCCESS)
+      {
+         return log<software_error, -1>({__FILE__, __LINE__, "ANDOR SDK SetShutter failed: " + andorSDKErrorName(error)});
+      }
+
       m_shutterState = 0;
    }
    else //Open
    {
-      SetShutter(1,1,50,50);
+      int error = SetShutter(1,1,500,500);
+      if(error != DRV_SUCCESS)
+      {
+         return log<software_error, -1>({__FILE__, __LINE__, "ANDOR SDK SetShutter failed: " + andorSDKErrorName(error)});
+      }
+
       m_shutterState = 1;
    }
 
@@ -1612,17 +1621,13 @@ int andorCtrl::getFPS()
 
    m_expTime = exptime;
 
-   //std::cerr << accumCycletime << " " << kinCycletime << "\n";
-
    float readoutTime;
    error = GetReadOutTime(&readoutTime);
    if(error != DRV_SUCCESS)
    {
       return log<software_error,-1>({__FILE__, __LINE__, "ANDOR SDK error from GetReadOutTime: " + andorSDKErrorName(error)});
    }
 
-   //if(readoutTime < exptime) m_fps = 1./m_expTime;
-   //else m_fps = 1.0/readoutTime;
    m_fps = 1.0/accumCycletime;
 
    return 0;
@@ -1916,7 +1921,7 @@ int andorCtrl::loadImageIntoStream(void * dest)
    if( frameGrabber<andorCtrl>::loadImageIntoStreamCopy(dest, m_image_p, m_width, m_height, m_typeSize) == nullptr) return -1;
 
    return 0;
-   }
+ }
 
 inline
 int andorCtrl::reconfig()

apps/bmcCtrl/bmcCtrl.hpp

@@ -519,8 +519,7 @@ int bmcCtrl::releaseDM()
 
    if(!m_dmopen)
    {
-      log<text_log>("dm is not initialized", logPrio::LOG_ERROR);
-      return -1;
+      return 0;
    }
 
    state(stateCodes::READY);
@@ -530,7 +529,7 @@ int bmcCtrl::releaseDM()
       pthread_kill(m_smThread.native_handle(), SIGUSR1);
    }
 
-   sleep(1); ///\todo need to trigger shmimMonitor loop to pause it.
+   sleep(1);
 
    if(zeroDM() < 0)
    {