Merge branch 'nikitinvv-master'

xray-imaging · Feb 19, 2021 · 7d2f1de · 7d2f1de
2 parents dd25065 + bf936a9
commit 7d2f1de
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Showing 6 changed files with 66 additions and 20 deletions.
diff --git a/docs/source/tomoStreamApp.rst b/docs/source/tomoStreamApp.rst
@@ -65,6 +65,9 @@ tomoStream PVA Names
   * - $(P)$(R)FlatPVAName
     - stringout
     - Contains the name of the TomoScan PVA where the flat images are stored
+  * - $(P)$(R)ThetaPVAName
+    - stringout
+    - Contains the name of the TomoScan PVA where the rotation angle positions are stored
   * - $(P)$(R)ReconPVAName
     - stringout
     - Contains the name of the TomoStream PVA where the the selected 3 orthogonal slices are stored

diff --git a/iocBoot/iocTomoStream/tomoStream.substitutions b/iocBoot/iocTomoStream/tomoStream.substitutions
@@ -1,6 +1,6 @@
 file "$(TOP)/db/tomoStream.template"
 {
 pattern
-{  P,      R, TOMO_SCAN, IMAGE_P, DARK_PVA, FLAT_PVA, RECON_PVA}
-{2bmb:, TomoStream:, 2bmb:TomoScan:, 2bmb:TomoScan:PvaPluginPVPrefix, 2bmb:TomoScan:StreamDarkFields, 2bmb:TomoScan:StreamFlatFields, 2bmb:TomoStream:StreamRecon}
+{  P,      R, TOMO_SCAN, IMAGE_P, DARK_PVA, FLAT_PVA, RECON_PVA, THETA_PVA}
+{2bmb:, TomoStream:, 2bmb:TomoScanStream:, 2bmb:TomoScanStream:PvaPluginPVPrefix, 2bmb:TomoScanStream:StreamDarkFields, 2bmb:TomoScanStream:StreamFlatFields, 2bmb:TomoStream:StreamRecon, 2bmb:TomoStream:StreamTheta}
 }
diff --git a/tomoStreamApp/Db/tomoStream.template b/tomoStreamApp/Db/tomoStream.template
@@ -30,6 +30,11 @@ record(stringout, "$(P)$(R)FlatPVAName")
    field(VAL,  "$(FLAT_PVA)")
 }
 
+record(stringout, "$(P)$(R)ThetaPVAName")
+{
+   field(VAL,  "$(THETA_PVA)")
+}
+
 record(stringout, "$(P)$(R)ReconPVAName")
 {
    field(VAL,  "$(RECON_PVA)")

diff --git a/tomoStreamApp/Db/tomoStream_settings.req b/tomoStreamApp/Db/tomoStream_settings.req
@@ -15,10 +15,11 @@ $(P)$(R)TomoScanPVPrefix
 ######################
 # tomoStream PVA names
 ######################
+$(P)$(R)ImagePVAPName
 $(P)$(R)DarkPVAName
 $(P)$(R)FlatPVAName
+$(P)$(R)ThetaPVAName
 $(P)$(R)ReconPVAName
-$(P)$(R)ImagePVAPName
 
 ############################
 # Streaming analysis control

diff --git a/tomoStreamApp/op/adl/tomoStreamEPICS_PVs.adl b/tomoStreamApp/op/adl/tomoStreamEPICS_PVs.adl
@@ -5,10 +5,10 @@ file {
 }
 display {
 	object {
-		x=1854
-		y=159
-		width=455
-		height=190
+		x=6064
+		y=37
+		width=456
+		height=205
 	}
 	clr=14
 	bclr=4
@@ -115,7 +115,7 @@ rectangle {
 		x=5
 		y=40
 		width=445
-		height=140
+		height=160
 	}
 	"basic attribute" {
 		clr=14
@@ -241,7 +241,7 @@ text {
 "text entry" {
 	object {
 		x=220
-		y=150
+		y=173
 		width=225
 		height=20
 	}
@@ -257,7 +257,7 @@ text {
 text {
 	object {
 		x=100
-		y=150
+		y=173
 		width=110
 		height=20
 	}
@@ -267,3 +267,32 @@ text {
 	textix="Recon PVA"
 	align="horiz. right"
 }
+text {
+	object {
+		x=101
+		y=150
+		width=110
+		height=20
+	}
+	"basic attribute" {
+		clr=14
+	}
+	textix="Theta PVA"
+	align="horiz. right"
+}
+"text entry" {
+	object {
+		x=221
+		y=150
+		width=225
+		height=20
+	}
+	control {
+		chan="$(P)$(R)ThetaPVAName"
+		clr=14
+		bclr=51
+	}
+	format="string"
+	limits {
+	}
+}
diff --git a/tomostream/tomostream.py b/tomostream/tomostream.py
@@ -50,18 +50,20 @@ def __init__(self, pv_files, macros):
 
         self.epics_pvs['RotationStep']       = PV(prefix + 'RotationStep')
 
-        self.epics_pvs['PSOPVPrefix']        = PV(prefix + 'PSOPVPrefix')
-        if self.epics_pvs['PSOPVPrefix'].get(as_string=True) == None:
-            log.error("TomoScan is down")
-            log.error("Type exit() here and start TomoScan first")
-            return
-        self.epics_pvs['ThetaArray']         = PV(self.epics_pvs['PSOPVPrefix'].get(as_string=True) + 'motorPos.AVAL')
-    
+        # Replace PSOPVPrefix to link to check a TomoScanStream PV so it returns if scan IOC is down
+        # self.epics_pvs['PSOPVPrefix']        = PV(prefix + 'PSOPVPrefix')
+        # if self.epics_pvs['PSOPVPrefix'].get(as_string=True) == None:
+        #     log.error("TomoScan is down")
+        #     log.error("Type exit() here and start TomoScan first")
+        #     return
+
         # pva type channel for flat and dark fields pv broadcasted from the detector machine
         self.epics_pvs['PvaDark']        = pva.Channel(self.epics_pvs['DarkPVAName'].get())
         self.pva_dark = self.epics_pvs['PvaDark']
         self.epics_pvs['PvaFlat']        = pva.Channel(self.epics_pvs['FlatPVAName'].get())
         self.pva_flat = self.epics_pvs['PvaFlat']   
+        self.epics_pvs['PvaTheta']        = pva.Channel(self.epics_pvs['ThetaPVAName'].get())
+        self.pva_theta = self.epics_pvs['PvaTheta']   
 
         # pva type channel that contains projection and metadata
         image_pv_name = PV(self.epics_pvs['ImagePVAPName'].get()).get()
@@ -142,7 +144,10 @@ def reinit_monitors(self):
         height = pva_image_data['dimension'][1]['size']
         self.pv_rec['dimension'] = [{'size': 3*width, 'fullSize': 3*width, 'binning': 1},
                                     {'size': width, 'fullSize': width, 'binning': 1}]
-        self.theta = self.epics_pvs['ThetaArray'].get()[:self.epics_pvs['NumAngles'].get()]                
+        # self.theta = self.epics_pvs['ThetaArray'].get()[:self.epics_pvs['NumAngles'].get()]                
+        self.theta = self.pva_theta.get()['value']
+        print(self.theta)
+        #exit()
         # update limits on sliders
         # epics_pvs['OrthoXlimit'].put(width-1)
         # epics_pvs['OrthoYlimit'].put(width-1)
@@ -224,7 +229,9 @@ def add_dark(self, pv):
         if(self.stream_is_running and len(pv['value'])==self.width*self.height):  # if pv with dark field has cocrrect sizes
             data = pv['value'].reshape(self.height, self.width)
             self.slv.set_dark(data)
-            log.warning('new dark fields acquired')
+            print('Norm dark', np.linalg.norm(data))
+            log.error('new dark fields acquired')
+
 
     def add_flat(self, pv):
         """PV monitoring function for reading new flat fields from manually running pv server 
@@ -233,7 +240,8 @@ def add_flat(self, pv):
         if(self.stream_is_running and len(pv['value'])==self.width*self.height):  # if pv with flat has correct sizes
             data = pv['value'].reshape(self.height, self.width)
             self.slv.set_flat(data)
-            log.warning('new flat fields acquired')
+            print('Norm flat', np.linalg.norm(data))
+            log.error('new flat fields acquired')
 
     def begin_stream(self):
         """Run streaming reconstruction by sending new incoming projections from the queue to the solver class,