68 epics key error for epuangle device and progressive stack serialization error

README.md

@@ -152,6 +152,21 @@ The nx_server service must be installed on a computer that
 has a mount point to the data computer such that the ```/etc/fstab``` file contains the entry in its list of mount 
 points.
 
+The service relies on the environment variable set in the file ```nx_server.env``` to determine the port to listen on 
+and the base data directory. 
+
+Create the file in the nx_server directory called ```nx_server.env``` and add the following entry to tell the service
+the IP address of nx_server:
+
+```shell
+vi pyStxm/nx_server/nx_server.env
+```
+Then in nx_server.env add the following line, replacing the IP address with the IP address of the computer that is 
+running nx_server:
+```shell
+NX_SERVER_HOST=IP-ADDR-HERE
+```
+
 **Service Commands**:
 
     - Enable the service: 
@@ -170,6 +185,34 @@ points.
         >sudo systemctl restart nx_server.service 
 
 
+In order for the logs of nx_server service to not use all diskspace on **/var/log**
+the messages will be sent to **/etc/var/log/nx_server.log** and **logrotate** will be used
+to rotate the logs when they reach 10MB in size, keeping 5 rotated logs and
+compressing them to save space. 
+
+
+Create the file **/etc/logrotate.d/nx_server** and add the contents below:
+
+```
+/var/log/nx_server.log {
+    size 10M
+    rotate 5
+    compress
+    missingok
+    notifempty
+    copytruncate
+}
+````
+
+Then run:
+```shell
+    sudo logrotate -f /etc/logrotate.d/nx_server
+````
+
+You can continue to view live output with:
+```shell
+    tail -f /var/log/nx_server.log
+````
 --------------------------------------
 ### Configure pyStxm with Pixelator
 

bcm/devices/ophyd/ad_tucsen.py

@@ -143,7 +143,7 @@ def make_filename(self):
             Path that the IOC can write to or is it the path that this application can write to?
 
             ('a9b3ed47-bd2e-47af-ab20',
-             '\/opt/test_data/C167092/',
+             '/opt/test_data/C167092/',
              '/opt/test_data/C167092')
         '''
         #dont over ride what was previously set to these signals likely from the scan plan
@@ -269,7 +269,7 @@ def make_filename(self):
             Path that the IOC can write to or is it the path that this application can write to?
 
             ('a9b3ed47-bd2e-47af-ab20',
-             '\directory\\test_data\\C167092\\',
+             '/directory/test_data/C167092/',
              '/opt/test_data/C167092')
         '''
         #dont over ride what was previously set to these signals likely from the scan plan

bcm/devices/zmq/pixelator/pixelator_dcs_server_api.py

@@ -531,14 +531,17 @@ def intake_scan_line_data(self, resp, selected_det_names):
         # calc the progress
         all_scans_progress = int(float((self.ttl_points_received / self._total_num_points) * 100.0)/len(selected_det_names))
         cur_img_progress = int(float((self.cur_img_points_received / (self.npoints_rows * self.npoints_cols)) * 100.0)/len(selected_det_names))
+        # cur_img_progress keeps a running total so reset it to zero on start of every new image
+        if sl_dct['img_idx'] > 0:
+            cur_img_progress = cur_img_progress - 100.0 * sl_dct['img_idx']
+
         self._scan_line_data_cntr += 1
         return {'det_name': selected_det_names[sl_dct['det_chan_idx']], 'row': sl_dct['row'], 'col': sl_dct['col'], 'shape': sl_dct['data_shape'],
                 'value': sl_dct['data'], 'is_tiled': self.tiling, 'is_partial': True if not self.tiling else False,
                 'img_idx': sl_dct['img_idx'],
                 "tile_num": sl_dct['tile_num'], "ev_idx": sl_dct['outer_idx'], "prog": cur_img_progress, "pol_idx": sl_dct['tile_num'],
                 "total_prog": all_scans_progress}
 
-
     def handle_scanStarted(self, scan_request):
         """
         parse the scan request and set the member variables

cls/appWidgets/main_object.py

@@ -136,6 +136,7 @@ def __init__(self, name, endstation, beamline_cfg_dct=None, splash=None, main_cf
         self.dcs_settings = None
         self.data_dir = beamline_cfg_dct["BL_CFG_MAIN"]['data_dir']
         self.default_detector = beamline_cfg_dct["BL_CFG_MAIN"].get('default_detector', None)
+        self.striptool_scaling_factor = float(beamline_cfg_dct["BL_CFG_MAIN"].get('striptool_scaling_factor', 1))
         self.data_sub_context = zmq.Context()
         self.nx_server_master_seq_dct = None
         self._progressive_stack_data = {} # this is a dict of detector names each containing a list of lists that

cls/app_data/app_dflts.json

@@ -83,7 +83,7 @@
                 "OSA_IDX": 1,
                 "ZP_A1": -4.859,
                 "ZP_D": 240.0,
-                "ZP_IDX": 6
+                "ZP_IDX": 0
             }
         },
         "PREFERENCESPARAMS": {
@@ -185,8 +185,8 @@
                 0
             ],
             "RANGE": [
-                1000.0,
-                1000.0,
+                933.33,
+                933.33,
                 0,
                 0
             ],
@@ -197,8 +197,8 @@
                 -10.0
             ],
             "STEP": [
-                71.42857142857143,
-                71.42857142857143,
+                66.66642857142857,
+                66.66642857142857,
                 0,
                 0
             ],
@@ -296,8 +296,8 @@
             ],
             "DWELL": 1.0,
             "NPOINTS": [
-                15,
-                15,
+                30,
+                30,
                 0,
                 0
             ],
@@ -314,8 +314,8 @@
                 -10.0
             ],
             "STEP": [
-                5.714285714285714,
-                5.714285714285714,
+                2.7586206896551726,
+                2.7586206896551726,
                 0,
                 0
             ],

cls/applications/pyStxm/app.ini

@@ -4,8 +4,8 @@ autoSaveData = true
 
 # which beamline configuration to use for the devices, this is the name of the .ini file in the bl_configs directory
 # of the same name <lab>_<beamline>_<endstation>.ini
-# bl_config = sls_x07da_polLux
-bl_config = amb_bl10ID1
+bl_config = sls_x07da_polLux
+# bl_config = amb_bl10ID1
 # bl_config = uhv_bl10ID1
 mongo_db_nm = pystxm_amb_bl10ID1
 nx_server_port = 5555

cls/applications/pyStxm/bl_configs/amb_bl10ID1/amb_bl10ID1.ini

@@ -18,8 +18,9 @@ ptychography_enabled=false
 min_ptycho_dwell_ms=300.0 # ms
 tomography_enabled=false #requires GONIX and GONIY to exist
 use_e712_hdw_accel=true
-save_progressive_stack_data=true
+save_progressive_stack_data=false
 default_detector=DNM_PMT
+striptool_scaling_factor=10.0
 
 #plugin_dir=endstation_prefix
 #support for Pixelator required override the plugin dir so that it will use the common pixelator scan plugins

cls/applications/pyStxm/bl_configs/amb_bl10ID1/devs.py

@@ -1,5 +1,5 @@
 
-SIM =False 
+SIM =  True
 dev_dct = {}
 
 
@@ -9,16 +9,16 @@
         "name": "DNM_SAMPLE_FINE_X",
         "desc": "Fine_X",
         "class": "e712_sample_motor",
-        #"dcs_nm": "PZAC1610-3-I12-40",
-        "dcs_nm": "TB_ASTXMIOC:m700" if SIM else "PZAC1610-3-I12-40",
+        "dcs_nm": "PZAC1610-3-I12-40",
+        #"dcs_nm": "TB_ASTXMIOC:m700" if SIM else "PZAC1610-3-I12-40",
         "pos_type": "POS_TYPE_ES",
     },
     {
         "name": "DNM_SAMPLE_FINE_Y",
         "desc": "Fine_Y",
         "class": "e712_sample_motor",
-        #"dcs_nm": "PZAC1610-3-I12-41",
-        "dcs_nm": "TB_ASTXMIOC:m701" if SIM else "PZAC1610-3-I12-41",
+        "dcs_nm": "PZAC1610-3-I12-41",
+        #"dcs_nm": "TB_ASTXMIOC:m701" if SIM else "PZAC1610-3-I12-41",
         "pos_type": "POS_TYPE_ES",
     },
     {
@@ -34,71 +34,71 @@
         "desc": "OSA_Y",
         "class": "MotorQt",
         #"dcs_nm": "PZAC1610-3-I12-44",
-        "dcs_nm": "TB_ASTXMIOC:m702" if SIM else "PZAC1610-3-I12-44",
+        "dcs_nm": "TB_ASTXMIOC:m703" if SIM else "PZAC1610-3-I12-44",
         "pos_type": "POS_TYPE_ES",
     },
     {
         "name": "DNM_ZONEPLATE_Z",
         "Zoneplate_Z": "FineX",
         "class": "MotorQt",
         #"dcs_nm": "SMTR1610-3-I12-51",
-        "dcs_nm": "TB_ASTXMIOC:m703" if SIM else "SMTR1610-3-I12-51",
+        "dcs_nm": "TB_ASTXMIOC:m704" if SIM else "SMTR1610-3-I12-51",
         "pos_type": "POS_TYPE_ES",
     },
     {
         "name": "DNM_COARSE_X",
         "desc": "Coarse_X",
         "class": "MotorQt",
-        #"dcs_nm": "SMTR1610-3-I12-45",
-        "dcs_nm": "TB_ASTXMIOC:m704" if SIM else "SMTR1610-3-I12-45",
+        "dcs_nm": "SMTR1610-3-I12-45",
+        #"dcs_nm": "TB_ASTXMIOC:m705" if SIM else "SMTR1610-3-I12-45",
         "pos_type": "POS_TYPE_ES",
     },
     {
         "name": "DNM_COARSE_Y",
         "desc": "Coarse_Y",
         "class": "MotorQt",
-        #"dcs_nm": "SMTR1610-3-I12-46",
-        "dcs_nm": "TB_ASTXMIOC:m705" if SIM else "SMTR1610-3-I12-46",
+        "dcs_nm": "SMTR1610-3-I12-46",
+        #"dcs_nm": "TB_ASTXMIOC:m706" if SIM else "SMTR1610-3-I12-46",
         "pos_type": "POS_TYPE_ES",
     },
     {
         "name": "DNM_COARSE_Z",
         "desc": "Coarse_Z",
         "class": "MotorQt",
         #"dcs_nm": "SMTR1610-3-I12-47",
-        "dcs_nm": "TB_ASTXMIOC:m706" if SIM else "SMTR1610-3-I12-47",
+        "dcs_nm": "TB_ASTXMIOC:m707" if SIM else "SMTR1610-3-I12-47",
         "pos_type": "POS_TYPE_ES",
     },
     {
         "name": "DNM_DETECTOR_X",
         "desc": "Detector_X",
         "class": "MotorQt",
         #"dcs_nm": "SMTR1610-3-I12-48",
-        "dcs_nm": "TB_ASTXMIOC:m707" if SIM else "SMTR1610-3-I12-48",
+        "dcs_nm": "TB_ASTXMIOC:m708" if SIM else "SMTR1610-3-I12-48",
         "pos_type": "POS_TYPE_ES",
     },
     {
         "name": "DNM_DETECTOR_Y",
         "desc": "Detector_Y",
         "class": "MotorQt",
         #"dcs_nm": "SMTR1610-3-I12-49",
-        "dcs_nm": "TB_ASTXMIOC:m708" if SIM else "SMTR1610-3-I12-49",
+        "dcs_nm": "TB_ASTXMIOC:m709" if SIM else "SMTR1610-3-I12-49",
         "pos_type": "POS_TYPE_ES",
     },
     {
         "name": "DNM_DETECTOR_Z",
         "desc": "Detector_Z",
         "class": "MotorQt",
         #"dcs_nm": "SMTR1610-3-I12-50",
-        "dcs_nm": "TB_ASTXMIOC:m709" if SIM else "SMTR1610-3-I12-50",
+        "dcs_nm": "TB_ASTXMIOC:m710" if SIM else "SMTR1610-3-I12-50",
         "pos_type": "POS_TYPE_ES",
     },
     {
         "name": "DNM_SAMPLE_X",
         "desc": "Sample_X",
         "class": "sample_abstract_motor",
-        #"dcs_nm": "PSMTR1610-3-I12-00",
-        "dcs_nm": "TB_ASTXMIOC:m710" if SIM else "PSMTR1610-3-I12-00",
+        "dcs_nm": "PSMTR1610-3-I12-00",
+        #"dcs_nm": "TB_ASTXMIOC:m711" if SIM else "PSMTR1610-3-I12-00",
         "pos_type": "POS_TYPE_ES",
         "fine_mtr_name": "DNM_SAMPLE_FINE_X",
         "coarse_mtr_name": "DNM_COARSE_X"
@@ -107,8 +107,8 @@
         "name": "DNM_SAMPLE_Y",
         "desc": "Sample_Y",
         "class": "sample_abstract_motor",
-        #"dcs_nm": "PSMTR1610-3-I12-01",
-        "dcs_nm": "TB_ASTXMIOC:m711" if SIM else "PSMTR1610-3-I12-01",
+        "dcs_nm": "PSMTR1610-3-I12-01",
+        #"dcs_nm": "TB_ASTXMIOC:m712" if SIM else "PSMTR1610-3-I12-01",
         "pos_type": "POS_TYPE_ES",
         "fine_mtr_name": "DNM_SAMPLE_FINE_Y",
         "coarse_mtr_name": "DNM_COARSE_Y"
@@ -188,7 +188,8 @@
         "name": "DNM_EPU_ANGLE",
         "desc": "Epu_Angle",
         "class": "MotorQt",
-        "dcs_nm": "SIM_VBL1610-I12:epuAngle" if SIM else "BL1610-I10:epuAngle",
+        #"dcs_nm": "SIM_VBL1610-I12:epuAngle" if SIM else "BL1610-I10:epuAngle",
+        "dcs_nm": "BL1610-I10:epuAngle",
         "abstract_mtr": True,
         "pos_type": "POS_TYPE_BL",
     },
@@ -208,7 +209,7 @@
         "name": "DNM_SHUTTERTASKRUN",
         "class": "make_basedevice",
         # "dcs_nm": "ASTXM1610:Dio:shutter:Run",
-        "dcs_nm": "uhvDIO:shutter:Run",
+        "dcs_nm": "ASTXM1610:Dio:shutter:Run" if SIM else "uhvDIO:shutter:Run",
     },
 ]