update at 2024/09/13 XPD beamtime

NSLS-II-XPD · Sep 17, 2024 · 3902fdf · 3902fdf
1 parent d3ec673
commit 3902fdf
Show file tree

Hide file tree

Showing 6 changed files with 31 additions and 28 deletions.
diff --git a/scripts/_LDRD_Kafka.py b/scripts/_LDRD_Kafka.py
@@ -101,7 +101,7 @@ def _kafka_process():
 
 class dic_to_inputs():
     def __init__(self, parameters_dict, parameters_list):
-        """ Turn the input dict into class methods
+        """ Turn the input dict into class attributes
 
         Args:
             parameters_dict (dict): dict read from excel spreadsheet
@@ -122,14 +122,14 @@ def __init__(self, parameters_dict, parameters_list):
 class xlsx_to_inputs():
     def __init__(self, parameters_list, xlsx_fn, sheet_name='inputs', is_kafka=False):
         """ Read the excel spreadsheet according to the sheet name into a dict
-        Turn the dict read from excel into class methods
+        Turn the dict read from excel into class attributes
 
         Args:
             parameters_list (list): list for namespace deined above
             xlsx_fn (str): full path if excel file
             sheet_name (str, optional): sheet name of the excel file. Defaults to 'inputs'.
             is_kafka (bool, optional): if True, the namespace for the variables processed 
-                                        in Kafka will be turn into class methods. Defaults to False.
+                                        in Kafka will be turn into class attributes. Defaults to False.
         """
         self.parameters_list = parameters_list
         self.from_xlsx = xlsx_fn
@@ -294,7 +294,7 @@ def macro_agent(self, qserver_process, RM, check_target=False, is_1st=False):
                 print(f'\nReach the target, stop iteration, stop all pumps, and wash the loop.\n')
 
                 ### Stop all infusing pumps and wash loop
-                sq.wash_tube_queue2(qin.pump_list, qin.wash_tube, 'ul/min', 
+                sq.wash_tube_queue2(qin.pump_list, qin.if_wash, qin.wash_loop, 'ul/min', 
                                 zmq_control_addr=qin.zmq_control_addr[0],
                                 zmq_info_addr=qin.zmq_info_addr[0])
 
@@ -317,7 +317,7 @@ def macro_agent(self, qserver_process, RM, check_target=False, is_1st=False):
         if len(self.agent.table) < 2:
             acq_func = "qr"
         else:
-            acq_func = "qei"
+            acq_func = "qem"
 
         new_points = self.agent.ask(acq_func, n=1)
 
@@ -1083,10 +1083,10 @@ def macro_17_add_queue(self, stream_name, qserver_process, RM):
                 print('*** qsever aborted due to too many bad scans, please check setup ***\n')
 
                 ### Stop all infusing pumps and wash loop
-                sq.wash_tube_queue2(qin.pump_list, qin.wash_tube, 'ul/min', 
+                sq.wash_tube_queue2(qin.pump_list, qin.if_wash, qin.wash_loop, 'ul/min', 
                                 zmq_control_addr=qin.zmq_control_addr[0],
                                 zmq_info_addr=qin.zmq_info_addr[0])
-                
+
                 RM.queue_stop()
 
             elif (len(self.good_data) <= 2) and (self.inputs.use_good_bad[0]):

diff --git a/scripts/_data_export.py b/scripts/_data_export.py
@@ -6,7 +6,8 @@
 import os
 import json
 import importlib
-importlib.import_module("_data_export")
+# importlib.import_module("_data_analysis")
+from _data_analysis import *
 
 """ This module provides functions for data export.
     Usually imported as de.
@@ -63,7 +64,7 @@ def _fn_generator(uid, beamline_acronym='xpd'):
     date, ttime = _readable_time(metadata_dic['time'])
     full_uid = metadata_dic['uid']
     fn = f'{sample_type}_{date}-{ttime}_{full_uid[0:8]}'
-    return fn
+    return fnkafka_test
 
 
 ## Auto generate sample name with given prefix and infuse_rate

diff --git a/scripts/_synthesis_queue_RM.py b/scripts/_synthesis_queue_RM.py
@@ -163,13 +163,13 @@ def synthesis_queue_xlsx(parameter_obj):
 
 
 
-  		## 4.0 Configure area detector in Qserver
-		if det1 == 'pe1c' or det1 == 'pe2c':
-			scanplan = BPlan('configure_area_det', 
-							det=det1, 
-							exposure=1, 
-							acq_time=det1_frame_rate)
-			RM.item_add(scanplan, pos=pos)
+  		# ## 4.0 Configure area detector in Qserver
+		# if det1 == 'pe1c' or det1 == 'pe2c':
+		# 	scanplan = BPlan('configure_area_det', 
+		# 					det=det1, 
+		# 					exposure=1, 
+		# 					acq_time=det1_frame_rate)
+		# 	RM.item_add(scanplan, pos=pos)
 
 
 		## 4-1. Take a fluorescence peak to check reaction

diff --git a/scripts/inputs_qserver_kafka_v2.xlsx b/scripts/inputs_qserver_kafka_v2.xlsx
diff --git a/scripts/kafka_consumer_iterate_XPD_v2.py b/scripts/kafka_consumer_iterate_XPD_v2.py
@@ -39,11 +39,11 @@
 xlsx_fn = '/home/xf28id2/.ipython/profile_collection_ldrd20-31/scripts/inputs_qserver_kafka_v2.xlsx'
 
 ## Input varaibales for Qserver, reading from xlsx_fn by given sheet name
-qserver_process = LK.xlsx_to_inputs(LK._qserver_inputs(), xlsx_fn=xlsx_fn, sheet_name='qserver_test')
+qserver_process = LK.xlsx_to_inputs(LK._qserver_inputs(), xlsx_fn=xlsx_fn, sheet_name='qserver_XPD')
 qin = qserver_process.inputs
 
 ## Input varaibales for Kafka, reading from xlsx_fn by given sheet name
-kafka_process = LK.xlsx_to_inputs(LK._kafka_inputs(), xlsx_fn=xlsx_fn, sheet_name='kafka_test', is_kafka=True)
+kafka_process = LK.xlsx_to_inputs(LK._kafka_inputs(), xlsx_fn=xlsx_fn, sheet_name='kafka_process', is_kafka=True)
 kin = kafka_process.inputs
 
 ## Define RE Manager API as RM 
@@ -54,9 +54,11 @@
     first_points = kafka_process.macro_agent(qserver_process, RM, check_target=False, is_1st=True)
     rate_list = kafka_process.auto_rate_list(qin.pump_list, first_points, kin.fix_Br_ratio)
     if kin.post_dilute[0]:
-        rate_list.append(sum(rate_list)*kin.post_dilute[1])
+        sum_active = sum(rate_list)
+        rate_list.append(sum_active/9)   ## append PF rate
+        rate_list.append(sum_active*kin.post_dilute[1])  ## append toluene rate
     qin.infuse_rates = rate_list
-
+    print(f'\n{rate_list = }\n')
 
 ## Import Qserver parameters to RE Manager
 sq.synthesis_queue_xlsx(qserver_process)

diff --git a/scripts/prepare_agent_pdf.py b/scripts/prepare_agent_pdf.py
@@ -13,17 +13,17 @@
 
 def build_agent(peak_target=660, peak_tolerance=5, size_target=6, agent_data_path='/', use_OAm=False):
     # data_path = '/home/xf28id2/data_ZnCl2'
-    #data_path = '/home/xf28id2/data'
-    agent_data_path = agent_data_path
+    agent_data_path = '/home/xf28id2/Documents/ChengHung/agent_data/Cl_02'
+    # agent_data_path = agent_data_path
 
 
     if use_OAm:
         dofs = [
-            DOF(description="CsPb(oleate)3", name="infusion_rate_CsPb", units="uL/min", search_domain=(10, 30)),
+            DOF(description="CsPb(oleate)3", name="infusion_rate_CsPb", units="uL/min", search_domain=(20, 80)),
             # DOF(description="TOABr", name="infusion_rate_Br", units="uL/min", search_domain=(50, 200)),
-            DOF(description="ZnI2", name="infusion_rate_I2", units="uL/min", search_domain=(0, 250)), 
-            DOF(description="ZnCl2", name="infusion_rate_Cl", units="uL/min", search_domain=(0, 250)),
-            DOF(description="OAm_Tol", name="infusion_rate_OAm", units="uL/min", search_domain=(0, 30)),
+            DOF(description="ZnI2", name="infusion_rate_I2", units="uL/min", search_domain=(10, 190)), 
+            DOF(description="ZnCl2", name="infusion_rate_Cl", units="uL/min", search_domain=(10, 190)),
+            DOF(description="OAm_Tol", name="infusion_rate_OAm", units="uL/min", search_domain=(0, 70)),
         ]
 
     else:
@@ -43,7 +43,7 @@ def build_agent(peak_target=660, peak_tolerance=5, size_target=6, agent_data_pat
     ratio_down = 1-(510-peak_down)*0.99/110
 
     objectives = [
-        Objective(description="Peak emission", name="Peak", target=(peak_down, peak_up), weight=100, max_noise=0.25),
+        Objective(description="Peak emission", name="Peak", target=(peak_down, peak_up), weight=100., max_noise=0.25),
         Objective(description="Peak width", name="FWHM", target="min", transform="log", weight=5., max_noise=0.25),
         Objective(description="Quantum yield", name="PLQY", target="max", transform="log", weight=1., max_noise=0.25),
         # Objective(description="Particle size", name="Br_size", target=(size_target-1.5, size_target+1.5), transform="log", weight=0.1, max_noise=0.25),
@@ -72,7 +72,7 @@ def build_agent(peak_target=660, peak_tolerance=5, size_target=6, agent_data_pat
         agent.dofs.infusion_rate_Cl.deactivate()
         agent.dofs.infusion_rate_Cl.device.put(0)
 
-    elif peak_target < 500:        
+    elif peak_target < 510:        
         agent.dofs.infusion_rate_I2.deactivate()
         agent.dofs.infusion_rate_I2.device.put(0)