Data security updates at PDF

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.gitignore

@@ -88,3 +88,6 @@ history.sqlite
 Link\ to\ startup
 
 .vscode/
+# pixi environments
+.pixi/*
+!.pixi/config.toml

pixi.toml

@@ -0,0 +1,65 @@
+[workspace]
+channels = ["conda-forge"]
+name = "pdf-profile-collection"
+platforms = ["linux-64"]
+version = "2025.3.1"
+
+[system-requirements]
+libc = "2.17"
+
+[feature.profile.dependencies]
+bluesky-base = "==1.14.6"
+bluesky-queueserver = "*"
+matplotlib-base= ">=3.9.3,<4"
+networkx = ">=3.4.2,<4"
+nslsii = "==0.11.4"
+numpy = "*"
+ophyd = ">=1.11.0"
+pyepics = "*"
+python = ">=3.12,<3.13"
+semver = ">=3.0.4,<4"
+tiled-client = ">=0.1.6"
+bluesky-darkframes = ">=0.6.0,<0.7"
+xpdacq = ">=1.1.4,<2"
+xpdan = ">=0.8.2,<0.9"
+lmfit = ">=1.3.4,<2"
+databroker = "==2.0.0"
+bluesky-tiled-plugins = ">=2.0.0b68"
+tifffile = ">=2025.5.10,<2026"
+setuptools = "<81"
+hdf5-external-filter-plugins = ">=0.1.0,<0.2"
+blosc-hdf5-plugin = ">=1.0.1,<2"
+epicscorelibs = ">=7.0.7.99.1.1,<8"
+ophyd-async = ">=0.13.7,<0.14"
+
+
+[feature.profile.pypi-dependencies]
+pvxslibs = ">=1.3.2, <2"
+
+
+[feature.qs.dependencies]
+bluesky-queueserver = "*"
+bluesky-httpserver = "*"
+
+[feature.qs.tasks]
+# This section needs some development work to understand the best way to
+# thread the required configuration through both the task and files checked into
+# the profile.  These will interact with the ansible roles for pushing out the
+# systemd units
+qs-backend = "start-re-manager --profile-dir=."
+qs-server = "uvicorn --host localhost --port 60610 bluesky_httpserver.server:app"
+
+
+[feature.terminal.dependencies]
+ipython = ">=9.5.0"
+pyside6 = "*"
+numpy = ">2"
+
+
+[feature.terminal.tasks]
+start = "unset SESSION_MANAGER PYTHONPATH && MPLBACKEND=qtagg ipython --profile-dir=."
+pvs = "ipython --profile-dir=. -c 'get_pv_types(); exit()'"
+
+[environments]
+terminal = {features=["profile", "terminal"], solve-group="profile"}
+qs = {features=["profile", "qs"], solve-group="profile"}

scripts/Battery_Coincell/Battery_Coincell.py

@@ -0,0 +1,59 @@
+
+
+from epics import PV
+from epics import caget, caput
+import datetime
+import numpy as np
+import pylab
+from pylab import *
+import os
+from tifffile import imsave,  imread
+import sys
+
+
+####Only XRD measurement
+####Detector position on XRD measurement
+
+sample_ID = []
+scan_plan = []
+
+xstage = OT_stage_2_X
+ystage = OT_stage_2_Y
+
+pos_x = [158.15, 158.15, 158.15, 158.15, 158.15, 158.15]
+pos_y = [158.15, 158.15, 158.15, 158.15, 158.15, 158.15]
+
+det_exp_time = []
+
+sleep_time = [60,60,60,60,60,60] # or put list = [x,x,x,x,x,x] length needs to be same as sample_ID
+
+glbl['dk_window']=0.1
+glbl['frame_acq_time']=0.1 #XRD det exposure time in situ cells 
+xpd_configuration["area_det"] = pe1c #pilatus1 # pe1c, pe2c
+
+#if you use Pilatus detector
+# dark_strategy = no_dark
+
+#if you use PE detector
+dark_strategy = None
+
+number_of_repeat = 10000
+
+def tqdm_sleep(rest_time, message='Sleep'):
+    from tqdm import tqdm
+    for j in tqdm(range(0,100), desc=message):
+        time.sleep(rest_time/100)
+
+
+for num in range (number_of_repeat):  #10000$$$$$$$$$$$$$
+
+    for i in range(len(sample_ID)):
+
+        glbl['frame_acq_time'] = det_exp_time[i]
+        RE(mv(xstage, pos_x[i], ystage, pos_y[i]))
+        xrun(sample_ID[i], scan_plan[i], useful_info = measurement_data(), dark_strategy=dark_strategy)
+
+        try:
+            tqdm_sleep(sleep_time[i], message='Sleep after changing sample')    #if you use "list", use tqdm_sleep(sleep_time, )
+        except (KeyError, ValueError):
+            tqdm_sleep(sleep_time[0], message='Sleep after changing sample')

scripts/Eurotherm3504_Linkam_T96_0903_2025/eurotherm3504_Linkam_T96_0903_2025.py

@@ -76,9 +76,9 @@ def measurement(num_repeat, sleep_clear=1, frame_time=0.1, Settle_time=10):
 	DetZ.append(round(Det_1_Z.position))
 
 	try:
-		tset = thermal_device.setpoint.get()  #for linkham get target temperature
+		tset = thermal_device.setpoint.get()  #for eurotherm/linkham get target temperature
 	except AttributeError:
-		tset = thermal_device.setpoint        #for eurotherm 
+		tset = thermal_device.setpoint        ## After revision on 2025/09/17, eurotherm and linkam use the same attribute to read temperature
 
 	tqdm_sleep(Settle_time, message='Wait for thermal equilibrium')
 
@@ -125,7 +125,8 @@ def measurement(num_repeat, sleep_clear=1, frame_time=0.1, Settle_time=10):
 		glbl['frame_acq_time'] = det_exp_PDF
 		# RE(mv(thermal_device,Tlist[i]))
 		print(f'\nmove {thermal_device.name} to {Tlist[i]}\n')
-		thermal_device.move(Tlist[i])    
+		# thermal_device.move(Tlist[i])
+		RE(pbar_set_temp(temp_controller = thermal_device, ramprate = 5, setpoint = Tlist[i], ))
 		#Det_1_Z.move(D1)
 		move_PDF()
 		measurement(num_repaet_PDF, rest_time=sleep_clear, frame_time=det_exp_PDF, Settle_time=Settle_time)
@@ -143,7 +144,8 @@ def measurement(num_repeat, sleep_clear=1, frame_time=0.1, Settle_time=10):
 	move_PDF()
 	for i in range(len(Tlist)):
 		print(f'\nmove {thermal_device.name} to {Tlist[i]}\n')
-		thermal_device.move(Tlist[i])
+		# thermal_device.move(Tlist[i])
+		RE(pbar_set_temp(temp_controller = thermal_device, ramprate = 5, setpoint = Tlist[i], ))
 		measurement(num_repaet_PDF, rest_time=sleep_clear, frame_time=det_exp_PDF, Settle_time=Settle_time)
 		tqdm_sleep(st2, message='Sleep after PDF')
 
@@ -153,7 +155,8 @@ def measurement(num_repeat, sleep_clear=1, frame_time=0.1, Settle_time=10):
 	move_XRD()
 	for i in range(len(Tlist)):
 		print(f'\nmove {thermal_device.name} to {Tlist[i]}\n')
-		thermal_device.move(Tlist[i])
+		# thermal_device.move(Tlist[i])
+		RE(pbar_set_temp(temp_controller = thermal_device, ramprate = 5, setpoint = Tlist[i], ))
 		measurement(num_repaet_XRD, rest_time=sleep_clear, frame_time=det_exp_XRD, Settle_time=Settle_time)
 		tqdm_sleep(st2, message='Sleep after XRD')
 

scripts/Hotairblower/1008_2025/Hotairblower_list.py

@@ -0,0 +1,60 @@
+# Cryostat T-dependent XRD and PDF measurements
+# Created: 11/09/2020 (MA)
+
+import time
+import pylab
+from pylab import *
+import numpy as np
+import os
+from tifffile import imread, imsave
+import matplotlib.pyplot as plt 
+import shutil 
+
+#======================================== Definition of variables =======================================
+# Users plese change variables as necessay
+
+A = [450, 500, 550] + [600]*3 + [650] + [700]*3 + [30]
+
+# A = [25, 28, 25]
+
+T_threshold = 1	     	     # T-setpoint +-threshold
+Settle_time = 60		     # Settle time after HAB reach the setpoint	Temperature
+
+smpi_PDF = 8                # sample index for PDF
+spi_PDF = 5                  # scan plan index for PDF
+frame_time = 1.5            # frame acquisition time for PDF and XRD
+
+smpi_XRD = 8                # for XRD
+spi_XRD = 5                  # for XRD
+
+glbl['frame_acq_time'] = 0.1   # Deatector frame acquasition time
+glbl['dk_window'] = 30         # dark current acquasition window
+st2 = 5                 	# sleep timebefore each measuement
+temp_controller = hotairblower
+
+#======================================= Definition of Measuremet =======================================
+# Do not change anyhing below.  
+
+i = 0
+for t in A:
+
+    RE(pbar_set_temp(temp_controller=temp_controller, setpoint=t, tolerance=T_threshold))
+
+    tqdm_sleep(Settle_time, message='Wait for thermal equilibrium...')
+
+    print('\nMove to PDF Setup\n')
+    set_PDF()
+    glbl['frame_acq_time'] = frame_time
+    xrun(smpi_PDF, spi_PDF, more_info = measurement_data())
+    glbl['frame_acq_time'] = 0.1
+    tqdm_sleep(st2, message='Sleep and Change to XRD')
+
+    print('\nMove to XRD Setup')
+    set_XRD()
+    glbl['frame_acq_time'] = frame_time
+    xrun(smpi_XRD, spi_XRD, more_info = measurement_data())
+    glbl['frame_acq_time'] = 0.1
+
+    print('\nGo to next Temperature...\n')
+
+

scripts/Hotairblower/1008_2025/definitions.py

@@ -0,0 +1,89 @@
+
+temp_controller = lakeshore336_2
+#------------------------------------------= ''' Do not change anything  below !!!'''---------------------.move----------------
+config_dir = "/nsls2/data3/pdf/pdfhack/legacy/processed/xpdacq_data/user_data/config_base/" 
+
+
+def set_PDF(): # Move PDF poni and mask files to config directory
+    xpd_configuration['area_det']=pilatus1
+    Grid_Z.move(1972)
+    # xpd_configuration['area_det']=pe1c
+    # Det_1_Z.move(2679)
+
+    try:
+        os.remove(config_dir + "xpdAcq_calib_info.poni")
+    except Exception:
+        pass      
+    shutil.copy(config_dir + "/pilatus_PDF/" + "xpdAcq_calib_info.poni" , config_dir)
+    try:
+        os.remove(config_dir + "Mask.npy")
+    except Exception:
+        pass
+    shutil.copy(config_dir + "/pilatus_PDF/" + "Mask.npy" , config_dir)
+
+def set_XRD(): # Move XRD poni and mask files to config directory
+    # xpd_configuration['area_det']=pe1c
+    # Det_1_Z.move(2679+700)
+    xpd_configuration['area_det']=pilatus1
+    Grid_Z.move(1972+700)
+
+    try:
+        os.remove(config_dir + "xpdAcq_calib_info.poni")
+    except Exception:
+        pass     
+    shutil.copy(config_dir + "/pilatus_XRD/" + "xpdAcq_calib_info.poni" , config_dir)
+    try:
+        os.remove(config_dir + "Mask.npy")
+    except Exception:
+        pass
+    shutil.copy(config_dir + "/pilatus_XRD/" + "Mask.npy" , config_dir)
+
+
+## run the following commmand before using scan_shifter_pos(OT_stage_2_X, -128, -218, 400)
+def set_scan_pos():
+    Grid_X.move(0)
+    Grid_Y.move(130)
+
+    xpd_configuration['area_det']=pe1c
+    glbl['frame_acq_time']=0.1
+
+
+
+def measurement_data(): # .......Captures metadata   
+    info_dict = {}
+    info_dict['OT_stage_1_X'] = OT_stage_1_X.read()
+    info_dict['OT_stage_1_Y'] = OT_stage_1_Y.read()
+    info_dict['Det_1_X'] = Det_1_X.read()
+    info_dict['Det_1_Y'] = Det_1_Y.read()
+    info_dict['Det_1_Z'] = Det_1_Z.read()
+    info_dict['Grid_X'] = Grid_X.read()
+    info_dict['Grid_Y'] = Grid_Y.read()
+    info_dict['Grid_Z'] = Grid_Z.read()
+    info_dict['ring_current'] = ring_current.read()
+    info_dict['frame_acq_time'] = glbl['frame_acq_time']
+    info_dict['dk_window'] = glbl['dk_window']
+    # info_dict['cryostat_A'] = lakeshore336.read()['lakeshore336_temp_A_T']['value']
+    # info_dict['cryostat_A_V'] = caget('XF:28ID1-ES{LS336:1-Chan:A}Val:Sens-I')
+    # info_dict['cryostat_B'] = lakeshore336.read()['lakeshore336_temp_B_T']['value']
+    # info_dict['cryostat_B_V'] = caget('XF:28ID1-ES{LS336:1-Chan:B}Val:Sens-I')
+    # info_dict['cryostat_C'] = lakeshore336.read()['lakeshore336_temp_C_T']['value']
+    # info_dict['cryostat_C_V'] = caget('XF:28ID1-ES{LS336:1-Chan:C}Val:Sens-I')
+    # info_dict['cryostat_D'] = lakeshore336.read()['lakeshore336_temp_D_T']['value']
+    # info_dict['cryostat_D_V'] = caget('XF:28ID1-ES{LS336:1-Chan:D}Val:Sens-I')
+    # info_dict['hotairblower'] = hotairblower.read()['hotairblower_readback']['value']
+    info_dict['Measurement_time'] = time.time()
+    return info_dict
+
+# def Det_scan(SI, SP, repeat): # Pilatus three position scan
+#     for j in range(repeat):
+#         # det_x = [40.644, 31.356, 36]
+#         # det_y = [-3.356, -12.644, -8]
+#         # for i in range(len(det_x)):
+#         #     Grid_X.move(det_x[i])
+#         #     Grid_Y.move(det_y[i])
+#         #     #xrun(SI, jog([pilatus1], SP, OT_stage_2_Y, use_ypos-.5, use_ypos+.5), dark_strategy=no_dark,  more_info = useful_info())
+#         xrun(SI, SP, dark_strategy= no_dark, more_info = measurement_data(), user_config = my_config)
+
+
+
+