Combine collection and ldrd20-31 profiles to use with blop

README.md

@@ -0,0 +1,64 @@
+We need to generate `integration` files and tiff files (`dark_sub`)
+
+What we have now via Kafka:
+
+```bash
+2024-05-28/20:20:49 mrakitin@xf28id2-ws3:XPD (RHEL8.9) /nsls2/data/xpd-new/proposals/commissioning/pass-315985/ldrd/unnamed_sample $ tree
+.
+├── fq
+│   └── unnamed_sample_20240528-202016_2f28e7_0001.fq
+├── mask
+├── meta
+│   └── unnamed_sample_20240528-202016_2f28e7.yaml
+├── pdf
+│   └── unnamed_sample_20240528-202016_2f28e7_0001.gr
+└── sq
+    └── unnamed_sample_20240528-202016_2f28e7_0001.sq
+```
+
+
+Good example (from ZMQ):
+
+```bash
+2024-05-28/20:24:59 mrakitin@xf28id2-ws3:XPD (RHEL8.9) /nsls2/data/xpd-new/proposals/commissioning/pass-315985/tmp/unnamed_sample $ tree .
+.
+├── dark_sub
+│   ├── unnamed_sample_20240517-184225_2f003e_primary-dk_sub_image-00000.tiff
+│   └── unnamed_sample_20240528-191335_29af22_primary-dk_sub_image-00000.tiff
+├── fq
+│   ├── unnamed_sample_20240528-183014_ca6f1a_0001.fq
+│   ├── unnamed_sample_20240528-185345_79aec5_0001.fq
+│   ├── unnamed_sample_20240528-185612_15c0fd_0001.fq
+│   ├── unnamed_sample_20240528-190023_c55fbd_0001.fq
+│   ├── unnamed_sample_20240528-191335_29af22_0001.fq
+│   └── unnamed_sample_20240528-201210_786aad_0001.fq
+├── integration
+│   ├── unnamed_sample_20240528-191335_29af22_primary-1_mean_q.chi
+│   └── unnamed_sample_20240528-191335_29af22_primary-1_mean_tth.chi
+├── mask
+│   ├── unnamed_sample_20240517-184225_2f003e_primary-mask-1.npy
+│   └── unnamed_sample_20240528-191335_29af22_primary-mask-1.npy
+├── meta
+│   ├── unnamed_sample_20240517-184225_2f003e.yaml
+│   ├── unnamed_sample_20240528-191335_29af22.yaml
+│   └── unnamed_sample_20240528-201210_786aad.yaml
+├── pdf
+│   ├── unnamed_sample_20240528-183014_ca6f1a_0001.gr
+│   ├── unnamed_sample_20240528-185345_79aec5_0001.gr
+│   ├── unnamed_sample_20240528-185612_15c0fd_0001.gr
+│   ├── unnamed_sample_20240528-190023_c55fbd_0001.gr
+│   ├── unnamed_sample_20240528-191335_29af22_0001.gr
+│   └── unnamed_sample_20240528-201210_786aad_0001.gr
+├── scalar_data
+│   ├── unnamed_sample_20240517-184225_2f003e_primary.csv
+│   └── unnamed_sample_20240528-191335_29af22_primary.csv
+└── sq
+    ├── unnamed_sample_20240528-183014_ca6f1a_0001.sq
+    ├── unnamed_sample_20240528-185345_79aec5_0001.sq
+    ├── unnamed_sample_20240528-185612_15c0fd_0001.sq
+    ├── unnamed_sample_20240528-190023_c55fbd_0001.sq
+    ├── unnamed_sample_20240528-191335_29af22_0001.sq
+    └── unnamed_sample_20240528-201210_786aad_0001.sq
+
+8 directories, 29 files
+```

startup/00-startup.py

@@ -1,15 +1,30 @@
 # Make ophyd listen to pyepics.
 import nslsii
 import ophyd.signal
+import logging
+from IPython import get_ipython
+
+ip = get_ipython()
+
+print(f"Loading {__file__} from {ip.profile_dir.startup_dir}.")
+
+logger = logging.getLogger("startup_profile")
+
+from bluesky_queueserver import is_re_worker_active
 
 ophyd.signal.EpicsSignal.set_defaults(connection_timeout=5)
 # See docstring for nslsii.configure_base() for more details
 # this command takes away much of the boilerplate for settting up a profile
 # (such as setting up best effort callbacks etc)
+
 nslsii.configure_base(get_ipython().user_ns, 'xpd', pbar=True, bec=True,
                       magics=True, mpl=True, epics_context=False,
                       publish_documents_with_kafka=True)
 
+del one_1d_step
+del one_nd_step
+del one_shot
+
 # At the end of every run, verify that files were saved and
 # print a confirmation message.
 from bluesky.callbacks.broker import verify_files_saved, post_run

startup/02-adaptive.py

@@ -1,4 +1,4 @@
-"""Plan for running pgcam AE with a gradient TiCu sample."""
+"""Plan for running gpcam AE with a gradient TiCu sample."""
 import uuid
 import itertools
 import time
@@ -192,7 +192,7 @@ def adaptive_plan(
     reccomender_timeout=1,
     exposure=30,
     max_runs=1,
-    take_data=rocking_ct,
+    take_data=None,
     num=None,
     rocking_range=2,
 ):
@@ -270,6 +270,8 @@ def snap(Ti, temperature, time):
         it up for dead.
 
     """
+    if take_data is None:
+        take_data=rocking_ct
 
     # unpack the real motors
     x_motor, y_motor = real_motors

startup/03-back_search.py

@@ -72,9 +72,12 @@ def batch_scan(
     rocking_num=3,
     real_motors,
     exposure=20,
-    take_data=stepping_ct,
+    take_data=None,
     transform_pair
 ):
+    if take_data is None:
+        take_data = stepping_ct
+
     # unpack the real motors
     x_motor, y_motor = real_motors
     # make the soft pseudo axis

startup/10-motors.py

@@ -28,7 +28,7 @@
 
 # RPI DIFFRACTOMETER motors ### Change th only after changing in other plans
 th = EpicsMotor('XF:28IDC-ES:1{Dif:1-Ax:Th}Mtr', name='th')
-tth = EpicsMotor('XF:28IDC-ES:1{Dif:1-Ax:2ThI}Mtr', name='tth')
+#tth = EpicsMotor('XF:28IDC-ES:1{Dif:1-Ax:2ThI}Mtr', name='tth')
 diff_x = EpicsMotor('XF:28IDC-ES:1{Dif:1-Ax:X}Mtr', name='diff_x')
 diff_y = EpicsMotor('XF:28IDC-ES:1{Dif:1-Ax:Y}Mtr', name='diff_y')
 diff_tth_i = EpicsMotor('XF:28IDC-ES:1{Dif:1-Ax:2ThI}Mtr', name='diff_tth_i')

startup/1001-remoteplan.py

@@ -162,18 +162,23 @@ def xpd_mscan_flt(sample_list, pos_list, ht_list, scanplan, motor=sample_x, dela
 # -----start temperature scan plans ------------------
 
 def xpd_temp_list(smpl, Temp_list, exp_time, delay=1, dets=[]):
-    '''
-    example
-        xpd_temp_list(1, [300, 350, 400], 5, delay=1)
-        sample 1, at temperature 300, 350 and 400, exposure time 5sec, wait 1 second after each temperature.
+    '''The plan to perform a scan over temperature list.
+
+    Parameters
+    ----------
+
+    smpl: sample index ID in sample list
+    Temp_list: temperature list
+    exp_time : total exposure time for each sample, in seconds
+    delay: sleep time after each temperature changes, for temperature controller to stable
+    dets: list of motors, temperatures controllers, which will be recorded in table.
+
+    Examples
+    --------
 
-        parameters:
-        smpl: sample index ID in sample list
-        Temp_list: temperature list
-        exp_time : total exposure time for each sample, in seconds
-        delay: sleep time after each temperature changes, for temperature controller to stable
-        dets: list of motors, temperatures controllers, which will be recorded in table.
+    >>> xpd_temp_list(1, [300, 350, 400], 5, delay=1)
 
+    sample 1, at temperature 300, 350 and 400, exposure time 5sec, wait 1 second after each temperature.
     '''
     #RE(_configure_area_det(exp_time))
     T_controller = xpd_configuration["temp_controller"]
@@ -193,16 +198,19 @@ def xpd_temp_list(smpl, Temp_list, exp_time, delay=1, dets=[]):
 
 def xpd_temp_ramp(smpl, Tstart, Tstop, Tstep, exp_time, delay = 1, dets=[]):
     '''
-    example:
-        xpd_temp_ramp(1, 300, 400, 10, 5, delay=1)
-        sample 1, from 300K to 400K, 10K steps, exposure time 5sec, wait 1 second after each temperature.
-
-        parameters:
-        smpl: sample index ID in sample list
-        Tstart, Tstop, Tstep: temperature range(Tstart, Tend), step size: Tstep
-        scanplan : scanplan index ID in scanplan list
-        delay: sleep time after each temperature changes, for temperature controller to stable
-        dets: list of motors, temperatures controllers, which will be recorded in table.
+    Parameters
+    ----------
+    smpl: sample index ID in sample list
+    Tstart, Tstop, Tstep: temperature range(Tstart, Tend), step size: Tstep
+    scanplan : scanplan index ID in scanplan list
+    delay: sleep time after each temperature changes, for temperature controller to stable
+    dets: list of motors, temperatures controllers, which will be recorded in table.
+
+    Examples
+    --------
+    >>> xpd_temp_ramp(1, 300, 400, 10, 5, delay=1)
+
+    sample 1, from 300K to 400K, 10K steps, exposure time 5sec, wait 1 second after each temperature.
     '''
     #RE(_configure_area_det(exp_time))
     T_controller = xpd_configuration["temp_controller"]

startup/16-electrometer.py

@@ -26,6 +26,6 @@ def set_primary(self, n, value=None):
             cur.mean_value = Kind.hinted
 
 
-# qem1 = XPDQuadEM("XF:28IDC-BI{IM:04}EM180:", name="qem1")
-# for det in [qem1]:
-#     det.read_attrs = ['current2', 'current2.mean_value','current3', 'current3.mean_value']
+qem1 = XPDQuadEM("XF:28IDC-BI{IM:02}EM180:", name="qem1")
+for det in [qem1]:
+    det.read_attrs = ['current2', 'current2.mean_value','current3', 'current3.mean_value']