WIP: Fixes to work with collection-2020-2.0rc8 conda env

startup/00-startup.py

@@ -6,7 +6,7 @@
 # Set up a Broker.
 # TODO clean this up
 from bluesky_kafka import Publisher
-from databroker import Broker
+from databroker.v0 import Broker
 from databroker.headersource.mongo import MDS
 from databroker.assets.mongo import Registry
 
@@ -254,8 +254,17 @@ def bulk_register_datum_table(self, resource_uid, dkwargs_table, validate=False)
 
 
 mds_db1 = MDS(_mds_config_db1, auth=False)
-db1 = Broker(mds_db1, CompositeRegistry(_fs_config_db1))
+cr1 = CompositeRegistry(_fs_config_db1)
+db1 = Broker(mds_db1, cr1)
 
+# Broker 2
+
+mds_db2 = MDS(_mds_config_db2, auth=False)
+cr2 = CompositeRegistry(_fs_config_db2)
+db2 = Broker(mds_db2, cr2)
+
+
+# wrapper for two databases
 class CompositeBroker(Broker):
     """wrapper for two databases"""
 
@@ -521,7 +530,15 @@ def _epicssignal_get(self, *, as_string=None, connection_timeout=1.0, **kwargs):
     if as_string is None:
         as_string = self._string
 
-    with self._lock:
+    ###########################################
+    # Usedf only for old ophyd 1.3.3 and older.
+    from distutils.version import LooseVersion
+    import ophyd
+    if ophyd.__version__ < LooseVersion('1.4'):
+        self._metadata_lock = self._lock
+    ###########################################
+
+    with self._metadata_lock:
         if not self._read_pv.connected:
             if not self._read_pv.wait_for_connection(connection_timeout):
                 raise TimeoutError('Failed to connect to %s' %
@@ -560,7 +577,7 @@ def _epicssignal_get(self, *, as_string=None, connection_timeout=1.0, **kwargs):
 from ophyd import EpicsSignalRO
 from ophyd.areadetector import EpicsSignalWithRBV
 
+
 EpicsSignal.get = _epicssignal_get
 EpicsSignalRO.get = _epicssignal_get
 EpicsSignalWithRBV.get = _epicssignal_get
-

startup/13-mll.py

@@ -32,9 +32,9 @@ class HxnMLLSample(NamedDevice):
     sz = Cpt(EpicsMotor, 'XF:03IDC-ES{ANC350:3-Ax:2}Mtr', doc='coarse z')
 
     kill = Cpt(EpicsSignal, 'XF:03IDC-ES{Ppmac:1}KillAll-Cmd.PROC',
-               doc='kill all piezos')
+               doc='kill all piezos', kind='omitted')
     zero = Cpt(EpicsSignal, 'XF:03IDC-ES{Ppmac:1}KillZero-Cmd.PROC',
-               doc='zero all piezos')
+               doc='zero all piezos', kind='omitted')
     # sz1 = Cpt(EpicsMotor, 'XF:03IDC-ES{ANC350:3-Ax:3}Mtr', doc='coarse z1')
     # sz1 was replaced with vz when controller 2 died
 
@@ -74,7 +74,7 @@ class HxnMLLDiffractionSample(NamedDevice):
     dssz = Cpt(EpicsMotor, 'XF:03IDC-ES{Ppmac:1-dssz}Mtr', doc='fine_z')
 
     kill = Cpt(EpicsSignal, 'XF:03IDC-ES{Ppmac:1-Diff}Kill-Cmd.PROC',
-               doc='kill all piezos')
+               doc='kill all piezos', kind='omitted')
 
 
 smlld = HxnMLLDiffractionSample('', name='smlld')

startup/15-zp.py

@@ -58,8 +58,8 @@ class HxnZPSample(NamedDevice):
     smarthy = Cpt(SmarpodRotationAxis, axis=3, doc='smarpod theta around y')
     smarthz = Cpt(SmarpodRotationAxis, axis=1, doc='smarpod theta around z')
 
-    kill = Cpt(EpicsSignal, 'XF:03IDC-ES{Ppmac:1-ZP}Kill-Cmd.PROC')
-    zero = Cpt(EpicsSignal, 'XF:03IDC-ES{Ppmac:1-ZP}Zero-Cmd.PROC')
+    kill = Cpt(EpicsSignal, 'XF:03IDC-ES{Ppmac:1-ZP}Kill-Cmd.PROC', kind='omitted')
+    zero = Cpt(EpicsSignal, 'XF:03IDC-ES{Ppmac:1-ZP}Zero-Cmd.PROC', kind='omitted')
     mode = Cpt(EpicsSignal, 'XF:03IDC-ES{Ppmac:1-ZP}Mode-I')
 
 

startup/21-xspress3.py

@@ -1,7 +1,7 @@
 from ophyd.device import (Component as Cpt)
 
-from hxntools.detectors.xspress3 import (Xspress3FileStore,
-                                         Xspress3Channel)
+from nslsii.detectors.xspress3 import (Xspress3FileStore,
+                                       Xspress3Channel)
 from hxntools.detectors.hxn_xspress3 import HxnXspress3DetectorBase
 import threading
 from ophyd import DeviceStatus
@@ -139,7 +139,12 @@ def unstage(self, *args, **kwargs):
 
 
 # Create directories on the xspress3 server, otherwise scans can fail:
-xspress3.make_directories.put(True)
+#====================================================================
+# Note from DAMA: commented it out during the 2020-2 deployment visit.
+# The corresponding code is in
+# https://github.com/NSLS-II/nslsii/blob/master/nslsii/detectors/xspress3.py
+#====================================================================
+# xspress3.make_directories.put(True)
 
 
 elem_K_list = np.array(['Na','Mg','Al','Si','P','S','Cl','Ar','K','Ca','Sc','Ti','V','Cr','Mn','Fe','Co','Ni','Cu','Zn','Ga','Ge','As','Se','Br','Kr','Rb','Sr','Y','Zr','Nb','Mo','Tc','Ru','Rh','Pd','Ag','Cd','In','Sn','Sb','Te','I','Xe','Cs','Ba','La','Hf','Ta','W','Re','Os','Ir','Pt','Au','Hg','Tl','Pb','Bi','Po','At','Rn','Fr','Ra','Ac','Ce','Pr','Nd','Pm','Sm','Eu','Gd','Tb','Dy','Ho','Er','Tm','Yb','Lu','Th','Pa','U','Np','Pu','Am','Cm','Bk','Cf'])

startup/70-users_plans.py

@@ -111,7 +111,12 @@ def mll_z_fly2d(z_start, z_end, z_num, mot1, start1, end1, num1, mot2, start2, e
     yield from bps.mov(smlld.sbz, init_sz)
     save_page()
 
+
 def zp_z_2dscan(z_start, z_end, z_num, mot1, start1, end1, num1, mot2, start2, end2, num2, acq_time, elem='Co'):
+    """This function hasn't been used for a while.
+
+    TODO: convert to use 'yield from ...'.
+    """
     z_step = (z_end - z_start)/z_num
     init_sz = zps.zpsz.position
     movr(zps.zpsz, z_start/1000)
@@ -122,6 +127,7 @@ def zp_z_2dscan(z_start, z_end, z_num, mot1, start1, end1, num1, mot2, start2, e
         movr(zps.zpsz, z_step/1000)
     mov(zps.zpsz, init_sz)
 
+
 def go_det(det):
 
     if det == 'merlin':
@@ -242,7 +248,7 @@ def mll_mosaic_scan(x_start, x_end, x_num, x_block, y_start, y_end, y_num, y_blo
     #start mosaic scan
     for i in range(y_block):
         for j in range(x_block):
-            smll_sync_piezos()
+            yield from smll_sync_piezos()
             RE(fly2d(smll.ssx, x_start, x_end, x_num, smll.ssy, y_start, y_end, y_num, acq_time, return_speed=40))
             dx = x_block_size
             movr_sx(dx)
@@ -2154,11 +2160,13 @@ def mono_m1(pf_start, pf_end, pf_num, b_start, b_end, b_num):
 
 
 def smll_kill_piezos():
-    smll.kill.put(1)
+    # smll.kill.put(1)
+    yield from bps.mv(smll.kill, 1)
     yield from bps.sleep(5)
 
 def smll_zero_piezos():
-    smll.zero.put(1)
+    # smll.zero.put(1)
+    yield from bps.mv(smll.zero, 1)
     yield from bps.sleep(3)
 
 def smll_sync_piezos():
@@ -2177,7 +2185,7 @@ def movr_sx(dist):
     print('Current ssy = %.3f' % c_ssy)
     print('Current ssz = %.3f' % c_ssz)
 
-    smll_kill_piezos()
+    yield from smll_kill_piezos()
 
     t_ssx = c_ssx + dist
 
@@ -2186,20 +2194,20 @@ def movr_sx(dist):
 
     dx, dz = sample_to_lab(dxp, dzp, alpha)
 
-    movr(sx, dx)
-    movr(sz, dz)
+    yield from bps.movr(sx, dx)
+    yield from bps.movr(sz, dz)
 
     dy = c_ssy -smll.ssy.position
 
-    movr(sy, dy)
+    yield from bps.movr(sy, dy)
 
-    sleep(5)
+    yield from bps.sleep(5)
 
-    smll_sync_piezos()
+    yield from smll_sync_piezos()
 
-    mov(ssx, t_ssx)
-    mov(ssy, c_ssy)
-    mov(ssz, c_ssz)
+    yield from bps.mov(ssx, t_ssx)
+    yield from bps.mov(ssy, c_ssy)
+    yield from bps.mov(ssz, c_ssz)
 
     print('Post-move x = %.3f' % smll.ssx.position)
     print('Post-move y = %.3f' % smll.ssy.position)
@@ -2215,7 +2223,7 @@ def mov_sx(t_pos):
     print('Current ssy = %.3f' % c_ssy)
     print('Current ssz = %.3f' % c_ssz)
 
-    smll_kill_piezos()
+    yield from smll_kill_piezos()
 
     t_ssx = t_pos
 
@@ -2224,19 +2232,19 @@ def mov_sx(t_pos):
 
     dx, dz = sample_to_lab(dxp, dzp, alpha)
 
-    movr(sx, dx)
-    movr(sz, dz)
+    yield from bps.movr(sx, dx)
+    yield from bps.movr(sz, dz)
 
     dy = c_ssy - smll.ssy.position
 
-    movr(sy, dy)
+    yield from bps.movr(sy, dy)
 
-    sleep(5)
+    yield from bps.sleep(5)
 
-    smll_sync_piezos()
-    mov(ssx, t_ssx)
-    mov(ssy, c_ssy)
-    mov(ssz, c_ssz)
+    yield from smll_sync_piezos()
+    yield from bps.mov(ssx, t_ssx)
+    yield from bps.mov(ssy, c_ssy)
+    yield from bps.mov(ssz, c_ssz)
 
     print('Post-move x = %.3f' % (smll.ssx.position))
     print('Post-move y = %.3f' % (smll.ssy.position))
@@ -2253,26 +2261,26 @@ def movr_sy(dist):
     print('Current ssy = %.3f' % c_ssy)
     print('Current ssz = %.3f' % c_ssz)
 
-    smll_kill_piezos()
+    yield from smll_kill_piezos()
 
     t_ssy = c_ssy + dist
     dy = t_ssy - smll.ssy.position
-    movr(sy, dy)
+    yield from bps.movr(sy, dy)
 
     dxp = c_ssx - smll.ssx.position
     dzp = c_ssz - smll.ssz.position
 
     dx, dz = sample_to_lab(dxp, dzp, alpha)
 
-    movr(sx, dx)
-    movr(sz, dz)
+    yield from bps.movr(sx, dx)
+    yield from bps.movr(sz, dz)
 
-    sleep(5)
+    yield from bps.sleep(5)
 
-    smll_sync_piezos()
-    mov(ssx, c_ssx)
-    mov(ssy, t_ssy)
-    mov(ssz, c_ssz)
+    yield from smll_sync_piezos()
+    yield from bps.mov(ssy, t_ssy)
+    yield from bps.mov(ssz, c_ssz)
+    yield from bps.mov(ssx, c_ssx)
 
     print('Post-move x = %.3f' % smll.ssx.position)
     print('Post-move y = %.3f' % smll.ssy.position)
@@ -2288,26 +2296,26 @@ def mov_sy(t_pos):
     print('Current ssy = %.3f' % c_ssy)
     print('Current ssz = %.3f' % c_ssz)
 
-    smll_kill_piezos()
+    yield from smll_kill_piezos()
 
     t_ssy = t_pos
     dy = t_ssy - smll.ssy.position
-    movr(sy, dy)
+    yield from bps.movr(sy, dy)
 
     dxp = c_ssx - smll.ssx.position
     dzp = c_ssz - smll.ssz.position
 
     dx, dz = sample_to_lab(dxp, dzp, alpha)
 
-    movr(sbx, dx)
-    movr(sbz, dz)
+    yield from bps.movr(sbx, dx)
+    yield from bps.movr(sbz, dz)
 
-    sleep(5)
+    yield from bps.sleep(5)
 
-    smll_sync_piezos()
-    mov(ssx, c_ssx)
-    mov(ssy, t_ssy)
-    mov(ssz, c_ssz)
+    yield from smll_sync_piezos()
+    yield from bps.mov(ssx, c_ssx)
+    yield from bps.mov(ssy, t_ssy)
+    yield from bps.mov(ssz, c_ssz)
 
     print('Post-move x = %.3f' % (smll.ssx.position))
     print('Post-move y = %.3f' % (smll.ssy.position))
@@ -2324,20 +2332,20 @@ def movr_sz(dist):
     print('Current ssy = %.3f' % c_ssy)
     print('Current ssz = %.3f' % c_ssz)
 
-    smll_kill_piezos()
+    yield from smll_kill_piezos()
 
     t_ssz = c_ssz + dist*np.cos(alpha)
     dz = t_ssz - smll.dssz.position
     dy = c_ssy - smll.dssy.position
 
-    movr(sbz, dz)
-    movr(dsy, dy/1000.0)
+    yield from bps.movr(sbz, dz)
+    yield from bps.movr(dsy, dy/1000.0)
 
-    sleep(5)
+    yield from bps.sleep(5)
 
-    smll_sync_piezos()
-    mov(dssy, c_ssy)
-    mov(dssz, t_ssz)
+    yield from smll_sync_piezos()
+    yield from bps.mov(dssy, c_ssy)
+    yield from bps.mov(dssz, t_ssz)
 
     print('post-move x = %.3f' % smll.dssx.position)
     print('Post-move y = %.3f' % smll.dssy.position)
@@ -2354,20 +2362,20 @@ def mov_sz(t_pos):
     print('Current ssy = %.3f' % c_ssy)
     print('Current ssz = %.3f' % c_ssz)
 
-    smll_kill_piezos()
+    yield from smll_kill_piezos()
 
     t_ssz = t_pos
     dz = (t_ssz - smll.ssz.position)/np.cos(alpha)
     dy = c_ssy - smll.ssy.position
 
-    movr(sz, dz)
-    movr(sy, dy)
+    yield from bps.movr(sz, dz)
+    yield from bps.movr(sy, dy)
 
-    sleep(5)
+    yield from bps.sleep(5)
 
-    smll_sync_piezos()
-    mov(ssy, c_ssy)
-    mov(ssz, t_ssz)
+    yield from smll_sync_piezos()
+    yield from bps.mov(ssy, c_ssy)
+    yield from bps.mov(ssz, t_ssz)
 
     print('Post-move x = %.3f' % smll.ssx.position)
     print('Post-move y = %.3f' % smll.ssy.position)