Merge pull request #11 from NSLS-II-SST/Issue10-bug-long-pause-after-…

…completion-of-each-scan

Issue10 bug long pause after completion of each scan

rsoxs/Functions/alignment.py

@@ -154,8 +154,7 @@ def duplicate_sample(samp_num,name_suffix):
      newsamp['sample_name']+=f'_{name_suffix}'
      newsamp['sample_id']+=f'_{name_suffix}'
      rsoxs_config['bar'].append(newsamp)
-     #rsoxs_config.write()
-
+
 
 def move_to_location(locs=get_sample_location()):
     for item in locs:
@@ -466,7 +465,6 @@ def samxscan():
 
 
 
-#@finalize_decorator(#rsoxs_config.write_plan)
 def spiralsearch(
     diameter=0.6,
     stepsize=0.2,
@@ -603,76 +601,12 @@ def spiralsearch(
 
 
 
-# Bar imaging utilities:
-
-# usage:
-
-# load bar onto imager, load bar file, and do image_bar(bar,path='path_to_image')
-
-# this will automatically go into image tagging, but to pick up where you left off, do
-
-# locate_samples_from_image(bar,'path_to_image')
-
-# Find alignment fiducials in chamber
-#
-# Helpful Functions goto_af1() goto_af2() and find_af1x(),find_af1y(),find_af2x(),find_af2y()
-#
-# and then remap the bar using
-# correct_bar(bar,af1x,af1y,af2x,af2y)
-
-
-# def find_fiducials(f2=[7.5, 3.5, -2.5, 1.1]):
-#     thoffset = 0
-#     angles = [-90 + thoffset, 0 + thoffset, 90 + thoffset, 180 + thoffset]
-#     xrange = 3.5
-#     xnum = 36
-#     startxss = [f2, [4.2, 3.5, 1, 1.1]]
-#     yield from bps.mv(Shutter_enable, 0)
-#     yield from bps.mv(Shutter_control, 0)
-#     yield from load_configuration("SAXSNEXAFS")
-#     Beamstop_SAXS.kind = "hinted"
-#     # yield from bps.mv(DiodeRange, 7)
-#     # bec.enable_plots() # TODO: need to turn on plotting temporarilly for this function
-#     startys = [3, -187.0]  # af2 first because it is a safer location
-#     maxlocs = []
-#     for startxs, starty in zip(startxss, startys):
-#         yield from bps.mv(sam_Y, starty, sam_X, startxs[1], sam_Th, 0, sam_Z, 0)
-#         yield from bps.mv(Shutter_control, 1)
-#         yield from bp.rel_scan([Beamstop_SAXS], sam_Y, -1, 0.5, 16) # TODO: replace with flymax
-#         yield from bps.mv(Shutter_control, 0)
-#         #maxlocs.append(bec.peaks.max["SAXS Beamstop"][0]) #TODO: need to find maxiumum another way
-#         # yield from bps.mv(sam_Y, bec.peaks.max["SAXS Beamstop"][0])
-#         for startx, angle in zip(startxs, angles):
-#             yield from bps.mv(sam_X, startx, sam_Th, angle)
-#             yield from bps.mv(Shutter_control, 1)
-#             yield from bp.scan( # TODO: replace with flymax
-#                 [Beamstop_SAXS],
-#                 sam_X,
-#                 startx - 0.5 * xrange,
-#                 startx + 0.5 * xrange,
-#                 xnum,
-#             )
-#             yield from bps.mv(Shutter_control, 0)
-#             yield from bps.sleep(3)
-#             # maxlocs.append(bec.peaks.max["SAXS Beamstop"][0]) #TODO: need to find maxiumum another way
-#     print(maxlocs)  # [af2y,af2xm90,af2x0,af2x90,af2x180,af1y,af1xm90,af1x0,af1x90,af1x180]
-#     accept = input(f"Do you want to apply this correction (y,n)?")
-#     if accept in ['y','Y','yes']:
-#         back = False
-#         #rsoxs_config.read()
-#         for samp in rsoxs_config['bar']:
-#             if samp['front'] ==False:
-#                 back = True
-#         correct_bar(maxlocs,include_back=back)
-#     # bec.disable_plots()
-
 
 def rotate_now(theta, force=False):
     if theta is not None:
         samp = get_sample_dict()
         samp["angle"] = theta
         rotate_sample(samp, force)
-        #rsoxs_config.write()
         yield from load_sample(samp)
 
 
@@ -686,7 +620,6 @@ def jog_samp_zoff(id_or_num,jog_val,write_default=True,move=True):
             samp['bar_loc']['zoff'] += jog_val
             if write_default:
                 rotate_sample(samp) # this will write the new rotated positions into the position (without moving anything)
-            #rsoxs_config.write() # this saves the zoff and the new rotated position to the persistent sample list
             if(move):
                 RE(load_samp(id_or_num))
         else:

rsoxs/Functions/alignment_local.py

@@ -23,7 +23,6 @@
 
 def sample_by_value_match(key, string, bar=None):
     if bar == None:
-        ##rsoxs_config.read()
         bar = rsoxs_config['bar']
     results = [d for (index, d) in enumerate(bar) if d[key].find(string) >= 0]
     if len(results) == 1:
@@ -41,7 +40,6 @@ def sample_by_name( name, bar=None):
 
 def list_samples(bar=None):
     if bar == None:
-        ##rsoxs_config.read()
         bar = rsoxs_config['bar']
     text = "  i  Sample Name"
     for index, sample in enumerate(bar):
@@ -123,12 +121,10 @@ def sanatize_angle(samp, force=False):
         samp["bar_loc"]["th"] = 195.0
     if samp["bar_loc"]["th"] <= -155:
         samp["bar_loc"]["th"] = -155.0
-    ##rsoxs_config.write()
-
+
 
 
 def samp_dict_from_id_or_num(num_or_id):
-    ##rsoxs_config.read()
     if isinstance(num_or_id,str):
         sam_dict = [d for (index, d) in enumerate(rsoxs_config['bar']) if d['sample_id'].find(num_or_id) >= 0]
         if len(sam_dict) > 0:
@@ -146,7 +142,6 @@ def samp_dict_from_id_or_num(num_or_id):
 
 def offset_bar(xoff, yoff, zoff, thoff, bar=None):
     if bar == None:
-        ##rsoxs_config.read()
         bar = rsoxs_config['bar']
     for samp in bar:
         for mot in samp["location"]:
@@ -160,8 +155,7 @@ def offset_bar(xoff, yoff, zoff, thoff, bar=None):
                 mot["position"] += thoff
         sample_recenter_sample(samp)
 
-    ##rsoxs_config.write()
-
+
 def default_sample(name,proposal_id,institution='NIST',grazing=False,front=True):
     return {
         "institution": institution,
@@ -206,7 +200,6 @@ def stop(self, doc):
 import bluesky.preprocessors as bpp
 def image_bar( path=None, front=True, bar=None):
     if bar == None:
-        ##rsoxs_config.read()
         bar = rsoxs_config['bar']
     global loc_Q
     loc_Q = queue.Queue(1)
@@ -226,7 +219,6 @@ def image_bar( path=None, front=True, bar=None):
 
 def locate_samples_from_image( impath, front=True, bar=None):
     if bar == None:
-        ##rsoxs_config.read()
         bar = rsoxs_config['bar']
     # if the image was just taken itself, before a bar was compiled, then this can be run to just load that image
     # and then interactively place the elements of bar
@@ -249,7 +241,6 @@ def update_bar(loc_Q, front, inbar=None):
     updated with whether we are pointing at the front or the back of the bar
     """
     if inbar == None:
-        ##rsoxs_config.read()
         inbar = rsoxs_config['bar']
     from threading import Thread
 
@@ -277,6 +268,7 @@ def worker():
             gbar.insert(0, AF1)
             gbar.insert(1, AF2)
             gbar.insert(2, diode)
+            ## Appending fiducials/diodes to the end does not always reliably add image position into rsoxs_config (Issue #2, also encountered during 20241006 beam time), so it is simpler to add these at the beginnng.
 
 
 
@@ -300,7 +292,6 @@ def worker():
             AF2 = default_sample("AF2_back",proposal_id=gbar[0]['proposal_id'],institution=gbar[0]['institution'],front=False)
             gbar.insert(1, AF1)  # inserts in the second position
             gbar.insert(-1, AF2)  # inserts in the second to last position
-        ##rsoxs_config.write()
         while True:
             #        for sample in bar:
             sample = gbar[samplenum]
@@ -338,8 +329,6 @@ def worker():
                     sample["bar_loc"]["th0"] = float(180)
                 annotateImage(sample_image_axes, item, sample["sample_name"])
                 # advance sample and loop
-                #rsoxs_config['bar'] = gbar
-                #rsoxs_config.write()
                 samplenum += 1
             elif item == "escape":
                 print("aborting")
@@ -352,8 +341,6 @@ def worker():
                 samplenum -= 1
             if samplenum >= len(gbar):
                 print("done")
-                #rsoxs_config['bar'] = gbar
-                #rsoxs_config.write()
                 break
 
     t = Thread(target=worker)
@@ -448,7 +435,6 @@ def plot_key_press(event):
 def offset_bar( xoff, yoff, zoff, thoff, bar = None):
 
     if bar == None:
-        #rsoxs_config.read()
         bar = rsoxs_config['bar']
     for samp in bar:
         for mot in samp["location"]:
@@ -460,8 +446,7 @@ def offset_bar( xoff, yoff, zoff, thoff, bar = None):
                 mot["position"] += zoff
             if mot["motor"] == "th":
                 mot["position"] += thoff
-    #rsoxs_config.write()
-
+
 
 def correct_bar(fiduciallist, include_back, training_wheels=True, bar = None):
     """
@@ -475,7 +460,6 @@ def correct_bar(fiduciallist, include_back, training_wheels=True, bar = None):
     fiducial list is the list output by find_fiducials()
     """
     if bar == None:
-        #rsoxs_config.read()
         bar = deepcopy(rsoxs_config['bar'])
     af2y = fiduciallist[0]
     af2xm90 = fiduciallist[1]
@@ -606,8 +590,7 @@ def correct_bar(fiduciallist, include_back, training_wheels=True, bar = None):
         rotate_sample(samp)  # this will take the positions found above and the desired incident angle and
         # rotate the location of the sample accordingly
     rsoxs_config['bar'] = bar #event_model.sanitize_doc() #rsoxs_config['bar'] = orjson.dumps(bar)
-    #rsoxs_config.write()
-
+
 def zoffset(af1zoff, af2zoff, y, front=True, height=0.25, af1y=-186.3, af2y=4):
     """
     Using the z offset of the fiducial positions from the center of rotation,
@@ -688,7 +671,6 @@ def rotate_sample(samp, force=False):
             motor["position"] = theta_new
         if motor["motor"] == "y":
             motor["position"] = y0
-    # #rsoxs_config.write()
     # in future, updating y (if the rotation axis is not perfectly along y
     # and z (to keep the sample-detector distance constant) as needed would be good as well
     # newz = rotatedz(newx, th, zoff, af1xoff)
@@ -715,13 +697,11 @@ def sample_recenter_sample(samp):
     samp["bar_loc"]["x0"] = newx0
     samp["bar_loc"]["y0"] = newy  # y and y0 are the same, so we can just copy this
     samp["angle"] = newangle
-    # #rsoxs_config.write()
-
+
 
 
 def read_positions(bar=None):
     if bar == None:
-        #rsoxs_config.read()
         bar = rsoxs_config['bar']
     # for when the positions are altered by hand in the excel sheet, (i.e. after spiral scans)
     # this reads those positions and sets the default positions (x0 and y0) to match
@@ -731,7 +711,6 @@ def read_positions(bar=None):
 
 def resolve_spirals(bar=None):
     if bar == None:
-        #rsoxs_config.read()
         bar = rsoxs_config['bar']
     for samp in bar:
         if len(str(samp['bar_loc'].get('spiral_started',''))) > 0 and len(samp['bar_loc'].get('spiral_done','')) == 0:
@@ -757,7 +736,6 @@ def resolve_spirals(bar=None):
                             newsamp['sample_name']+=f'_{i}'
                             newsamp['sample_id']+=f'_{i}'
                             rsoxs_config['bar'].append(newsamp)
-                            #rsoxs_config.write()
                     else:
                         accept = input(f"image {im} at ({xs[im],ys[im]}) is correct (y,n)?")
                         if accept in ['y','Y','yes']:
@@ -767,14 +745,9 @@ def resolve_spirals(bar=None):
                                                 {'motor':'z','position':z}]
                             samp['bar_loc']['spiral_done']={"scan":h['start']['uid'],
                                                 'best_num':im}
-                            #rsoxs_config.write()
-
+
 
 
-#def clear_bar():
-#    accept = input(f"Are you sure you want to clear the presistant bar? (y,n)?")
-#    if accept in ['y','Y','yes']:
-        #rsoxs_config.clear_bar()
 
 def acq(id_or_num,acq_num=0):
     samp = samp_dict_from_id_or_num(id_or_num)

rsoxs/Functions/energyscancore.py

@@ -103,7 +103,6 @@ def cleanup():
     yield from bps.mv(Shutter_control, 0)
 
 
-#@finalize_decorator(##rsoxs_config.write_plan)
 def NEXAFS_step_scan_core(
     dets=None,    # a list of detectors to run at each step - must be scalar type detectors wtih set_exp functions
     energy=None,  # optional energy object to set energy commands to - sets to energy by default, but allows for simulation
@@ -342,7 +341,6 @@ def NEXAFS_step_scan_core(
 
 
 
-#@finalize_decorator(#rsoxs_config.write_plan)
 def new_en_scan_core(
     dets=None,    # a list of detectors to run at each step - get from md by default
     energy=None,  # optional energy object to set energy commands to - sets to energy by default, but allows for simulation
@@ -668,7 +666,6 @@ def final():
 
 
 
-#@finalize_decorator(#rsoxs_config.write_plan)
 def NEXAFS_old_fly_scan_core(
     scan_params,
     openshutter=True,
@@ -795,7 +792,6 @@ def NEXAFS_old_fly_scan_core(
 
 
 
-#@finalize_decorator(#rsoxs_config.write_plan)
 def NEXAFS_fly_scan_core(
     scan_params,
     openshutter=True,

rsoxs/Functions/fly_alignment.py

@@ -32,6 +32,7 @@
     BeamStopS)
 from .alignment import load_configuration, rsoxs_config,correct_bar
 
+## TODO: Not sure why this is redefined identically as the function in flystream_wrapper.py, but end goal is to move to Jamie's function.
 def flystream_during_wrapper(plan, flyers, stream=False):
     """
     Kickoff and collect "flyer" (asynchronously collect) objects during runs.
@@ -334,8 +335,6 @@ def find_optimum_motor_pos(db, uid, motor_name='RSoXS Sample Up-Down', signal_na
 
 
 
-#@finalize_decorator(#rsoxs_config.write_plan)
-#RE(fly_find_fiducials(f2=[3.5,-1,-2.4,1.5],f1=[2.0,-0.9,-1.5,0.8],y1=-187.5,y2=2)) # new encoders
 #def fly_find_fiducials(f2=[7.5,5,-2.5,0],f1=[4.6, 4, 1, 1.1],y2=2.5,y1=-188):
 def fly_find_fiducials(f2=[3.5,-1,-2.4,1.5],f1=[2.0,-0.9,-1.5,0.8],y1=-187.5,y2=2):
     thoffset = 0
@@ -380,7 +379,6 @@ def fly_find_fiducials(f2=[3.5,-1,-2.4,1.5],f1=[2.0,-0.9,-1.5,0.8],y1=-187.5,y2=
     accept = input(f"Do you want to apply this correction (y,n)?")
     if accept in ['y','Y','yes']:
         back = False
-        #rsoxs_config.read()
         for samp in rsoxs_config['bar']:
             if samp['front'] ==False:
                 back = True

rsoxs/Functions/flystream_wrapper.py

@@ -8,6 +8,7 @@
 from bluesky.preprocessors import plan_mutator
 
 
+## TODO: This is intended to be centralized in Jamie Titus's nbs-bl package.  Switch the imports after moving to all the new packages.
 def flystream_during_wrapper(plan, flyers, stream=False):
     """
     Kickoff and collect "flyer" (asynchronously collect) objects during runs.

rsoxs/Functions/rsoxs_plans.py

@@ -34,7 +34,6 @@
 motors = {"temp_ramp_rate": tem_tempstage.ramp_rate}
 
 
-#@finalize_decorator(#rsoxs_config.write_plan)
 def run_bar(
     bar=None,
     sort_by=["apriority"],
@@ -72,7 +71,6 @@ def run_bar(
         _description_
     """
     if bar == None:
-        #rsoxs_config.read()
         bar = rsoxs_config['bar']
     if dry_run:
         verbose = True
@@ -120,7 +118,6 @@ def run_bar(
         message += f'total time {time_sec(actual_total_time)}, expected {time_sec(queue_step["time_before"]+queue_step["acq_time"])}\n'
         message += f'expected time remaining {time_sec(queue_step["time_after"])} plus overhead\n'
 
-    #rsoxs_config.write() # bar may have changed - added annotations etc
     message = message[:message.rfind('expected')]
     message += f"End of Queue"
     rsoxs_bot.send_message(message)

rsoxs/Functions/spreadsheets.py

@@ -7,7 +7,6 @@ def load_sheet(path):
     newbar = load_samplesxlsx(path)
     if isinstance(newbar, list):
         rsoxs_config['bar'] = newbar
-        ##rsoxs_config.write()
         print(f'replaced persistent bar with bar loaded from {path}')
         return