Defaults BLISS scans¶
BLISS step-by-step scan functions¶
BLISS provides functions to perform step-by-step scans. The acquisition
chain for those scans is built using the DefaultChain class.
Parameters (common to all scans)¶
Counters parameters¶
counter_args (counter-providing objects): each parameter provides
counters to be integrated in the scan. if no counter parameters are
provided, use the active measurement group.
Optional parameters¶
Common keyword arguments that can be used in all scans:
name (str): scan name in data nodes tree and directories [default: ‘scan’]title (str): scan title [default: ‘a2scan… ‘] save (bool): save scan data to file [default: True]save_images (bool or None): save image files [default: None, means it follows the save argument]sleep_time (float): sleep time between 2 points [default: None]run (bool): ifTrue(default), run the scan.Falsemeans to just create scan object and acquisition chain.return_scan (bool): True by default ???
Scan example¶
ascan(<mot>, <start>, <stop>, <intervals>, <acq_time>, <title>) ascan( sy, 1, 2, 4, 0.5, title="Jadarite_LiNaSiB3O7(OH)")
This command performs a scan of five 500ms-counts of current measurement group
counters at <sy> motor positions: 1, 1.25, 1.5, 1.75 and 2.
ascan dscan¶
ascan(motor, start, stop, intervals, count_time, *counter_args, **kwargs)
Absolute scan of one motor, as specified by <motor>. The motor starts at
the position given by <start> and ends at the position given by <stop>.
The step size is: (<stop>-<start>)/<intervals>
The number of points will be <intervals> + 1.
Count time is given by <count_time> (seconds).
At the end of the scan, the motor will stay at stopping position
(<stop> position in case of success).
Idem for dscan but using relative positions:
dscan(motor, rel_start, rel_stop, intervals, count_time, *counter_args, **kwargs)
Scans one motor, as specified by <motor>. If the motor is at position X
before the scan begins, the scan will run from X+rel_start to X+rel_stop.
The step size is: (<rel_stop>-<rel_start>)/<intervals>. The number of points
will be <intervals>+1. Count time is given by <count_time> (in seconds).
At the end of a dscan (even in case of error or scan abortion, on a ctrl-c
for example) the motor will return to its initial position.
a2scan¶
a2scan( motor1, start1, stop1, motor2, start2, stop2, intervals, count_time, *counter_args, **kwargs)
Absolute 2 motors scan.
Scans two motors, as specified by <motor1> and <motor2>. The
motors start at the positions given by <start1> and <start2> and
end at the positions given by <stop1> and <stop2>. The step size
for each motor is given by (<stopN>-<startN>)/<intervals>. The
number of points will be <intervals>+1. Count time is given by
<count_time> (in seconds).
d2scan¶
Relative 2 motors scan.
Scans two motors, as specified by <motor1> and <motor2>. Each motor moves
the same number of points. If a motor is at position X
before the scan begins, the scan will run from X+<start> to X+<end>.
The step size of a motor is (<stopN>-<startN>)/<intervals>. The number
of points will be <intervals>+1. Count time is given by <count_time>
(in seconds).
At the end of the scan (even in case of error) the motors will return to their initial positions.
a3scan a4scan a5scan¶
Similary to a2scan, aNscan functions are provided fo N in {3,4,5}.
example for 9 intervals:
DEMO [2]: a5scan(m1,1,2, m2,3,4, m3,5,6, m4,7,8, m5,8,9, 9, 0.1) Scan 2 Fri Oct 26 16:07:08 2018 /tmp/scans/demo/ a5scan m1 1 2 m2 3 4 m3 5 6 m4 7 8 m5 8 9 10 0.1 # dt[s] m1 m2 m3 m4 m5 simct1 0 0 1 3 5 7 8 0.038648 1 0.432173 1.11 3.11 5.11 7.11 8.11 0.022345 2 0.850866 1.22 3.22 5.22 7.22 8.22 0.119345 3 1.25996 1.33 3.33 5.33 7.33 8.33 1.06995 4 1.74734 1.44 3.44 5.44 7.44 8.44 3.45354 5 2.16594 1.56 3.56 5.56 7.56 8.56 3.47793 6 2.57817 1.67 3.67 5.67 7.67 8.67 1.01595 7 2.98574 1.78 3.78 5.78 7.78 8.78 0.128783 8 3.4303 1.89 3.89 5.89 7.89 8.89 0.073870 9 3.84454 2 4 6 8 9 0.019919 Took 0:00:05.226827 Out [2]: Scan(name=a5scan_2, run_number=2, path=/tmp/scans/demo/)
aNscan dNscan¶
In case a scan for more than 5 motors is needed, anscan and dnscan functions
can be used with a slightly different list of parameters:
anscan(<counting_time>, <intervals>, (<mot>, <start>, <stop>)*)
(<mot>, <start>, <stop>) can be repeated as much as needed.
idem for dnscan with relative start and stop positions:
anscan(<counting_time>, <intervals>, (<mot>, <rel_start>, <rel_stop>)*)
amesh¶
amesh( motor1, start1, stop1, intervals1, motor2, start2, stop2, intervals2, count_time, *counter_args, **kwargs)
Mesh scan.
The amesh scan traces out a grid using motor <motor1> and motor
<motor2>. The first motor scans from position <start1> to <end1> using the
specified number of intervals + 1 as points number. The second motor similarly
scans from <start2> to <end2>. Each point is counted for for <count_time>
seconds (or monitor counts).
The scan of <motor1> is done at each point scanned by <motor2>. That is, the
first motor scan is nested within the second motor scan. (<motor1> is the
“fast” axis, <motor2> the “slow” axis)
Special parameter:
backnforth: if True, do back and forth on the first motor.
dmesh¶
Relative amesh.
lineup¶
Relative scan.
lineup(motor, start, stop, intervals, count_time, *counter_args, **kwargs)
lineup performs a dscan and then goes to the maximum value of first counter.
timescan¶
Scan without movement.
timescan(count_time, *counter_args, **kwargs)
Performs <npoints> counts for <count_time>. If <npoints> is 0, it
counts forever.
Special parameters:
<output_mode> (str): valid are ‘tail’ (append each line to output) or ‘monitor’ (refresh output in single line) [default: ‘tail’]<npoints> (int): number of points [default: 0, meaning infinite number of points]
loopscan¶
loopscan(npoints, count_time, *counter_args, **kwargs)
Similar to timescan but <npoints> is mandatory.
ct¶
ct(count_time, *counter_args, **kwargs)
Counts for a specified time.
pointscan¶
Performs a scan over many positions given as a list.
pointscan(motor, positions_list, count_time, *counter_args, **kwargs)
Scans one motor, as specified by <motor>. The motor starts at the
position given by the first value in <positions_list> and ends at the
position given by last value <positions_list>. Count time is given by
<count_time> (in seconds).
Special parameter:
<positions_list>: List of positions to scan for<motor>motor.
lookupscan¶
Previous multi-motors scans (aNscan, dNscan) are based on the generic
lookupscan. It can take a variable number of motors associated to a
list of positions to use for the scan.
usage:
lookupscan(counting_time, (<mot>, <positions_list>)*, <counter>*)
example:
import numpy as np lookupscan(0.1, m0, np.arange(0, 2, 0.5), m1, np.linspace(1, 3, 4), diode2)
Scans behaviour¶
- create acquisition device
prepare()start()trigger()called<nbpoints>times.stop()
| Scan | nbpoints | start/stop type |
|---|---|---|
| def. | N | list |
| timescan | 0 | [] |
| loopscan | N | [] |
| pointscan | N | float |
| ct | 1 | [] |
Default chain¶
All standard scans (step scans) are build the same way using the
DefaultAcquisitionChain object accessible via the global variable
DEFAULT_CHAIN, if you are in a session. It’s the entry point to
parameterise detectors in a step scan procedure. It is
easy to set acquisition parameters and saving parameters for any
detector, be it for step scans or to change it’s master.
Note
Acquisition parameters are all the parameters that define the
number of triggers and points, trigger type, exposure time and so on.
Other detector parameters should not be part of the DefaultAcquisitionChain
configuration.
For example Image configuration of a Lima device like binning, flip,
rotation and so on, should be excluded from this configuration and
set before any scan.
Saving parameters are parameters on some devices (like: Lima)
that configure the saving.
This means that for instance on Lima devices saving_mode, saving_format
and so on, may be part of the DEFAULT_CHAIN configuration.
Example: Two basler cameras with a hardware trigger provided by your counter
card. Most of the time the configuration comes from Beacon and the
yaml file may look like this:
- name: default_acq_chain plugin: default chain_config: - device: $basler_1 acquisition_settings: acq_trigger_mode: EXTERNAL_TRIGGER_MULTI saving_format: "HDF5" master: $p201_0 - device: $basler_2 acquisition_settings: acq_trigger_mode: EXTERNAL_TRIGGER_MULTI saving_format: "HDF5" master: $p201_0
In this example you notice that both cameras are triggered externally (EXTERNAL_TRIGGER_MULTI) and their saving format HDF5. Their master will be the p201 counter card. To activate this setting for all steps scan of your session do as follows in the session setup file :
DEFAULT_CHAIN.set_settings(default_acq_chain['chain_config'])
ChainPreset can also be added to
the DEFAULT_CHAIN. Usually this is also done in the session setup
like this:
DEFAULT_CHAIN.add_preset(my_preset)
To go further…¶
Steps scans¶
Most unusual step scans can be defined using one of the existing standard scans.
n-regions scan example¶
In this example you want to define a scan with several regions. The regions have to be defined as a list of tuples like: [(start1,stop1,npoints1),(start2,stop2,npoints2),…]
import numpy from bliss.common.scans import pointscan def n_region_scan(motor, regions, count_time, *counter_args, **kwargs): positions = list() for start,stop,npoints in regions: positions.extend(numpy.linspace(start,stop,npoints)) # change to new defined scan kwargs.setdefault('type', f'{len(regions)}_region_scan') # Build a **meaning** title kwargs.setdefault('title',f'{kwargs.get("type")} on {motor.name}') return pointscan(motor,positions,count_time,*counter_args,**kwargs)
Execute :
DEMO [1]: s = n_region_scan(roby,[(0,2,3),(10,15,11)],0.1,diode,save=False) Scan 9 Tue Apr 02 14:58:33 2019 <no saving> demo user = seb 2_region_scan on roby # dt[s] roby diode 0 0 0 23.8889 1 0.232985 1 23.5556 2 0.46471 2 -2.11111 3 0.823396 10 16.5556 4 1.01696 10.5 -8.88889 5 1.20862 11 -17.3333 6 1.39964 11.5 20.6667 7 1.59078 12 0.444444 8 1.78076 12.5 17.7778 9 1.97064 13 -0.111111 10 2.16226 13.5 26 11 2.35261 14 28.2222 12 2.54606 14.5 -1.55556 13 2.7383 15 59.2222 Took 0:00:03.366149
ascans, which take step size rather than the number of intervals¶
import numpy from bliss.common.scans import ascan def step_scan(motor, start, stop, step_size, count_time, *counter_args, **kwargs): intervals = int(numpy.ceil(abs(start-stop)/step_size)) - 1 return ascan(motor, start, stop, intervals, count_time, *counter_args, **kwargs)
Execute :
TEST_SESSION [42]: s = step_scan(roby, 0, 1, 0.2, 0.1, diode) Scan 17 Tue Apr 02 16:04:31 2019 /tmp/..../data.h5 test_session user = seb ascan roby 0 1 5 0.1 # dt[s] roby diode 0 0 0 -9.33333 1 0.193154 0.25 -38.5556 2 0.385237 0.5 -6.55556 3 0.575978 0.75 -13.5556 4 0.765097 1 -9.55556 Took 0:00:01.229621
Using ‘presets’ to customize a scan¶
In this example, the scan will pump a certain amount of liquid using a syringe before each point. To do this we will use ChainPreset.
from bliss.scanning.chain import ChainPreset,ChainIterationPreset from bliss.common.scans import ascan class Syringe: def __init__(self, available_liquid): self._available_liquid = available_liquid def pump(self,amount): if self._available_liquid < amount: raise RuntimeError("No more liquid to pump") self._available_liquid -= amount my_syringe = Syringe(10) # liquid volume == 10 def syringe_ascan(syringe, liquid_amount, motor, start, stop, intervals, count_time, *counter_args, **kwargs): class Preset(ChainPreset): class Point(ChainIterationPreset): def prepare(self): syringe.pump(liquid_amount) def get_iterator(self,acq_chain): while True: yield Preset.Point() kwargs.setdefault('run',False) s = ascan(motor, start, stop, intervals, count_time, *counter_args, **kwargs) preset = Preset() s.acq_chain.add_preset(preset) s.run() return s
Execute :
TEST_SESSION [16]: syringe_ascan(my_syringe, 1, roby, 0, 1, 15, 0.1, diode) Scan 22 Tue Apr 02 16:37:24 2019 /tmp/..../data.h5 test_session user = seb ascan roby 0 1 15 0.1 # dt[s] roby diode 0 0 0 12.6667 1 0.19153 0.0714 -12.2222 2 0.381468 0.1429 9 3 0.570563 0.2143 11.6667 4 0.761761 0.2857 -12.1111 5 0.953436 0.3571 10.8889 6 1.14317 0.4286 -1.44444 7 1.33038 0.5 -21.3333 8 1.51747 0.5714 51.3333 9 1.7079 0.6429 9.77778 !!! === RuntimeError: No more liquid to pump === !!! Took 0:00:02.008699 !!! === RuntimeError: No more liquid to pump === !!!
In this example, before each point preparation the syringe will pump one unit of a volume and raises an error when the syringe is empty.
Note
Any exception in Preset method stop the scan.
More complex scans¶
For more complex scans, you may need to use a lower level api. see: Scan engine.