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Light weight data acquisition framework for orchestrating beamline experiments.

Project description

acquisition-framework

Light weight data acquisition framework for orchestrating beamline experiments.

The code is organized as a library containing various classes. A beamline is set up simply by making instances for detectors, motors, and any other devices directly in ipython. See dummy_beamline.py for example.

macros

A macro is a short expression in command line syntax which can be directly run at the ipython prompt. The following is a macro.

mv samx 12.4

In this framework, macros are created by writing a class with certain properties and marking that class with a decorator. This registers the macro as a magic ipython command. All available macros are stored in a central list, and can be listed with the lsmac command. The macro syntax is similar to sardana and spec.

In [2]: lsmac

name            class                                          
---------------------------------------------------------------
ascan           <class 'lib.scans.AScan.AScan'>                
ct              <class 'lib.scans.Scan.Ct'>                    
dmesh           <class 'lib.scans.Mesh.DMesh'>                 
dscan           <class 'lib.scans.AScan.DScan'>                
liveplot        <class 'lib.recorders.PlotRecorder.LivePlot'>  
loopscan        <class 'lib.scans.Scan.LoopScan'>              
lsdet           <class 'lib.detectors.Detector.LsDet'>         
lsm             <class 'lib.motors.Motor.LsM'>                 
lsmac           <class 'lib.environment.LsMac'>                
lsrec           <class 'lib.recorders.Recorder.LsRec'>         
mesh            <class 'lib.scans.Mesh.Mesh'>                  
mv              <class 'lib.motors.Motor.Mv'>                  
mvd             <class 'lib.motors.Motor.Mvd'>                 
mvr             <class 'lib.motors.Motor.Mvr'>                 
npointflyscan   <class 'lib.scans.NpointFlyscan.NpointFlyscan'>
setlim          <class 'lib.motors.Motor.SetLim'>              
setpos          <class 'lib.motors.Motor.SetPos'>              
spiralscan      <class 'lib.scans.Spiral.SpiralScan'>          
startlive       <class 'lib.detectors.Detector.StartLive'>     
stoplive        <class 'lib.detectors.Detector.StopLive'>      
tweak           <class 'lib.scans.Tweak.Tweak'>                
userlevel       <class 'lib.environment.UserLevel'>            
wa              <class 'lib.motors.Motor.Wa'>                  
wm              <class 'lib.motors.Motor.Wm'>                  

Do <macro-name>? (without <>) for more information.

Note how macros aren't stored in a special library. They are written throughout the library wherever they make sense. For example, in Detector.py where the detector base classes are defined, the lsdet macro is defined as follows.

@macro
class LsDet(object):
    def run(self):
        dct = {d.name: d.__class__ for d in Detector.getinstances()}
        print(utils.dict_to_table(dct, titles=('name', 'class')))

Note that a macro is different from a script. Anyone can easily write a macro, but for composite operations where existing macros are just combined it is faster to write a script. The following is a script, not a macro, but uses a special runCommand function to interface with the command line syntax.

from lib.environment import runCommand

for i in range(5):
    runCommand('mv samy %d' % new_y_pos)
    runCommand('ascan samx 0 1 5 .1')

environment variables

No global environment variables are used. Instead, a central object in the environment module is used to store values such as scan number etc.

In [24]: from lib.environment import env

In [25]: env.nextScanID
Out[25]: 1

detector selection

Detectors have an active attribute which determines if they are included in data acquisition such as scans. The macro lsdet indicates if each detector is active with an asterisk.

In [2]: lsdet

  name   class                                          
--------------------------------------------------------
* det2   <class 'lib.detectors.Dummies.DummyDetector'>  
* det3   <class 'lib.detectors.Dummies.Dummy1dDetector'>
* det1   <class 'lib.detectors.Dummies.DummyDetector'>  

In [3]: ct
det2 : 0.5862324427414796
det3 : (100,)
det1 : 0.815299279368746

In [4]: det3.active=False

In [5]: lsdet

  name   class                                          
--------------------------------------------------------
* det2   <class 'lib.detectors.Dummies.DummyDetector'>  
  det3   <class 'lib.detectors.Dummies.Dummy1dDetector'>
* det1   <class 'lib.detectors.Dummies.DummyDetector'>  

In [6]: ct
det2 : 0.26999817158517125
det1 : 0.4045182722290984

instance tracking

The framework has no databases or central registries. Instead, objects are related through inheritance. A common base class Gadget is inherited by detectors, motors, as all the rest. Gadget and all of its subclasses keep track of their instances. An example follows.

In [1]: [m.name for m in Motor.getinstances()]
Out[1]: ['gap', 'samy', 'samx']

In [2]: [d.name for d in Detector.getinstances()]
Out[2]: ['det1', 'det3', 'det2']

In [3]: [g.name for g in Gadget.getinstances()]
Out[3]: ['gap', 'detgrp', 'det1', 'samy', 'samx', 'det3', 'det2', 'hdf5recorder']

recorders

Data is captured by recorders. Recorders are run in separate processes and get data through queues, avoiding holding up the main acquisition loop because of I/O. They can do anything with the data, for example saving to hdf5 files or live plotting. See the Hdf5Recorder and PlotRecorder classes for examples. The former is very primitive still, but the latter is quite nice.

Note how easy it is to write these recorders, and how easy it would be to integrate online data analysis, for example writing a recorder which serves data (or links to data) for an on-the-fly ptycho engine to grab.

The lsrec macro lists currently running recorders.

In [30]: lsrec

name           class                                            
----------------------------------------------------------------
hdf5recorder   <class 'lib.recorders.Hdf5Recorder.Hdf5Recorder'>
name           <class 'lib.recorders.PlotRecorder.PlotRecorder'>

user levels

All Gadget instances have an associated user level. This means that certain motors can be hidden and protected while others are exposed through the macros. In this example, two sample motors are available to everyone while the undulator gap is higher level. This is not a security feature but meant to simplify the environment and reduce the risk of mistakes

In [7]: env.userLevel
Out[7]: 1

In [8]: wa
samy 0.0
samx 0.0

In [9]: env.userLevel = 5

In [10]: wa
samy 0.0
gap 0.0
samx 0.0

direct access to python objects

If Gadget objects operate on underlying Tango devices, then Tango attributes are directly accessible on the objects themselvs. PyTango provides tab completion and so these can be easily checked or corrected. Of course Gadgetsubclasses can provide nice getter and setter methods, but fixes are easily done.

In [7]: pilatus.det.energy
Out[7]: 10.0

In[8]: pilatus.lima.saving_mode
Out[8]: 'MANUAL'

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