Experiments¶
This section describes how to write an experiment with Pychron. A Pychron experiment
in Mass Spec parlance is a Multiple Runs Sequence
.
Conditionals¶
Conditionals are conditional actions that are executed are various times throughout an automated analysis Multiple types of conditionals exist
Truncation - truncate the current run and continue experiment.
Termination - immediately terminate run and stop experiment.
Action - do a specified action.
QueueAction - used to run blanks, airs, etc. based on a condition
There are also multiple levels at which conditionals may be specified.
System - use these conditionals for every experiment and run.
Queue - use these conditionals for every run in the queue.
Run - use these conditionals for this run.
System conditionals are specified in spectrometer/default_conditionals.yml
Queue conditionals files are located in queue_conditionals
Run conditionals file are located in scripts/conditionals
Note
QueueActions may only be specified at the Queue level
Testable Attributes
Name |
Modifiers |
age |
|
<Valid Isotope> |
bs_corrected, bs, current[cur], std_dev[sd,stddev] |
kca |
|
kcl |
|
cak |
|
clk |
|
<Detector> |
inactive, deflection |
<m1>/<m2> |
Functions ==================== ========================================================== Name Example ——————– ———————————————————- min min(Ar40) max max(Ar40) average average(Ar40) slope slope(Ar40) ==================== ==========================================================
Position Rules¶
The following is a list of rules for how a position entry is interpreted
4 or p4 (Goto position 4)
3,4,5 (Goto positions 3,4,5. Treat as one analysis)
7-12 (Goto positions 7,8,9,10,11,12. Treat as individual analyses)
7:12 (Same as #3)
10:16:2 (Goto positions 10,12,14,16. Treat as individual analyses)
D1 (Drill position 1)
T1-2 (Goto named position T1-2 i.e transect 1, point 2)
L3 (Trace path L3)
1-6;9;11;15-20 (Combination of rules 2. and 3. Treat all positions as individual analyses)
Here are a few examples of how Rule #9 is processed
user_input= 1-6;9
#resulting positions
positions= 1,2,3,4,5,6,9
user_input= 1-3;9;11-13
#resulting positions
positions= 1,2,3,4,5,6,9,11,12,13
The starting position, i.e 1 in the above case, can be greater than the end position i.e 6. If the start > end, positions will decrease from start to end
user_input= 9;6-1
#resulting positions
positions= 9,6,5,4,3,2,1
If auto-increment position is enabled pychron starts incrementing from the last value and follows the same pattern as the rule.
user_input= 1-6;9
#resulting auto-incremented positions
positions= 10-15;18
user_input= 1-6
#resulting auto-incremented positions
positions= 7-12