nicoeinsidler/pigor

Quick analysis tool for the beam lines at Atominstitut of TU Wien in Vienna, Austria.

PIGOR

Pigor is a lightweight analysis tool for the polarimeter instrument NEPTUN at the tangential beam port of the 250kW research reactor hosted at Atominstitut of TU Wien, Austria. For more information visit our homepage.

Documentation has moved: The documentation has moved to PIGOR.org. (Alternatively you can find it in doc/_build/html)

pigor's Issues

Choose order of poly fit

Hy, it would be nice to choose the order of the polynomial fit (<=5), as sometimes we know that the theoretical curve of the measurement should be e.g. of order 2 (as for the DCZ sweeps, which are currently using poly5 and therefore falsify the actual minima.

path to links not valid in index_pigor.html

the links in the index_pigor.html cannot be opened

in my case the testfiles folder appears two times in the path

file:///D:/Users/richard/pigor/testfiles/testfiles/polarimeter/2019_02_20_1340_dc2z_scan.dat

Negative Contrast

In e.g. the testfile 2018-11-23-1545-scan-dc2x.html
there is a negative contrast for the sine_lin fit
Contrast for fit #0: -0.9358090416273662
-> has to be positive

ps: and the number should be truncated to 2 or three digits after the comma
(see issue #8)

fit improvement

Dear Nico,

as discussed, I am sending you an example of a bad sinusoidal fit which nonetheless has about the right frequency.
Thanks a lot that you are still open to work on your code.

I am not sure what files you need. I renamed the .dat file as .txt so I can attach it. Please let know in case this didn't work or you need something else.

Armin

PS: how do I add a bug label or do only you do that?

Edit: Initially, I accidentally attached a fit which worked quite good ;)

2020_06_18_1017_100s_comp_tilt9_DC4_scan_sine_fit_functions.txt
2020_06_18_1017_100s_comp_tilt9_DC4_scan_sine - Copy.txt

phase in degree instead of radians

Stephan requested this feature.

html - index file

it would be nice if in the root testfile directory a html index file would be created,
that lists and links to all html output files.

html/md - output of covariance matrix

give the output in nice matrix arrangement.

currently all is in one row without line breaks (see below):

Covariance:

['[[ 1.16085301e-04, \n 5.77137574e+01, \n-2.16962168e+02],\n [ 5.77137574e+01, \n 4.12751257e+08, \n-1.73398906e+08],\n [-2.16962168e+02, \n-1.73398906e+08, \n 9.14644609e+08]]']
</EXAMPLE>

Minima and Maxima of Fit

Minimal and maximal values and their corresponding x-axis values are not yet implemented.

error when processing position scan

Problem finding Position File

Note: This issue was originally posted from Armin Danner on Bitbucket and has been migrated to Github.

Terminal output:

 C:\Users\admin\ownCloud! Exp Data\3 Output POVM Uncertainty\Experiment\Raw D ata\2019-03-28-pigor tests\2019_03_08_1200_axis8_pos.dat: Detected measurement t ype POS. The following exception occured during runtime:

Each lower bound must be strictly less than each upper bound. \Continuing operation.

Here is 2019_03_08_1200_axis8_pos.dat

Start Motor Scan on 08/03/2019@12:06 | Measure Time (sec):100| Bg detector (cnts/sec):0.000000| Bg monitor (cnts/sec):0.000000100| Mon.lim.  (cnts/sec):  0
Ioff (cnts/sec): 0.096569   ErrIoff: 0.004037  Pp.d.Pa:  0.000000  ErrPp.d.Pal:  0.000000	Pol: 0.000000	ErrPol: 0.000000
Power Supply 1 (mA): 0| Power Supply 2 (mA): 0| Power Supply 3 (mA): 0| Power Supply 4 (mA): 0| Power Supply 5 (mA): OFF| Power Supply 6 (mA): OFF   
Position (Steps)Detector (cnts):   Monitor_Max,Min (cnts/sec):   Norm(1/s):   err(1/s) :     FlippRatio:     ErrFlippRatio        
-1900000.00000000	498.00000000	6.00000000	0.00000000	1.93774319	0.14882931	0.04983565	0.00435779
-1850000.00000000	941.00000000	8.00000000	0.00000000	3.61923077	0.25357492	0.02668211	0.00217686
-1800000.00000000	1303.00000000	8.00000000	0.00000000	5.40663900	0.37911441	0.01786113	0.00145807
-1750000.00000000	1437.00000000	7.00000000	0.00000000	5.67984190	0.38724958	0.01700200	0.00135970
-1700000.00000000	1375.00000000	7.00000000	0.00000000	5.39215686	0.36765026	0.01790910	0.00143229
-1650000.00000000	1010.00000000	7.00000000	0.00000000	3.92996109	0.27456761	0.02457243	0.00200056
-1600000.00000000	604.00000000	7.00000000	0.00000000	2.60344828	0.20108961	0.03709261	0.00325765

[i] init functionality - image format (file extension)

same problem as with the [y/n]

If I skip the question for the image format with enter - the next time round the option is [.png]
<e.g>
What image format should the plots have? (.png,.svg,.eps,.pdf) [.svg]
ENTER
What image format should the plots have? (.png,.svg,.eps,.pdf) [.png]
ENTER
</e.g>
remark
same with the
Which file extention should PIGOR look for? (string) [.dat]

Joining Plots

Would it be possible to join several graphs?

Bad Sine Fit

Hey Nico,
I have an issue with the Sinje Fits your are using, they tend to be quite inaccurate when there are single deviations from the typical pattern in the data we are using.

2019-04-24 - DC3 measurements at different axis 4 positions.zip

name of index-HTML - > index_pigor.html

export_meta() not working with multiprocessing

Multiprocessing not working

Note: This issue was migrated over from Bitbucket.

I ran into this problem when I introduced export_meta() in the Measurement class. When performance becomes an issue, this should be fixed again, but for now the sequential analysis works quite fast.

Terminal output on this one:

✅  testfiles\2019_02_20_1340_dc2z_scan.dat: Detected measurement type DC.
📍  testfiles\subdirectory_test\2018-11-23-0900-degree-of-polarisation.pos: Position file read: testfiles\2018-11-23-1325-degree-of-pol.dat
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "C:\Users\Nico Einsidler\AppData\Local\Programs\Python\Python37-32\lib\multiprocessing\pool.py", line 121, in worker
    result = (True, func(*args, **kwds))
  File "C:\Users\Nico Einsidler\AppData\Local\Programs\Python\Python37-32\lib\multiprocessing\pool.py", line 44, in mapstar
    return list(map(*args))
  File "C:\Users\Nico Einsidler\Documents\pigor\measurement.py", line 707, in export_meta
    if self.popt:
AttributeError: 'Measurement' object has no attribute 'popt'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "pigor.py", line 121, in <module>
    main()
  File "pigor.py", line 117, in main
    analyse_files(all_files)
  File "pigor.py", line 72, in analyse_files
    pool.map(measurement.Measurement.export_meta, m)
  File "C:\Users\Nico Einsidler\AppData\Local\Programs\Python\Python37-32\lib\multiprocessing\pool.py", line 268, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "C:\Users\Nico Einsidler\AppData\Local\Programs\Python\Python37-32\lib\multiprocessing\pool.py", line 657, in get
    raise self._value
AttributeError: 'Measurement' object has no attribute 'popt'

SVG, PDF and EPS support

Vector Graphics Support for PIGOR

Note: This issue was originally posted from Armin Danner on Bitbucket and has been migrated to Github.

Option to choose from different file formats for the standard plot output of PIGOR. => pigor.config

function: choose fit function

we get sine_lin fits but want bare sine fit. can we choose the used fit function?

Export Fit Function

... into a .txt that is interpretable by Mathematica

Nested Config Files

Subfolders can have their own config files which overrule parent config files.

Min/Max of Fit Functions

It is highly relevant for the "Extreme Values"-Section of the analyzed files that the min/max of the FIT FUNCTION is added --> If possible also give information about local minimas (e.g. the typical sine-shaped function of the DC X fields has two local minimas, both are relevant).
Please give x and y coordinates of ALL local/global minimas of the fit function (local is just needed for DC X, as stated).

[i] init functionality - default option not taken (y/n)

in the init option y/n selection has a problem
e.g.
OUT: Should PIGOR look for files recursively? (y/n) [y]
OUT: boo
IN: -> type Enter
next time it will read
OUT: Should PIGOR look for files recursively? (y/n) [n]
OUT: nool
side remark why the bool output above?

PIGOR_ROOT lost setting after quit

after quitting igor - [q] and restarting PIGOR_ROOT is back to default!

find_boundaries() for poly5 not implemented yet

Analysis for a DC#Z fails

The analysis of the compensation field (z component of DC coils) fails with the error:

🔴  C:\Users\Nico Einsidler\Documents\pigor\testfiles\polarimeter\2019_02_2
0_1340_dc2z_scan.dat: Error writing boundaries into file: zip argument #2 must support iteration

format of numbers - open for discussion

I dont like the long numbers .
maybe stick to only 2, 3 or 4 decimal places.
May even depend on the integer part