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A Python application for the analysis of β-NMR and β-NQR data taken at TRIUMF.

Home Page: https://pypi.org/project/bfit/

License: GNU General Public License v3.0

Python 94.69% C 1.98% C++ 1.18% TeX 1.53% Cython 0.63%

b-nmr b-nqr triumf

bfit's People

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ethoeng rmlmcfadden

bfit's Issues

In parameter draw plot, allow mouseover to show info (if no annotation) and on click draw in new window the data and fit line. This will require a new class in the backend similar to the FunctionPlacer.

Fit should only apply to checked files

To ease switching fitting between data sets. Also, have force check state on by default.

Fit seems to ignore bad bins

the fit ignores removing bad bins (no change in fit when bad bins are
removed, and the spectra visible changes after bin removal and clearly
mismatches the fit)

Need labeling runs by year

Internal labelling by run only causes the issue of being unable to re-fetch a run from a different year, especially if it was selected accidentally.

Alignment of lines in fetch files is bad

Rather than have each line have it's own frame, if you grid to the containing frame, it may align things better.

Or just find a way to make the line frames align.

Checkboxes in Fetch Data tab unclear

In the current version of bfit on muesli the fit button in the Fetch Data tab does not appear to be working.

Annotations broken

Not showing

Annotate fit parameter draw window

Allow for annotation using this module.

Significant Figures of Magnetic Field in Tesla

Under the Fetch Data tab it shows a list of runs with the year, run number, temperature, magnetic field, implantation bias, etc. I am currently working on some low field data and the magnetic field is automatically converted from Gauss to Tesla. That is great, but my data at 150 G is showing up as 0.02 T. I think you need to increase the significant figures or change the way it is shown.

Coded file input

Input a switch to change between simple run list input and coded input in file fetcher.

Coded input idea:

Type in a string using the variable "r" which when true will fetch that file.
Backend appends string to lambda function then uses eval function to turn string to executable.

Could be useful for getting every other file, or all but one. Run numbers would have to be fetched from file names in year directory.

Examples:

45010 < r (get latest files)
(40001 <= r < 40100) and r not in [40010] and r%10 == 0 (get every 10th but not 40010)

When appended to lambda r : would return true if we should draw it

Periodic redraw in same figure

Behaviour should be as follows:

Upon checking periodic redraw, the next draw (the one associated with the periodicity) should assign a figure number. This figure is then selected on every redraw, and then the focus should be passed back to whatever figure the use was looking at.

Combine runs

Allow for file fetch to combine checked runs by taking weighted mean

See global chisquared

Display this somewhere

Improvements to data storage and backend

Need improvement in tracking which data has been taken, what has been fitted. Stores fitdata objects.

Can do this either in bfit object or new external object.

Comb runs cannot be plotted while acquiring data if a non-comb run has been run prior

This evening we noticed while switching between 1f and 1w runs that if a 1f run was acquired before the 1w run, then the 1w run will not plot while the data is acquiring. However, it can be plotted just fine once the data acquisition is finalized. The runs I noticed this on were: 2019: 40193.

Drawing with same label

Drawing runs with the same label (ex: temperature) will remove previous runs with the same label.

Fit helicities independently

Completely separate.

Add split helicity fitting

Add link to musr run search site

Make a link to this site: http://musr.ca/mud/runSel.html

Add run label to fitting tab

Have the titles of the runs reflect the labels. Could do something like

[ run number -- label ]

if label != run

Logging needed

Should add proper logging, limiting filesize. Specify location on desktop to put files such as these (ex: ~/.bfit/).

Add 1000/T to draw parameter menus

Fit parameters reset on highlight

The fit parameter selection goes back to the first entry when the input fields are highlighted.

Seems to reselect combobox for some reason

2019-02-22 18:49:44,963 DEBUG    fit_files_tab.get_selected_run() [1052] -- Selected combobx[1] (run 40178)
2019-02-22 18:49:45,660 DEBUG    fit_files_tab.set_display() [1160] -- Setting display for run 40178
2019-02-22 18:49:45,661 DEBUG    fit_files_tab.get_selected_run() [1052] -- Selected combobx[0] (run 40173)

Increase max size of run number select box

In fit data tab. No reason for this to not take the whole screen. Make sure grid resizing still works.

Add beta avg to draw parameter menus

Add chisq to annotation menu

Fix draw fitting for large number of fits

Make multiple windows? Multiple sub plots?

Graphical P0: Setting 1F Multicomp

Issue #11 added graphical setting of P0. Setting new lines means altering the amplitudes of the old lines already set. This should not happen. Users specify peak height. This value should be fixed, regardless of other components set.

Ability to fit defined time range?

Have you considered implementing the ability to fit a part of the time range?

For example, sometimes I look at the first second of the data to get a good estimate of the initial asymmetry. I will do this specially if I am looking at a sample with a potential missing fraction.

Graphical setting of P0

Fit parameters should be able to set via graphical interface. (i.e. select peak and width or lor fits). Needed mostly for 1f

Removing data

Removing data sometimes leaves remnants of data untracked (fit page doesn't load run, thinks there's a run with blank mode, etc).

Possibly when there's an error elsewhere?

Fitting function resetting

Fitting function resets on file fetch, annoying when fitting a different set of files

Vanishing fitting parameter input

Fit parameters which are set by the user are reset after file fetch. Do not change for non-fetched files.

Memory leak

After 18h usage, shows large (50%) usage of RAM

Fetch files tab is slow

Especially when fetching a large number of files. This needs to be sped up.

Drawing in split hel does not remove legend properly

Fix set group parameters

Current function: update on next button press. New function: update on user input.

Limit the number of entry boxes and linked parameters. Just save values in fitdata objects.

Also have group parameters checkbox true by default.

Fetch run 40123, 2018
Fit
Fetch run 40127, 2018
Draw all
Fit, with error.

Log output:

2019-03-12 20:27:38,828 INFO     bfit.__init__() [157] -- Initializing --------------------------------------------------
2019-03-12 20:27:39,166 DEBUG    fileviewer_tab.__init__() [71] -- Initializing
2019-03-12 20:27:39,181 DEBUG    bfit.get_latest_year() [850] -- Latest year with data: 2018 (NMR: True, NQR: True)
2019-03-12 20:27:39,217 DEBUG    fileviewer_tab.__init__() [175] -- Initialization success.
2019-03-12 20:27:39,218 DEBUG    fetch_files_tab.__init__() [66] -- Initializing
2019-03-12 20:27:39,228 DEBUG    bfit.get_latest_year() [850] -- Latest year with data: 2018 (NMR: True, NQR: True)
2019-03-12 20:27:39,295 DEBUG    fetch_files_tab.__init__() [259] -- Initialization success.
2019-03-12 20:27:39,295 DEBUG    fit_files_tab.__init__() [57] -- Initializing
2019-03-12 20:27:39,362 DEBUG    bfit.__init__() [326] -- Initialization success. Starting mainloop.
2019-03-12 20:27:39,374 DEBUG    bfit.set_tab_change() [1030] -- Changing to tab 0
2019-03-12 20:27:42,670 DEBUG    bfit.set_tab_change() [1030] -- Changing to tab 1
2019-03-12 20:27:44,770 DEBUG    bfit.return_binder() [880] -- Calling return key command for notebook index 1
2019-03-12 20:27:44,772 DEBUG    fetch_files_tab.return_binder() [480] -- Focus is: run or year entry
2019-03-12 20:27:44,772 DEBUG    fetch_files_tab.get_data() [375] -- Fetching runs
2019-03-12 20:27:44,772 DEBUG    fetch_files_tab.string2run() [543] -- Parsed "40123" to run numbers (len: 1) [40123]
2019-03-12 20:27:44,781 DEBUG    fitdata.__init__() [56] -- Initializing run 40123 (2018).
2019-03-12 20:27:44,781 DEBUG    fetch_files_tab.get_data() [422] -- Fetching runs of mode 20
2019-03-12 20:27:44,787 DEBUG    bfit.set_asym_calc_mode_box() [1057] -- Setting fileviewer asym combobox values for mode "20"
2019-03-12 20:27:44,789 DEBUG    fetch_files_tab.__init__() [596] -- Initializing run 40123 (2018)
2019-03-12 20:27:44,825 DEBUG    bfit.get_label() [794] -- Fetching plot label for "Run Number"
2019-03-12 20:27:44,827 DEBUG    fit_files_tab.populate() [211] -- Populating data. Groups: [1]
2019-03-12 20:27:44,828 DEBUG    fit_files_tab.populate_param() [278] -- Populating fit parameters
2019-03-12 20:27:44,828 DEBUG    fit_files_tab.__init__() [942] -- Initalizing fit tab group 1
2019-03-12 20:27:44,829 DEBUG    fit_files_tab.create() [955] -- Creating graphics for fit input group 1
2019-03-12 20:27:44,842 DEBUG    fit_files_tab.populate_param() [278] -- Populating fit parameters
2019-03-12 20:27:44,842 DEBUG    fit_files_tab.get_new_parameters() [1024] -- Fetching new parameters
2019-03-12 20:27:44,843 DEBUG    fitdata.set_fitpar() [135] -- Fit parameters set to {'p0': {'amp': 0.07277506954176316, '1/T1': 0.8474576271186439, 'baseline': 0.004470859270959627, 'beta': 0.5}, 'blo': {'amp': 0, '1/T1': 0, 'baseline': -inf, 'beta': 0}, 'bhi': {'amp': inf, '1/T1': inf, 'baseline': inf, 'beta': 1}, 'res': {}, 'dres': {}, 'chi': {}, 'fixed': {}, 'shared': {}}
2019-03-12 20:27:44,844 DEBUG    fit_files_tab.populate_param() [1074] -- Populating parameter list with ('1/T1', 'amp', 'baseline')
2019-03-12 20:27:44,845 DEBUG    fit_files_tab.get_selected_run() [1054] -- Selected combobx[0] (run 40123)
2019-03-12 20:27:44,848 DEBUG    fit_files_tab.set_display() [1162] -- Setting display for run 40123
2019-03-12 20:27:44,848 DEBUG    fit_files_tab.get_selected_run() [1054] -- Selected combobx[0] (run 40123)
2019-03-12 20:27:44,850 INFO     fetch_files_tab.get_data() [457] -- Fetched runs [40123]
2019-03-12 20:27:46,527 DEBUG    bfit.set_tab_change() [1030] -- Changing to tab 2
2019-03-12 20:27:46,527 DEBUG    fit_files_tab.populate() [211] -- Populating data. Groups: [1]
2019-03-12 20:27:46,528 DEBUG    fit_files_tab.update() [1280] -- Updating fit tab for group 1
2019-03-12 20:27:46,528 DEBUG    fit_files_tab.set_display() [1162] -- Setting display for run 40123
2019-03-12 20:27:46,528 DEBUG    fit_files_tab.get_selected_run() [1054] -- Selected combobx[0] (run 40123)
2019-03-12 20:27:47,475 INFO     fit_files_tab.do_fit() [314] -- Fitting with "Exp" with 1 components
2019-03-12 20:27:47,476 DEBUG    fit_files_tab.do_fit() [323] -- Group 1 contains runs [40123]
2019-03-12 20:27:47,744 INFO     fit_files_tab.do_fit() [415] -- Fitting run 40123 (2018): [{'1/T1': [0.84746, 0.0, inf, False, False], 'amp': [0.07278, 0.0, inf, False, False], 'baseline': [0.00447, -inf, inf, False, False]}, {'rebin': 1, 'group': 1}]
2019-03-12 20:27:47,788 DEBUG    fitdata.set_fitresult() [153] -- Setting fit results to {'p0': {'amp': 0.07278, '1/T1': 0.84746, 'baseline': 0.00447, 'beta': 0.5}, 'blo': {'amp': 0.0, '1/T1': 0.0, 'baseline': -inf, 'beta': 0}, 'bhi': {'amp': inf, '1/T1': inf, 'baseline': inf, 'beta': 1}, 'res': {'1/T1': 1.283244280404294, 'amp': 0.09377768860389923, 'baseline': -0.0015603664610268156}, 'dres': {'1/T1': 0.050978671670798344, 'amp': 0.0011112704100392585, 'baseline': 0.0011822237261787266}, 'chi': {'1/T1': 1.3870614424311014, 'amp': 1.3870614424311014, 'baseline': 1.3870614424311014}, 'fixed': {'1/T1': False, 'amp': False, 'baseline': False}, 'shared': {'1/T1': False, 'amp': False, 'baseline': False}}
2019-03-12 20:27:47,788 DEBUG    fit_files_tab.set_display() [1162] -- Setting display for run 40123
2019-03-12 20:27:47,788 DEBUG    fit_files_tab.get_selected_run() [1054] -- Selected combobx[0] (run 40123)
2019-03-12 20:27:47,789 DEBUG    fetch_files_tab.draw_all() [318] -- Drawing all data (ignore check: False)
2019-03-12 20:27:47,790 DEBUG    fetch_files_tab.draw_all() [328] -- Draw style: "stack"
2019-03-12 20:27:47,790 DEBUG    fetch_files_tab.draw() [770] -- Draw run 40123 (2018)
2019-03-12 20:27:47,793 INFO     bfit.draw() [366] -- Drawing run 40123 (2018). mode: c, rebin: 1, option: , style: stack, {'label': '40123'}
2019-03-12 20:27:48,268 DEBUG    bfit.draw() [724] -- Drawing success.
2019-03-12 20:27:48,268 INFO     fit_files_tab.draw_fit() [603] -- Drawing fit for run 40123. {}
2019-03-12 20:27:49,816 DEBUG    bfit.set_tab_change() [1030] -- Changing to tab 1
2019-03-12 20:27:49,816 DEBUG    bfit.set_asym_calc_mode_box() [1057] -- Setting fileviewer asym combobox values for mode "20"
2019-03-12 20:27:52,972 DEBUG    bfit.return_binder() [880] -- Calling return key command for notebook index 1
2019-03-12 20:27:52,972 DEBUG    fetch_files_tab.return_binder() [480] -- Focus is: run or year entry
2019-03-12 20:27:52,973 DEBUG    fetch_files_tab.get_data() [375] -- Fetching runs
2019-03-12 20:27:52,973 DEBUG    fetch_files_tab.string2run() [543] -- Parsed "40123,40127" to run numbers (len: 2) [40123, 40127]
2019-03-12 20:27:52,977 DEBUG    fitdata.__init__() [56] -- Initializing run 40123 (2018).
2019-03-12 20:27:52,982 DEBUG    fitdata.__init__() [56] -- Initializing run 40127 (2018).
2019-03-12 20:27:52,982 DEBUG    fetch_files_tab.get_data() [422] -- Fetching runs of mode 20
2019-03-12 20:27:52,983 DEBUG    bfit.set_asym_calc_mode_box() [1057] -- Setting fileviewer asym combobox values for mode "20"
2019-03-12 20:27:52,983 DEBUG    fetch_files_tab.__init__() [596] -- Initializing run 40127 (2018)
2019-03-12 20:27:53,002 DEBUG    bfit.get_label() [794] -- Fetching plot label for "Run Number"
2019-03-12 20:27:53,003 DEBUG    fit_files_tab.populate() [211] -- Populating data. Groups: [1]
2019-03-12 20:27:53,003 DEBUG    fit_files_tab.update() [1280] -- Updating fit tab for group 1
2019-03-12 20:27:53,004 DEBUG    fit_files_tab.set_display() [1162] -- Setting display for run 40123
2019-03-12 20:27:53,004 DEBUG    fit_files_tab.get_selected_run() [1054] -- Selected combobx[0] (run 40123)
2019-03-12 20:27:53,004 DEBUG    fit_files_tab.get_new_parameters() [1024] -- Fetching new parameters
2019-03-12 20:27:53,005 DEBUG    fitdata.set_fitpar() [135] -- Fit parameters set to {'p0': {'amp': 0.07277506954176316, '1/T1': 0.8474576271186439, 'baseline': 0.004470859270959627, 'beta': 0.5}, 'blo': {'amp': 0, '1/T1': 0, 'baseline': -inf, 'beta': 0}, 'bhi': {'amp': inf, '1/T1': inf, 'baseline': inf, 'beta': 1}, 'res': {}, 'dres': {}, 'chi': {}, 'fixed': {}, 'shared': {}}
2019-03-12 20:27:53,005 INFO     fetch_files_tab.get_data() [457] -- Fetched runs [40123, 40127]
2019-03-12 20:27:55,808 DEBUG    bfit.set_tab_change() [1030] -- Changing to tab 2
2019-03-12 20:27:55,809 DEBUG    fit_files_tab.populate() [211] -- Populating data. Groups: [1]
2019-03-12 20:27:55,811 DEBUG    fit_files_tab.update() [1280] -- Updating fit tab for group 1
2019-03-12 20:27:55,812 DEBUG    fit_files_tab.set_display() [1162] -- Setting display for run 40123
2019-03-12 20:27:55,812 DEBUG    fit_files_tab.get_selected_run() [1054] -- Selected combobx[0] (run 40123)
2019-03-12 20:27:56,355 DEBUG    bfit.set_tab_change() [1030] -- Changing to tab 1
2019-03-12 20:27:56,356 DEBUG    bfit.set_asym_calc_mode_box() [1057] -- Setting fileviewer asym combobox values for mode "20"
2019-03-12 20:27:57,857 DEBUG    fetch_files_tab.draw_all() [318] -- Drawing all data (ignore check: False)
2019-03-12 20:27:57,858 DEBUG    fetch_files_tab.draw_all() [328] -- Draw style: "stack"
2019-03-12 20:27:57,858 DEBUG    fetch_files_tab.draw() [770] -- Draw run 40123 (2018)
2019-03-12 20:27:57,860 INFO     bfit.draw() [366] -- Drawing run 40123 (2018). mode: c, rebin: 1, option: , style: stack, {'label': '40123'}
2019-03-12 20:27:58,025 DEBUG    bfit.draw() [724] -- Drawing success.
2019-03-12 20:27:58,025 DEBUG    fetch_files_tab.draw() [770] -- Draw run 40127 (2018)
2019-03-12 20:27:58,027 INFO     bfit.draw() [366] -- Drawing run 40127 (2018). mode: c, rebin: 1, option: , style: stack, {'label': '40127'}
2019-03-12 20:27:58,068 DEBUG    bfit.draw() [724] -- Drawing success.
2019-03-12 20:27:59,729 DEBUG    bfit.set_tab_change() [1030] -- Changing to tab 2
2019-03-12 20:27:59,730 DEBUG    fit_files_tab.populate() [211] -- Populating data. Groups: [1]
2019-03-12 20:27:59,730 DEBUG    fit_files_tab.update() [1280] -- Updating fit tab for group 1
2019-03-12 20:27:59,731 DEBUG    fit_files_tab.set_display() [1162] -- Setting display for run 40123
2019-03-12 20:27:59,731 DEBUG    fit_files_tab.get_selected_run() [1054] -- Selected combobx[0] (run 40123)
2019-03-12 20:28:00,691 INFO     fit_files_tab.do_fit() [314] -- Fitting with "Exp" with 1 components
2019-03-12 20:28:00,692 DEBUG    fit_files_tab.do_fit() [323] -- Group 1 contains runs [40123, 40127]
2019-03-12 20:28:01,038 INFO     fit_files_tab.do_fit() [415] -- Fitting run 40123 (2018): [{'1/T1': [0.84746, 0.0, inf, False, False], 'amp': [0.07278, 0.0, inf, False, False], 'baseline': [0.00447, -inf, inf, False, False]}, {'rebin': 0, 'group': 0}]
2019-03-12 20:28:01,038 INFO     fit_files_tab.do_fit() [415] -- Fitting run 40127 (2018): [{'1/T1': [0.84746, 0.0, inf, False, False], 'amp': [0.07278, 0.0, inf, False, False], 'baseline': [0.00447, -inf, inf, False, False]}, {'rebin': 1, 'group': 1}]
2019-03-12 20:28:01,041 ERROR    fit_files_tab.do_fit() [423] -- Fitting error
Traceback (most recent call last):
  File "/home/fuji/Documents/Research/src/bfit/bfit/gui/fit_files_tab.py", line 421, in do_fit
    hist_select=self.bfit.hist_select)
  File "/home/fuji/Documents/Research/src/bfit/bfit/fitting/default_routines.py", line 141, in __call__
    hist_select=hist_select,p0=p0,bounds=bounds)
  File "/home/fuji/Documents/Research/src/bfit/bfit/fitting/fit_bdata.py", line 127, in fit_list
    p,s,c = fit_single(r,y,fn,om,re,hist_select,p0=p,bounds=b,xlim=xl,**kwargs)
  File "/home/fuji/Documents/Research/src/bfit/bfit/fitting/fit_bdata.py", line 181, in fit_single
    x,y,dy = data.asym('c',omit=omit,rebin=rebin,hist_select=hist_select)
  File "/home/fuji/Documents/Research/src/bdata/bdata/bdata.py", line 1059, in asym
    raise RuntimeError('Rebinning factor must be int >= 1.')
RuntimeError: Rebinning factor must be int >= 1.
2019-03-12 20:31:46,753 INFO     bfit.on_closing() [863] -- Closing all windows.
2019-03-12 20:31:47,055 INFO     bfit.on_closing() [866] -- Finished     --------------------------------------------------

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