gammaspec.py changes #1046

KennellyT · 2018-06-04T16:13:35Z

Functions are now undercase with underscore, added extra line on the bottom of gammaspec.py, and added a test to test spectrometry.py

scopatz · 2018-06-04T19:54:50Z

tests/test_spectrometry.py

@@ -91,7 +91,21 @@ def test_gross_counts():
 def test_net_count():
    nc=sa.net_counts(gspec1, 475, 484, 1)

-
+def test_read_spec_id_file():


How is this working? You don't seem to actually call read_spec_id_file()

it's called at global scope

KennellyT · 2018-06-04T20:00:11Z

@scopatz, It seems I forgot to add another gspec variable to call read_spec_id_file(). Ill edit this file to add gspec3 which calls read_spec_id_file().

scopatz · 2018-06-04T20:02:23Z

OK! Just post to this issue when you have it figured out!

KennellyT · 2018-06-08T14:15:58Z

gspec3 variable has been added to test_spectrometry.py and test_read_spec_id_file() has been edited to test the read_spec_id() function. I also added another module called gamma_effect.py that calculates the compton edge energy, backscatter energy ,single escape energy, and double escape energy when given an input energy. A test function has been created for this module and is called test_gamma_effects.py.
I will be drafting a tutorial on how to use gammaspec as well as gamma_effects to analyze .spe files within the week.

scopatz · 2018-06-08T14:30:25Z

pyne/gamma_effects.py

+    """Returns compton edge energy from a given gamma energy"""  
+    E_compton = E- E/(1+(2*E/mec2))
+    return E_compton
+def backscatter(E):


PEP8: two spaces between functions.

scopatz · 2018-06-08T14:30:43Z

pyne/gamma_effects.py

+
+"""
+
+mec2 = 511. #keV # Rest mass energy of an electron #.511 MeV 


global variables should be ALL_UPPERCASE

scopatz · 2018-06-08T14:32:15Z

Thanks @KennellyT - just let me know here, when you think this PR is ready to go!

KennellyT · 2018-06-08T14:42:25Z

Changed pull request to mirror comments. Also added srim_read.py, a function that reads srim files. Also added writecsv function in gammaspec.py.

KennellyT · 2018-06-13T02:24:06Z

Update of the above pull requests:
gammaspec.py:

read_spec_id_file()- reads and collects data from .spe files of the 'spec_id' format.
write_csv()-takes energy,counts, and channels from spectrum and writes them to csv file to be named by user.

srim_read.py
read_srim_output()-Reads a srim file

spectanalysis.py
net_area()-Calculates the net area under a peak by subtracting background from total
counts under the peak.
end_point_average_area()- Calculates the net area under a peak by end point averaging the
background counts and subtracting the background from total
counts under the peak.

gaussian_fit()-Plots the Gaussian fit of the counts versus channel number.

fwhm()- Calculates the full width half maximum of a peak.

scopatz · 2018-06-14T17:55:09Z

pyne/gamma_effects.py

@@ -0,0 +1,35 @@
+"""Purpose:


We use numpydoc format. So you don't need "purpose" and the following lines shouldn't be indented. thanks!

scopatz · 2018-06-14T17:55:57Z

pyne/gamma_effects.py

+
+def compton_edge(E):
+    """Returns compton edge energy from a given gamma energy"""  
+    E_compton = E- E/(1+(2*E/MEC_2))


There should be a single space in front of the minus: E - E/

scopatz · 2018-06-14T17:56:31Z

pyne/gamma_effects.py

+def single_escape(E):
+    """Returns single escape energy from a given gamma energy"""
+    if (E < 1022):	#keV
+        raise RuntimeError('E needs to be equal to or greater than 1022 keV to be valid')


This should be a ValueError instead of a RuntimeError, I would think.

scopatz · 2018-06-14T17:56:56Z

pyne/gamma_effects.py

+def double_escape(E):
+    """Returns double escape energy from a given gamma energy"""
+    if (E < 1022):	#keV
+        raise RuntimeError('E needs to be equal to or greater than 1022 keV to be valid')


ValueError again.

scopatz · 2018-06-14T17:58:52Z

pyne/srim_read.py

+                 long_straggs=None,long_stragg_units=None,lat_straggs=None,
+                 lat_stragg_units=None):
+        """Define srim specific variables """
+        super(srim, self).__init__()


You shouldn't need to call super, but it doesn't hurt.

scopatz · 2018-06-14T17:59:35Z

pyne/srim_read.py

+warn(__name__ + " is not yet QA compliant.", QAWarning)
+
+
+class srim(object):


Class name should be CapCase, so this should be Srim or similar.

scopatz · 2018-06-14T18:00:08Z

pyne/srim_read.py

+
+
+class srim(object):
+    """srim class includes srim specific variables"""


This docstring doesn't help users who don't know what srim is. Could you expand please? Thanks!

scopatz · 2018-06-14T18:00:59Z

pyne/srim_read.py

+                 ion_units=None,proj_ranges=None,proj_range_units=None,
+                 long_straggs=None,long_stragg_units=None,lat_straggs=None,
+                 lat_stragg_units=None):
+        """Define srim specific variables """


This docstring should include the meaning and type of all of the arguments and keyword arguments (except self, which doesn't need to be documented.)

scopatz · 2018-06-14T18:01:48Z

pyne/srim_read.py

+        return print_string
+
+def read_srim_output(filepath):
+    #def read_srim_output(file_path):


Please remove commented out code line

scopatz · 2018-06-14T18:02:30Z

tests/test_spectrometry.py

 import warnings
 from pyne.utils import QAWarning
 warnings.simplefilter("ignore", QAWarning)

-from pyne import gammaspec
+#from pyne import gammaspec


please remove commented out lines like this.

scopatz · 2018-06-14T18:04:04Z

tests/test_spectrometry.py

+
+def test_end_point_average_area():
+    nc = sa.end_point_average_area(gspec1,475,484,var=5)
+    #assert_equal(nc,20355.5) 


Shouldn't the tests here have an assert? Is the problem that you are doing a float comparison? You should probably use assert_almost_equals in this case

scopatz · 2018-06-14T18:04:25Z

Thanks for the update @KennellyT!

KennellyT · 2018-06-15T16:33:19Z

@scopatz- I took your comments and advice and implemented them into the pull request. readme.rst file had an issue where it states:

conda install -c conda-forge pyne

where VERSION should be replaced with the version number to be installed.

but version is not in the conda install -c statement nor is it needed to install pyne via conda via https://anaconda.org/conda-forge/pyne

I have updated srim_read and class by adding the meaning of the variables.
Thank you

py1sl · 2018-07-18T08:13:34Z

@KennellyT pleased to see this get some attention, its been on my todo list since I first wrote the initial read functions, when I was first learning python
It would be good to add peak find methods as well, i believe i wrote a mariscotti peak find routine for spectanalysis but didn't test it, not needed for this PR

KennellyT · 2018-07-18T19:12:48Z

@py1sl - I'll look at your mariscotti peak find routine/code as I have developed a peak finder function using the second derivative test and Savitzky Golay filter but I have not fully tested the function on a wide variety of gamma spectra.

katyhuff · 2018-09-13T13:34:15Z

@KennellyT ... this seems ready to merge to me.

I see that @py1sl has suggested a peak finding method as well. Perhaps we can merge this and add a future issue for peak finding. What do you think?

gonuke

Thanks for this contribution @KennellyT - sorry that it has been sitting untended for so long...

I have a few little comments, but will otherwise look to merge this soon.

gonuke · 2019-01-08T06:09:19Z

pyne/spectanalysis.py

+    y = spec.counts[c1:c2]
+    n = len(x)
+    mean = sum(x*y)/n                   
+    sigma = np.sqrt(sum(y*(x-mean)**2)/n)


Is this sigma ever used?

So the sigma variable goes into the gauss function (line 240) def gauss(x,amp,x_center,sigma):but in hindsight, this operation can be done in a much cleaner and more efficient manner. I'll take out the gauss function (line 240) and replace it with either its own variable or make the function separate from the gaussian_fit function.

But this sigma does NOT get used in the gauss() function.... that function has an argument named sigma that gets populated automatically by the curve_fit method. The initial guess for this value appears to be n/2.

Ah, I now see the sigma issue. I'll replace the n/2 with sigma. Thank you!

gonuke · 2019-01-08T06:10:09Z

pyne/spectanalysis.py

+    return end_point_average
+
+def gaussian_fit(spec,c1,c2):
+    """Plots the gaussian fit to the raw data. 


It might make sense to separate the curve fitting from the plotting in case users want to fit without plotting. This would let you reuse it in the fwhm() function below.

I concur and I will separate this function into two

gonuke · 2019-01-08T06:12:43Z

pyne/spectanalysis.py

+    net_area = p - ((n/2.0)*(count1+count2))
+    return net_area
+
+def end_point_average_area(spec,c1,c2,var=5):


Should this be equivalent to net_area if var = 1. I don’t think it is, thanks to python indexing. If it should be, then net_area should just Call this with var=1

KennellyT · 2019-01-10T14:42:28Z

Appears that my additions are failing in test_decay.py when trying to download http://data.pyne.io/origen-benchmark-hdf5-1.8.14.h5: E. It seems that the link is down: urllib.error.HTTPError: HTTP Error 404: Not Found or Unable to open/create file 'origen-benchmark-hdf5-1.8.14.h5'

gonuke · 2019-01-10T15:23:12Z

You might need to rebase your code against develop. We've recently moved that file to a different location because data.pyne.io has gone down. The default branch now gets this code from the github pyne/data repository

gonuke · 2019-03-21T11:37:49Z

I'd like to push for a merge on this @KennellyT - let me know if you want any assistance in rebasing and moving this foward

… gammaspec.py and added test to test_spectometry.py

…d new module srim_read.py with files Helium and test_srim_read.py

…rometry after reviewing comments

…y_poly

ahnaf-tahmid-chowdhury · 2024-02-16T16:42:22Z

Hi @KennellyT, are you still working on this?

scopatz reviewed Jun 4, 2018

View reviewed changes

scopatz reviewed Jun 8, 2018

View reviewed changes

scopatz reviewed Jun 14, 2018

View reviewed changes

gonuke reviewed Jan 8, 2019

View reviewed changes

gammaspec.py has a new function read_SPEC_ID_file that reads these files

f04e13a

KennellyT added 22 commits March 22, 2019 09:27

function names are undercase with underscore, added line to bottom of…

eb595d4

… gammaspec.py and added test to test_spectometry.py

calls read_spec_id_file in test

957011f

gamma_effects and tests added

7ff363b

Updated gamma_effects.py, gammaspec.py and test_spectrometry.py. Adde…

6f384c2

…d new module srim_read.py with files Helium and test_srim_read.py

gammaspec.py write_csv function changed

dad8843

srim_read.py changed

afe4438

tests srim fixed

ffd4507

spectanalysis new area functions and tests

c00e624

tests for spec updated

233f8e0

new function gaussian_fit added

6c6d784

spectanalysis.py edit

196ba3d

took out gaussian test

4fdd8bb

spectanalysis update

b4026df

changed gamma_effects, spectanalysis, srim_read,readme.rst,test_spect…

eebcd2f

…rometry after reviewing comments

assert_almost_equal

15e49e9

python 2 division issue with spectanalysis.py

8212d12

gammaspec epoly function, spectanalysis fwhm

29c890a

Added gv_format_spect2 to tests folder

4dc92ef

circleci did not accept printed equation that outputs from calc_energ…

1841771

…y_poly

assert_almost_equal used for float

f42f678

new functions epoly_fit, resolution added

d4e1a47

sigma usage in gaussian_fit

72796b1

KennellyT force-pushed the experimental_KennellyT branch from fc94593 to 72796b1 Compare March 22, 2019 14:29

gonuke added this to the Deferred milestone Aug 16, 2020

Merge branch 'develop' into experimental_KennellyT

193bdec


		"""

		mec2 = 511. #keV # Rest mass energy of an electron #.511 MeV

		warn(__name__ + " is not yet QA compliant.", QAWarning)


		class srim(object):



		class srim(object):
		"""srim class includes srim specific variables"""

gammaspec.py changes #1046

Are you sure you want to change the base?

gammaspec.py changes #1046

Conversation

KennellyT commented Jun 4, 2018

Choose a reason for hiding this comment

Choose a reason for hiding this comment

KennellyT commented Jun 4, 2018

scopatz commented Jun 4, 2018

KennellyT commented Jun 8, 2018

Choose a reason for hiding this comment

Choose a reason for hiding this comment

scopatz commented Jun 8, 2018

KennellyT commented Jun 8, 2018 • edited

KennellyT commented Jun 13, 2018

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

scopatz commented Jun 14, 2018

KennellyT commented Jun 15, 2018 • edited

py1sl commented Jul 18, 2018

KennellyT commented Jul 18, 2018

katyhuff commented Sep 13, 2018

gonuke left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

KennellyT commented Jan 10, 2019

gonuke commented Jan 10, 2019 • edited

gonuke commented Mar 21, 2019

ahnaf-tahmid-chowdhury commented Feb 16, 2024

KennellyT commented Jun 8, 2018 •

edited

KennellyT commented Jun 15, 2018 •

edited

gonuke commented Jan 10, 2019 •

edited