Xsvs1 #299
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Xsvs1 #299
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This collapesses 50 commit into one to make rebasing on to the inverted library easier. WIP: added the functions for static tests for image data, before doing xsvs DOC: fixed the documentation for the funstions ENH: added a time bining function for integration C: added documentation for static tests BUG: fixed a bug in the static tests function BUG: removed a bug in the time_bin function ENH: added a new function to find the maximum speckle count in any image TST: added tests to test_time_bining, test_max_counts, test_intesnity_distribution STY: both files are fixed with pep8 DOC: fixed the documentation,and change the order of the functions API: added new function to find the suitable center for the speckle pattern API: added a seperate dir for xsvs, and move the static tests module to that TST: start working on tests for the speckle_visibility module sttaic tests BUG: fixed the bug in dict.iteritems(0 for python 3 BUG: fixed the bug for python 3 -remove the iteritems BUG: changed the dict.items() back to dict.iteritems() -Problem with python 3 DOC: changed the documentation for speckle_visibility.py DOC: fixed the documentation of suitable center API: added new function for saxs_circular_average TST: added test function for circular_average function to find saxs integration TST: fixed the nx=6 in the tests for circular_average ENH: added the pixel_size to the circular_average function BUG: fixed the bug with python 3 ( dict.iteritem() not working) API moved the circular_average function to core.py and the test to test_core.py BUG: finxed the bug with python 3 in dict.values() BUG: python 3 TST: added tests to check the static_tests one label ENH: moved the circular_average function to speckle_visibility.py ENH: changes to documentation TST: fixed the static_tests() and remove the unwanted parts in the core.py BUG: added list() to dict.values) for python 3 STY: fixed with pepe8 API: changed the static_test_functions and tests for them Doc: added more documentation ENH: changes after comments, fixed the documentation, change the function names and fix teh bugs STY: fixed with pep8 and changes in importing skimage ENH: added threshold mask to the bin_ceners in circular_average function DOC: fixed the documentation API: moved the speckle_visibility file, del the speckle_visibility dir, and rename the module to speckle_analysis.py BUG: removed the label_num = np.unique(labels)[1:] API: changed the skxray/tests/test_speckle_visibility.py to skxray/tests/test_speckle_analysis.py PI: added new function for speckle count of pixels within required ROI labels API: moved the geometrics_bin_edges to core and fixed the changes according to Tom's comments ENH: fixed the py3 issue ENH: ENH: changed the mean_intensity functions BUG: fixed the bugs in the code, fixed after Toms' comments, Added inde_list when combining the mean intensity of label arrays, not to add into wrong labels API: changed the function name geometric_bin_edges to geometric_series ENH: added index(labels list) to roi_pixels functions ENH: made the num in roi_kymograph as required ENH: changed according to Tom's comments BUG: fixed in the combine_mean_int BUG: fixed the combine_mean_intensity function using np.vstack DOC: fixed the documentation images dimensions are: (num_img, num_rows, num_cols)
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@ericdill any more comments? |
Closed
| @@ -1223,3 +1223,44 @@ def multi_tau_lags(multitau_levels, multitau_channels): | |||
| lag_steps = np.append(lag_steps, np.array(lag)) | |||
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| return tot_channels, lag_steps | |||
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| def geometric_series(common_ratio, number_of_images, first_term=1): | |||
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Previous conversation in other thread:
@sameera2004 what is the purpose of this function? It does not appear anywhere else in this PR except for its test
@ericdill All these functions are going to use in XSVS2.
As an example in XSVS they collect 100 images, each take in1ms,
Then they choose ROI and see the photon count probability density in that ROI for 1ms, 2ms, 4ms, 8s, 16ms, etc
or 1ms, 3ms, 9ms, 27ms, etc like,
This will create for 100 images, common ratio=2, geometric_series = 1, 2, 4, 8, 16, 32, 64
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But this function is not used in your other pr, #293
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@sameera2004 can you upload the data that you use for this notebook somewhere? google drive or dropbox would work |
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can you update the notebook that goes along with this PR? |
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@ericdill I sent you the data I used for this analysis |
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merging for now. will probably edit during review of #293 |
ericdill
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re-basing of #283