X-Ray Speckle Visibility Spectroscopy #293

sameera2004 · 2015-06-28T04:48:07Z

No description provided.

sameera2004 · 2015-06-28T04:49:22Z

skxray/speckle_visibility/xsvs.py

+    # number of ROI's
+    num_roi = np.max(label_array)
+
+    # create integration times


@tacaswell geometric_bin_edges wil create this time_bin for integration

@ericdill earlier I used to call the geometric_series as time_series here they are going to use that function

ericdill · 2015-07-21T13:50:59Z

skxray/speckle_visibility/xsvs.py

+
+
+def xsvs(image_sets, label_array, timebin_num=2, number_of_img=50):
+    """


can you describe what this function is doing?

Sure I will,(more description)

ericdill · 2015-07-21T13:55:15Z

Do you have an example notebook for this?

sameera2004 · 2015-07-21T14:04:43Z

@ericdill Yes I have example notebook, but some of the function name changed (like geometric_series), If @tacaswell didn't start to rebase this PR,
I will rebase and do the changes and add more documentation and can add the example notebook?

codecov-io · 2015-07-29T13:56:11Z

Uncovered Suggestions

+0.28% via ...skxray/core/utils.py#120...132
+0.28% via ...skxray/core/utils.py#120...132
+0.24% via ...kxray/io/avizo_io.py#119...129
See 7 more...

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sameera2004 · 2015-08-11T18:00:01Z

notebook

http://nbviewer.ipython.org/github/sameera2004/my_ipy_notebook/blob/master/speckle_analysis/xsvs_analysis.ipynb

danielballan · 2015-08-11T18:51:25Z

Thanks for the notebook link, @sameera2004.

sameera2004 · 2015-08-12T14:57:23Z

@danielballan sure, I will put this in skxray-examples with more clarification.

sameera2004 · 2015-08-17T18:07:54Z

Ready for review

sameera2004 · 2015-08-18T18:27:40Z

@ericdill I removed the xsvs_fitting module ready for review

# The first commit's message is: WIP: added the functions for static tests for image data, before doing xsvs # This is the 2nd commit message: DOC: fixed the documentation for the funstions # This is the 3rd commit message: ENH: added a time bining function for integration # This is the 4th commit message: C: added documentation for static tests # This is the 5th commit message: BUG: fixed a bug in the static tests function # This is the 6th commit message: BUG: removed a bug in the time_bin function # This is the 7th commit message: ENH: added a new function to find the maximum speckle count in any image # This is the 8th commit message: TST: added tests to test_time_bining, test_max_counts, test_intesnity_distribution

…attern Conflicts: skxray/speckle_visibility.py API: added a seperate dir for xsvs, and move the static tests module to that API: added new function to find the suitable center for the speckle pattern Conflicts: skxray/speckle_visibility.py 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

(Negative binomial distribution, poission distribution, gamma distribution, etc ..)

DOC: fixed the documentation DOC: fixed the documentation ENH DOC: fixed the documentation ENH BUG: fixed the bug in dict.iteritems(0 for python 3 BUG: fixed the bug for python 3 -remove the iteritems DOC: finxed the documentation ENH 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: finxed the documentation ENH 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: finxed the documentation ENH 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 DOC: finxed the documentation ENH 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 DOC: finxed the documentation ENH 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 DOC: added more documentation DOC: added more documentation ENH: added the pixel_size to the circular_average function ENH: changes to the bi edges

DOC: fixed the documentationof the xsvs.py _process 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 DOC: fixed the documentationof the xsvs.py _process 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 DOC: fixed the documentationof the xsvs.py _process 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

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 STY: fixed with pepe8 BUG: fixed the bug with python 3 in dict.values() BUG: python 3 STY: fixed with pepe8 BUG: fixed the bug with python 3 in dict.values() BUG: python 3 TST: added tests to check the static_tests one label ENH:fixed the core.py ENH:fixed the core.py ENH: moved the circular_average function to speckle_visibility.py ENH: changes to documentation Conflicts: skxray/speckle_visibility/speckle_visibility.py skxray/tests/test_speckle_visibility.py ENH: changes to documentation Conflicts: skxray/speckle_visibility/speckle_visibility.py skxray/tests/test_speckle_visibility.py TST: fixed the static_tests() and remove the unwanted parts in the core.py ENH: changes to documentation Conflicts: skxray/speckle_visibility/speckle_visibility.py skxray/tests/test_speckle_visibility.py 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 Conflicts: skxray/tests/test_speckle_visibility.py STY: fixed with pepe8 Conflicts: skxray/tests/test_speckle_visibility.py API: changed the static_test_functions and tests for them Doc: added more documentation Conflicts: skxray/core/utils.py

…tion names and fix teh bugs Conflicts: skxray/speckle_visibility/speckle_visibility.py skxray/tests/test_speckle_visibility.py Conflicts: skxray/speckle_visibility/speckle_visibility.py

ENH: added threshold mask to the bin_ceners in circular_average function

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 API: added new function for speckle count of pixels within required ROI labels ENH: added ENH API: removed the xsvs1 functions API:removed the circular_average function DOC: fixed the documentation DOC:fixed the documentation

… bin centers

…value and model value

…mize it

ericdill · 2015-09-04T18:13:52Z

skxray/core/speckle.py

+    # number of pixels per ROI
+    num_pixels = np.bincount(labels, minlength=(num_roi+1))[1:]
+
+    # probability density of detecting speckles


The docstring says that this is the probability density of detecting photons. Which one is correct?

This comment has not been addressed. Your in-line comments and docstrings do not match up

I checked the paper, it should be probability density of detecting photons, so I fixed it

sameera2004 · 2015-09-08T15:09:54Z

@ericdill I fixed this PR ready for review(docstrings and other suggestions)

ericdill · 2015-09-08T15:30:14Z

skxray/core/speckle.py

+    max_cts : int, optional
+       the brightest pixel in any ROI in any image in the image set.
+       default None; if not provided can be use roi_max_counts function
+       in skxray.roi module


Can you rewrite

default None; if not provided can be use roi_max_counts function in skxray.roi module

to say

defaults to using skxray.core.roi.roi_max_counts to determine the brightest pixel in any of the ROIs

* upstream/master: (31 commits) DOC: added spaces and fixed the documentation BUG: changed the mean_intensity to an array instead of returning a list STY: fixed with pep8 TST: fixed the bug in the tests ENH: changed the return of the mean_intensity function to an array(ealier it was returning a list) ENH: took out one [0] from the kymograph function and took out returning strings on the mean intensity function TST: took out the python 3 issue with dict_values() BLD: add updated .travis.yml file TST: took out pandas dependency in the test suite BLD: changed pip install to conda install pandas in .travis.yml APi: removed the mean_image_sets to combine mean_image_sets BLD: install pandas TST: fixed the issues with the mean intensity tests added new function to get combine mean intensities for image sets MNT: Remove pandas dep. ENH: Remove helper function TST: Rework and fix tests MNT: Mostly documentation DOC: Update the docstrings MNT: Remove lingering merge conflict TST: Remove test of private function ...

sameera2004 · 2015-09-09T16:45:25Z

@ericdill I changed the bin_edges Thanks for the suggestion, added the example notebook in skxray-examples , this is ready for review

sameera2004 · 2015-09-10T16:11:54Z

@ericdill I fixed the documentation and ready for review

ericdill · 2015-09-10T19:12:35Z

skxray/core/speckle.py

+########################################################################
+
+"""
+    X-ray speckle visibility spectroscopy(XSVS) - Dynamic information of


Remove the tabs from this module docstring

sameera2004 · 2015-09-10T20:16:36Z

@ericdill , I fixed this PR according to the comments, ready for review

ericdill · 2015-09-10T20:52:14Z

Looks good!

X-Ray Speckle Visibility Spectroscopy

sameera2004 · 2015-09-10T21:13:33Z

@ericdill Thanks for all the help and suggestions!

sameera2004 reviewed Jun 28, 2015
View reviewed changes

sameera2004 added the in progress label Jun 28, 2015

ericdill mentioned this pull request Jul 21, 2015

Xsvs1 #299

Merged

ericdill reviewed Jul 21, 2015
View reviewed changes

sameera2004 added PR: Review and removed in progress labels Aug 12, 2015

sameera2004 added 16 commits August 18, 2015 15:25

API: added new module containing fitting functions for XSVS

558270d

(Negative binomial distribution, poission distribution, gamma distribution, etc ..)

WPI: adding the main function for xsvs

a735748

ENH: changes after comments, fixed the documentation, change the func…

95470d6

…tion names and fix teh bugs Conflicts: skxray/speckle_visibility/speckle_visibility.py skxray/tests/test_speckle_visibility.py Conflicts: skxray/speckle_visibility/speckle_visibility.py

STY: fixed with pep8 and changes in importing skimage

d59d965

ENH: added threshold mask to the bin_ceners in circular_average function

API: added a new function to find normalized bin edges and normalized…

75fb1bf

… bin centers

API: added __init__.py and fixed the documentation

882a3a7

API: added new functions to do the fiiting, minmize the experimental …

9212960

…value and model value

API: added new function for diffusive_motion_contrast_factor and mini…

aae0f9b

…mize it

ENH: working with diffusion coff functions

1be549c

DOC: added more description to the documentation

f81441b

ericdill reviewed Sep 4, 2015
View reviewed changes

sameera2004 added 2 commits September 8, 2015 10:43

DOC: changed photons to speckles

180db89

ENH: changed cur

4b783d4

ericdill reviewed Sep 8, 2015
View reviewed changes

sameera2004 added 2 commits September 9, 2015 10:40

ENH: changed the bin_edges

be553a8

sameera2004 added 2 commits September 9, 2015 14:38

DOC: fixed the issue with speckles or photons

5811f1e

DOC: fixed the documentation "max_cts" docstrings

de067b9

ericdill reviewed Sep 10, 2015
View reviewed changes

ENH: changed according to comments

64a31a9

ericdill added a commit that referenced this pull request Sep 10, 2015

Merge pull request #293 from sameera2004/xsvs2

b764d5c

X-Ray Speckle Visibility Spectroscopy

ericdill merged commit b764d5c into scikit-beam:master Sep 10, 2015

sameera2004 deleted the xsvs2 branch September 28, 2015 14:17

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X-Ray Speckle Visibility Spectroscopy #293

X-Ray Speckle Visibility Spectroscopy #293

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		def xsvs(image_sets, label_array, timebin_num=2, number_of_img=50):
		"""

X-Ray Speckle Visibility Spectroscopy #293

X-Ray Speckle Visibility Spectroscopy #293

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