RCv0.3 #44

carterbox · 2017-05-05T21:12:17Z

Introduces polytope for approximate beam / polygon intersections #30
Implements __repr__ for saving and loading phantoms #40
Restructures phantoms as hierarchical structures. Removes the Feature class. #43.
Uses sphinxnb to automatically integrate demo notebooks into documentation.

…before computing intersection. Also adding distance function to Beam because it is different than Line.

…circ now required knowledge of what a Beam is which would make geometry no longer selfcontained.

…n the same Beam every time instead of making copies.

…as incorrect after they were moved from the geometry to the acquisition module.

…m` classes. Initial benchmarch shows it cuts sinogram time in half because the half_space is transformed instead if being resolved after each transformation.

…PI change.

Realized that there was no test already in existance to make sure that a sinogram is computed consistently. This test is important to make sure that changes to the underlying computational geometry does not alter the higher level behavior.

The contains functions for Circle and Polygon were incomplete because they only worked for points. This adds the ability to provide Circle, Polygons, and Meshes as input for this function. As a side effect, the edges property is added to the Polygon class.

Making hierarchical structures and organizing Features into groups was impossible or difficult. By combining Feature and Phantom into one class and allowing child parent tree-like relationships the construction of complex phantoms should be easier.

Previously polygons were not self-containting. e.g. A.contains(A) would be false, but this is inconsistent with Point behavior.

Default Phantom needs to have deep copyies of vertices otherwise rotation moves vertices multiple times.

The save and load functions were broken by the tranisition to hierarchical phantoms. This update moves the save and load functions outside of the `Phantom` class definition and uses the `repr` function to store a `Phantom` as a string.

Conflicts: xdesign/geometry.py

Rename multiple mtf functions to include authors initials. Remove phase probability computation function.

beamintersect functions were defined twice: once in geometry and once in acquistion. Removed redundant copy in geometry. Also removed text references to Feature and fixed up WetCircles.

Conflicts: xdesign/acquisition.py

It's recommended by numpy.

sinogram and angleogram didn't return the probe which made them unfit for use by art, sirt, and mlem.

carterbox · 2017-05-05T21:18:03Z

I forgot that this is going to fail because it requires a version of polytope that hasn't been released yet.

coveralls · 2017-05-07T02:48:46Z

Changes Unknown when pulling 9254d8f on RCv0.3 into ** on master**.

Moved module doc strings to top so they are picked out by sphinx. Replaced Mock module with unittest.mock. Add pages for formats and constants.

Added nbsphinx extension to allow demo notebooks to be directly converted to the webpage.

Sphinxnb

coveralls · 2017-05-18T00:15:40Z

Changes Unknown when pulling ff28b81 on RCv0.3 into ** on master**.

coveralls · 2017-05-18T00:15:41Z

Changes Unknown when pulling ff28b81 on RCv0.3 into ** on master**.

coveralls · 2017-05-23T21:35:16Z

Changes Unknown when pulling 7597008 on RCv0.3 into ** on master**.

huyuhuster · 2020-09-23T13:37:36Z

xdesign/geometry.py

@@ -67,8 +67,6 @@
 __docformat__ = 'restructuredtext en'
 __all__ = ['Entity',
           'Point',
-        #    'Superellipse',


Hello, I wonder why you deleted the ellipse here. Sometimes I need to add an ellipse phantom.

Hi @huyuhuster, there is no algorithm implemented to compute the area of intersection between a rectangle and a superellipse. Therefore, these entities cannot be used in phantoms for data acquisition simulation. If you want to try to use these entities anyways, they are still there, just removed from __all__; you can import then directly.

Hi @carterbox , thanks for your reply. Do you plan to implement the algorithm? By the way, when I simulating the acquisition, it will be very slow if the size of the probe is small, such as 1/1000. Do you have any method to speed it? Often I need to cost several hours to simulate one phantom.

I have no such plans because I'm working on other things. PRs are welcome though. 😁

OK，do you have any suggestion of speed the acquisition simulation?

No. I haven't looked at this codebase in more than a year.

carterbox and others added 30 commits November 13, 2016 02:55

Adding bounding circles to meshes and polygons to do collision check …

3111ca7

…before computing intersection. Also adding distance function to Beam because it is different than Line.

Moving beamintersect functions to the acquisition module because beam…

ba183a1

…circ now required knowledge of what a Beam is which would make geometry no longer selfcontained.

Changed the raster_scan and angle_scan functions such that they retur…

30a3bdd

…n the same Beam every time instead of making copies.

BUG: test_geometry was failing because import beamcirc and beampoly w…

cdb8f43

…as incorrect after they were moved from the geometry to the acquisition module.

Integrating new polytope rotation functions with Polygon and `Bea…

a25e9c2

…m` classes. Initial benchmarch shows it cuts sinogram time in half because the half_space is transformed instead if being resolved after each transformation.

Merge branch 'master' into polytope

f2e6ab1

Bumped some debugging print statements to the logger.

0e4b9a8

BUG: Probe did not properly translate beam.

e2f1fbd

MAINT: Update calls to polytope translation and rotation because of A…

26c1bea

…PI change.

TST: Add tests for geometry.contains()

40d310f

ENH: Add __repr__ to geometry module

6183542

ENH: Add XDesignDefault for internal testing of XDesign

3152098

BUG: Made entities self-containing

de9d792

Previously polygons were not self-containting. e.g. A.contains(A) would be false, but this is inconsistent with Point behavior.

PEP8: Removing line overflow and renaming ambiguous variables

e71bce9

API: Remove Ellipse and Superellipse from public API

ffe73f3

BUG: Fix rotation for DefaultPhantom

0b0ca48

Default Phantom needs to have deep copyies of vertices otherwise rotation moves vertices multiple times.

BUG: Fix plot_phantom_color_map by using float massatten

d4d41fc

TST: Convert material tests for new save and load

598d6aa

Merge branch 'polytope' into dev

3e5afcb

Merge branch 'tree-phantom' into dev

a926f64

Conflicts: xdesign/geometry.py

API: Make metrics compatible new hierarchical phantom

cc3b439

Rename multiple mtf functions to include authors initials. Remove phase probability computation function.

DOC: Rephase doc strings and add deprecation warnings

0fee299

Merge branch 'tree-phantom' into dev

b37be8a

TST: Remove Feature from sinogram_test

6093d71

BUG: Remove redundant function definitions left over from merge

f0290d8

beamintersect functions were defined twice: once in geometry and once in acquistion. Removed redundant copy in geometry. Also removed text references to Feature and fixed up WetCircles.

ENH: Add __repr__ to Beam and Probe

19a57e1

carterbox added 7 commits May 4, 2017 14:36

TST: Add logger.debug statement

fd66220

DOC: Improve documentation for algorithm module.

2cd929f

DOC: Improve docstrings for acquistion module.

0e11040

Conflicts: xdesign/acquisition.py

DOC: Remove traces of Feature class from docs

1de3bdb

REF: Replace hstack and vstack with concatenate and stack

fb0e42d

It's recommended by numpy.

API: Add Probe to things returned by sinogram, angleogram

74f6c67

sinogram and angleogram didn't return the probe which made them unfit for use by art, sirt, and mlem.

DOC: Updating demonstrations to use sinogram

b23d2a3

REL: Add polytope to requirements

9254d8f

carterbox added this to the 0.3.0 milestone May 7, 2017

carterbox added 5 commits May 17, 2017 14:14

DOC: Update documentation

2259cef

Moved module doc strings to top so they are picked out by sphinx. Replaced Mock module with unittest.mock. Add pages for formats and constants.

DOC: Make doc index more informative

28b1b49

DOC: Run notebooks automatically for doc page

47d1a44

Added nbsphinx extension to allow demo notebooks to be directly converted to the webpage.

DOC: Clean up mock modules for readthedocs build

092cbf3

Merge pull request #47 from tomography/sphinxnb

ff28b81

Sphinxnb

REL: Bump version to 0.3

7597008

carterbox closed this May 23, 2017

carterbox reopened this May 23, 2017

carterbox merged commit e6036dd into master May 23, 2017

carterbox deleted the RCv0.3 branch May 23, 2017 21:38

huyuhuster reviewed Sep 23, 2020

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RCv0.3 #44

RCv0.3 #44

carterbox commented May 5, 2017 •

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huyuhuster Sep 23, 2020

carterbox Sep 23, 2020

huyuhuster Sep 25, 2020

carterbox Sep 25, 2020

huyuhuster Sep 25, 2020

carterbox Sep 25, 2020

RCv0.3 #44

RCv0.3 #44

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carterbox commented May 5, 2017 •

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