Merge pull request #57 from tomography/tike

Scope reduction and API change

.gitignore

@@ -103,3 +103,4 @@ Thumbs.db
 .spyderworkspace
 *.*~
 *~
+.*

.travis.yml

@@ -2,8 +2,8 @@ language: python
 
 python:
   - "2.7"
-  - "3.4"
   - "3.5"
+  - "3.6"
 
 os:
   - linux
@@ -30,13 +30,18 @@ before_install:
   - conda install anaconda-client
 
 install:
-  - conda install python=$TRAVIS_PYTHON_VERSION nose six numpy scipy matplotlib python-coveralls pillow cached-property setuptools
-  - pip install phasepack polytope
+  - conda install python=$TRAVIS_PYTHON_VERSION setuptools
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "3.5" ]]; then
+      conda install python-coveralls;
+    fi
+  - conda install nose six numpy scipy matplotlib requests cached-property
+  - pip install phasepack
   - conda info -a
   - python setup.py build_ext --inplace
-
 script:
-  - nosetests tests --with-coverage
+  - nosetests tests -vs --with-coverage
 
 after_success:
-  - coveralls
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "3.5" ]]; then
+      coveralls;
+    fi

docs/source/api/xdesign.acquisition.rst

@@ -16,5 +16,4 @@
 
   .. autosummary::
 
-    sinogram
-    raster_scan
+    raster_scan2D

docs/source/bibtex/refs.bib

@@ -1,3 +1,34 @@
+@article{Gordon1970,
+author = {Gordon, Richard and Bender, Robert and Herman, Gabor T.},
+doi = {10.1016/0022-5193(70)90109-8},
+isbn = {0022-5193 (Print)$\backslash$n0022-5193 (Linking)},
+issn = {10958541},
+journal = {Journal of Theoretical Biology},
+month = {dec},
+number = {3},
+pages = {471--481},
+pmid = {5492997},
+title = {{Algebraic Reconstruction Techniques (ART) for three-dimensional electron microscopy and X-ray photography}},
+url = {https://doi.org/10.1016/0022-5193(70)90109-8},
+volume = {29},
+year = {1970}
+}
+
+
+@article{Gilbert1972,
+abstract = {A method of reconstruction (ART) has recently been proposed (Gordon, Bender {\&} Herman, 1970) which consists in iteratively changing a trial structure until its projections are consistent with the original projections of the unknown structure. It is shown that in general ART produces erroneous reconstructions. An alternative iterative method is proposed which will give correct reconstructions under certain conditions. One of the potential applications of this method is in determining the three-dimensional structure of objects from electron micrographs. {\textcopyright} 1972.},
+author = {Gilbert, Peter},
+doi = {10.1016/0022-5193(72)90180-4},
+isbn = {0022-5193},
+issn = {10958541},
+journal = {Journal of Theoretical Biology},
+pmid = {5070894},
+title = {{Iterative methods for the three-dimensional reconstruction of an object from projections}},
+year = {1972},
+url = {https://doi.org/10.1016/0022-5193(72)90180-4}
+}
+
+
 @article{AlRaoush:03,
 author  = {Al-Raoush R and Thompson K and Willson CS},
 title   = {Comparison of network generation techniques for unconsolidated porous media},

docs/source/conf.py

@@ -336,7 +336,7 @@ def __getattr__(cls, name):
 MOCK_MODULES = ['numpy',
                 'matplotlib', 'matplotlib.pyplot', 'matplotlib.patches',
                 'matplotlib.path', 'matplotlib.patheffects', 'matplotlib.axis',
-                'polytope',
+                'matplotlib.collections',
                 'cached_property',
                 'scipy', 'scipy.stats', 'scipy.ndimage', 'scipy.spatial',
                 'cycler',

meta.yaml

@@ -20,6 +20,7 @@ requirements:
     - six
     - matplotlib
     - phasepack
+    - pyfftw
     - cached-property
     - polytope
 

requirements.txt

@@ -4,7 +4,6 @@ six
 numpy
 scipy
 matplotlib
+requests
 phasepack
 cached-property
-polytope >= 0.1.4
-requests

tests/DynamicRange[10, False].txt

@@ -1 +1 @@
-Phantom(geometry=Polygon(vertices=[Point([1.0, 1.0]), Point([0.0, 1.0]), Point([0.0, 0.0]), Point([1.0, 0.0])], sign=1), children=[Phantom(geometry=Circle(center=Point([0.44538880985485596, 0.84280137568431979]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=4.0)), Phantom(geometry=Circle(center=Point([0.90570491543840059, 0.39801132897255548]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=256.0)), Phantom(geometry=Circle(center=Point([0.75525940832233152, 0.52528305478379145]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=16.0)), Phantom(geometry=Circle(center=Point([0.12465655092315107, 0.13873813723884812]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=512.0)), Phantom(geometry=Circle(center=Point([0.080191097760285004, 0.79104236485444579]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=2.0)), Phantom(geometry=Circle(center=Point([0.74338715708111913, 0.82376062971596675]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=64.0)), Phantom(geometry=Circle(center=Point([0.91879104945366852, 0.76176374368963318]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=128.0)), Phantom(geometry=Circle(center=Point([0.16599012263531657, 0.62243089366158333]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=8.0)), Phantom(geometry=Circle(center=Point([0.51911728153131276, 0.42532919749170817]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.67292729643635674, 0.1151972876756111]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=32.0))], material=None)
+Phantom(geometry=Rectangle(Point([-0.5, -0.5]), [1, 1]), children=[Phantom(geometry=Circle(center=Point([-0.55461119014514404, -0.15719862431568021]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=4.0)), Phantom(geometry=Circle(center=Point([-0.094295084561599407, -0.60198867102744447]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=256.0)), Phantom(geometry=Circle(center=Point([-0.24474059167766848, -0.47471694521620855]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=16.0)), Phantom(geometry=Circle(center=Point([-0.87534344907684891, -0.86126186276115191]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=512.0)), Phantom(geometry=Circle(center=Point([-0.91980890223971501, -0.20895763514555421]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=2.0)), Phantom(geometry=Circle(center=Point([-0.25661284291888087, -0.17623937028403325]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=64.0)), Phantom(geometry=Circle(center=Point([-0.081208950546331482, -0.23823625631036682]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=128.0)), Phantom(geometry=Circle(center=Point([-0.83400987736468346, -0.37756910633841667]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=8.0)), Phantom(geometry=Circle(center=Point([-0.4808827184686873, -0.57467080250829183]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([-0.32707270356364326, -0.8848027123243889]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=32.0))], material=None)

tests/DynamicRange[10, True].txt

@@ -1 +1 @@
-Phantom(geometry=Polygon(vertices=[Point([1.0, 1.0]), Point([0.0, 1.0]), Point([0.0, 0.0]), Point([1.0, 0.0])], sign=1), children=[Phantom(geometry=Circle(center=Point([0.11719840140783656, 0.065027299680040715]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=4.0)), Phantom(geometry=Circle(center=Point([0.42397162509775999, 0.16657748069349226]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=256.0)), Phantom(geometry=Circle(center=Point([0.68295784506262869, 0.1597695938687313]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=16.0)), Phantom(geometry=Circle(center=Point([0.86043018985322217, 0.17125151853085241]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=512.0)), Phantom(geometry=Circle(center=Point([0.16146562976033307, 0.43482729277909549]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=2.0)), Phantom(geometry=Circle(center=Point([0.37861186496911303, 0.41239482052709042]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=64.0)), Phantom(geometry=Circle(center=Point([0.63350557013674158, 0.37018492028161648]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=128.0)), Phantom(geometry=Circle(center=Point([0.92819957978658263, 0.4100661470358069]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=8.0)), Phantom(geometry=Circle(center=Point([0.071379507274735868, 0.57728430323361668]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.32339116246269262, 0.64249012766594049]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=32.0))], material=None)
+Phantom(geometry=Rectangle(Point([0.0, 0.0]), [1, 1]), children=[Phantom(geometry=Circle(center=Point([-0.38280159859216345, -0.43497270031995927]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=4.0)), Phantom(geometry=Circle(center=Point([-0.076028374902240015, -0.33342251930650774]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=256.0)), Phantom(geometry=Circle(center=Point([0.18295784506262869, -0.3402304061312687]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=16.0)), Phantom(geometry=Circle(center=Point([0.36043018985322217, -0.32874848146914759]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=512.0)), Phantom(geometry=Circle(center=Point([-0.33853437023966693, -0.065172707220904513]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=2.0)), Phantom(geometry=Circle(center=Point([-0.12138813503088697, -0.087605179472909578]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=64.0)), Phantom(geometry=Circle(center=Point([0.13350557013674158, -0.12981507971838352]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=128.0)), Phantom(geometry=Circle(center=Point([0.42819957978658263, -0.089933852964193095]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=8.0)), Phantom(geometry=Circle(center=Point([-0.42862049272526415, 0.07728430323361668]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([-0.17660883753730738, 0.14249012766594049]), radius=0.0625, sign=1), children=[], material=SimpleMaterial(mass_attenuation=32.0))], material=None)

tests/HyperbolicConcentric[].txt

@@ -1 +1 @@
-Phantom(geometry=None, children=[Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.5), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.4898979485566356), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.4795831523312719), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.469041575982343), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.458257569495584), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.447213595499958), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.43588989435406744), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.4242640687119285), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.41231056256176607), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.4), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.3872983346207417), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.37416573867739417), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.36055512754639896), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.34641016151377546), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.33166247903554), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.316227766016838), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.30000000000000004), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.28284271247461906), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.2645751311064591), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.2449489742783178), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.223606797749979), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.2), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.17320508075688773), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.14142135623730953), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.5, 0.5]), radius=0.1), children=[], material=SimpleMaterial(mass_attenuation=1.0))], material=None)
+Phantom(geometry=None, children=[Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.5, sign=1), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.4898979485566356, sign=1), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.4795831523312719, sign=1), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.469041575982343, sign=1), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.458257569495584, sign=1), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.447213595499958, sign=1), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.43588989435406744, sign=1), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.4242640687119285, sign=1), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.41231056256176607, sign=1), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.4, sign=1), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.3872983346207417, sign=1), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.37416573867739417, sign=1), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.36055512754639896, sign=1), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.34641016151377546, sign=1), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.33166247903554, sign=1), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.316227766016838, sign=1), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.30000000000000004, sign=1), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.28284271247461906, sign=1), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.2645751311064591, sign=1), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.2449489742783178, sign=1), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.223606797749979, sign=1), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.2, sign=1), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.17320508075688773, sign=1), children=[], material=SimpleMaterial(mass_attenuation=1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.14142135623730953, sign=1), children=[], material=SimpleMaterial(mass_attenuation=-1.0)), Phantom(geometry=Circle(center=Point([0.0, 0.0]), radius=0.1, sign=1), children=[], material=SimpleMaterial(mass_attenuation=1.0))], material=None)