docs: fix builds, other code cleanup, isolate fan stuff

README.rst

@@ -3,7 +3,7 @@ radontea
 
 |PyPI Version| |Tests Status| |Coverage Status| |Docs Status|
 
-Algorithms to compute the inverse Radon trannsform (e.g. SART, backprojection, Fourier interpolation).
+Algorithms to compute the inverse Radon transform (e.g. SART, backprojection, Fourier interpolation).
 
 
 Documentation

docs/code_reference.rst

@@ -2,28 +2,24 @@
 Code reference
 ==============
 
-
-
 Parallel beam geometry
 ::::::::::::::::::::::
+.. currentmodule:: radontea
 .. autosummary:: 
-    art
+    radon_parallel
     backproject
     fourier_map
-    radon
+    integrate
+    art
     sart
-    sum
-
+
 
 Radon transform
 ---------------
-.. automodule:: radontea._Radon
-.. currentmodule:: radontea
-.. autofunction:: radon
+.. autofunction:: radon_parallel
 
 Non-iterative reconstruction
 ----------------------------
-.. currentmodule:: radontea
 Computes the inverse Radon transform with non-iterative techniques.
 The linear system of equations that describes the forward process can be
 inverted with several algorithms, most notably the backprojection
@@ -41,19 +37,17 @@ Fourier mapping
 .. autofunction:: fourier_map
 
 
-Sum
-~~~
+Slow integration
+~~~~~~~~~~~~~~~~
 .. autofunction:: integrate
 
 
 Iterative reconstruction
 ------------------------
-.. currentmodule:: radontea
 Inversion of Radon-based tomography methods using iterative algorithms.
 The convegence of these algorithms might be slow. The implementation
 is not optimized.
 
-
 ART
 ~~~
 .. autofunction:: art
@@ -65,32 +59,23 @@ SART
 
 Fan beam geometry
 :::::::::::::::::
-.. currentmodule:: radontea
-
 .. autosummary:: 
-    get_det_coords
-    get_fan_coords
-    lino2sino
-    radon_fan_translation
-    sa_interpolate
+    fan.radon_fan
+    fan.get_det_coords
+    fan.get_fan_coords
+    fan.lino2sino
+    fan.fan_rec
 
 
 Coordinate transforms
 ---------------------
 
-.. autofunction:: get_det_coords
-.. autofunction:: get_fan_coords
-.. autofunction:: lino2sino
-.. autofunction:: radon_fan_translation
-
-
-Non-iterative reconstruction
-----------------------------
-.. currentmodule:: radontea
-The inverse Radon transform with non-iterative techniques for
-a fan-beam geometry.
+.. autofunction:: radontea.fan.get_det_coords
+.. autofunction:: radontea.fan.get_fan_coords
+.. autofunction:: radontea.fan.radon_fan
+.. autofunction:: radontea.fan.lino2sino
 
-Interpolation
-~~~~~~~~~~~~~
-.. autofunction:: sa_interpolate
 
+Reconstruction
+--------------
+.. autofunction:: radontea.fan.fan_rec

docs/conf.py

@@ -33,16 +33,11 @@
 autodoc_member_order = 'bysource'
 autodoc_mock_imports = install_requires
 
-# There should be a file "setup.py" that has the property "version"
-from setup import author, authors, description, name, version, year
-projectname = name
-projectdescription = description
-
 # Display link to GitHub repo instead of doc on rtfd
 rst_prolog = """
 :github_url: https://github.com/RI-imaging/radontea
 """
-
+print("ASDASD")
 
 # -- General configuration ------------------------------------------------
 
@@ -77,16 +72,18 @@
 master_doc = 'index'
 
 # General information about the project.
-project = projectname
-copyright = year+", "+author
+project = 'radontea'
+copyright = '2017, Paul Müller'
+author = 'Paul Müller'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
 # The full version, including alpha/beta/rc tags.
-release = version
+exec(open(op.join(pdir, "radontea/_version.py")).read())
+release = version #@UndefinedVariable
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -203,7 +200,7 @@
 #html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = projectname+'doc'
+htmlhelp_basename = project+'doc'
 
 
 # -- Options for LaTeX output ---------------------------------------------
@@ -223,7 +220,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-  ('index', projectname+'.tex', projectname+' Documentation',
+  ('index', project+'.tex', project+' Documentation',
    author, 'manual'),
 ]
 
@@ -253,8 +250,8 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', projectname, projectname+' Documentation',
-     authors, 1)
+    ('index', project, project+' Documentation',
+     author, 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -267,9 +264,9 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', projectname, projectname+u' Documentation',
-   author, projectname,
-   projectdescription,
+  ('index', project, project + ' Documentation',
+   author, project,
+   "Methods for the inversion of the Radon transform",
    'Numeric'),
 ]
 

radontea/__init__.py

@@ -4,10 +4,9 @@
 from .alg_art import art  # noqa F401
 from .alg_sart import sart  # noqa F401
 
-from .fan import fan_rec, lino2sino  # noqa F401
+from . import fan  # noqa F401
 
 from .rdn_prl import radon_parallel  # noqa F401
-from .rdn_fan import radon_fan  # noqa F401
 
 from .threed import volume_recon  # noqa F401
 

radontea/fan.py

@@ -2,9 +2,10 @@
 import scipy.interpolate
 
 from .rdn_fan import get_fan_coords
+from .rdn_fan import get_det_coords, radon_fan  # noqa F401
 
 
-def fan_rec(linogram, lDS, method, stepsize=1, det_spacing=1,
+def fan_rec(linogram, lds, method, stepsize=1, det_spacing=1,
             numang=None, count=None, max_count=None, **kwargs):
     """2D synthetic aperture reconstruction
 
@@ -16,7 +17,7 @@ def fan_rec(linogram, lDS, method, stepsize=1, det_spacing=1,
     ----------
     linogram: 2d ndarray of shape (D, A)
         Input linogram from the synthetic aprture measurement.
-    lDS: float
+    lds: float
         Distance in pixels between source and detector.
     method: callable
         Reconstruction method, e.g. `radontea.backproject`.
@@ -31,30 +32,22 @@ def fan_rec(linogram, lDS, method, stepsize=1, det_spacing=1,
         of `count.value` is incremented.
     **kwargs: dict
         Keyword arguments for `method`.
-
-
-    See Also
-    --------
-    radon_fan_translation
-        The forward process.
-    lino2sino
-        Linogram to sinogram conversion.
     """
-    sino, angles = lino2sino(linogram, lDS, numang=numang, retang=True,
+    sino, angles = lino2sino(linogram, lds, numang=numang, retang=True,
                              stepsize=stepsize, det_spacing=det_spacing,
                              count=count, max_count=max_count)
     return method(sino, angles, **kwargs)
 
 
-def lino2sino(linogram, lDS, stepsize=1, det_spacing=1, numang=None,
+def lino2sino(linogram, lds, stepsize=1, det_spacing=1, numang=None,
               retang=False, count=None, max_count=None):
     """Convert linogram to sinogram for an equispaced detector.
 
     Parameters
     ----------
     linogram: real 2d ndarray of shape (D, A*)
         Linogram from synthetic aperture measurements.
-    lDS: float
+    lds: float
         Distance from point source to detector in au.
     stepsize: float
         Translational increment of object in au (stepsize in D).
@@ -70,28 +63,18 @@ def lino2sino(linogram, lDS, stepsize=1, det_spacing=1, numang=None,
         by the total number of steps. At each step, the value
         of `count.value` is incremented.
 
-
     Returns
     -------
     sinogram: 2d ndarray of shape (D, A)
         The distortion-corrected sinogram.
         If retang is True, then the equispaced angles are returned as
         well.
 
-
     Notes
     -----
     This function can be used to convert a linogram obtained with
     fan-beam tomography to a sinogram, which then can be reconstructed
     with the backprojection or fourier mapping algorithms.
-
-
-    See Also
-    --------
-    radon_fan_translation
-        The forward process.
-    sa_interpolate
-        Backprojection that uses this function.
     """
     if not np.isreal(linogram):
         raise ValueError("`linogram` must be a real-valued array!")
@@ -107,7 +90,7 @@ def lino2sino(linogram, lDS, stepsize=1, det_spacing=1, numang=None,
         max_count.value += D + A
 
     # equispaced angles and corresponding lateral detector positions.
-    angles, xang = get_fan_coords(det_size, det_spacing, lDS, A)
+    angles, xang = get_fan_coords(det_size, det_spacing, lds, A)
 
     uorig = linogram
     lino = np.zeros((D, A))
@@ -135,7 +118,7 @@ def lino2sino(linogram, lDS, stepsize=1, det_spacing=1, numang=None,
         # depends on the current angle.
         # What is the distance b/w the center of the object (centered at
         # lDS/2) to the axis alpha = 0?
-        deltaD = np.tan(alpha) * lDS / 2
+        deltaD = np.tan(alpha) * lds / 2
 
         # Shearing:
         # At larger angles, the object seems bigger on the screen.

radontea/rdn_fan.py

@@ -5,7 +5,7 @@
 
 
 def get_det_coords(size, spacing):
-    """Compute pixel-center positions for 2d detector
+    """Compute pixel-center positions for 2D detector
 
     The centers of the pixels of a detector are usually not aligned to
     a pixel grid. If we center the detector at the origin, odd images
@@ -51,13 +51,11 @@ def get_fan_coords(size, spacing, distance, numang):
     numang: int
         Number of angles.
 
-
     Returns
     -------
     angles, latpos: two 1D ndarrays
         Angles and pixel coordinates at the detector.
 
-
     Notes
     -----
     Actually one would not need to define spacing and distance, but for
@@ -108,7 +106,6 @@ def radon_fan(arr, det_size, det_spacing=1, shift_size=1,
     that its lower boundary starts at (det_size/2, 0) and its upper
     boundary ends at (-det_size/2, 0) at increments of `shift_size`.
 
-
     Parameters
     ----------
     arr: ndarray, shape (N,N)
@@ -134,20 +131,16 @@ def radon_fan(arr, det_size, det_spacing=1, shift_size=1,
         by the total number of steps. At each step, the value
         of `count.value` is incremented.
 
-
     Returns
     -------
     outarr: ndarray of floats, shape (N+det_size,det_size)
         Linogram of the input image. Where N+det_size determines the
         lateral position of the sample.
 
-
     See Also
     --------
     scipy.ndimage.interpolation.rotate :
         The interpolator used to rotate the image.
-    radon_prl
-        The original Radon transform.
     """
     N = arr.shape[0]
     if lD is None:

radontea/threed.py

@@ -3,11 +3,6 @@
 import time
 
 
-def run(method, kwargs, target, target_index):
-    res = method(**kwargs)
-    target[target_index] = res
-
-
 def do_work(in_queue, out_list, count, max_count):
     while True:
         item = in_queue.get()
@@ -46,7 +41,7 @@ def volume_recon(func2d, sinogram=None, angles=None,
         value of `max_count.value` is set initially and the value
         of `count.value` is incremented until it reaches the end
         of the algorithm (`max_count.value`).
-    *kwargs: dict
+    **kwargs: dict
         Additional keyword arguments to `func2d`.
 
     Returns