pyrost.simulation and pyrost.abberations_fit are fully revamped, v 0.3.0

MANIFEST.in

 graft tests
 graft pyrost/config
 graft pyrost/bin
+graft pyrost/ini_templates
 exclude dev.pyx
 include pytest.ini
 include LICENSE

dev.pxd

 #cython: language_level=3, boundscheck=False, wraparound=False, initializedcheck=False, cdivision=True, embedsignature=True
-cdef extern from "gsl/gsl_math.h":
-
-    ctypedef struct gsl_function:
-        double (* function) (double x, void * params) nogil
-        void * params
-
-cdef extern from "gsl/gsl_integration.h":
-
-    ctypedef struct gsl_integration_workspace
-    ctypedef struct gsl_integration_qaws_table
-    ctypedef struct gsl_integration_qawo_table
-    ctypedef struct gsl_integration_cquad_workspace
-    cdef enum:
-        GSL_INTEG_GAUSS15 = 1
-        GSL_INTEG_GAUSS21 = 2
-        GSL_INTEG_GAUSS31 = 3
-        GSL_INTEG_GAUSS41 = 4
-        GSL_INTEG_GAUSS51 = 5
-        GSL_INTEG_GAUSS61 = 6
-    cdef enum gsl_integration_qawo_enum:
-        GSL_INTEG_COSINE, GSL_INTEG_SINE
-
-    gsl_integration_cquad_workspace *  gsl_integration_cquad_workspace_alloc (size_t n) nogil
-    
-    void  gsl_integration_cquad_workspace_free (gsl_integration_cquad_workspace * w) nogil
-
-    int gsl_integration_cquad (gsl_function * f, double a, double b, double epsabs, double epsrel, gsl_integration_cquad_workspace * workspace, double * result, double * abserr, size_t * nevals) nogil
-
-    gsl_integration_workspace *  gsl_integration_workspace_alloc(size_t n) nogil
-
-    void  gsl_integration_workspace_free(gsl_integration_workspace * w) nogil
-
-    int  gsl_integration_qag(gsl_function *f, double a, double b, double epsabs, double epsrel, size_t limit, int key, gsl_integration_workspace * workspace, double * result, double * abserr) nogil
-
 cdef extern from "gsl/gsl_rng.h":
 
     ctypedef struct gsl_rng_type

dev.pyxbld

 def make_ext(modname, pyxfilename):
-    from distutils.extension import Extension
+    from distutils.core import Extension
     import numpy
     from Cython.Build import cythonize
     import os

docs/conf.py

@@ -22,7 +22,7 @@ copyright = '2020, Nikolay Ivanov'
 author = 'Nikolay Ivanov'
 
 # The full version, including alpha/beta/rc tags
-release = '0.2.0'
+release = '0.3.0'
 
 
 # -- General configuration ---------------------------------------------------

docs/reference/c_funcs/aperture_wp.rst

-aperture_wp
-===========
-
-.. autofunction:: pyrost.bin.aperture_wp
\ No newline at end of file

docs/reference/c_funcs/bar_positions.rst

+bar_positions
+=============
+
+.. autofunction:: pyrost.bin.bar_positions
\ No newline at end of file

docs/reference/c_funcs/fft_convolve.rst

+fft_convolve
+============
+
+.. autofunction:: pyrost.bin.fft_convolve
\ No newline at end of file

docs/reference/c_funcs/fft_convolve_scan.rst

+fft_convolve_scan
+=================
+
+.. autofunction:: pyrost.bin.fft_convolve_scan
\ No newline at end of file

docs/reference/c_funcs/fhf_wp.rst

+fhf_wp
+======
+
+.. autofunction:: pyrost.bin.fhf_wp
\ No newline at end of file

docs/reference/c_funcs/fhf_wp_scan.rst

+fhf_wp_scan
+===========
+
+.. autofunction:: pyrost.bin.fhf_wp_scan
\ No newline at end of file

docs/reference/c_funcs/fraunhofer_1d.rst

-fraunhofer_1d
-=============
-
-.. autofunction:: pyrost.bin.fraunhofer_1d
\ No newline at end of file

docs/reference/c_funcs/fraunhofer_1d_scan.rst

-fraunhofer_1d_scan
-==================
-
-.. autofunction:: pyrost.bin.fraunhofer_1d_scan
\ No newline at end of file

docs/reference/c_funcs/lens_wp.rst

-lens_wp
-=======
-
-.. autofunction:: pyrost.bin.lens_wp
\ No newline at end of file

docs/reference/c_funcs/rsc_wp.rst

+rsc_wp
+======
+
+.. autofunction:: pyrost.bin.rsc_wp
\ No newline at end of file

docs/reference/classes/st_sim.rst

@@ -2,4 +2,7 @@ STSim
 =====
 
 .. autoclass:: pyrost.simulation.STSim
-    :members:
\ No newline at end of file
+    :members:
+    :exclude-members: update_bar_positions
+
+    .. automethod:: update_bar_positions
\ No newline at end of file

docs/reference/st_sim_c_ref.rst

@@ -12,10 +12,12 @@ the wavefronts. All the functions are written in `Cython`_.
     :maxdepth: 1
     :caption: Contents
 
-    c_funcs/lens_wp
-    c_funcs/aperture_wp
-    c_funcs/fraunhofer_1d
-    c_funcs/fraunhofer_1d_scan
+    c_funcs/rsc_wp
+    c_funcs/fhf_wp
+    c_funcs/fhf_wp_scan
+    c_funcs/bar_positions
     c_funcs/barcode_profile
+    c_funcs/fft_convolve
+    c_funcs/fft_convolve_scan
     c_funcs/make_frames
     c_funcs/make_whitefield
\ No newline at end of file

docs/tutorials/1d_sim.rst

@@ -151,6 +151,7 @@ In the end you can save the results to a CXI file.
     /frame_selector          Group
     /frame_selector/good_frames Dataset {200}
     /speckle_tracking        Group
+    /speckle_tracking/error_frame Dataset {1, 2000}
     /speckle_tracking/dfs    Dataset {SCALAR}
     /speckle_tracking/dss    Dataset {SCALAR}
     /speckle_tracking/mask   Dataset {1, 2000}

docs/tutorials/diatom.rst

@@ -158,8 +158,10 @@ the phase profile with polynomial function using :class:`pyrost.AbberationsFit`.
 .. doctest::
 
     >>> data.update_phase(st_res)
-    >>> fit_ss = data.fit_phase(axis=0, max_order=3)
-    >>> fit_fs = data.fit_phase(axis=1, max_order=3)
+    >>> fit_obj_ss = data.get_fit(axis=0)
+    >>> fit_ss = fit_obj_ss.fit(max_order=3)
+    >>> fit_obj_fs = data.get_fit(axis=1)
+    >>> fit_fs = fit_obj_fs.fit(max_order=3)
 
     >>> fig, ax = plt.subplots(figsize=(10, 10)) # doctest: +SKIP
     >>> ax.imshow(data.get('phase')) # doctest: +SKIP
@@ -176,12 +178,12 @@ the phase profile with polynomial function using :class:`pyrost.AbberationsFit`.
 .. doctest::
 
     >>> fig, axes = plt.subplots(1, 2, figsize=(16, 6)) # doctest: +SKIP
-    >>> axes[0].plot(data.get('phase').mean(axis=0), label='Reconstructed profile') # doctest: +SKIP
-    >>> axes[0].plot(data.get_fit(axis=1).phase_model(fit_fs['ph_fit'], fit_fs['pixels']), # doctest: +SKIP
-    >>>              label='Polynomial fit') # doctest: +SKIP
+    >>> axes[0].plot(fit_obj_fs.pixels, fit_obj_fs.phase, label='Reconstructed profile') # doctest: +SKIP
+    >>> axes[0].plot(fit_obj_fs.pixels, fit_obj_fs.model(fit_fs['ph_fit']), # doctest: +SKIP
+                     label='Polynomial fit') # doctest: +SKIP
     >>> axes[0].set_xlabel('fast axis', fontsize=15) # doctest: +SKIP
-    >>> axes[1].plot(data.get('phase').mean(axis=1), label='Reconstructed profile') # doctest: +SKIP
-    >>> axes[1].plot(data.get_fit(axis=0).phase_model(fit_ss['ph_fit'], fit_ss['pixels']), # doctest: +SKIP
+    >>> axes[1].plot(fit_obj_ss.pixels, fit_obj_ss.phase, label='Reconstructed profile') # doctest: +SKIP
+    >>> axes[1].plot(fit_obj_ss.pixels, fit_obj_ss.model(fit_ss['ph_fit']), # doctest: +SKIP
     >>>              label='Polynomial fit') # doctest: +SKIP
     >>> axes[1].set_xlabel('slow axis') # doctest: +SKIP
     >>> for ax in axes: # doctest: +SKIP
@@ -224,6 +226,7 @@ In the end you can save the results to a CXI file.
     /frame_selector          Group
     /frame_selector/good_frames Dataset {120}
     /speckle_tracking        Group
+    /speckle_tracking/error_frame Dataset {516, 1556}
     /speckle_tracking/dfs    Dataset {SCALAR}
     /speckle_tracking/dss    Dataset {SCALAR}
     /speckle_tracking/mask   Dataset {516, 1556}