Merge branch 'dev0'

README.md

+## Current build status
+[![PyPI](https://img.shields.io/pypi/v/pyrost?color=brightgreen)](https://pypi.org/project/pyrost/)
+[![Documentation Status](https://readthedocs.org/projects/robust-speckle-tracking/badge/?version=latest)](https://robust-speckle-tracking.readthedocs.io/en/latest/?badge=latest)
+
 # pyrost
 Python Robust Speckle Tracking (**pyrost**) is a library for wavefront metrology
 and sample imaging based on ptychographic speckle tracking algorithm. This
@@ -15,7 +19,6 @@ The documentation can be found on [Read the Docs](https://robust-speckle-trackin
 - [h5py](https://www.h5py.org) 2.10.0 or later.
 - [NumPy](https://numpy.org) 1.19.0 or later.
 - [SciPy](https://scipy.org) 1.5.2 or later.
-- [pyFFTW](https://github.com/pyFFTW/pyFFTW) 0.12.0 or later.
 
 ## Installation
 We recommend **not** building from source, but install the release from [pypi](https://test.pypi.org/project/rst/)

docs/conf.py

@@ -22,7 +22,7 @@ copyright = '2020, Nikolay Ivanov'
 author = 'Nikolay Ivanov'
 
 # The full version, including alpha/beta/rc tags
-release = '0.1.0'
+release = '0.1.1'
 
 
 # -- General configuration ---------------------------------------------------

docs/install.rst

@@ -16,12 +16,10 @@ pyrost has the following **mandatory** runtime dependencies:
   CXI files.
 * `NumPy <https://numpy.org>`_ 1.19.0 or later.
 * `SciPy <https://scipy.org>`_ 1.5.2 or later.
-* `pyFFTW <https://github.com/pyFFTW/pyFFTW>`_ 0.12.0 or later, which is used
-  for the Fourier Transform wavefront reconstruction (:func:`pyrost.bin.ct_integrate`).
 
 Packages
 --------
-pyrost packages are available through `pypi <https://test.pypi.org/project/rst/>`_ on
+pyrost packages are available through `pypi <https://pypi.org/project/pyrost/>`_ on
 OS X as for now.
 
 pip

docs/rtd_environment.yml

@@ -15,5 +15,4 @@ dependencies:
   - sphinx
   - sphinx_rtd_theme
   - mock
-  - pillow
-  - pyfftw
+  - pillow
\ No newline at end of file
\ No newline at end of file

environment.yml

@@ -10,5 +10,4 @@ dependencies:
   - llvm-openmp
   - h5py
   - numpy
-  - scipy
-  - pyfftw
+  - scipy
\ No newline at end of file
\ No newline at end of file

pyrost/bin/st_utils.pyx

@@ -5,7 +5,6 @@ from libc.math cimport sqrt, exp, pi, floor
 from cython.parallel import prange
 cimport openmp
 from posix.time cimport clock_gettime, timespec, CLOCK_REALTIME
-from pyfftw import FFTW, empty_aligned
 
 ctypedef fused float_t:
     np.float64_t
@@ -631,12 +630,9 @@ def ct_integrate(float_t[:, ::1] sx_arr, float_t[:, ::1] sy_arr):
     dtype = np.float64 if float_t is np.float64_t else np.float32
     cdef:
         int a = sx_arr.shape[0], b = sx_arr.shape[1], i, j, ii, jj
+        float_t[:, ::1] s_asdi = np.empty((2 * a, 2 * b), dtype=dtype)
+        complex_t[:, ::1] sf_asdi = np.empty((2 * a, 2 * b), dtype=np.complex128)
         float_t xf, yf
-        np.ndarray[np.complex128_t, ndim=2] s_asdi = empty_aligned((2 * a, 2 * b), dtype='complex128')
-        np.ndarray[np.complex128_t, ndim=2] sf_asdi = empty_aligned((2 * a, 2 * b), dtype='complex128')
-        np.ndarray[np.complex128_t, ndim=2] w_asdi = empty_aligned((2 * a, 2 * b), dtype='complex128')
-    fft_obj = FFTW(s_asdi, sf_asdi, axes=(0, 1))
-    ifft_obj = FFTW(sf_asdi, w_asdi, axes=(0, 1), direction='FFTW_BACKWARD')
     for i in range(a):
         for j in range(b):
             s_asdi[i, j] = -sx_arr[a - i - 1, b - j - 1]
@@ -649,7 +645,7 @@ def ct_integrate(float_t[:, ::1] sx_arr, float_t[:, ::1] sy_arr):
     for i in range(a):
         for j in range(b):
             s_asdi[i + a, j + b] = sx_arr[i, j]
-    cdef np.ndarray[np.complex128_t, ndim=2] sfx_asdi = fft_obj().copy()
+    cdef np.ndarray[np.complex128_t, ndim=2] sfx_asdi = np.fft.fft2(s_asdi)
     for i in range(a):
         for j in range(b):
             s_asdi[i, j] = -sy_arr[a - i - 1, b - j - 1]
@@ -662,12 +658,11 @@ def ct_integrate(float_t[:, ::1] sx_arr, float_t[:, ::1] sy_arr):
     for i in range(a):
         for j in range(b):
             s_asdi[i + a, j + b] = sy_arr[i, j]
-    cdef np.ndarray[np.complex128_t, ndim=2] sfy_asdi = fft_obj().copy()
+    cdef np.ndarray[np.complex128_t, ndim=2] sfy_asdi = np.fft.fft2(s_asdi)
     for i in range(2 * a):
         xf = <float_t>(i) / 2 / a - i // a
         for j in range(2 * b):
             yf = <float_t>(j) / 2 / b - j // b
             sf_asdi[i, j] = (xf * sfx_asdi[i, j] + yf * sfy_asdi[i, j]) / (2j * pi * (xf**2 + yf**2))
     sf_asdi[0, 0] = 0
-    ifft_obj()
-    return np.asarray(w_asdi.real[a:, b:], dtype=dtype)
+    return np.asarray(np.fft.ifft2(sf_asdi).real[a:, b:], dtype=dtype)

requirements.txt

@@ -2,5 +2,4 @@ Cython>=0.29.21
 CythonGSL>=0.2.2
 h5py>=2.10.0
 numpy>=1.19.0
-scipy>=1.5.2
-pyfftw>=0.12.0
+scipy>=1.5.2
\ No newline at end of file
\ No newline at end of file

setup.py

@@ -53,7 +53,7 @@ with open('README.md', 'r') as readme:
     long_description = readme.read()
 
 setup(name='pyrost',
-      version='0.1.0',
+      version='0.1.1',
       author='Nikolay Ivanov',
       author_email="nikolay.ivanov@desy.de",
       long_description=long_description,