diff --git a/README.md b/README.md
index de980114f2e09d141fb8a2f277fa18c71eef8a98..03362f7ae47bec62548b3cb067cf516a3ad225ac 100755
--- a/README.md
+++ b/README.md
@@ -1,3 +1,7 @@
+## Current build status
+[](https://pypi.org/project/pyrost/)
+[](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/)
diff --git a/docs/conf.py b/docs/conf.py
index 3873f34cb76c8432bdadf488b52173f18b073ac9..6e4cee92c829c941ed938ac3043a10b5dd4a14d9 100755
--- a/docs/conf.py
+++ b/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 ---------------------------------------------------
diff --git a/docs/install.rst b/docs/install.rst
old mode 100644
new mode 100755
index 3f4abe083748bd9e5bc6419ac1d3f5eaf15dd7db..9f52fccabec05516c9cb078b951b5db7ab9e80b5
--- a/docs/install.rst
+++ b/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
diff --git a/docs/rtd_environment.yml b/docs/rtd_environment.yml
old mode 100644
new mode 100755
index 7ac27455e001087ad9a9bc6566698bb580f18bcf..f7714abcca1aa7fb1cf7020249c51bf5d285bfbc
--- a/docs/rtd_environment.yml
+++ b/docs/rtd_environment.yml
@@ -15,5 +15,4 @@ dependencies:
- sphinx
- sphinx_rtd_theme
- mock
- - pillow
- - pyfftw
\ No newline at end of file
+ - pillow
\ No newline at end of file
diff --git a/environment.yml b/environment.yml
old mode 100644
new mode 100755
index 17be69909663ffcccc80a77f7a0497f31d4e0a7f..1dbb1ed917d2453507d66be6ae3fef694ce1da9d
--- a/environment.yml
+++ b/environment.yml
@@ -10,5 +10,4 @@ dependencies:
- llvm-openmp
- h5py
- numpy
- - scipy
- - pyfftw
\ No newline at end of file
+ - scipy
\ No newline at end of file
diff --git a/pyrost/bin/st_utils.pyx b/pyrost/bin/st_utils.pyx
index 564ea94906d671ca312bad60d778021e49012d8f..d141dccd0e86f327df6c50fdea5021aea38b3f35 100755
--- a/pyrost/bin/st_utils.pyx
+++ b/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)
diff --git a/requirements.txt b/requirements.txt
old mode 100644
new mode 100755
index 0e426768e147f30cfbd4fa638d0fbc55c750a4ae..2a3e40622d4bf739300cb58d3f41c6f7bb657ac4
--- a/requirements.txt
+++ b/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
\ No newline at end of file
+scipy>=1.5.2
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 6ba748b6f54a5e3da6e7d9b9fbc4e905c47207f6..49a0cbe63f7f7b5a2b7c394498f9553cc3f37852 100644
--- a/setup.py
+++ b/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,