diff --git a/MANIFEST.in b/MANIFEST.in
old mode 100644
new mode 100755
index 523902ae46b58a1345f8fb9541aa9d2c4c3b5f0b..273f97285be35932338beea1a8b651dc7a238e12
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,2 +1,6 @@
-global-include *.pyx
-global-include *.c
\ No newline at end of file
+graft tests
+graft pyrost/config
+graft pyrost/bin
+exclude dev.pyx
+global-exclude *.py[cod]
+global-exclude *.so
\ No newline at end of file
diff --git a/dev.ipynb b/dev.ipynb
index 825fd1531afef0ad3d3ef0a533e0f8848484c817..58de49180e67cdb8134d664585acc6a4667bad98 100755
--- a/dev.ipynb
+++ b/dev.ipynb
@@ -8,7 +8,7 @@
{
"data": {
"text/plain": [
- "(None, <pyximport.pyximport.PyxImporter at 0x7f9d187e8590>)"
+ "(None, <pyximport.pyximport.PyxImporter at 0x7fa6306d8bd0>)"
]
},
"execution_count": 1,
@@ -217,7 +217,7 @@
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
@@ -229,73 +229,36 @@
},
{
"cell_type": "code",
- "execution_count": 8,
+ "execution_count": 9,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
- "2020-11-27 17:58:02,589 - STSim - INFO - Initializing\n",
- "2020-11-27 17:58:02,591 - STSim - INFO - Current parameters\n",
- "2020-11-27 17:58:02,591 - STSim - INFO - Initializing coordinate arrays at the sample's plane\n",
- "2020-11-27 17:58:02,592 - STSim - INFO - Number of points in x axis: 1287\n",
- "2020-11-27 17:58:02,593 - STSim - INFO - Number of points in y axis: 1810\n",
- "2020-11-27 17:58:02,594 - STSim - INFO - Generating wavefields at the sample's plane\n",
- "2020-11-27 17:58:02,599 - STSim - INFO - The wavefields have been generated\n",
- "2020-11-27 17:58:02,601 - STSim - INFO - Generating barcode's transmission coefficients\n",
- "2020-11-27 17:58:02,603 - STSim - INFO - The coefficients have been generated\n",
- "2020-11-27 17:58:02,604 - STSim - INFO - Generating wavefields at the detector's plane\n",
- "2020-11-27 17:58:02,830 - STSim - INFO - The wavefields have been generated\n",
- "2020-11-27 17:58:02,831 - STSim - INFO - Making ptychograph...\n",
- "2020-11-27 17:58:02,832 - STSim - INFO - Source blur size: 100.000000 um\n",
- "2020-11-27 17:58:02,835 - STSim - INFO - The ptychograph is generated, data shape: (10, 1, 2000)\n",
- "2020-11-27 17:58:02,836 - STSim - INFO - Saving data in the directory: results/test_sim\n",
- "2020-11-27 17:58:02,837 - STSim - INFO - Making ini files...\n",
- "2020-11-27 17:58:02,854 - STSim - INFO - results/test_sim/update_pixel_map.ini saved\n",
- "2020-11-27 17:58:02,856 - STSim - INFO - results/test_sim/zernike.ini saved\n",
- "2020-11-27 17:58:02,858 - STSim - INFO - results/test_sim/calculate_phase.ini saved\n",
- "2020-11-27 17:58:02,859 - STSim - INFO - results/test_sim/make_reference.ini saved\n",
- "2020-11-27 17:58:02,861 - STSim - INFO - results/test_sim/calc_error.ini saved\n",
- "2020-11-27 17:58:02,863 - STSim - INFO - results/test_sim/speckle_gui.ini saved\n",
- "2020-11-27 17:58:02,865 - STSim - INFO - results/test_sim/generate_pixel_map.ini saved\n",
- "2020-11-27 17:58:02,867 - STSim - INFO - results/test_sim/update_translations.ini saved\n",
- "2020-11-27 17:58:02,869 - STSim - INFO - results/test_sim/parameters.ini saved\n",
- "2020-11-27 17:58:02,871 - STSim - INFO - results/test_sim/protocol.ini saved\n",
- "2020-11-27 17:58:02,872 - STSim - INFO - Making a cxi file...\n",
- "2020-11-27 17:58:02,873 - STSim - INFO - Using the following cxi protocol:\n",
- "2020-11-27 17:58:02,874 - STSim - INFO - basis_vectors [float]: '/entry_1/instrument_1/detector_1/basis_vectors' \n",
- "2020-11-27 17:58:02,875 - STSim - INFO - data [float]: '/entry_1/data_1/data' \n",
- "2020-11-27 17:58:02,876 - STSim - INFO - defocus [float]: '/speckle_tracking/defocus' \n",
- "2020-11-27 17:58:02,878 - STSim - INFO - defocus_fs [float]: '/speckle_tracking/dfs' \n",
- "2020-11-27 17:58:02,879 - STSim - INFO - defocus_ss [float]: '/speckle_tracking/dss' \n",
- "2020-11-27 17:58:02,880 - STSim - INFO - distance [float]: '/entry_1/instrument_1/detector_1/distance' \n",
- "2020-11-27 17:58:02,881 - STSim - INFO - energy [float]: '/entry_1/instrument_1/source_1/energy' \n",
- "2020-11-27 17:58:02,882 - STSim - INFO - good_frames [int]: '/frame_selector/good_frames' \n",
- "2020-11-27 17:58:02,883 - STSim - INFO - m0 [int]: '/speckle_tracking/m0' \n",
- "2020-11-27 17:58:02,884 - STSim - INFO - mask [bool]: '/speckle_tracking/mask' \n",
- "2020-11-27 17:58:02,885 - STSim - INFO - n0 [int]: '/speckle_tracking/n0' \n",
- "2020-11-27 17:58:02,887 - STSim - INFO - phase [float]: '/speckle_tracking/phase' \n",
- "2020-11-27 17:58:02,888 - STSim - INFO - pixel_map [float]: '/speckle_tracking/pixel_map' \n",
- "2020-11-27 17:58:02,889 - STSim - INFO - pixel_abberations [float]: '/speckle_tracking/pixel_abberations' \n",
- "2020-11-27 17:58:02,890 - STSim - INFO - pixel_translations [float]: '/speckle_tracking/pixel_translations' \n",
- "2020-11-27 17:58:02,891 - STSim - INFO - reference_image [float]: '/speckle_tracking/reference_image' \n",
- "2020-11-27 17:58:02,892 - STSim - INFO - roi [int]: '/speckle_tracking/roi' \n",
- "2020-11-27 17:58:02,893 - STSim - INFO - translations [float]: '/entry_1/sample_1/geometry/translations' \n",
- "2020-11-27 17:58:02,895 - STSim - INFO - wavelength [float]: '/entry_1/instrument_1/source_1/wavelength' \n",
- "2020-11-27 17:58:02,896 - STSim - INFO - whitefield [float]: '/speckle_tracking/whitefield' \n",
- "2020-11-27 17:58:02,897 - STSim - INFO - x_pixel_size [float]: '/entry_1/instrument_1/detector_1/x_pixel_size' \n",
- "2020-11-27 17:58:02,898 - STSim - INFO - y_pixel_size [float]: '/entry_1/instrument_1/detector_1/y_pixel_size' \n",
- "2020-11-27 17:58:02,918 - STSim - INFO - results/test_sim/data.cxi saved\n"
+ "2020-11-29 13:02:50,237 - STSim - INFO - Initializing\n",
+ "2020-11-29 13:02:50,237 - STSim - INFO - Current parameters\n",
+ "2020-11-29 13:02:50,238 - STSim - INFO - Initializing coordinate arrays at the sample's plane\n",
+ "2020-11-29 13:02:50,238 - STSim - INFO - Number of points in x axis: 1287\n",
+ "2020-11-29 13:02:50,239 - STSim - INFO - Number of points in y axis: 1810\n",
+ "2020-11-29 13:02:50,241 - STSim - INFO - Generating wavefields at the sample's plane\n",
+ "2020-11-29 13:02:50,248 - STSim - INFO - The wavefields have been generated\n",
+ "2020-11-29 13:02:50,249 - STSim - INFO - Generating barcode's transmission coefficients\n",
+ "2020-11-29 13:02:50,252 - STSim - INFO - The coefficients have been generated\n",
+ "2020-11-29 13:02:50,252 - STSim - INFO - Generating wavefields at the detector's plane\n",
+ "2020-11-29 13:02:50,454 - STSim - INFO - The wavefields have been generated\n",
+ "2020-11-29 13:02:50,455 - STSim - INFO - Making ptychograph...\n",
+ "2020-11-29 13:02:50,456 - STSim - INFO - Source blur size: 100.000000 um\n",
+ "2020-11-29 13:02:50,459 - STSim - INFO - The ptychograph is generated, data shape: (10, 1, 2000)\n"
]
}
],
"source": [
"st_params = st_sim.parameters(**params)\n",
- "st_conv = st_sim.STConverter()\n",
+ "st_conv = st_sim.converter()\n",
"with st_sim.STSim(st_params) as sim_obj:\n",
" data = sim_obj.ptychograph()\n",
- " st_conv.save_sim(data, sim_obj, 'results/test_sim')"
+ " st_data = st_conv.export_data(data, st_params)"
]
},
{
diff --git a/docs/conf.py b/docs/conf.py
index 7b5a172374835e89e5de2c06673f59a3530ada52..786ec05d72bc032d7f39978906ab07f7ec4f5f4a 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 = '0.1.2'
+release = '0.1.3'
# -- General configuration ---------------------------------------------------
diff --git a/pyrost/data_processing.py b/pyrost/data_processing.py
index 7a8a5307d96a01a21b806872966b4073a751f6a8..e9921a1b62e1b74b1774d9e845b1a6d88bf009ed 100755
--- a/pyrost/data_processing.py
+++ b/pyrost/data_processing.py
@@ -693,7 +693,8 @@ class SpeckleTracking(DataContainer):
return {'pixel_map': pixel_map}
def iter_update(self, sw_fs, sw_ss=0, ls_pm=3., ls_ri=10.,
- n_iter=5, f_tol=3e-3, verbose=True, method='search'):
+ n_iter=5, f_tol=3e-3, verbose=True, method='search',
+ return_errors=True):
"""Perform iterative Robust Speckle Tracking update. `ls_ri` and
`ls_pm` define high frequency cut-off to supress the noise.
Iterative update terminates when the difference between total
@@ -723,6 +724,8 @@ class SpeckleTracking(DataContainer):
* 'newton' : Iterative Newton's method based on
finite difference gradient approximation.
* 'search' : Grid search along the search window.
+ return_errors : bool, optional
+ Return errors array if True.
Returns
-------
@@ -730,7 +733,8 @@ class SpeckleTracking(DataContainer):
A new :class:`SpeckleTracking` object with the updated
`pixel_map` and `reference_image`.
list
- List of total MSE values for each iteration.
+ List of total MSE values for each iteration. Only if
+ `return_errors` is True.
"""
obj = self.update_reference(ls_ri=ls_ri, sw_ss=sw_ss, sw_fs=sw_fs)
errors = [obj.total_mse(ls_ri=ls_ri)]
@@ -759,7 +763,10 @@ class SpeckleTracking(DataContainer):
print('Iteration No. {:d}: Total MSE = {:.3f}'.format(it, errors[-1]))
if errors[-2] - errors[-1] <= f_tol:
break
- return obj, errors
+ if return_errors:
+ return obj, errors
+ else:
+ return obj
def total_mse(self, ls_ri=3.):
"""Return average mean-squared-error (MSE) per pixel.
diff --git a/pyrost/simulation/__init__.py b/pyrost/simulation/__init__.py
index 52326949c39d0be0f3cf642aa51961c5bfa36eb9..ee6275bccc096b7fc6ede7a9023b242058b28207 100755
--- a/pyrost/simulation/__init__.py
+++ b/pyrost/simulation/__init__.py
@@ -3,4 +3,4 @@ Speckle Tracking scans. Wavefront propagation is based on
the Fresnel diffraction theory.
"""
from .st_sim_param import STParams, parameters
-from .st_sim import STSim, STConverter
\ No newline at end of file
+from .st_sim import STSim, STConverter, converter
diff --git a/pyrost/simulation/st_sim.py b/pyrost/simulation/st_sim.py
index 4ed04495557565d38c9ee1165e6a434cc64213c7..3cd9b9f5a6613aff6d7668fce2738b9103b687ac 100755
--- a/pyrost/simulation/st_sim.py
+++ b/pyrost/simulation/st_sim.py
@@ -118,14 +118,18 @@ class STSim:
def __init__(self, st_params, bsteps=None):
self.parameters = st_params
- self.__dict__.update(**self.parameters.export_dict())
self._init_logging()
self._init_coord()
self._init_lens()
self._init_barcode(bsteps)
self._init_detector()
+ def __getattr__(self, attr):
+ if attr in self.parameters:
+ return self.parameters.__getattr__(attr)
+
def _init_logging(self):
+ os.makedirs(self.log_dir, exist_ok=True)
self.logger = logging.getLogger(self.__class__.__name__)
self.logger.level = logging.INFO
filename = os.path.join(self.log_dir, datetime.datetime.now().strftime('%d-%m-%Y_%H-%M-%S.log'))
@@ -508,6 +512,28 @@ class STConverter:
if logger:
logger.info("{:s} saved".format(os.path.join(dir_path, 'data.cxi')))
+def converter(coord_ratio=1e-6, float_precision='float64'):
+ """Return the default simulation converter.
+
+ Parameters
+ ----------
+ coord_ratio : float, optional
+ Coordinates ratio between the simulated and saved data.
+ float_precision: {'float32', 'float64'}, optional
+ Floating point precision.
+
+ Returns
+ -------
+ STConverter
+ Default simulation data converter.
+
+ See Also
+ --------
+ STConverter : Full converter class description.
+ """
+ return STConverter(protocol=cxi_protocol(float_precision),
+ coord_ratio=coord_ratio)
+
def main():
"""Main fuction to run Speckle Tracking simulation and save the results to a CXI file.
"""
diff --git a/pyrost/simulation/st_sim_param.py b/pyrost/simulation/st_sim_param.py
index c6e0e3623ae3d9c8956bec68095d34669cb06b7d..590a2db87bc3b888bc514578eaa61752b4241949 100755
--- a/pyrost/simulation/st_sim_param.py
+++ b/pyrost/simulation/st_sim_param.py
@@ -126,6 +126,12 @@ class STParams(INIParser):
super(STParams, self).__init__(**kwargs)
self.__dict__['_lookup'] = self.lookup_dict()
+ def __iter__(self):
+ return self._lookup.__iter__()
+
+ def __contains__(self, attr):
+ return attr in self._lookup
+
def __getattr__(self, attr):
if attr in self._lookup:
return self.__dict__[self._lookup[attr]][attr]
diff --git a/pytest.ini b/pytest.ini
index b30dddcd92a195a3dde59278db4f7f16d82c230a..6e7ae8f6073cc6bdfd5a6073298ccba274d18590 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -1,4 +1,5 @@
[pytest]
markers =
st_sim: test Speckle Tracking simulation package
- rst: rest Robust Speckle Tracking package
\ No newline at end of file
+ rst: test Robust Speckle Tracking package
+ standalone: standalone test
\ No newline at end of file
diff --git a/setup.py b/setup.py
old mode 100644
new mode 100755
index c8bcbf8cde004404ede7f38e3d5106c408bb0e10..c4a850a8a034992851946031fb1208e2eb84db9f
--- a/setup.py
+++ b/setup.py
@@ -42,7 +42,7 @@ with open('README.md', 'r') as readme:
long_description = readme.read()
setup(name='pyrost',
- version='0.1.2',
+ version='0.1.3',
author='Nikolay Ivanov',
author_email="nikolay.ivanov@desy.de",
long_description=long_description,
diff --git a/test_pyrost.py b/tests/test_pyrost.py
similarity index 80%
rename from test_pyrost.py
rename to tests/test_pyrost.py
index 32e46351b890028cf3db01a5cd6e79e928265841..0ed993abca8b7a37caaab6287caa27e38b0ecaa1 100755
--- a/test_pyrost.py
+++ b/tests/test_pyrost.py
@@ -45,10 +45,17 @@ def exp_data_2d(request):
@pytest.fixture(params=['float32', 'float64'])
def loader(request):
"""
- Return a default cxi protocol
+ Return the default loader.
"""
return rst.loader(request.param)
+@pytest.fixture(params=['float32', 'float64'])
+def converter(request):
+ """
+ Return the default loader.
+ """
+ return st_sim.converter(float_precision=request.param)
+
@pytest.fixture(scope='function')
def ini_path():
"""Return a path to the experimental speckle tracking data.
@@ -68,8 +75,8 @@ def test_st_params(st_params, ini_path):
@pytest.mark.st_sim
def test_st_sim(st_params):
- sim = st_sim.STSim(st_params)
- ptych = sim.ptychograph()
+ with st_sim.STSim(st_params) as sim_obj:
+ ptych = sim_obj.ptychograph()
assert len(ptych.shape) == 3
assert ptych.shape[0] == st_params.n_frames
@@ -95,6 +102,7 @@ def test_iter_update(sim_data, loader):
data_path = os.path.join(sim_data, 'data.cxi')
assert os.path.isfile(data_path)
st_data = loader.load(data_path, roi=(0, 1, 400, 1450))
+ assert st_data.data.dtype == loader.protocol.known_types['float']
st_obj = st_data.get_st()
pixel_map0 = st_obj.pixel_map.copy()
st_obj.iter_update(sw_ss=0, sw_fs=150, ls_pm=2.5, ls_ri=15,
@@ -108,3 +116,15 @@ def test_data_process_routines(exp_data_2d, loader):
data = loader.load(**exp_data_2d)
data = data.make_mask(method='eiger-bad')
assert (data.get('whitefield') <= 65535).all()
+
+@pytest.mark.standalone
+def test_full(st_params, converter):
+ with st_sim.STSim(st_params) as sim_obj:
+ ptych = sim_obj.ptychograph()
+ data = converter.export_data(ptych, st_params)
+ assert data.data.dtype == converter.protocol.known_types['float']
+ st_obj = data.get_st()
+ st_res = st_obj.iter_update(sw_fs=20, ls_pm=3, ls_ri=5,
+ verbose=True, n_iter=10, return_errors=False)
+ assert (st_obj.pixel_map != st_res.pixel_map).any()
+ assert st_res.pixel_map.dtype == converter.protocol.known_types['float']
\ No newline at end of file