syned 1.0.38__tar.gz → 1.0.40__tar.gz

{syned-1.0.38 → syned-1.0.40}/MANIFEST.in

@@ -1,5 +1,5 @@
 recursive-include syned *.pyx
 recursive-include syned *.py
 
-include README.txt
+include README.rst
 include LICENSE

{syned-1.0.38 → syned-1.0.40}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: syned
-Version: 1.0.38
+Version: 1.0.40
 Summary: SYNED (SYNchrotron Elements Dictionary) kernel library
 Home-page: https://github.com/oasys-kit/syned
 Download-URL: https://github.com/oasys-kit/syned
@@ -23,6 +23,9 @@ Classifier: Intended Audience :: Education
 Classifier: Intended Audience :: Science/Research
 Classifier: Intended Audience :: Developers
 License-File: LICENSE
+Requires-Dist: setuptools
+Requires-Dist: numpy
+Requires-Dist: scipy
 
 =====
 syned

syned-1.0.40/examples/example_get_source.py

@@ -0,0 +1,48 @@
+
+
+from syned.storage_ring.magnetic_structures.undulator import Undulator
+from syned.storage_ring.magnetic_structures.wiggler import Wiggler
+from syned.storage_ring.magnetic_structures.bending_magnet import BendingMagnet
+from syned.storage_ring.light_source import LightSource
+from syned.storage_ring.electron_beam import ElectronBeam
+
+from syned.beamline.beamline import Beamline
+
+if __name__ == "__main__":
+
+
+
+    src1 = ElectronBeam.initialize_as_pencil_beam(energy_in_GeV=6.0,current=0.2)
+    src2 = Undulator()
+    src = LightSource("test",src1,src2)
+    magnetic_structure = src.get_magnetic_structure()
+
+    print(magnetic_structure)
+    if isinstance(magnetic_structure, Undulator):
+        print(" I am undulator")
+    elif isinstance(magnetic_structure, Wiggler):
+        print("I am wiggler")
+    elif isinstance(magnetic_structure, BendingMagnet):
+        print("I am a Bending Magnet")
+    else:
+        print("I do not know what I am...")
+
+
+    #
+    #
+    #
+
+    a = Beamline()
+    magnetic_structure = a.get_light_source().get_magnetic_structure()
+
+    print(magnetic_structure)
+    if isinstance(magnetic_structure, Undulator):
+        print(" I am undulator")
+    elif isinstance(magnetic_structure, Wiggler):
+        print("I am wiggler")
+    elif isinstance(magnetic_structure, BendingMagnet):
+        print("I am a Bending Magnet")
+    else:
+        print("I do not know what I am...")
+
+

{syned-1.0.38 → syned-1.0.40}/setup.py

@@ -1,8 +1,6 @@
 #! /usr/bin/env python3
 
-from importlib.machinery import SourceFileLoader
 import os
-import subprocess
 
 try:
     from setuptools import find_packages, setup
@@ -11,7 +9,7 @@ except AttributeError:
 
 NAME = 'syned'
 
-VERSION = '1.0.38'
+VERSION = '1.0.40'
 ISRELEASED = True
 
 DESCRIPTION = 'SYNED (SYNchrotron Elements Dictionary) kernel library'
@@ -58,81 +56,29 @@ SETUP_REQUIRES = (
     'setuptools',
 )
 
-
-# Return the git revision as a string
-def git_version():
-    """Return the git revision as a string.
-
-    Copied from numpy setup.py
-    """
-    def _minimal_ext_cmd(cmd):
-        # construct minimal environment
-        env = {}
-        for k in ['SYSTEMROOT', 'PATH']:
-            v = os.environ.get(k)
-            if v is not None:
-                env[k] = v
-        # LANGUAGE is used on win32
-        env['LANGUAGE'] = 'C'
-        env['LANG'] = 'C'
-        env['LC_ALL'] = 'C'
-        out = subprocess.Popen(cmd, stdout=subprocess.PIPE, env=env).communicate()[0]
-        return out
-
-    try:
-        out = _minimal_ext_cmd(['git', 'rev-parse', 'HEAD'])
-        GIT_REVISION = out.strip().decode('ascii')
-    except OSError:
-        GIT_REVISION = "Unknown"
-
-    return GIT_REVISION
-
-
-def write_version_py(filename='syned/version.py'):
-    # Copied from numpy setup.py
-    cnt = """
-# THIS FILE IS GENERATED FROM syned SETUP.PY
-short_version = '%(version)s'
-version = '%(version)s'
-full_version = '%(full_version)s'
-git_revision = '%(git_revision)s'
-release = %(isrelease)s
-
-if not release:
-    version = full_version
-    short_version += ".dev"
-"""
-    FULLVERSION = VERSION
-    if os.path.exists('.git'):
-        GIT_REVISION = git_version()
-    elif os.path.exists('syned/version.py'):
-        # must be a source distribution, use existing version file
-        version = SourceFileLoader('syned.version', 'syned/version.py').load_module()
-        GIT_REVISION = version.git_revision
-    else:
-        GIT_REVISION = "Unknown"
-
-    if not ISRELEASED:
-        FULLVERSION += '.dev0+' + GIT_REVISION[:7]
-
-    a = open(filename, 'w')
-    try:
-        a.write(cnt % {'version': VERSION,
-                       'full_version': FULLVERSION,
-                       'git_revision': GIT_REVISION,
-                       'isrelease': str(ISRELEASED)})
-    finally:
-        a.close()
-
-
-PACKAGES = find_packages(exclude=('*.tests', '*.tests.*', 'tests.*', 'tests'))
+PACKAGES = [
+    "syned",
+    "syned.beamline",
+    "syned.beamline.optical_elements",
+    "syned.beamline.optical_elements.absorbers",
+    "syned.beamline.optical_elements.crystals",
+    "syned.beamline.optical_elements.gratings",
+    "syned.beamline.optical_elements.ideal_elements",
+    "syned.beamline.optical_elements.mirrors",
+    "syned.beamline.optical_elements.refractors",
+    "syned.beamline.optical_elements.ideal_elements",
+    "syned.beamline.optical_elements.ideal_elements",
+    "syned.storage_ring",
+    "syned.storage_ring.magnetic_structures",
+    "syned.util",
+    "syned.widget",
+]
 
 PACKAGE_DATA = {
 }
 
 
 def setup_package():
-    write_version_py()
     setup(
         name=NAME,
         version=VERSION,

syned-1.0.40/shadow4/examples/optical_elements/examples_crystal.py

@@ -0,0 +1,134 @@
+
+import numpy
+
+from shadow4.sources.source_geometrical.source_geometrical import SourceGeometrical
+from shadow4.beamline.optical_elements.crystals.s4_plane_crystal import S4PlaneCrystal, S4PlaneCrystalElement
+
+
+from shadow4.tools.graphics import plotxy
+
+from syned.beamline.element_coordinates import ElementCoordinates
+
+from syned.beamline.optical_elements.crystals.crystal import Crystal, DiffractionGeometry
+
+
+def get_sigmas_radiation(photon_energy,undulator_length):
+    import scipy.constants as codata
+    lambdan = 1e-10 * codata.h*codata.c/codata.e*1e10 / photon_energy # in m
+    print("wavelength in m",lambdan)
+    return 1e6*2.740/4/numpy.pi*numpy.sqrt(lambdan*undulator_length),1e6*0.69*numpy.sqrt(lambdan/undulator_length)
+
+
+def crystal_diffraction_with_collimated_beam(do_plot=True):
+
+    #
+    # collimated source
+    #
+
+    if True:
+        src = SourceGeometrical()
+        src.set_energy_distribution_singleline(value=8000, unit='eV')
+        src.set_spatial_type_rectangle(width=1e-3, height=1e-3)
+        src.set_angular_distribution_uniform(0,0,-100e-6,100e-6)
+        src.set_polarization(polarization_degree= 0.5, phase_diff=numpy.pi/4, coherent_beam=True)
+        beam = src.get_beam()
+
+        print(beam.info())
+        SX, SZ = (1e6*beam.get_standard_deviation(1),1e6*beam.get_standard_deviation(3))
+
+
+    #
+    # crystal definition
+    #
+
+
+    if False:
+        crystal1 = S4PlaneCrystalElement(
+                                optical_element=S4PlaneCrystal(
+                                    name="Plane crystal",
+                                    boundary_shape=None,
+                                    material="Si",
+                                    diffraction_geometry=DiffractionGeometry.BRAGG,  # ?? not supposed to be in syned...
+                                    miller_index_h=1,
+                                    miller_index_k=1,
+                                    miller_index_l=1,
+                                    asymmetry_angle=0.0,
+                                    thickness=0.010, # this is thick crystal approximation
+                                    f_central=True,
+                                    f_phot_cent=0,
+                                    phot_cent=8000.0,
+                                    file_refl="",
+                                    f_bragg_a=False,
+                                    # a_bragg=0.0,
+                                    f_johansson=False,
+                                    r_johansson=1.0,
+                                    f_mosaic=False,
+                                    spread_mos=0.4 * numpy.pi / 180,
+                                    f_ext=0,                                    ),
+                                coordinates=ElementCoordinates(p=0.0, q=5000.0e-3,
+                                            angle_radial=0.0, angle_azimuthal=0.0, angle_radial_out=0.0),
+                                input_beam=beam)
+    else:
+        crystal1 = S4PlaneCrystalElement()
+        optical_element =             S4PlaneCrystal(
+                name="Plane crystal",
+                boundary_shape=None,
+                material="Si",
+                diffraction_geometry=DiffractionGeometry.BRAGG,  # ?? not supposed to be in syned...
+                miller_index_h=1,
+                miller_index_k=1,
+                miller_index_l=1,
+                asymmetry_angle=0.0,
+                thickness=0.010,  # this is thick crystal approximation
+                f_central=True,
+                f_phot_cent=0,
+                phot_cent=8000.0,
+                file_refl="",
+                f_bragg_a=False,
+                # a_bragg=0.0,
+                f_johansson=False,
+                r_johansson=1.0,
+                f_mosaic=False,
+                spread_mos=0.4 * numpy.pi / 180,
+                f_ext=0, )
+
+        crystal1.set_optical_element(optical_element)
+        crystal1.set_coordinates(
+            ElementCoordinates(p=0.0, q=5000.0e-3,
+                                           angle_radial=0.0, angle_azimuthal=0.0, angle_radial_out=0.0))
+        crystal1.set_input_beam(beam)
+
+
+    # print(crystal1.info())
+    # print(crystal1.get_optical_element().get_surface_shape().get_conic_coefficients())
+    #
+    # trace
+    #
+
+    beam2, mirr2 = crystal1.trace_beam()
+
+    if do_plot:
+        plotxy(beam2, 6, 23, nbins=100, title="INTENSITY VS Z'")
+
+    #
+    # #
+    # if do_plot:
+    #     plotxy(beam2, 1, 3, nbins=100, title="FOCAL PLANE")
+    #     plotxy(mirr2, 1, 3, nbins=100, title="LENS HEIGHT")
+    #     # plotxy(mirr2, 4, 5, nbins=100, title="FOOT DIV")
+    #
+    # FX, FZ = (1e6*beam2.get_standard_deviation(1),1e6*beam2.get_standard_deviation(3))
+    # print("Source dimensions: %f %f um"%(SX,SZ))
+    # print("Focal dimensions: %f %f um"%(FX,FZ))
+    # print("Demagnification: %g %g"%(SX/FX,SX/FZ))
+
+
+
+
+if __name__ == "__main__":
+    from srxraylib.plot.gol import set_qt
+    set_qt()
+
+    crystal_diffraction_with_collimated_beam(do_plot=True)
+
+

syned-1.0.40/shadow4/examples/optical_elements/examples_crystal_asymmetric.py

@@ -0,0 +1,134 @@
+
+import numpy
+
+from shadow4.sources.source_geometrical.source_geometrical import SourceGeometrical
+from shadow4.beamline.optical_elements.crystals.s4_plane_crystal import S4PlaneCrystal, S4PlaneCrystalElement
+
+
+from shadow4.tools.graphics import plotxy
+
+from syned.beamline.element_coordinates import ElementCoordinates
+
+from syned.beamline.optical_elements.crystals.crystal import Crystal, DiffractionGeometry
+
+
+def get_sigmas_radiation(photon_energy,undulator_length):
+    import scipy.constants as codata
+    lambdan = 1e-10 * codata.h*codata.c/codata.e*1e10 / photon_energy # in m
+    print("wavelength in m",lambdan)
+    return 1e6*2.740/4/numpy.pi*numpy.sqrt(lambdan*undulator_length),1e6*0.69*numpy.sqrt(lambdan/undulator_length)
+
+
+def crystal_diffraction_with_collimated_beam(do_plot=True):
+
+    #
+    # collimated source
+    #
+
+    if True:
+        src = SourceGeometrical(nrays=300)
+        src.set_energy_distribution_singleline(value=8000, unit='eV')
+        src.set_spatial_type_rectangle(width=1e-3, height=1e-3)
+        src.set_angular_distribution_uniform(0,0,-100e-6,100e-6)
+        src.set_polarization(polarization_degree= 0.5, phase_diff=numpy.pi/4, coherent_beam=True)
+        beam = src.get_beam()
+
+        print(beam.info())
+        SX, SZ = (1e6*beam.get_standard_deviation(1),1e6*beam.get_standard_deviation(3))
+
+
+    #
+    # crystal definition
+    #
+
+
+    if False:
+        crystal1 = S4PlaneCrystalElement(
+                                optical_element=S4PlaneCrystal(
+                                    name="Plane crystal",
+                                    boundary_shape=None,
+                                    material="Si",
+                                    diffraction_geometry=DiffractionGeometry.BRAGG,  # ?? not supposed to be in syned...
+                                    miller_index_h=1,
+                                    miller_index_k=1,
+                                    miller_index_l=1,
+                                    asymmetry_angle=0.0,
+                                    thickness=0.010, # this is thick crystal approximation
+                                    f_central=True,
+                                    f_phot_cent=0,
+                                    phot_cent=8000.0,
+                                    file_refl="",
+                                    f_bragg_a=False,
+                                    # a_bragg=0.0,
+                                    f_johansson=False,
+                                    r_johansson=1.0,
+                                    f_mosaic=False,
+                                    spread_mos=0.4 * numpy.pi / 180,
+                                    f_ext=0,                                    ),
+                                coordinates=ElementCoordinates(p=0.0, q=5000.0e-3,
+                                            angle_radial=0.0, angle_azimuthal=0.0, angle_radial_out=0.0),
+                                input_beam=beam)
+    else:
+        crystal1 = S4PlaneCrystalElement()
+        optical_element =             S4PlaneCrystal(
+                name="Plane crystal",
+                boundary_shape=None,
+                material="Si",
+                diffraction_geometry=DiffractionGeometry.BRAGG,  # ?? not supposed to be in syned...
+                miller_index_h=1,
+                miller_index_k=1,
+                miller_index_l=1,
+                asymmetry_angle=numpy.radians(10.0),
+                thickness=0.010,  # this is thick crystal approximation
+                f_central=True,
+                f_phot_cent=0,
+                phot_cent=8000.0,
+                file_refl="",
+                f_bragg_a=False,
+                # a_bragg=0.0,
+                f_johansson=False,
+                r_johansson=1.0,
+                f_mosaic=False,
+                spread_mos=0.4 * numpy.pi / 180,
+                f_ext=0, )
+
+        crystal1.set_optical_element(optical_element)
+        crystal1.set_coordinates(
+            ElementCoordinates(p=0.0, q=5000.0e-3,
+                                           angle_radial=0.0, angle_azimuthal=0.0, angle_radial_out=0.0))
+        crystal1.set_input_beam(beam)
+
+
+    # print(crystal1.info())
+    # print(crystal1.get_optical_element().get_surface_shape().get_conic_coefficients())
+    #
+    # trace
+    #
+
+    beam2, mirr2 = crystal1.trace_beam()
+
+    if do_plot:
+        plotxy(beam2, 6, 23, nbins=100, title="INTENSITY VS Z'")
+
+    #
+    # #
+    # if do_plot:
+    #     plotxy(beam2, 1, 3, nbins=100, title="FOCAL PLANE")
+    #     plotxy(mirr2, 1, 3, nbins=100, title="LENS HEIGHT")
+    #     # plotxy(mirr2, 4, 5, nbins=100, title="FOOT DIV")
+    #
+    # FX, FZ = (1e6*beam2.get_standard_deviation(1),1e6*beam2.get_standard_deviation(3))
+    # print("Source dimensions: %f %f um"%(SX,SZ))
+    # print("Focal dimensions: %f %f um"%(FX,FZ))
+    # print("Demagnification: %g %g"%(SX/FX,SX/FZ))
+
+
+
+
+if __name__ == "__main__":
+    from srxraylib.plot.gol import set_qt
+    set_qt()
+
+    crystal_diffraction_with_collimated_beam(do_plot=True)
+
+

syned-1.0.40/shadow4/examples/optical_elements/examples_crystal_yb66.py

@@ -0,0 +1,124 @@
+
+import numpy
+
+from shadow4.sources.source_geometrical.source_geometrical import SourceGeometrical
+from shadow4.beamline.optical_elements.crystals.s4_plane_crystal import S4PlaneCrystal, S4PlaneCrystalElement
+
+
+from shadow4.tools.graphics import plotxy
+
+from syned.beamline.element_coordinates import ElementCoordinates
+
+from syned.beamline.optical_elements.crystals.crystal import Crystal, DiffractionGeometry
+
+
+def get_sigmas_radiation(photon_energy,undulator_length):
+    import scipy.constants as codata
+    lambdan = 1e-10 * codata.h*codata.c/codata.e*1e10 / photon_energy # in m
+    print("wavelength in m",lambdan)
+    return 1e6*2.740/4/numpy.pi*numpy.sqrt(lambdan*undulator_length),1e6*0.69*numpy.sqrt(lambdan/undulator_length)
+
+
+def crystal_diffraction_with_collimated_beam(do_plot=True):
+
+    #
+    # collimated source
+    #
+
+    if True:
+        src = SourceGeometrical()
+        src.set_energy_distribution_singleline(value=8000, unit='eV')
+        src.set_spatial_type_rectangle(width=1e-3, height=1e-3)
+        src.set_angular_distribution_uniform(0,0,-100e-6,100e-6)
+        src.set_polarization(polarization_degree=0.5, phase_diff=numpy.pi/4, coherent_beam=True)
+
+        beam = src.get_beam()
+
+        print(beam.info())
+        SX, SZ = (1e6*beam.get_standard_deviation(1),1e6*beam.get_standard_deviation(3))
+
+
+    #
+    # crystal definition
+    #
+
+    if True: # create preprocessor file
+        descriptor = 'YB66'
+        SCANFROM = 0  # in microradiants
+        SCANTO = 100  # in microradiants
+        TEMPER = 1.0
+        ENERGY = 8040.0
+        SCANPOINTS = 200
+
+        print("Using crystal descriptor: ", descriptor)
+        from xoppylib.crystals.tools import bragg_calc2
+        from dabax.dabax_xraylib import DabaxXraylib
+        bragg_dictionary = bragg_calc2(descriptor=descriptor,
+                                       hh=4, kk=0, ll=0,
+                                       temper=1.0,
+                                       emin=ENERGY - 100.0, emax=ENERGY + 100.0,
+                                       estep=(SCANTO - SCANFROM) / SCANPOINTS, fileout="xcrystal.bra",
+                                       material_constants_library=DabaxXraylib())
+
+    crystal1 = S4PlaneCrystalElement(
+                                optical_element=S4PlaneCrystal(
+                                    name="Plane crystal",
+                                    boundary_shape=None,
+                                    material="YB66",
+                                    diffraction_geometry=DiffractionGeometry.BRAGG,  # ?? not supposed to be in syned...
+                                    miller_index_h=4,
+                                    miller_index_k=4,
+                                    miller_index_l=0,
+                                    asymmetry_angle=0.0,
+                                    thickness=0.010,  ###########################
+                                    f_central=True,
+                                    f_phot_cent=0,
+                                    phot_cent=8000.0,
+                                    file_refl="xcrystal.bra",
+                                    f_bragg_a=False,
+                                    # a_bragg=0.0,
+                                    f_johansson=False,
+                                    r_johansson=1.0,
+                                    f_mosaic=False,
+                                    spread_mos=0.4 * numpy.pi / 180,
+                                    f_ext=0,
+                                    material_constants_library_flag=3, # 0=xraylib, 1=dabax
+                                    # 2=shadow preprocessor file v1
+                                    # 3=shadow preprocessor file v2
+                                ),
+                                coordinates=ElementCoordinates(p=0.0, q=5000.0e-3,
+                                            angle_radial=0.0, angle_azimuthal=0.0, angle_radial_out=0.0),
+                                input_beam=beam)
+
+    # print(crystal1.info())
+    # print(crystal1.get_optical_element().get_surface_shape().get_conic_coefficients())
+    #
+    # trace
+    #
+
+    beam2, mirr2 = crystal1.trace_beam()
+
+    if do_plot:
+        plotxy(beam2, 6, 23, nbins=100, title="INTENSITY VS Z'")
+    #
+    # #
+    # if do_plot:
+    #     plotxy(beam2, 1, 3, nbins=100, title="FOCAL PLANE")
+    #     plotxy(mirr2, 1, 3, nbins=100, title="LENS HEIGHT")
+    #     # plotxy(mirr2, 4, 5, nbins=100, title="FOOT DIV")
+    #
+    # FX, FZ = (1e6*beam2.get_standard_deviation(1),1e6*beam2.get_standard_deviation(3))
+    # print("Source dimensions: %f %f um"%(SX,SZ))
+    # print("Focal dimensions: %f %f um"%(FX,FZ))
+    # print("Demagnification: %g %g"%(SX/FX,SX/FZ))
+
+
+
+
+if __name__ == "__main__":
+    from srxraylib.plot.gol import set_qt
+    set_qt()
+
+    crystal_diffraction_with_collimated_beam(do_plot=True)
+
+