add more accelerated cupy templates (#547)

ptypy/utils/scripts.py

@@ -728,7 +728,7 @@ def phase_from_dpc(dpc_row, dpc_col):
     sh = np.asarray(sh)
     fac = np.ones_like(sh)
     fac[-2:] = 2
-    f = np.zeros(sh * fac, dtype=np.complex)
+    f = np.zeros(sh * fac, dtype=complex)
     c = px + 1j*py
     f[..., :sh[-2], :sh[-1]] = c
     f[..., :sh[-2], sh[-1]:] = c[..., :, ::-1]

templates/accelerate/ptypy_i13_AuStar_farfield_cupy.py

@@ -0,0 +1,116 @@
+"""
+This script is a test for ptychographic reconstruction in the absence
+of actual data. It uses a simulated Au Siemens star pattern under  
+experimental farfield conditions in the hard X-ray regime.
+"""
+from ptypy.core import Ptycho
+from ptypy import utils as u
+import ptypy
+ptypy.load_gpu_engines(arch="cupy")
+
+import tempfile
+tmpdir = tempfile.gettempdir()
+
+### PTYCHO PARAMETERS
+p = u.Param()
+p.verbose_level = "info"
+p.run = None
+
+p.data_type = "single"
+p.run = None
+p.io = u.Param()
+p.io.home = "/".join([tmpdir, "ptypy"])
+p.io.autosave = u.Param(active=False)
+p.io.autoplot = u.Param(active=False, layout="nearfield")
+p.io.interaction = u.Param(active=False)
+
+# Simulation parameters
+sim = u.Param()
+sim.energy = 9.7
+sim.distance = 8.46e-2
+sim.psize = 100e-9
+sim.shape = 1024
+sim.xy = u.Param()
+sim.xy.override = u.parallel.MPIrand_uniform(0.0,10e-6,(20,2))
+#sim.xy.positions = np.random.normal(0.0,3e-6,(20,2))
+sim.verbose_level = 1
+
+sim.illumination = u.Param()
+sim.illumination.model = None
+sim.illumination.photons = 1e11
+sim.illumination.aperture = u.Param()
+sim.illumination.aperture.diffuser = (8.0, 10.0)
+sim.illumination.aperture.form = "circ"
+sim.illumination.aperture.size = 90e-6
+sim.illumination.aperture.central_stop = 0.15
+sim.illumination.propagation = u.Param()
+sim.illumination.propagation.focussed = None#0.08
+sim.illumination.propagation.parallel = 0.005
+sim.illumination.propagation.spot_size = None
+
+sim.sample = u.Param()
+sim.sample.model = u.xradia_star((1200,1200),minfeature=3,contrast=0.8)
+sim.sample.process = u.Param()
+sim.sample.process.offset = (0,0)
+sim.sample.process.zoom = 1.0
+sim.sample.process.formula = "Au"
+sim.sample.process.density = 19.3
+sim.sample.process.thickness = 700e-9
+sim.sample.process.ref_index = None
+sim.sample.process.smoothing = None
+sim.sample.fill = 1.0+0.j
+
+sim.detector = 'GenericCCD32bit'
+sim.plot = False
+
+# Scan model and initial value parameters
+p.scans = u.Param()
+p.scans.scan00 = u.Param()
+p.scans.scan00.name = 'BlockFull'
+
+p.scans.scan00.coherence = u.Param()
+p.scans.scan00.coherence.num_probe_modes = 1
+p.scans.scan00.coherence.num_object_modes = 1
+p.scans.scan00.coherence.energies = [1.0]
+
+p.scans.scan00.sample = u.Param()
+
+# (copy simulation illumination and modify some things)
+p.scans.scan00.illumination = sim.illumination.copy(99)
+p.scans.scan00.illumination.aperture.size = 105e-6
+p.scans.scan00.illumination.aperture.central_stop = None
+
+# Scan data (simulation) parameters
+p.scans.scan00.data=u.Param()
+p.scans.scan00.data.name = 'SimScan'
+p.scans.scan00.data.propagation = 'nearfield'
+p.scans.scan00.data.save = None #'append'
+p.scans.scan00.data.shape = None
+p.scans.scan00.data.num_frames = None
+p.scans.scan00.data.update(sim)
+
+# Reconstruction parameters
+p.engines = u.Param()
+p.engines.engine00 = u.Param()
+p.engines.engine00.name = 'DM_cupy'
+p.engines.engine00.numiter = 100
+p.engines.engine00.object_inertia = 1.
+p.engines.engine00.numiter_contiguous = 1
+p.engines.engine00.probe_support = None
+p.engines.engine00.probe_inertia = 0.001
+p.engines.engine00.obj_smooth_std = 10
+p.engines.engine00.clip_object = None
+p.engines.engine00.alpha = 1
+p.engines.engine00.probe_update_start = 2
+p.engines.engine00.update_object_first = True
+p.engines.engine00.overlap_converge_factor = 0.5
+p.engines.engine00.overlap_max_iterations = 100
+p.engines.engine00.fourier_relax_factor = 0.05
+
+p.engines.engine01 = u.Param()
+p.engines.engine01.name = 'ML_cupy'
+p.engines.engine01.numiter = 50
+
+if __name__ == "__main__":
+    P = Ptycho(p,level=5)
+

templates/accelerate/ptypy_i13_AuStar_nearfield_cupy.py

@@ -0,0 +1,118 @@
+"""
+This script is a test for ptychographic reconstruction in the absence
+of actual data. It uses a simulated Au Siemens star pattern under  
+experimental nearfield conditions in the hard X-ray regime.
+"""
+from ptypy.core import Ptycho
+from ptypy import utils as u
+import ptypy
+ptypy.load_gpu_engines(arch="cupy")
+
+import tempfile
+tmpdir = tempfile.gettempdir()
+
+### PTYCHO PARAMETERS
+p = u.Param()
+p.verbose_level = "info"
+p.run = None
+p.frames_per_block = 20
+
+p.data_type = "single"
+p.run = None
+p.io = u.Param()
+p.io.home = "/".join([tmpdir, "ptypy"])
+p.io.autosave = u.Param(active=False)
+p.io.autoplot = u.Param(active=False, layout="nearfield")
+p.io.interaction = u.Param(active=False)
+
+# Simulation parameters
+sim = u.Param()
+sim.energy = 9.7
+sim.distance = 8.46e-2
+sim.psize = 100e-9
+sim.shape = 1024
+sim.xy = u.Param()
+sim.xy.override = u.parallel.MPIrand_uniform(0.0,10e-6,(20,2))
+#sim.xy.positions = np.random.normal(0.0,3e-6,(20,2))
+sim.verbose_level = 1
+
+sim.illumination = u.Param()
+sim.illumination.model = None
+sim.illumination.photons = 1e11
+sim.illumination.aperture = u.Param()
+sim.illumination.aperture.diffuser = (8.0, 10.0)
+sim.illumination.aperture.form = "circ"
+sim.illumination.aperture.size = 90e-6
+sim.illumination.aperture.central_stop = 0.15
+sim.illumination.propagation = u.Param()
+sim.illumination.propagation.focussed = None#0.08
+sim.illumination.propagation.parallel = 0.005
+sim.illumination.propagation.spot_size = None
+
+sim.sample = u.Param()
+sim.sample.model = u.xradia_star((1200,1200),minfeature=3,contrast=0.8)
+sim.sample.process = u.Param()
+sim.sample.process.offset = (0,0)
+sim.sample.process.zoom = 1.0
+sim.sample.process.formula = "Au"
+sim.sample.process.density = 19.3
+sim.sample.process.thickness = 700e-9
+sim.sample.process.ref_index = None
+sim.sample.process.smoothing = None
+sim.sample.fill = 1.0+0.j
+
+sim.detector = 'GenericCCD32bit'
+sim.plot = False
+
+# Scan model and initial value parameters
+p.scans = u.Param()
+p.scans.scan00 = u.Param()
+p.scans.scan00.name = 'BlockFull'
+p.scans.scan00.propagation = "nearfield"
+
+p.scans.scan00.coherence = u.Param()
+p.scans.scan00.coherence.num_probe_modes = 1
+p.scans.scan00.coherence.num_object_modes = 1
+p.scans.scan00.coherence.energies = [1.0]
+
+p.scans.scan00.sample = u.Param()
+
+# (copy simulation illumination and modify some things)
+p.scans.scan00.illumination = sim.illumination.copy(99)
+p.scans.scan00.illumination.aperture.size = 105e-6
+p.scans.scan00.illumination.aperture.central_stop = None
+
+# Scan data (simulation) parameters
+p.scans.scan00.data=u.Param()
+p.scans.scan00.data.name = 'SimScan'
+p.scans.scan00.data.propagation = 'nearfield'
+p.scans.scan00.data.save = None #'append'
+p.scans.scan00.data.shape = None
+p.scans.scan00.data.num_frames = None
+p.scans.scan00.data.update(sim)
+
+# Reconstruction parameters
+p.engines = u.Param()
+p.engines.engine00 = u.Param()
+p.engines.engine00.name = 'DM_cupy'
+p.engines.engine00.numiter = 100
+p.engines.engine00.object_inertia = 1.
+p.engines.engine00.numiter_contiguous = 1
+p.engines.engine00.probe_support = None
+p.engines.engine00.probe_inertia = 0.001
+p.engines.engine00.obj_smooth_std = 10
+p.engines.engine00.clip_object = None
+p.engines.engine00.alpha = 1
+p.engines.engine00.probe_update_start = 2
+p.engines.engine00.update_object_first = True
+p.engines.engine00.overlap_converge_factor = 0.5
+p.engines.engine00.overlap_max_iterations = 100
+p.engines.engine00.fourier_relax_factor = 0.05
+
+p.engines.engine01 = u.Param()
+p.engines.engine01.name = 'ML_cupy'
+p.engines.engine01.numiter = 50
+
+if __name__ == "__main__":
+    P = Ptycho(p,level=5)
+

templates/accelerate/ptypy_id22ni_AuStar_focused_cupy.py

@@ -0,0 +1,120 @@
+"""
+This script is a test for ptychographic reconstruction in the absence
+of actual data. It uses a simulated Au Siemens star pattern under  
+experimental farfield conditions and with a focused beam in the hard X-ray regime.
+"""
+from ptypy.core import Ptycho
+from ptypy import utils as u
+import ptypy
+ptypy.load_gpu_engines(arch="cupy")
+
+import numpy as np
+import tempfile
+tmpdir = tempfile.gettempdir()
+
+p = u.Param()
+
+### PTYCHO PARAMETERS
+p.verbose_level = "info"
+
+p.data_type = "single"
+p.run = None
+
+p.io = u.Param()
+p.io.home = "/".join([tmpdir, "ptypy"])
+p.io.autosave = u.Param(active=False)
+p.io.autoplot = u.Param(active=False, layout="weak")
+p.io.interaction = u.Param(active=False)
+
+# Simulation parameters
+sim = u.Param()
+sim.energy = 17.0
+sim.distance = 2.886
+sim.psize = 51e-6
+sim.shape = 256
+sim.xy = u.Param()
+sim.xy.model = "round"
+sim.xy.spacing = 250e-9
+sim.xy.steps = 30
+sim.xy.extent = 4e-6
+
+sim.illumination = u.Param()
+sim.illumination.model = None
+sim.illumination.photons = 3e8
+sim.illumination.aperture = u.Param()
+sim.illumination.aperture.diffuser = None
+sim.illumination.aperture.form = "rect"
+sim.illumination.aperture.size = 35e-6
+sim.illumination.aperture.central_stop = None
+sim.illumination.propagation = u.Param()
+sim.illumination.propagation.focussed = 0.08
+sim.illumination.propagation.parallel = 0.0014
+sim.illumination.propagation.spot_size = None
+
+sim.sample = u.Param()
+sim.sample.model = u.xradia_star((1000,1000),minfeature=3,contrast=0.0)
+sim.sample.process = u.Param()
+sim.sample.process.offset = (100,100)
+sim.sample.process.zoom = 1.0
+sim.sample.process.formula = "Au"
+sim.sample.process.density = 19.3
+sim.sample.process.thickness = 2000e-9
+sim.sample.process.ref_index = None
+sim.sample.process.smoothing = None
+sim.sample.fill = 1.0+0.j
+
+#sim.detector = 'FRELON_TAPER'
+sim.detector = 'GenericCCD32bit'
+sim.verbose_level = 1
+sim.psf = 1. # emulates partial coherence
+sim.plot = False
+
+# Scan model and initial value parameters
+p.scans = u.Param()
+p.scans.scan00 = u.Param()
+p.scans.scan00.name = 'BlockFull'
+
+p.scans.scan00.coherence = u.Param()
+p.scans.scan00.coherence.num_probe_modes = 4
+p.scans.scan00.coherence.num_object_modes = 1
+p.scans.scan00.coherence.energies = [1.0]
+
+p.scans.scan00.sample = u.Param()
+p.scans.scan00.sample.model = 'stxm'
+p.scans.scan00.sample.process =  None
+
+# (copy the simulation illumination and change specific things)
+p.scans.scan00.illumination = sim.illumination.copy(99)
+p.scans.scan00.illumination.aperture.form = 'circ'
+p.scans.scan00.illumination.propagation.focussed = 0.06
+p.scans.scan00.illumination.diversity = u.Param()
+p.scans.scan00.illumination.diversity.power = 0.1
+p.scans.scan00.illumination.diversity.noise = (np.pi,3.0)
+
+# Scan data (simulation) parameters
+p.scans.scan00.data = u.Param()
+p.scans.scan00.data.name = 'SimScan'
+p.scans.scan00.data.update(sim)
+p.scans.scan00.data.save = None
+
+# Reconstruction parameters
+p.engines = u.Param()
+p.engines.engine00 = u.Param()
+p.engines.engine00.name = 'DM_cupy'
+p.engines.engine00.numiter = 150
+p.engines.engine00.fourier_relax_factor = 0.05
+p.engines.engine00.numiter_contiguous = 1
+p.engines.engine00.probe_support = 0.7
+p.engines.engine00.probe_inertia = 0.01
+p.engines.engine00.object_inertia = 0.1
+p.engines.engine00.clip_object = (0, 1.)
+p.engines.engine00.alpha = 1
+p.engines.engine00.probe_update_start = 2
+p.engines.engine00.update_object_first = True
+p.engines.engine00.overlap_converge_factor = 0.05
+p.engines.engine00.overlap_max_iterations = 100
+p.engines.engine00.obj_smooth_std = 5
+
+u.verbose.set_level("info")
+if __name__ == "__main__":
+    P = Ptycho(p,level=5)