Merge branch 'master' into gretchko

proxtoolbox/experiments/orbitaltomography/planar_molecule.py

@@ -5,7 +5,7 @@ import matplotlib.pyplot as plt
 
 from proxtoolbox.experiments.orbitaltomography.orbitExperiment import OrbitalTomographyExperiment
 from proxtoolbox.utils.visualization.complex_field_visualization import complex_to_rgb
-from proxtoolbox.utils.OrbitalTomog import bin_array, shifted_fft, shifted_ifft, fourier_interpolate, roll_to_pos
+from proxtoolbox.utils.orbitaltomog import bin_array, shifted_fft, shifted_ifft, fourier_interpolate, roll_to_pos
 
 
 class PlanarMolecule(OrbitalTomographyExperiment):
@@ -192,12 +192,15 @@ class PlanarMolecule(OrbitalTomographyExperiment):
             bx4.set_ylabel('Gap')
         f.tight_layout()
 
-        h, ax = plt.subplots(1,3,figsize=(9,3))
+        h, ax = plt.subplots(1, 3, figsize=(9,3))
         ax[0].imshow(self.data)
+        ax[0].set_title("Measured data")
         prop = self.propagator(self)
         u_hat = prop.eval(self.algorithm.prox1.eval(self.algorithm.u))
         ax[1].imshow(abs(u_hat))
+        ax[1].set_title("Predicted measurement intensity")
         ax[2].imshow(complex_to_rgb(u_hat))
+        ax[2].set_title("Predicted phase (by color)")
         h.tight_layout()
         plt.show()
 

proxtoolbox/experiments/orbitaltomography/planar_molecule_demo.py

@@ -2,7 +2,6 @@ import sys, os
 # set proxpython path
 sys.path.append(os.path.dirname(os.path.realpath(__file__)) + "/../../..")
 
-
 from proxtoolbox.experiments.orbitaltomography import planar_molecule as pm
 
 if __name__ == "__main__":  # prevent execution when generating documentation
@@ -13,7 +12,8 @@ if __name__ == "__main__":  # prevent execution when generating documentation
                             use_sparsity_with_support=True,
                             sparsity_parameter=40,
                             TOL=1e-10,
-                            lambda_0=0.85, lambda_max=0.5, lambda_switch=30)
+                            lambda_0=0.85, lambda_max=0.5, lambda_switch=30,
+                            rnd_seed=None)  # Disable fixed pseudo-random number generator
     # exp_pm.plotInputData()
     exp_pm.run()
     exp_pm.show()

proxtoolbox/proxoperators/P_M.py

@@ -37,7 +37,7 @@ class P_M(ProxOperator):
         """
         m = self.data
         a = self.prop.eval(u)
-        b = magproj(a, m)
+        b = magproj(m, a)
         return self.invprop.eval(b)
 
 
@@ -70,7 +70,7 @@ class P_M_masked(P_M):
         array_like - p_M: the projection IN THE PHYSICAL (time) DOMAIN
         """
         fourier_space_iterate = self.prop.eval(u)
-        constrained = magproj(fourier_space_iterate.copy(), self.data)
+        constrained = magproj(self.data, fourier_space_iterate.copy())
         update = where(self.mask, fourier_space_iterate, constrained)
         return self.invprop(update)
 
@@ -97,7 +97,7 @@ class Approx_P_M(P_M):
         # Now see that the propagated field is within the ball around the data (if any).
         # If not, the projection is calculated, otherwise we do nothing.
         if h_u_hat >= self.data_ball + self.TOL2:
-            b = magproj(u_hat, self.data)
+            b = magproj(self.data, u_hat)
             return self.invprop.eval(b)
         else:
             return u
@@ -124,7 +124,7 @@ class Approx_P_M_masked(P_M_masked):
         # Now see that the propagated field is within the ball around the data (if any).
         # If not, the projection is calculated, otherwise we do nothing.
         if h_u_hat >= self.data_ball + self.TOL2:
-            constrained = magproj(u_hat.copy(), self.data)  # Apply constraint
+            constrained = magproj(self.data, u_hat.copy())  # Apply constraint
             update = where(self.mask, u_hat, constrained)  # Masking operation
             return self.invprop(update)  # Propagate back
         else:

proxtoolbox/proxoperators/P_Sparsity.py

 from numpy import zeros_like, unravel_index, sum, max
 import numpy as np
 from proxtoolbox.proxoperators.proxoperator import ProxOperator
-from proxtoolbox.utils.OrbitalTomog import tile_array, bin_array
+from proxtoolbox.utils.orbitaltomog import tile_array, bin_array
 from proxtoolbox.utils.size import size_matlab
 
 __all__ = ['P_Sparsity', 'P_Sparsity_real', 'P_Sparsity_Symmetric', 'P_Sparsity_Symmetric_real',

proxtoolbox/proxoperators/propagators.py

 from numpy import pi, sqrt, conj
 from numpy.fft import fft2, ifft2, fft, ifft
-from proxtoolbox.utils.OrbitalTomog import shifted_ifft, shifted_fft
+from proxtoolbox.utils.orbitaltomog import shifted_ifft, shifted_fft
 
 __all__ = ['PropagatorFFTn', 'InvPropagatorFFTn',
            'PropagatorFFT2', 'InvPropagatorFFT2',

pyproject.toml

+[tool.poetry]
+name = "ProxPython"
+version = "1.0.4"
+description = ""
+authors = ["Russell Luke <r.luke@math.uni-goettingen.de>"]
+
+[tool.poetry.dependencies]
+python = "^3.8"
+numpy = "^1.19.2"
+scikit-image = "^0.17.2"
+matplotlib = "^3.3.2"
+scipy = "^1.5.2"
+
+[tool.poetry.dev-dependencies]
+
+[build-system]
+requires = ["poetry>=0.12"]
+build-backend = "poetry.masonry.api"

singularity.def

+Bootstrap: docker
+From: python:3.8.5-slim-buster
+
+%setup
+    mkdir -p $SINGULARITY_ROOTFS/code
+    cp poetry.lock $SINGULARITY_ROOTFS/code/  
+    cp pyproject.toml $SINGULARITY_ROOTFS/code/
+
+
+
+%post
+    apt-get -qyy update
+    env DEBIAN_FRONTEND=noninteractive apt-get -qyy install -o APT::Install-Recommends=false -o APT::Install-Suggests=false \
+        git cmake ninja-build libscalapack-openmpi-dev \
+        build-essential curl
+    apt-get clean
+    export POETRY_HOME=/etc/poetry
+    curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python
+    ln -s /etc/poetry/bin/poetry /usr/local/bin/poetry
+    chmod a+rX /etc/poetry/bin/poetry
+
+    export PIP_NO_CACHE_DIR=off
+    export PIP_DISABLE_PIP_VERSION_CHECK=on
+
+    cd /code
+    poetry config virtualenvs.create false
+    poetry install  --no-interaction --no-ansi
+
+%runscript
+    exec poetry shell "$@"
+