Merge branch 'master' into 'NoLips'

# Conflicts:
#   env.nix

.gitignore

@@ -6,4 +6,5 @@ build
 dist
 .vscode/launch.json
 .vscode/settings.json
-tests/orb_tomog_regression_tests.py
\ No newline at end of file
+tests/orb_tomog_regression_tests.py
+/env

README.md

@@ -18,9 +18,9 @@ Institute for Numerical and Applied Mathematics at the University of Göttingen.
 
 ## Python version
 
-**1.0.4**:
-* [Sources](https://gitlab.gwdg.de/nam/ProxPython/-/releases/1.0.4)
-* [Documentation](https://num.math.uni-goettingen.de/proxtoolbox/versions/1.0.4)
+**1.0.5**:
+* [Sources](https://gitlab.gwdg.de/nam/ProxPython/-/releases/1.0.5)
+* [Documentation](https://num.math.uni-goettingen.de/proxtoolbox/versions/1.0.5)
 
 
 The documentation includes a tutorial.

demos/Elser_RRR.py

+import pdb
+import SetProxPythonPath
+from proxtoolbox.experiments.phase.Elser_Experiment import Elser_Experiment
+
+Elser = Elser_Experiment(Atoms=400, category='H', algorithm='RRR', lambda_0=0.95, lambda_max=0.95, anim=True)
+Elser.run()
+Elser.show()

demos/JWST_ADMM.py

@@ -2,6 +2,6 @@
 import SetProxPythonPath
 from proxtoolbox.experiments.phase.JWST_Experiment import JWST_Experiment
 
-JWST = JWST_Experiment(algorithm='ADMM', lambda_0=3.0, lambda_max=3.0)
+JWST = JWST_Experiment(algorithm='ADMM', lambda_0=4.0, lambda_max=4.0, anim=True)
 JWST.run()
 JWST.show()

demos/JWST_ADMM_noise.py

@@ -3,6 +3,6 @@ import SetProxPythonPath
 from proxtoolbox.experiments.phase.JWST_Experiment import JWST_Experiment
 
 JWST = JWST_Experiment(algorithm='ADMM', lambda_0=3.0, lambda_max=3.0,
-                       MAXIT=300, noise = True, rotate = True)
+                       MAXIT=300, noise = True, rotate = True, anim=True)
 JWST.run()
 JWST.show()

demos/JWST_DRl.py

-
+import pdb
 import SetProxPythonPath
 from proxtoolbox.experiments.phase.JWST_Experiment import JWST_Experiment
 

docs/Tutorial/addingExperiment.rst

@@ -69,7 +69,7 @@ A concrete experiment class needs to override the
       GetData.getData('Phase')
 
       print('Loading data file CDI_intensity')
-      f = loadmat('../InputData/Phase/CDI_intensity.mat')
+      f = loadmat(datadir/'Phase'/'CDI_intensity.mat')
       # diffraction pattern
       dp = f['intensity']['img'][0, 0]
       orig_res = max(dp.shape[0], dp.shape[1])  # actual data size

env.nix

@@ -30,4 +30,3 @@ poetry2nix.mkPoetryEnv {
     });
   });
 }
-

proxtoolbox/__init__.py

@@ -36,6 +36,7 @@ from .experiments import *
 from .proxoperators import *
 from .utils import *
 
+
 __all__ = ["algorithms",
            "experiments",
            "proxoperators",

proxtoolbox/experiments/CT/ART_Experiment.py

@@ -6,6 +6,7 @@ from proxtoolbox.utils.graphics import addColorbar
 
 #for downloading data
 import proxtoolbox.utils.GetData as GetData
+from proxtoolbox.utils.GetData import datadir
 
 import numpy as np
 from scipy.io import loadmat
@@ -74,7 +75,7 @@ class ART_Experiment(Experiment):
         # load data
         if not self.silent:
             print('Loading data file ART_SheppLogan.mat ')
-        data_Shepp = loadmat('../InputData/CT/ART_SheppLogan.mat')
+        data_Shepp = loadmat(datadir/'CT'/'ART_SheppLogan.mat')
         N = data_Shepp['N'].item()
         p = data_Shepp['p'].item()
         theta = data_Shepp['theta']

proxtoolbox/experiments/orbitaltomography/degenerate_orbits.py

@@ -5,14 +5,16 @@ from proxtoolbox.experiments.orbitaltomography.planar_molecule import PlanarMole
 from proxtoolbox.utils.orbitaltomog import shifted_fft, fourier_interpolate
 from proxtoolbox.utils.visualization.complex_field_visualization import complex_to_rgb
 
+#for downloading data
+import proxtoolbox.utils.GetData as GetData
+from proxtoolbox.utils.GetData import datadir
 
 class DegenerateOrbital(PlanarMolecule):
     @staticmethod
     def getDefaultParameters():
         defaultParams = {
             'experiment_name': '2D ARPES',
-            'data_filename': '..\\Inputdata\\OrbitalTomog'
-                             + '\\2020_10_27_coronene_Homo1+2_ARPES_2e6counts_corrected_80x80.tif',
+            'data_filename': datadir/'OrbitalTomog'/'2020_10_27_coronene_Homo1+2_ARPES_2e6counts_corrected_80x80.tif',
             'from_intensity_data': True,
             'object': 'real',
             'degeneracy': 2,  # Number of degenerate states to reconstruct
@@ -59,6 +61,10 @@ class DegenerateOrbital(PlanarMolecule):
             - threshold_for_support: float, in range [0,1], fraction of the maximum at which to threshold when
                 determining support or support for sparsity
         """
+
+        # make sure input data can be found, otherwise download it
+        GetData.getData('OrbitalTomog')
+        
         super(DegenerateOrbital, self).loadData()
 
     def createRandomGuess(self):

proxtoolbox/experiments/orbitaltomography/molecule_3d.py

@@ -7,6 +7,9 @@ from proxtoolbox.experiments.orbitaltomography.orbitExperiment import OrbitalTom
 from proxtoolbox.utils.visualization.stack_viewer import XYZStackViewer
 from proxtoolbox.utils.orbitaltomog import shifted_fft
 
+#for downloading data
+import proxtoolbox.utils.GetData as GetData
+from proxtoolbox.utils.GetData import datadir
 
 class Molecule3D(OrbitalTomographyExperiment):
     @staticmethod
@@ -56,6 +59,9 @@ class Molecule3D(OrbitalTomographyExperiment):
         """
         Load data and set in the correct format for reconstruction
         """
+        # make sure input data can be found, otherwise download it
+        GetData.getData('OrbitalTomog')
+        
         # TODO: copy from data processor
         raise NotImplementedError
 

proxtoolbox/experiments/orbitaltomography/orbitExperiment.py

@@ -6,6 +6,9 @@ from glob import glob
 from proxtoolbox.utils.h5 import write_dict_to_h5
 import numpy as np
 
+#for downloading data
+import proxtoolbox.utils.GetData as GetData
+from proxtoolbox.utils.GetData import datadir
 
 class OrbitalTomographyExperiment(Experiment):
     @staticmethod
@@ -30,6 +33,10 @@ class OrbitalTomographyExperiment(Experiment):
         self.output_ignore_keys = ['u1', 'u2', 'plots']
 
     def loadData(self):
+        
+        # make sure input data can be found, otherwise download it
+        GetData.getData('OrbitalTomog')
+
         """
         Load or generate the dataset that will be used for
         this experiment. Create the initial iterate.