Merge remote-tracking branch 'origin/dornheim' into dornheim

Current_state.txt

+Written 18th October 2019 by Alexander Dornheim
+
+Current state of ProxPython (to my knowledge):
+
+Folders:
+docs: haven't worked on this
+GUI_Python: haven't worked on this
+InputData: folder for input data, input data for Phase, ART should be automatically downloaded into this folder
+Nanoscale_Photonic_Imaging_demos: haven't worked on this, to contain demos for Russels book (so far 1 demo)
+proxgui: haven't worked on this
+proxtoolbox: most code, see below
+TestSuite: testing/demos, see below
+
+Files:
+changes_in_Matlab_since_NahmeZiehe.txt: old, delete
+manual.pdf: old
+ProxPython_for_Dummies_README.txt: Mostly wrote it in Feb 2018 for students, still most up to date ReadMe. Contains list of demos which should work properly.
+ProxPython_how_to_run_demos_on_Windows_for_dummies.txt: Short ReadMe for Windows by students (recent). Contains list of files students had problem running.
+ReadMe.md: old, doesn't contain much information
+setup.py: never touched this setup file
+
+Proposed clean up:
+Are both GUI folders needed? Are they working? -> Jochen
+docs -> new documentation by Sylvain in future
+delete changes_in_Matlab_since_NahmeZiehe.txt
+Combine ReadMes
+manual.pdf ?
+
+TestSuite Folder
+
+Phase_test_data: some output from the matlab version which I used for tests, need to talk to Sylvain if he wants to keep this. My tests are very basic, need to be done better using unitest
+testing_Algortihms: folder with tests for the algortihms Robin implemented using unitest, haven't touched it personally
+testing_ProxOperators: folder with tests for the proxoperators Robin implemented using unitest, haven't touched it personally
+*_demo.py: Relocate/ structure in folders: Phase/ART demos etc. List of demos that should be working see ReadMe
+
+to be continued...
+
+
+
+
+
+
+
+
+
+
+

ProxPython_for_Dummies_README.txt

@@ -36,30 +36,30 @@ I. Phase Retrieval:
         d. Phase_JWST_DRAP_demo.py  (Douglas-Rachford-Alternating Projectons hybrid proposed by Nguyen, 2017)     DRAP not yet in ProxPython
 
     2. Siemens data set:  far field Siemens star tests
-		a.  Phase_Siemens_amplitude_demo.py (phase object)
+        a.  Phase_Siemens_amplitude_demo.py (phase object)
         b.  Phase_Siemens_nonneg_demo.py (nonnegative object)
-		c.  Phase_Siemens_real_demo.py (real object - possibly negative valued!?)
+        c.  Phase_Siemens_real_demo.py (real object - possibly negative valued!?)
 
     3. Goettingen data set:
         a. tasse_ap_demo (far field optical diffraction - experimental data)
-		b. tasse_raar_demo (far field optical diffraction - experimental data)
-		c. Near_field_synthetic_demo (near field cell with noise - simulated)        
+        b. tasse_raar_demo (far field optical diffraction - experimental data)
+        c. Near_field_synthetic_demo (near field cell with noise - simulated)        
         d. Phase_near_field_Siemens_experimental_demo(near feild x-ray of Siemens star phase object with structured beam)
-		e. Near_field_living_worm_demo (near field x-ray image of a living worm-  not sure parameters are correct) 
+        e. Near_field_living_worm_demo (near field x-ray image of a living worm-  not sure parameters are correct) 
 
 II. Computed Tomography:
     1.  BLOCK_RAAR_parallel_ART_demo.py (parallelized RAAR, Luke 2005, for CT)
     2.  BLOCK_RAAR_sequential_ART_demo.py (RAAR, Luke 2005, for CT)
     3.  ART_alternating_proj_demo.py (cyclic projections)
     4.  ART_averaged_proj_demo.py (Cimmino algorithm)
-	5.  BLOCK_GRAAL_parallel_ART_demo.py (Golden Ratio Algorithm of Malitskyi, 2017)
+    5.  BLOCK_GRAAL_parallel_ART_demo.py (Golden Ratio Algorithm of Malitskyi, 2017)
     7.  BLOCK_AP_parallel_ART_demo.py (Block parallelized Cimmino)
 
     Not implemented:
     6.  BLOCK_ART_averaged_proj_in (Block Cimmino algorithm)    seems to do the same as demo 7 in ProxToolbox
 
 V. Sudoku:
-	1. Sudoku_demo.py (RAAR for Sudoku following Elser's 2007 model)
+    1. Sudoku_demo.py (RAAR for Sudoku following Elser's 2007 model)
 
 
 

ProxPython_how_to_run_demos_on_Windows_for_dummies.txt

+How to run a demo of ProxPython in Windows starting at 0:
+
+Download python at https://www.python.org/downloads/ .
+Download the ProxPython file from GitLab by clicking on the little cloud icon.
+
+Open the command window by typing in cmd in the search bar.
+In the command window, change your current folder to ProxPython/Testsuite by typing chdir "adress of the testsuite folder" (without the quotation marks).
+You can get the adress by typing in Testsuite in the search bar, right-clicking on the folder and going for copy full path. Now you can paste it by rightclicking in the command window
+Now you need to download some libraries which are needed for the demos. Type in the command window the following 4 commands:
+py -m pip install numpy
+py -m pip install scipy
+py -m pip install h5py
+py -m pip install matplotlib
+
+Now you can run any of the demo files by typing py "name of the file.py" (without the quotation marks), for example py Sudoku_demo.py.
+
+Demos which don't seem to work:
+
+ART_alternating_proj_demo.py (Calculates for a long time without getting any result)
+BLOCK_HAAR_sequential_ART_demo.py (module proxtoolbox.Algorithms has no attribute HAAR)
+BLOCK_QNAP_sequential_ART_demo.py (module proxtoolbox.Algorithms has no attribute QNAP)
+DRprotein_demo.py ( No such file or directory: '../InputData/Protein/1PTQ.pdb)
+Ptychography_demo.py (Seems to loop some kind of runtimeerror)
+sudoku_in.py (runs, but has no output. Might be in the wrong directory?)
+Testing_problems.py (no module named 'proxtoolbox')
+Testing_Utilities.py (no module named 'proxtoolbox')
+TestSuite_all.py (no module named 'TestSuite')
+
+
+
+
+
+
+

TestSuite/Phase_JWST_DRAP_demo.py

+"""              Phase_JWST_DRAP_demo
+            written on Sep 17. 2019 by
+            Constantin Höing
+            Inst. Fuer Numerische und Angewandte Mathematik
+            Universität Göttingen
+
+    
+            
+    """
+    
+    
+    
+
+import sys
+sys.path.append('../proxtoolbox/Problems/Phase') # find out what should be in the string
+sys.path.append("..")
+import JWST_data_processor
+import JWST_DRAP_in
+from phase import Phase
+
+
+JWST = Phase(JWST_DRAP_in.new_config)
+JWST.solve()
+JWST.show()
+

TestSuite/Phase_JWST_HPR_demo.py

+"""              Phase_JWST_DRAP_demo
+            written on Sep 17. 2019 by
+            Constantin Höing
+            Inst. Fuer Numerische und Angewandte Mathematik
+            Universität Göttingen
+
+    
+            
+    """
+    
+    
+    
+
+import sys
+sys.path.append('../proxtoolbox/Problems/Phase') # find out what should be in the string
+sys.path.append("..")
+import JWST_data_processor
+import JWST_HPR_in
+from phase import Phase
+
+
+JWST = Phase(JWST_HPR_in.new_config)
+JWST.solve()
+JWST.show()
+

TestSuite/WIP_CDP_1D_AltP_cold_demo.py

+import sys
+sys.path.append('../proxtoolbox/Problems/Phase')
+sys.path.append('..')
+import CDP_processor
+import CDP_1D_AltP_cold_in
+from phase import Phase
+
+CDP = Phase(CDP_1D_AltP_cold_in.new_config)
+CDP.solve()
+CDP.show()

TestSuite/WIP_CDP_1D_AltP_warm_demo.py

+import sys
+sys.path.append('../proxtoolbox/Problems/Phase')
+sys.path.append('..')
+import CDP_processor
+import CDP_1D_AltP_warm_in
+from phase import Phase
+
+CDP = Phase(CDP_1D_AltP_warm_in.new_config)
+CDP.solve()
+CDP.show()

TestSuite/WIP_CDP_1D_DRAP_warm_demo.py

+import sys
+sys.path.append('../proxtoolbox/Problems/Phase')
+sys.path.append('..')
+import CDP_processor
+import CDP_1D_DRAP_warm_in
+from phase import Phase
+
+CDP = Phase(CDP_1D_DRAP_warm_in.new_config)
+CDP.solve()
+CDP.show()

TestSuite/WIP_CDP_1D_QNAP_cold_demo.py

+import sys
+sys.path.append('../proxtoolbox/Problems/Phase')
+sys.path.append('..')
+import CDP_processor
+import CDP_1D_QNAP_cold_in
+from phase import Phase
+
+CDP = Phase(CDP_1D_QNAP_cold_in.new_config)
+CDP.solve()
+CDP.show()

TestSuite/WIP_CDP_1D_RAAR_warm_demo.py

+import sys
+sys.path.append('../proxtoolbox/Problems/Phase')
+sys.path.append('..')
+import CDP_processor
+import CDP_1D_RAAR_warm_in
+from phase import Phase
+
+CDP = Phase(CDP_1D_RAAR_warm_in.new_config)
+CDP.solve()
+CDP.show()

TestSuite/WIP_CDP_1D_Wirt_cold_demo.py

+import sys
+sys.path.append('../proxtoolbox/Problems/Phase')
+sys.path.append('..')
+import CDP_processor
+import CDP_1D_Wirt_cold_in
+from phase import Phase
+
+CDP = Phase(CDP_1D_Wirt_cold_in.new_config)
+CDP.solve()
+CDP.show()

TestSuite/WIP_CDP_2D_ALtP_cold_demo.py

+import sys
+sys.path.append('../proxtoolbox/Problems/Phase')
+sys.path.append('..')
+import CDP_processor
+import CDP_2D_AltP_cold_in
+from phase import Phase
+
+CDP = Phase(CDP_2D_AltP_cold_in.new_config)
+CDP.solve()
+CDP.show()

TestSuite/WIP_CDP_2D_DRAP_cold_demo.py

+import sys
+sys.path.append('../proxtoolbox/Problems/Phase')
+sys.path.append('..')
+import CDP_processor
+import CDP_2D_DRAP_cold_in
+from phase import Phase
+
+CDP = Phase(CDP_2D_DRAP_cold_in.new_config)
+CDP.solve()
+CDP.show()

TestSuite/WIP_CDP_2D_QNAP_warm_demo.py

+import sys
+sys.path.append('../proxtoolbox/Problems/Phase')
+sys.path.append('..')
+import CDP_processor
+import CDP_2D_QNAP_warm_in
+from phase import Phase
+
+CDP = Phase(CDP_2D_QNAP_warm_in.new_config)
+CDP.solve()
+CDP.show()

TestSuite/WIP_CDP_2D_Wirt_cold_demo.py

+import sys
+sys.path.append('../proxtoolbox/Problems/Phase')
+sys.path.append('..')
+import CDP_processor
+import CDP_2D_Wirt_cold_in
+from phase import Phase
+
+CDP = Phase(CDP_2D_Wirt_cold_in.new_config)
+CDP.solve()
+CDP.show()

TestSuite/demo_tool.py

+"""              demo_tool.py
+            written on Sep 13 2019 by
+            Constantin Höing
+            Inst. Fuer Numerische und Angewandte Mathematik
+            Universität Göttingen
+
+    Description: A tool to list all demos (if added to the folder this is in) and then run a demo the user choose.
+                
+    
+    """
+    
+    
+
+
+
+
+
+
+
+from os import listdir
+from os.path import realpath
+
+
+
+def main():
+    L = listdir(realpath(__file__)[:-13])
+    newL = []
+    for val in L:
+        if "demo" in val:
+            newL.append(val)
+    L = newL
+    del newL
+
+    L.remove("demo_tool.py")
+
+    print("All available demos will be listet. Enter the corresponding number to run that demo\n")
+    L.append("exit")
+
+    
+    while True:
+        print("\n\n\n\n")
+        for idx, val in enumerate(L):
+            print("({})\t{}".format(idx, val))
+        
+    
+        choice = int(input("Which demo do you want to run ?: "))
+        if L[choice] != "exit":
+            exec("import " + L[choice][:-3])
+        else:
+            quit()
+        
+        
+
+
+
+
+    
+
+
+main()
\ No newline at end of file

TestSuite/testing_Algorithms/test_CAARL.py

+import numpy as np
+import unittest
+from proxtoolbox.Algorithms.CAARL import *
+from proxtoolbox.ProxOperators.P_binary import *
+from proxtoolbox.ProxOperators.P_RN import *
+from proxtoolbox.ProxOperators.P_M import *
+class test_CAARL(unittest.TestCase):
+    def test_CAARL(self):
+        config={'proxoperators':[P_binary,P_RN,P_M],'beta0':2 ,'beta_max':2,'beta_switch':1,'prox_idx':2,'iter':10,'prox_idx':2,'support_idx':np.array([1,2]),'Nx':8,'Ny':0,'Nz':0,'Prox':[P_binary,P_RN], 'norm_data':1, 'product_space_dimension':5,'beta_0':2,'M':np.array([1,2,2,2,2,12])}
+        self.pro= CAARL(config)
+        u = np.array([1,2,5,6,-5,-6])
+        self.assertEqual(self.pro.evaluate(u).tolist(),np.array([ -1.8703690419340218+8.437742860180073j , 2.5477381663013103+8.807889679799857j,-7.613529601089619+0.3701468196197832j, -12.384068573713796-8.437742860180071j, 9.483898643023636-8.807889679799857j, 9.836330407412484-0.3701468196197823j]).tolist())
+if __name__ == '__main__':
+    unittest.main()
+#inut:u=[1,2,5,6,-5,-6]
+#output:[ -1.8703690419340218+8.437742860180073j , 2.5477381663013103+8.807889679799857j,-7.613529601089619+0.3701468196197832j, -12.384068573713796-8.437742860180071j, 9.483898643023636-8.807889679799857j, 9.836330407412484-0.3701468196197823j]

TestSuite/testing_Algorithms/test_CADRl.py

+import numpy as np
+import unittest
+from proxtoolbox.Algorithms.CADRl import *
+from proxtoolbox.ProxOperators.P_binary import *
+from proxtoolbox.ProxOperators.P_RN import *
+from proxtoolbox.ProxOperators.P_M import *
+class test_CADRl(unittest.TestCase):
+    def test_CADRl(self):
+        config={'proxoperators':[P_RN,P_M,P_binary],'beta0':2 ,'beta_max':2,'beta_switch':1,'prox_idx':2,'iter':10,'prox_idx':2,'support_idx':np.array([1,2]),'Nx':8,'Ny':0,'Nz':0,'Prox':[P_binary,P_RN], 'norm_data':1, 'product_space_dimension':5,'beta_0':2,'M':np.array([1,2,2,2,2,12])}
+        self.pro= CADRl(config)
+        u = np.array([1,2,5,6,-5,-6])
+        self.assertEqual(self.pro.evaluate(u).tolist(),np.array([ (-1.9356980627875102+3.0408182027976864j) ,0.8580885402990752+2.7029495135979418j,-1.1271369416921422-0.3378686891997414j,-1.779020587713914-3.0408182027976864j,1.062835004479652-2.7029495135979418j, 1.9209320474148388+0.3378686891997414j]).tolist())
+if __name__ == '__main__':
+    unittest.main()

TestSuite/testing_Algorithms/test_CDRl.py

+import numpy as np
+import unittest
+from proxtoolbox.Algorithms.CDRl import *
+from proxtoolbox.ProxOperators.P_binary import *
+from proxtoolbox.ProxOperators.P_RN import *
+from proxtoolbox.ProxOperators.P_M import *
+class test_CDRl(unittest.TestCase):
+    def test_CDRl(self):
+        config={'proxoperators':[P_binary,P_RN,P_M],'beta0':2 ,'beta_max':2,'beta_switch':1,'prox_idx':2,'iter':10,'prox_idx':2,'support_idx':np.array([1,2]),'Nx':8,'Ny':0,'Nz':0,'Prox':[P_binary,P_RN], 'norm_data':1, 'product_space_dimension':5,'beta_0':2,'M':np.array([1,2,2,2,2,12]),'lambda0':2,'lambda_max':2,'lambda_switch':1,'lambda_0':2}
+        self.pro= CDRl(config)
+        u = np.array([1,2,5,6,-5,-6])
+        self.assertEqual(self.pro.evaluate(u).tolist(),np.array([  0.9510576492339013-2.7982183410847505j,1.2326217479829011-2.9678073314535216j ,16.23359565239013-0.169588990368774j ,19.54586980521637+2.798218341084751j ,-16.18465330162403+2.967807331453521j , -19.778491553199267+0.169588990368774j]).tolist())
+if __name__ == '__main__':
+    unittest.main()
+