Added automatic regression tests (in new tests folder)

demos/SetProxPythonPath.py

-#Sylvain
-
 # Module to be imported by test modules to set the ProxPython path
 # after this is called, can use import statements like this one:
 # from proxtoolbox.experiments.phase import Phase, JWST_AltP_in

demos/Sudoku_DRl.py

@@ -4,16 +4,16 @@ from proxtoolbox.experiments.sudoku.sudokuExperiment import SudokuExperiment
 
 # if a puzzle is not specified, the sudoku experiment uses the
 # default puzzle, which is the same as the one below:
-puzzle = ((2,0,0,0,0,1,0,3,0),
-         (4,0,0,0,8,6,1,0,0),
-         (0,0,0,0,0,0,0,0,0),
-         (0,0,0,0,1,0,0,0,0),
-         (0,0,0,0,0,0,9,0,0),
-         (0,0,5,0,0,3,0,0,7),
-         (0,0,0,0,0,0,0,0,0),
-         (1,0,0,0,0,7,4,9,0),
-         (0,2,4,1,0,0,0,0,0))
+# puzzle = ((2,0,0,0,0,1,0,3,0),
+#          (4,0,0,0,8,6,1,0,0),
+#          (0,0,0,0,0,0,0,0,0),
+#          (0,0,0,0,1,0,0,0,0),
+#          (0,0,0,0,0,0,9,0,0),
+#          (0,0,5,0,0,3,0,0,7),
+#          (0,0,0,0,0,0,0,0,0),
+#          (1,0,0,0,0,7,4,9,0),
+#          (0,2,4,1,0,0,0,0,0))
 
-Sudoku = SudokuExperiment(algorithm='DRl', sudoku=puzzle)
+Sudoku = SudokuExperiment(algorithm='DRl')
 Sudoku.run()
 Sudoku.show()

proxtoolbox/algorithms/iterateMonitor.py

@@ -28,6 +28,7 @@ class IterateMonitor:
         self.anim = experiment.anim
         self.anim_callback = experiment.animate
         self.anim_step = experiment.anim_step
+        self.silent = experiment.silent
 
         self.changes = None
 
@@ -82,7 +83,7 @@ class IterateMonitor:
         alg : instance of Algorithm class
             Algorithm being monitored.
         """
-        if self.anim and self.anim_callback is not None \
+        if (not self.silent) and self.anim and self.anim_callback is not None \
                 and alg.iter % self.anim_step == 0:
             self.anim_callback(alg)
 

proxtoolbox/algorithms/samsara/samsara.py

@@ -374,7 +374,7 @@ class Samsara():
     def __first_step(self):
         """Initialise variables.
         """
-        print('First iteration: initialising...')
+        #print('First iteration: initialising...')
         ##################################################
         # Initialisation
         ##################################################

proxtoolbox/experiments/CT/ART_Experiment.py

@@ -72,7 +72,8 @@ class ART_Experiment(Experiment):
         GetData.getData('CT')
         
         # load data
-        print('Loading data file ART_SheppLogan.mat ')
+        if not self.silent:
+            print('Loading data file ART_SheppLogan.mat ')
         data_Shepp = loadmat('../InputData/CT/ART_SheppLogan.mat')
         N = data_Shepp['N'].item()
         p = data_Shepp['p'].item()

proxtoolbox/experiments/experiment.py

@@ -101,6 +101,8 @@ class Experiment(metaclass=ExperimentMetaClass):
                  accelerator_name=None,
                  rotate=False,
                  verbose=0,
+                 silent=False, # if set to True, means no print statement should be executed
+                               # (including what would have been generated with verbose mode)
                  graphics=0,
                  anim=False,
                  anim_step = 2, # Tell how frequently the animation is updated, i.e., every `anim_step` step(s)
@@ -150,6 +152,7 @@ class Experiment(metaclass=ExperimentMetaClass):
         self.data_ball = data_ball
         self.diagnostic = diagnostic
         self.verbose = verbose
+        self.silent = silent
         self.graphics = graphics
         self.anim = anim
         self.anim_step = anim_step
@@ -266,10 +269,10 @@ class Experiment(metaclass=ExperimentMetaClass):
         Run the algorithm associated with this experiment.
         The initial iterate is obtained from the loadData() method.
         """
-        # TODO: implement multiple runs
 
-        print("Running " + self.algorithm_name + " on " + self.experiment_name + "...")
-        if self.verbose:
+        if not self.silent:
+            print("Running " + self.algorithm_name + " on " + self.experiment_name + "...")
+        if self.verbose and not self.silent:
             self.printInput()
 
         t = time.time()
@@ -278,15 +281,16 @@ class Experiment(metaclass=ExperimentMetaClass):
 
         self.output['stats']['time'] = time.time() - t
 
-        print("Took", self.output['stats']['iter'], "iterations and",
-              self.output['stats']['time'], "seconds.")
+        if not self.silent:
+            print("Took", self.output['stats']['iter'], "iterations and",
+                self.output['stats']['time'], "seconds.")
 
         self.postprocess()
         
         if self.save_output:
             self.saveOutput()
 
-        if self.verbose:
+        if self.verbose and not self.silent:
             self.printBenchmark()
 
         if self.anim and mpl.is_interactive():

proxtoolbox/experiments/phase/CDI_Experiment.py

@@ -75,8 +75,8 @@ class CDI_Experiment(PhaseExperiment):
 
         # make sure input data can be found, otherwise download it
         GetData.getData('Phase')
-
-        print('Loading data file CDI_intensity')
+        if not self.silent:
+            print('Loading data file CDI_intensity')
         f = loadmat('../InputData/Phase/CDI_intensity.mat')
         # diffraction pattern
         dp = f['intensity']['img'][0, 0]
@@ -115,7 +115,8 @@ class CDI_Experiment(PhaseExperiment):
 
         self.magn = 1  # magnification factor
         self.farfield = True
-        print('Using farfield formula.')
+        if not self.silent:
+            print('Using farfield formula.')
 
         self.rt_data = Cell(1)
         self.rt_data[0] = M

proxtoolbox/experiments/phase/JWST_Experiment.py

@@ -89,7 +89,8 @@ class JWST_Experiment(PhaseExperiment):
         # works well.
         snr = 1e-8 
 
-        print('Loading data.')
+        if not self.silent:
+            print('Loading data.')
         with open('../InputData/Phase/pupil.pmod','r') as fid:
         # read lower endian float <f
             Xi_A = np.fromfile(fid, dtype='<f')

proxtoolbox/experiments/phase/Krueger_Experiment.py

@@ -85,7 +85,8 @@ class Krueger_Experiment(PhaseExperiment):
         WG = WG['WG']
 
         # hologram
-        print('Loading data hologram_not-normalized.mat')
+        if not self.silent:
+            print('Loading data hologram_not-normalized.mat')
         I_exp = loadmat('../InputData/Phase/hologram_not-normalized.mat')
         I_exp = I_exp['I_exp']
 

proxtoolbox/experiments/phase/Phasepack_Experiment.py

@@ -84,7 +84,8 @@ class Phasepack_Experiment(PhaseExperiment):
                 print('*************************************************************************')
                 raise IOError(errMsg)
 
-        print("Loading data. This may take a while...")
+        if not self.silent:
+            print("Loading data. This may take a while...")
 
         # transmission matrix
         XH_test_dict = loadMatFile(data_dir + filenames[2])

proxtoolbox/experiments/ptychography/ptychographyExperiment.py

@@ -266,7 +266,8 @@ class PtychographyExperiment(Experiment):
         # Average total intensity in experimental diffraction pattern
         I_sum = np.sum(np.sum(self.I_exp,axis=1),axis=0)
         I_avg = np.mean(I_sum)
-        print("Average intensity of single frame is {:.2e} photons".format(I_avg))
+        if not self.silent:
+            print("Average intensity of single frame is {:.2e} photons".format(I_avg))
 
         # Maximum average intensity in a single experimental frame
         I_max_avg = np.amax(I_sum) / (self.Nx*self.Ny)
@@ -697,7 +698,8 @@ class PtychographyExperiment(Experiment):
 
         if self.warmup:
             # run warmup algorithm
-            print("Running warmup algorithm " + self.warmupExp.algorithm_name)
+            if not self.silent:
+                print("Running warmup algorithm " + self.warmupExp.algorithm_name)
             warmup_out = self.warmupExp.algorithm.run(self.warmupExp.u0)
             warmup_u = warmup_out['u'] 
             u0 = Cell(3)
@@ -707,7 +709,8 @@ class PtychographyExperiment(Experiment):
         else:
             u0 = self.u0
 
-        print("Running main algorithm (" + self.algorithm_name + ")")
+        if not self.silent:
+            print("Running main algorithm (" + self.algorithm_name + ")")
         output = super(PtychographyExperiment, self).runAlgorithm(u0) # call parent's method
         return output
         

tests/SetProxPythonPath.py

+# Module to be imported by test modules to set the ProxPython path
+# after this is called, can use import statements like this one:
+# from proxtoolbox.experiments.phase import Phase, JWST_AltP_in
+
+import sys
+import os
+# add the proxpython directory into the Python's path
+sys.path.append(os.path.dirname(os.path.realpath(__file__)) + "/..")
+