changed reference to the Data Folder globally

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

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
 
+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

proxtoolbox/experiments/orbitaltomography/orbit_kpeem.py

@@ -7,6 +7,8 @@ from proxtoolbox.experiments.orbitaltomography.planar_molecule import PlanarMole
 from proxtoolbox.utils.orbitaltomog import shifted_fft, fourier_interpolate, bin_array, shifted_ifft
 from proxtoolbox.utils.visualization.complex_field_visualization import complex_to_rgb
 
+from proxtoolbox.utils.GetData import datadir
+
 
 class OrbitalMomentumMicroscope(PlanarMolecule):
     """
@@ -17,8 +19,9 @@ class OrbitalMomentumMicroscope(PlanarMolecule):
     def getDefaultParameters():
         defaultParams = {
             'experiment_name': 'Momentum microscopy',
-            'data_filename': '..\\Inputdata\\OrbitalTomog'
-                             + '\\2020_11_05_Coronene_HOMO_near_degenerate_noisefree.tif',
+            'data_filename': datadir
+                            + '\OrbitalTomog'
+                            + '\\2020_11_05_Coronene_HOMO_near_degenerate_noisefree.tif',
             'from_intensity_data': False,
             'object': 'real',
             'constraint': 'sparse real',

proxtoolbox/experiments/orbitaltomography/orthogonal_orbits.py

@@ -7,13 +7,16 @@ from proxtoolbox.experiments.orbitaltomography.planar_molecule import PlanarMole
 from proxtoolbox.utils.orbitaltomog import shifted_fft, fourier_interpolate, bin_array, shifted_ifft
 from proxtoolbox.utils.visualization.complex_field_visualization import complex_to_rgb
 
+from proxtoolbox.utils.GetData import datadir
+
 
 class OrthogonalOrbitals(PlanarMolecule):
     @staticmethod
     def getDefaultParameters():
         defaultParams = {
             'experiment_name': '2D ARPES',
-            'data_filename': '..\\Inputdata\\OrbitalTomog'
+            'data_filename':  datadir
+                             + '\OrbitalTomog'
                              + '\\2020_10_27_coronene_Homo_stack_ARPES_2e6counts_corrected_80x80.tif',
             'from_intensity_data': False,
             'object': 'real',

proxtoolbox/experiments/orbitaltomography/planar_molecule.py

@@ -7,6 +7,7 @@ from proxtoolbox.experiments.orbitaltomography.orbitExperiment import OrbitalTom
 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.GetData import datadir
 
 class PlanarMolecule(OrbitalTomographyExperiment):
     @staticmethod
@@ -14,7 +15,7 @@ class PlanarMolecule(OrbitalTomographyExperiment):
         # TODO: optimize parameters and proxoperators to get good & consistent phase retrieval using the demo
         defaultParams = {
             'experiment_name': 'noisy 2D ARPES', # '2D ARPES', #
-            'data_filename': '../InputData/OrbitalTomog/coronene_homo1.tif',
+            'data_filename': datadir/'OrbitalTomog'/'coronene_homo1.tif',
             'from_intensity_data': False,
             'object': 'real',
             'constraint': 'sparse real',

proxtoolbox/experiments/phase/CDI_Experiment.py

@@ -7,6 +7,7 @@ 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 numpy import exp, sqrt, log2, log10, ceil, floor, unravel_index, argmax, zeros
@@ -77,7 +78,7 @@ class CDI_Experiment(PhaseExperiment):
         GetData.getData('Phase')
         if not self.silent:
             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

proxtoolbox/experiments/phase/CDP_Experiment.py

@@ -13,6 +13,8 @@ from numpy.linalg import norm
 from numpy.fft import fft2, ifft2
 import time
 
+from proxtoolbox.utils.GetData import datadir
+
 
 class CDP_Experiment(PhaseExperiment):
     """
@@ -91,18 +93,18 @@ class CDP_Experiment(PhaseExperiment):
         # make image
         if debug:
             if n2 == 1:
-                x_dict = loadMatFile('../InputData/Phase/CDP_1D_x.mat')
+                x_dict = loadMatFile(datadir/'Phase'/'CDP_1D_x.mat')
                 debug_image = x_dict['x']
-                masks_dict = loadMatFile('../InputData/Phase/CDP_1D_Masks.mat')
+                masks_dict = loadMatFile(datadir/'Phase'/'CDP_1D_Masks.mat')
                 debug_masks = masks_dict['Masks']
-                z0_dict = loadMatFile('../InputData/Phase/CDP_1D_z0.mat')
+                z0_dict = loadMatFile(datadir/'Phase'/'CDP_1D_z0.mat')
                 debug_z0 = z0_dict['z0']
             elif n2 == 256:
-                x_dict = loadMatFile('../InputData/Phase/CDP_2D_x.mat')
+                x_dict = loadMatFile(datadir/'Phase'/'CDP_2D_x.mat')
                 debug_image = x_dict['x']
-                masks_dict = loadMatFile('../InputData/Phase/CDP_2D_Masks.mat')
+                masks_dict = loadMatFile(datadir/'Phase'/'CDP_2D_Masks.mat')
                 debug_masks = masks_dict['Masks']
-                z0_dict = loadMatFile('../InputData/Phase/CDP_2D_z0.mat')
+                z0_dict = loadMatFile(datadir/'Phase'/'CDP_2D_z0.mat')
                 debug_z0 = z0_dict['z0']
             x = debug_image
         else:

proxtoolbox/experiments/phase/JWST_Experiment.py

@@ -12,6 +12,7 @@ from proxtoolbox.utils.cell import Cell, isCell
 
 #for downloading data
 import proxtoolbox.utils.GetData as GetData
+from proxtoolbox.utils.GetData import datadir
 
 import matplotlib
 import matplotlib.pyplot as plt
@@ -91,7 +92,7 @@ class JWST_Experiment(PhaseExperiment):
 
         if not self.silent:
             print('Loading data.')
-        with open('../InputData/Phase/pupil.pmod','r') as fid:
+        with open(datadir/'Phase'/'pupil.pmod','r') as fid:
         # read lower endian float <f
             Xi_A = np.fromfile(fid, dtype='<f')
             Xi_A = Xi_A.astype(np.float64)
@@ -99,13 +100,13 @@ class JWST_Experiment(PhaseExperiment):
 
         diversity = 3
 
-        with open('../InputData/Phase/phase_p37.pmod','r') as fid:
+        with open(datadir/'Phase'/'phase_p37.pmod','r') as fid:
         # read lower endian float <f
             temp1 = np.fromfile(fid, dtype='<f')
             temp1 = temp1.astype(np.float64)
             temp1 = temp1.reshape(512,512).T
 
-        with open('../InputData/Phase/phase_m37.pmod','r') as fid:
+        with open(datadir/'Phase'/'phase_m37.pmod','r') as fid:
         # read lower endian float <f
             temp2 = np.fromfile(fid, dtype='<f')
             temp2 = temp2.astype(np.float64)

proxtoolbox/experiments/phase/Krueger_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 numpy import exp, sqrt, log2, log10, ceil, floor, unravel_index, argmax, zeros
@@ -81,13 +82,13 @@ class Krueger_Experiment(PhaseExperiment):
         # parameters see below
 
         # empty waveguide (WG) beam
-        WG = loadmat('../InputData/Phase/WG_beam.mat')
+        WG = loadmat(datadir/'Phase'/'WG_beam.mat')
         WG = WG['WG']
 
         # hologram
         if not self.silent:
             print('Loading data hologram_not-normalized.mat')
-        I_exp = loadmat('../InputData/Phase/hologram_not-normalized.mat')
+        I_exp = loadmat(datadir/'Phase'/'hologram_not-normalized.mat')
         I_exp = I_exp['I_exp']
 
         I_exp[np.isnan(I_exp)] = 1

proxtoolbox/experiments/phase/Phasepack_Experiment.py

@@ -17,6 +17,7 @@ from matplotlib.pyplot import subplots, show, figure
 import os.path
 import time
 
+from proxtoolbox.utils.GetData import datadir
 
 class Phasepack_Experiment(PhaseExperiment):
     '''
@@ -70,7 +71,7 @@ class Phasepack_Experiment(PhaseExperiment):
         # so that we can use the automatic data loading feature (i.e., GetData.getData("Phasepack")).
         # Another possibility is to write code that downloads the data files directly from 
         # the original website (https://rice.app.box.com/v/TransmissionMatrices)
-        data_dir = "../InputData/Phase/" + self.dataset + '/'
+        data_dir = datadir/'Phase' + self.dataset
         filenames = ['A_GS.mat', 'YH_squared_test.mat', 'XH_test.mat']
         for filename in filenames:
             data_path = data_dir + filename

proxtoolbox/experiments/ptychography/ptychographyExperiment.py

@@ -11,6 +11,7 @@ from proxtoolbox.experiments.ptychography.ptychographyUtils import circ, \
 
 #for downloading data
 import proxtoolbox.utils.GetData as GetData
+from proxtoolbox.utils.GetData import datadir
 
 import numpy as np
 from numpy import exp, sqrt, log2, log10, ceil, floor, unravel_index, argmax, zeros
@@ -44,7 +45,7 @@ class PtychographyExperiment(Experiment):
             'experiment_name' : 'Ptychography',
             'object': 'complex',
             'constraint': 'amplitude only',
-            'data_dir': '../InputData/Ptychography/',
+            'data_dir': datadir/'Ptychography',
             'datafile': 'data_NTT_01_26210_192x192',
             'farfield': True,
             'noise': None,
@@ -93,7 +94,7 @@ class PtychographyExperiment(Experiment):
 
 
     def __init__(self, 
-                 data_dir = '../InputData/Ptychography/',
+                 data_dir = datadir/'Ptychography',
                  datafile = 'data_NTT_01_26210_192x192',
                  farfield = True,   
                  poissonfactor = 5,