Prepare for waveorder==1.0.0 release (#114)

* Remove io folder and tests * remove multiprocessing examples * np.int to int * maintain examples/2D_QLIPP_simulation * maintain `3D_PODT_phase_simulation` * local file names * np.int to int * clean PTI_simulation * simple CI/CD for testing examples * add PTI examples to automated tests * turn off GPU for tests * reorganize folders and add README * fix tests * make default PTI simulation smaller * remove pdb * typo * docs typo * remove unmaintained python scripts * remove unused imports and variables * depend on numpy >= 1.21 * fix formatting * naming fix * refactor example tests
mehta-lab · Apr 18, 2023 · 5e05b1c · 5e05b1c
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diff --git a/examples/2D_QLIPP_simulation/2D_QLIPP_forward.ipynb b/examples/2D_QLIPP_simulation/2D_QLIPP_forward.ipynb
diff --git a/examples/2D_QLIPP_simulation/2D_QLIPP_forward.py b/examples/2D_QLIPP_simulation/2D_QLIPP_forward.py
@@ -16,7 +16,7 @@
 
 import waveorder as wo
 
-# ### Key parameters
+# Key parameters
 N = 256  # number of pixel in y dimension
 M = 256  # number of pixel in x dimension
 mag = 40  # magnification
@@ -29,7 +29,7 @@
 z_defocus = (np.r_[:5] - 2) * 1.757  # a set of defocus plane
 chi = 0.03 * 2 * np.pi  # swing of Polscope analyzer
 
-# ## Sample : star with uniform phase, uniform retardance, and radial orientation
+# Sample : star with uniform phase, uniform retardance, and radial orientation
 # generate Siemens star pattern
 star, theta, _ = wo.genStarTarget(N, M)
 wo.plot_multicolumn(np.array([star, theta]), num_col=2, size=5)
@@ -54,8 +54,8 @@
 )
 plt.show()
 
-# ## Forward model of QLIPP <br> (polarization-diverse and depth-diverse acquisition)
-# #### Source pupil
+# Forward model of QLIPP <br> (polarization-diverse and depth-diverse acquisition)
+# Source pupil
 # Subsample source pattern for speed
 
 xx, yy, fxx, fyy = wo.gen_coordinate((N, M), ps)
@@ -67,7 +67,7 @@
 plt.imshow(fftshift(Source_discrete), cmap="gray")
 plt.show()
 
-# #### Initialize microscope simulator with above source pattern and uniform imaging pupil
+# Initialize microscope simulator with above source pattern and uniform imaging pupil
 # Microscope object generation
 
 simulator = wo.waveorder_microscopy_simulator(
@@ -83,7 +83,7 @@
     Source=Source_discrete,
 )
 
-# ## Compute image volumes and Stokes volumes
+# Compute image volumes and Stokes volumes
 I_meas, Stokes_out = simulator.simulate_waveorder_measurements(
     t_eigen, sa, multiprocess=False
 )
@@ -96,8 +96,8 @@
     np.random.poisson(I_meas / np.max(I_meas) * photon_count + const_bg)
 ).astype("float64")
 
-# #### Save simulation
-output_file = "/data_sm/home/lihao/project/Polscope/Simulation/3D_Pol_Phase/PTI_repo_demo/2D_QLIPP_simulation"
+# Save simulation
+output_file = "./2D_QLIPP_simulation.npz"
 np.savez(
     output_file,
     I_meas=I_meas_noise,

diff --git a/examples/2D_QLIPP_simulation/2D_QLIPP_recon.ipynb b/examples/2D_QLIPP_simulation/2D_QLIPP_recon.ipynb
diff --git a/examples/2D_QLIPP_simulation/2D_QLIPP_recon.py b/examples/2D_QLIPP_simulation/2D_QLIPP_recon.py
@@ -19,7 +19,7 @@
 # Load simulations
 
 
-file_name = "/data_sm/home/lihao/project/Polscope/Simulation/3D_Pol_Phase/PTI_repo_demo/2D_QLIPP_simulation.npz"
+file_name = "./2D_QLIPP_simulation.npz"
 
 array_loaded = np.load(file_name)
 list_of_array_names = sorted(array_loaded)

diff --git a/examples/3D_PODT_phase_simulation/3D_PODT_Phase_forward.ipynb b/examples/3D_PODT_phase_simulation/3D_PODT_Phase_forward.ipynb
diff --git a/examples/3D_PODT_phase_simulation/3D_PODT_Phase_forward.py b/examples/3D_PODT_phase_simulation/3D_PODT_Phase_forward.py
@@ -15,7 +15,7 @@
 from numpy.fft import fft, ifft, fft2, ifft2, fftshift, ifftshift, fftn, ifftn
 import waveorder as wo
 
-# ### Experiment parameters
+# Experiment parameters
 N = 256  # number of pixel in y dimension
 M = 256  # number of pixel in x dimension
 L = 100  # number of layers in z dimension
@@ -27,7 +27,7 @@
 NA_obj = 1.2  # objective NA
 NA_illu = 0.9  # illumination NA
 
-# ### Sample creation
+# Sample creation
 radius = 5
 blur_size = 2 * ps
 sphere, _, _ = wo.gen_sphere_target((N, M, L), ps, psz, radius, blur_size)
@@ -53,7 +53,7 @@
 )
 plt.show()
 
-# ### Setup acquisition
+# Setup acquisition
 # Subsampled Source pattern
 
 xx, yy, fxx, fyy = wo.gen_coordinate((N, M), ps)
@@ -155,7 +155,7 @@
 
 
 # Save simulations
-output_file = "/data_sm/home/lihao/project/Polscope/Simulation/3D_Pol_Phase/PTI_repo_demo/3D_PODT_simulation"
+output_file = "./3D_PODT_simulation.npz"
 np.savez(
     output_file,
     I_meas=I_meas,

diff --git a/examples/3D_PODT_phase_simulation/3D_PODT_Phase_recon.ipynb b/examples/3D_PODT_phase_simulation/3D_PODT_Phase_recon.ipynb
diff --git a/examples/3D_PODT_phase_simulation/3D_PODT_Phase_recon.py b/examples/3D_PODT_phase_simulation/3D_PODT_Phase_recon.py
@@ -18,9 +18,9 @@
 
 import waveorder as wo
 
-# ### Load data
+# Load data
 # Load simulations
-file_name = "/data_sm/home/lihao/project/Polscope/Simulation/3D_Pol_Phase/PTI_repo_demo/3D_PODT_simulation.npz"
+file_name = "./3D_PODT_simulation.npz"
 array_loaded = np.load(file_name)
 list_of_array_names = sorted(array_loaded)
 for array_name in list_of_array_names:
@@ -30,7 +30,7 @@
 N, M, L = I_meas.shape
 
 
-# ### Refractive index reconstruction
+# Refractive index reconstruction
 z_defocus = (np.r_[:L] - L // 2) * psz
 chi = 0.1 * 2 * np.pi
 setup = wo.waveorder_microscopy(