waveorder 1.0.0rc1__tar.gz → 1.0.0rc3__tar.gz

waveorder-1.0.0rc3/.git-blame-ignore-revs

@@ -0,0 +1,4 @@
+# .git-blame-ignore-revs
+# created as described in: https://docs.github.com/en/repositories/working-with-files/using-files/viewing-a-file#ignore-commits-in-the-blame-view
+# black-format files
+07517c3353c392106cabae003d589946ea25918a

{waveorder-1.0.0rc1 → waveorder-1.0.0rc3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: waveorder
-Version: 1.0.0rc1
+Version: 1.0.0rc3
 Summary: Wave optical simulations and deconvolution of optical properties
 Home-page: https://github.com/mehta-lab/waveorder
 Author: Computational Microscopy Platform, CZ Biohub
@@ -10,6 +10,7 @@ Project-URL: Bug Tracker, https://github.com/mehta-lab/waveorder/issues
 Project-URL: Documentation, https://github.com/mehta-lab/waveorder
 Project-URL: Source Code, https://github.com/mehta-lab/waveorder
 Project-URL: User Support, https://github.com/mehta-lab/waveorder/issues
+Platform: UNKNOWN
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: BSD License
@@ -62,7 +63,7 @@ PTI provides volumetric reconstructions of mean permittivity ($\propto$ material
 
 ![Data_flow](https://github.com/mehta-lab/waveorder/blob/main/Fig_Readme.png?raw=true)
 
-The [example notebooks](examples/) illustrate simulations and reconstruction for 2D QLIPP, 3D PODT, and 2D/3D PTI methods.
+The [example notebooks](https://github.com/mehta-lab/waveorder/tree/main/examples) illustrate simulations and reconstruction for 2D QLIPP, 3D PODT, and 2D/3D PTI methods.
 
 If you are interested in deploying QLIPP or PODT for label-free imaging at scale, checkout our [napari plugin](https://www.napari-hub.org/plugins/recOrder-napari),  [`recOrder-napari`](https://github.com/mehta-lab/recOrder).
 
@@ -72,7 +73,7 @@ In addition to label-free reconstruction algorithms, `waveorder` also implements
 
 1. Correlative measurements of biomolecular density and orientation from polarization-diverse widefield imaging ([multimodal Instant PolScope](https://opg.optica.org/boe/fulltext.cfm?uri=boe-13-5-3102&id=472350))
 
-We provide an [example notebook](examples/fluorescence_deconvolution/) for widefield fluorescence deconvolution.
+We provide an [example notebook](https://github.com/mehta-lab/waveorder/blob/main/examples/experimental_reconstructions/fluorescence_deconvolution/fluorescence_deconv.ipynb) for widefield fluorescence deconvolution.
 
 ## Citation
 
@@ -116,3 +117,5 @@ python
 ```
 
 To use GPUs in `waveorder` set ```use_gpu=True``` when initializing the simulator and reconstructor classes.
+
+

{waveorder-1.0.0rc1 → waveorder-1.0.0rc3}/README.md

@@ -29,7 +29,7 @@ PTI provides volumetric reconstructions of mean permittivity ($\propto$ material
 
 ![Data_flow](https://github.com/mehta-lab/waveorder/blob/main/Fig_Readme.png?raw=true)
 
-The [example notebooks](examples/) illustrate simulations and reconstruction for 2D QLIPP, 3D PODT, and 2D/3D PTI methods.
+The [example notebooks](https://github.com/mehta-lab/waveorder/tree/main/examples) illustrate simulations and reconstruction for 2D QLIPP, 3D PODT, and 2D/3D PTI methods.
 
 If you are interested in deploying QLIPP or PODT for label-free imaging at scale, checkout our [napari plugin](https://www.napari-hub.org/plugins/recOrder-napari),  [`recOrder-napari`](https://github.com/mehta-lab/recOrder).
 
@@ -39,7 +39,7 @@ In addition to label-free reconstruction algorithms, `waveorder` also implements
 
 1. Correlative measurements of biomolecular density and orientation from polarization-diverse widefield imaging ([multimodal Instant PolScope](https://opg.optica.org/boe/fulltext.cfm?uri=boe-13-5-3102&id=472350))
 
-We provide an [example notebook](examples/fluorescence_deconvolution/) for widefield fluorescence deconvolution.
+We provide an [example notebook](https://github.com/mehta-lab/waveorder/blob/main/examples/experimental_reconstructions/fluorescence_deconvolution/fluorescence_deconv.ipynb) for widefield fluorescence deconvolution.
 
 ## Citation
 

{waveorder-1.0.0rc1 → waveorder-1.0.0rc3}/examples/2D_QLIPP_simulation/2D_QLIPP_forward.py

@@ -16,7 +16,7 @@ from numpy.fft import fft2, ifft2, fftshift, ifftshift
 
 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 @@ NA_illu_in = 0.4  # illumination NA (phase contrast inner ring)
 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 @@ wo.plot_multicolumn(
 )
 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.figure(figsize=(10, 10))
 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 @@ simulator = wo.waveorder_microscopy_simulator(
     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 @@ I_meas_noise = (
     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,

{waveorder-1.0.0rc1 → waveorder-1.0.0rc3}/examples/2D_QLIPP_simulation/2D_QLIPP_recon.py

@@ -19,7 +19,7 @@ import waveorder as wo
 # 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)

{waveorder-1.0.0rc1 → waveorder-1.0.0rc3}/examples/3D_PODT_phase_simulation/3D_PODT_Phase_forward.py

@@ -15,7 +15,7 @@ import matplotlib.pyplot as plt
 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 @@ lambda_illu = 0.532  # wavelength
 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.imshow(
 )
 plt.show()
 
-# ### Setup acquisition
+# Setup acquisition
 # Subsampled Source pattern
 
 xx, yy, fxx, fyy = wo.gen_coordinate((N, M), ps)
@@ -155,7 +155,7 @@ plt.show()
 
 
 # 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,

{waveorder-1.0.0rc1 → waveorder-1.0.0rc3}/examples/3D_PODT_phase_simulation/3D_PODT_Phase_recon.py

@@ -18,9 +18,9 @@ from numpy.fft import fft, ifft, fft2, ifft2, fftn, ifftn, fftshift, ifftshift
 
 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 @@ print(list_of_array_names)
 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(

{waveorder-1.0.0rc1 → waveorder-1.0.0rc3}/examples/PTI_simulation/PTI_Simulation_Forward_2D3D.py

@@ -43,11 +43,11 @@ import waveorder as wo
 ### Parameters of sample
 
 sample_type = "2D"  # 2D or 3D
-N = 200  # number of pixel in y dimension
-M = 200  # number of pixel in x dimension
-L = 100  # number of layers in z dimension
-z_layer = 50  # default z-slice to display in XY views.
-y_layer = 100  # default y-slice to display in XZ views.
+N = 50  # number of pixel in y dimension
+M = 50  # number of pixel in x dimension
+L = 26  # number of layers in z dimension
+z_layer = L // 2  # default z-slice to display in XY views.
+y_layer = M // 2  # default y-slice to display in XZ views.
 
 ### Parameters of imaging system
 
@@ -60,7 +60,7 @@ NA_obj = 1.47  # objective NA
 NA_illu = 1.4  # illumination NA
 chi = 0.25 * 2 * np.pi  # swing of the microscope
 z_defocus = (np.r_[:L] - L // 2) * psz  # defocus position
-use_gpu = True  # option to use gpu
+use_gpu = False  # option to use gpu
 gpu_id = 0  # gpu to be used
 
 ### Sample pattern
@@ -80,21 +80,25 @@ if sample_type == "3D":
     azimuth = np.round(azimuth / np.pi / 2 * 16) / 16 * np.pi * 2
 elif sample_type == "2D":
     ## 2D spoke pattern, azimuth aligned with spokes, and the inclination set to 60 degrees ##
-    target, azimuth, _ = wo.genStarTarget(N, M, blur_px=1 * ps, margin=60)
+    target, azimuth, _ = wo.genStarTarget(N, M, blur_px=1 * ps, margin=10)
     inclination = np.ones_like(target) * np.pi / 3
     azimuth = azimuth % (np.pi * 2)
     azimuth = np.round(azimuth / np.pi / 2 * 16) / 16 * np.pi * 2
 
     # pad zero in the z direction outside of the focal plane to mimic thin specimens
     target = np.pad(
-        target[:, :, np.newaxis], ((0, 0), (0, 0), (50, 49)), mode="constant"
+        target[:, :, np.newaxis],
+        ((0, 0), (0, 0), (L // 2, L // 2 - 1)),
+        mode="constant",
     )
     azimuth = np.pad(
-        azimuth[:, :, np.newaxis], ((0, 0), (0, 0), (50, 49)), mode="constant"
+        azimuth[:, :, np.newaxis],
+        ((0, 0), (0, 0), (L // 2, L // 2 - 1)),
+        mode="constant",
     )
     inclination = np.pad(
         inclination[:, :, np.newaxis],
-        ((0, 0), (0, 0), (50, 49)),
+        ((0, 0), (0, 0), (L // 2, L // 2 - 1)),
         mode="constant",
     )
 else:
@@ -470,7 +474,7 @@ I_meas_noise = I_meas_SEAGLE / np.mean(I_meas_SEAGLE) * photon_count
 
 # Save simulations
 
-output_dir = "/home/lihao.yeh/Desktop/recorder_test/processed_data/"
+output_dir = "./"
 
 if sample_type == "3D":
     output_file = "PTI_simulation_data_NA_det_147_NA_illu_140_3D_spoke_discrete_no_1528_ne_1553_no_noise_Born"

{waveorder-1.0.0rc1 → waveorder-1.0.0rc3}/examples/PTI_simulation/PTI_Simulation_Recon2D.py

@@ -19,7 +19,7 @@ import waveorder as wo
 ## Initialization
 ## Load simulated images and parameters
 
-file_name = "/data_sm/home/lihao/project/Polscope/Simulation/3D_Pol_Phase/PTI_repo_demo/PTI_simulation_data_NA_det_147_NA_illu_140_2D_spoke_discrete_no_1528_ne_1553_no_noise_Born.npz"
+file_name = "./PTI_simulation_data_NA_det_147_NA_illu_140_2D_spoke_discrete_no_1528_ne_1553_no_noise_Born.npz"
 
 array_loaded = np.load(file_name)
 list_of_array_names = sorted(array_loaded)
@@ -29,7 +29,8 @@ for array_name in list_of_array_names:
 
 print(list_of_array_names)
 
-I_meas = np.transpose(I_meas[:, :, :, :, 50], (0, 2, 3, 1))
+L = I_meas.shape[-1]
+I_meas = np.transpose(I_meas[:, :, :, :, L // 2], (0, 2, 3, 1))
 z_defocus = np.array([0])
 
 I_meas = I_meas[1:]
@@ -41,7 +42,7 @@ print(I_meas.shape)
 _, N, M, _ = I_meas.shape
 cali = False
 bg_option = "global"
-use_gpu = True
+use_gpu = False
 gpu_id = 0
 
 # chi = pi/2
@@ -166,13 +167,13 @@ phase_nm, absorption_nm, retardance_pr_nm = [
     )
 ]
 
-# clean up GPU memory leftorver
+# # clean up GPU memory leftorver
 
-import gc
-import cupy as cp
+# import gc
+# import cupy as cp
 
-gc.collect()
-cp.get_default_memory_pool().free_all_blocks()
+# gc.collect()
+# cp.get_default_memory_pool().free_all_blocks()
 
 ## Visualize reconstructed physical properties of simulated sample
 ### Phase, principal retardance, azimuth, inclination, and optic sign

{waveorder-1.0.0rc1 → waveorder-1.0.0rc3}/examples/PTI_simulation/PTI_Simulation_Recon3D.py

@@ -16,7 +16,7 @@ import waveorder as wo
 ## Initialization
 ## Load simulated images and parameters
 
-file_name = "/data_sm/home/lihao/project/Polscope/Simulation/3D_Pol_Phase/PTI_repo_demo/PTI_simulation_data_NA_det_147_NA_illu_140_2D_spoke_discrete_no_1528_ne_1553_no_noise_Born.npz"
+file_name = "./PTI_simulation_data_NA_det_147_NA_illu_140_2D_spoke_discrete_no_1528_ne_1553_no_noise_Born.npz"
 
 array_loaded = np.load(file_name)
 list_of_array_names = sorted(array_loaded)
@@ -32,7 +32,7 @@ print(I_meas.shape)
 _, _, N, M, L = I_meas.shape
 cali = False
 bg_option = "global"
-use_gpu = True
+use_gpu = False
 gpu_id = 0
 
 
@@ -169,11 +169,11 @@ phase_PT, absorption_PT, retardance_pr_PT = [
 
 # clean up GPU memory leftorver
 
-import gc
-import cupy as cp
+# import gc
+# import cupy as cp
 
-gc.collect()
-cp.get_default_memory_pool().free_all_blocks()
+# gc.collect()
+# cp.get_default_memory_pool().free_all_blocks()
 
 ## Visualize reconstructed physical properties of simulated sample
 ### Reconstructed phase, absorption, principal retardance, azimuth, and inclination assuming (+) and (-) optic sign
@@ -225,9 +225,9 @@ plt.show()
 ######################################
 
 ## display parameters for 2D dataset ##
-z_layer = 50
-y_layer = 100
-x_layer = 100
+z_layer = L // 2
+y_layer = M // 2
+x_layer = N // 2
 phase_min = -0.012
 phase_max = 0.012
 ret_min = 0
@@ -499,9 +499,9 @@ z_step = psz
 
 ### select slices to plot ###
 spacing = 4
-z_layer = 50
-x_layer = 100
-y_layer = 100
+z_layer = L // 2
+x_layer = N // 2
+y_layer = M // 2
 linelength_scale = 20
 #########################
 

waveorder-1.0.0rc3/examples/README.md

@@ -0,0 +1,12 @@
+This folder of examples consists of:
+
+1) A set of simulations that will run as is. Any of the files in these folders 
+can be run with `python <script-name>.py`, and these files are included in 
+`waveorder`'s automated testing.  
+- `/2D_QLIPP_simulation/`
+- `/3D_PODT_Phase_simulation/`
+- `/PTI_simulation/`
+
+2) A set of data-dependent reconstructions in `/experimental_reconstructions/`. 
+These files serve as a form of documentation for the types of reconstructions
+that `waveorder` can perform. 

{waveorder-1.0.0rc1 → waveorder-1.0.0rc3}/setup.cfg

@@ -36,12 +36,11 @@ include_package_data = True
 python_requires = >=3.8
 setup_requires = setuptools_scm
 install_requires = 
-	numpy>=1.17.4
+	numpy>=1.21
 	matplotlib>=3.1.1
 	scipy>=1.3.0
 	pywavelets>=1.1.1
 	ipywidgets>=7.5.1
-	opencv-python>=3.4.1
 	tifffile>=2021.11.2
 	zarr>=2.6.1
 	natsort>=7.1.1

waveorder-1.0.0rc3/tests/test_examples.py

@@ -0,0 +1,40 @@
+import subprocess
+import os
+from pathlib import Path
+
+
+def _run_scripts(scripts):
+    for script in scripts:
+        path = os.path.join(os.getcwd(), "examples/", script)
+        completed_process = subprocess.run(["python", path])
+        assert completed_process.returncode == 0
+
+
+# Currently, these tests will run in the background if no screen is available
+# If you do have a screen available, plots will appear, and you'll need to
+# close them to make the tests pass.
+# TODO: see if we can make these run locally w/o showing matplotlib
+# @patch("matplotlib.pyplot.show")
+def test_qlipp_examples():
+    scripts = [
+        "2D_QLIPP_simulation/2D_QLIPP_forward.py",
+        "2D_QLIPP_simulation/2D_QLIPP_recon.py",
+    ]
+    _run_scripts(scripts)
+
+
+def test_phase_examples():
+    scripts = [
+        "3D_PODT_phase_simulation/3D_PODT_Phase_forward.py",
+        "3D_PODT_phase_simulation/3D_PODT_Phase_recon.py",
+    ]
+    _run_scripts(scripts)
+
+
+def test_pti_examples():
+    scripts = [
+        "PTI_simulation/PTI_Simulation_Forward_2D3D.py",
+        "PTI_simulation/PTI_Simulation_Recon2D.py",
+        "PTI_simulation/PTI_Simulation_Recon3D.py",
+    ]
+    _run_scripts(scripts)

{waveorder-1.0.0rc1 → waveorder-1.0.0rc3}/waveorder/_version.py

@@ -1,5 +1,4 @@
-# coding: utf-8
 # file generated by setuptools_scm
 # don't change, don't track in version control
-__version__ = version = '1.0.0rc1'
+__version__ = version = '1.0.0rc3'
 __version_tuple__ = version_tuple = (1, 0, 0)