black and isort

examples/documentation/PTI_experiment/PTI_Experiment_Recon3D_anisotropic_target_small.py

@@ -1,16 +1,16 @@
 # %%
 # This notebook-style script requires a ~500 MB download from https://www.ebi.ac.uk/biostudies/files/S-BIAD1063/PTI-BIA/Anisotropic_target_small.zip
 
-import numpy as np
+from pathlib import Path
+
 import matplotlib.pyplot as plt
+import numpy as np
+import zarr
+from iohub import open_ome_zarr
 from numpy.fft import fftshift
 
 import waveorder as wo
-from waveorder import optics, waveorder_reconstructor, util
-
-import zarr
-from pathlib import Path
-from iohub import open_ome_zarr
+from waveorder import optics, util, waveorder_reconstructor
 from waveorder.visuals import jupyter_visuals
 
 # %%
@@ -62,10 +62,12 @@
 I_cali_mean = np.array(PTI_file.I_cali_mean)
 
 # source polarization, instrument matrix calibration
-E_in, A_matrix, I_cali_mean = (
-    wo.waveorder_reconstructor.instrument_matrix_and_source_calibration(
-        I_cali_mean, handedness="RCP"
-    )
+(
+    E_in,
+    A_matrix,
+    I_cali_mean,
+) = wo.waveorder_reconstructor.instrument_matrix_and_source_calibration(
+    I_cali_mean, handedness="RCP"
 )
 
 # %%
@@ -238,15 +240,18 @@
 # "negative" -> only solution of negatively uniaxial material
 # "unknown" -> both solutions of positively and negatively uniaxial material + optic sign estimation
 
-differential_permittivity, azimuth, theta, mat_map = (
-    setup.scattering_potential_tensor_to_3D_orientation(
-        f_tensor,
-        S_image_tm,
-        material_type="unknown",
-        reg_ret_pr=reg_differential_permittivity,
-        itr=10,
-        fast_gpu_mode=True,
-    )
+(
+    differential_permittivity,
+    azimuth,
+    theta,
+    mat_map,
+) = setup.scattering_potential_tensor_to_3D_orientation(
+    f_tensor,
+    S_image_tm,
+    material_type="unknown",
+    reg_ret_pr=reg_differential_permittivity,
+    itr=10,
+    fast_gpu_mode=True,
 )
 
 # %%
@@ -264,7 +269,10 @@
     [
         ((-1) ** i)
         * util.wavelet_softThreshold(
-            ((-1) ** i) * differential_permittivity_PT[i], "db8", 0.00303, level=1
+            ((-1) ** i) * differential_permittivity_PT[i],
+            "db8",
+            0.00303,
+            level=1,
         )
         for i in range(2)
     ]
@@ -374,17 +382,27 @@
 
 # compute the physical properties from the scattering potential tensor
 
-differential_permittivity_p, azimuth_p, theta_p = (
-    optics.scattering_potential_tensor_to_3D_orientation_PN(
-        f_tensor, material_type="positive", reg_ret_pr=reg_differential_permittivity
-    )
-)
-differential_permittivity_n, azimuth_n, theta_n = (
-    optics.scattering_potential_tensor_to_3D_orientation_PN(
-        f_tensor, material_type="negative", reg_ret_pr=reg_differential_permittivity
-    )
+(
+    differential_permittivity_p,
+    azimuth_p,
+    theta_p,
+) = optics.scattering_potential_tensor_to_3D_orientation_PN(
+    f_tensor,
+    material_type="positive",
+    reg_ret_pr=reg_differential_permittivity,
+)
+(
+    differential_permittivity_n,
+    azimuth_n,
+    theta_n,
+) = optics.scattering_potential_tensor_to_3D_orientation_PN(
+    f_tensor,
+    material_type="negative",
+    reg_ret_pr=reg_differential_permittivity,
+)
+differential_permittivity = np.array(
+    [differential_permittivity_p, differential_permittivity_n]
 )
-differential_permittivity = np.array([differential_permittivity_p, differential_permittivity_n])
 azimuth = np.array([azimuth_p, azimuth_n])
 theta = np.array([theta_p, theta_n])
 
@@ -402,7 +420,10 @@
     [
         ((-1) ** i)
         * util.wavelet_softThreshold(
-            ((-1) ** i) * differential_permittivity_PT[i], "db8", 0.00303, level=1
+            ((-1) ** i) * differential_permittivity_PT[i],
+            "db8",
+            0.00303,
+            level=1,
         )
         for i in range(2)
     ]

examples/maintenance/PTI_simulation/PTI_Simulation_Forward_2D3D.py

@@ -9,14 +9,11 @@
 #  density and anisotropy," bioRxiv 2020.12.15.422951 (2020).```   #
 ####################################################################
 
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
 from numpy.fft import fftshift
-from waveorder import (
-    optics,
-    waveorder_simulator,
-    util,
-)
+
+from waveorder import optics, util, waveorder_simulator
 from waveorder.visuals import jupyter_visuals
 
 #####################################################################

examples/maintenance/PTI_simulation/PTI_Simulation_Recon2D.py

@@ -9,14 +9,11 @@
 #  density and anisotropy," bioRxiv 2020.12.15.422951 (2020).```   #
 ####################################################################
 
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
 from numpy.fft import fftshift
 
-from waveorder import (
-    optics,
-    waveorder_reconstructor,
-)
+from waveorder import optics, waveorder_reconstructor
 from waveorder.visuals import jupyter_visuals
 
 ## Initialization
@@ -271,7 +268,6 @@
 # in-plane orientation
 from matplotlib.colors import hsv_to_rgb
 
-
 ret_min_color = 0
 ret_max_color = 1.5
 

examples/maintenance/PTI_simulation/PTI_Simulation_Recon3D.py

@@ -8,13 +8,11 @@
 #  "uPTI: uniaxial permittivity tensor imaging of intrinsic        #
 #  density and anisotropy," bioRxiv 2020.12.15.422951 (2020).```   #
 ####################################################################
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
 from numpy.fft import fftshift
-from waveorder import (
-    optics,
-    waveorder_reconstructor,
-)
+
+from waveorder import optics, waveorder_reconstructor
 from waveorder.visuals import jupyter_visuals
 
 ## Initialization

examples/maintenance/QLIPP_simulation/2D_QLIPP_forward.py

@@ -10,14 +10,11 @@
 #####################################################################################################
 
 
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
 from numpy.fft import fftshift
-from waveorder import (
-    optics,
-    waveorder_simulator,
-    util,
-)
+
+from waveorder import optics, util, waveorder_simulator
 from waveorder.visuals import jupyter_visuals
 
 # Key parameters

examples/maintenance/QLIPP_simulation/2D_QLIPP_recon.py

@@ -10,13 +10,11 @@
 #  eLife 9:e55502 (2020).```                                                                        #
 #####################################################################################################
 
-import numpy as np
 import matplotlib.pyplot as plt
-from waveorder import (
-    waveorder_reconstructor,
-)
-from waveorder.visuals import jupyter_visuals
+import numpy as np
 
+from waveorder import waveorder_reconstructor
+from waveorder.visuals import jupyter_visuals
 
 # ### Load simulated data
 # Load simulations

examples/models/inplane_oriented_thick_pol3d_vector.py

@@ -1,9 +1,7 @@
-import torch
 import napari
+import torch
 
-from waveorder.models import (
-    inplane_oriented_thick_pol3d_vector,
-)
+from waveorder.models import inplane_oriented_thick_pol3d_vector
 
 # Parameters
 # all lengths must use consistent units e.g. um
@@ -25,20 +23,22 @@
 )
 
 # Calculate transfer function
-sfZYX_transfer_function, intensity_to_stokes_matrix, singular_system = (
-    inplane_oriented_thick_pol3d_vector.calculate_transfer_function(
-        swing,
-        scheme,
-        zyx_shape,
-        yx_pixel_size,
-        z_pixel_size,
-        wavelength_illumination,
-        z_padding,
-        index_of_refraction_media,
-        numerical_aperture_illumination,
-        numerical_aperture_detection,
-        fourier_oversample_factor=fourier_oversample_factor,
-    )
+(
+    sfZYX_transfer_function,
+    intensity_to_stokes_matrix,
+    singular_system,
+) = inplane_oriented_thick_pol3d_vector.calculate_transfer_function(
+    swing,
+    scheme,
+    zyx_shape,
+    yx_pixel_size,
+    z_pixel_size,
+    wavelength_illumination,
+    z_padding,
+    index_of_refraction_media,
+    numerical_aperture_illumination,
+    numerical_aperture_detection,
+    fourier_oversample_factor=fourier_oversample_factor,
 )
 
 # Display transfer function

examples/models/isotropic_thin_3d.py

@@ -5,7 +5,7 @@
 
 import napari
 import numpy as np
-from waveorder import util
+
 from waveorder.models import isotropic_thin_3d
 
 # Parameters

examples/models/phase_thick_3d.py

@@ -5,7 +5,7 @@
 
 import napari
 import numpy as np
-from waveorder import util
+
 from waveorder.models import phase_thick_3d
 
 # Parameters

examples/visuals/plot_greens_tensor.py

@@ -1,17 +1,19 @@
-from skimage import measure
+import os
+
 import napari
-from napari.experimental import link_layers
 import numpy as np
 import torch
-import os
-from waveorder import util, optics
+from napari.experimental import link_layers
 from scipy.ndimage import gaussian_filter
+from skimage import measure
+
+from waveorder import optics, util
 
 # Parameters
 # all lengths must use consistent units e.g. um
 output_dirpath = "./greens_plots"
 os.makedirs(output_dirpath, exist_ok=True)
-grid_size = 100 # 300 for publication
+grid_size = 100  # 300 for publication
 blur_width = grid_size // 35  # blurring to smooth sharp corners
 zyx_shape = 3 * (grid_size,)
 yx_pixel_size = 6.5 / 63

examples/visuals/plot_vector_transfer_function_support.py

@@ -1,7 +1,7 @@
+import os
+
 import napari
 import numpy as np
-import os
-import matplotlib.pyplot as plt
 
 
 def plot_otf_support(
@@ -28,8 +28,14 @@ def plot_otf_support(
     points = np.array(
         [
             [0, 0],
-            [det_na - ill_na, (1 - ill_na**2) ** 0.5 - (1 - det_na**2) ** 0.5],
-            [det_na + ill_na, (1 - ill_na**2) ** 0.5 - (1 - det_na**2) ** 0.5],
+            [
+                det_na - ill_na,
+                (1 - ill_na**2) ** 0.5 - (1 - det_na**2) ** 0.5,
+            ],
+            [
+                det_na + ill_na,
+                (1 - ill_na**2) ** 0.5 - (1 - det_na**2) ** 0.5,
+            ],
             [2 * ill_na, 0],
         ]
     )
@@ -203,7 +209,6 @@ def plot_otf_support(
 ]
 
 for my_color in my_colors:
-
     plot_otf_support(
         ill_na,
         det_na,

tests/models/test_isotropic_fluorescent_thick_3d.py

@@ -1,4 +1,3 @@
-import pytest
 import torch
 
 from waveorder.models import isotropic_fluorescent_thick_3d

tests/models/test_phase_thick_3d.py

@@ -1,5 +1,6 @@
-import pytest
 import numpy as np
+import pytest
+
 from waveorder.models import phase_thick_3d
 
 
@@ -27,7 +28,6 @@ def simulate_phase_recon(
     z_pixel_size_um=0.1,
     yx_pixel_size_um=6.5 / 63,
 ):
-
     z_fov_um = 50
     yx_fov_um = 50
 
@@ -98,4 +98,4 @@ def test_phase_invariance():
 
     # test yx pixel size invariance
     recon2 = simulate_phase_recon(yx_pixel_size_um=0.7 * 6.5 / 63)
-    assert np.abs((recon2 - recon) / recon) < 0.02
+    assert np.abs((recon2 - recon) / recon) < 0.02

tests/test_examples.py

@@ -1,8 +1,9 @@
-import subprocess
 import os
-import pytest
+import subprocess
 import sys
 
+import pytest
+
 
 def _run_scripts(scripts):
     for script in scripts:

tests/test_focus_estimator.py

@@ -1,5 +1,6 @@
-import pytest
 import numpy as np
+import pytest
+
 from waveorder import focus