waveorder 2.1.0__py3-none-any.whl → 2.2.0rc0__py3-none-any.whl

waveorder/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '2.1.0'
-__version_tuple__ = version_tuple = (2, 1, 0)
+__version__ = version = '2.2.0rc0'
+__version_tuple__ = version_tuple = (2, 2, 0)

waveorder/focus.py

@@ -3,6 +3,7 @@ from typing import Literal, Optional
 from waveorder import util
 import matplotlib.pyplot as plt
 import numpy as np
+import warnings
 
 
 def focus_from_transverse_band(
@@ -60,10 +61,19 @@ def focus_from_transverse_band(
     >>> slice = focus_from_transverse_band(zyx_array, NA_det=0.55, lambda_ill=0.532, pixel_size=6.5/20)
     >>> in_focus_data = data[slice,:,:]
     """
-    minmaxfunc = _check_focus_inputs(
-        zyx_array, NA_det, lambda_ill, pixel_size, midband_fractions, mode
+    minmaxfunc = _mode_to_minmaxfunc(mode)
+
+    _check_focus_inputs(
+        zyx_array, NA_det, lambda_ill, pixel_size, midband_fractions
     )
 
+    # Check for single slice
+    if zyx_array.shape[0] == 1:
+        warnings.warn(
+            "The dataset only contained a single slice. Returning trivial slice index = 0."
+        )
+        return 0
+
     # Calculate coordinates
     _, Y, X = zyx_array.shape
     _, _, fxx, fyy = util.gen_coordinate((Y, X), pixel_size)
@@ -94,25 +104,35 @@ def focus_from_transverse_band(
     # Plot
     if plot_path is not None:
         _plot_focus_metric(
-            plot_path, midband_sum, peak_index, in_focus_index, peak_results, threshold_FWHM
+            plot_path,
+            midband_sum,
+            peak_index,
+            in_focus_index,
+            peak_results,
+            threshold_FWHM,
         )
 
     return in_focus_index
 
 
+def _mode_to_minmaxfunc(mode):
+    if mode == "min":
+        minmaxfunc = np.argmin
+    elif mode == "max":
+        minmaxfunc = np.argmax
+    else:
+        raise ValueError("mode must be either `min` or `max`")
+    return minmaxfunc
+
+
 def _check_focus_inputs(
-    zyx_array, NA_det, lambda_ill, pixel_size, midband_fractions, mode
+    zyx_array, NA_det, lambda_ill, pixel_size, midband_fractions
 ):
     N = len(zyx_array.shape)
     if N != 3:
         raise ValueError(
             f"{N}D array supplied. `focus_from_transverse_band` only accepts 3D arrays."
         )
-    if zyx_array.shape[0] == 1:
-        print(
-            "WARNING: The dataset only contained a single slice. Returning trivial slice index = 0."
-        )
-        return 0
 
     if NA_det < 0:
         raise ValueError("NA must be > 0")
@@ -121,7 +141,7 @@ def _check_focus_inputs(
     if pixel_size < 0:
         raise ValueError("pixel_size must be > 0")
     if not 0.4 < lambda_ill / pixel_size < 10:
-        print(
+        warnings.warn(
             f"WARNING: lambda_ill/pixel_size = {lambda_ill/pixel_size}."
             f"Did you use the same units?"
             f"Did you enter the pixel size in (demagnified) object-space units?"
@@ -134,17 +154,15 @@ def _check_focus_inputs(
         raise ValueError("midband_fractions[0] must be between 0 and 1")
     if not (0 <= midband_fractions[1] <= 1):
         raise ValueError("midband_fractions[1] must be between 0 and 1")
-    if mode == "min":
-        minmaxfunc = np.argmin
-    elif mode == "max":
-        minmaxfunc = np.argmax
-    else:
-        raise ValueError("mode must be either `min` or `max`")
-    return minmaxfunc
 
 
 def _plot_focus_metric(
-    plot_path, midband_sum, peak_index, in_focus_index, peak_results, threshold_FWHM
+    plot_path,
+    midband_sum,
+    peak_index,
+    in_focus_index,
+    peak_results,
+    threshold_FWHM,
 ):
     _, ax = plt.subplots(1, 1, figsize=(4, 4))
     ax.plot(midband_sum, "-k")

waveorder/models/isotropic_fluorescent_thick_3d.py

@@ -81,7 +81,24 @@ def visualize_transfer_function(viewer, optical_transfer_function, zyx_scale):
     viewer.dims.order = (0, 1, 2)
 
 
-def apply_transfer_function(zyx_object, optical_transfer_function, z_padding):
+def apply_transfer_function(
+    zyx_object, optical_transfer_function, z_padding, background=10
+):
+    """Simulate imaging by applying a transfer function
+
+    Parameters
+    ----------
+    zyx_object : torch.Tensor
+    optical_transfer_function : torch.Tensor
+    z_padding : int
+    background : int, optional
+        constant background counts added to each voxel, by default 10
+
+    Returns
+    -------
+    Simulated data : torch.Tensor
+        
+    """
     if (
         zyx_object.shape[0] + 2 * z_padding
         != optical_transfer_function.shape[0]
@@ -99,7 +116,7 @@ def apply_transfer_function(zyx_object, optical_transfer_function, z_padding):
     zyx_data = zyx_obj_hat * optical_transfer_function
     data = torch.real(torch.fft.ifftn(zyx_data))
 
-    data += 10  # Add a direct background
+    data += background  # Add a direct background
     return data
 
 

waveorder/models/phase_thick_3d.py

@@ -12,7 +12,6 @@ def generate_test_phantom(
     zyx_shape,
     yx_pixel_size,
     z_pixel_size,
-    wavelength_illumination,
     index_of_refraction_media,
     index_of_refraction_sample,
     sphere_radius,
@@ -24,12 +23,9 @@ def generate_test_phantom(
         radius=sphere_radius,
         blur_size=2 * yx_pixel_size,
     )
-    zyx_phase = (
-        sphere
-        * (index_of_refraction_sample - index_of_refraction_media)
-        * z_pixel_size
-        / wavelength_illumination
-    )  # phase in radians
+    zyx_phase = sphere * (
+        index_of_refraction_sample - index_of_refraction_media
+    )  # refractive index increment
 
     return zyx_phase
 
@@ -120,12 +116,19 @@ def visualize_transfer_function(
 
 
 def apply_transfer_function(
-    zyx_object, real_potential_transfer_function, z_padding
+    zyx_object, real_potential_transfer_function, z_padding, brightness
 ):
     # This simplified forward model only handles phase, so it resuses the fluorescence forward model
     # TODO: extend to absorption
-    return isotropic_fluorescent_thick_3d.apply_transfer_function(
-        zyx_object, real_potential_transfer_function, z_padding
+    return (
+        isotropic_fluorescent_thick_3d.apply_transfer_function(
+            zyx_object,
+            real_potential_transfer_function,
+            z_padding,
+            background=0,
+        )
+        * brightness
+        + brightness
     )
 
 
@@ -134,8 +137,6 @@ def apply_inverse_transfer_function(
     real_potential_transfer_function: Tensor,
     imaginary_potential_transfer_function: Tensor,
     z_padding: int,
-    z_pixel_size: float,  # TODO: MOVE THIS PARAM TO OTF? (leaky param)
-    wavelength_illumination: float,  # TOOD: MOVE THIS PARAM TO OTF? (leaky param)
     absorption_ratio: float = 0.0,
     reconstruction_algorithm: Literal["Tikhonov", "TV"] = "Tikhonov",
     regularization_strength: float = 1e-3,
@@ -158,14 +159,6 @@ def apply_inverse_transfer_function(
     z_padding : int
         Padding for axial dimension. Use zero for defocus stacks that
         extend ~3 PSF widths beyond the sample. Pad by ~3 PSF widths otherwise.
-    z_pixel_size : float
-        spacing between axial samples in sample space
-        units must be consistent with wavelength_illumination
-        TODO: move this leaky parameter to calculate_transfer_function
-    wavelength_illumination : float,
-        illumination wavelength
-        units must be consistent with z_pixel_size
-        TODO: move this leaky parameter to calculate_transfer_function
     absorption_ratio : float, optional,
         Absorption-to-phase ratio in the sample.
         Use default 0 for purely phase objects.
@@ -223,4 +216,4 @@ def apply_inverse_transfer_function(
     if z_padding != 0:
         f_real = f_real[z_padding:-z_padding]
 
-    return f_real * z_pixel_size / 4 / np.pi * wavelength_illumination
+    return f_real

waveorder/optics.py

@@ -270,7 +270,7 @@ def Source_subsample(Source_cont, NAx_coord, NAy_coord, subsampled_NA=0.1):
             illu_list.append(i)
             first_idx = False
         elif (
-            np.product(
+            np.prod(
                 (NAx_list[i] - NAx_list[illu_list]) ** 2
                 + (NAy_list[i] - NAy_list[illu_list]) ** 2
                 >= subsampled_NA**2
@@ -739,19 +739,23 @@ def compute_weak_object_transfer_function_3D(
 
     H1 = torch.fft.ifft2(torch.conj(SPHz_hat) * PG_hat, dim=(1, 2))
     H1 = H1 * window[:, None, None]
-    H1 = torch.fft.fft(H1, dim=0) * z_pixel_size
+    H1 = torch.fft.fft(H1, dim=0)
 
     H2 = torch.fft.ifft2(SPHz_hat * torch.conj(PG_hat), dim=(1, 2))
     H2 = H2 * window[:, None, None]
-    H2 = torch.fft.fft(H2, dim=0) * z_pixel_size
+    H2 = torch.fft.fft(H2, dim=0)
 
-    I_norm = torch.sum(
+    direct_intensity = torch.sum(
         illumination_pupil_support
         * detection_pupil
         * torch.conj(detection_pupil)
     )
-    real_potential_transfer_function = (H1 + H2) / I_norm
-    imag_potential_transfer_function = 1j * (H1 - H2) / I_norm
+    real_potential_transfer_function = (H1 + H2) / direct_intensity
+    imag_potential_transfer_function = 1j * (H1 - H2) / direct_intensity
+
+    # Discretization factor for unitless input and output
+    real_potential_transfer_function *= z_pixel_size
+    imag_potential_transfer_function *= z_pixel_size
 
     return real_potential_transfer_function, imag_potential_transfer_function
 

{waveorder-2.1.0.dist-info → waveorder-2.2.0rc0.dist-info}/METADATA

@@ -1,43 +1,66 @@
 Metadata-Version: 2.1
 Name: waveorder
-Version: 2.1.0
-Summary: Wave optical simulations and deconvolution of optical properties
-Home-page: https://github.com/mehta-lab/waveorder
-Author: Computational Microscopy Platform, CZ Biohub
-Author-email: shalin.mehta@czbiohub.org
+Version: 2.2.0rc0
+Summary: Wave-optical simulations and deconvolution of optical properties
+Author-email: CZ Biohub SF <compmicro@czbiohub.org>
+Maintainer-email: Talon Chandler <talon.chandler@czbiohub.org>, Shalin Mehta <shalin.mehta@czbiohub.org>
 License: BSD 3-Clause License
-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
+        
+        Copyright (c) 2019, Chan Zuckerberg Biohub
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: Homepage, https://github.com/mehta-lab/waveorder
+Project-URL: Repository, https://github.com/mehta-lab/waveorder
+Project-URL: Issues, https://github.com/mehta-lab/waveorder/issues
+Keywords: simulation,optics,phase,scattering,polarization,label-free,permittivity,reconstruction-algorithm,qlipp,mipolscope,permittivity-tensor-imaging
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: BSD License
-Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Image Processing
-Classifier: Topic :: Scientific/Engineering :: Visualization
-Classifier: Topic :: Scientific/Engineering :: Information Analysis
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Operating System :: POSIX :: Linux
 Classifier: Operating System :: Microsoft :: Windows
-Classifier: Operating System :: POSIX
-Classifier: Operating System :: Unix
 Classifier: Operating System :: MacOS
-Requires-Python: >=3.8
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy >=1.21
+Requires-Dist: numpy <2,>=1.21
 Requires-Dist: matplotlib >=3.1.1
 Requires-Dist: scipy >=1.3.0
 Requires-Dist: pywavelets >=1.1.1
 Requires-Dist: ipywidgets >=7.5.1
-Requires-Dist: torch >=2.0.0
+Requires-Dist: torch >=2.2.1
 Provides-Extra: dev
-Requires-Dist: flake8 ; extra == 'dev'
-Requires-Dist: pytest >=5.0.0 ; extra == 'dev'
+Requires-Dist: pytest ; extra == 'dev'
 Requires-Dist: pytest-cov ; extra == 'dev'
 
 # waveorder
@@ -93,7 +116,7 @@ Please cite this repository, along with the relevant preprint or paper, if you u
 (Optional but recommended) install [anaconda](https://www.anaconda.com/products/distribution) and create a virtual environment:
 
 ```sh
-conda create -y -n waveorder python=3.9
+conda create -y -n waveorder python=3.11
 conda activate waveorder
 ```
 

{waveorder-2.1.0.dist-info → waveorder-2.2.0rc0.dist-info}/RECORD

@@ -1,20 +1,20 @@
 waveorder/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-waveorder/_version.py,sha256=N_eoCB5RSZeFANRJsHZ9FylE5ILLKrp6YmjX8ezqFpA,411
+waveorder/_version.py,sha256=y62tGqTh86kx1L4FG_Wu91vm4c-zkqBUqEkv0mTr0sY,414
 waveorder/background_estimator.py,sha256=gCIO6-232H0CGH4o6gnqW9KSYGOrXf5E9nD67WeF304,12399
 waveorder/correction.py,sha256=N0Ic6mqw3U7mqow4dKTOkNx2QYOLwedGNH7HiKV-M6s,3460
-waveorder/focus.py,sha256=bx6mbYdCJlKnS68344kFO0_qqowbpI3JNlV4ouT3vJo,6125
-waveorder/optics.py,sha256=64vFUq8DmmaHqBjXdLifWlnwpoXloQYsvm2KWTV7dkE,37478
+waveorder/focus.py,sha256=4mg84Fe4V-oFplsuaU_VQU1_TEDoEfPggIAv6Is2dE4,6312
+waveorder/optics.py,sha256=-mHYRMzDUNAz8kwF8xAR8RFuAEkWZzczKv2wnU5NuVs,37640
 waveorder/stokes.py,sha256=Wk9ZimzICIZLh1CkB0kQSCSBLeugkDeydwXTPd-M-po,15186
 waveorder/util.py,sha256=3k810fpb7pIEcc4fii6gP4wTerxCtFYgG82SiDzUTtQ,69898
 waveorder/visual.py,sha256=SFzkQdMit3HyqTqrgzX4w5bRwz8QuwGumzVayi3DwDM,58171
 waveorder/waveorder_reconstructor.py,sha256=5-jlbK8gcJqHbFhiWt-TcETV5cdLHSAXq9O3JupPXD0,151942
 waveorder/waveorder_simulator.py,sha256=_HCmDZkACUGzgwnaI-q0PjsL1gRE55IQuaWw-wtAjCU,45856
 waveorder/models/inplane_oriented_thick_pol3d.py,sha256=Z7rfufrDeEkUYf2MlZsXyvKsZWHIJWujK357_z1BBg0,5809
-waveorder/models/isotropic_fluorescent_thick_3d.py,sha256=H6BFI25PaWXhtx62Gsf42Y85cCdflwhKk_nKlcuD9T8,5007
+waveorder/models/isotropic_fluorescent_thick_3d.py,sha256=Pzi2kM1OGmwQIrI6b5h9OeIOGzHssG30Wv8zDi4n4PQ,5395
 waveorder/models/isotropic_thin_3d.py,sha256=E__ly_xF6Tw_bHLSHHPpd3p60t01LhIPiFrqfd5u1r4,8493
-waveorder/models/phase_thick_3d.py,sha256=U3RMHCFaKvxptoARt_lyJEHMElfj1tSJpVHJNnceIcs,7158
-waveorder-2.1.0.dist-info/LICENSE,sha256=auz4oGH1A-xZtoiR2zuXIk-Hii4v9aGgFVBqn7nfpms,1509
-waveorder-2.1.0.dist-info/METADATA,sha256=IsQbwt64BSCXnO1CboPAFOWUPiUzMoD7gK0LQBSHcqM,6656
-waveorder-2.1.0.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-waveorder-2.1.0.dist-info/top_level.txt,sha256=i3zReXiiMTnyPk93W7aEz_oEfsLnfR_Kzl7PW7kUslA,10
-waveorder-2.1.0.dist-info/RECORD,,
+waveorder/models/phase_thick_3d.py,sha256=itGav-JUDcs7YXxxtdtFK95CuaKR759o9ubL7ms8lBk,6590
+waveorder-2.2.0rc0.dist-info/LICENSE,sha256=auz4oGH1A-xZtoiR2zuXIk-Hii4v9aGgFVBqn7nfpms,1509
+waveorder-2.2.0rc0.dist-info/METADATA,sha256=KItkcQO-Bl3Gj-rutxx1V89YkVGYovr-QFo-OUPnAHI,8249
+waveorder-2.2.0rc0.dist-info/WHEEL,sha256=Z4pYXqR_rTB7OWNDYFOm1qRk0RX6GFP2o8LgvP453Hk,91
+waveorder-2.2.0rc0.dist-info/top_level.txt,sha256=i3zReXiiMTnyPk93W7aEz_oEfsLnfR_Kzl7PW7kUslA,10
+waveorder-2.2.0rc0.dist-info/RECORD,,

{waveorder-2.1.0.dist-info → waveorder-2.2.0rc0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.2)
+Generator: setuptools (70.3.0)
 Root-Is-Purelib: true
 Tag: py3-none-any