midas-2d 0.1.0__tar.gz

midas_2d-0.1.0/LICENSE

@@ -0,0 +1,53 @@
+Copyright (c) 2012, UChicago Argonne, LLC
+ 
+All Rights Reserved
+ 
+MIDAS Microstructural Imaging using Diffraction Analysis Software
+
+Materials Physics and Engineering
+Computational X-ray Science
+Advanced Photon Source
+Argonne National Laboratory
+
+Contributing Authors:
+Hemant Sharma (hsharma@anl.gov)
+
+OPEN SOURCE LICENSE
+ 
+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.  Software changes,  
+   modifications, or derivative works, should be noted with comments and  
+   the author and organization's name.
+ 
+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 names of UChicago Argonne, LLC or the Department of Energy  
+   nor the names of its contributors may be used to endorse or promote  
+   products derived from this software without specific prior written  
+   permission.
+ 
+4. The software and the end-user documentation included with the  
+   redistribution, if any, must include the following acknowledgment:
+ 
+   "This product includes software produced by UChicago Argonne, LLC  
+   under Contract No. DE-AC02-06CH11357 with the Department of Energy."
+ 
+****************************************************************************
+ 
+DISCLAIMER
+ 
+THE SOFTWARE IS SUPPLIED "AS IS" WITHOUT WARRANTY OF ANY KIND.
+ 
+Neither the United States GOVERNMENT, nor the United States Department  
+of Energy, NOR UChicago Argonne, LLC, nor any of their employees, makes  
+any warranty, express or implied, or assumes any legal liability or  
+responsibility for the accuracy, completeness, or usefulness of any  
+information, data, apparatus, product, or process disclosed, or  
+represents that its use would not infringe privately owned rights.
+ 
+****************************************************************************

midas_2d-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: midas-2d
+Version: 0.1.0
+Summary: Differentiable diffraction for 2D / few-layer & ultrafast experiments: finite-size interference (Laue oscillations), crystal-truncation rods, and rocking curves on top of midas-hkls.
+Author-email: Hemant Sharma <hsharma@anl.gov>
+License-Expression: BSD-3-Clause
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20
+Requires-Dist: torch>=2.0
+Requires-Dist: midas-hkls>=0.5
+Requires-Dist: midas-pink>=0.1
+Requires-Dist: midas-invert>=0.1
+Provides-Extra: viz
+Requires-Dist: matplotlib>=3.5; extra == "viz"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: matplotlib>=3.5; extra == "dev"
+Dynamic: license-file
+
+# midas-2d
+
+Differentiable diffraction for **2D / few-layer & ultrafast** experiments,
+built on `midas-hkls` (structure factors, form factors, lattice math, HKL
+enumeration) and `midas-pink` (energy spectrum). All forward paths are
+torch-differentiable and run on CPU / CUDA / MPS.
+
+See `../MIDAS_2D_ULTRAFAST_DIFFRACTION_PLAN.md` for the full phased plan and the
+collaborator-driven scope (Schaller/Flanders ultrafast nanoplatelets;
+Hruszkewycz BCDI; Cherukara ML inversion; Sankaranarayanan MD).
+
+## Status: Phases 1-4 implemented (38 tests, MPS/CPU verified)
+
+### Phase 1 -- finite-size forward core
+- **`shape_factor`** -- Laue interference `|S(q)|^2 = prod sin^2(N_i pi x_i)/
+  sin^2(pi x_i)` (thickness fringes / Laue oscillations), its `N -> inf`
+  crystal-truncation-rod limit, `nanoplatelet_rod`. Differentiable in a
+  real-valued layer count `N`, with finite/correct gradients at the Bragg peak.
+- **`forward`** -- continuous-q structure factor `F(q)` (reuses `midas-hkls`
+  form-factor / metric / DWF physics, no integer rounding), assembled into
+  `I(q) = |F|^2 . |S|^2 . Lp`.
+- **`energy`** -- swappable mono/pink/white via `midas_pink.ParameterisedSpectrum`.
+- **`io`** -- zinc-blende CdSe builder.
+
+### Phase 3 -- MD-coupled engine (`debye`)  *(the novel core)*
+Diffraction straight from atomic coordinates, **differentiable w.r.t. the atom
+positions**:
+- `coherent_amplitude` / `coherent_intensity` -- oriented `|sum f e^{iQ.r}|^2`
+  (reproduces the Phase-1 analytic fringes to 2e-3 -- cross-checked).
+- `debye_intensity` -- orientationally-averaged Debye equation (colloidal case).
+- `ensemble_intensity` -- average over MD frames; **the spread of coordinates
+  *is* the disorder**, so anisotropic Debye-Waller falloff emerges with no DWF
+  assumed.
+- `io.cdse_supercell`, `io.load_xyz_frames` -- explicit structures / trajectories.
+
+### Phase 2 -- transient anisotropic disorder, rocking, inversion, UQ
+- **`disorder`** -- `AnisotropicMSD` / `TransientMSD` (fittable, time-resolved
+  out-of-plane vs in-plane MSD) and `msd_tensor_from_frames` (read the same
+  tensor off an MD trajectory -- closes the loop with `debye`).
+- **`rocking`** -- `rocking_curve`, `fwhm`, `thickness_from_fwhm` (FWHM ~ 0.886/N),
+  `reciprocal_space_map`; rod models from either the analytic or MD forward.
+- **`inverse`** -- `fit` (Adam/L-BFGS), `cosine_loss` (smooth scale-invariant
+  shape loss), `laplace_uncertainty` (Hessian-at-optimum error bars).
+
+### Phase 4 -- coherent / BCDI (`coherent`)
+- `coherent_speckle`, `bcdi_forward` (`|FFT(psi)|^2`), and `phase_retrieval`
+  (autograd phase retrieval inside a support -- the differentiable ER/HIO
+  alternative and a slot for learned priors).
+
+### Diffraction-as-a-loss-on-dynamics (`dynamics`)  *(novel closure)*
+- `thermal_ensemble` -- differentiable thermal cloud from anisotropic spring
+  constants (reparameterisation trick), `stiffness_from_msd` (equipartition),
+  `recover_stiffness` -- fit `(k_par, k_perp)` straight from diffraction, so a
+  transient drop in `k_perp` (lattice softening) is read off the patterns.
+
+### Coherent phonons (`phonon`)
+- `strain_wave`, `bragg_timeseries`, `fit_coherent_phonon` -- a damped
+  out-of-plane breathing mode modulates a Bragg reflection; recover its
+  frequency, damping and amplitude from the time series.
+
+### Amortised ML inference (`ml`)
+- `make_dataset` (forward model = data generator), `ParameterMLP`,
+  `train_surrogate` -- one network pass maps a pattern to {N3, u_perp}
+  (held-out N3 MAE ~0.07 cell).
+
+### Instrument realism + real data (`instrument`, `realdata`)
+- `project_to_detector` (Ewald-correct), `solid_angle_polarization`,
+  `poisson_nll` / `add_poisson_noise`, `resolution_convolve`;
+  `load_profile` and `debye_reference_numpy` (independent NumPy Debye oracle,
+  agrees with the torch path to 1e-14).
+
+### Multi-reflection (`rocking.thickness_loss_scan`)
+- Joint thickness loss over several rods -- breaks the single-rod thickness
+  multimodality (one basin per integer N3) to a unique minimum.
+
+### Depth-resolved strain + unified thermal (`strain_profile`)
+- A per-atom out-of-plane displacement `u_z(z)` makes the Bragg peak asymmetric
+  (the d-spacing-vs-depth signal); `recover_depth_strain` inverts the asymmetric
+  peak back to the depth profile.  `thermal_rod` drives BOTH the shift (thermal
+  expansion) and the amplitude (local Debye-Waller) from one `T(z)` field.
+  Builders: `linear_strain`, `exponential_strain`, `acoustic_pulse` (Thomsen).
+
+### Diffraction -> transport/coupling coefficients (`thermal_transport`)
+- `two_temperature_model` + `fit_electron_phonon_coupling` -- recover the
+  **electron-phonon coupling g** from the Bragg-amplitude transient.
+- `heat_diffusion_1d` + `fit_thermal_diffusivity` -- recover the **thermal
+  diffusivity kappa** from the depth-resolved strain front.
+
+### Differentiable MD -> learn the potential (`md_integrator`)
+- `velocity_verlet` (autograd through every step), `bragg_from_trajectory`,
+  `coherent_mode_kick`, `recover_potential_from_movie` -- recover the
+  **interatomic spring constant** by differentiating an MD trajectory to match a
+  Bragg-intensity oscillation.  (Uses a non-uniform standing-wave mode: a
+  uniform kick is a rigid translation that |A|^2 cannot see; the intensity rings
+  at 2*omega.)
+
+### Frontier tier
+- **`multimodal`** -- joint X-ray + optical (transient-absorption) inversion.
+  `fit_multimodal` recovers the **deformation potential Xi** and thermal
+  coefficient; the optical channel pins the carrier dynamics. (Honest finding:
+  when electronic/thermal timescales are well separated, the X-ray strain shape
+  alone already localizes Xi -- see `xray_only_degeneracy`.)
+- **`latent_dynamics`** -- `discover_eom` recovers the equation of motion
+  (e.g. a damped phonon `v_dot = -omega^2 x - gamma v`) from a structural
+  trajectory by sparse regression (SINDy/STLSQ), *without assuming the form*;
+  the spurious cubic term is thresholded to zero.
+- **`ensemble`** -- `recover_thickness_distribution`: deconvolve the thickness
+  *distribution* of a polydisperse sample from the smeared fringes.
+- **`active_learning`** -- `fisher_information` / `next_best_measurement`: rank
+  candidate delays/reflections by how much they constrain a target parameter
+  (autonomous-beamline experiment design).
+
+### Showcase demos (write to `dev/paper/figures/`)
+- `tutorial_npl_fringes` -- 3/4/5-monolayer Laue oscillations (fringe count = N3-1).
+- `tutorial_md_transient_disorder` -- **anisotropic transient disordering from
+  the atoms + differentiable recovery of u_perp(t); planted = MD-derived =
+  recovered.**
+- `tutorial_coherent_rsm` -- coherent reciprocal-space map + phase retrieval.
+- `tutorial_stiffness_and_phonon` -- transient lattice softening k_perp(t) +
+  coherent-phonon frequency/damping, both recovered from diffraction.
+- `tutorial_ml_and_detector` -- amortised-inference parity plot + a coherent
+  pattern Ewald-projected onto a detector with Poisson noise.
+- `tutorial_depth_strain` -- depth-resolved lattice-displacement reconstruction
+  from an asymmetric Bragg peak (the d-spacing-vs-depth signal).
+- `tutorial_transport_and_md` -- recover electron-phonon coupling g, thermal
+  diffusivity kappa, and interatomic stiffness k, all from diffraction.
+- `tutorial_frontier` -- deformation potential (multi-modal), equation-of-motion
+  discovery, and ensemble thickness distribution.
+
+## Quick start
+
+```python
+import torch
+from midas_2d import cdse_supercell, coherent_intensity
+
+# Diffraction straight from atoms, differentiable in the coordinates:
+coords, elements, cell = cdse_supercell((8, 8, 4))     # few-layer CdSe platelet
+coords.requires_grad_(True)
+q = (2 * torch.pi / 6.077) * torch.tensor([[1., 1., 1.0]])
+I = coherent_intensity(coords, elements, q)            # I.backward() -> per-atom grads
+```
+
+```bash
+python -m midas_2d.examples.tutorial_md_transient_disorder   # the headline figure
+pytest                                                       # 38 tests (set KMP_DUPLICATE_LIB_OK=TRUE on macOS)
+```
+
+## Not yet implemented
+
+- Phase 5: ML inversion / amortized-inference surrogates (uses the
+  differentiable forwards as data generators + consistency layer).
+- Multi-reflection / multi-Bragg joint BCDI; absolute-scale spectral weighting.

midas_2d-0.1.0/README.md

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+# midas-2d
+
+Differentiable diffraction for **2D / few-layer & ultrafast** experiments,
+built on `midas-hkls` (structure factors, form factors, lattice math, HKL
+enumeration) and `midas-pink` (energy spectrum). All forward paths are
+torch-differentiable and run on CPU / CUDA / MPS.
+
+See `../MIDAS_2D_ULTRAFAST_DIFFRACTION_PLAN.md` for the full phased plan and the
+collaborator-driven scope (Schaller/Flanders ultrafast nanoplatelets;
+Hruszkewycz BCDI; Cherukara ML inversion; Sankaranarayanan MD).
+
+## Status: Phases 1-4 implemented (38 tests, MPS/CPU verified)
+
+### Phase 1 -- finite-size forward core
+- **`shape_factor`** -- Laue interference `|S(q)|^2 = prod sin^2(N_i pi x_i)/
+  sin^2(pi x_i)` (thickness fringes / Laue oscillations), its `N -> inf`
+  crystal-truncation-rod limit, `nanoplatelet_rod`. Differentiable in a
+  real-valued layer count `N`, with finite/correct gradients at the Bragg peak.
+- **`forward`** -- continuous-q structure factor `F(q)` (reuses `midas-hkls`
+  form-factor / metric / DWF physics, no integer rounding), assembled into
+  `I(q) = |F|^2 . |S|^2 . Lp`.
+- **`energy`** -- swappable mono/pink/white via `midas_pink.ParameterisedSpectrum`.
+- **`io`** -- zinc-blende CdSe builder.
+
+### Phase 3 -- MD-coupled engine (`debye`)  *(the novel core)*
+Diffraction straight from atomic coordinates, **differentiable w.r.t. the atom
+positions**:
+- `coherent_amplitude` / `coherent_intensity` -- oriented `|sum f e^{iQ.r}|^2`
+  (reproduces the Phase-1 analytic fringes to 2e-3 -- cross-checked).
+- `debye_intensity` -- orientationally-averaged Debye equation (colloidal case).
+- `ensemble_intensity` -- average over MD frames; **the spread of coordinates
+  *is* the disorder**, so anisotropic Debye-Waller falloff emerges with no DWF
+  assumed.
+- `io.cdse_supercell`, `io.load_xyz_frames` -- explicit structures / trajectories.
+
+### Phase 2 -- transient anisotropic disorder, rocking, inversion, UQ
+- **`disorder`** -- `AnisotropicMSD` / `TransientMSD` (fittable, time-resolved
+  out-of-plane vs in-plane MSD) and `msd_tensor_from_frames` (read the same
+  tensor off an MD trajectory -- closes the loop with `debye`).
+- **`rocking`** -- `rocking_curve`, `fwhm`, `thickness_from_fwhm` (FWHM ~ 0.886/N),
+  `reciprocal_space_map`; rod models from either the analytic or MD forward.
+- **`inverse`** -- `fit` (Adam/L-BFGS), `cosine_loss` (smooth scale-invariant
+  shape loss), `laplace_uncertainty` (Hessian-at-optimum error bars).
+
+### Phase 4 -- coherent / BCDI (`coherent`)
+- `coherent_speckle`, `bcdi_forward` (`|FFT(psi)|^2`), and `phase_retrieval`
+  (autograd phase retrieval inside a support -- the differentiable ER/HIO
+  alternative and a slot for learned priors).
+
+### Diffraction-as-a-loss-on-dynamics (`dynamics`)  *(novel closure)*
+- `thermal_ensemble` -- differentiable thermal cloud from anisotropic spring
+  constants (reparameterisation trick), `stiffness_from_msd` (equipartition),
+  `recover_stiffness` -- fit `(k_par, k_perp)` straight from diffraction, so a
+  transient drop in `k_perp` (lattice softening) is read off the patterns.
+
+### Coherent phonons (`phonon`)
+- `strain_wave`, `bragg_timeseries`, `fit_coherent_phonon` -- a damped
+  out-of-plane breathing mode modulates a Bragg reflection; recover its
+  frequency, damping and amplitude from the time series.
+
+### Amortised ML inference (`ml`)
+- `make_dataset` (forward model = data generator), `ParameterMLP`,
+  `train_surrogate` -- one network pass maps a pattern to {N3, u_perp}
+  (held-out N3 MAE ~0.07 cell).
+
+### Instrument realism + real data (`instrument`, `realdata`)
+- `project_to_detector` (Ewald-correct), `solid_angle_polarization`,
+  `poisson_nll` / `add_poisson_noise`, `resolution_convolve`;
+  `load_profile` and `debye_reference_numpy` (independent NumPy Debye oracle,
+  agrees with the torch path to 1e-14).
+
+### Multi-reflection (`rocking.thickness_loss_scan`)
+- Joint thickness loss over several rods -- breaks the single-rod thickness
+  multimodality (one basin per integer N3) to a unique minimum.
+
+### Depth-resolved strain + unified thermal (`strain_profile`)
+- A per-atom out-of-plane displacement `u_z(z)` makes the Bragg peak asymmetric
+  (the d-spacing-vs-depth signal); `recover_depth_strain` inverts the asymmetric
+  peak back to the depth profile.  `thermal_rod` drives BOTH the shift (thermal
+  expansion) and the amplitude (local Debye-Waller) from one `T(z)` field.
+  Builders: `linear_strain`, `exponential_strain`, `acoustic_pulse` (Thomsen).
+
+### Diffraction -> transport/coupling coefficients (`thermal_transport`)
+- `two_temperature_model` + `fit_electron_phonon_coupling` -- recover the
+  **electron-phonon coupling g** from the Bragg-amplitude transient.
+- `heat_diffusion_1d` + `fit_thermal_diffusivity` -- recover the **thermal
+  diffusivity kappa** from the depth-resolved strain front.
+
+### Differentiable MD -> learn the potential (`md_integrator`)
+- `velocity_verlet` (autograd through every step), `bragg_from_trajectory`,
+  `coherent_mode_kick`, `recover_potential_from_movie` -- recover the
+  **interatomic spring constant** by differentiating an MD trajectory to match a
+  Bragg-intensity oscillation.  (Uses a non-uniform standing-wave mode: a
+  uniform kick is a rigid translation that |A|^2 cannot see; the intensity rings
+  at 2*omega.)
+
+### Frontier tier
+- **`multimodal`** -- joint X-ray + optical (transient-absorption) inversion.
+  `fit_multimodal` recovers the **deformation potential Xi** and thermal
+  coefficient; the optical channel pins the carrier dynamics. (Honest finding:
+  when electronic/thermal timescales are well separated, the X-ray strain shape
+  alone already localizes Xi -- see `xray_only_degeneracy`.)
+- **`latent_dynamics`** -- `discover_eom` recovers the equation of motion
+  (e.g. a damped phonon `v_dot = -omega^2 x - gamma v`) from a structural
+  trajectory by sparse regression (SINDy/STLSQ), *without assuming the form*;
+  the spurious cubic term is thresholded to zero.
+- **`ensemble`** -- `recover_thickness_distribution`: deconvolve the thickness
+  *distribution* of a polydisperse sample from the smeared fringes.
+- **`active_learning`** -- `fisher_information` / `next_best_measurement`: rank
+  candidate delays/reflections by how much they constrain a target parameter
+  (autonomous-beamline experiment design).
+
+### Showcase demos (write to `dev/paper/figures/`)
+- `tutorial_npl_fringes` -- 3/4/5-monolayer Laue oscillations (fringe count = N3-1).
+- `tutorial_md_transient_disorder` -- **anisotropic transient disordering from
+  the atoms + differentiable recovery of u_perp(t); planted = MD-derived =
+  recovered.**
+- `tutorial_coherent_rsm` -- coherent reciprocal-space map + phase retrieval.
+- `tutorial_stiffness_and_phonon` -- transient lattice softening k_perp(t) +
+  coherent-phonon frequency/damping, both recovered from diffraction.
+- `tutorial_ml_and_detector` -- amortised-inference parity plot + a coherent
+  pattern Ewald-projected onto a detector with Poisson noise.
+- `tutorial_depth_strain` -- depth-resolved lattice-displacement reconstruction
+  from an asymmetric Bragg peak (the d-spacing-vs-depth signal).
+- `tutorial_transport_and_md` -- recover electron-phonon coupling g, thermal
+  diffusivity kappa, and interatomic stiffness k, all from diffraction.
+- `tutorial_frontier` -- deformation potential (multi-modal), equation-of-motion
+  discovery, and ensemble thickness distribution.
+
+## Quick start
+
+```python
+import torch
+from midas_2d import cdse_supercell, coherent_intensity
+
+# Diffraction straight from atoms, differentiable in the coordinates:
+coords, elements, cell = cdse_supercell((8, 8, 4))     # few-layer CdSe platelet
+coords.requires_grad_(True)
+q = (2 * torch.pi / 6.077) * torch.tensor([[1., 1., 1.0]])
+I = coherent_intensity(coords, elements, q)            # I.backward() -> per-atom grads
+```
+
+```bash
+python -m midas_2d.examples.tutorial_md_transient_disorder   # the headline figure
+pytest                                                       # 38 tests (set KMP_DUPLICATE_LIB_OK=TRUE on macOS)
+```
+
+## Not yet implemented
+
+- Phase 5: ML inversion / amortized-inference surrogates (uses the
+  differentiable forwards as data generators + consistency layer).
+- Multi-reflection / multi-Bragg joint BCDI; absolute-scale spectral weighting.

midas_2d-0.1.0/midas_2d/__init__.py

@@ -0,0 +1,211 @@
+"""midas-2d -- differentiable diffraction for 2D / few-layer & ultrafast work.
+
+Phase 1 (finite-size forward core):
+    from midas_2d import (
+        interference_factor, truncation_rod, nanoplatelet_rod,
+        rod_intensity, structure_factor_q,
+        cdse_zincblende, build_crystal_tensor,
+        make_spectrum, monochromatic,
+    )
+
+Builds on midas-hkls (structure factors, form factors, lattice, hkl gen) and
+midas-pink (energy spectrum).  See MIDAS_2D_ULTRAFAST_DIFFRACTION_PLAN.md.
+"""
+from .coherent import bcdi_forward, coherent_speckle, phase_retrieval
+from .debye import (
+    atomic_form_factors,
+    coherent_amplitude,
+    coherent_intensity,
+    debye_intensity,
+    ensemble_intensity,
+)
+from .disorder import (
+    AnisotropicMSD,
+    TransientMSD,
+    dwf_amplitude,
+    msd_tensor_from_frames,
+)
+from .dynamics import (
+    msd_from_stiffness,
+    recover_stiffness,
+    stiffness_from_msd,
+    thermal_ensemble,
+)
+from .energy import make_spectrum, monochromatic
+from .instrument import (
+    add_poisson_noise,
+    poisson_nll,
+    project_to_detector,
+    resolution_convolve,
+    solid_angle_polarization,
+)
+from .inverse import cosine_loss, fit, laplace_uncertainty, relative_l2_loss
+from .ml import ParameterMLP, make_dataset, train_surrogate
+from .phonon import (
+    apply_out_of_plane_strain,
+    bragg_timeseries,
+    fit_coherent_phonon,
+    strain_wave,
+)
+from .realdata import debye_reference_numpy, load_profile
+from .active_learning import (
+    fisher_information,
+    next_best_measurement,
+    rank_measurements,
+    sensitivity,
+)
+from .ensemble import polydisperse_rod, recover_thickness_distribution
+from .latent_dynamics import discover_eom, integrate_latent_ode, library_terms
+from .md_integrator import (
+    bragg_from_trajectory,
+    coherent_mode_kick,
+    harmonic_force,
+    recover_potential_from_movie,
+    velocity_verlet,
+)
+from .multimodal import (
+    carrier_density,
+    fit_multimodal,
+    lattice_temperature_from_carriers,
+    optical_signal,
+    strain_two_channel,
+    xray_only_degeneracy,
+)
+from .strain_profile import (
+    acoustic_pulse,
+    apply_depth_displacement,
+    depth_resolved_amplitude,
+    depth_resolved_intensity,
+    exponential_strain,
+    linear_strain,
+    recover_depth_strain,
+    strain_to_displacement,
+    temperature_to_displacement,
+    temperature_to_msd,
+    thermal_rod,
+)
+from .thermal_transport import (
+    fit_electron_phonon_coupling,
+    fit_thermal_diffusivity,
+    heat_diffusion_1d,
+    lattice_T_to_intensity_ratio,
+    two_temperature_model,
+)
+from .rocking import (
+    analytic_rod_model,
+    fwhm,
+    md_rod_model,
+    reciprocal_space_map,
+    rocking_curve,
+    thickness_from_fwhm,
+    thickness_loss_scan,
+)
+from .forward import rod_intensity, structure_factor_q
+from .io import (
+    build_crystal_tensor,
+    cdse_supercell,
+    cdse_zincblende,
+    load_xyz_frames,
+    supercell_from_crystal,
+)
+from .shape_factor import (
+    interference_factor,
+    laue_interference_1d,
+    nanoplatelet_rod,
+    truncation_rod,
+)
+
+__version__ = "0.1.0"
+
+__all__ = [
+    "interference_factor",
+    "laue_interference_1d",
+    "nanoplatelet_rod",
+    "truncation_rod",
+    "rod_intensity",
+    "structure_factor_q",
+    "cdse_zincblende",
+    "build_crystal_tensor",
+    "cdse_supercell",
+    "supercell_from_crystal",
+    "load_xyz_frames",
+    "atomic_form_factors",
+    "coherent_amplitude",
+    "coherent_intensity",
+    "debye_intensity",
+    "ensemble_intensity",
+    "AnisotropicMSD",
+    "TransientMSD",
+    "dwf_amplitude",
+    "msd_tensor_from_frames",
+    "analytic_rod_model",
+    "md_rod_model",
+    "rocking_curve",
+    "fwhm",
+    "thickness_from_fwhm",
+    "reciprocal_space_map",
+    "thickness_loss_scan",
+    "fit",
+    "laplace_uncertainty",
+    "relative_l2_loss",
+    "cosine_loss",
+    "coherent_speckle",
+    "bcdi_forward",
+    "phase_retrieval",
+    "stiffness_from_msd",
+    "msd_from_stiffness",
+    "thermal_ensemble",
+    "recover_stiffness",
+    "strain_wave",
+    "apply_out_of_plane_strain",
+    "bragg_timeseries",
+    "fit_coherent_phonon",
+    "make_dataset",
+    "ParameterMLP",
+    "train_surrogate",
+    "project_to_detector",
+    "solid_angle_polarization",
+    "poisson_nll",
+    "add_poisson_noise",
+    "resolution_convolve",
+    "load_profile",
+    "debye_reference_numpy",
+    "depth_resolved_amplitude",
+    "depth_resolved_intensity",
+    "apply_depth_displacement",
+    "linear_strain",
+    "exponential_strain",
+    "acoustic_pulse",
+    "strain_to_displacement",
+    "temperature_to_displacement",
+    "temperature_to_msd",
+    "thermal_rod",
+    "recover_depth_strain",
+    "two_temperature_model",
+    "lattice_T_to_intensity_ratio",
+    "fit_electron_phonon_coupling",
+    "heat_diffusion_1d",
+    "fit_thermal_diffusivity",
+    "harmonic_force",
+    "velocity_verlet",
+    "bragg_from_trajectory",
+    "coherent_mode_kick",
+    "recover_potential_from_movie",
+    "carrier_density",
+    "lattice_temperature_from_carriers",
+    "strain_two_channel",
+    "optical_signal",
+    "fit_multimodal",
+    "xray_only_degeneracy",
+    "library_terms",
+    "integrate_latent_ode",
+    "discover_eom",
+    "polydisperse_rod",
+    "recover_thickness_distribution",
+    "sensitivity",
+    "fisher_information",
+    "rank_measurements",
+    "next_best_measurement",
+    "make_spectrum",
+    "monochromatic",
+]

midas_2d-0.1.0/midas_2d/active_learning.py

@@ -0,0 +1,13 @@
+"""Experiment design -- now provided by the shared ``midas_invert`` leaf.
+
+Thin re-export so existing ``midas_2d`` imports are unchanged.
+"""
+from midas_invert.design import (
+    fisher_information,
+    next_best_measurement,
+    rank_measurements,
+    sensitivity,
+)
+
+__all__ = ["sensitivity", "fisher_information", "rank_measurements",
+           "next_best_measurement"]