redbirdpy 0.1.0__tar.gz → 0.2.0__tar.gz

{redbirdpy-0.1.0 → redbirdpy-0.2.0}/Makefile

@@ -81,7 +81,11 @@ docs:
 
 # Format code (requires black)
 format:
-	$(PYTHON) -m black redbirdpy/ test/
+	$(PYTHON) -m black redbirdpy/ test/ example/*.py setup.py
+
+# Run all demo scripts
+demo:
+	cd example && for demo in demo*.py; do echo $$demo; time $(PYTHON) $$demo 0; done
 
 # Type checking (requires mypy)
 typecheck:
@@ -99,5 +103,3 @@ info:
 version:
 	@$(PYTHON) -c "import redbirdpy; print(redbirdpy.__version__)"
 
-pretty:
-	$(PYTHON) -m black test/*.py example/*.py redbirdpy/*.py setup.py

{redbirdpy-0.1.0 → redbirdpy-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: redbirdpy
-Version: 0.1.0
+Version: 0.2.0
 Summary: A Python toolbox for Diffuse Optical Tomography (DOT) and Near-Infrared Spectroscopy (NIRS)
 Home-page: https://github.com/fangq/redbirdpy
 Author: Qianqian Fang
@@ -14,7 +14,7 @@ Project-URL: Repository, https://github.com/fangq/redbirdpy
 Project-URL: Bug Tracker, https://github.com/fangq/redbirdpy/issues
 Keywords: Diffuse Optical Tomography,DOT,NIRS,Near-Infrared Spectroscopy,FEM,Finite Element Method,Biomedical Optics,Image Reconstruction,Inverse Problem,Photon Migration,Diffusion Equation,Tissue Optics
 Platform: any
-Classifier: Development Status :: 3 - Alpha
+Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Healthcare Industry
@@ -37,14 +37,12 @@ Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 Requires-Dist: numpy>=1.15.0
 Requires-Dist: scipy>=1.0.0
-Provides-Extra: mesh
-Requires-Dist: iso2mesh>=0.5.4; extra == "mesh"
+Requires-Dist: iso2mesh>=0.5.0
 Provides-Extra: dev
 Requires-Dist: pytest>=6.0; extra == "dev"
 Requires-Dist: pytest-cov>=2.0; extra == "dev"
 Requires-Dist: flake8>=3.0; extra == "dev"
 Provides-Extra: all
-Requires-Dist: iso2mesh>=0.5.4; extra == "all"
 Requires-Dist: matplotlib>=3.0; extra == "all"
 Dynamic: author
 Dynamic: home-page
@@ -53,13 +51,13 @@ Dynamic: maintainer
 Dynamic: platform
 Dynamic: requires-python
 
-![Redbird Banner](./doc/images/redbird_banner.png)
+![Redbird Banner](https://raw.githubusercontent.com/fangq/redbird/refs/heads/master/doc/images/redbird_banner.png)
 
 # RedbirdPy - A Model-Based Diffuse Optical Imaging Toolbox for Python
 
-* **Copyright**: (C) Qianqian Fang (2005–2025) \<q.fang at neu.edu>
+* **Copyright**: (C) Qianqian Fang (2005–2026) \<q.fang at neu.edu>
 * **License**: GNU Public License V3 or later
-* **Version**: 0.1.0
+* **Version**: 0.2.0 (Flamingo)
 * **GitHub**: [https://github.com/fangq/redbirdpy](https://github.com/fangq/redbirdpy)
 * **Acknowledgement**: This project is supported by the US National Institute of Health (NIH)
   grant [R01-CA204443](https://reporter.nih.gov/project-details/10982160)
@@ -88,7 +86,7 @@ Dynamic: requires-python
 
 ## Introduction
 
-**Redbird-Python** is a Python translation of the [Redbird MATLAB toolbox](https://github.com/fangq/redbird) for diffuse optical imaging (DOI) and diffuse optical tomography (DOT). It provides a fast, experimentally-validated forward solver for the diffusion equation using the finite-element method (FEM), along with advanced non-linear image reconstruction algorithms.
+**RedbirdPy** is a Python translation of the [Redbird MATLAB toolbox](https://github.com/fangq/redbird) for diffuse optical imaging (DOI) and diffuse optical tomography (DOT). It provides a fast, experimentally-validated forward solver for the diffusion equation using the finite-element method (FEM), along with advanced non-linear image reconstruction algorithms.
 
 Redbird is the result of over two decades of active research in DOT and image reconstruction. It has been the core data analysis tool in numerous publications related to optical breast imaging, prior-guided reconstruction techniques, multi-modal imaging, and wide-field DOT systems.
 
@@ -104,7 +102,7 @@ Redbird is the result of over two decades of active research in DOT and image re
 
 ### Validation
 
-The forward solver is carefully validated against Monte Carlo solvers—**MCX** and **MMC**. The diffusion approximation is valid in high-scattering media where the reduced scattering coefficient (μs') is much greater than the absorption coefficient (μa).
+The forward solver is carefully validated against Monte Carlo solvers - **MCX** and **MMC**. The diffusion approximation is valid in high-scattering media where the reduced scattering coefficient (μs') is much greater than the absorption coefficient (μa).
 
 ---
 
@@ -112,15 +110,15 @@ The forward solver is carefully validated against Monte Carlo solvers—**MCX**
 
 ### Requirements
 
-- Python 3.8+
+- Python 3.6+
 - NumPy
 - SciPy
+- Iso2Mesh
 
 ### Basic Installation
 
 ```bash
 pip install numpy scipy
-# For mesh generation
 pip install iso2mesh  # or from https://github.com/NeuroJSON/pyiso2mesh
 ```
 
@@ -131,7 +129,7 @@ pip install iso2mesh  # or from https://github.com/NeuroJSON/pyiso2mesh
 pip install numba          # JIT compilation
 
 # For accelerated solvers
-pip install blocksolver  # or from https://github.com/fangq/
+pip install blocksolver  # or from https://github.com/fangq/blit
 
 # For other linear solvers
 pip install pypardiso      # Intel MKL PARDISO (fastest direct solver)
@@ -147,7 +145,7 @@ cd redbirdpy
 pip install -e .
 ```
 
-Or simply add the `redbirdpy` folder to your Python path.
+Or simply import `redbirdpy` from inside the repository's top folder.
 
 ---
 
@@ -201,12 +199,12 @@ Redbird performs two main tasks:
 
 Redbird supports four types of image reconstructions:
 
-| Mode | Description |
-|------|-------------|
-| **Bulk Fitting** | Estimate single set of properties for entire domain |
-| **Segmented** | One property set per labeled tissue segment ("hard-prior") |
+| Mode | Description                                                   |
+|------|---------------------------------------------------------------|
+| **Bulk Fitting** | Estimate single set of properties for the entire domain       |
+| **Segmented** | One property set per labeled tissue segment ("hard-prior")    |
 | **Soft-Prior** | Spatial priors as soft constraints (Laplacian, compositional) |
-| **Unconstrained** | Independent properties per node with Tikhonov regularization |
+| **Unconstrained** | Independent properties per node with Tikhonov regularization  |
 
 ---
 
@@ -265,9 +263,9 @@ Redbird supports four types of image reconstructions:
 | Function | Description |
 |----------|-------------|
 | `femsolve(A, b, method)` | Solve linear system with auto-selection |
-| `get_solver_info()` | Query available solver backends |
+| `solverinfo()` | Query available solver backends |
 
-Supported solvers: `pardiso`, `umfpack`, `cholmod`, `superlu`, `blqmr`, `cg`, `cg+amg`, `gmres`, `bicgstab`
+Supported solvers: `pardiso`, `umfpack`, `cholmod`, `superlu`, `blqmr`, `cg`, `cg+amg`, `gmres`, `minres`, `minres+amg`, `qmr`, `bicgstab`
 
 ### `redbirdpy.analytical` - Analytical Solutions
 
@@ -395,8 +393,8 @@ Configure similarly using `dettype`, `detparam1`, `detparam2`, `detpattern`.
 
 ```python
 cfg['prop'] = {
-    '690': np.array([[0, 0, 1, 1], [0.012, 1.1, 0, 1.37]]),
-    '830': np.array([[0, 0, 1, 1], [0.008, 0.9, 0, 1.37]])
+    '690': [[0, 0, 1, 1], [0.012, 1.1, 0, 1.37]],
+    '830': [[0, 0, 1, 1], [0.008, 0.9, 0, 1.37]]
 }
 ```
 
@@ -498,7 +496,7 @@ recon['prop'] = np.tile(cfg['prop'][1,:], (recon['node'].shape[0], 1))
 newrecon, resid = rb.run(cfg, recon, detphi0, lambda_=1e-4)[:2]
 ```
 
-### Wide-Field Reconstruction
+### Wide-Field Forward and Reconstruction
 
 ```python
 # Create illumination patterns
@@ -585,12 +583,12 @@ If you use Redbird in your research, please cite:
 
 ## License
 
-GNU General Public License v3.0 or later - see [LICENSE](LICENSE) file for details.
+GNU General Public License v3.0 or later - see [LICENSE](LICENSE.txt) file for details.
 
 ## Author
 
 **Qianqian Fang** (q.fang@neu.edu)
-Computational Optics & Translational Imaging Lab
+Computational Optics & Translational Imaging (COTI) Lab
 Northeastern University
 
-Python translation based on the [Redbird MATLAB toolbox](https://github.com/fangq/redbirdpy).
+Python translation based on the [Redbird MATLAB toolbox](https://github.com/fangq/redbird).

{redbirdpy-0.1.0 → redbirdpy-0.2.0}/README.md

@@ -1,10 +1,10 @@
-![Redbird Banner](./doc/images/redbird_banner.png)
+![Redbird Banner](https://raw.githubusercontent.com/fangq/redbird/refs/heads/master/doc/images/redbird_banner.png)
 
 # RedbirdPy - A Model-Based Diffuse Optical Imaging Toolbox for Python
 
-* **Copyright**: (C) Qianqian Fang (2005–2025) \<q.fang at neu.edu>
+* **Copyright**: (C) Qianqian Fang (2005–2026) \<q.fang at neu.edu>
 * **License**: GNU Public License V3 or later
-* **Version**: 0.1.0
+* **Version**: 0.2.0 (Flamingo)
 * **GitHub**: [https://github.com/fangq/redbirdpy](https://github.com/fangq/redbirdpy)
 * **Acknowledgement**: This project is supported by the US National Institute of Health (NIH)
   grant [R01-CA204443](https://reporter.nih.gov/project-details/10982160)
@@ -33,7 +33,7 @@
 
 ## Introduction
 
-**Redbird-Python** is a Python translation of the [Redbird MATLAB toolbox](https://github.com/fangq/redbird) for diffuse optical imaging (DOI) and diffuse optical tomography (DOT). It provides a fast, experimentally-validated forward solver for the diffusion equation using the finite-element method (FEM), along with advanced non-linear image reconstruction algorithms.
+**RedbirdPy** is a Python translation of the [Redbird MATLAB toolbox](https://github.com/fangq/redbird) for diffuse optical imaging (DOI) and diffuse optical tomography (DOT). It provides a fast, experimentally-validated forward solver for the diffusion equation using the finite-element method (FEM), along with advanced non-linear image reconstruction algorithms.
 
 Redbird is the result of over two decades of active research in DOT and image reconstruction. It has been the core data analysis tool in numerous publications related to optical breast imaging, prior-guided reconstruction techniques, multi-modal imaging, and wide-field DOT systems.
 
@@ -49,7 +49,7 @@ Redbird is the result of over two decades of active research in DOT and image re
 
 ### Validation
 
-The forward solver is carefully validated against Monte Carlo solvers—**MCX** and **MMC**. The diffusion approximation is valid in high-scattering media where the reduced scattering coefficient (μs') is much greater than the absorption coefficient (μa).
+The forward solver is carefully validated against Monte Carlo solvers - **MCX** and **MMC**. The diffusion approximation is valid in high-scattering media where the reduced scattering coefficient (μs') is much greater than the absorption coefficient (μa).
 
 ---
 
@@ -57,15 +57,15 @@ The forward solver is carefully validated against Monte Carlo solvers—**MCX**
 
 ### Requirements
 
-- Python 3.8+
+- Python 3.6+
 - NumPy
 - SciPy
+- Iso2Mesh
 
 ### Basic Installation
 
 ```bash
 pip install numpy scipy
-# For mesh generation
 pip install iso2mesh  # or from https://github.com/NeuroJSON/pyiso2mesh
 ```
 
@@ -76,7 +76,7 @@ pip install iso2mesh  # or from https://github.com/NeuroJSON/pyiso2mesh
 pip install numba          # JIT compilation
 
 # For accelerated solvers
-pip install blocksolver  # or from https://github.com/fangq/
+pip install blocksolver  # or from https://github.com/fangq/blit
 
 # For other linear solvers
 pip install pypardiso      # Intel MKL PARDISO (fastest direct solver)
@@ -92,7 +92,7 @@ cd redbirdpy
 pip install -e .
 ```
 
-Or simply add the `redbirdpy` folder to your Python path.
+Or simply import `redbirdpy` from inside the repository's top folder.
 
 ---
 
@@ -146,12 +146,12 @@ Redbird performs two main tasks:
 
 Redbird supports four types of image reconstructions:
 
-| Mode | Description |
-|------|-------------|
-| **Bulk Fitting** | Estimate single set of properties for entire domain |
-| **Segmented** | One property set per labeled tissue segment ("hard-prior") |
+| Mode | Description                                                   |
+|------|---------------------------------------------------------------|
+| **Bulk Fitting** | Estimate single set of properties for the entire domain       |
+| **Segmented** | One property set per labeled tissue segment ("hard-prior")    |
 | **Soft-Prior** | Spatial priors as soft constraints (Laplacian, compositional) |
-| **Unconstrained** | Independent properties per node with Tikhonov regularization |
+| **Unconstrained** | Independent properties per node with Tikhonov regularization  |
 
 ---
 
@@ -210,9 +210,9 @@ Redbird supports four types of image reconstructions:
 | Function | Description |
 |----------|-------------|
 | `femsolve(A, b, method)` | Solve linear system with auto-selection |
-| `get_solver_info()` | Query available solver backends |
+| `solverinfo()` | Query available solver backends |
 
-Supported solvers: `pardiso`, `umfpack`, `cholmod`, `superlu`, `blqmr`, `cg`, `cg+amg`, `gmres`, `bicgstab`
+Supported solvers: `pardiso`, `umfpack`, `cholmod`, `superlu`, `blqmr`, `cg`, `cg+amg`, `gmres`, `minres`, `minres+amg`, `qmr`, `bicgstab`
 
 ### `redbirdpy.analytical` - Analytical Solutions
 
@@ -340,8 +340,8 @@ Configure similarly using `dettype`, `detparam1`, `detparam2`, `detpattern`.
 
 ```python
 cfg['prop'] = {
-    '690': np.array([[0, 0, 1, 1], [0.012, 1.1, 0, 1.37]]),
-    '830': np.array([[0, 0, 1, 1], [0.008, 0.9, 0, 1.37]])
+    '690': [[0, 0, 1, 1], [0.012, 1.1, 0, 1.37]],
+    '830': [[0, 0, 1, 1], [0.008, 0.9, 0, 1.37]]
 }
 ```
 
@@ -443,7 +443,7 @@ recon['prop'] = np.tile(cfg['prop'][1,:], (recon['node'].shape[0], 1))
 newrecon, resid = rb.run(cfg, recon, detphi0, lambda_=1e-4)[:2]
 ```
 
-### Wide-Field Reconstruction
+### Wide-Field Forward and Reconstruction
 
 ```python
 # Create illumination patterns
@@ -530,12 +530,12 @@ If you use Redbird in your research, please cite:
 
 ## License
 
-GNU General Public License v3.0 or later - see [LICENSE](LICENSE) file for details.
+GNU General Public License v3.0 or later - see [LICENSE](LICENSE.txt) file for details.
 
 ## Author
 
 **Qianqian Fang** (q.fang@neu.edu)
-Computational Optics & Translational Imaging Lab
+Computational Optics & Translational Imaging (COTI) Lab
 Northeastern University
 
-Python translation based on the [Redbird MATLAB toolbox](https://github.com/fangq/redbirdpy).
+Python translation based on the [Redbird MATLAB toolbox](https://github.com/fangq/redbird).

{redbirdpy-0.1.0 → redbirdpy-0.2.0}/example/demo_redbird_basic.py

@@ -196,7 +196,7 @@ if __name__ == "__main__":
             subplot=133,
             parent=hh,
         )
-        plt.show()
+        plt.show(block=(len(sys.argv) == 1))
 
     except Exception as e:
         print(f"Plotting skipped: {e}")

{redbirdpy-0.1.0 → redbirdpy-0.2.0}/example/demo_redbird_forward.py

@@ -80,7 +80,7 @@ node_with_data = np.column_stack([cfg["node"], phi_log])
 # plotmesh with slice 'y>60'
 plotmesh(node_with_data, cfg["elem"], "y>60")
 
-plt.show()
+plt.show(block=(len(sys.argv) == 1))
 
 # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 # %   Print summary

{redbirdpy-0.1.0 → redbirdpy-0.2.0}/example/demo_redbird_forward_expert.py

@@ -215,4 +215,4 @@ ax.set_ylabel("log10(Detector Value)")
 ax.set_title("Detector Readings vs Distance")
 ax.legend()
 
-plt.show()
+plt.show(block=(len(sys.argv) == 1))

{redbirdpy-0.1.0 → redbirdpy-0.2.0}/example/demo_redbird_forward_heterogeneous.py

@@ -197,4 +197,4 @@ ax2.set_title("Forward solution from detector")
 plt.colorbar(tc2, ax=ax2, label="log10(fluence)")
 
 plt.tight_layout()
-plt.show()
+plt.show(block=(len(sys.argv) == 1))

{redbirdpy-0.1.0 → redbirdpy-0.2.0}/example/demo_redbird_forward_layered.py

@@ -219,4 +219,4 @@ plt.colorbar(tc3, ax=ax3, label="log10(fluence)")
 ax3.legend()
 
 plt.tight_layout()
-plt.show()
+plt.show(block=(len(sys.argv) == 1))

{redbirdpy-0.1.0 → redbirdpy-0.2.0}/example/demo_redbird_recon.py

@@ -169,4 +169,4 @@ ax.set_ylabel("Residual")
 ax.set_title("Reconstruction Convergence")
 ax.grid(True)
 
-plt.show()
+plt.show(block=(len(sys.argv) == 1))

redbirdpy-0.2.0/example/demo_redbird_recon_expert.py

@@ -0,0 +1,186 @@
+"""
+Redbird - A Diffusion Solver for Diffuse Optical Tomography
+Copyright Qianqian Fang, 2018
+
+Continuous-Wave (CW) reconstruction of absorption (mua) target
+(explicit iterative loop to show internal steps of rbrun)
+
+This file is part of Redbird URL: https://github.com/fangq/redbirdpy
+
+INDEX CONVENTION: iso2mesh returns 1-based elem/face indices.
+tsearchn returns 1-based element indices to match MATLAB convention.
+"""
+
+import numpy as np
+import time
+import sys
+import os
+
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..")))
+
+import redbirdpy as rb
+from redbirdpy import forward
+from redbirdpy.recon import reginv, matreform
+import iso2mesh as i2m
+import matplotlib.pyplot as plt
+
+# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+# %   prepare simulation input
+# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+if __name__ == "__main__":
+    s0 = [70, 50, 20]
+
+    nobbx, fcbbx, _ = i2m.meshabox(
+        [40, 0, 0], [160, 120, 60], 10
+    )  # elem/face are 1-based
+    nosp, fcsp, _ = i2m.meshasphere(s0, 5, 1)
+    no, fc = i2m.mergemesh(nobbx, fcbbx, nosp, fcsp[:, :3])
+
+    node, elem, _ = i2m.s2m(
+        no, fc[:, :3], 1, 10, "tetgen", [[41, 1, 1], s0]
+    )  # elem is 1-based
+
+    xi, yi = np.meshgrid(np.arange(60, 141, 20), np.arange(20, 101, 20))
+
+    cfg0 = {
+        "node": node,
+        "elem": elem[:, :4],  # 1-based
+        "seg": elem[:, 4].astype(int),
+        "srcpos": np.c_[xi.flat, yi.flat, np.zeros(xi.size)],
+        "detpos": np.c_[xi.flat, yi.flat, 60 * np.ones(xi.size)],
+        "srcdir": [0, 0, 1],
+        "detdir": [0, 0, -1],
+        "prop": np.array([[0, 0, 1, 1], [0.008, 1, 0, 1.37], [0.016, 1, 0, 1.37]]),
+        "omega": 0,
+    }
+
+    cfg = {k: v.copy() if hasattr(v, "copy") else v for k, v in cfg0.items()}
+    cfg0 = rb.meshprep(cfg0)[0]
+
+    # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    # %   Run forward for the heterogeneous domain
+    # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+    detphi0 = rb.run(cfg0)[0]
+
+    # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    # %   Reset the domain to a homogeneous medium for recon
+    # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+    node, face, elem = i2m.meshabox([40, 0, 0], [160, 120, 60], 10)  # 1-based
+    cfg = rb.setmesh(cfg, node, elem, cfg["prop"], np.ones(node.shape[0], dtype=int))
+
+    sd = rb.sdmap(cfg)
+
+    # create coarse reconstruction mesh
+    recon = {}
+    recon["node"], _, recon["elem"] = i2m.meshabox(
+        [40, 0, 0], [160, 120, 60], 20
+    )  # 1-based
+    recon["mapid"], recon["mapweight"] = i2m.tsearchn(
+        recon["node"], recon["elem"], cfg["node"]
+    )  # mapid is 0-based
+
+    # Check for NaN (points outside recon mesh)
+    nan_count = np.isnan(recon["mapid"]).sum()
+    if nan_count > 0:
+        print(f"WARNING: {nan_count} forward nodes outside recon mesh")
+
+    # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    # %   Initialize properties for reconstruction
+    # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+    maxiter = 10
+    resid = np.zeros(maxiter)
+
+    # initialize reconstruction to homogeneous (label=1)
+    recon["prop"] = np.tile(cfg["prop"][1, :], (recon["node"].shape[0], 1))
+    cfg["prop"] = np.tile(cfg["prop"][1, :], (cfg["node"].shape[0], 1))
+    cfg.pop("seg", None)
+
+    # prepare mesh for forward solver
+    cfg = rb.meshprep(cfg)[0]
+
+    # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    # %  Explicit iterative reconstruction
+    # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+    for i in range(maxiter):
+        tic = time.perf_counter()
+
+        # run forward on forward mesh
+        detphi, phi = forward.runforward(cfg, sd=sd, method="blqmr", rhsblock=4)
+        # build Jacobian for mua (cfg["elem"] is 1-based, jac handles conversion internally)
+        # Jmua shape: (nsd, nn_forward)
+        Jmua, _ = forward.jac(sd, phi, cfg["deldotdel"], cfg["elem"], cfg["evol"])
+
+        # remap Jacobian to coarse recon mesh
+        Jmua_recon = i2m.meshremap(
+            Jmua.T,
+            recon["mapid"],
+            recon["mapweight"],
+            recon["elem"],
+            recon["node"].shape[0],
+        ).T
+
+        # create inverse problem (real-valued formulation)
+        Jmua_recon, misfit, _ = matreform(
+            Jmua_recon, detphi0.flatten(), detphi.flatten(), "real"
+        )
+
+        # store residual
+        resid[i] = np.sum(np.abs(misfit))
+
+        # normalize Jacobian
+        blockscale = 1.0 / np.sqrt(np.sum(Jmua_recon**2))
+        Jmua_recon = Jmua_recon * blockscale
+
+        # solve for update on recon mesh
+        dmu_recon = reginv(Jmua_recon, misfit, 1e-3)
+
+        # de-normalize
+        dmu_recon = dmu_recon * blockscale
+
+        # update recon mesh mua
+        recon["prop"][:, 0] = recon["prop"][:, 0] + dmu_recon
+
+        # interpolate update to forward mesh
+        # meshinterp: interpolate from recon nodes to forward nodes
+        cfg["prop"] = i2m.meshinterp(
+            recon["prop"],
+            recon["mapid"],
+            recon["mapweight"],
+            recon["elem"],
+            cfg["prop"],
+        )
+
+        elapsed = time.perf_counter() - tic
+        print(
+            f"iter [{i+1:4d}]: residual={resid[i]:.6e}, relres={resid[i]/resid[0]:.6e} (time={elapsed:.4f} s)"
+        )
+
+    # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    # %  Plotting results
+    # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+    cutpos, cutval, facedata = i2m.qmeshcut(
+        cfg["elem"][:, :4], cfg["node"][:, :3], cfg["prop"][:, 0], "z = 20"
+    )[:3]
+    hh = i2m.plotmesh(
+        np.c_[cutpos, np.log10(np.abs(cutval) + 1e-20)],
+        facedata.tolist(),
+        subplot=121,
+        hold="on",
+    )
+    cutpos, cutval, facedata = i2m.qmeshcut(
+        cfg["elem"][:, :4], cfg["node"][:, :3], cfg["prop"][:, 0], "x = 70"
+    )[:3]
+    i2m.plotmesh(
+        np.c_[cutpos, np.log10(np.abs(cutval) + 1e-20)],
+        facedata.tolist(),
+        subplot=122,
+        parent=hh,
+    )
+
+    plt.show(block=(len(sys.argv) == 1))

{redbirdpy-0.1.0 → redbirdpy-0.2.0}/example/demo_redbird_recon_widefield.py

@@ -167,4 +167,4 @@ i2m.plotmesh(
     parent=hh,
 )
 
-plt.show()
+plt.show(block=(len(sys.argv) == 1))

{redbirdpy-0.1.0 → redbirdpy-0.2.0}/example/demo_redbird_widefield.py

@@ -261,4 +261,4 @@ if HAS_MCX and fcw is not None:
     ]
     ax.legend(handles=legend_elements, loc="upper right")
 
-plt.show()
+plt.show(block=(len(sys.argv) == 1))

{redbirdpy-0.1.0 → redbirdpy-0.2.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "redbirdpy"
-version = "0.1.0"
+version = "0.2.0"
 description = "A Python toolbox for Diffuse Optical Tomography (DOT) and Near-Infrared Spectroscopy (NIRS)"
 readme = "README.md"
 license = {text = "GPL-3.0"}
@@ -29,7 +29,7 @@ keywords = [
     "Tissue Optics",
 ]
 classifiers = [
-    "Development Status :: 3 - Alpha",
+    "Development Status :: 4 - Beta",
     "Intended Audience :: Science/Research",
     "Intended Audience :: Developers",
     "Intended Audience :: Healthcare Industry",
@@ -52,17 +52,16 @@ requires-python = ">=3.6"
 dependencies = [
     "numpy>=1.15.0",
     "scipy>=1.0.0",
+    "iso2mesh>=0.5.0",
 ]
 
 [project.optional-dependencies]
-mesh = ["iso2mesh>=0.5.4"]
 dev = [
     "pytest>=6.0",
     "pytest-cov>=2.0",
     "flake8>=3.0",
 ]
 all = [
-    "iso2mesh>=0.5.4",
     "matplotlib>=3.0",
 ]
 

{redbirdpy-0.1.0 → redbirdpy-0.2.0}/redbirdpy/__init__.py

@@ -52,7 +52,7 @@ Author: Translated from Redbird MATLAB toolbox by Qianqian Fang (q.fang <at> neu
 License: GPL version 3
 """
 
-__version__ = "0.1.0"
+__version__ = "0.2.0"
 __author__ = "Qianqian Fang"
 
 from . import forward