Update with latest changes for publication of thesis.

Author: janbrumm

CHANGELOG.md

@@ -4,6 +4,12 @@ All notable changes to the **LayerModel_lib** project will be documented in this
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+##  [2.4.0] 
+### Changed
+- add all dielectric properties to install using MANIFEST.in
+- update README for published version of thesis
+- some cosmetic changes for plotting the abdominal surfaces of the phantoms
+
 ##  [2.3.0] - 2023-01-19
 ### Added
 - Polynomial Channel Model and its parameters for all phantoms and TX/RX locations

LayerModel_lib/voxelmodel.py

@@ -674,13 +674,15 @@ def show_3d_model(self, model_type: str,
                       show_clusters: Optional[bool] = False,
                       colored_endpoint_indices: List[Tuple] = None,
                       colored_surf3d_indices: List[Tuple] = None,
+                      default_face_color: Tuple = (1, 1, 1, 0.5),
                       show_surf3d_indices: bool = False,
                       show_endpoint_indices: bool = False,
                       x_min_limit: float = None, x_max_limit: float = None,
                       y_min_limit: float = None, y_max_limit: float = None,
                       z_min_limit: float = None, z_max_limit: float = None,
                       plot_origin: np.ndarray = None, plot_radius: float = None,
-                      transformation_vector: Coordinate = None) -> Tuple:
+                      transformation_vector: Coordinate = None,
+                      axes_off = True) -> Tuple:
         """
         Open a plot showing the 3D model of the model_type given.
 
@@ -695,6 +697,7 @@ def show_3d_model(self, model_type: str,
         :param colored_surf3d_indices:  same as 'colored_endpoint_indices' only that indices into
                                         model['trunk'].surface_3d are given.
         :param show_surf3d_indices: Show the index of each surface patch
+        :param default_face_color: Default color of the patches given as (r, g, b, alpha) tuple.
         :param x_max_limit: maximum x value to plot
         :param x_min_limit: minimum x value to plot
         :param y_max_limit: maximum y value to plot
@@ -704,6 +707,7 @@ def show_3d_model(self, model_type: str,
         :param plot_origin: origin for setting axis scaling equal -> handed over to set_axes_equal()
         :param plot_radius: radius for setting axis scaling equal -> handed over to set_axes_equal()
         :param transformation_vector: a vector giving the translation applied to all patches before drawing
+        :param axes_off: turns axes of the figure off by default
         :return:
         """
 
@@ -734,12 +738,11 @@ def show_3d_model(self, model_type: str,
                              if index in indices]
                 colored_surf3d.append((color, hatch, endpoints))
 
-        # the default face color:
-        default_face_color = (1, 1, 1, 0.5)
 
         fig = plt.figure()
         ax = fig.add_subplot(111, projection='3d')
-        ax.set_aspect('equal')
+        # ax.set_aspect('equal')
+        ax.set_box_aspect((1, 1, 1))
 
         # save a list of min. and max. X, Y, Z coordinates
         x_min, y_min, z_min = [1e10] * 3
@@ -902,7 +905,8 @@ def show_3d_model(self, model_type: str,
         ax.elev = 19
         ax.azim = 10
         ax.dist = 6
-        ax.set_axis_off()
+        if axes_off:
+            ax.set_axis_off()
         return fig, ax
 
     def determine_physical_endpoint_mapping(self):
@@ -1071,7 +1075,7 @@ def plot_abdominal_endpoint_patches(self, endpoint_colors: Dict = None,
         Plot all the abdominal endpoint patches as viewed from the front of the body.
 
         :param endpoint_colors: Dict containing the colors for each abdominal endpoint.
-                                key = endpoint index, value = color. For all endpoints not in the dict, the
+                                key = endpoint index, value = list of colors. For all endpoints not in the dict, the
                                 default_color will be used. The color value may be a tuple or list of colors.
         :param default_color: The default color of the patches
         :param hf  Figure handle to plot the data in

MANIFEST.in

@@ -1,5 +1,8 @@
 include LayerModel_lib/ColeColeConstants.TissueProperties
 include LayerModel_lib/PhantomColormap.npy
+include LayerModel_lib/channel_model.h5
+include LayerModel_lib/tissue_properties_fornesleal.json
+include LayerModel_lib/tissue_properties_gabriel.json
 include README.md
 recursive-include examples *.py *.md
 recursive-include phantom_import *.py *.md

README.md

@@ -7,13 +7,13 @@
 
 This repository provides a library to calculate transfer functions, path loss, channel capacity and various 
 other properties of in-body to on-body ultra wideband commincation using the layer modeling approach as introduced 
-in [BB17]. Instead of simulating the wave propagation inside the human body using numerical methods, the transmission 
-form transmitter TX to receiver RX is simplified by a plane wave travelling through a multi-layered dielectric.
+in [Bru24]. Instead of simulating the wave propagation inside the human body using numerical methods, the transmission 
+from transmitter TX to receiver RX is simplified by a plane wave travelling through a multi-layered dielectric.
 The layers of this multi-layered dielectric can be determined from arbitrary voxel models.  
 
-It was shown in [BB17b], [BKB19], and [BB19] that the results from this layer modeling approach fit well to the results that 
+It was shown in [Bru24], [BB17b], [BKB19], and [BB19] that the results from this layer modeling approach fit well to the results that 
 have been published in the literature so far for similar transmission setups. For more details on this modeling
-technique refer to [BB17b] or [TT+12]. The actual results in [BB17a], [BB17b], [BB17c] and [BKB19] were computed using MATLAB. 
+technique refer to [Bru24]. The actual results in [BB17a], [BB17b], [BB17c] and [BKB19] were computed using MATLAB. 
 `LayerModel_lib` is a Python implementation of the same functionality. 
 
 The results from [BB19] were simulated using this library and the resulting data 
@@ -23,8 +23,8 @@ can be found in int/in-body/ismict2019>.
 This code is distributed under [MIT license](LICENSE). When using this code or parts of it for publications or research
 please cite this repository as:
 
-[Bru19] J.-C. Brumm, "LayerModel_lib. A Python toolkit to compute the transmission behaviour of plane 
-electromagnetic waves through human tissue." DOI: 10.5281/zenodo.3507610 
+[Bru23] J.-C. Brumm, "LayerModel_lib. A Python toolkit to compute the transmission behaviour of plane 
+electromagnetic waves through human tissue." DOI: 10.5281/zenodo.10459541 
 
 ## Installation and Requirements
 1. Download and install at least Python 3.6
@@ -80,6 +80,9 @@ More examples can be found in the [examples](examples/README.md) folder.
 
 ## References 
 
+[Bru24] J.-C. Brumm, "Channel Modeling and Performance Analysis of Ultra Wideband In-Body Communication", 
+PhD thesis, TU Hamburg, 2024, https://doi.org/10.15480/882.9047
+
 [BB19] J.-C. Brumm, and G. Bauch, “Influence of Physiological Properties on the
 Channel Capacity for Ultra Wideband In-Body Communication,” in *13th International Symposium on Medical 
 Information and Communication Technology (ISMICT'2019)*. Oslo, 2019.