Merge branch 'main' of https://github.com/IPASC/PACFISH

# Conflicts:
#	pacfish/iohandler/file_reader.py
#	pacfish_matlab/@kwave_adapter/kwave_adapter.m

.github/workflows/continuous-integration-testing.yml

@@ -5,7 +5,7 @@ name: Test PACFISH
 
 on:
   push:
-    branches: [ main ]
+    branches: [ main, release ]
   pull_request:
     branches: [ main ]
 
@@ -56,17 +56,3 @@ jobs:
         pip install
         build
         --user
-    - name: Build a binary wheel and a source tarball
-      if: github.repository == 'IPASC/PACFISH' && matrix.python-version == 3.9 && matrix.os == 'ubuntu-latest'
-      run: >-
-        python -m
-        build
-        --sdist
-        --wheel
-        --outdir dist/
-        .
-    - name: Publish to PyPI
-      if: github.repository == 'IPASC/PACFISH' && matrix.python-version == 3.9 && matrix.os == 'ubuntu-latest'
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        password: ${{ secrets.PYPI }}

.github/workflows/release_integration.yml

@@ -0,0 +1,57 @@
+# This workflow will install Python dependencies, run unit_tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Test PACFISH
+
+on:
+  push:
+    branches: [release ]
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      python-version: ["3.9"]
+      os: [ubuntu-latest]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        python -m pip install -r requirements.txt
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest --cov=pacfish --cov-report=xml --cov-report=term-missing
+        coverage xml
+    - name: Install pypa/build
+      run: >-
+        python -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: >-
+        python -m
+        build
+        --sdist
+        --wheel
+        --outdir dist/
+        .
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.PYPI }}

CONTRIBUTING.md

@@ -6,10 +6,12 @@ people that have contributed to this project.
 
 | Name | Institution | Contributions |
 | ---- | --- | ------------- |
+| Ben Cox | University College London | MATLAB API |
 | Kris Dreher | German Cancer Research Center | IO Handling |
 | Janek Gröhl | University of Cambridge | General Maintenance; Python API |
 | Lina Hacker | University of Cambridge | Python API |
 | François Varray | Creatis, Université de Lyon | MATLAB API |
+| Jeffrey Sackey | University College London | MATLAB API |
 | Lawrence Yip | Lawson Health Research Institute | Adapter Implementation, Bug Fixing |
 
 # How to contribute

VERSION

@@ -1 +1 @@
-0.4.3
+0.4.5

pacfish/visualize_device.py

@@ -27,6 +27,8 @@ def visualize_device(device_dictionary: dict, save_path: str = None, title: str
         Optional parameter whether the figure legend should be shown (default: True)
     """
 
+    MARGIN = 0.001
+
     def define_boundary_values(_device_dictionary: dict):
         mins = np.ones(3) * 100000
         maxs = np.ones(3) * -100000
@@ -59,17 +61,20 @@ def define_boundary_values(_device_dictionary: dict):
             if fov[2 * i + 1] > maxs[i]:
                 maxs[i] = fov[2 * i + 1]
 
-        MARGIN = 0.001
         maxs += MARGIN
         mins -= MARGIN
         return mins, maxs
 
     def add_arbitrary_plane(_device_dictionary: dict, _mins, _maxs, _axes, _draw_axis):
         _draw_axis.set_xlim(_mins[_axes[0]], _maxs[_axes[0]])
         _draw_axis.set_ylim(_maxs[_axes[1]], _mins[_axes[1]])
+        x_ticks = np.asarray(np.round(np.linspace(_mins[_axes[0]] + MARGIN, _maxs[_axes[0]] - MARGIN, 5), decimals=4))
+        y_ticks = np.asarray(np.round(np.linspace(_mins[_axes[1]] + MARGIN, _maxs[_axes[1]] - MARGIN, 5), decimals=4))
+        _draw_axis.set_xticks(x_ticks, x_ticks*100)
+        _draw_axis.set_yticks(y_ticks, y_ticks * 100)
         _draw_axis.set_title(f"axes {_axes[0]}/{_axes[1]} projection view")
-        _draw_axis.set_xlabel(f"{_axes[0]}-axis [m]")
-        _draw_axis.set_ylabel(f"{_axes[1]}-axis [m]")
+        _draw_axis.set_xlabel(f"{_axes[0]}-axis [cm]")
+        _draw_axis.set_ylabel(f"{_axes[1]}-axis [cm]")
 
         fov = _device_dictionary["general"][MetadataDeviceTags.FIELD_OF_VIEW.tag]
 
@@ -84,10 +89,10 @@ def add_arbitrary_plane(_device_dictionary: dict, _mins, _maxs, _axes, _draw_axi
                 _device_dictionary["detectors"][detector][MetadataDeviceTags.DETECTOR_GEOMETRY.tag])
 
             if detector_geometry_type == "CUBOID":
-                if detector_geometry[_axes[0]] == 0:
-                    detector_geometry[_axes[0]] = 0.0001
-                if detector_geometry[_axes[1]] == 0:
-                    detector_geometry[_axes[1]] = 0.0001
+                if detector_geometry[_axes[0]] < 0.001:
+                    detector_geometry[_axes[0]] = 0.001
+                if detector_geometry[_axes[1]] < 0.001:
+                    detector_geometry[_axes[1]] = 0.001
                 _draw_axis.add_patch(Rectangle((detector_position[_axes[0]] - detector_geometry[_axes[0]] / 2,
                                                 detector_position[_axes[1]] - detector_geometry[_axes[1]] / 2),
                                                detector_geometry[_axes[0]], detector_geometry[_axes[1]], color="blue"))
@@ -147,8 +152,8 @@ def add_arbitrary_plane(_device_dictionary: dict, _mins, _maxs, _axes, _draw_axi
         plt.figure(figsize=(10, 4))
     plt.suptitle(title)
     ax = plt.subplot(1, num_subplots, 1)
-    ax.axes.xaxis.set_visible(False)
-    ax.axes.yaxis.set_visible(False)
+    # ax.axes.xaxis.set_visible(False)
+    # ax.axes.yaxis.set_visible(False)
     add_arbitrary_plane(device_dictionary, mins, maxs, _axes=(0, 2), _draw_axis=ax)
     if not only_show_xz:
         ax = plt.subplot(1, num_subplots, 2)

pacfish_matlab/@kwave_adapter/kwave_adapter.m

@@ -24,7 +24,7 @@
     end
 
     methods
-                
+
         %% Constructor for the api
         function obj = kwave_adapter(varargin)
             if (nargin<=4)
@@ -274,8 +274,8 @@
                             orientation3 = 180 - acosd(costheta3);	
                             % Stores the 3 orientations made as the
                             % detector orientation
+
                             device_struct.detectors.(index).detector_orientation = [orientation1 orientation3 orientation2];
-
                             device_struct.detectors.(index).detector_geometry = [elem.length elem.width elem.length];
                         end
                     case 3 % 2D with position elements used as detector
@@ -429,6 +429,7 @@
                         end
                 end
 
+
                 if any(obj.fov) % Checks whether FOV was given as an input (was previously checked above)
                     device_struct.general.field_of_view = obj.fov; 
                 else