Merge branch '2.4.0' into 'master'

Version update for new release.

See merge request inm-1/fa/sli/tools/slix!23

.gitlab-ci.yml

@@ -1,42 +1,59 @@
+include:
+    - template: Code-Quality.gitlab-ci.yml
+
 stages:
     - test
     - install
     - pack
 
-before_script:
-    - apt-get update -qq && apt-get upgrade -y
-    - apt-get install -y python3 python3-pip
-    - /usr/bin/python3 -m pip install --upgrade pip
+code_quality_html:
+  extends: code_quality
+  variables:
+    REPORT_FORMAT: html
+  artifacts:
+    paths: [gl-code-quality-report.html]
 
-lint:python3:
+test:python3:
     stage: test
-    allow_failure: true
     image: cupy/cupy:v8.0.0
     script:
-        - pip3 install flake8
-        - flake8 SLIX/ --count --select=E9,F63,F7,F82 --show-source --statistics
-        - flake8 SLIX/ --count --exit-zero --max-complexity=10 --statistics
+        - apt-get update -qq && apt-get upgrade -y
+        - apt-get install -y python3 python3-pip
+        - /usr/bin/python3 -m pip install --upgrade pip
+        - pip3 install tifffile numpy nibabel h5py pillow numba matplotlib pytest pytest-cov
+        # Online preview of tests that did run successfully
+        - pytest tests --junitxml=report.xml    
+    artifacts:
+        when: always
+        reports:
+            junit: report.xml
     tags:
         - docker
-        - gpu
-
-test:python3:
+        - gpu 
+        
+test_with_coverage:python3:
     stage: test
     image: cupy/cupy:v8.0.0
     script:
+        - apt-get install -y python3 python3-pip
+        - /usr/bin/python3 -m pip install --upgrade pip
         - pip3 install tifffile numpy nibabel h5py pillow numba matplotlib pytest pytest-cov
-        - pytest --cov=SLIX --cov-config=.coveragerc tests --cov-report=html
+        - coverage run -m pytest --cov-config=.coveragerc tests
+        - coverage report
+        - coverage xml
     artifacts:
-            paths:
-                - htmlcov/
-    tags:
-        - docker
-        - gpu 
+        reports:
+            cobertura: coverage.xml
+    only:
+        - merge_requests
 
 install:python3:
     stage: install
     image: cupy/cupy:v8.0.0
     script:
+        - apt-get update -qq && apt-get upgrade -y
+        - apt-get install -y python3 python3-pip
+        - /usr/bin/python3 -m pip install --upgrade pip
         - pip3 install .
     tags:
     - docker
@@ -46,8 +63,11 @@ pack:python3:
     stage: pack
     image: cupy/cupy:v8.0.0
     script:
+        - apt-get update -qq && apt-get upgrade -y
+        - apt-get install -y python3 python3-pip
+        - /usr/bin/python3 -m pip install --upgrade pip
         - pip3 install pep517
         - python3 -m pep517.build --source --binary --out-dir dist/ .
     tags:
     - docker
-    - gpu 
+    - gpu 

CHANGELOG.md

@@ -1,5 +1,29 @@
 # Changelog
 
+## v2.4.0
+### Added
+- Added vector weighting option available for SLIXVisualizeParameter with the parameter `--weight_map`. This parameter is used to weight the length of the shown vectors in both the unit vector visualization as well as the vector distribution.
+- Added new options to SLIXVisualizeParameter to allow the user to customize the appearance of the resulting parameter maps such as the vector maps and the FOM.
+- Added a new interface to SLIX.visualize called Colormaps. This class contains basic colormaps that can be used to visualize the results of the SLIX.visualize methods.
+- Currently this class holds the following color maps:
+  - Colomaps.rgb
+  - Colormaps.hsv_black
+  - Colormaps.hsv_white
+  - Colormaps.hsv_black_reverse
+  - Colormaps.hsv_white_reverse
+  - Colormaps.rgb_reverse
+- Added command line parameters for the user to choose the color maps when calling SLIXVisualizeParameter (`-c, --colormap`).
+- Added a new color_bubble method to SLIX.visualize.
+- Added an inclination parameter to SLIXVisualizeParameter [...] fom to allow the user to choose the inclination of the FOM.
+- 
+### Changed
+- When calling SLIXVisualizeParameter, a color bubble associated with the written image will be written as well. This can be disabled by using the `--disable_colorbubble` option.
+- Added a new method to SLIX.toolbox to get unit vectors from both direction and inclination images (3D instead of 2D only).
+- Added the name of the color map to the filename.
+- Added optional paramer name for the directions in SLIXVisualizeParameter (`--direction`).
+- 
+### Fixed
+- Fixed a bug in SLIXVisualizeParameter and SLIX.visualize.unit_vectors which caused the unit vectors to be drawn in the wrong direction.
 
 ## v2.3.0
 ### Added

SLIX/CPU/_toolbox.py

@@ -133,7 +133,7 @@ def _peakdistance(peak_image, centroids, number_of_peaks):
                 elif number_of_peaks[idx] % 2 == 0:
                     left = (i + sub_centroid_array[i]) * 360.0 / \
                            len(sub_peak_array)
-                    right_side_peak = number_of_peaks[idx]//2
+                    right_side_peak = number_of_peaks[idx] // 2
                     current_position = i
                     while right_side_peak > 0 and \
                             current_position < len(sub_peak_array):
@@ -152,7 +152,7 @@ def _peakdistance(peak_image, centroids, number_of_peaks):
 
                     current_pair += 1
 
-                if current_pair == number_of_peaks[idx]//2:
+                if current_pair == number_of_peaks[idx] // 2:
                     break
     return result_image
 
@@ -204,8 +204,8 @@ def _direction(peak_array, centroids, number_of_peaks, num_directions, correctdi
                         if right_side_peak == 0:
                             right = (current_position +
                                      sub_centroid_array[current_position]) * \
-                                     360.0 / len(sub_peak_array) + \
-                                     numpy.float32(correctdir)
+                                    360.0 / len(sub_peak_array) + \
+                                    numpy.float32(correctdir)
                             # If our peaks are around 180° ± 35° apart,
                             # we can calculate the direction.
                             if number_of_peaks[idx] > 2 and \
@@ -217,7 +217,7 @@ def _direction(peak_array, centroids, number_of_peaks, num_directions, correctdi
                                 (270.0 - ((left + right) / 2.0)) % 180
                             current_direction += 1
 
-                    if current_direction == number_of_peaks[idx]//2:
+                    if current_direction == number_of_peaks[idx] // 2:
                         break
     return result_image
 

SLIX/CPU/toolbox.py

@@ -474,3 +474,30 @@ def unit_vectors(direction):
     UnitY[numpy.isclose(direction, -1)] = 0
 
     return UnitX, UnitY
+
+
+def unit_vectors_3d(direction, inclination):
+    """
+    Calculate the unit vectors (UnitX, UnitY, UnitZ) from a given direction angle.
+
+    Args:
+
+        direction: 3D NumPy array - direction angles in degrees
+
+        inclination: 3D NumPy array - inclination angles in degrees
+
+    Returns:
+
+        UnitX, UnitY, UnitZ: 3D NumPy array, 3D NumPy array
+            x- and y-vector component in arrays
+    """
+    directions_rad = numpy.deg2rad(direction)
+    UnitX = -numpy.sin(0.5 * numpy.pi) * numpy.cos(directions_rad)
+    UnitY = numpy.sin(0.5 * numpy.pi) * numpy.sin(directions_rad)
+    UnitZ = numpy.sin(inclination)
+
+    UnitX[numpy.isclose(direction, -1)] = 0
+    UnitY[numpy.isclose(direction, -1)] = 0
+    UnitZ[numpy.isclose(direction, -1)] = 0
+
+    return UnitX, UnitY, UnitZ

SLIX/GPU/toolbox.py

@@ -656,3 +656,44 @@ def unit_vectors(direction, return_numpy=True):
     if return_numpy:
         return UnitX.get(), UnitY.get()
     return UnitX, UnitY
+
+
+def unit_vectors_3d(direction, inclination, return_numpy=True):
+    """
+    Calculate the unit vectors (UnitX, UnitY, UnitZ) from a given direction angle.
+
+    Args:
+
+        direction: 3D NumPy array - direction angles in degrees
+
+        inclination: 3D NumPy array - inclination angles in degrees
+
+        return_numpy: Necessary if using `use_gpu`. Specifies if a CuPy or Numpy
+        array will be returned.
+
+    Returns:
+
+        UnitX, UnitY, UnitZ: 3D NumPy array, 3D NumPy array
+            x- and y-vector component in arrays
+    """
+    direction_gpu = cupy.array(direction)
+    direction_gpu_rad = cupy.deg2rad(direction_gpu)
+    UnitX = -cupy.sin(0.5 * cupy.pi) * cupy.cos(direction_gpu_rad)
+    UnitY = cupy.sin(0.5 * cupy.pi) * cupy.sin(direction_gpu_rad)
+    del direction_gpu_rad
+
+    UnitX[cupy.isclose(direction_gpu, -1)] = 0
+    UnitY[cupy.isclose(direction_gpu, -1)] = 0
+
+    inclination_gpu = cupy.array(inclination)
+    inclination_gpu_rad = cupy.deg2rad(inclination_gpu)
+    UnitZ = cupy.sin(inclination_gpu_rad)
+    del inclination_gpu_rad
+
+    UnitZ[cupy.isclose(direction_gpu, -1)] = 0
+    del direction_gpu
+    del inclination_gpu
+
+    if return_numpy:
+        return UnitX.get(), UnitY.get(), UnitZ.get()
+    return UnitX, UnitY, UnitZ

SLIX/__init__.py

@@ -1,8 +1,9 @@
 """
-Scattered Light Imaging ToolboX (SLIX) – an open-source Python package that allows a fully automated evaluation of SLI measurements and the generation of different parameter maps
+Scattered Light Imaging ToolboX (SLIX) – an open-source Python package that allows a fully automated evaluation of SLI
+measurements and the generation of different parameter maps
 """
-__version__ = '2.3.0'
+__version__ = '2.4.0-alpha2'
 __all__ = ['toolbox', 'io', 'visualization', 'preparation',
-           'attributemanager']
+           'attributemanager', 'classification']
 
-from . import toolbox, io, visualization, preparation, attributemanager
+from . import toolbox, io, visualization, preparation, attributemanager, classification