Merge branch 'feature/qt6-optim' into 'develop'

Change decorators

See merge request !8

src/gnomon_package_tissueimagemesh/algorithm/cellComplexFromCellImage/cellReconstructionDracoStem.py

@@ -9,11 +9,11 @@ from cellcomplex.property_topomesh.analysis import compute_topomesh_property
 from cellcomplex.property_topomesh.extraction import clean_topomesh
 from timagetk_geometry.draco import DracoMesh
 
-from gnomon.utils import corePlugin
+from gnomon.utils import algorithmPlugin
 from gnomon.utils.decorators import cellImageInput, cellComplexOutput
 
 
-@corePlugin(version="0.3.0", coreversion="0.81.0", name="DRACO Reconstruction")
+@algorithmPlugin(version="0.3.0", coreversion="0.81.0", name="DRACO Reconstruction")
 @cellImageInput('tissue', data_plugin="gnomonCellImageDataTissueImage")
 @cellComplexOutput('topomesh', data_plugin="gnomonCellComplexDataPropertyTopomesh")
 class cellReconstructionDracoStem(gnomonAbstractCellComplexFromCellImage):

src/gnomon_package_tissueimagemesh/algorithm/cellComplexFromCellImage/cellReconstructionGrifone.py

@@ -10,11 +10,11 @@ from cellcomplex.property_topomesh.extraction import clean_topomesh
 
 from timagetk_geometry.grifone.grifone import segmentation_topological_element_cell_topomesh
 
-from gnomon.utils import corePlugin
+from gnomon.utils import algorithmPlugin
 from gnomon.utils.decorators import cellImageInput, cellComplexOutput
 
 
-@corePlugin(version="0.3.0", coreversion="0.81.0", name="GRIFONE Reconstruction")
+@algorithmPlugin(version="0.3.0", coreversion="0.81.0", name="GRIFONE Reconstruction")
 @cellImageInput('seg_img', data_plugin="gnomonCellImageDataTissueImage")
 @cellComplexOutput('element_topomesh', data_plugin="gnomonCellComplexDataPropertyTopomesh")
 class cellReconstructionGrifone(gnomonAbstractCellComplexFromCellImage):

src/gnomon_package_tissueimagemesh/algorithm/meshFromImage/imageSurfaceMesh.py

@@ -7,7 +7,7 @@ from dtkcore import d_int, d_inliststring, d_real
 import gnomon.core
 from gnomon.core import gnomonAbstractMeshFromImage
 
-from gnomon.utils import corePlugin
+from gnomon.utils import algorithmPlugin
 
 from gnomon.utils.decorators import imageInput, meshOutput
 
@@ -18,7 +18,7 @@ from cellcomplex.property_topomesh.creation import triangle_topomesh
 from cellcomplex.utils import array_dict
 
 
-@corePlugin(version="0.3.0", coreversion="0.81.0", name="Surface Mesh")
+@algorithmPlugin(version="0.3.0", coreversion="0.81.0", name="Surface Mesh")
 @imageInput("img", data_plugin='gnomonImageDataMultiChannelImage')
 @meshOutput("topomesh", data_plugin="gnomonMeshDataPropertyTopomesh")
 class imageSurfaceMesh(gnomonAbstractMeshFromImage):

src/gnomon_package_tissueimagemesh/algorithm/meshFromImage/segmentationSurfaceMesh.py

@@ -7,7 +7,7 @@ from dtkcore import d_bool, d_int, d_inliststring, d_real
 import gnomon.core
 from gnomon.core import gnomonAbstractMeshFromImage
 
-from gnomon.utils import corePlugin
+from gnomon.utils import algorithmPlugin
 
 from gnomon.utils.decorators import cellImageInput, meshOutput
 
@@ -16,7 +16,7 @@ from timagetk_geometry.image_surface.tissue_image_mesh import tissue_image_surfa
 from cellcomplex.property_topomesh.analysis import compute_topomesh_property
 
 
-@corePlugin(version="0.3.0", coreversion="0.81.0", name="Segmentation Surface Mesh")
+@algorithmPlugin(version="0.3.0", coreversion="0.81.0", name="Segmentation Surface Mesh")
 @cellImageInput("seg_img", data_plugin='gnomonCellImageDataTissueImage')
 @meshOutput("topomesh", data_plugin="gnomonMeshDataPropertyTopomesh")
 class segmentationSurfaceMesh(gnomonAbstractMeshFromImage):
@@ -34,6 +34,7 @@ class segmentationSurfaceMesh(gnomonAbstractMeshFromImage):
         self._parameters['orientation'] = d_inliststring('Orientation', "up", ["up", "down"], "Whether to keep upper or lower part")
         self._parameters['down_facing_threshold'] = d_real("Normal z threshold", 0, -1, 1, 2, "The z coordinate below which a normal vector is considered to face downwards")
         self._parameters['fill_holes'] = d_bool("Fill holes", False, "Whether to fill holes in the segmented image to generate the surface mesh")
+        self._parameters['padding'] = d_bool("Padding", False, "Whether to pad the image with background before generating the surface mesh")
 
         self._parameter_groups = {}
 
@@ -57,7 +58,7 @@ class segmentationSurfaceMesh(gnomonAbstractMeshFromImage):
                 resampling_voxelsize=resampling_voxelsize,
                 orientation=(1 if self['orientation']=="up" else -1),
                 surface_matching='cell',
-                padding=False,
+                padding=self['padding'],
                 down_facing_threshold=self['down_facing_threshold'],
                 fill_holes=self['fill_holes']
             )

src/gnomon_package_tissueimagemesh/algorithm/meshFromImage/segmentationWallMesh.py

@@ -6,7 +6,7 @@ from dtkcore import d_bool, d_int, d_inliststringlist, d_real
 import gnomon.core
 from gnomon.core import gnomonAbstractMeshFromImage
 
-from gnomon.utils import corePlugin
+from gnomon.utils import algorithmPlugin
 from gnomon.utils.decorators import cellImageInput, meshOutput
 
 from timagetk_geometry.image_surface.wall_mesh import tissue_image_wall_topomesh
@@ -14,7 +14,7 @@ from timagetk_geometry.image_surface.wall_mesh import tissue_image_wall_topomesh
 from cellcomplex.property_topomesh.analysis import compute_topomesh_property
 
 
-@corePlugin(version="0.3.0", coreversion="0.81.0", name="Cell Wall Meshes")
+@algorithmPlugin(version="0.3.0", coreversion="0.81.0", name="Cell Wall Meshes")
 @cellImageInput("seg_img", data_plugin='gnomonCellImageDataTissueImage')
 @meshOutput("topomesh", data_plugin="gnomonMeshDataPropertyTopomesh")
 class segmentationWallMesh(gnomonAbstractMeshFromImage):