Remove redundant "Optimized-" models (#196)

* Remove redundant "Optimized-" models

* Remove references in swcc project

* Lint fix of migration file

* Remove reference in tasks

* Remove implicit references in swcc project

shapeworks_cloud/core/filters.py

@@ -67,16 +67,8 @@ class Meta:
         fields = ['project', 'mesh']
 
 
-class OptimizedShapeModelFilter(FilterSet):
-    project = ModelChoiceFilter(queryset=models.Project.objects.all())
-
-    class Meta:
-        models = models.OptimizedShapeModel
-        fields = ['project']
-
-
 class OptimizedParticlesFilter(FilterSet):
-    shape_model = ModelChoiceFilter(queryset=models.OptimizedShapeModel.objects.all())
+    project = ModelChoiceFilter(queryset=models.Project.objects.all())
     original_segmentation = ModelChoiceFilter(
         field_name='groomed_segmentation__segmentation',
         queryset=models.Segmentation.objects.all(),
@@ -97,11 +89,3 @@ class Meta:
             'original_segmentation',
             'original_mesh',
         ]
-
-
-class OptimizedPCAModelFilter(FilterSet):
-    shape_model = ModelChoiceFilter(queryset=models.OptimizedShapeModel.objects.all())
-
-    class Meta:
-        models = models.OptimizedParticles
-        fields = ['shape_model']

shapeworks_cloud/core/migrations/0013_remove_redundant_models.py

@@ -0,0 +1,50 @@
+# Generated by Django 3.2.15 on 2022-09-27 14:38
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('core', '0012_analysis_models'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='optimizedshapemodel',
+            name='project',
+        ),
+        migrations.RemoveField(
+            model_name='optimizedsurfacereconstruction',
+            name='particles',
+        ),
+        migrations.RemoveField(
+            model_name='optimizedsurfacereconstructionmeta',
+            name='shape_model',
+        ),
+        migrations.RemoveField(
+            model_name='optimizedparticles',
+            name='shape_model',
+        ),
+        migrations.AddField(
+            model_name='optimizedparticles',
+            name='project',
+            field=models.ForeignKey(
+                default=None, on_delete=django.db.models.deletion.CASCADE, to='core.project'
+            ),
+            preserve_default=False,
+        ),
+        migrations.DeleteModel(
+            name='OptimizedPCAModel',
+        ),
+        migrations.DeleteModel(
+            name='OptimizedShapeModel',
+        ),
+        migrations.DeleteModel(
+            name='OptimizedSurfaceReconstruction',
+        ),
+        migrations.DeleteModel(
+            name='OptimizedSurfaceReconstructionMeta',
+        ),
+    ]

shapeworks_cloud/core/models.py

@@ -109,26 +109,13 @@ class GroomedMesh(TimeStampedModel, models.Model):
     project = models.ForeignKey(Project, on_delete=models.CASCADE, related_name='groomed_meshes')
 
 
-class OptimizedShapeModel(TimeStampedModel, models.Model):
-    project = models.ForeignKey(
-        Project,
-        on_delete=models.CASCADE,
-        related_name='optimized_shape_models',
-    )
-    parameters = models.JSONField(default=dict)
-
-
 class OptimizedParticles(TimeStampedModel, models.Model):
+    project = models.ForeignKey(Project, on_delete=models.CASCADE)
     world = S3FileField()
     local = S3FileField()
     transform = S3FileField()
     constraints = S3FileField(null=True)
 
-    shape_model = models.ForeignKey(
-        OptimizedShapeModel,
-        on_delete=models.CASCADE,
-        related_name='particles',
-    )
     groomed_segmentation = models.ForeignKey(
         GroomedSegmentation,
         on_delete=models.CASCADE,
@@ -143,41 +130,3 @@ class OptimizedParticles(TimeStampedModel, models.Model):
         blank=True,
         null=True,
     )
-
-
-class OptimizedSurfaceReconstructionMeta(TimeStampedModel, models.Model):
-    method = models.CharField(max_length=255)  # TODO: Should be choices
-    reconstruction_params = S3FileField()
-    template_reconstruction = S3FileField()
-
-    shape_model = models.ForeignKey(
-        OptimizedShapeModel,
-        on_delete=models.CASCADE,
-        related_name='+',
-    )
-
-
-class OptimizedSurfaceReconstruction(TimeStampedModel, models.Model):
-    particles = models.OneToOneField(
-        OptimizedParticles,
-        on_delete=models.CASCADE,
-        related_name='surface_reconstruction',
-        primary_key=True,
-    )
-    sample_reconstruction = S3FileField()
-
-
-class OptimizedPCAModel(TimeStampedModel, models.Model):
-    shape_model = models.OneToOneField(
-        OptimizedShapeModel,
-        on_delete=models.CASCADE,
-        related_name='pca_model',
-        primary_key=True,
-    )
-
-    mean_particles = S3FileField()
-    pca_modes = S3FileField()
-    eigen_spectrum = S3FileField()
-
-
-# TODO: checkpoints... what about pca model reference?

shapeworks_cloud/core/rest.py

@@ -116,34 +116,12 @@ class GroomedMeshViewSet(BaseViewSet):
     filterset_class = filters.GroomedMeshFilter
 
 
-class OptimizedShapeModelViewSet(BaseViewSet):
-    queryset = models.OptimizedShapeModel.objects.all()
-    serializer_class = serializers.OptimizedShapeModelSerializer
-    filterset_class = filters.OptimizedShapeModelFilter
-
-
 class OptimizedParticlesViewSet(BaseViewSet):
     queryset = models.OptimizedParticles.objects.all()
     serializer_class = serializers.OptimizedParticlesSerializer
     filterset_class = filters.OptimizedParticlesFilter
 
 
-class OptimizedSurfaceReconstructionMetaViewSet(BaseViewSet):
-    queryset = models.OptimizedSurfaceReconstructionMeta.objects.all()
-    serializer_class = serializers.OptimizedSurfaceReconstructionMetaSerializer
-
-
-class OptimizedSurfaceReconstructionViewSet(BaseViewSet):
-    queryset = models.OptimizedSurfaceReconstruction.objects.all()
-    serializer_class = serializers.OptimizedSurfaceReconstructionSerializer
-
-
-class OptimizedPCAModelViewSet(BaseViewSet):
-    queryset = models.OptimizedPCAModel.objects.all()
-    serializer_class = serializers.OptimizedPCAModelSerializer
-    filterset_class = filters.OptimizedPCAModelFilter
-
-
 class CachedAnalysisViewSet(BaseViewSet):
     queryset = models.CachedAnalysis.objects.all()
 

shapeworks_cloud/core/serializers.py

@@ -122,14 +122,6 @@ def get_id(self, obj) -> int:
         return obj.mesh_id
 
 
-class OptimizedShapeModelSerializer(serializers.ModelSerializer):
-    parameters = serializers.DictField()
-
-    class Meta:
-        model = models.OptimizedShapeModel
-        fields = '__all__'
-
-
 class OptimizedParticlesSerializer(serializers.ModelSerializer):
     world = S3FileSerializerField()
     local = S3FileSerializerField()
@@ -139,34 +131,3 @@ class OptimizedParticlesSerializer(serializers.ModelSerializer):
     class Meta:
         model = models.OptimizedParticles
         fields = '__all__'
-
-
-class OptimizedSurfaceReconstructionMetaSerializer(serializers.ModelSerializer):
-    reconstruction_params = S3FileSerializerField()
-    template_reconstruction = S3FileSerializerField()
-
-    class Meta:
-        model = models.OptimizedSurfaceReconstructionMeta
-        fields = '__all__'
-
-
-class OptimizedSurfaceReconstructionSerializer(serializers.ModelSerializer):
-    sample_reconstruction = S3FileSerializerField()
-
-    class Meta:
-        model = models.OptimizedSurfaceReconstruction
-        fields = '__all__'
-
-
-class OptimizedPCAModelSerializer(serializers.ModelSerializer):
-    id = serializers.SerializerMethodField()
-    mean_particles = S3FileSerializerField()
-    pca_modes = S3FileSerializerField()
-    eigen_spectrum = S3FileSerializerField()
-
-    class Meta:
-        model = models.OptimizedPCAModel
-        fields = '__all__'
-
-    def get_id(self, obj) -> int:
-        return obj.shape_model.id

shapeworks_cloud/core/tasks.py

@@ -189,7 +189,7 @@ def post_command_function(project, download_dir, project_dfs, project_filename):
 def optimize(user_id, project_id, form_data):
     def pre_command_function():
         # delete any previous results
-        models.OptimizedShapeModel.objects.filter(project=project_id).delete()
+        models.OptimizedParticles.objects.filter(project=project_id).delete()
 
     def post_command_function(project, download_dir, project_dfs, project_filename):
         save_dfs_to_project_spreadsheet(
@@ -211,13 +211,10 @@ def post_command_function(project, download_dir, project_dfs, project_filename):
             target_mesh = project_groomed_meshes.filter(
                 file__endswith=groomed_filename,
             ).first()
-            result_shape_object = models.OptimizedShapeModel.objects.create(
-                project=project, parameters=form_data
-            )
             result_particles_object = models.OptimizedParticles.objects.create(
                 groomed_segmentation=target_segmentation,
                 groomed_mesh=target_mesh,
-                shape_model=result_shape_object,
+                project=project,
             )
             result_particles_object.world.save(
                 row['world_particles_1'].split('/')[-1],

shapeworks_cloud/urls.py

@@ -20,15 +20,9 @@
     'groomed-segmentations', rest.GroomedSegmentationViewSet, basename='groomed_segmentation'
 )
 router.register('groomed-meshes', rest.GroomedMeshViewSet, basename='groomed_mesh')
-router.register(
-    'optimized-shape-models', rest.OptimizedShapeModelViewSet, basename='optimized_shape_model'
-)
 router.register(
     'optimized-particles', rest.OptimizedParticlesViewSet, basename='optimized_particles'
 )
-router.register(
-    'optimized-pca-model', rest.OptimizedPCAModelViewSet, basename='optimized_pca_model'
-)
 router.register('cached-analysis', rest.CachedAnalysisViewSet, basename='cached_analysis')
 router.register(
     'cached-analysis-mode', rest.CachedAnalysisModeViewSet, basename='cached_analysis_mode'

swcc/swcc/models/__init__.py

@@ -5,8 +5,6 @@
     Image,
     Mesh,
     OptimizedParticles,
-    OptimizedPCAModel,
-    OptimizedShapeModel,
     Segmentation,
 )
 from .project import Project
@@ -19,8 +17,6 @@
     'Image',
     'Mesh',
     'OptimizedParticles',
-    'OptimizedPCAModel',
-    'OptimizedShapeModel',
     'Project',
     'Segmentation',
     'Subject',

swcc/swcc/models/other_models.py

@@ -1,14 +1,9 @@
 from __future__ import annotations
 
-from pathlib import Path
-
 try:
-    from typing import Any, Dict, Iterator, List, Literal, Optional
+    from typing import List, Literal, Optional
 except ImportError:
     from typing import (
-        Any,
-        Dict,
-        Iterator,
         List,
         Optional,
     )
@@ -67,57 +62,18 @@ class GroomedMesh(ApiModel):
     project: Project
 
 
-class OptimizedShapeModel(ApiModel):
-    _endpoint = 'optimized-shape-models'
-
-    project: Project
-    parameters: Dict[str, Any]
-
-    @property
-    def particles(self) -> Iterator[OptimizedParticles]:
-        return OptimizedParticles.list(shape_model=self)
-
-    def add_particles(
-        self,
-        world: Path,
-        local: Path,
-        transform: Path,
-        groomed_segmentation: Optional[GroomedSegmentation],
-        groomed_mesh: Optional[GroomedMesh],
-        constraints: Path,
-    ) -> OptimizedParticles:
-        return OptimizedParticles(
-            world=world,
-            local=local,
-            transform=transform,
-            shape_model=self,
-            groomed_segmentation=groomed_segmentation,
-            groomed_mesh=groomed_mesh,
-            constraints=constraints,
-        ).create()
-
-
 class OptimizedParticles(ApiModel):
     _endpoint = 'optimized-particles'
 
     world: FileType[Literal['core.OptimizedParticles.world']]
     local: FileType[Literal['core.OptimizedParticles.local']]
     transform: FileType[Literal['core.OptimizedParticles.transform']]
-    shape_model: OptimizedShapeModel
+    project: Project
     groomed_segmentation: Optional[GroomedSegmentation]
     groomed_mesh: Optional[GroomedMesh]
     constraints: Optional[FileType[Literal['core.OptimizedParticles.constraints']]] = None
 
 
-class OptimizedPCAModel(ApiModel):
-    _endpoint = 'optimized-pca-model'
-
-    mean_particles: FileType[Literal['core.OptimizedPCAModel.mean_particles']]
-    pca_modes: FileType[Literal['core.OptimizedPCAModel.pca_modes']]
-    eigen_spectrum: FileType[Literal['core.OptimizedPCAModel.eigen_spectrum']]
-    shape_model: OptimizedShapeModel
-
-
 class CachedAnalysisModePCA(ApiModel):
     _endpoint = 'cached-analysis-mode-pca'
 
@@ -152,6 +108,4 @@ class CachedAnalysis(ApiModel):
 Image.update_forward_refs()
 GroomedSegmentation.update_forward_refs()
 GroomedMesh.update_forward_refs()
-OptimizedShapeModel.update_forward_refs()
 OptimizedParticles.update_forward_refs()
-OptimizedPCAModel.update_forward_refs()