mobiedantic 0.1.0__py3-none-any.whl

mobiedantic/__init__.py

@@ -0,0 +1,170 @@
+from __future__ import annotations
+
+import json
+from pathlib import Path
+
+from mobiedantic.generated import Dataset as DatasetSchema
+from mobiedantic.generated import ImageDisplay, ImageDisplay1, MergedGrid, Name, Source
+from mobiedantic.generated import Project as ProjectSchema
+
+
+class Dataset:
+    path: Path
+    model: DatasetSchema = None
+
+    def __init__(self, path: Path) -> None:
+        self.path = Path(path)
+        if self.path.exists() and not self.path.is_dir():
+            message = "'path' needs to point to a directory."
+            raise ValueError(message)
+
+    def save(self, *, create_directory: bool = True):
+        if self.model is None:
+            message = 'Dataset not initialized.'
+            raise ValueError(message)
+        if not self.path.exists() and not create_directory:
+            message = "Dataset folder doesn't exist yet and may not be created."
+            raise ValueError(message)
+        self.path.mkdir(exist_ok=True)
+        with open(self.path / 'dataset.json', 'w') as dataset_file:
+            dataset_file.write(
+                json.dumps(
+                    self.model.model_dump(exclude_none=True, by_alias=True), indent=2
+                )
+            )
+
+    def load(self):
+        dataset_path = self.path / 'dataset.json'
+        if not dataset_path.exists():
+            message = f'Dataset file not found: {dataset_path}'
+            raise ValueError(message)
+        with open(dataset_path) as dataset_file:
+            data = json.loads(dataset_file.read())
+            self.model = DatasetSchema(**data)
+
+    def set_model(self, model: DatasetSchema):
+        self.model = model
+
+    def initialize_with_paths(
+        self,
+        path_dict: dict[str, Path],
+        *,
+        is2d: bool,
+        channel_index: int = 0,
+        data_format: str = 'ome.zarr',
+    ) -> None:
+        sources = {}
+        for name in path_dict:
+            try:
+                source_path = {
+                    'channel': channel_index,
+                    'relativePath': str(
+                        Path(path_dict[name]).relative_to(
+                            self.path.parent, walk_up=True
+                        )
+                    ),
+                }
+            except (ValueError, TypeError):
+                source_path = {
+                    'channel': channel_index,
+                    'absolutePath': str(Path(path_dict[name]).absolute()),
+                }
+            data = {
+                'image': {
+                    'imageData': {
+                        data_format: source_path,
+                    }
+                }
+            }
+            sources[name] = Source(**data)
+        views_dict = {'default': {'uiSelectionGroup': 'view', 'isExclusive': True}}
+        self.model = DatasetSchema(
+            is2D=is2d,
+            sources=sources,
+            views=views_dict,
+        )
+
+    def add_merged_grid(
+        self,
+        name: str,
+        sources: list[str],
+        positions: list[tuple[int, int]] | None = None,
+        *,
+        view_name: str = 'default',
+    ) -> None:
+        if self.model.views[view_name].sourceTransforms is None:
+            self.model.views[view_name].sourceTransforms = []
+        self.model.views[view_name].sourceTransforms.append(
+            MergedGrid(
+                mergedGrid={
+                    'sources': sources,
+                    'positions': positions,
+                    'mergedGridSourceName': name,
+                }
+            )
+        )
+        if self.model.views[view_name].sourceDisplays is None:
+            self.model.views[view_name].sourceDisplays = []
+        self.model.views[view_name].sourceDisplays.append(
+            ImageDisplay(
+                imageDisplay=ImageDisplay1(
+                    name=name,
+                    color='white',
+                    opacity=1.0,
+                    contrastLimits=[0, 255],  # TODO: get from histograms/data
+                    sources=[name],
+                )
+            )
+        )
+
+    # @classmethod
+    # def create(cls, path: Path, *, is2d: bool) -> "Dataset":
+    #     empty_schema = DatasetSchema(
+    #         is2D=is2d,
+    #     )
+
+
+class Project:
+    path: Path
+    model: ProjectSchema = None
+
+    def __init__(self, path: Path) -> None:
+        self.path = Path(path)
+
+    def initialize_model(self, description: str) -> None:
+        self.model = ProjectSchema(
+            datasets=[], defaultDataset='', description=description, specVersion='0.3.0'
+        )
+
+    def new_dataset(
+        self, name: str, *, make_default: bool = False, overwrite: bool = True
+    ) -> Dataset:
+        if self.model is None:
+            message = 'Project not initialized.'
+            raise ValueError(message)
+        if len(self.model.datasets) == 0:
+            make_default = True
+        dataset_folder = self.path / name
+        dataset_folder.mkdir(exist_ok=overwrite, parents=True)
+        self.model.datasets.append(Name(name))
+        if make_default:
+            self.model.defaultDataset = name
+        return Dataset(path=dataset_folder)
+
+    def save(self, *, create_directory: bool = True):
+        if self.model is None:
+            message = 'Project not initialized.'
+            raise ValueError(message)
+        if not self.path.exists() and not create_directory:
+            message = "Project folder doesn't exist yet and may not be created."
+            raise ValueError(message)
+        self.path.mkdir(exist_ok=True)
+        with open(self.path / 'project.json', 'w') as project_file:
+            project_file.write(
+                json.dumps(
+                    self.model.model_dump(exclude_none=True, by_alias=True), indent=2
+                )
+            )
+
+    # @classmethod
+    # def create(cls, path: Path) -> "Project":