Merge pull request #283 from arayabrain/feature/microscope/main

Merge microscope format modules

.codespellignore

@@ -3,3 +3,6 @@ afterAll
 xdescribe
 optinist
 Optinist
+nnumber
+nNumber
+NNUMBER

.pre-commit-config.yaml

@@ -28,5 +28,6 @@ repos:
     rev: v2.2.4
     hooks:
     -   id: codespell
+        args: [-I, .codespellignore]
         additional_dependencies:
         -   tomli

studio/app/optinist/microscopes/.gitignore

@@ -0,0 +1,7 @@
+dll/
+testdata/
+
+/*.out.json
+/*.out.tiff
+/*.out.*.json
+/*.out.*.tiff

studio/app/optinist/microscopes/IsxdReader.py

@@ -0,0 +1,99 @@
+import sys
+
+try:
+    import isx
+except ModuleNotFoundError:
+    pass
+
+from MicroscopeDataReaderBase import MicroscopeDataReaderBase, OMEDataModel
+
+
+class IsxdReader(MicroscopeDataReaderBase):
+    """Inscopix isxd data reader"""
+
+    SDK_MODULE_NAME = "isx"
+
+    @staticmethod
+    def get_library_path() -> str:
+        """Returns the path of the library (dll) file"""
+        # Note: In inscopix SDK, library (ddl) files are not used directly.
+        return None  # do nothing.
+
+    @staticmethod
+    def is_available() -> bool:
+        """Determine if library is available"""
+        return __class__.SDK_MODULE_NAME in sys.modules
+
+    def _init_library(self):
+        # Note: in inscopix sdk, there is no library (ddl)
+        #         initialization process. (using pip module)
+        pass  # do nothing.
+
+    def _load_file(self, data_file_path: str) -> object:
+        handle = isx.Movie.read(data_file_path)
+        return (handle,)
+
+    def _build_original_metadata(self, data_name: str) -> dict:
+        movie: isx.Movie = None
+        (movie,) = self.resource_handles
+
+        spacing: isx.Spacing = movie.spacing
+        timing: isx.Timing = movie.timing
+
+        original_metadata = {
+            "data_name": data_name,
+            "spacing": {
+                "width": spacing.num_pixels[0],
+                "height": spacing.num_pixels[1],
+            },
+            "timing": {
+                "start": timing.start.to_datetime().strftime("%Y-%m-%d %H:%M:%S"),
+                "period_msec": timing.period.to_msecs(),
+                "num_samples": timing.num_samples,
+                "dropped": timing.dropped,
+                "cropped": timing.cropped,
+                "blank": timing.blank,
+            },
+        }
+
+        return original_metadata
+
+    def _build_ome_metadata(self, original_metadata: dict) -> OMEDataModel:
+        """
+        @link OME/NativeND2Reader
+        """
+
+        spacing = original_metadata["spacing"]
+        timing = original_metadata["timing"]
+
+        omeData = OMEDataModel(
+            image_name=original_metadata["data_name"],
+            size_x=spacing["width"],
+            size_y=spacing["height"],
+            size_t=timing["num_samples"],
+            size_z=0,  # Note: currently unsettled
+            size_c=0,  # Note: currently unsettled
+            acquisition_date=timing["start"],
+            objective_model=None,  # Note: currently unsettled
+            fps=(1000 / timing["period_msec"]),
+        )
+
+        return omeData
+
+    def _build_lab_specific_metadata(self, original_metadata: dict) -> dict:
+        # Note: Not currently supported
+        return None
+
+    def _release_resources(self) -> None:
+        # Note: in inscopix sdk, there is no library (ddl) release process.
+        pass  # do nothing.
+
+    def _get_image_stacks(self) -> list:
+        movie: isx.Movie = None
+        (movie,) = self.resource_handles
+
+        image_frames = [
+            movie.get_frame_data(i) for i in range(movie.timing.num_samples)
+        ]
+
+        return image_frames

studio/app/optinist/microscopes/MicroscopeDataReaderBase.py

@@ -0,0 +1,137 @@
+import os
+from abc import ABCMeta, abstractmethod
+from dataclasses import dataclass
+
+
+@dataclass
+class OMEDataModel:
+    """OME(Open Microscopy Environment) aware metadata
+    @link https://ome-model.readthedocs.io/en/stable/ome-xml/
+    """
+
+    image_name: str
+    size_x: int  # width
+    size_y: int  # height
+    size_t: int  # time frames
+    size_z: int  # axis z frames
+    size_c: int  # channels
+    acquisition_date: str
+    objective_model: str  # objective lens model
+    fps: int  # frames_per_second  # Note: extended from OME format
+
+
+class MicroscopeDataReaderBase(metaclass=ABCMeta):
+    """Microscope data reader base class"""
+
+    LIBRARY_DIR_KEY = "MICROSCOPES_LIBRARY_DIR"
+
+    def __init__(self):
+        """
+        Initialization
+        """
+        self._init_library()
+
+        # init members
+        self.__data_file_path = None
+        self.__resource_handles = None
+        self.__original_metadata = None
+        self.__ome_metadata = None
+        self.__lab_specific_metadata = None
+
+    def __del__(self):
+        """
+        Destructor
+        """
+        if self.__resource_handles is not None:
+            self._release_resources()
+            self.__resource_handles = None
+
+    def load(self, data_file_path: str):
+        """
+        Release resources
+        """
+        if self.__resource_handles is not None:
+            raise Exception("Reader module already initialized.")
+
+        """
+        Reset data
+        """
+        self.__original_metadata = None
+        self.__ome_metadata = None
+        self.__lab_specific_metadata = None
+
+        """
+        Load data file
+        """
+        handles = self._load_file(data_file_path)
+        self.__resource_handles = handles
+        self.__data_file_path = data_file_path
+        data_name = os.path.basename(data_file_path)
+
+        """
+        Read metadata
+        """
+        self.__original_metadata = self._build_original_metadata(data_name)
+        self.__ome_metadata = self._build_ome_metadata(self.__original_metadata)
+        self.__lab_specific_metadata = self._build_lab_specific_metadata(
+            self.__original_metadata
+        )
+
+    def get_image_stacks(self) -> list:
+        """Return microscope image stacks"""
+        return self._get_image_stacks()
+
+    @abstractmethod
+    def _init_library(self) -> dict:
+        """Initialize microscope library"""
+        pass
+
+    @abstractmethod
+    def _load_file(self, data_file_path: str) -> object:
+        """Return metadata specific to microscope instruments"""
+        pass
+
+    @abstractmethod
+    def _build_original_metadata(self, data_name: str) -> dict:
+        """Build metadata specific to microscope instruments"""
+        pass
+
+    @abstractmethod
+    def _build_ome_metadata(self, original_metadata: dict) -> OMEDataModel:
+        """Build OME(Open Microscopy Environment) aware metadata"""
+        pass
+
+    @abstractmethod
+    def _build_lab_specific_metadata(self, original_metadata: dict) -> dict:
+        """Build metadata in lab-specific format"""
+        pass
+
+    @abstractmethod
+    def _release_resources() -> None:
+        """Release microscope library resources"""
+        pass
+
+    @abstractmethod
+    def _get_image_stacks(self) -> list:
+        """Return microscope image stacks"""
+        pass
+
+    @property
+    def data_file_path(self) -> str:
+        return self.__data_file_path
+
+    @property
+    def resource_handles(self) -> list:
+        return self.__resource_handles
+
+    @property
+    def original_metadata(self) -> dict:
+        return self.__original_metadata
+
+    @property
+    def ome_metadata(self) -> dict:
+        return self.__ome_metadata
+
+    @property
+    def lab_specific_metadata(self) -> dict:
+        return self.__lab_specific_metadata