Update bdv_metadata.py

.gitignore

@@ -299,3 +299,4 @@ test.xml
 /docs/source/05_reference/_autosummary
 /docs/source/05_reference/_autosummary
 codex.md
+AGENTS.MD

src/navigate/model/data_sources/bdv_data_source.py

@@ -70,9 +70,11 @@ def __init__(self, file_name: str = None, mode: str = "w") -> None:
         Parameters
         ----------
         file_name : str
-            The name of the file to write to.
-        mode : str
-            The mode to open the file in. Must be "w" for write or "r" for read.
+            Path to the output. For BDV/HDF5 use a ".h5" file; for BDV/N5 use a
+            ".n5" file; for TIFF-based filelist export use a directory containing
+            ".tif" or ".tiff" files.
+        mode : {'w', 'r'}
+            Mode to open the file in. Must be 'w' for write (export) or 'r' for read.
         """
         #: np.array: The image.
         self.image = None
@@ -86,7 +88,8 @@ def __init__(self, file_name: str = None, mode: str = "w") -> None:
         #: str: The file type.
         self.__file_type = os.path.splitext(os.path.basename(file_name))[-1][1:].lower()
 
-        if self.__file_type not in ["h5", "n5"]:
+        # Allow HDF5, N5, and TIFF (filelist) outputs for BigDataViewer metadata
+        if self.__file_type not in ["h5", "n5", "tif", "tiff"]:
             error_statement = f"Unknown file type {self.__file_type}."
             logger.error(error_statement)
             raise ValueError(error_statement)

src/navigate/model/data_sources/tiff_data_source.py

@@ -35,6 +35,7 @@
 import uuid
 from pathlib import Path
 import logging
+from typing import Dict, Any
 
 # Third Party Imports
 import tifffile
@@ -45,6 +46,7 @@
 from .data_source import DataSource, DataReader
 from ..metadata_sources.metadata import Metadata
 from ..metadata_sources.ome_tiff_metadata import OMETIFFMetadata
+from ..metadata_sources.bdv_metadata import BigDataViewerMetadata
 
 
 # Logger Setup
@@ -74,26 +76,36 @@ def __init__(
         """
         #: np.ndarray: Image data
         self.image = None
+
+        #: list: List of positions on a per-slice basis.
         self._views = []
 
         super().__init__(file_name=file_name, mode=mode)
 
         #: str: Directory to save the data to.
         self.save_directory = Path(self.file_name).parent
 
-        # Is this an OME-TIFF?
-        # TODO: check the header, rather than use the file extension
+        # Check if the file is OME-TIFF and create the appropriate metadata object
         if self.file_name.endswith(".ome.tiff") or self.file_name.endswith(".ome.tif"):
+            #: bool: Is this an OME-TIFF file?
             self._is_ome = True
+
             #: Metadata: Metadata object
             self.metadata = OMETIFFMetadata()
         else:
+            #: bool: Is this an OME-TIFF file?
             self._is_ome = False
+
+            # Metadata: Metadata object
             self.metadata = Metadata()
 
+        #: BigDataViewerMetadata: Metadata for BigDataViewer
+        self.bdv_metadata = BigDataViewerMetadata()
+
+        #: bool: Is this a bigtiff file?
         self._is_bigtiff = is_bigtiff
 
-        # For file writing, do we assume all files end with tiff or tif?
+        #: bool: For file writing, do we assume all files end with tiff or tif?
         self.__double_f = self.file_name.endswith("tiff")
 
         # Keep track of z, time, channel indices
@@ -170,7 +182,7 @@ def get_data(
         channel: int = 0,
         z: int = -1,
         resolution: int = 1,
-    ) -> npt.ArrayLike:
+    ) -> npt.ArrayLike or None:
         """Get data according to timepoint, position, channel and z-axis id
 
         Parameters
@@ -226,13 +238,18 @@ def write(self, data: npt.ArrayLike, **kw) -> None:
         data : npt.ArrayLike
             Data to write to file.
         kw : dict
-            Keyword arguments to pass to tifffile.imsave.
+            Keyword arguments to pass to tifffile.imsave. Includes stage coordinates
+            in format {'x': 11259.4, 'y': 11759.4, 'z': 68.0, 'theta': 0.0, 'f': 100.0}
         """
         self.mode = "w"
 
+        # Get the current frame and position
         c, z, self._current_time, self._current_position = self._cztp_indices(
             self._current_frame, self.metadata.per_stack
-        )  # find current channel
+        )
+
+        # If it is the first frame of the stack, create a new image file.
+        ome_xml = None
         if z == 0:
             if c == 0:
                 # Make sure we're set up for writing
@@ -241,10 +258,10 @@ def write(self, data: npt.ArrayLike, **kw) -> None:
                 ome_xml = self.metadata.to_xml(
                     c=c, t=self._current_time, file_name=self.file_name, uid=self.uid
                 ).encode()
-        else:
-            ome_xml = None
 
         if len(kw) > 0:
+            # On a per-stack basis, we store the stage coordinates.
+            # Resets for each stack.
             self._views.append(kw)
 
         if self.is_ome:
@@ -269,8 +286,7 @@ def write(self, data: npt.ArrayLike, **kw) -> None:
         self._current_frame += 1
 
         # Check if this was the last frame to write
-        # print("Switch")
-        c, z, _, _ = self._cztp_indices(self._current_frame, self.metadata.per_stack)
+        c, z, t, p = self._cztp_indices(self._current_frame, self.metadata.per_stack)
         if (z == 0) and (c == 0):
             self.close(True)
 
@@ -369,9 +385,49 @@ def close(self, internal=False) -> None:
                     )
         else:
             self.image.close()
+
         if not internal:
             self._closed = True
 
+        # Write the metadata to XML
+        if len(self._views) > 0:
+            self.bdv_metadata.write_xml(
+                os.path.join(self.save_directory, "dataset.xml"), self._views
+            )
+
+    def set_metadata_from_configuration_experiment(
+        self, configuration: Dict[str, Any], microscope_name: str = None
+    ) -> None:
+        """Sets the metadata from according to the microscope configuration.
+
+        Child method also provides information to the BigDataViewerMetadata.
+
+        Parameters
+        ----------
+        configuration : Dict[str, Any]
+            Configuration experiment.
+        microscope_name : str
+            The microscope name
+        """
+        self.metadata.active_microscope = microscope_name
+        self.metadata.configuration = configuration
+        self.get_shape_from_metadata()
+
+        self.bdv_metadata.active_microscope = microscope_name
+        self.bdv_metadata.configuration = configuration
+
+    def set_metadata(self, metadata_config: dict) -> None:
+        """Sets the metadata
+
+        Parameters
+        ----------
+        metadata_config : dict
+            shape configuration: "c", "z", "t", "p", "is_dynamic", "per_stack"
+        """
+        self.metadata.set_from_dict(metadata_config)
+        self.bdv_metadata.set_from_dict(metadata_config)
+        self.get_shape_from_metadata()
+
 
 class TiffReader(DataReader):
     def __init__(self, tiff_file: tifffile.TiffFile):

src/navigate/model/features/image_writer.py

@@ -139,6 +139,7 @@ def __init__(
         # camera flip flags
         if self.microscope_name is None:
             self.microscope_name = self.model.active_microscope_name
+
         camera_config = self.model.configuration["configuration"]["microscopes"][
             self.microscope_name
         ]["camera"]
@@ -151,13 +152,14 @@ def __init__(
         self.disk_space_check_interval = 60
 
         #: int: Minimum disk space required in bytes.
-        self.min_disk_space = 10 * 1024 * 1024 * 1024 # 10 GB
+        self.min_disk_space = 10 * 1024 * 1024 * 1024  # 10 GB
 
         #: float: Time of last disk space check
         self.last_disk_space_check = 0
 
         #: bool: Flag to indicate if initialized before
         self.initialized = False
+
         # initialize saving
         self.initialize_saving(sub_dir, image_name)
 
@@ -177,7 +179,10 @@ def save_image(self, frame_ids):
                 continue
 
             # Check disk space at regular intervals to prevent running out of space
-            if time.time() - self.last_disk_space_check > self.disk_space_check_interval:
+            if (
+                time.time() - self.last_disk_space_check
+                > self.disk_space_check_interval
+            ):
                 _, _, free = shutil.disk_usage(self.save_directory)
                 logger.info(f"Free Disk Space: {free / 1024 / 1024 / 1024} GB")
                 if free < self.min_disk_space:
@@ -349,9 +354,7 @@ def get_saving_file_name(self, sub_dir="", image_name=None):
                 os.makedirs(self.save_directory)
                 logger.debug(f"Save Directory Created - {self.save_directory}")
             except (PermissionError, OSError, FileNotFoundError):
-                logger.debug(
-                    f"Unable to Create Save Directory - {self.save_directory}"
-                )
+                logger.debug(f"Unable to Create Save Directory - {self.save_directory}")
                 self.model.stop_acquisition = True
                 self.model.event_queue.put(
                     "warning",
@@ -378,6 +381,7 @@ def get_saving_file_name(self, sub_dir="", image_name=None):
 
     def initialize_saving(self, sub_dir="", image_name=None):
 
+        # Check if previously initialized data source exists and close it
         if self.data_source is not None:
             self.data_source.close()
             self.data_source = None
@@ -393,9 +397,7 @@ def initialize_saving(self, sub_dir="", image_name=None):
                 os.makedirs(self.mip_directory)
                 logger.debug(f"MIP Directory Created - {self.mip_directory}")
             except (PermissionError, OSError, FileNotFoundError):
-                logger.debug(
-                    f"Unable to Create MIP Directory - {self.mip_directory}"
-                )
+                logger.debug(f"Unable to Create MIP Directory - {self.mip_directory}")
                 self.model.stop_acquisition = True
                 self.model.event_queue.put(
                     "warning",