Fix tiff channel handling (it was saving each channel as a separate i…

…mage in the TIFF)

src/sim_recon/images/__init__.py

@@ -58,8 +58,9 @@ def dv_to_tiff(
                 channel.array = complex_to_interleaved_float(channel.array)
     write_tiff(
         tiff_path,
-        *image_data.channels,
+        image_data.channels,
         resolution=image_data.resolution,
         overwrite=overwrite,
+        allow_missing_channel_info=True,
     )
     return Path(tiff_path)

src/sim_recon/images/dv.py

@@ -149,7 +149,7 @@ def handle_float_array(
 
 def write_dv(
     output_file: str | PathLike[str],
-    *channels: ImageChannel[Wavelengths],
+    channels: Collection[ImageChannel[Wavelengths]],
     input_dv: mrc.Mrc,
     resolution: ImageResolution,
     overwrite: bool = False,

src/sim_recon/images/tiff.py

@@ -2,6 +2,7 @@
 
 import logging
 from pathlib import Path
+import numpy as np
 import tifffile as tf
 from typing import TYPE_CHECKING
 
@@ -14,7 +15,8 @@
 )
 
 if TYPE_CHECKING:
-    from typing import Any, Generator
+    from typing import Any
+    from collections.abc import Generator, Collection
     from os import PathLike
     from numpy.typing import NDArray
     from .dataclasses import Wavelengths
@@ -57,23 +59,46 @@ def generate_channels_from_tiffs(
 
 def write_tiff(
     output_path: str | PathLike[str],
-    *channels: ImageChannel,
+    *images: Collection[ImageChannel[Wavelengths] | ImageChannel[None]],
     resolution: ImageResolution | None = None,
     ome: bool = True,
     allow_empty_channels: bool = False,
+    allow_missing_channel_info: bool = False,
     overwrite: bool = False,
 ) -> Path:
-    def get_channel_dict(channel: ImageChannel) -> dict[str, Any] | None:
-        channel_dict: dict[str, Any] = {}
-        if channel.wavelengths is None:
-            return None
-        if channel.wavelengths.excitation_nm is not None:
-            channel_dict["ExcitationWavelength"] = channel.wavelengths.excitation_nm
-            channel_dict["ExcitationWavelengthUnits"] = "nm"
-        if channel.wavelengths.emission_nm is not None:
-            channel_dict["EmissionWavelength"] = channel.wavelengths.emission_nm
-            channel_dict["EmissionWavelengthUnits"] = "nm"
-        return channel_dict
+    def get_ome_channel_dict(*channels: ImageChannel) -> dict[str, Any] | None:
+        names: list[str] = []
+        excitation_wavelengths: list[float | None] = []
+        excitation_wavelength_units: list[str | None] = []
+        emission_wavelengths: list[float | None] = []
+        emission_wavelength_units: list[str | None] = []
+        for i, channel in enumerate(channels, 1):
+            if channel.wavelengths is None:
+                if not allow_missing_channel_info:
+                    raise UndefinedValueError(f"Missing wavelengths for channel {i}")
+                names.append(f"Channel {i}")
+                excitation_wavelengths.append(None)
+                excitation_wavelength_units.append(None)
+                emission_wavelengths.append(None)
+                emission_wavelength_units.append(None)
+
+            else:
+                names.append(
+                    f"Channel {i}"
+                    if channel.wavelengths.emission_nm_int is None
+                    else str(channel.wavelengths.emission_nm_int)
+                )
+                excitation_wavelengths.append(channel.wavelengths.excitation_nm)
+                excitation_wavelength_units.append("nm")
+                emission_wavelengths.append(channel.wavelengths.emission_nm)
+                emission_wavelength_units.append("nm")
+        return {
+            "Name": names,
+            "ExcitationWavelength": excitation_wavelengths,
+            "ExcitationWavelengthUnits": excitation_wavelength_units,
+            "EmissionWavelength": emission_wavelengths,
+            "EmissionWavelengthUnits": emission_wavelength_units,
+        }
 
     output_path = Path(output_path)
 
@@ -86,10 +111,11 @@ def get_channel_dict(channel: ImageChannel) -> dict[str, Any] | None:
         else:
             raise PySimReconFileExistsError(f"File {output_path} already exists")
 
+    tiff_metadata: dict[str, Any] = {}
     tiff_kwargs: dict[str, Any] = {
         "software": f"PySIMRecon {__version__}",
         "photometric": "MINISBLACK",
-        "metadata": {},
+        "metadata": tiff_metadata,
     }
 
     if resolution is not None:
@@ -103,15 +129,16 @@ def get_channel_dict(channel: ImageChannel) -> dict[str, Any] | None:
         )  # Use CENTIMETER for maximum compatibility
 
     if ome:
+        tiff_metadata["Name"] = output_path.name
         if resolution is not None:
             # OME PhysicalSize:
-            tiff_kwargs["metadata"]["PhysicalSizeX"] = resolution.x
-            tiff_kwargs["metadata"]["PhysicalSizeXUnit"] = "µm"
-            tiff_kwargs["metadata"]["PhysicalSizeY"] = resolution.x
-            tiff_kwargs["metadata"]["PhysicalSizeYUnit"] = "µm"
+            tiff_metadata["PhysicalSizeX"] = resolution.x
+            tiff_metadata["PhysicalSizeXUnit"] = "µm"
+            tiff_metadata["PhysicalSizeY"] = resolution.x
+            tiff_metadata["PhysicalSizeYUnit"] = "µm"
             if resolution.z is not None:
-                tiff_kwargs["metadata"]["PhysicalSizeZ"] = resolution.z
-                tiff_kwargs["metadata"]["PhysicalSizeYUnit"] = "µm"
+                tiff_metadata["PhysicalSizeZ"] = resolution.z
+                tiff_metadata["PhysicalSizeYUnit"] = "µm"
 
     with tf.TiffWriter(
         output_path,
@@ -120,24 +147,43 @@ def get_channel_dict(channel: ImageChannel) -> dict[str, Any] | None:
         ome=ome,
         shaped=not ome,
     ) as tiff:
-        for channel in channels:
-            if channel.array is None:
-                if allow_empty_channels:
-                    logger.warning(
-                        "Channel %s has no array to write",
-                        channel.wavelengths,
+        for channels in images:
+            channels_to_write = []
+            for channel in channels:
+                if channel.array is None:
+                    if allow_empty_channels:
+                        logger.warning(
+                            "Channel %s has no array to write",
+                            channel.wavelengths,
+                        )
+                        continue
+                    raise UndefinedValueError(
+                        f"{output_path} will not be created as channel {channel.wavelengths} has no array to write",
                     )
-                    continue
-                raise UndefinedValueError(
-                    f"{output_path} will not be created as channel {channel.wavelengths} has no array to write",
-                )
-            channel_kwargs = tiff_kwargs.copy()
-            channel_kwargs["metadata"]["axes"] = (
-                "YX" if channel.array.ndim == 2 else "ZYX"
-            )
+                channels_to_write.append(channel)
+
+            array = np.stack(
+                [_.array for _ in channels], axis=0
+            )  # adds another axis, even if only 1 channel
+
+            image_kwargs = tiff_kwargs.copy()
+            if array.ndim == 3:
+                # In case the images are 2D
+                tiff_metadata["axes"] = "CYX"
+            else:
+                tiff_metadata["axes"] = "CZYX"
+
             if ome:
-                channel_dict = get_channel_dict(channel)
-                if channel_dict is not None:
-                    channel_kwargs["metadata"]["Channel"] = channel_dict
-            tiff.write(channel.array, **channel_kwargs)
+                try:
+                    channel_dict = get_ome_channel_dict(*channels)
+                    if channel_dict is not None:
+                        tiff_metadata["Channel"] = channel_dict
+                except UndefinedValueError as e:
+                    if not allow_missing_channel_info:
+                        logger.error("Failed to write image '%s': %s", output_path, e)
+                        raise
+                    logger.warning(
+                        "Writing without OME Channel metadata due to error: %s", e
+                    )
+            tiff.write(array, **image_kwargs)
     return output_path

src/sim_recon/recon.py

@@ -191,7 +191,7 @@ def reconstruct_from_processing_info(processing_info: ProcessingInfo) -> Process
     recon_pixel_size = float(processing_info.kwargs["xyres"]) / zoomfact
     write_tiff(
         processing_info.output_path,
-        ImageChannel(processing_info.wavelengths, rec_array),
+        (ImageChannel(processing_info.wavelengths, rec_array),),
         resolution=ImageResolution(recon_pixel_size, recon_pixel_size),
         overwrite=True,
     )
@@ -266,12 +266,15 @@ def _reconstructions_to_output(
                 zzoom = zoom_factors[0][1]
                 write_output(
                     output_image_path,
-                    *generate_channels_from_tiffs(*output_wavelengths_path_tuples),
+                    tuple(
+                        generate_channels_from_tiffs(*output_wavelengths_path_tuples)
+                    ),
                     resolution=ImageResolution(
                         input_resolution.x / zoom_fact,
                         input_resolution.y / zoom_fact,
                         input_resolution.z / zzoom,
-                    ))
+                    ),
+                )
             return
         except InvalidValueError as e:
             logger.warning("Unable to stitch files due to error: %s", e)
@@ -294,7 +297,11 @@ def _reconstructions_to_output(
         zzoom = processing_info.kwargs["zzoom"]
         write_output(
             output_image_path,
-            *generate_channels_from_tiffs((processing_info.wavelengths, processing_info.output_path)),
+            tuple(
+                generate_channels_from_tiffs(
+                    (processing_info.wavelengths, processing_info.output_path)
+                )
+            ),
             resolution=ImageResolution(
                 input_resolution.x / zoom_fact,
                 input_resolution.y / zoom_fact,
@@ -454,7 +461,7 @@ def run_reconstructions(
                             processing_info_dict=processing_info_dict,
                             stitch_channels=stitch_channels,
                             overwrite=overwrite,
-                            file_type=output_file_type
+                            file_type=output_file_type,
                         )
                     finally:
                         proc_log_files: list[Path] = []
@@ -649,7 +656,7 @@ def _prepare_files(
             )
             write_tiff(
                 split_file_path,
-                channel,
+                (channel,),
                 resolution=image_data.resolution,
             )