napari-tmidas 0.2.0__py3-none-any.whl → 0.2.2__py3-none-any.whl

napari_tmidas/processing_functions/basic.py

@@ -1,8 +1,14 @@
 # processing_functions/basic.py
 """
-Basic image processing functions that don't require additional dependencies.
+Basic image processing functions
 """
+import concurrent.futures
+import os
+import traceback
+
+import dask.array as da
 import numpy as np
+import tifffile
 
 from napari_tmidas._registry import BatchProcessingRegistry
 
@@ -161,24 +167,47 @@ def max_z_projection_tzyx(image: np.ndarray) -> np.ndarray:
 
 
 @BatchProcessingRegistry.register(
-    name="Split Channels",
-    suffix="_split_channels",
+    name="Split Color Channels",
+    suffix="_split_color_channels",
     description="Splits the color channels of the image",
     parameters={
         "num_channels": {
-            "type": "integer",
+            "type": int,
             "default": 3,
+            "min": 2,
+            "max": 4,
             "description": "Number of color channels in the image",
-        }
+        },
+        "time_steps": {
+            "type": int,
+            "default": 0,
+            "min": 0,
+            "max": 1000,
+            "description": "Number of time steps (leave 0 if not a time series)",
+        },
+        "output_format": {
+            "type": str,
+            "default": "python",
+            "options": ["python", "fiji"],
+            "description": "Output dimension order: python (standard) or fiji (ImageJ/Fiji compatible)",
+        },
     },
 )
-def split_channels(image: np.ndarray, num_channels: int = 3) -> np.ndarray:
+def split_channels(
+    image: np.ndarray,
+    num_channels: int = 3,
+    time_steps: int = 0,
+    output_format: str = "python",
+) -> np.ndarray:
     """
     Split the image into separate channels based on the specified number of channels.
+    Can handle various dimensional orderings including time series data.
 
     Args:
         image: Input image array (at least 3D: XYC or higher dimensions)
         num_channels: Number of channels in the image (default: 3)
+        time_steps: Number of time steps if time series (default: 0, meaning not a time series)
+        output_format: Dimension order format, either "python" (standard) or "fiji" (ImageJ compatible)
 
     Returns:
         Stacked array of channels with shape (num_channels, ...)
@@ -190,30 +219,153 @@ def split_channels(image: np.ndarray, num_channels: int = 3) -> np.ndarray:
         )
 
     print(f"Image shape: {image.shape}")
-    num_channels = int(num_channels)
-    # Identify the channel axis
-    possible_axes = [
-        axis
-        for axis, dim_size in enumerate(image.shape)
-        if dim_size == num_channels
-    ]
-    # print(f"Possible axes: {possible_axes}")
-    if len(possible_axes) != 1:
-
+    is_timelapse = time_steps > 0
+    is_3d = (
+        image.ndim > 3
+    )  # More than 3 dimensions likely means 3D + channels or time series
+
+    # Find channel axis based on provided channel count
+    channel_axis = None
+    for axis, dim_size in enumerate(image.shape):
+        if dim_size == num_channels:
+            # Found a dimension matching the specified channel count
+            channel_axis = axis
+            # If we have multiple matching dimensions, prefer the one that's not likely spatial
+            if (
+                axis < image.ndim - 2
+            ):  # Not one of the last two dimensions (likely spatial)
+                break
+
+    # If channel axis is not found with exact match, look for other possibilities
+    if channel_axis is None:
+        # Try to infer channel axis using heuristics
+        ndim = image.ndim
+
+        # Check dimensions for a small value (1-16) that could be channels
+        for i, dim_size in enumerate(image.shape):
+            # Skip dimensions that are likely spatial (Y,X) - typically the last two
+            if i >= ndim - 2:
+                continue
+            # Skip first dimension if this is a time series
+            if is_timelapse and i == 0:
+                continue
+            # A dimension with size 1-16 is likely channels
+            if 1 <= dim_size <= 16:
+                channel_axis = i
+                break
+
+        # If still not found, check even the spatial dimensions (for RGB images)
+        if channel_axis is None and image.shape[-1] <= 16:
+            channel_axis = ndim - 1
+
+    if channel_axis is None:
         raise ValueError(
-            f"Could not uniquely identify a channel axis with {num_channels} channels. "
-            f"Found {len(possible_axes)} possible axes: {possible_axes}. "
-            f"Image shape: {image.shape}"
+            f"Could not identify a channel axis. Please check if the number of channels ({num_channels}) "
+            f"matches any dimension in your image shape {image.shape}"
         )
 
-    channel_axis = possible_axes[0]
     print(f"Channel axis identified: {channel_axis}")
 
-    # Split and process channels
+    # Generate dimensional understanding for better handling
+    # Create axes string to understand dimension ordering
+    axes = [""] * image.ndim
+
+    # Assign channel axis
+    axes[channel_axis] = "C"
+
+    # Assign time axis if present
+    if is_timelapse and 0 not in [
+        channel_axis
+    ]:  # If channel is not at position 0
+        axes[0] = "T"
+
+    # Assign remaining spatial dimensions
+    remaining_dims = [i for i in range(image.ndim) if axes[i] == ""]
+    spatial_axes = []
+    if is_3d and len(remaining_dims) > 2:
+        # We have Z dimension
+        spatial_axes.append("Z")
+
+    # Add Y and X
+    spatial_axes.extend(["Y", "X"])
+
+    # Assign remaining dimensions
+    for i, dim in enumerate(remaining_dims):
+        if i < len(spatial_axes):
+            axes[dim] = spatial_axes[i]
+        else:
+            axes[dim] = "A"  # Anonymous dimension
+
+    axes_str = "".join(axes)
+    print(f"Inferred dimension order: {axes_str}")
+
+    # Split along the channel axis
+    actual_channels = image.shape[channel_axis]
+    if actual_channels != num_channels:
+        print(
+            f"Warning: Specified {num_channels} channels but found {actual_channels} in the data. Using {actual_channels}."
+        )
+        num_channels = actual_channels
+
+    # Split channels
     channels = np.split(image, num_channels, axis=channel_axis)
-    # channels = [np.squeeze(ch, axis=channel_axis) for ch in channels]
 
-    return np.stack(channels, axis=0)
+    # Process output format
+    result_channels = []
+    for i, channel_img in enumerate(channels):
+        # Get original axes without channel
+        axes_without_channel = axes.copy()
+        del axes_without_channel[channel_axis]
+        axes_without_channel_str = "".join(axes_without_channel)
+
+        # For fiji format, reorganize dimensions to TZYX order
+        if output_format.lower() == "fiji":
+            # Map dimensions to positions
+            dim_indices = {
+                dim: i for i, dim in enumerate(axes_without_channel_str)
+            }
+
+            # Build target order and transpose indices
+            target_order = ""
+            transpose_indices = []
+
+            # Add T if exists
+            if "T" in dim_indices:
+                target_order += "T"
+                transpose_indices.append(dim_indices["T"])
+
+            # Add Z if exists
+            if "Z" in dim_indices:
+                target_order += "Z"
+                transpose_indices.append(dim_indices["Z"])
+
+            # Add Y and X (should always exist)
+            if "Y" in dim_indices and "X" in dim_indices:
+                target_order += "YX"
+                transpose_indices.append(dim_indices["Y"])
+                transpose_indices.append(dim_indices["X"])
+
+            # Only transpose if order is different and we have enough dimensions
+            if (
+                axes_without_channel_str != target_order
+                and len(transpose_indices) > 1
+                and len(transpose_indices) == len(axes_without_channel)
+            ):
+                print(
+                    f"Channel {i}: Transposing from {axes_without_channel_str} to {target_order}"
+                )
+                result_channels.append(
+                    np.transpose(channel_img, transpose_indices)
+                )
+            else:
+                # Keep as is
+                result_channels.append(channel_img)
+        else:
+            # For python format, keep as is
+            result_channels.append(channel_img)
+
+    # Stack channels along a new first dimension
+    return np.stack(result_channels, axis=0)
 
 
 @BatchProcessingRegistry.register(
@@ -287,3 +439,322 @@ def rgb_to_labels(
         label_image[mask] = label
     # Return the label image
     return label_image
+
+
+@BatchProcessingRegistry.register(
+    name="Split TZYX into ZYX TIFs",
+    suffix="_split",
+    description="Splits a 4D TZYX image stack into separate 3D ZYX TIFs for each time point using parallel processing",
+    parameters={
+        "output_name_format": {
+            "type": str,
+            "default": "{basename}_t{timepoint:03d}",
+            "description": "Format for output filenames. Use {basename} and {timepoint} as placeholders",
+        },
+        "preserve_scale": {
+            "type": bool,
+            "default": True,
+            "description": "Preserve scale/resolution metadata when saving",
+        },
+        "use_compression": {
+            "type": bool,
+            "default": True,
+            "description": "Apply zlib compression to output files",
+        },
+        "num_workers": {
+            "type": int,
+            "default": 4,
+            "min": 1,
+            "max": 16,
+            "description": "Number of worker processes for parallel processing",
+        },
+    },
+)
+def split_tzyx_stack(
+    image: np.ndarray,
+    output_name_format: str = "{basename}_t{timepoint:03d}",
+    preserve_scale: bool = True,
+    use_compression: bool = True,
+    num_workers: int = 4,
+) -> np.ndarray:
+    """
+    Split a 4D TZYX stack into separate 3D ZYX TIF files using parallel processing.
+
+    This function takes a 4D TZYX image stack and saves each time point as
+    a separate 3D ZYX TIF file. Files are processed in parallel for better performance.
+    The original 4D stack is returned unchanged.
+
+    Parameters:
+    -----------
+    image : numpy.ndarray
+        Input 4D TZYX image stack
+    output_name_format : str
+        Format string for output filenames. Use {basename} and {timepoint} as placeholders.
+        Default: "{basename}_t{timepoint:03d}"
+    preserve_scale : bool
+        Whether to preserve scale/resolution metadata when saving
+    use_compression : bool
+        Whether to apply zlib compression to output files
+    num_workers : int
+        Number of worker processes for parallel file saving
+
+    Returns:
+    --------
+    numpy.ndarray
+        The original image (unchanged)
+    """
+    # Validate input dimensions
+    if image.ndim != 4:
+        print(
+            f"Warning: Expected 4D TZYX input, got {image.ndim}D. Returning original image."
+        )
+        return image
+
+    # Use dask array to optimize memory usage when processing slices
+    chunks = (1,) + image.shape[1:]  # Each timepoint is a chunk
+    dask_image = da.from_array(image, chunks=chunks)
+
+    # Store processing parameters for post-processing
+    split_tzyx_stack.dask_image = dask_image
+    split_tzyx_stack.output_name_format = output_name_format
+    split_tzyx_stack.preserve_scale = preserve_scale
+    split_tzyx_stack.use_compression = use_compression
+    split_tzyx_stack.num_workers = min(
+        num_workers, image.shape[0]
+    )  # Limit workers to number of timepoints
+
+    # Mark for post-processing with multiple output files
+    split_tzyx_stack.requires_post_processing = True
+    split_tzyx_stack.produces_multiple_files = True
+    # Tell the processing system to skip creating the original output file
+    split_tzyx_stack.skip_original_output = True
+
+    # Get dimensions for informational purposes
+    t_size, z_size, y_size, x_size = image.shape
+    print(f"TZYX stack dimensions: {image.shape}, dtype: {image.dtype}")
+    print(f"Will generate {t_size} separate ZYX files")
+    print(f"Parallelization: {split_tzyx_stack.num_workers} workers")
+
+    # The actual file saving will happen in the post-processing step
+    return image
+
+
+# Monkey patch ProcessingWorker.process_file to handle parallel TZYX splitting
+try:
+    # Import tifffile here to ensure it's available for the monkey patch
+    import tifffile
+
+    from napari_tmidas._file_selector import ProcessingWorker
+
+    # Define function to save a single timepoint
+    def save_timepoint(
+        t: int,
+        data: np.ndarray,
+        output_filepath: str,
+        resolution=None,
+        use_compression=True,
+    ) -> str:
+        """
+        Save a single timepoint to disk.
+
+        Parameters:
+        -----------
+        t : int
+            Timepoint index for logging
+        data : np.ndarray
+            3D ZYX data to save
+        output_filepath : str
+            Path to save the file
+        resolution : tuple, optional
+            Resolution metadata to preserve
+        use_compression : bool
+            Whether to use compression
+
+        Returns:
+        --------
+        str
+            Path to the saved file
+        """
+        try:
+            # Create output directory if it doesn't exist
+            os.makedirs(os.path.dirname(output_filepath), exist_ok=True)
+
+            # Determine the appropriate compression parameter
+            # Note: tifffile uses 'compression', not 'compress'
+            compression_arg = "zlib" if use_compression else None
+
+            # Calculate approximate file size for BigTIFF decision
+            size_gb = (data.size * data.itemsize) / (1024**3)
+            use_bigtiff = size_gb > 4.0
+
+            # Save the file with proper parameters
+            tifffile.imwrite(
+                output_filepath,
+                data,
+                resolution=resolution,
+                compression=compression_arg,
+                bigtiff=use_bigtiff,
+            )
+
+            print(f"✓ Saved timepoint {t} to {output_filepath}")
+            return output_filepath
+        except Exception as e:
+            print(f"✘ Error saving timepoint {t}: {str(e)}")
+            traceback.print_exc()
+            raise
+
+    # Store the original process_file function
+    original_process_file = ProcessingWorker.process_file
+
+    # Define the custom process_file function
+    def process_file_with_tzyx_splitting(self, filepath):
+        """Modified process_file function that handles parallel TZYX splitting."""
+        # First call the original function to get the initial result
+        result = original_process_file(self, filepath)
+
+        # Skip further processing if there's no result or no processed_file
+        if not isinstance(result, dict) or "processed_file" not in result:
+            return result
+
+        # Get the output path from the original processing
+        output_path = result["processed_file"]
+        processing_func = self.processing_func
+
+        # Check if our function has the required attributes for TZYX splitting
+        if (
+            hasattr(processing_func, "requires_post_processing")
+            and processing_func.requires_post_processing
+            and hasattr(processing_func, "dask_image")
+            and hasattr(processing_func, "produces_multiple_files")
+            and processing_func.produces_multiple_files
+        ):
+            try:
+                # Get the Dask image and processing parameters
+                dask_image = processing_func.dask_image
+                output_name_format = processing_func.output_name_format
+                preserve_scale = processing_func.preserve_scale
+                use_compression = processing_func.use_compression
+                num_workers = processing_func.num_workers
+
+                # Extract base filename without extension
+                basename = os.path.splitext(os.path.basename(output_path))[0]
+                dirname = os.path.dirname(output_path)
+
+                # Try to get scale info from original file if needed
+                resolution = None
+                if preserve_scale:
+                    try:
+                        with tifffile.TiffFile(filepath) as tif:
+                            if hasattr(tif, "pages") and tif.pages:
+                                page = tif.pages[0]
+                                if hasattr(page, "resolution"):
+                                    resolution = page.resolution
+                    except (OSError, AttributeError, KeyError) as e:
+
+                        print(
+                            f"Warning: Could not read original resolution: {e}"
+                        )
+
+                # Get number of timepoints
+                t_size = dask_image.shape[0]
+                print(f"Processing {t_size} timepoints in parallel...")
+
+                # Prepare output paths for each timepoint
+                output_filepaths = []
+                for t in range(t_size):
+                    # Format the output filename
+                    output_filename = output_name_format.format(
+                        basename=basename, timepoint=t
+                    )
+                    # Add extension
+                    output_filepath = os.path.join(
+                        dirname, f"{output_filename}.tif"
+                    )
+                    output_filepaths.append(output_filepath)
+
+                # Process timepoints in parallel
+                processed_files = []
+
+                # Use ThreadPoolExecutor for parallel file saving
+                with concurrent.futures.ThreadPoolExecutor(
+                    max_workers=num_workers
+                ) as executor:
+                    # Submit tasks for each timepoint
+                    future_to_timepoint = {}
+                    for t in range(t_size):
+                        # Extract this timepoint's data using Dask
+                        timepoint_array = dask_image[t].compute()
+
+                        # Submit the task to save this timepoint
+                        future = executor.submit(
+                            save_timepoint,
+                            t,
+                            timepoint_array,
+                            output_filepaths[t],
+                            resolution,
+                            use_compression,
+                        )
+                        future_to_timepoint[future] = t
+
+                    total = len(future_to_timepoint)
+                    for completed, future in enumerate(
+                        concurrent.futures.as_completed(future_to_timepoint),
+                        start=1,
+                    ):
+                        t = future_to_timepoint[future]
+                        try:
+                            output_filepath = future.result()
+                            processed_files.append(output_filepath)
+                        except (OSError, concurrent.futures.TimeoutError) as e:
+                            print(f"Failed to save timepoint {t}: {e}")
+
+                        # Update progress
+                        if completed % 5 == 0 or completed == total:
+                            percent = int(completed * 100 / total)
+                            print(
+                                f"Progress: {completed}/{total} timepoints ({percent}%)"
+                            )
+
+                # Update the result with the list of processed files
+                if processed_files:
+                    print(
+                        f"Successfully generated {len(processed_files)} ZYX files from TZYX stack"
+                    )
+                    result["processed_files"] = processed_files
+
+                    # Skip creating the original consolidated output file if requested
+                    if (
+                        hasattr(processing_func, "skip_original_output")
+                        and processing_func.skip_original_output
+                    ):
+                        # Remove the original file if it was already created
+                        if os.path.exists(output_path):
+                            try:
+                                os.remove(output_path)
+                                print(
+                                    f"Removed unnecessary consolidated file: {output_path}"
+                                )
+                            except OSError as e:
+                                print(
+                                    f"Warning: Could not remove consolidated file: {e}"
+                                )
+
+                        # Remove the entry from the result to prevent its display
+                        if "processed_file" in result:
+                            del result["processed_file"]
+
+                else:
+                    print("Warning: No ZYX files were successfully generated")
+
+            except (OSError, ValueError, RuntimeError) as e:
+
+                traceback.print_exc()
+                print(f"Error in TZYX splitting post-processing: {e}")
+
+        return result
+
+    # Apply the monkey patch
+    ProcessingWorker.process_file = process_file_with_tzyx_splitting
+
+except (NameError, AttributeError) as e:
+    print(f"Warning: Could not apply TZYX splitting patch: {e}")