Save tiff stack

qim3d/io/save.py

@@ -4,13 +4,19 @@ import os
 import tifffile
 import numpy as np
 from qim3d.io.logger import log
+from qim3d.utils.internal_tools import sizeof, stringify_path
+
 
 class DataSaver:
     """Utility class for saving data to different file formats.
 
     Attributes:
         replace (bool): Specifies if an existing file with identical path is replaced.
-        compression (bool): Specifies if the file is with Deflate compression.
+        compression (bool): Specifies if the file is saved with Deflate compression (lossless).
+        basename (str): Specifies the basename for a TIFF stack saved as several files
+            (only relevant for TIFF stacks).
+        sliced_dim (int): Specifies the dimension that is sliced in case a TIFF stack is saved
+            as several files (only relevant for TIFF stacks)
 
     Methods:
         save_tiff(path,data): Save data to a TIFF file to the given path.
@@ -30,9 +36,15 @@ class DataSaver:
                 Default is False.
             compression (bool, optional): Specifies if the file should be saved with Deflate compression.
                 Default is False.
+            basename (str, optional): Specifies the basename for a TIFF stack saved as several files
+                (only relevant for TIFF stacks). Default is None
+            sliced_dim (int, optional): Specifies the dimension that is sliced in case a TIFF stack is saved
+                as several files (only relevant for TIFF stacks). Default is 0, i.e., the first dimension.
         """
         self.replace = kwargs.get("replace", False)
         self.compression = kwargs.get("compression", False)
+        self.basename = kwargs.get("basename", None)
+        self.sliced_dim = kwargs.get("sliced_dim", 0)
 
     def save_tiff(self, path, data):
         """Save data to a TIFF file to the given path.
@@ -43,6 +55,41 @@ class DataSaver:
         """
         tifffile.imwrite(path, data, compression=self.compression)
 
+    def save_tiff_stack(self, path, data):
+        """Save data as a TIFF stack containing slices in separate files to the given path.
+        The slices will be named according to the basename plus a suffix with a zero-filled
+        value corresponding to the slice number
+
+        Args:
+            path (str): The directory to save files to
+            data (numpy.ndarray): The data to be saved
+        """
+        extension = ".tif"
+
+        if data.ndim <= 2:
+            path = os.path.join(path, self.basename, ".tif")
+            self.save_tiff(path, data)
+        else:
+            # get number of total slices
+            no_slices = data.shape[self.sliced_dim]
+            # Get number of zero-fill values as the number of digits in the total number of slices
+            zfill_val = len(str(no_slices))
+
+            # Create index list
+            idx = [slice(None)] * data.ndim
+
+            # Iterate through each slice and save
+            for i in range(no_slices):
+                idx[self.sliced_dim] = i
+                sliced = data[tuple(idx)]
+                filename = self.basename + str(i).zfill(zfill_val) + extension
+                filepath = os.path.join(path, filename)
+                self.save_tiff(filepath, sliced)
+
+            pattern_string = filepath[:-(len(extension)+zfill_val)] + "-"*zfill_val + extension
+
+            log.info(f"Total of {no_slices} files saved following the pattern '{pattern_string}'")
+
     def save(self, path, data):
         """Save data to the given path.
 
@@ -51,8 +98,9 @@ class DataSaver:
             data (numpy.ndarray): The data to be saved
 
         Raises:
+            ValueError: If the provided path is an existing directory and self.basename is not provided
             ValueError: If the file format is not supported.
-            ValueError: If the specified folder does not exist.
+            ValueError: If the provided path does not exist and self.basename is not provided
             ValueError: If a file extension is not provided.
             ValueError: if a file with the specified path already exists and replace=False.
 
@@ -60,32 +108,69 @@ class DataSaver:
             image = qim3d.examples.blobs_256x256
             saver = qim3d.io.DataSaver(compression=True)
             saver.save("image.tif",image)
+
         """
 
-        folder = os.path.dirname(path) or '.'
-        # Check if directory exists
-        if os.path.isdir(folder):
+        path = stringify_path(path)
+        isdir = os.path.isdir(path)
         _, ext = os.path.splitext(path)
-            # Check if provided path contains file extension
+
+        # If path is an existing directory
+        if isdir:
+            # If basename is provided
+            if self.basename:
+                # Save as tiff stack
+                return self.save_tiff_stack(path, data)
+            # If basename is not provided
+            else:
+                raise ValueError(
+                    f"To save a stack as several TIFF files to the directory '{path}', please provide the keyword argument 'basename'. "
+                    + "Otherwise, to save a single file, please provide a full path with a filename and valid extension."
+                )
+
+        # If path is not an existing directory
+        else:
+            # If there is no file extension in path and basename is provided
+            if not ext and self.basename:
+                # Make directory and save as tiff stack
+                os.mkdir(path)
+                log.info("Created directory '%s'!", path)
+                return self.save_tiff_stack(path, data)
+
+            # Check if a parent directory exists
+            parentdir = os.path.dirname(path) or "."
+            if os.path.isdir(parentdir):
+                # If there is a file extension in the path
                 if ext:
+                    # If there is a basename
+                    if self.basename:
+                        # It will be unused and the user is informed accordingly
+                        log.info("'basename' argument is unused")
                     # Check if a file with the given path already exists
                     if os.path.isfile(path) and not self.replace:
-                    raise ValueError("A file with the provided path already exists. To replace it set 'replace=True'")
+                        raise ValueError(
+                            "A file with the provided path already exists. To replace it set 'replace=True'"
+                        )
 
                     if path.endswith((".tif", ".tiff")):
                         return self.save_tiff(path, data)
                     else:
                         raise ValueError("Unsupported file format")
+                # If there is no file extension in the path
                 else:
-                raise ValueError('Please provide a file extension')
+                    raise ValueError(
+                        "Please provide a file extension if you want to save as a single file."
+                        + " Otherwise, please provide a basename to save as a TIFF stack"
+                    )
             else:
-            raise ValueError(f'The directory {folder} does not exist. Please provide a valid directory')
+                raise ValueError(
+                    f"The directory '{parentdir}' does not exist.\n"
+                    + "Please provide a valid directory or specify a basename if you want to save a tiff stack as several files to a folder that does not yet exist"
+                )
+
 
-def save(path,
-        data,
-        replace=False,
-        compression=False,
-        **kwargs
+def save(
+    path, data, replace=False, compression=False, basename=None, sliced_dim=0, **kwargs
 ):
     """Save data to a specified file path.
 
@@ -96,6 +181,10 @@ def save(path,
             Default is False.
         compression (bool, optional): Specifies if the file should be saved with Deflate compression (lossless).
             Default is False.
+        basename (str, optional): Specifies the basename for a TIFF stack saved as several files
+            (only relevant for TIFF stacks). Default is None
+        sliced_dim (int, optional): Specifies the dimension that is sliced in case a TIFF stack is saved
+            as several files (only relevant for TIFF stacks). Default is 0, i.e., the first dimension.
         **kwargs: Additional keyword arguments to be passed to the DataSaver constructor
 
     Example:
@@ -103,4 +192,10 @@ def save(path,
         qim3d.io.save("image.tif",image,compression=True)
     """
 
-    DataSaver(replace=replace, compression=compression, **kwargs).save(path, data)
\ No newline at end of file
+    DataSaver(
+        replace=replace,
+        compression=compression,
+        basename=basename,
+        sliced_dim=sliced_dim,
+        **kwargs,
+    ).save(path, data)