diff --git a/qim3d/io/save.py b/qim3d/io/save.py
index ad988b9a73b534f2381bc23f5973312e83e47952..73cea5c5115f6893a537cd4e98ed66828bde29df 100644
--- a/qim3d/io/save.py
+++ b/qim3d/io/save.py
@@ -4,17 +4,23 @@ 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.
- load(path,data): Save data to the given path.
+ load(path,data): Save data to the given path.
Example:
image = qim3d.examples.blobs_256x256
@@ -26,33 +32,75 @@ class DataSaver:
"""Initializes a new instance of the DataSaver class.
Args:
- replace (bool, optional): Specifies if an existing file with identical path should be replaced.
+ replace (bool, optional): Specifies if an existing file with identical path should be replaced.
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.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):
+ def save_tiff(self, path, data):
"""Save data to a TIFF file to the given path.
- Args:
+ Args:
path (str): The path to save file to
- data (numpy.ndarray): The data to be saved
+ data (numpy.ndarray): The data to be saved
+ """
+ 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
"""
- tifffile.imwrite(path,data,compression=self.compression)
+ 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.
- Args:
+ Args:
path (str): The path to save file to
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.
@@ -60,47 +108,94 @@ 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):
- _, ext = os.path.splitext(path)
- # Check if provided path contains file extension
- if ext:
- # 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'")
-
- if path.endswith((".tif",".tiff")):
- return self.save_tiff(path,data)
- else:
- raise ValueError("Unsupported file format")
+ path = stringify_path(path)
+ isdir = os.path.isdir(path)
+ _, ext = os.path.splitext(path)
+
+ # 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('Please provide a file extension')
+ 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:
- raise ValueError(f'The directory {folder} does not exist. Please provide a valid directory')
-
-def save(path,
- data,
- replace=False,
- compression=False,
- **kwargs
- ):
+ # 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'"
+ )
+
+ 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 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 '{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, basename=None, sliced_dim=0, **kwargs
+):
"""Save data to a specified file path.
Args:
path (str): The path to save file to
- data (numpy.ndarray): The data to be saved
- replace (bool, optional): Specifies if an existing file with identical path should be replaced.
+ data (numpy.ndarray): The data to be saved
+ replace (bool, optional): Specifies if an existing file with identical path should be replaced.
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:
image = qim3d.examples.blobs_256x256
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)
diff --git a/qim3d/tests/io/test_save.py b/qim3d/tests/io/test_save.py
index cf15140757d4f46dc1e3842a2d1988db6b9a3ae7..87e4a6b26703387b1d33943d3d643f834e3c127f 100644
--- a/qim3d/tests/io/test_save.py
+++ b/qim3d/tests/io/test_save.py
@@ -127,11 +127,13 @@ def test_no_file_ext():
# Create filename without extension
filename = 'test_image'
+ message = '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'
+
# Create temporary directory
with tempfile.TemporaryDirectory() as temp_dir:
image_path = os.path.join(temp_dir,filename)
- with pytest.raises(ValueError,match='Please provide a file extension'):
+ with pytest.raises(ValueError,match=message):
# Try to save the test image to a path witout file extension
qim3d.io.save(image_path,test_image)
@@ -142,8 +144,10 @@ def test_folder_doesnt_exist():
# Create invalid path
invalid_path = os.path.join('this','path','doesnt','exist.tif')
- message = f'The directory {re.escape(os.path.dirname(invalid_path))} does not exist. Please provide a valid directory'
-
+ #message = f'The directory {re.escape(os.path.dirname(invalid_path))} does not exist. Please provide a valid directory'
+ message = f"""The directory {re.escape(os.path.dirname(invalid_path))} does not exist. 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"""
+
with pytest.raises(ValueError,match=message):
# Try to save test image to an invalid path
qim3d.io.save(invalid_path,test_image)
@@ -162,6 +166,62 @@ def test_unsupported_file_format():
# Try to save test image with an unsupported file extension
qim3d.io.save(image_path,test_image)
+def test_no_basename():
+ # Create random test image
+ test_image = np.random.randint(0,256,(100,100,100),'uint8')
+
+ # Create temporary directory
+ with tempfile.TemporaryDirectory() as temp_dir:
+ message = f"""Please provide a basename with the keyword argument 'basename' if you want to save
+ a TIFF stack as several files to '{re.escape(temp_dir)}'. Otherwise, please provide a path with a valid filename"""
+
+ with pytest.raises(ValueError,match=message):
+ # Try to save test image to an existing directory (indicating
+ # that you want to save as several files) without providing a basename
+ qim3d.io.save(temp_dir,test_image)
+
+def test_mkdir_tiff_stack():
+ # Create random test image
+ test_image = np.random.randint(0,256,(10,100,100),'uint8')
+
+ # create temporary directory
+ with tempfile.TemporaryDirectory() as temp_dir:
+ # Define a folder that does not yet exist
+ path2save= os.path.join(temp_dir,'tempfolder')
+
+ # Save to this folder with a basename
+ qim3d.io.save(path2save,test_image,basename='test')
+
+ # Assert that folder is created
+ assert os.path.isdir(path2save)
+
+def test_tiff_stack_naming():
+ # Create random test image
+ test_image = np.random.randint(0,256,(10,100,100),'uint8')
+
+ # Define expected filenames
+ basename = 'test'
+ expected_filenames = [basename + str(i).zfill(2) + '.tif' for i,_ in enumerate(test_image)]
+
+ # create temporary directory
+ with tempfile.TemporaryDirectory() as temp_dir:
+ qim3d.io.save(temp_dir,test_image,basename=basename)
+
+ assert expected_filenames==sorted(os.listdir(temp_dir))
+
+
+def test_tiff_stack_slicing_dim():
+ # Create random test image where the three dimensions are not the same length
+ test_image = np.random.randint(0,256,(5,10,15),'uint8')
+
+ with tempfile.TemporaryDirectory() as temp_dir:
+ # Iterate thorugh all three dims and save the image as slices in
+ # each dimension in separate folder and assert the number of files
+ # match the shape of the image
+ for dim in range(3):
+ path2save = os.path.join(temp_dir,'dim'+str(dim))
+ qim3d.io.save(path2save,test_image,basename='test',sliced_dim=dim)
+ assert len(os.listdir(path2save))==test_image.shape[dim]
def calculate_image_hash(image):
image_bytes = image.tobytes()