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Save tiff stack

Merged Save tiff stack
save_tiff_stack into main
Merged s184058 requested to merge save_tiff_stack into main
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qim3d/io/save.py
+ 135
− 40
@@ -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)