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Commit b4beb644 authored by s184058's avatar s184058 Committed by fima
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Save tiff stack

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qim3d/io/save.py
+ 135
− 40
View file @ b4beb644
......@@ -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)
qim3d/tests/io/test_save.py
+ 63
− 3
View file @ b4beb644
......@@ -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)
......@@ -142,7 +144,9 @@ 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
......@@ -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()
......
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