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Load common formats

Merged Load common formats
load_common_formats into main
Merged s184058 requested to merge load_common_formats into main
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qim3d/io/load.py
+ 47
− 14
@@ -11,6 +11,7 @@ import qim3d
from qim3d.io.logger import log
from qim3d.utils.internal_tools import sizeof, stringify_path
from qim3d.utils.system import Memory
from PIL import Image, UnidentifiedImageError
class DataLoader:
@@ -45,7 +46,7 @@ class DataLoader:
stack when loading files. Default is False.
dataset_name (str, optional): Specifies the name of the dataset to be loaded
in case multiple dataset exist within the same file. Default is None (only for HDF5 files)
return_metadata (bool, optional): Specifies whether to return metadata or not. Default is False (only for HDF5 and TXRM/TXM/XRM files)
return_metadata (bool, optional): Specifies whether to return metadata or not. Default is False (only for HDF5, TXRM/TXM/XRM and NIfTI files)
contains (str, optional): Specifies a part of the name that is common for the TIFF file stack to be loaded (only for TIFF stacks).
Default is None.
"""
@@ -61,7 +62,8 @@ class DataLoader:
path (str): The path to the TIFF file.
Returns:
numpy.ndarray: The loaded volume as a NumPy array.
numpy.ndarray or numpy.memmap: The loaded volume.
If 'self.virtual_stack' is True, returns a numpy.memmap object.
"""
if self.virtual_stack:
@@ -80,7 +82,8 @@ class DataLoader:
path (str): The path to the HDF5 file.
Returns:
numpy.ndarray or tuple: The loaded volume as a NumPy array.
numpy.ndarray, h5py._hl.dataset.Dataset or tuple: The loaded volume.
If 'self.virtual_stack' is True, returns a h5py._hl.dataset.Dataset object
If 'self.return_metadata' is True, returns a tuple (volume, metadata).
Raises:
@@ -161,7 +164,8 @@ class DataLoader:
path (str): The path to the stack of TIFF files.
Returns:
numpy.ndarray: The loaded volume as a NumPy array.
numpy.ndarray or numpy.memmap: The loaded volume.
If 'self.virtual_stack' is True, returns a numpy.memmap object.
Raises:
ValueError: If the 'contains' argument is not specified.
@@ -214,7 +218,7 @@ class DataLoader:
path (str): The path to the HDF5 file.
Returns:
numpy.ndarray or tuple: The loaded volume as a NumPy array.
numpy.ndarray or tuple: The loaded volume.
If 'self.return_metadata' is True, returns a tuple (volume, metadata).
Raises:
@@ -252,7 +256,8 @@ class DataLoader:
path (str): The path to the NIfTI file.
Returns:
numpy.ndarray or tuple: The loaded volume as a NumPy array.
numpy.ndarray, nibabel.arrayproxy.ArrayProxy or tuple: The loaded volume.
If 'self.virtual_stack' is True, returns a nibabel.arrayproxy.ArrayProxy object
If 'self.return_metadata' is True, returns a tuple (volume, metadata).
"""
@@ -272,6 +277,17 @@ class DataLoader:
return vol, metadata
else:
return vol
def load_pil(self, path):
"""Load a PIL image from the specified path
Args:
path (str): The path to the image supported by PIL.
Returns:
numpy.ndarray: The loaded image/volume.
"""
return np.array(Image.open(path))
def load(self, path):
"""
@@ -281,8 +297,9 @@ class DataLoader:
path (str or os.PathLike): The path to the file or directory.
Returns:
numpy.ndarray: The loaded volume as a NumPy array.
numpy.ndarray, numpy.memmap, h5py._hl.dataset.Dataset, nibabel.arrayproxy.ArrayProxy or tuple: The loaded volume.
If 'self.virtual_stack' is True, returns numpy.memmap, h5py._hl.dataset.Dataset or nibabel.arrayproxy.ArrayProxy depending on file format
If 'self.return_metadata' is True and file format is either HDF5, NIfTI or TXRM/TXM/XRM, returns a tuple (volume, metadata).
Raises:
ValueError: If the format is not supported
ValueError: If the file or directory does not exist.
@@ -292,6 +309,7 @@ class DataLoader:
data = loader.load("image.tif")
"""
# Stringify path in case it is not already a string
path = stringify_path(path)
# Load a file
@@ -306,7 +324,10 @@ class DataLoader:
elif path.endswith((".nii",".nii.gz")):
return self.load_nifti(path)
else:
raise ValueError("Unsupported file format")
try:
return self.load_pil(path)
except UnidentifiedImageError:
raise ValueError("Unsupported file format")
# Load a directory
elif os.path.isdir(path):
@@ -357,8 +378,9 @@ def load(
to the DataLoader constructor.
Returns:
numpy.ndarray: The loaded volume as a NumPy array.
If 'return_metadata' is True and file format is either HDF5 or TXRM/TXM/XRM, returns a tuple (volume, metadata).
numpy.ndarray, numpy.memmap, h5py._hl.dataset.Dataset, nibabel.arrayproxy.ArrayProxy or tuple: The loaded volume.
If 'virtual_stack' is True, returns numpy.memmap, h5py._hl.dataset.Dataset or nibabel.arrayproxy.ArrayProxy depending on file format
If 'return_metadata' is True and file format is either HDF5, NIfTI or TXRM/TXM/XRM, returns a tuple (volume, metadata).
Example:
data = qim3d.io.load("image.tif", virtual_stack=True)
@@ -374,16 +396,27 @@ def load(
data = loader.load(path)
if not virtual_stack:
def log_memory_info(data):
mem = Memory()
log.info(
"Volume using %s of memory\n",
sizeof(data[0].nbytes if return_metadata else data.nbytes),
sizeof(data[0].nbytes if isinstance(data, tuple) else data.nbytes),
)
mem.report()
if return_metadata and not isinstance(data,tuple):
log.warning('The file format does not contain metadata')
if not virtual_stack:
log_memory_info(data)
else:
log.info("Using virtual stack")
# Only log if file type is not a np.ndarray, i.e., it is some kind of memmap object
if not isinstance( data[0] if isinstance(data,tuple) else data, np.ndarray ):
log.info("Using virtual stack")
else:
log.warning('Virtual stack is not supported for this file format')
log_memory_info(data)
return data