diff --git a/qim3d/io/load.py b/qim3d/io/load.py
index 880f7b7a5fe25af0a846a5b6effa3a0a352490df..4d67274de5f4ea26099b39a846ecf369d5abd33b 100644
--- a/qim3d/io/load.py
+++ b/qim3d/io/load.py
@@ -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
diff --git a/qim3d/utils/system.py b/qim3d/utils/system.py
index 383060df8c8fad875df4c4984325b7fb0f92ed6a..57ac08c2a3c1e1d6d886e28dec42d878843f0baf 100644
--- a/qim3d/utils/system.py
+++ b/qim3d/utils/system.py
@@ -19,7 +19,7 @@ class Memory:
self.total = mem.total
self.free = mem.available
- self.free_pct = (mem.free / mem.total) * 100
+ self.free_pct = (mem.available / mem.total) * 100
self.used = mem.total - mem.available
self.used_pct = mem.percent
@@ -28,7 +28,7 @@ class Memory:
"System memory:\n • Total.: %s\n • Used..: %s (%s%%)\n • Free..: %s (%s%%)",
sizeof(self.total),
sizeof(self.used),
- round(self.used_pct, 2),
+ round(self.used_pct, 1),
sizeof(self.free),
- round(self.free_pct, 2),
+ round(self.free_pct, 1),
)