diff --git a/qim3d/io/load.py b/qim3d/io/load.py
index c00988e2b12945d19d531b0379b3db6ae344ae95..8c8ea8d7f1b0e0559e151a70e6b7e7c3808d8c57 100644
--- a/qim3d/io/load.py
+++ b/qim3d/io/load.py
@@ -15,7 +15,7 @@ class DataLoader:
Args:
virtual_stack (bool, optional): Specifies whether to use virtual stack
- when loading TIFF files. Default is False.
+ when loading files. Default is False.
Attributes:
virtual_stack (bool): Specifies whether virtual stack is enabled.
@@ -24,6 +24,7 @@ class DataLoader:
load_tiff(path): Load a TIFF file from the specified path.
load_h5(path): Load an HDF5 file from the specified path.
load_tiff_stack(path): Load a stack of TIFF files from the specified path.
+ load_txrm(path): Load a TXRM/TXM/XRM file from the specified path
load(path): Load a file or directory based on the given path.
Raises:
@@ -40,7 +41,7 @@ class DataLoader:
Args:
path (str): The path to the file or directory.
virtual_stack (bool, optional): Specifies whether to use virtual
- stack when loading TIFF and HDF5 files. Default is False.
+ 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 files)
@@ -87,11 +88,11 @@ class DataLoader:
ValueError: If the specified dataset_name is not found or is invalid.
ValueError: If the dataset_name is not specified in case of multiple datasets in the HDF5 file
ValueError: If no datasets are found in the file.
-
"""
+
# Read file
f = h5py.File(path, "r")
- data_keys = self._get_h5_dataset_keys(f)
+ data_keys = _get_h5_dataset_keys(f)
datasets = []
metadata = {}
for key in data_keys:
@@ -169,8 +170,8 @@ class DataLoader:
Raises:
ValueError: If the 'contains' argument is not specified.
ValueError: If the 'contains' argument matches multiple TIFF stacks in the directory
-
"""
+
if not self.contains:
raise ValueError(
"Please specify a part of the name that is common for the TIFF file stack with the argument 'contains'"
@@ -191,7 +192,7 @@ class DataLoader:
raise ValueError(f"The provided part of the filename for the TIFF stack matches multiple TIFF stacks: {unique_names}.\nPlease provide a string that is unique for the TIFF stack that is intended to be loaded")
- vol = tifffile.imread([os.path.join(path, file) for file in tiff_stack])
+ vol = tifffile.imread([os.path.join(path, file) for file in tiff_stack],out='memmap')
if not self.virtual_stack:
vol = np.copy(vol) # Copy to memory
@@ -204,6 +205,40 @@ class DataLoader:
return vol
+ def load_txrm(self,path):
+ """Load a TXRM/XRM/TXM file from the specified path.
+
+ Args:
+ path (str): The path to the HDF5 file.
+
+ Returns:
+ numpy.ndarray or tuple: The loaded volume as a NumPy array.
+ If 'return_metadata' is True, returns a tuple (volume, metadata).
+
+ Raises:
+ ValueError: If the dxchange library is not installed
+ """
+
+ try:
+ import dxchange
+ except ImportError:
+ raise ValueError('The library dxchange is required to load TXRM files. Please find installation instructions at https://dxchange.readthedocs.io/en/latest/source/install.html')
+
+ vol, metadata = dxchange.read_txrm(path)
+ vol = vol.squeeze() # In case of an XRM file, the third redundant dimension is removed
+
+
+ log.info("Loaded shape: %s", vol.shape)
+ log.info("Using %s of memory", sizeof(sys.getsizeof(vol)))
+
+ if self.virtual_stack:
+ raise NotImplementedError("Using virtual stack for TXRM files is not implemented yet")
+
+ if self.return_metadata:
+ return vol, metadata
+ else:
+ return vol
+
def load(self, path):
"""
Load a file or directory based on the given path.
@@ -229,6 +264,8 @@ class DataLoader:
return self.load_tiff(path)
elif path.endswith(".h5"):
return self.load_h5(path)
+ elif path.endswith((".txrm",".txm",".xrm")):
+ return self.load_txrm(path)
else:
raise ValueError("Unsupported file format")
@@ -250,12 +287,12 @@ class DataLoader:
else:
raise ValueError("Invalid path")
- def _get_h5_dataset_keys(self, f):
- keys = []
- f.visit(
- lambda key: keys.append(key) if isinstance(f[key], h5py.Dataset) else None
- )
- return keys
+def _get_h5_dataset_keys(f):
+ keys = []
+ f.visit(
+ lambda key: keys.append(key) if isinstance(f[key], h5py.Dataset) else None
+ )
+ return keys
def load(path, virtual_stack=False, dataset_name=None, return_metadata=False, contains=None, **kwargs):
@@ -268,7 +305,7 @@ def load(path, virtual_stack=False, dataset_name=None, return_metadata=False, co
stack when loading TIFF and HDF5 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 files)
+ return_metadata (bool, optional): Specifies whether to return metadata or not. Default is False (only for HDF5 and TXRM 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)
**kwargs: Additional keyword arguments to be passed
to the DataLoader constructor.