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Commit dfe9eb41 authored by Felipe Delestro Matos's avatar Felipe Delestro Matos
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Solving conflicts

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qim3d/io/load.py
+ 0
− 116
View file @ dfe9eb41
......@@ -24,10 +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.
<<<<<<< HEAD
=======
load_txrm(path): Load a TXRM/TXM/XRM file from the specified path
>>>>>>> main
load(path): Load a file or directory based on the given path.
Raises:
......@@ -44,11 +41,7 @@ class DataLoader:
Args:
path (str): The path to the file or directory.
virtual_stack (bool, optional): Specifies whether to use virtual
<<<<<<< HEAD
stack when loading TIFF and HDF5 files. Default is False.
=======
stack when loading files. Default is False.
>>>>>>> main
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)
......@@ -95,8 +88,6 @@ 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.
<<<<<<< HEAD
=======
"""
# Read file
......@@ -175,98 +166,11 @@ class DataLoader:
Returns:
numpy.ndarray: The loaded volume as a NumPy array.
>>>>>>> main
Raises:
ValueError: If the 'contains' argument is not specified.
ValueError: If the 'contains' argument matches multiple TIFF stacks in the directory
"""
<<<<<<< HEAD
# Read file
f = h5py.File(path, "r")
data_keys = self._get_h5_dataset_keys(f)
datasets = []
metadata = {}
for key in data_keys:
if (
f[key].ndim > 1
): # Data is assumed to be a dataset if it is two dimensions or more
datasets.append(key)
if f[key].attrs.keys():
metadata[key] = {
"value": f[key][()],
**{attr_key: val for attr_key, val in f[key].attrs.items()},
}
# Only one dataset was found
if len(datasets) == 1:
if self.dataset_name:
log.info(
"'dataset_name' argument is unused since there is only one dataset in the file"
)
name = datasets[0]
vol = f[name]
# Multiple datasets were found
elif len(datasets) > 1:
if self.dataset_name in datasets: # Provided dataset name is valid
name = self.dataset_name
vol = f[name]
else:
if self.dataset_name: # Dataset name is provided
similar_names = difflib.get_close_matches(
self.dataset_name, datasets
) # Find closest matching name if any
if similar_names:
suggestion = similar_names[0] # Get the closest match
raise ValueError(
f"Invalid dataset name. Did you mean '{suggestion}'?"
)
else:
raise ValueError(
f"Invalid dataset name. Please choose between the following datasets: {datasets}"
)
else:
raise ValueError(
f"Found multiple datasets: {datasets}. Please specify which of them that you want to load with the argument 'dataset_name'"
)
# No datasets were found
else:
raise ValueError(f"Did not find any data in the file: {path}")
if not self.virtual_stack:
vol = vol[()] # Load dataset into memory
f.close()
else:
log.info("Using virtual stack")
log.info("Loaded the following dataset: %s", name)
log.info("Loaded shape: %s", vol.shape)
log.info("Using %s of memory", sizeof(sys.getsizeof(vol)))
if self.return_metadata:
return vol, metadata
else:
return vol
def load_tiff_stack(self, path):
"""Load a stack of TIFF files from the specified path.
Args:
path (str): The path to the stack of TIFF files.
Returns:
numpy.ndarray: The loaded volume as a NumPy array.
Raises:
ValueError: If the 'contains' argument is not specified.
ValueError: If the 'contains' argument matches multiple TIFF stacks in the directory
"""
=======
>>>>>>> main
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'"
......@@ -287,11 +191,7 @@ 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")
<<<<<<< HEAD
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')
>>>>>>> main
if not self.virtual_stack:
vol = np.copy(vol) # Copy to memory
......@@ -304,8 +204,6 @@ class DataLoader:
return vol
<<<<<<< HEAD
=======
def load_txrm(self,path):
"""Load a TXRM/XRM/TXM file from the specified path.
......@@ -340,7 +238,6 @@ class DataLoader:
else:
return vol
>>>>>>> main
def load(self, path):
"""
Load a file or directory based on the given path.
......@@ -389,21 +286,12 @@ class DataLoader:
else:
raise ValueError("Invalid path")
<<<<<<< HEAD
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
>>>>>>> main
def load(path, virtual_stack=False, dataset_name=None, return_metadata=False, contains=None, **kwargs):
......@@ -416,11 +304,7 @@ 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)
<<<<<<< HEAD
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)
>>>>>>> main
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.
......
qim3d/viz/__init__.py
+ 0
− 4
View file @ dfe9eb41
<<<<<<< HEAD
from .img import grid_pred, grid_overview
from .visualizations import plot_metrics
=======
from .img import grid_pred, grid_overview, slice_viz
>>>>>>> main
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