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Commit 77f73208 authored by Stefan Peter Engelmann Jensen's avatar Stefan Peter Engelmann Jensen
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Refactoring and updated docstrings in load.py + hotfix in system.py

parent a48a138a
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1 merge request!29Load common formats
This commit is part of merge request !29. Comments created here will be created in the context of that merge request.
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qim3d/io/load.py
+ 31
− 14
View file @ 77f73208
...@@ -46,7 +46,7 @@ class DataLoader: ...@@ -46,7 +46,7 @@ class DataLoader:
stack when loading files. Default is False. stack when loading files. Default is False.
dataset_name (str, optional): Specifies the name of the dataset to be loaded 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) 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). 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. Default is None.
""" """
...@@ -62,7 +62,8 @@ class DataLoader: ...@@ -62,7 +62,8 @@ class DataLoader:
path (str): The path to the TIFF file. path (str): The path to the TIFF file.
Returns: 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: if self.virtual_stack:
...@@ -81,7 +82,8 @@ class DataLoader: ...@@ -81,7 +82,8 @@ class DataLoader:
path (str): The path to the HDF5 file. path (str): The path to the HDF5 file.
Returns: 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). If 'self.return_metadata' is True, returns a tuple (volume, metadata).
Raises: Raises:
...@@ -162,7 +164,8 @@ class DataLoader: ...@@ -162,7 +164,8 @@ class DataLoader:
path (str): The path to the stack of TIFF files. path (str): The path to the stack of TIFF files.
Returns: 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: Raises:
ValueError: If the 'contains' argument is not specified. ValueError: If the 'contains' argument is not specified.
...@@ -215,7 +218,7 @@ class DataLoader: ...@@ -215,7 +218,7 @@ class DataLoader:
path (str): The path to the HDF5 file. path (str): The path to the HDF5 file.
Returns: 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). If 'self.return_metadata' is True, returns a tuple (volume, metadata).
Raises: Raises:
...@@ -253,7 +256,8 @@ class DataLoader: ...@@ -253,7 +256,8 @@ class DataLoader:
path (str): The path to the NIfTI file. path (str): The path to the NIfTI file.
Returns: 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). If 'self.return_metadata' is True, returns a tuple (volume, metadata).
""" """
...@@ -281,7 +285,7 @@ class DataLoader: ...@@ -281,7 +285,7 @@ class DataLoader:
path (str): The path to the image supported by PIL. path (str): The path to the image supported by PIL.
Returns: Returns:
numpy.ndarray: The loaded image/volume as a NumPy array. numpy.ndarray: The loaded image/volume.
""" """
return np.array(Image.open(path)) return np.array(Image.open(path))
...@@ -293,8 +297,9 @@ class DataLoader: ...@@ -293,8 +297,9 @@ class DataLoader:
path (str or os.PathLike): The path to the file or directory. path (str or os.PathLike): The path to the file or directory.
Returns: 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: Raises:
ValueError: If the format is not supported ValueError: If the format is not supported
ValueError: If the file or directory does not exist. ValueError: If the file or directory does not exist.
...@@ -373,8 +378,9 @@ def load( ...@@ -373,8 +378,9 @@ def load(
to the DataLoader constructor. to the DataLoader constructor.
Returns: 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 'return_metadata' is True and file format is either HDF5 or TXRM/TXM/XRM, returns a tuple (volume, metadata). 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: Example:
data = qim3d.io.load("image.tif", virtual_stack=True) data = qim3d.io.load("image.tif", virtual_stack=True)
...@@ -390,16 +396,27 @@ def load( ...@@ -390,16 +396,27 @@ def load(
data = loader.load(path) data = loader.load(path)
if not virtual_stack:
def log_memory_info(data):
mem = Memory() mem = Memory()
log.info( log.info(
"Volume using %s of memory\n", "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() 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: else:
# 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") log.info("Using virtual stack")
else:
log.warning('Virtual stack is not supported for this file format')
log_memory_info(data)
return data return data
......
qim3d/utils/system.py
+ 3
− 3
View file @ 77f73208
...@@ -19,7 +19,7 @@ class Memory: ...@@ -19,7 +19,7 @@ class Memory:
self.total = mem.total self.total = mem.total
self.free = mem.available 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 = mem.total - mem.available
self.used_pct = mem.percent self.used_pct = mem.percent
...@@ -28,7 +28,7 @@ class Memory: ...@@ -28,7 +28,7 @@ class Memory:
"System memory:\n • Total.: %s\n • Used..: %s (%s%%)\n • Free..: %s (%s%%)", "System memory:\n • Total.: %s\n • Used..: %s (%s%%)\n • Free..: %s (%s%%)",
sizeof(self.total), sizeof(self.total),
sizeof(self.used), sizeof(self.used),
round(self.used_pct, 2), round(self.used_pct, 1),
sizeof(self.free), sizeof(self.free),
round(self.free_pct, 2), round(self.free_pct, 1),
) )
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