diff --git a/model_server/base/accessors.py b/model_server/base/accessors.py
index b250605d4df5de6b1cd18d3a2570a85ed532f319..43d400f9587253b4e2fd2fc62a59ceb1acd39857 100644
--- a/model_server/base/accessors.py
+++ b/model_server/base/accessors.py
@@ -24,6 +24,10 @@ class GenericImageDataAccessor(ABC):
"""
pass
+ @property
+ def loaded(self):
+ return self._data is not None
+
@property
def chroma(self):
return self.shape_dict['C']
@@ -38,6 +42,7 @@ class GenericImageDataAccessor(ABC):
def is_3d(self):
return True if self.shape_dict['Z'] > 1 else False
+ # TODO: no direct calls to self._data outside load/unload methods
def is_mask(self):
return is_mask(self._data)
@@ -198,7 +203,7 @@ class InMemoryDataAccessor(GenericImageDataAccessor):
self._data = self.conform_data(data)
class GenericImageFileAccessor(GenericImageDataAccessor): # image data is loaded from a file
- def __init__(self, fpath: Path):
+ def __init__(self, fpath: Path, lazy=False):
"""
Interface for image data that originates in an image file
:param fpath: absolute path to image file
@@ -208,6 +213,15 @@ class GenericImageFileAccessor(GenericImageDataAccessor): # image data is loaded
raise FileAccessorError(f'Could not find file at {fpath}')
self.fpath = fpath
+ if not lazy:
+ self._data = self.load()
+ else:
+ self._data = None
+
+ @abstractmethod
+ def load(self):
+ pass
+
@staticmethod
def read(fp: Path):
return generate_file_accessor(fp)
@@ -219,12 +233,12 @@ class GenericImageFileAccessor(GenericImageDataAccessor): # image data is loaded
return d
class TifSingleSeriesFileAccessor(GenericImageFileAccessor):
- def __init__(self, fpath: Path):
- super().__init__(fpath)
+ def load(self):
+ fpath = self.fpath
try:
tf = tifffile.TiffFile(fpath)
- self.tf = tf
+ self.tf = tf # TODO: close file connection
except Exception:
raise FileAccessorError(f'Unable to access data in {fpath}')
@@ -251,14 +265,15 @@ class TifSingleSeriesFileAccessor(GenericImageFileAccessor):
[0, 1, 2, 3]
)
- self._data = self.conform_data(yxcz.reshape(yxcz.shape[0:4]))
+ return self.conform_data(yxcz.reshape(yxcz.shape[0:4]))
+ # TODO: remove
def __del__(self):
self.tf.close()
class PngFileAccessor(GenericImageFileAccessor):
- def __init__(self, fpath: Path):
- super().__init__(fpath)
+ def load(self):
+ fpath = self.fpath
try:
arr = imread(fpath)
@@ -266,19 +281,19 @@ class PngFileAccessor(GenericImageFileAccessor):
FileAccessorError(f'Unable to access data in {fpath}')
if len(arr.shape) == 3: # rgb
- self._data = np.expand_dims(arr, 3)
+ return np.expand_dims(arr, 3)
else: # mono
- self._data = np.expand_dims(arr, (2, 3))
+ return np.expand_dims(arr, (2, 3))
class CziImageFileAccessor(GenericImageFileAccessor):
"""
- Image that is stored in a Zeiss .CZI file; may be multi-channel, and/or a z-stack,
- but not a time series or multiposition acquisition.
+ Image that is stored in a Zeiss .CZI file; may be multi-channel, and/or a z-stack, but not a time series
+ or multiposition acquisition. Read the whole file as a single accessor, no interaction with subblocks.
"""
- def __init__(self, fpath: Path):
- super().__init__(fpath)
-
+ def load(self):
+ fpath = self.fpath
try:
+ # TODO: persist metadata then remove file connection
cf = czifile.CziFile(fpath)
self.czifile = cf
except Exception:
@@ -302,7 +317,7 @@ class CziImageFileAccessor(GenericImageFileAccessor):
[cf.axes.index(ch) for ch in idx],
[0, 1, 2, 3]
)
- self._data = self.conform_data(yxcz.reshape(yxcz.shape[0:4]))
+ return self.conform_data(yxcz.reshape(yxcz.shape[0:4]))
def __del__(self):
self.czifile.close()
@@ -363,21 +378,21 @@ def write_accessor_data_to_file(fpath: Path, acc: GenericImageDataAccessor, mkdi
return True
-def generate_file_accessor(fpath):
+def generate_file_accessor(fpath, **kwargs):
"""
Given an image file path, return an image accessor, assuming the file is a supported format and represents
a single position array, which may be single or multichannel, single plane or z-stack.
"""
if str(fpath).upper().endswith('.TIF') or str(fpath).upper().endswith('.TIFF'):
- return TifSingleSeriesFileAccessor(fpath)
+ return TifSingleSeriesFileAccessor(fpath, **kwargs)
elif str(fpath).upper().endswith('.CZI'):
- return CziImageFileAccessor(fpath)
+ return CziImageFileAccessor(fpath, **kwargs)
elif str(fpath).upper().endswith('.PNG'):
- return PngFileAccessor(fpath)
+ return PngFileAccessor(fpath, **kwargs)
else:
raise FileAccessorError(f'Could not match a file accessor with {fpath}')
-
+# TODO: implement lazy loading at patch stack level
class PatchStack(InMemoryDataAccessor):
axes = 'PYXCZ'
diff --git a/model_server/base/session.py b/model_server/base/session.py
index 1dfd8f3078d9adba0f103e776821f3691d2adb47..5f8c6611e7cd476a4d4a83cc53289d6b94744635 100644
--- a/model_server/base/session.py
+++ b/model_server/base/session.py
@@ -163,10 +163,11 @@ class _Session(object):
if accessor_id is None:
idx = len(self.accessors)
accessor_id = f'acc_{idx:06d}'
- self.accessors[accessor_id] = {'loaded': True, 'object': acc, **acc.info}
+ self.accessors[accessor_id] = {'loaded': acc.loaded, 'object': acc, **acc.info}
self.log_info(f'Added accessor {accessor_id}')
return accessor_id
+ # TODO: divergent cases between lazy file-backed accessor (with its own loaded state) and in-memory ones
def del_accessor(self, accessor_id: str) -> str:
"""
Remove accessor object but retain its info dictionary
diff --git a/tests/base/test_accessors.py b/tests/base/test_accessors.py
index e73e347029f5ec42cd01696ebdf01a0ae4c0cff0..f17053988cb814d83b047036f37762d33328255d 100644
--- a/tests/base/test_accessors.py
+++ b/tests/base/test_accessors.py
@@ -228,6 +228,9 @@ class TestCziImageFileAccess(unittest.TestCase):
)
)
+ def test_lazy_load(self):
+ cf = generate_file_accessor(data['czifile']['path'])
+ self.assertEqual(1, 0)
class TestPatchStackAccessor(unittest.TestCase):
def setUp(self) -> None: