diff --git a/model_server/base/accessors.py b/model_server/base/accessors.py
index c6a787bc4c12918b64d06e95c97c50cf4ad2fc53..fec80c819ad808a1f8ca2afa09b6b0fd65a8b4fe 100644
--- a/model_server/base/accessors.py
+++ b/model_server/base/accessors.py
@@ -185,6 +185,14 @@ class CziImageFileAccessor(GenericImageFileAccessor):
def write_accessor_data_to_file(fpath: Path, accessor: GenericImageDataAccessor, mkdir=True) -> bool:
+ """
+ Export an image accessor to file.
+ :param fpath: complete path including filename and extension
+ :param accessor: image accessor to be written
+ :param mkdir: create any needed subdirectories in fpath if True
+ :return: True
+ """
+
if mkdir:
fpath.parent.mkdir(parents=True, exist_ok=True)
try:
@@ -207,6 +215,10 @@ def write_accessor_data_to_file(fpath: Path, accessor: GenericImageDataAccessor,
def generate_file_accessor(fpath):
+ """
+ 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 multi-channel, single plane or z-stack.
+ """
if str(fpath).upper().endswith('.TIF') or str(fpath).upper().endswith('.TIFF'):
return TifSingleSeriesFileAccessor(fpath)
elif str(fpath).upper().endswith('.CZI'):
@@ -216,27 +228,6 @@ def generate_file_accessor(fpath):
else:
raise FileAccessorError(f'Could not match a file accessor with {fpath}')
-class Error(Exception):
- pass
-
-class FileAccessorError(Error):
- pass
-
-class FileNotFoundError(Error):
- pass
-
-class DataShapeError(Error):
- pass
-
-class FileWriteError(Error):
- pass
-
-class InvalidAxisKey(Error):
- pass
-
-class InvalidDataShape(Error):
- pass
-
class PatchStack(InMemoryDataAccessor):
@@ -293,6 +284,7 @@ class PatchStack(InMemoryDataAccessor):
[0, 3, 4, 1, 2],
[0, 1, 2, 3, 4]
)
+
@property
def shape(self):
return self.data.shape
@@ -300,3 +292,41 @@ class PatchStack(InMemoryDataAccessor):
@property
def shape_dict(self):
return dict(zip(('P', 'Y', 'X', 'C', 'Z'), self.data.shape))
+
+
+def make_patch_stack_from_file(fpath): # interpret z-dimension as patch position
+ if not Path(fpath).exists():
+ raise FileNotFoundError(f'Could not find {fpath}')
+
+ pyxc = np.moveaxis(
+ generate_file_accessor(fpath).data, # yxcz
+ [0, 1, 2, 3],
+ [1, 2, 3, 0]
+ )
+ pyxcz = np.expand_dims(pyxc, axis=3)
+ return PatchStack(pyxcz)
+
+
+class Error(Exception):
+ pass
+
+class FileAccessorError(Error):
+ pass
+
+class FileNotFoundError(Error):
+ pass
+
+class DataShapeError(Error):
+ pass
+
+class FileWriteError(Error):
+ pass
+
+class InvalidAxisKey(Error):
+ pass
+
+class InvalidDataShape(Error):
+ pass
+
+
+
diff --git a/model_server/extensions/chaeo/accessors.py b/model_server/extensions/chaeo/accessors.py
index 2307d80ccb0b90bd70e2ca03c6a3b14800069e65..7c9f74e57caf5413e515e89eff49622967cd4c2c 100644
--- a/model_server/extensions/chaeo/accessors.py
+++ b/model_server/extensions/chaeo/accessors.py
@@ -1,25 +1,11 @@
-from pathlib import Path
-
import numpy as np
from skimage.io import imsave
from tifffile import imwrite
from base.process import make_rgb
-from model_server.base.accessors import generate_file_accessor, InMemoryDataAccessor
-
-
-class MonoPatchStackFromFile(MonoPatchStack):
- def __init__(self, fpath):
- if not Path(fpath).exists():
- raise FileNotFoundError(f'Could not find {fpath}')
- self.file_acc = generate_file_accessor(fpath)
- super().__init__(self.file_acc.data[:, :, 0, :])
-
- @property
- def fpath(self):
- return self.file_acc.fpath
+# TODO: move this as method in base.accessors
def write_patch_to_file(where, fname, yxcz):
ext = fname.split('.')[-1].upper()
where.mkdir(parents=True, exist_ok=True)
@@ -52,7 +38,4 @@ class Error(Exception):
class InvalidDataForPatchStackError(Error):
pass
-class FileNotFoundError(Error):
- pass
-
diff --git a/model_server/extensions/chaeo/models.py b/model_server/extensions/chaeo/models.py
index 1a969db316e2e4a469f4c879770ae83c37d03e68..58235d81ed8d56845d220cd6203b7ed22ec6624c 100644
--- a/model_server/extensions/chaeo/models.py
+++ b/model_server/extensions/chaeo/models.py
@@ -5,16 +5,15 @@ import h5py
import numpy as np
import skimage
-from model_server.extensions.chaeo.accessors import MonoPatchStackFromFile
-
+from model_server.extensions.chaeo.accessors import PatchStack
def generate_ilastik_object_classifier(
template_ilp: Path,
target_ilp: Path,
- raw_stack: MonoPatchStackFromFile,
- mask_stack: MonoPatchStackFromFile,
- label_stack: MonoPatchStackFromFile,
+ raw_stack: PatchStack,
+ mask_stack: PatchStack,
+ label_stack: PatchStack,
label_names: list,
lane: int = 0,
allow_multiple_objects=True,
diff --git a/model_server/extensions/chaeo/tests/test_accessors.py b/model_server/extensions/chaeo/tests/test_accessors.py
index a92c058c6d9c490ba47f9b5d0d250c7acd8a8030..c51f31ca49af2694c0cec8306920ff557d463b75 100644
--- a/model_server/extensions/chaeo/tests/test_accessors.py
+++ b/model_server/extensions/chaeo/tests/test_accessors.py
@@ -3,8 +3,7 @@ import unittest
import numpy as np
from model_server.conf.testing import monozstackmask
-from model_server.extensions.chaeo.accessors import MonoPatchStackFromFile
-from base.accessors import PatchStack
+from base.accessors import PatchStack, make_patch_stack_from_file, FileNotFoundError
class TestMultipositionCziImageFileAccess(unittest.TestCase):
@@ -36,16 +35,15 @@ class TestMultipositionCziImageFileAccess(unittest.TestCase):
w = monozstackmask['w']
c = monozstackmask['c']
n = monozstackmask['z']
- acc = MonoPatchStackFromFile(monozstackmask['path'])
+
+ acc = make_patch_stack_from_file(monozstackmask['path'])
self.assertEqual(acc.hw, (h, w))
self.assertEqual(acc.count, n)
- self.assertEqual(acc.make_tczyx().shape, (n, c, 1, h, w))
- self.assertEqual(acc.fpath, monozstackmask['path'])
+ self.assertEqual(acc.pyxcz.shape, (n, h, w, c, 1))
def test_raises_filenotfound(self):
- from model_server.extensions.chaeo.accessors import FileNotFoundError
with self.assertRaises(FileNotFoundError):
- acc = MonoPatchStackFromFile('c:/fake/file/name.tif')
+ acc = make_patch_stack_from_file('c:/fake/file/name.tif')
def test_make_3d_patch_stack_from_nonuniform_list(self):
w = 256