base.accessors method to make patch mask from file

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
+
+
+

model_server/extensions/chaeo/accessors.py

-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
-
 

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,

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