diff --git a/model_server/base/accessors.py b/model_server/base/accessors.py
index 712bbacf19296201775e1d7d49ef45b356ac1d1d..c6a787bc4c12918b64d06e95c97c50cf4ad2fc53 100644
--- a/model_server/base/accessors.py
+++ b/model_server/base/accessors.py
@@ -8,6 +8,7 @@ from skimage.io import imread
import czifile
import tifffile
+from extensions.chaeo.accessors import InvalidDataForPatchStackError
from model_server.base.process import is_mask
class GenericImageDataAccessor(ABC):
@@ -234,4 +235,68 @@ class InvalidAxisKey(Error):
pass
class InvalidDataShape(Error):
- pass
\ No newline at end of file
+ pass
+
+
+class PatchStack(InMemoryDataAccessor):
+
+ def __init__(self, data):
+ """
+ A sequence of n (generally) color 3D images of the same size
+ :param data: either a list of np.ndarrays of size YXCZ, or np.ndarray of size PYXCZ
+ """
+
+ if isinstance(data, list): # list of YXCZ patches
+ n = len(data)
+ yxcz_shape = np.array([e.shape for e in data]).max(axis=0)
+ nda = np.zeros(
+ (n, *yxcz_shape), dtype=data[0].dtype
+ )
+ for i in range(0, len(data)):
+ s = tuple([slice(0, c) for c in data[i].shape])
+ nda[i][s] = data[i]
+
+ elif isinstance(data, np.ndarray) and len(data.shape) == 5: # interpret as PYXCZ
+ nda = data
+ else:
+ raise InvalidDataForPatchStackError(f'Cannot create accessor from {type(data)}')
+
+ assert nda.ndim == 5
+ self._data = nda
+
+ def iat(self, i):
+ return self.data[i, :, :, :, :]
+
+ def iat_yxcz(self, i):
+ return self.iat(i)
+
+ @property
+ def count(self):
+ return self.shape_dict['P']
+
+ @property
+ def shape_dict(self):
+ return dict(zip(('P', 'Y', 'X', 'C', 'Z'), self.data.shape))
+
+ def get_list(self):
+ n = self.nz
+ return [self.data[:, :, 0, zi] for zi in range(0, n)]
+
+ @property
+ def pyxcz(self):
+ return self.data
+
+ @property
+ def pczyx(self):
+ return np.moveaxis(
+ self.data,
+ [0, 3, 4, 1, 2],
+ [0, 1, 2, 3, 4]
+ )
+ @property
+ def shape(self):
+ return self.data.shape
+
+ @property
+ def shape_dict(self):
+ return dict(zip(('P', 'Y', 'X', 'C', 'Z'), self.data.shape))
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 608e9d0965f5ea68f6186b36eb9c591dcb91f6fa..819f8552660f1051f2bf3e713faf74d21e58d508 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -17,7 +17,8 @@ from model_server.base.accessors import GenericImageDataAccessor, InMemoryDataAc
from model_server.base.models import InstanceSegmentationModel
from model_server.base.process import pad, rescale, resample_to_8bit, make_rgb
from base.annotators import draw_box_on_patch, draw_contours_on_patch, draw_boxes_on_3d_image
-from model_server.extensions.chaeo.accessors import write_patch_to_file, PatchStack
+from model_server.extensions.chaeo.accessors import write_patch_to_file
+from base.accessors import PatchStack
from base.process import mask_largest_object
diff --git a/model_server/extensions/chaeo/accessors.py b/model_server/extensions/chaeo/accessors.py
index 45eee67b63847ba4df80814fd2d6a1fc0f154550..2307d80ccb0b90bd70e2ca03c6a3b14800069e65 100644
--- a/model_server/extensions/chaeo/accessors.py
+++ b/model_server/extensions/chaeo/accessors.py
@@ -7,67 +7,6 @@ from tifffile import imwrite
from base.process import make_rgb
from model_server.base.accessors import generate_file_accessor, InMemoryDataAccessor
-class MonoPatchStack(InMemoryDataAccessor):
-
- def __init__(self, data):
- """
- A sequence of n monochrome images of the same size
- :param data: either np.ndarray of dimensions YXn, or a list of np.ndarrays of size YX
- """
-
- if isinstance(data, np.ndarray):
- if data.ndim == 3: # interpret as YXZ
- self._data = np.expand_dims(data, 2)
- elif data.ndim == 4: # interpret as a copy another patch stack
- self._data = data
- else:
- raise InvalidDataForPatchStackError()
- elif isinstance(data, list): # list of YX patches
- if len(data) == 0:
- self._data = np.ndarray([0, 0, 0, 0], dtype='uin9')
- elif len(data) == 1:
- self._data = np.expand_dims(
- np.array(
- data[0].squeeze()
- ),
- (2, 3)
- )
- else:
- nda = np.array(data).squeeze()
- assert nda.ndim == 3
- self._data = np.expand_dims(
- np.moveaxis(
- nda,
- [1, 2, 0],
- [0, 1, 2]),
- 2
- )
- else:
- raise InvalidDataForPatchStackError(f'Cannot create accessor from {type(data)}')
-
- def make_tczyx(self):
- assert self.chroma == 1
- tyx = np.moveaxis(
- self.data[:, :, 0, :], # YX(C)Z
- [2, 0, 1],
- [0, 1, 2]
- )
- return np.expand_dims(tyx, (1, 2))
-
- @property
- def count(self):
- return self.nz
-
- def iat(self, i):
- return self.data[:, :, 0, i]
-
- def iat_yxcz(self, i):
- return np.expand_dims(self.iat(i), (2, 3))
-
- def get_list(self):
- n = self.nz
- return [self.data[:, :, 0, zi] for zi in range(0, n)]
-
class MonoPatchStackFromFile(MonoPatchStack):
def __init__(self, fpath):
@@ -81,70 +20,6 @@ class MonoPatchStackFromFile(MonoPatchStack):
return self.file_acc.fpath
-class PatchStack(InMemoryDataAccessor):
-
- def __init__(self, data):
- """
- A sequence of n (generally) color 3D images of the same size
- :param data: either a list of np.ndarrays of size YXCZ, or np.ndarray of size PYXCZ
- """
-
- if isinstance(data, list): # list of YXCZ patches
- n = len(data)
- yxcz_shape = np.array([e.shape for e in data]).max(axis=0)
- nda = np.zeros(
- (n, *yxcz_shape), dtype=data[0].dtype
- )
- for i in range(0, len(data)):
- s = tuple([slice(0, c) for c in data[i].shape])
- nda[i][s] = data[i]
-
- elif isinstance(data, np.ndarray) and len(data.shape) == 5: # interpret as PYXCZ
- nda = data
- else:
- raise InvalidDataForPatchStackError(f'Cannot create accessor from {type(data)}')
-
- assert nda.ndim == 5
- self._data = nda
-
- def iat(self, i):
- return self.data[i, :, :, :, :]
-
- def iat_yxcz(self, i):
- return self.iat(i)
-
- @property
- def count(self):
- return self.shape_dict['P']
-
- @property
- def shape_dict(self):
- return dict(zip(('P', 'Y', 'X', 'C', 'Z'), self.data.shape))
-
- def get_list(self):
- n = self.nz
- return [self.data[:, :, 0, zi] for zi in range(0, n)]
-
- @property
- def pyxcz(self):
- return self.data
-
- @property
- def pczyx(self):
- return np.moveaxis(
- self.data,
- [0, 3, 4, 1, 2],
- [0, 1, 2, 3, 4]
- )
- @property
- def shape(self):
- return self.data.shape
-
- @property
- def shape_dict(self):
- return dict(zip(('P', 'Y', 'X', 'C', 'Z'), self.data.shape))
-
-
def write_patch_to_file(where, fname, yxcz):
ext = fname.split('.')[-1].upper()
where.mkdir(parents=True, exist_ok=True)
diff --git a/model_server/extensions/chaeo/tests/test_accessors.py b/model_server/extensions/chaeo/tests/test_accessors.py
index 0aa364c794de074524ecc231ee602208a8c99b4a..a92c058c6d9c490ba47f9b5d0d250c7acd8a8030 100644
--- a/model_server/extensions/chaeo/tests/test_accessors.py
+++ b/model_server/extensions/chaeo/tests/test_accessors.py
@@ -3,8 +3,8 @@ import unittest
import numpy as np
from model_server.conf.testing import monozstackmask
-from model_server.extensions.chaeo.accessors import MonoPatchStackFromFile, PatchStack
-
+from model_server.extensions.chaeo.accessors import MonoPatchStackFromFile
+from base.accessors import PatchStack
class TestMultipositionCziImageFileAccess(unittest.TestCase):
diff --git a/model_server/extensions/ilastik/models.py b/model_server/extensions/ilastik/models.py
index 9a6de5e86bf9d13a1aa2d7e62af7ba974acd2920..91493a2bed5fc0f676206a3cf1b75a3ff4f7c00b 100644
--- a/model_server/extensions/ilastik/models.py
+++ b/model_server/extensions/ilastik/models.py
@@ -5,7 +5,7 @@ import numpy as np
import vigra
import model_server.extensions.ilastik.conf
-from extensions.chaeo.accessors import PatchStack
+from base.accessors import PatchStack
from model_server.base.accessors import GenericImageDataAccessor, InMemoryDataAccessor
from model_server.base.models import Model, ImageToImageModel, InstanceSegmentationModel, InvalidInputImageError, ParameterExpectedError, SemanticSegmentationModel