From 4d16baa59f4e86e8d43e964764de9ef957d1147e Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 26 Oct 2023 15:40:02 +0200
Subject: [PATCH] Split out patch/patch mask creation for file export;
implemented and test accessor abstraction for patch arrays
---
extensions/chaeo/accessors.py | 51 ++++++++++++++++
extensions/chaeo/products.py | 76 ++++++++++++++++++++----
extensions/chaeo/tests/test_accessors.py | 27 +++++++++
3 files changed, 141 insertions(+), 13 deletions(-)
create mode 100644 extensions/chaeo/accessors.py
create mode 100644 extensions/chaeo/tests/test_accessors.py
diff --git a/extensions/chaeo/accessors.py b/extensions/chaeo/accessors.py
new file mode 100644
index 00000000..32fb7020
--- /dev/null
+++ b/extensions/chaeo/accessors.py
@@ -0,0 +1,51 @@
+import numpy as np
+from model_server.accessors import 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): # interpret as YXZ
+ assert len(data.shape) == 3
+ self._data = np.expand_dims(data, 2)
+ elif isinstance(data, list): # list of YX patches
+ self._data = np.expand_dims(
+ np.moveaxis(
+ np.array(data),
+ [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 get_list(self):
+ n = self.nz
+ return [self.data[:, :, 0, zi] for zi in range(0, n)]
+
+
+class Error(Exception):
+ pass
+
+class InvalidDataForPatchStackError(Error):
+ pass
\ No newline at end of file
diff --git a/extensions/chaeo/products.py b/extensions/chaeo/products.py
index e665d878..a9310e37 100644
--- a/extensions/chaeo/products.py
+++ b/extensions/chaeo/products.py
@@ -9,6 +9,7 @@ from skimage.io import imsave
from skimage.measure import find_contours, shannon_entropy
from tifffile import imwrite
+from extensions.chaeo.accessors import MonoPatchStack
from extensions.chaeo.annotators import draw_box_on_patch, draw_contours_on_patch
from model_server.accessors import GenericImageDataAccessor, InMemoryDataAccessor
from model_server.process import pad, rescale, resample_to_8bit
@@ -55,16 +56,13 @@ def _write_patch_to_file(where, fname, data):
else:
raise Exception(f'Unsupported file extension: {ext}')
-def export_patch_masks_from_zstack(
- where: Path,
+def get_patch_masks_from_zmask_meta(
stack: GenericImageDataAccessor,
zmask_meta: list,
pad_to: int = 256,
- prefix='mask',
-):
- exported = []
+) -> MonoPatchStack:
+ patches = []
for mi in zmask_meta:
- obj = mi['info']
sl = mi['slice']
rbb = mi['relative_bounding_box']
@@ -82,27 +80,48 @@ def export_patch_masks_from_zstack(
if pad_to:
patch = pad(patch, pad_to)
+ patches.append(patch)
+ return MonoPatchStack(patches)
+
+def export_patch_masks_from_zstack(
+ where: Path,
+ stack: GenericImageDataAccessor,
+ zmask_meta: list,
+ pad_to: int = 256,
+ prefix='mask',
+ **kwargs
+):
+ patches_acc = get_patch_masks_from_zmask_meta(
+ stack,
+ zmask_meta,
+ pad_to=pad_to,
+ **kwargs
+ )
+ assert len(zmask_meta) == patches_acc.count
+
+ exported = []
+ for i in range(0, len(zmask_meta)):
+ mi = zmask_meta[i]
+ obj = mi['info']
+ patch = patches_acc.iat(i)
ext = 'png'
fname = f'{prefix}-la{obj.label:04d}-zi{obj.zi:04d}.{ext}'
_write_patch_to_file(where, fname, patch)
exported.append(fname)
return exported
-def export_patches_from_zstack(
- where: Path,
+def get_patches_from_zmask_meta(
stack: GenericImageDataAccessor,
zmask_meta: list,
rescale_clip: float = 0.0,
pad_to: int = 256,
make_3d: bool = False,
- prefix='patch',
focus_metric: str = None,
**kwargs
-):
-
- exported = []
+) -> MonoPatchStack:
+ patches = []
for mi in zmask_meta:
- obj = mi['info']
+
sl = mi['slice']
rbb = mi['relative_bounding_box']
idx = mi['df_index']
@@ -177,6 +196,37 @@ def export_patches_from_zstack(
if pad_to:
patch = pad(patch, pad_to)
+ patches.append(patch)
+ return MonoPatchStack(patches)
+
+def export_patches_from_zstack(
+ where: Path,
+ stack: GenericImageDataAccessor,
+ zmask_meta: list,
+ rescale_clip: float = 0.0,
+ pad_to: int = 256,
+ make_3d: bool = False,
+ prefix='patch',
+ focus_metric: str = None,
+ **kwargs
+):
+ patches_acc = get_patches_from_zmask_meta(
+ stack,
+ zmask_meta,
+ rescale_clip=rescale_clip,
+ pad_to=pad_to,
+ make_3d=make_3d,
+ focus_metric=focus_metric,
+ **kwargs
+ )
+ assert len(zmask_meta) == patches_acc.count
+
+ exported = []
+ for i in range(0, len(zmask_meta)):
+ mi = zmask_meta[i]
+ patch = patches_acc.iat(i)
+ obj = mi['info']
+ idx = mi['df_index']
ext = 'tif' if make_3d else 'png'
fname = f'{prefix}-la{obj.label:04d}-zi{obj.zi:04d}.{ext}'
diff --git a/extensions/chaeo/tests/test_accessors.py b/extensions/chaeo/tests/test_accessors.py
new file mode 100644
index 00000000..465f15e0
--- /dev/null
+++ b/extensions/chaeo/tests/test_accessors.py
@@ -0,0 +1,27 @@
+import unittest
+
+import numpy as np
+
+from extensions.chaeo.accessors import MonoPatchStack
+
+
+
+class TestCziImageFileAccess(unittest.TestCase):
+ def setUp(self) -> None:
+ pass
+
+ def test_make_patch_stack_from_list(self):
+ w = 256
+ h = 512
+ n = 4
+ acc = MonoPatchStack(np.random.rand(h, w, n))
+ assert acc.count == n
+ assert acc.hw == (h, w)
+
+ def test_make_patch_stack_from_3d_array(self):
+ w = 256
+ h = 512
+ n = 4
+ acc = MonoPatchStack([np.random.rand(h, w) for _ in range(0, 4)])
+ assert acc.count == n
+ assert acc.hw == (h, w)
\ No newline at end of file
--
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