From eb0b6e033f71911c1b90fc05121507fb0795f6c5 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 19 Feb 2024 11:32:50 +0100
Subject: [PATCH] Converge to a single PatchStack accessor class
---
model_server/base/roiset.py | 4 +-
model_server/extensions/chaeo/accessors.py | 45 ++++++++++--------
.../extensions/chaeo/tests/test_accessors.py | 46 ++++++-------------
3 files changed, 42 insertions(+), 53 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 0314c4f9..09fc6c42 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -17,7 +17,7 @@ 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, MonoPatchStack, Multichannel3dPatchStack
+from model_server.extensions.chaeo.accessors import write_patch_to_file, MonoPatchStack, PatchStack
from base.process import mask_largest_object
@@ -234,7 +234,7 @@ class RoiSet(object):
if channel is not None or self.acc_raw.chroma == 1:
return MonoPatchStack(patches)
else:
- return Multichannel3dPatchStack(patches)
+ return PatchStack(patches)
def export_annotated_zstack(self, where, prefix='zstack', **kwargs):
annotated = InMemoryDataAccessor(draw_boxes_on_3d_image(self, **kwargs))
diff --git a/model_server/extensions/chaeo/accessors.py b/model_server/extensions/chaeo/accessors.py
index 1f1278a3..ee9bfd07 100644
--- a/model_server/extensions/chaeo/accessors.py
+++ b/model_server/extensions/chaeo/accessors.py
@@ -80,30 +80,33 @@ class MonoPatchStackFromFile(MonoPatchStack):
def fpath(self):
return self.file_acc.fpath
-# TODO: unify this into one accessor
-class Multichannel3dPatchStack(InMemoryDataAccessor):
+
+class PatchStack(InMemoryDataAccessor):
def __init__(self, data):
"""
A sequence of n (generally) color 3D images of the same size
- :param data: a list of np.ndarrays of size YXCZ
+ :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
- nda = np.zeros((len(data), *np.array([e.shape for e in data]).max(axis=0)), dtype=data[0].dtype)
+ 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)):
- nzi = data[i].shape[-1]
- nda[i, :, :, :, 0:nzi] = data[i]
- assert nda.ndim == 5
- # self._data = np.moveaxis( # pos-YXCZ
- # nda,
- # [0, 1, 2, 0, 3],
- # [0, 1, 2, 3]
- # )
- self._data = nda
+ 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, :, :, :, :]
@@ -115,11 +118,15 @@ class Multichannel3dPatchStack(InMemoryDataAccessor):
return self.shape_dict['P']
@property
- def data(self):
- """
- Return data as 5d with axes in order of pos, Y, X, C, Z
- :return: np.ndarray
- """
+ 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
@@ -141,7 +148,7 @@ def write_patch_to_file(where, fname, yxcz):
assert yxcz.shape[3] == 1, f'Cannot export z-stacks as PNGs'
if yxcz.shape[2] == 1:
outdata = yxcz[:, :, 0, 0]
- elif yxcz.shape[2] == 2: # add a blank blue channel
+ elif yxcz.shape[2] == 2: # add a blank blue channel
outdata = make_rgb(yxcz)
else: # preserve RGB order
outdata = yxcz[:, :, :, 0]
diff --git a/model_server/extensions/chaeo/tests/test_accessors.py b/model_server/extensions/chaeo/tests/test_accessors.py
index a717c2ac..086b405c 100644
--- a/model_server/extensions/chaeo/tests/test_accessors.py
+++ b/model_server/extensions/chaeo/tests/test_accessors.py
@@ -3,7 +3,7 @@ import unittest
import numpy as np
from model_server.conf.testing import monozstackmask
-from model_server.extensions.chaeo.accessors import MonoPatchStack, MonoPatchStackFromFile, Multichannel3dPatchStack
+from model_server.extensions.chaeo.accessors import MonoPatchStackFromFile, PatchStack
@@ -15,27 +15,21 @@ class TestMultipositionCziImageFileAccess(unittest.TestCase):
w = 256
h = 512
n = 4
- acc = MonoPatchStack(np.random.rand(h, w, n))
+ acc = PatchStack(np.random.rand(n, h, w, 1, 1))
self.assertEqual(acc.count, n)
self.assertEqual(acc.hw, (h, w))
- self.assertEqual(acc.make_tczyx().shape, (n, 1, 1, h, w))
+ self.assertEqual(acc.pyxcz.shape, (n, h, w, 1, 1))
def test_make_patch_stack_from_list(self):
w = 256
h = 512
n = 4
- acc = MonoPatchStack([np.random.rand(h, w) for _ in range(0, n)])
+ acc = PatchStack([np.random.rand(h, w, 1, 1) for _ in range(0, n)])
self.assertEqual(acc.count, n)
self.assertEqual(acc.hw, (h, w))
- self.assertEqual(acc.make_tczyx().shape, (n, 1, 1, h, w))
+ self.assertEqual(acc.pyxcz.shape, (n, h, w, 1, 1))
return acc
- def test_make_patch_stack_clone(self):
- w = 256
- h = 512
- n = 4
- acc = MonoPatchStack([np.random.rand(h, w) for _ in range(0, n)])
- self.assertEqual(MonoPatchStack(acc.data).shape, acc.shape)
def test_make_patch_stack_from_file(self):
h = monozstackmask['h']
@@ -53,30 +47,18 @@ class TestMultipositionCziImageFileAccess(unittest.TestCase):
with self.assertRaises(FileNotFoundError):
acc = MonoPatchStackFromFile('c:/fake/file/name.tif')
- def test_patch_as_yxcz_array(self):
- w = 256
- h = 512
- n = 4
- acc = MonoPatchStack([np.random.rand(h, w) for _ in range(0, 4)])
- self.assertEqual(acc.iat_yxcz(0).shape, (h, w, 1, 1))
-
- def test_make_3d_patch_stack_from_list(self):
+ def test_make_3d_patch_stack_from_nonuniform_list(self):
w = 256
h = 512
c = 1
nz = 5
n = 4
- acc = Multichannel3dPatchStack([np.random.rand(h, w, c, nz) for _ in range(0, n)])
- self.assertEqual(acc.count, n)
- self.assertEqual(acc.hw, (h, w))
- self.assertEqual(acc.chroma, c)
- self.assertEqual(acc.iat(0).shape, (h, w, c, nz))
- def test_3d_patch_as_yxcz_array(self):
- w = 256
- h = 512
- nz = 5
- c = 1
- n = 4
- acc = Multichannel3dPatchStack([np.random.rand(h, w, c, nz) for _ in range(0, n)])
- self.assertEqual(acc.iat_yxcz(0).shape, (h, w, c, nz))
\ No newline at end of file
+ patches = [np.random.rand(h, w, c, nz) for _ in range(0, n)]
+ patches.append(np.random.rand(h, 2 * w, c, nz))
+ acc = PatchStack(patches)
+ self.assertEqual(acc.count, n + 1)
+ self.assertEqual(acc.hw, (h, 2 * w))
+ self.assertEqual(acc.chroma, c)
+ self.assertEqual(acc.iat(0).shape, (h, 2 * w, c, nz))
+ self.assertEqual(acc.iat_yxcz(0).shape, (h, 2 * w, c, nz))
\ No newline at end of file
--
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