From 6debd9c3708776b76d41910319b005377ca5fe8c Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 26 Oct 2023 15:51:44 +0200
Subject: [PATCH] Use patch stack accessor in a batch script
---
extensions/chaeo/accessors.py | 7 +++-
...fer_labels_to_ilastik_object_classifier.py | 36 ++++++++-----------
extensions/chaeo/tests/test_accessors.py | 10 +++---
3 files changed, 26 insertions(+), 27 deletions(-)
diff --git a/extensions/chaeo/accessors.py b/extensions/chaeo/accessors.py
index 32fb7020..d1e9089c 100644
--- a/extensions/chaeo/accessors.py
+++ b/extensions/chaeo/accessors.py
@@ -1,5 +1,5 @@
import numpy as np
-from model_server.accessors import InMemoryDataAccessor
+from model_server.accessors import generate_file_accessor, InMemoryDataAccessor
class MonoPatchStack(InMemoryDataAccessor):
@@ -44,6 +44,11 @@ class MonoPatchStack(InMemoryDataAccessor):
return [self.data[:, :, 0, zi] for zi in range(0, n)]
+class MonoPatchStackFromFile(MonoPatchStack):
+ def __init__(self, fpath):
+ super().__init__(generate_file_accessor(fpath).data[:, :, 0, :])
+
+
class Error(Exception):
pass
diff --git a/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py b/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py
index 49de008f..9e07ec2b 100644
--- a/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py
+++ b/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py
@@ -8,6 +8,7 @@ import skimage
import uuid
import vigra
+from extensions.chaeo.accessors import MonoPatchStack, MonoPatchStackFromFile
from extensions.ilastik.models import IlastikObjectClassifierFromSegmentationModel
from model_server.accessors import generate_file_accessor, GenericImageDataAccessor, InMemoryDataAccessor, write_accessor_data_to_file
@@ -17,22 +18,13 @@ class PatchStackObjectClassifier(IlastikObjectClassifierFromSegmentationModel):
as time-series images where each frame contains only one object.
"""
- @staticmethod
- def make_tczyx(acc: GenericImageDataAccessor):
- assert acc.chroma == 1
- tyx = np.moveaxis(
- acc.data[:, :, 0, :], # YX(C)Z
- [2, 0, 1],
- [0, 1, 2]
- )
- return np.expand_dims(tyx, (1, 2))
- def infer(self, input_img: GenericImageDataAccessor, segmentation_img: GenericImageDataAccessor) -> (np.ndarray, dict):
- assert segmentation_img.is_mask()
- assert input_img.chroma == 1
+ def infer(self, input_acc: MonoPatchStack, segmentation_acc: MonoPatchStack) -> (np.ndarray, dict):
+ assert segmentation_acc.is_mask()
+ assert input_acc.chroma == 1
- tagged_input_data = vigra.taggedView(self.make_tczyx(input_img), 'tczyx')
- tagged_seg_data = vigra.taggedView(self.make_tczyx(segmentation_img), 'tczyx')
+ tagged_input_data = vigra.taggedView(input_acc.make_tczyx(), 'tczyx')
+ tagged_seg_data = vigra.taggedView(segmentation_acc.make_tczyx(), 'tczyx')
dsi = [
{
@@ -46,14 +38,14 @@ class PatchStackObjectClassifier(IlastikObjectClassifierFromSegmentationModel):
assert len(obmaps) == 1, 'ilastik generated more than one object map'
# for some reason ilastik scrambles these axes to Z(1)YX(1)
- assert obmaps[0].shape == (input_img.nz, 1, input_img.hw[0], input_img.hw[1], 1)
+ assert obmaps[0].shape == (input_acc.nz, 1, input_acc.hw[0], input_acc.hw[1], 1)
yxcz = np.moveaxis(
obmaps[0][:, :, :, :, 0],
[2, 3, 1, 0],
[0, 1, 2, 3]
)
- assert yxcz.shape == input_img.shape
+ assert yxcz.shape == input_acc.shape
return InMemoryDataAccessor(data=yxcz), {'success': True}
def get_dataset_info(h5: h5py.File, lane : int = 0):
@@ -236,16 +228,16 @@ if __name__ == '__main__':
def infer_and_compare_training_set(ilp, suffix):
# infer object labels from the same data used to train the classifier
- train_zstack_raw = generate_file_accessor(where_patch_stack / 'zstack_train_raw.tif')
- train_zstack_mask = generate_file_accessor(where_patch_stack / 'zstack_train_mask.tif')
- train_truth_labels = generate_file_accessor(where_patch_stack / f'zstack_train_label.tif')
+ train_zstack_raw = MonoPatchStackFromFile(where_patch_stack / 'zstack_train_raw.tif')
+ train_zstack_mask = MonoPatchStackFromFile(where_patch_stack / 'zstack_train_mask.tif')
+ train_truth_labels = MonoPatchStackFromFile(where_patch_stack / f'zstack_train_label.tif')
infer_and_compare(ilp, 'train', suffix, train_zstack_raw, train_zstack_mask, train_truth_labels)
def infer_and_compare_test_set(ilp, suffix):
# infer object labels from test dataset
- test_zstack_raw = generate_file_accessor(where_patch_stack / 'zstack_test_raw.tif')
- test_zstack_mask = generate_file_accessor(where_patch_stack / 'zstack_test_mask.tif')
- test_truth_labels = generate_file_accessor(where_patch_stack / f'zstack_test_label.tif')
+ test_zstack_raw = MonoPatchStackFromFile(where_patch_stack / 'zstack_test_raw.tif')
+ test_zstack_mask = MonoPatchStackFromFile(where_patch_stack / 'zstack_test_mask.tif')
+ test_truth_labels = MonoPatchStackFromFile(where_patch_stack / f'zstack_test_label.tif')
infer_and_compare(ilp, 'test', suffix, test_zstack_raw, test_zstack_mask, test_truth_labels)
def infer_and_compare(ilp, prefix, suffix, raw, mask, labels):
diff --git a/extensions/chaeo/tests/test_accessors.py b/extensions/chaeo/tests/test_accessors.py
index 465f15e0..842b8fbc 100644
--- a/extensions/chaeo/tests/test_accessors.py
+++ b/extensions/chaeo/tests/test_accessors.py
@@ -15,13 +15,15 @@ class TestCziImageFileAccess(unittest.TestCase):
h = 512
n = 4
acc = MonoPatchStack(np.random.rand(h, w, n))
- assert acc.count == n
- assert acc.hw == (h, w)
+ self.assertEqual(acc.count, n)
+ self.assertEqual(acc.hw, (h, w))
+ self.assertEqual(acc.make_tczyx().shape, (n, 1, 1, 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
+ self.assertEqual(acc.count, n)
+ self.assertEqual(acc.hw, (h, w))
+ self.assertEqual(acc.make_tczyx().shape, (n, 1, 1, h, w))
\ No newline at end of file
--
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