From 55af627bf4912096cec41410f1c2e493b5d27fb3 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 3 Jun 2024 16:16:27 +0200
Subject: [PATCH] Added and tested apply function to support pipeline-line
operations
---
model_server/base/accessors.py | 10 ++++++++++
tests/test_accessors.py | 3 +--
2 files changed, 11 insertions(+), 2 deletions(-)
diff --git a/model_server/base/accessors.py b/model_server/base/accessors.py
index 6f596ab7..f5db79c2 100644
--- a/model_server/base/accessors.py
+++ b/model_server/base/accessors.py
@@ -110,6 +110,16 @@ class GenericImageDataAccessor(ABC):
def shape_dict(self):
return dict(zip(('Y', 'X', 'C', 'Z'), self.data.shape))
+ def apply(self, func):
+ """
+ Apply func to data and return as a new in-memory accessor
+ :param func: function that receives and returns the same size np.ndarray
+ :return: InMemoryDataAccessor
+ """
+ return InMemoryDataAccessor(
+ func(self.data)
+ )
+
class InMemoryDataAccessor(GenericImageDataAccessor):
def __init__(self, data):
self._data = self.conform_data(data)
diff --git a/tests/test_accessors.py b/tests/test_accessors.py
index d2f06655..014eda2c 100644
--- a/tests/test_accessors.py
+++ b/tests/test_accessors.py
@@ -73,11 +73,10 @@ class TestCziImageFileAccess(unittest.TestCase):
def test_write_two_channel_png(self):
from model_server.base.process import resample_to_8bit
- ch = 2
cf = CziImageFileAccessor(czifile['path'])
acc = cf.get_channels([0, 1])
opa = output_path / f'{cf.fpath.stem}_2ch.png'
- acc_out = InMemoryDataAccessor(resample_to_8bit(acc.data))
+ acc_out = acc.apply(resample_to_8bit)
self.assertTrue(
write_accessor_data_to_file(opa, acc_out)
--
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