From 03786d1444782252b336c6630b5bb2eb91d0aa0a Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 3 Jun 2024 16:11:50 +0200
Subject: [PATCH] Renamed get_one_channel_data to get_mono
---
model_server/base/accessors.py | 2 +-
model_server/base/roiset.py | 2 +-
model_server/base/workflows.py | 2 +-
model_server/extensions/ilastik/models.py | 2 +-
model_server/extensions/ilastik/tests/test_ilastik.py | 4 ++--
tests/test_accessors.py | 10 +++++-----
tests/test_model.py | 2 +-
tests/test_roiset.py | 6 +++---
8 files changed, 15 insertions(+), 15 deletions(-)
diff --git a/model_server/base/accessors.py b/model_server/base/accessors.py
index 73cafd08..6f596ab7 100644
--- a/model_server/base/accessors.py
+++ b/model_server/base/accessors.py
@@ -56,7 +56,7 @@ class GenericImageDataAccessor(ABC):
nda = self.data.take(indices=carr, axis=self._ga('C'))
return self._derived_accessor(nda)
- def get_one_channel_data(self, channel: int, mip: bool = False):
+ def get_mono(self, channel: int, mip: bool = False):
return self.get_channels([channel], mip=mip)
def _gc(self, channels):
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 11deff15..69c45e39 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -358,7 +358,7 @@ class RoiSet(object):
raw_acc = self.get_patches_acc(channels=channels, expanded=False, pad_to=None) # all channels
if derived_channel_functions is not None:
- mono_data = [raw_acc.get_one_channel_data(c).data for c in range(0, raw_acc.chroma)]
+ mono_data = [raw_acc.get_mono(c).data for c in range(0, raw_acc.chroma)]
for fcn in derived_channel_functions:
der = fcn(raw_acc) # returns patch stack
if der.shape != mono_data[0].shape or der.dtype not in ['uint8', 'uint16']:
diff --git a/model_server/base/workflows.py b/model_server/base/workflows.py
index 912f6062..9ff6f57c 100644
--- a/model_server/base/workflows.py
+++ b/model_server/base/workflows.py
@@ -42,7 +42,7 @@ def classify_pixels(fpi: Path, model: SemanticSegmentationModel, where_output: P
"""
ti = Timer()
ch = kwargs.get('channel')
- img = generate_file_accessor(fpi).get_one_channel_data(ch)
+ img = generate_file_accessor(fpi).get_mono(ch)
ti.click('file_input')
outdata = model.label_pixel_class(img)
diff --git a/model_server/extensions/ilastik/models.py b/model_server/extensions/ilastik/models.py
index e8afb238..b40ed066 100644
--- a/model_server/extensions/ilastik/models.py
+++ b/model_server/extensions/ilastik/models.py
@@ -313,7 +313,7 @@ class IlastikObjectClassifierFromPixelPredictionsModel(IlastikModel, ImageToImag
raise InvalidInputImageError('Expecting input image and pixel probabilities to be the same shape')
pxch = kwargs.get('pixel_classification_channel', 0)
pxtr = kwargs.get('pixel_classification_threshold', 0.5)
- mask = img._derived_accessor(pxmap.get_one_channel_data(pxch).data > pxtr)
+ mask = img._derived_accessor(pxmap.get_mono(pxch).data > pxtr)
obmap, _ = self.infer(img, mask)
return obmap
diff --git a/model_server/extensions/ilastik/tests/test_ilastik.py b/model_server/extensions/ilastik/tests/test_ilastik.py
index f4e0b41c..c9358796 100644
--- a/model_server/extensions/ilastik/tests/test_ilastik.py
+++ b/model_server/extensions/ilastik/tests/test_ilastik.py
@@ -22,7 +22,7 @@ class TestIlastikPixelClassification(unittest.TestCase):
self.model = ilm.IlastikPixelClassifierModel(
params=ilm.IlastikPixelClassifierParams(project_file=ilastik_classifiers['px'].__str__())
)
- self.mono_image = self.cf.get_one_channel_data(self.channel)
+ self.mono_image = self.cf.get_mono(self.channel)
def test_faulthandler(self): # recreate error that is messing up ilastik
@@ -436,7 +436,7 @@ class TestIlastikOnMultichannelInputs(TestServerBaseClass):
class TestIlastikObjectClassification(unittest.TestCase):
def setUp(self):
stack = generate_file_accessor(roiset_test_data['multichannel_zstack']['path'])
- stack_ch_pa = stack.get_one_channel_data(roiset_test_data['pipeline_params']['patches_channel'])
+ stack_ch_pa = stack.get_mono(roiset_test_data['pipeline_params']['patches_channel'])
seg_mask = generate_file_accessor(roiset_test_data['multichannel_zstack']['mask_path'])
self.roiset = RoiSet(
diff --git a/tests/test_accessors.py b/tests/test_accessors.py
index 0375ee1a..d2f06655 100644
--- a/tests/test_accessors.py
+++ b/tests/test_accessors.py
@@ -45,7 +45,7 @@ class TestCziImageFileAccess(unittest.TestCase):
nz = 11
c = 3
cf = InMemoryDataAccessor(_random_int(h, w, nc, nz))
- sc = cf.get_one_channel_data(c)
+ sc = cf.get_mono(c)
self.assertEqual(sc.shape, (h, w, 1, nz))
def test_get_single_channel_mip_from_zstack(self):
@@ -55,13 +55,13 @@ class TestCziImageFileAccess(unittest.TestCase):
nz = 11
c = 3
cf = InMemoryDataAccessor(np.random.rand(h, w, nc, nz))
- sc = cf.get_one_channel_data(c, mip=True)
+ sc = cf.get_mono(c, mip=True)
self.assertEqual(sc.shape, (h, w, 1, 1))
def test_write_single_channel_tif(self):
ch = 4
cf = CziImageFileAccessor(czifile['path'])
- mono = cf.get_one_channel_data(ch)
+ mono = cf.get_mono(ch)
self.assertTrue(
write_accessor_data_to_file(
output_path / f'{cf.fpath.stem}_ch{ch}.tif',
@@ -246,7 +246,7 @@ class TestPatchStackAccessor(unittest.TestCase):
def test_get_one_channel(self):
acc = self.test_pczyx()
- mono = acc.get_one_channel_data(channel=1)
+ mono = acc.get_mono(channel=1)
for a in 'PXYZ':
self.assertEqual(mono.shape_dict[a], acc.shape_dict[a])
self.assertEqual(mono.shape_dict['C'], 1)
@@ -261,7 +261,7 @@ class TestPatchStackAccessor(unittest.TestCase):
def test_get_one_channel_mip(self):
acc = self.test_pczyx()
- mono_mip = acc.get_one_channel_data(channel=1, mip=True)
+ mono_mip = acc.get_mono(channel=1, mip=True)
for a in 'PXY':
self.assertEqual(mono_mip.shape_dict[a], acc.shape_dict[a])
for a in 'CZ':
diff --git a/tests/test_model.py b/tests/test_model.py
index 3f9f2872..91043f24 100644
--- a/tests/test_model.py
+++ b/tests/test_model.py
@@ -25,7 +25,7 @@ class TestCziImageFileAccess(unittest.TestCase):
def test_dummy_pixel_segmentation(self):
model = DummySemanticSegmentationModel()
- img = self.cf.get_one_channel_data(0)
+ img = self.cf.get_mono(0)
mask = model.label_pixel_class(img)
w = czifile['w']
diff --git a/tests/test_roiset.py b/tests/test_roiset.py
index ed1327de..efc0779f 100644
--- a/tests/test_roiset.py
+++ b/tests/test_roiset.py
@@ -19,7 +19,7 @@ class BaseTestRoiSetMonoProducts(object):
def setUp(self) -> None:
# set up test raw data and segmentation from file
self.stack = generate_file_accessor(roiset_test_data['multichannel_zstack']['path'])
- self.stack_ch_pa = self.stack.get_one_channel_data(roiset_test_data['pipeline_params']['patches_channel'])
+ self.stack_ch_pa = self.stack.get_mono(roiset_test_data['pipeline_params']['patches_channel'])
self.seg_mask = generate_file_accessor(roiset_test_data['multichannel_zstack']['mask_path'])
@@ -376,7 +376,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
)
result = generate_file_accessor(where / df_res.patch_path.iloc[0])
self.assertEqual(result.chroma, 3)
- self.assertEqual(result.get_one_channel_data(2).data.max(), 0) # blue channel is black
+ self.assertEqual(result.get_mono(2).data.max(), 0) # blue channel is black
def test_multichannel_to_multichannel_tif_patches(self):
where = output_path / 'multichannel' / 'multichannel_tif_patches'
@@ -523,7 +523,7 @@ class TestRoiSetSerialization(unittest.TestCase):
def setUp(self) -> None:
# set up test raw data and segmentation from file
self.stack = generate_file_accessor(roiset_test_data['multichannel_zstack']['path'])
- self.stack_ch_pa = self.stack.get_one_channel_data(roiset_test_data['pipeline_params']['segmentation_channel'])
+ self.stack_ch_pa = self.stack.get_mono(roiset_test_data['pipeline_params']['segmentation_channel'])
self.seg_mask_3d = generate_file_accessor(roiset_test_data['multichannel_zstack']['mask_path_3d'])
@staticmethod
--
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