From 3cc6ffd038960e1c82c90c48ae55133a07b94313 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 7 Sep 2023 10:56:31 +0200
Subject: [PATCH] Corrected and validated issue where axes are flipped in
exported TIFs
---
examples/ilastik3d.py | 5 +++--
model_server/ilastik.py | 22 +++++++++++-----------
model_server/image.py | 14 +++++++++-----
tests/test_ilastik.py | 4 ++--
tests/test_image.py | 24 ++++++++++++++++--------
5 files changed, 41 insertions(+), 28 deletions(-)
diff --git a/examples/ilastik3d.py b/examples/ilastik3d.py
index 0e381475..3f542533 100644
--- a/examples/ilastik3d.py
+++ b/examples/ilastik3d.py
@@ -65,6 +65,7 @@ if __name__ == '__main__':
resp_models = requests.get(uri + 'models')
- raise Exception('x, y axes are currently flipped in pixelmap')
+ # raise Exception('x, y axes are currently flipped in pixelmap')
- server_process.terminate()
\ No newline at end of file
+ server_process.terminate()
+ print('Finished')
\ No newline at end of file
diff --git a/model_server/ilastik.py b/model_server/ilastik.py
index d2490ba9..aad0f38c 100644
--- a/model_server/ilastik.py
+++ b/model_server/ilastik.py
@@ -57,22 +57,22 @@ class IlastikPixelClassifierModel(IlastikImageToImageModel):
return PixelClassificationWorkflow
def infer(self, input_img: GenericImageDataAccessor) -> (np.ndarray, dict):
- tagged_input_data = vigra.taggedView(input_img.data, 'xycz')
+ tagged_input_data = vigra.taggedView(input_img.data, 'yxcz')
dsi = [
{
'Raw Data': self.PreloadedArrayDatasetInfo(preloaded_array=tagged_input_data),
}
]
- pxmaps = self.shell.workflow.batchProcessingApplet.run_export(dsi, export_to_array=True) # [1 x w x h x n]
+ pxmaps = self.shell.workflow.batchProcessingApplet.run_export(dsi, export_to_array=True) # [z x h x w x n]
assert(len(pxmaps) == 1, 'ilastik generated more than one pixel map')
- xycz = np.moveaxis(
+ yxcz = np.moveaxis(
pxmaps[0],
- [2, 1, 3, 0],
+ [1, 2, 3, 0],
[0, 1, 2, 3]
)
- return InMemoryDataAccessor(data=xycz), {'success': True}
+ return InMemoryDataAccessor(data=yxcz), {'success': True}
class IlastikObjectClassifierModel(IlastikImageToImageModel):
model_id = 'ilastik_object_classification'
@@ -83,8 +83,8 @@ class IlastikObjectClassifierModel(IlastikImageToImageModel):
return ObjectClassificationWorkflow
def infer(self, input_img: GenericImageDataAccessor, pxmap_img: GenericImageDataAccessor) -> (np.ndarray, dict):
- tagged_input_data = vigra.taggedView(input_img.data, 'xycz')
- tagged_pxmap_data = vigra.taggedView(pxmap_img.data, 'xycz')
+ tagged_input_data = vigra.taggedView(input_img.data, 'yxcz')
+ tagged_pxmap_data = vigra.taggedView(pxmap_img.data, 'yxcz')
dsi = [
{
@@ -93,13 +93,13 @@ class IlastikObjectClassifierModel(IlastikImageToImageModel):
}
]
- obmaps = self.shell.workflow.batchProcessingApplet.run_export(dsi, export_to_array=True)
+ obmaps = self.shell.workflow.batchProcessingApplet.run_export(dsi, export_to_array=True) # [z x h x w x n]
assert (len(obmaps) == 1, 'ilastik generated more than one object map')
- xycz = np.moveaxis(
+ yxcz = np.moveaxis(
obmaps[0],
- [2, 1, 3, 0],
+ [1, 2, 3, 0],
[0, 1, 2, 3]
)
- return InMemoryDataAccessor(data=xycz), {'success': True}
+ return InMemoryDataAccessor(data=yxcz), {'success': True}
diff --git a/model_server/image.py b/model_server/image.py
index 8cbd37c1..d2b4da24 100644
--- a/model_server/image.py
+++ b/model_server/image.py
@@ -38,6 +38,10 @@ class GenericImageDataAccessor(ABC):
@property
def data(self):
+ """
+ Return data as 4d with axes in order of Y, X, C, Z
+ :return: np.ndarray
+ """
return self._data
@property
@@ -46,7 +50,7 @@ class GenericImageDataAccessor(ABC):
@property
def shape_dict(self):
- return dict(zip(('X', 'Y', 'C', 'Z'), self.data.shape))
+ return dict(zip(('Y', 'X', 'C', 'Z'), self.data.shape))
class InMemoryDataAccessor(GenericImageDataAccessor):
def __init__(self, data):
@@ -96,12 +100,12 @@ class CziImageFileAccessor(GenericImageFileAccessor):
def write_accessor_data_to_file(fpath: Path, accessor: GenericImageDataAccessor) -> bool:
try:
- zcxy = np.moveaxis(
- accessor.data,
- [3, 2, 1, 0],
+ zcyx= np.moveaxis(
+ accessor.data, # yxcz
+ [3, 2, 0, 1],
[0, 1, 2, 3]
)
- tifffile.imwrite(fpath, zcxy, imagej=True)
+ tifffile.imwrite(fpath, zcyx, imagej=True)
except:
raise FileWriteError(f'Unable to write data to file')
return True
diff --git a/tests/test_ilastik.py b/tests/test_ilastik.py
index 25c876b9..4af941d1 100644
--- a/tests/test_ilastik.py
+++ b/tests/test_ilastik.py
@@ -44,10 +44,10 @@ class TestIlastikPixelClassification(unittest.TestCase):
w = 512
h = 256
- input_img = InMemoryDataAccessor(data=np.random.rand(w, h, 1, 1))
+ input_img = InMemoryDataAccessor(data=np.random.rand(h, w, 1, 1))
pxmap, _ = model.infer(input_img)
- self.assertEqual(pxmap.shape, (w, h, 2, 1))
+ self.assertEqual(pxmap.shape, (h, w, 2, 1))
def test_run_pixel_classifier(self):
diff --git a/tests/test_image.py b/tests/test_image.py
index 00a746fe..6c085b6c 100644
--- a/tests/test_image.py
+++ b/tests/test_image.py
@@ -44,7 +44,9 @@ class TestCziImageFileAccess(unittest.TestCase):
self.assertEqual(cf.data.shape[3], mono.data.shape[2])
def test_conform_data_shorter_than_xycz(self):
- data = np.random.rand(256, 512, 1)
+ h = 256
+ w = 512
+ data = np.random.rand(h, w, 1)
acc = InMemoryDataAccessor(data)
self.assertEqual(
InMemoryDataAccessor.conform_data(data).shape,
@@ -52,7 +54,7 @@ class TestCziImageFileAccess(unittest.TestCase):
)
self.assertEqual(
acc.shape_dict,
- {'X': 256, 'Y': 512, 'C': 1, 'Z': 1}
+ {'Y': 256, 'X': 512, 'C': 1, 'Z': 1}
)
def test_conform_data_longer_than_xycz(self):
@@ -61,7 +63,7 @@ class TestCziImageFileAccess(unittest.TestCase):
acc = InMemoryDataAccessor(data)
- def test_write_multichannel_image_preserves_axes(self):
+ def test_write_multichannel_image_preserve_axes(self):
h = 256
w = 512
c = 3
@@ -69,12 +71,18 @@ class TestCziImageFileAccess(unittest.TestCase):
yxcz = (2**8 * np.random.rand(h, w, c, nz)).astype('uint8')
acc = InMemoryDataAccessor(yxcz)
+ fp = output_path / f'rand3d.tif'
self.assertTrue(
- write_accessor_data_to_file(
- output_path / f'rand3d.tif',
- acc
- )
+ write_accessor_data_to_file(fp, acc)
)
# need to sort out x,y flipping since np convention yxcz flips axes in 3d tif
self.assertEqual(acc.shape_dict['X'], w, acc.shape_dict)
- self.assertEqual(acc.shape_dict['Y'], h, acc.shape_dict)
\ No newline at end of file
+ self.assertEqual(acc.shape_dict['Y'], h, acc.shape_dict)
+
+ # re-open file and check axes order
+ from tifffile import TiffFile
+ fh = TiffFile(fp)
+ self.assertEqual(len(fh.series), 1)
+ se = fh.series[0]
+ fh_shape_dict = {se.axes[i]: se.shape[i] for i in range(0, len(se.shape))}
+ self.assertEqual(fh_shape_dict, acc.shape_dict, 'Axes are not preserved in TIF output')
--
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