From 7f82c04907eaca1355bb9da75eca72543f2ae46f Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Wed, 30 Aug 2023 10:44:40 +0200
Subject: [PATCH] Pixel map generation passes test, confirmed image orientation
and format are correct
---
model_server/ilastik.py | 24 ++++++++++++-----------
model_server/image.py | 7 ++++++-
tests/test_ilastik.py | 43 +++++++++++++++++++++++++++++------------
3 files changed, 50 insertions(+), 24 deletions(-)
diff --git a/model_server/ilastik.py b/model_server/ilastik.py
index 7be2269c..aadfad6a 100644
--- a/model_server/ilastik.py
+++ b/model_server/ilastik.py
@@ -7,6 +7,7 @@ from ilastik.workflows.pixelClassification import PixelClassificationWorkflow
from ilastik.workflows.objectClassification.objectClassificationWorkflow import ObjectClassificationWorkflow
import numpy as np
+import vigra
from model_server.image import GenericImageDataAccessor, InMemoryDataAccessor
from model_server.model import ImageToImageModel, ParameterExpectedError
@@ -14,11 +15,6 @@ from model_server.model import ImageToImageModel, ParameterExpectedError
class IlastikImageToImageModel(ImageToImageModel):
- # workflows = {
- # 'pixel_classification': PixelClassificationWorkflow,
- # 'object_classification': ObjectClassificationWorkflow,
- # }
-
def __init__(self, params, autoload=True):
if 'project_file' not in params or not os.path.exists(params['project_file']):
raise ParameterExpectedError('Ilastik model expects a project (*.ilp) file')
@@ -56,20 +52,26 @@ class IlastikImageToImageModel(ImageToImageModel):
return workflow.objectClassificationApplet.topLevelOperator
- # def infer(self, img, channel=None) -> (np.ndarray, dict):
- # assert self.operator.Classifier.ready()
-
class IlastikPixelClassifierModel(IlastikImageToImageModel):
workflow = PixelClassificationWorkflow
def infer(self, input_img: GenericImageDataAccessor, channel=None) -> (np.ndarray, dict):
+ tagged_input_data = vigra.taggedView(input_img.data, 'xycz')
dsi = [
{
- 'Raw Data': PreloadedArrayDatasetInfo(preloaded_array=input_img.data[0:3]),
+ 'Raw Data': PreloadedArrayDatasetInfo(preloaded_array=tagged_input_data),
}
]
- pxmaps = self.shell.workflow.batchProcessingApplet.run_export(dsi, export_to_array=True)
- return InMemoryDataAccessor(data=pxmaps[0])
+ pxmaps = self.shell.workflow.batchProcessingApplet.run_export(dsi, export_to_array=True) # [1 x w x h x n]
+
+ assert(len(pxmaps) == 1, 'ilastik generated more than on pixel map')
+
+ xycz = np.moveaxis(
+ pxmaps[0],
+ [2, 1, 3, 0],
+ [0, 1, 2, 3]
+ )
+ return InMemoryDataAccessor(data=xycz)
diff --git a/model_server/image.py b/model_server/image.py
index 863c2ec6..ca015a9c 100644
--- a/model_server/image.py
+++ b/model_server/image.py
@@ -95,7 +95,12 @@ class CziImageFileAccessor(GenericImageFileAccessor):
def write_accessor_data_to_file(fpath: Path, accessor: GenericImageDataAccessor) -> bool:
try:
- tifffile.imwrite(fpath, accessor.data)
+ zcxy = np.moveaxis(
+ accessor.data,
+ [3, 2, 0, 1],
+ [0, 1, 2, 3]
+ )
+ tifffile.imwrite(fpath, zcxy, 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 94a7cbbb..ac387a41 100644
--- a/tests/test_ilastik.py
+++ b/tests/test_ilastik.py
@@ -1,6 +1,9 @@
import unittest
+
+import numpy as np
+
from conf.testing import czifile, ilastik, output_path
-from model_server.image import CziImageFileAccessor, write_accessor_data_to_file
+from model_server.image import CziImageFileAccessor, InMemoryDataAccessor, write_accessor_data_to_file
from model_server.ilastik import IlastikPixelClassifierModel
class TestIlastikPixelClassification(unittest.TestCase):
@@ -18,21 +21,37 @@ class TestIlastikPixelClassification(unittest.TestCase):
with self.assertRaises(io.UnsupportedOperation):
faulthandler.enable(file=sys.stdout)
+ def test_run_pixel_classifier_on_random_data(self):
+ model = IlastikPixelClassifierModel({'project_file': ilastik['pixel_classifier']})
+ w = 512
+ h = 256
+
+ input_img = InMemoryDataAccessor(data=np.random.rand(w, h, 1, 1))
+
+ pxmap = model.infer(input_img)
+ self.assertEqual(pxmap.shape, (w, h, 2, 1))
+
def test_run_pixel_classifier(self):
channel = 2
model = IlastikPixelClassifierModel({'project_file': ilastik['pixel_classifier']})
cf = CziImageFileAccessor(czifile['path'])
- pxmap = model.infer(cf.get_one_channel_data(channel))
+ mono_image = cf.get_one_channel_data(channel)
+
+ self.assertEqual(mono_image.shape_dict['X'], czifile['w'])
+ self.assertEqual(mono_image.shape_dict['Y'], czifile['h'])
+ self.assertEqual(mono_image.shape_dict['C'], 1)
+ self.assertEqual(mono_image.shape_dict['Z'], 1)
+
+ pxmap = model.infer(mono_image)
+ self.assertEqual(pxmap.shape[0:2], cf.shape[0:2])
+ self.assertEqual(pxmap.shape_dict['C'], 2)
+ self.assertEqual(pxmap.shape_dict['Z'], 1)
print(pxmap.shape_dict)
+ self.assertTrue(
+ write_accessor_data_to_file(
+ output_path / f'pxmap_{cf.fpath.stem}_ch{channel}.tif',
+ pxmap
+ )
+ )
- # self.assertEqual(pxmap.shape[0:2], cf.shape[0:2])
- # self.assertEqual(pxmap.shape_dict['C'], 2)
- # self.assertEqual(pxmap.shape_dict['Z'], 1)
- #
- # self.assertTrue(
- # write_accessor_data_to_file(
- # output_path / f'pxmap_{cf.fpath.stem}_ch{channel}.tif',
- # pxmap
- # )
- # )
\ No newline at end of file
--
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