From e3162d6bf63329c90ca09eee9637dd4211a8d5e3 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Tue, 29 Aug 2023 15:58:18 +0200
Subject: [PATCH] Updated test for channel selection, and conforming image data
to XYCZ order
---
api.py | 2 +-
model_server/ilastik.py | 9 +++++----
model_server/image.py | 32 ++++++++++++++++++++++----------
model_server/model.py | 9 ++++-----
model_server/workflow.py | 4 ++--
tests/test_api.py | 15 +++++++++++----
tests/test_ilastik.py | 21 +++++++++++++++++----
tests/test_image.py | 20 +++++++++++++++++++-
tests/test_model.py | 8 ++++----
tests/test_workflow.py | 4 ++--
10 files changed, 87 insertions(+), 37 deletions(-)
diff --git a/api.py b/api.py
index 89e42d8f..1bf0f17d 100644
--- a/api.py
+++ b/api.py
@@ -30,7 +30,7 @@ def load_model(model_id: str, params: Dict[str, str] = None) -> dict:
session.load_model(model_id, params=params)
return session.describe_loaded_models()
-@app.put('/i2i/infer/{model_id}') # image file in, image file out
+@app.put('/i2i/infer/') # image file in, image file out
def infer_img(model_id: str, input_filename: str, channel: int = None) -> dict:
if model_id not in session.describe_loaded_models().keys():
raise HTTPException(
diff --git a/model_server/ilastik.py b/model_server/ilastik.py
index a345925f..7be2269c 100644
--- a/model_server/ilastik.py
+++ b/model_server/ilastik.py
@@ -8,7 +8,8 @@ from ilastik.workflows.objectClassification.objectClassificationWorkflow import
import numpy as np
-from model_server.model import GenericImageDataAccessor, ImageToImageModel, ParameterExpectedError
+from model_server.image import GenericImageDataAccessor, InMemoryDataAccessor
+from model_server.model import ImageToImageModel, ParameterExpectedError
class IlastikImageToImageModel(ImageToImageModel):
@@ -64,11 +65,11 @@ class IlastikPixelClassifierModel(IlastikImageToImageModel):
def infer(self, input_img: GenericImageDataAccessor, channel=None) -> (np.ndarray, dict):
dsi = [
{
- 'Raw Data': PreloadedArrayDatasetInfo(preloaded_array=input_img.data),
+ 'Raw Data': PreloadedArrayDatasetInfo(preloaded_array=input_img.data[0:3]),
}
]
- pxmap = self.shell.workflow.batchProcessingApplet.run_export(dsi, export_to_array=True)
- return pxmap
+ pxmaps = self.shell.workflow.batchProcessingApplet.run_export(dsi, export_to_array=True)
+ return InMemoryDataAccessor(data=pxmaps[0])
diff --git a/model_server/image.py b/model_server/image.py
index 2e314d1b..4bea66a1 100644
--- a/model_server/image.py
+++ b/model_server/image.py
@@ -14,7 +14,7 @@ class GenericImageDataAccessor(ABC):
def __init__(self):
"""
Abstract base class that exposes an interfaces for image data, irrespective of whether it is instantiated
- from file I/O or other means.
+ from file I/O or other means. Enforces X, Y, C, Z dimensions in that order.
"""
pass
@@ -22,23 +22,34 @@ class GenericImageDataAccessor(ABC):
def chroma(self):
return self.shape_dict['C']
+ @staticmethod
+ def conform_data(data):
+ if len(data.shape) > 4:
+ raise DataShapeError(f'Cannot handle image with dimensions other than X, Y, C, and Z: {data.shape}')
+ ones = [1 for i in range(0, 4 - len(data.shape))]
+ return data.reshape(*data.shape, *ones)
+
def is_3d(self):
return True if self.shape_dict['Z'] > 1 else False
def get_one_channel_data (self, channel: int):
- return InMemoryDataAccessor(self.data[:, :, channel, :])
+ return InMemoryDataAccessor(self.data[:, :, int(channel), :])
@property
- def data(self): # XYCZ enforced
+ def data(self):
return self._data
+ @property
+ def shape(self):
+ return self._data.shape
+
@property
def shape_dict(self):
return dict(zip(('X', 'Y', 'C', 'Z'), self.data.shape))
class InMemoryDataAccessor(GenericImageDataAccessor):
def __init__(self, data):
- self._data = data
+ self._data = self.conform_data(data)
class GenericImageFileAccessor(GenericImageDataAccessor): # image data is loaded from a file
def __init__(self, fpath: Path):
@@ -67,7 +78,7 @@ class CziImageFileAccessor(GenericImageFileAccessor):
sd = {ch: cf.shape[cf.axes.index(ch)] for ch in cf.axes}
if sd['S'] > 1 or sd['T'] > 1:
- raise FileShapeError(f'Cannot handle image with multiple positions or time points: {sd}')
+ raise DataShapeError(f'Cannot handle image with multiple positions or time points: {sd}')
idx = {k: sd[k] for k in ['X', 'Y', 'C', 'Z']}
xycz = np.moveaxis(
@@ -76,10 +87,11 @@ class CziImageFileAccessor(GenericImageFileAccessor):
[0, 1, 2, 3]
)
- try:
- self._data = xycz.reshape(xycz.shape[0:4])
- except Exception:
- raise FileShapeError(f'Cannot handle image with dimensions other than X, Y, C, and Z')
+ # try:
+ # self._data = xycz.reshape(xycz.shape[0:4])
+ # except Exception:
+ # raise FileShapeError(f'Cannot handle image with dimensions other than X, Y, C, and Z')
+ self._data = self.conform_data(xycz.reshape(xycz.shape[0:4]))
def __del__(self):
self.czifile.close()
@@ -108,7 +120,7 @@ class FileAccessorError(Error):
class FileNotFoundError(Error):
pass
-class FileShapeError(Error):
+class DataShapeError(Error):
pass
class FileWriteError(Error):
diff --git a/model_server/model.py b/model_server/model.py
index 672bb63d..8c07d2d8 100644
--- a/model_server/model.py
+++ b/model_server/model.py
@@ -4,7 +4,7 @@ import os
import numpy as np
-from model_server.image import GenericImageDataAccessor
+from model_server.image import GenericImageDataAccessor, InMemoryDataAccessor
class Model(ABC):
@@ -59,7 +59,7 @@ class ImageToImageModel(Model):
"""
@abstractmethod
- def infer(self, img) -> (np.ndarray, dict):
+ def infer(self, img) -> (GenericImageDataAccessor, dict):
super().infer(img)
class DummyImageToImageModel(ImageToImageModel):
@@ -69,14 +69,13 @@ class DummyImageToImageModel(ImageToImageModel):
def load(self):
return True
- def infer(self, img: GenericImageDataAccessor) -> (np.ndarray, dict):
+ def infer(self, img: GenericImageDataAccessor) -> GenericImageDataAccessor:
super().infer(img)
w = img.shape_dict['X']
h = img.shape_dict['Y']
result = np.zeros([h, w], dtype='uint8')
result[floor(0.25 * h) : floor(0.75 * h), floor(0.25 * w) : floor(0.75 * w)] = 255
- return (result, {'success': True})
-
+ return InMemoryDataAccessor(data=result)
class Error(Exception):
pass
diff --git a/model_server/workflow.py b/model_server/workflow.py
index ece9b1b4..38803ed6 100644
--- a/model_server/workflow.py
+++ b/model_server/workflow.py
@@ -28,7 +28,7 @@ def infer_image_to_image(fpi, model, where_output, **kwargs) -> dict:
# run model inference
# TODO: call this async / await and report out infer status to optional callback
- outdata, messages = model.infer(img)
+ outdata = model.infer(img)
dt_inf = time() - t0
# TODO: assert outdata format
@@ -49,7 +49,7 @@ def infer_image_to_image(fpi, model, where_output, **kwargs) -> dict:
model_id=model.model_id,
input_filepath=str(fpi),
output_filepath=str(outpath),
- success=messages['success'],
+ success=True,
timer_results=timer_results
)
diff --git a/tests/test_api.py b/tests/test_api.py
index e290d163..f5869bdd 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -62,8 +62,11 @@ class TestApiFromAutomatedClient(unittest.TestCase):
def test_i2i_inference_errors_model_not_found(self):
model_id = 'not_a_real_model'
resp = requests.put(
- self.uri + f'i2i/infer/{model_id}',
- params={'input_filename': 'not_a_real_file.name'}
+ self.uri + f'i2i/infer/',
+ params={
+ 'model_id': model_id,
+ 'input_filename': 'not_a_real_file.name'
+ }
)
print(resp.content)
self.assertEqual(resp.status_code, 409)
@@ -77,7 +80,11 @@ class TestApiFromAutomatedClient(unittest.TestCase):
self.assertEqual(resp_load.status_code, 200, f'Error loading {model.model_id}')
self.copy_input_file_to_server()
resp_infer = requests.put(
- self.uri + f'i2i/infer/{model.model_id}',
- params={'input_filename': czifile['filename']},
+ self.uri + f'i2i/infer/',
+ params={
+ 'model_id': model.model_id,
+ 'input_filename': czifile['filename'],
+ 'channel': 2,
+ },
)
self.assertEqual(resp_infer.status_code, 200, f'Error inferring from {model.model_id}')
\ No newline at end of file
diff --git a/tests/test_ilastik.py b/tests/test_ilastik.py
index 6fd34563..94a7cbbb 100644
--- a/tests/test_ilastik.py
+++ b/tests/test_ilastik.py
@@ -1,6 +1,6 @@
import unittest
-from conf.testing import czifile, ilastik
-from model_server.image import CziImageFileAccessor
+from conf.testing import czifile, ilastik, output_path
+from model_server.image import CziImageFileAccessor, write_accessor_data_to_file
from model_server.ilastik import IlastikPixelClassifierModel
class TestIlastikPixelClassification(unittest.TestCase):
@@ -18,8 +18,21 @@ class TestIlastikPixelClassification(unittest.TestCase):
with self.assertRaises(io.UnsupportedOperation):
faulthandler.enable(file=sys.stdout)
- def test_instantiate_pixel_classifier(self):
+ def test_run_pixel_classifier(self):
+ channel = 2
model = IlastikPixelClassifierModel({'project_file': ilastik['pixel_classifier']})
cf = CziImageFileAccessor(czifile['path'])
- model.infer(cf.get_one_channel_data(2))
+ pxmap = model.infer(cf.get_one_channel_data(channel))
+ print(pxmap.shape_dict)
+
+ # 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
diff --git a/tests/test_image.py b/tests/test_image.py
index 8aef0eaf..3ca3cb2e 100644
--- a/tests/test_image.py
+++ b/tests/test_image.py
@@ -1,6 +1,9 @@
import unittest
+
+import numpy as np
+
from conf.testing import czifile, output_path
-from model_server.image import CziImageFileAccessor, write_accessor_data_to_file
+from model_server.image import CziImageFileAccessor, DataShapeError, InMemoryDataAccessor, write_accessor_data_to_file
class TestCziImageFileAccess(unittest.TestCase):
def setUp(self) -> None:
@@ -13,6 +16,8 @@ class TestCziImageFileAccess(unittest.TestCase):
self.assertEqual(cf.chroma, czifile['c'])
self.assertFalse(cf.is_3d())
self.assertEqual(len(cf.data.shape), 4)
+ self.assertEqual(cf.shape[0], czifile['h'])
+ self.assertEqual(cf.shape[1], czifile['w'])
def test_write_single_channel_tif(self):
ch = 2
@@ -26,3 +31,16 @@ class TestCziImageFileAccess(unittest.TestCase):
)
self.assertEqual(cf.data.shape[0:2], mono.data.shape[0:2])
self.assertEqual(cf.data.shape[3], mono.data.shape[2])
+
+ def test_conform_data_shorter_than_xycz(self):
+ data = np.random.rand(256, 512)
+ acc = InMemoryDataAccessor(data)
+ self.assertEqual(
+ acc.shape_dict,
+ {'X': 256, 'Y': 512, 'C': 1, 'Z': 1}
+ )
+
+ def test_conform_data_longer_than_xycz(self):
+ data = np.random.rand(256, 512, 12, 8, 3)
+ with self.assertRaises(DataShapeError):
+ acc = InMemoryDataAccessor(data)
\ No newline at end of file
diff --git a/tests/test_model.py b/tests/test_model.py
index 2c1d7c64..9f4ab388 100644
--- a/tests/test_model.py
+++ b/tests/test_model.py
@@ -25,25 +25,25 @@ class TestCziImageFileAccess(unittest.TestCase):
def test_czifile_is_correct_shape(self):
model = DummyImageToImageModel()
- img, _ = model.infer(self.cf)
+ img = model.infer(self.cf)
w = czifile['w']
h = czifile['h']
self.assertEqual(
img.shape,
- (h, w),
+ (h, w, 1, 1),
'Inferred image is not the expected shape'
)
self.assertEqual(
- img[int(w/2), int(h/2)],
+ img.data[int(w/2), int(h/2)],
255,
'Middle pixel is not white as expected'
)
self.assertEqual(
- img[0, 0],
+ img.data[0, 0],
0,
'First pixel is not black as expected'
)
diff --git a/tests/test_workflow.py b/tests/test_workflow.py
index fff03bbc..83935d3d 100644
--- a/tests/test_workflow.py
+++ b/tests/test_workflow.py
@@ -10,7 +10,7 @@ class TestGetSessionObject(unittest.TestCase):
self.model = DummyImageToImageModel()
def test_single_session_instance(self):
- result = infer_image_to_image(czifile['path'], self.model, output_path)
+ result = infer_image_to_image(czifile['path'], self.model, output_path, channel=2)
self.assertTrue(result.success)
import tifffile
@@ -20,7 +20,7 @@ class TestGetSessionObject(unittest.TestCase):
self.assertEqual(
img.shape,
- (h, w),
+ (h, w, 1, 1),
'Inferred image is not the expected shape'
)
--
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