From 986066a0f1bbbb681a2f1b89f7440a22803d7565 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 6 May 2024 12:40:15 +0200
Subject: [PATCH] Moved project file into model.params; removed autogeneration
of segmentation model from pixel predictions model
---
model_server/extensions/ilastik/models.py | 33 +++++------------------
1 file changed, 6 insertions(+), 27 deletions(-)
diff --git a/model_server/extensions/ilastik/models.py b/model_server/extensions/ilastik/models.py
index 2c92c026..001b6a95 100644
--- a/model_server/extensions/ilastik/models.py
+++ b/model_server/extensions/ilastik/models.py
@@ -22,13 +22,13 @@ class IlastikModel(Model):
:param enforce_embedded:
raise an error if all input data are not embedded in the project file, i.e. on the filesystem
"""
- self.project_file = Path(params['project_file'])
+ self.params = params
+ pf = Path(params['project_file'])
self.enforce_embedded = enforce_embedded
- params['project_file'] = self.project_file.__str__()
- if self.project_file.is_absolute():
- pap = self.project_file
+ if pf.is_absolute():
+ pap = pf
else:
- pap = model_server.extensions.ilastik.conf.paths['project_files'] / self.project_file
+ pap = model_server.extensions.ilastik.conf.paths['project_files'] / pf
self.project_file_abspath = pap
if not pap.exists():
raise FileNotFoundError(f'Project file does not exist: {pap}')
@@ -62,7 +62,7 @@ class IlastikModel(Model):
assert True
if not isinstance(shell.workflow, self.get_workflow()):
raise ParameterExpectedError(
- f'Ilastik project file {self.project_file} does not describe an instance of {self.__class__}'
+ f'Ilastik project file {self.project_file_abspath} does not describe an instance of {self.__class__}'
)
self.shell = shell
@@ -300,27 +300,6 @@ class IlastikObjectClassifierFromPixelPredictionsModel(IlastikModel, ImageToImag
obmap, _ = self.infer(img, mask)
return obmap
- def make_instance_segmentation_model(self, px_ch: int):
- """
- Generate an instance segmentation model, i.e. one that takes binary masks instead of pixel probabilities as a
- second input.
- :param px_ch: channel of pixel probability map to use
- :return:
- InstanceSegmentationModel object
- """
- class _Mod(self.__class__, InstanceSegmentationModel):
- def label_instance_class(
- self, img: GenericImageDataAccessor, mask: GenericImageDataAccessor, **kwargs
- ) -> GenericImageDataAccessor:
- if mask.dtype == 'bool':
- norm_mask = 1.0 * mask.data
- else:
- norm_mask = mask.data / np.iinfo(mask.dtype).max
- norm_mask_acc = mask._derived_accessor(norm_mask.astype('float32'))
- return super().label_instance_class(img, norm_mask_acc, pixel_classification_channel=px_ch)
- return _Mod(params={'project_file': self.project_file})
-
-
class Error(Exception):
pass
--
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