From 92b0121a4004619211ee708089a1570cad57356d Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 21 Mar 2024 15:40:41 +0100
Subject: [PATCH] Raise error if ilastik data not embedded in project file; but
it appears that most test classifiers fail this
---
model_server/extensions/ilastik/models.py | 28 +++++++++++++++++++++--
1 file changed, 26 insertions(+), 2 deletions(-)
diff --git a/model_server/extensions/ilastik/models.py b/model_server/extensions/ilastik/models.py
index de25566a..00224805 100644
--- a/model_server/extensions/ilastik/models.py
+++ b/model_server/extensions/ilastik/models.py
@@ -12,8 +12,17 @@ from model_server.base.models import Model, ImageToImageModel, InstanceSegmentat
class IlastikModel(Model):
- def __init__(self, params, autoload=True):
+ def __init__(self, params, autoload=True, enforce_embedded=True):
+ """
+ Base class for models that run via ilastik shell API
+ :param params:
+ project_file: path to ilastik project file
+ :param autoload: automatically load model into memory if true
+ :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.enforce_embedded = enforce_embedded
params['project_file'] = self.project_file.__str__()
if self.project_file.is_absolute():
pap = self.project_file
@@ -42,6 +51,15 @@ class IlastikModel(Model):
args.project = self.project_file_abspath.__str__()
shell = app.main(args, init_logging=False)
+ # validate if inputs are embedded in project file
+ input_groups = shell.projectManager.currentProjectFile['Input Data']['infos']
+ lanes = input_groups.keys()
+ for ll in lanes:
+ input_types = input_groups[ll]
+ for tt in input_types:
+ ds_loc = input_groups[ll][tt].get('location', False)
+ if self.enforce_embedded and ds_loc and ds_loc[()] == b'FileSystem':
+ raise IlastikInputEmbedding('Cannot load ilastik project file where inputs are on filesystem')
if not isinstance(shell.workflow, self.get_workflow()):
raise ParameterExpectedError(
f'Ilastik project file {self.project_file} does not describe an instance of {shell.workflow.__class__}'
@@ -216,4 +234,10 @@ class PatchStackObjectClassifier(IlastikObjectClassifierFromSegmentationModel):
[0, 4, 1, 2, 3]
)
- return PatchStack(data=pyxcz), {'success': True}
\ No newline at end of file
+ return PatchStack(data=pyxcz), {'success': True}
+
+class Error(Exception):
+ pass
+
+class IlastikInputEmbedding(Error):
+ pass
\ No newline at end of file
--
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