From f7c02a0a7fc2e3971470f38752f5eb5e248f14de Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 27 Oct 2023 11:35:52 +0200
Subject: [PATCH] Moved patch stack-specific ilastik model
---
...fer_labels_to_ilastik_object_classifier.py | 42 ++----------------
extensions/chaeo/models.py | 43 +++++++++++++++++++
2 files changed, 46 insertions(+), 39 deletions(-)
create mode 100644 extensions/chaeo/models.py
diff --git a/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py b/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py
index 9e07ec2b..d780b4a5 100644
--- a/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py
+++ b/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py
@@ -6,47 +6,11 @@ import numpy as np
import pandas as pd
import skimage
import uuid
-import vigra
-from extensions.chaeo.accessors import MonoPatchStack, MonoPatchStackFromFile
-from extensions.ilastik.models import IlastikObjectClassifierFromSegmentationModel
-from model_server.accessors import generate_file_accessor, GenericImageDataAccessor, InMemoryDataAccessor, write_accessor_data_to_file
+from extensions.chaeo.accessors import MonoPatchStackFromFile
+from extensions.chaeo.models import PatchStackObjectClassifier
+from model_server.accessors import generate_file_accessor, GenericImageDataAccessor, write_accessor_data_to_file
-class PatchStackObjectClassifier(IlastikObjectClassifierFromSegmentationModel):
- """
- Wrap ilastik object classification for inputs comprising raw image and binary segmentation masks, both represented
- as time-series images where each frame contains only one object.
- """
-
-
- def infer(self, input_acc: MonoPatchStack, segmentation_acc: MonoPatchStack) -> (np.ndarray, dict):
- assert segmentation_acc.is_mask()
- assert input_acc.chroma == 1
-
- tagged_input_data = vigra.taggedView(input_acc.make_tczyx(), 'tczyx')
- tagged_seg_data = vigra.taggedView(segmentation_acc.make_tczyx(), 'tczyx')
-
- dsi = [
- {
- 'Raw Data': self.PreloadedArrayDatasetInfo(preloaded_array=tagged_input_data),
- 'Segmentation Image': self.PreloadedArrayDatasetInfo(preloaded_array=tagged_seg_data),
- }
- ]
-
- 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'
-
- # for some reason ilastik scrambles these axes to Z(1)YX(1)
- assert obmaps[0].shape == (input_acc.nz, 1, input_acc.hw[0], input_acc.hw[1], 1)
- yxcz = np.moveaxis(
- obmaps[0][:, :, :, :, 0],
- [2, 3, 1, 0],
- [0, 1, 2, 3]
- )
-
- assert yxcz.shape == input_acc.shape
- return InMemoryDataAccessor(data=yxcz), {'success': True}
def get_dataset_info(h5: h5py.File, lane : int = 0):
"""
diff --git a/extensions/chaeo/models.py b/extensions/chaeo/models.py
new file mode 100644
index 00000000..5900134e
--- /dev/null
+++ b/extensions/chaeo/models.py
@@ -0,0 +1,43 @@
+import numpy as np
+import vigra
+
+from extensions.chaeo.accessors import MonoPatchStack
+from extensions.ilastik.models import IlastikObjectClassifierFromSegmentationModel
+from model_server.accessors import InMemoryDataAccessor
+
+
+class PatchStackObjectClassifier(IlastikObjectClassifierFromSegmentationModel):
+ """
+ Wrap ilastik object classification for inputs comprising raw image and binary segmentation masks, both represented
+ as time-series images where each frame contains only one object.
+ """
+
+
+ def infer(self, input_acc: MonoPatchStack, segmentation_acc: MonoPatchStack) -> (np.ndarray, dict):
+ assert segmentation_acc.is_mask()
+ assert input_acc.chroma == 1
+
+ tagged_input_data = vigra.taggedView(input_acc.make_tczyx(), 'tczyx')
+ tagged_seg_data = vigra.taggedView(segmentation_acc.make_tczyx(), 'tczyx')
+
+ dsi = [
+ {
+ 'Raw Data': self.PreloadedArrayDatasetInfo(preloaded_array=tagged_input_data),
+ 'Segmentation Image': self.PreloadedArrayDatasetInfo(preloaded_array=tagged_seg_data),
+ }
+ ]
+
+ 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'
+
+ # for some reason ilastik scrambles these axes to Z(1)YX(1)
+ assert obmaps[0].shape == (input_acc.nz, 1, input_acc.hw[0], input_acc.hw[1], 1)
+ yxcz = np.moveaxis(
+ obmaps[0][:, :, :, :, 0],
+ [2, 3, 1, 0],
+ [0, 1, 2, 3]
+ )
+
+ assert yxcz.shape == input_acc.shape
+ return InMemoryDataAccessor(data=yxcz), {'success': True}
\ No newline at end of file
--
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