From 0a3039faad8e2427f9da0f3c8d65776b96b2f405 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 19 Feb 2024 13:05:19 +0100
Subject: [PATCH] Move patch stack wrapper to ilastik extension
---
.../chaeo/examples/batch_obj_cla.py | 2 +-
...fer_labels_to_ilastik_object_classifier.py | 3 +-
model_server/extensions/chaeo/models.py | 40 +------------------
model_server/extensions/ilastik/models.py | 36 +++++++++++++++++
4 files changed, 40 insertions(+), 41 deletions(-)
diff --git a/model_server/extensions/chaeo/examples/batch_obj_cla.py b/model_server/extensions/chaeo/examples/batch_obj_cla.py
index 7471034f..eef5e703 100644
--- a/model_server/extensions/chaeo/examples/batch_obj_cla.py
+++ b/model_server/extensions/chaeo/examples/batch_obj_cla.py
@@ -2,7 +2,7 @@ from pathlib import Path
from model_server.conf.testing import output_path
from model_server.base.util import autonumber_new_directory, get_matching_files, loop_workflow
-from model_server.extensions.chaeo.models import PatchStackObjectClassifier
+from extensions.ilastik.models import PatchStackObjectClassifier
from model_server.extensions.chaeo.workflows import infer_object_map_from_zstack
from model_server.extensions.ilastik.models import IlastikPixelClassifierModel
diff --git a/model_server/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py b/model_server/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py
index ae306745..5d9625b5 100644
--- a/model_server/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py
+++ b/model_server/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py
@@ -4,7 +4,8 @@ import pandas as pd
import skimage
from model_server.extensions.chaeo.accessors import MonoPatchStackFromFile
-from model_server.extensions.chaeo.models import generate_ilastik_object_classifier, PatchStackObjectClassifier
+from model_server.extensions.chaeo.models import generate_ilastik_object_classifier
+from extensions.ilastik.models import PatchStackObjectClassifier
from model_server.base.accessors import GenericImageDataAccessor, write_accessor_data_to_file
diff --git a/model_server/extensions/chaeo/models.py b/model_server/extensions/chaeo/models.py
index 7f8c08bd..1a969db3 100644
--- a/model_server/extensions/chaeo/models.py
+++ b/model_server/extensions/chaeo/models.py
@@ -4,48 +4,10 @@ import shutil
import h5py
import numpy as np
import skimage
-import vigra
-from model_server.extensions.chaeo.accessors import MonoPatchStack, MonoPatchStackFromFile
-from model_server.extensions.ilastik.models import IlastikObjectClassifierFromSegmentationModel
+from model_server.extensions.chaeo.accessors import MonoPatchStackFromFile
-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)
- yxz = np.moveaxis(
- obmaps[0][:, 0, :, :, 0],
- [1, 2, 0],
- [0, 1, 2]
- )
-
- assert yxz.shape[0:2] == input_acc.hw
- assert yxz.shape[2] == input_acc.nz
- return MonoPatchStack(data=yxz), {'success': True}
-
def generate_ilastik_object_classifier(
template_ilp: Path,
diff --git a/model_server/extensions/ilastik/models.py b/model_server/extensions/ilastik/models.py
index 1cdd5477..2cd56349 100644
--- a/model_server/extensions/ilastik/models.py
+++ b/model_server/extensions/ilastik/models.py
@@ -5,6 +5,7 @@ import numpy as np
import vigra
import model_server.extensions.ilastik.conf
+from extensions.chaeo.accessors import PatchStack
from model_server.base.accessors import GenericImageDataAccessor, InMemoryDataAccessor
from model_server.base.models import Model, ImageToImageModel, InstanceSegmentationModel, InvalidInputImageError, ParameterExpectedError, SemanticSegmentationModel
@@ -180,3 +181,38 @@ class IlastikObjectClassifierFromPixelPredictionsModel(IlastikModel, ImageToImag
return obmap
+class PatchStackObjectClassifier(IlastikObjectClassifierFromSegmentationModel):
+ """
+ Wrap ilastik object classification for inputs comprising single-object series of raw images and binary
+ segmentation masks.
+ """
+
+ def infer(self, input_acc: PatchStack, segmentation_acc: PatchStack) -> (np.ndarray, dict):
+ assert segmentation_acc.is_mask()
+ assert input_acc.chroma == 1
+
+ tagged_input_data = vigra.taggedView(input_acc.pczyx, 'tczyx')
+ tagged_seg_data = vigra.taggedView(segmentation_acc.pczyx, '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)
+ yxz = np.moveaxis(
+ obmaps[0][:, 0, :, :, 0],
+ [1, 2, 0],
+ [0, 1, 2]
+ )
+
+ assert yxz.shape[0:2] == input_acc.hw
+ assert yxz.shape[2] == input_acc.nz
+ return PatchStack(data=yxz), {'success': True}
--
GitLab