From 6942c0446877ca614e68879f58c013a74fb1ebda Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 16 Oct 2023 17:26:32 +0200
Subject: [PATCH] Needed to modify model wrapper to handle patch stacks
---
...fer_labels_to_ilastik_object_classifier.py | 51 +++++++++++++++++--
1 file changed, 46 insertions(+), 5 deletions(-)
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 2fee54bc..3c721d25 100644
--- a/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py
+++ b/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py
@@ -5,10 +5,51 @@ import json
import numpy as np
import pandas as pd
import uuid
+import vigra
from extensions.chaeo.util import autonumber_new_file
from extensions.ilastik.models import IlastikObjectClassifierFromSegmentationModel
-from model_server.accessors import generate_file_accessor, write_accessor_data_to_file
+from model_server.accessors import generate_file_accessor, GenericImageDataAccessor, InMemoryDataAccessor, write_accessor_data_to_file
+
+class PatchStackObjectClassifier(IlastikObjectClassifierFromSegmentationModel):
+
+ @staticmethod
+ def make_tczyx(acc):
+ assert acc.chroma == 1
+ tyx = np.moveaxis(
+ acc.data[:, :, 0, :], # YX(C)Z
+ [2, 0, 1],
+ [0, 1, 2]
+ )
+ return np.expand_dims(tyx, (1, 2))
+ # return tyx
+
+ def infer(self, input_img: GenericImageDataAccessor, segmentation_img: GenericImageDataAccessor) -> (np.ndarray, dict):
+ assert segmentation_img.is_mask()
+ assert input_img.chroma == 1
+
+ tagged_input_data = vigra.taggedView(self.make_tczyx(input_img), 'tczyx')
+ tagged_seg_data = vigra.taggedView(self.make_tczyx(segmentation_img), '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'
+ assert obmaps[0].shape == (input_img.nz, 1, input_img.hw[0], input_img.hw[1], 1) # z(1)yx(1)
+
+ yxcz = np.moveaxis(
+ obmaps[0][:, :, :, :, 0],
+ [2, 3, 1, 0],
+ [0, 1, 2, 3]
+ )
+ assert yxcz.shape == input_img.shape
+ return InMemoryDataAccessor(data=yxcz), {'success': True}
def get_dataset_info(h5, lane=0):
lns = f'{lane:04d}'
@@ -154,8 +195,8 @@ if __name__ == '__main__':
train_zstack_mask = generate_file_accessor(where_patch_stack / 'zstack_train_mask.tif')
new_ilp = root / 'exp0014/test_obj_from_seg.ilp'
- mod = IlastikObjectClassifierFromSegmentationModel({'project_file': new_ilp})
+ mod = PatchStackObjectClassifier({'project_file': new_ilp})
- result = mod.infer(train_zstack_raw, train_zstack_mask)
- write_accessor_data_to_file(where_patch_stack / 'result.tif', result)
- print(mod.project_file_abspath)
\ No newline at end of file
+ result_acc, _ = mod.infer(train_zstack_raw, train_zstack_mask)
+ write_accessor_data_to_file(where_patch_stack / 'result.tif', result_acc)
+ print(where_patch_stack / 'result.tif')
\ No newline at end of file
--
GitLab