From 3be7e5953ce944ede92e899e67136bb3be649d3a Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 30 Oct 2023 17:22:51 +0100
Subject: [PATCH] Batch workflow now running without errors and creating
meaningful output data
---
extensions/chaeo/workflows.py | 41 +++++++++++++++--------------------
1 file changed, 18 insertions(+), 23 deletions(-)
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index ce7714d7..61b9c3c4 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -265,36 +265,31 @@ def infer_object_map_from_zstack(
# send patches and mask stacks to object classifier
result_acc, _ = object_classifier.infer(patches_acc, patch_masks_acc)
- object_labels_map = np.copy(interm['label_map'])
- assert object_labels_map.shape == interm['label_map'].shape
- assert object_labels_map.dtype == interm['label_map'].dtype
+ labels_map = interm['label_map']
+ output_map = np.zeros(labels_map.shape, dtype=labels_map.dtype)
+ assert labels_map.shape == interm['label_map'].shape
+ assert labels_map.dtype == interm['label_map'].dtype
# assign labels to object map:
+ meta = []
for ii in range(0, len(zmask_meta)):
- mi = zmask_meta[ii]
- object_label_id = mi['info'].label
- result_label_map = mask_largest_object(result_acc.iat(ii))
- assert result_label_map.ndim == 2
- unique_values = np.unique(result_label_map)
- if not len(unique_values) == 2:
- mask_largest_object(result_label_map)
- raise Exception()
- assert unique_values[0] == 0
- ii_mask = object_labels_map == object_label_id
- object_labels_map[ii_mask] = unique_values[1]
- # object_labels_map[ii_mask] = np.unique(
- # mask_largest_object(
- # result_acc.iat(ii)
- # )
- # )[1]
- # patch = patches_acc.iat(ii)
+ object_id = zmask_meta[ii]['info'].label
+ result_patch = mask_largest_object(result_acc.iat(ii))
+ object_class = np.unique(result_patch)[1]
+ output_map[labels_map == object_id] = object_class
+ meta.append({'object_id': ii, 'object_class': object_id})
write_accessor_data_to_file(
- Path(output_folder_path) / 'obj_classes_' / (fstem + '.tif'),
- object_labels_map
+ Path(output_folder_path) / ('obj_classes_' + (fstem + '.tif')),
+ InMemoryDataAccessor(output_map)
)
ti.click('export_object_classes')
- return ti
+
+ return {
+ 'timer_results': ti.events,
+ 'dataframe': pd.DataFrame(meta),
+ 'interm': {},
+ }
--
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