From 33f832353306a2afd6593b728ded0cb5064dca1e Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 27 Oct 2023 14:26:07 +0200
Subject: [PATCH] Started testing object classification from z-stack via a
batch running script
---
extensions/chaeo/accessors.py | 6 ++-
extensions/chaeo/examples/batch_obj_cla.py | 45 ++++++++++++++++++++++
extensions/chaeo/workflows.py | 25 +++++++-----
3 files changed, 65 insertions(+), 11 deletions(-)
create mode 100644 extensions/chaeo/examples/batch_obj_cla.py
diff --git a/extensions/chaeo/accessors.py b/extensions/chaeo/accessors.py
index d1e9089c..b782c51b 100644
--- a/extensions/chaeo/accessors.py
+++ b/extensions/chaeo/accessors.py
@@ -10,12 +10,14 @@ class MonoPatchStack(InMemoryDataAccessor):
"""
if isinstance(data, np.ndarray): # interpret as YXZ
- assert len(data.shape) == 3
+ assert data.ndim == 3
self._data = np.expand_dims(data, 2)
elif isinstance(data, list): # list of YX patches
+ nda = np.array(data)
+ assert nda.squeeze().ndim == 3
self._data = np.expand_dims(
np.moveaxis(
- np.array(data),
+ nda,
[1, 2, 0],
[0, 1, 2]),
2
diff --git a/extensions/chaeo/examples/batch_obj_cla.py b/extensions/chaeo/examples/batch_obj_cla.py
new file mode 100644
index 00000000..105f8e46
--- /dev/null
+++ b/extensions/chaeo/examples/batch_obj_cla.py
@@ -0,0 +1,45 @@
+from pathlib import Path
+
+from conf.testing import output_path
+from model_server.util import autonumber_new_directory, get_matching_files, loop_workflow
+from extensions.chaeo.models import PatchStackObjectClassifier
+from extensions.chaeo.workflows import infer_object_map_from_zstack
+from extensions.ilastik.models import IlastikPixelClassifierModel
+
+
+
+if __name__ == '__main__':
+ where_czi = 'c:/Users/rhodes/projects/proj0004-marine-photoactivation/data/exp0038/AutoMic/20230906-163415/Selection'
+ where_output = autonumber_new_directory(
+ output_path,
+ 'zmask_to_automic',
+ )
+
+ px_ilp = Path.home() / 'model-server' / 'testing' / 'zmask' / 'AF405-bodies_boundaries.ilp'
+ ob_ilp = Path.home() / 'model-server' / 'testing' / 'zmask' / 'auto_obj_after.ilp'
+
+ params = {
+ 'pxmap_threshold': 0.25,
+ 'pxmap_foreground_channel': 0,
+ 'segmentation_channel': 0,
+ 'patches_channel': 4,
+ 'zmask_filters': {'area': (1e3, 1e8)},
+ }
+
+ input_files = get_matching_files(where_czi, 'czi', coord_filter={'P': (0, 10)}, )
+
+ models = [
+ IlastikPixelClassifierModel(params={'project_file': Path(px_ilp)}),
+ PatchStackObjectClassifier(params={'project_file': Path(ob_ilp)})
+ ]
+
+ loop_workflow(
+ input_files,
+ where_output,
+ infer_object_map_from_zstack,
+ models,
+ params,
+ catch_and_continue=False,
+ )
+
+ print('Finished')
\ No newline at end of file
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 7289c58e..3847d5e2 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -27,11 +27,9 @@ def get_zmask_meta(
pxmap_foreground_channel: int = 0,
zmask_zindex: int = None,
zmask_clip: int = None,
- zmask_expand_box_by: int = None,
zmask_filters: Dict = None,
zmask_type: str = 'boxes',
-
-
+ **kwargs,
) -> tuple:
ti = Timer()
stack = generate_file_accessor(Path(input_file_path))
@@ -63,7 +61,7 @@ def get_zmask_meta(
stack.get_one_channel_data(segmentation_channel),
mask_type=zmask_type,
filters=zmask_filters,
- expand_box_by=zmask_expand_box_by,
+ **kwargs,
)
ti.click('generate_zmasks')
@@ -210,7 +208,7 @@ def export_patches_from_multichannel_zstack(
'interm': interm,
}
-def get_object_map_from_zstack(
+def infer_object_map_from_zstack(
input_file_path: str,
output_folder_path: str,
models: List[Model],
@@ -222,7 +220,7 @@ def get_object_map_from_zstack(
zmask_clip: int = None,
zmask_type: str = 'boxes',
zmask_filters: Dict = None,
- zmask_expand_box_by: int = None,
+ # zmask_expand_box_by: int = None,
**kwargs,
) -> Dict:
assert len(models) == 2
@@ -239,17 +237,19 @@ def get_object_map_from_zstack(
pxmap_foreground_channel=pxmap_foreground_channel,
zmask_zindex=zmask_zindex,
zmask_clip=zmask_clip,
- zmask_expand_box_by=zmask_expand_box_by,
+ # zmask_expand_box_by=zmask_expand_box_by,
zmask_filters=zmask_filters,
zmask_type=zmask_type,
+ **kwargs
)
# extract patches to accessor
patches_acc = get_patches_from_zmask_meta(
- stack,
+ stack.get_one_channel_data(patches_channel),
zmask_meta,
rescale_clip=zmask_clip,
make_3d=False,
+ focus_metric='max_sobel',
**kwargs
)
@@ -274,14 +274,21 @@ def get_object_map_from_zstack(
mi = zmask_meta[ii]
object_label_id = mi['info'].label
result_label_map = result_acc.iat(ii)
+ assert (result_label_map.shape) == 2
unique_values = np.unique(result_label_map)
assert len(unique_values) == 2
assert unique_values[0] == 0
- inferred_class = result_acc.iat(ii)
ii_mask = object_labels_map == object_label_id
object_labels_map[ii_mask] = unique_values[1]
patch = patches_acc.iat(ii)
+ write_accessor_data_to_file(
+ Path(output_folder_path) / 'obj_classes_' / (fstem + '.tif'),
+ object_labels_map
+ )
+ ti.click('export_object_classes')
+ return ti
+
def transfer_ecotaxa_labels_to_patch_stacks(
--
GitLab