From 1c45425fd72d7e6fed2748d4da80601b5e2fb629 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Sun, 22 Oct 2023 08:36:21 +0200
Subject: [PATCH] Elevate whether to use a specific z-index or MIP to find best
focus in zmask
---
.../chaeo/actual_runs/20231008_Bilbao_PA.py | 64 +++++++++++++++++++
extensions/chaeo/workflows.py | 7 +-
2 files changed, 70 insertions(+), 1 deletion(-)
create mode 100644 extensions/chaeo/actual_runs/20231008_Bilbao_PA.py
diff --git a/extensions/chaeo/actual_runs/20231008_Bilbao_PA.py b/extensions/chaeo/actual_runs/20231008_Bilbao_PA.py
new file mode 100644
index 00000000..4312bccd
--- /dev/null
+++ b/extensions/chaeo/actual_runs/20231008_Bilbao_PA.py
@@ -0,0 +1,64 @@
+from pathlib import Path
+
+from extensions.chaeo.util import autonumber_new_directory, get_matching_files, loop_workflow
+from extensions.chaeo.workflows import export_patches_from_multichannel_zstack
+
+from model_server.accessors import CziImageFileAccessor, write_accessor_data_to_file, InMemoryDataAccessor
+from model_server.process import rescale
+
+
+def export_single_channel_tif_from_multichannel_czi(input_file_path, output_folder_path, channel, **kwargs):
+ in_acc = CziImageFileAccessor(input_file_path)
+ data = in_acc.get_one_channel_data(channel).data
+ if 'rescale_zmask_clip' in kwargs:
+ data = rescale(data, clip=kwargs['rescale_zmask_clip'])
+ outf = Path(output_folder_path) / (Path(input_file_path).stem + '.tif')
+ write_accessor_data_to_file(
+ outf,
+ InMemoryDataAccessor(data),
+ )
+ print(f'Wrote file: {outf}')
+
+if __name__ == '__main__':
+ root = Path('c:/Users/rhodes/projects/proj0012-trec-handoff/owncloud-sync/TREC-HD/Images/')
+ where_czi = (root / 'TREC_STOP_24_Bilbao/231008_automic/20231008-162336/Selection').__str__()
+ where_output = autonumber_new_directory(
+ 'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0017/output',
+ 'batch-output'
+ )
+
+ px_ilp = Path('c:/Users/rhodes/projects/proj0011-plankton-seg/exp0017/pxAF405_dim8bit.ilp').__str__()
+
+ params = {
+ 'ilastik_project_file': px_ilp,
+ 'pxmap_threshold': 0.25,
+ 'pixel_class': 0,
+ 'zmask_channel': 0,
+ 'zmask_zindex': 3,
+ 'patches_channel': 2,
+ 'mask_type': 'boxes',
+ 'zmask_filters': {'area': (1e3, 1e8)},
+ 'zmask_expand_box_by': (128, 3),
+ 'export_pixel_probabilities': True,
+ 'export_2d_patches_for_training': True,
+ 'draw_bounding_box_on_2d_patch': True,
+ 'export_2d_patches_for_annotation': True,
+ 'export_3d_patches': False,
+ 'export_annotated_zstack': True,
+ 'export_patch_masks': True,
+ 'rescale_zmask_clip': 0.01,
+ 'rgb_overlay_channels': (1, None, None),
+ 'rgb_overlay_weights': (0.5, 1.0, 1.0)
+ }
+
+ input_files = get_matching_files(where_czi, 'czi', coord_filter={})
+
+ loop_workflow(
+ input_files,
+ where_output,
+ export_patches_from_multichannel_zstack,
+ 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 bf1503e4..5e1b4e3c 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -23,6 +23,7 @@ def export_patches_from_multichannel_zstack(
pxmap_threshold: float,
pixel_class: int,
zmask_channel: int,
+ zmask_zindex: None, # None for MIP,
patches_channel: int,
rescale_zmask_clip: int = None,
mask_type: str = 'boxes',
@@ -46,7 +47,11 @@ def export_patches_from_multichannel_zstack(
ti.click('file_input')
# MIP and classify pixels
- zmask_data = stack.get_one_channel_data(channel=zmask_channel).data.max(axis=-1, keepdims=True)
+ if isinstance(zmask_zindex, int):
+ assert 0 < zmask_zindex < stack.nz
+ zmask_data = stack.get_one_channel_data(channel=zmask_channel).data[:, :, :, zmask_zindex]
+ else:
+ zmask_data = stack.get_one_channel_data(channel=zmask_channel).data.max(axis=-1, keepdims=True)
if rescale_zmask_clip:
zmask_data = rescale(zmask_data, rescale_zmask_clip)
mip = InMemoryDataAccessor(
--
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