From 0c3a9a03928f7c703a0ab2d419abbbe6ce314c9f Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 19 Oct 2023 15:41:57 +0200
Subject: [PATCH] Trying to run 2d kristineberg data through z-stack pipeline
---
.../actual_runs/20230805_kristineberg_PA.py | 42 +++++++++++++++++++
extensions/chaeo/actual_runs/__init__.py | 0
.../actual_runs/proj0004-exp0038-fixed.py | 41 ++++++++++++++++++
.../chaeo/examples/batch_run_patches.py | 10 +++--
extensions/chaeo/workflows.py | 2 +-
5 files changed, 90 insertions(+), 5 deletions(-)
create mode 100644 extensions/chaeo/actual_runs/20230805_kristineberg_PA.py
create mode 100644 extensions/chaeo/actual_runs/__init__.py
create mode 100644 extensions/chaeo/actual_runs/proj0004-exp0038-fixed.py
diff --git a/extensions/chaeo/actual_runs/20230805_kristineberg_PA.py b/extensions/chaeo/actual_runs/20230805_kristineberg_PA.py
new file mode 100644
index 00000000..f37da1a1
--- /dev/null
+++ b/extensions/chaeo/actual_runs/20230805_kristineberg_PA.py
@@ -0,0 +1,42 @@
+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
+
+if __name__ == '__main__':
+ where_czi = 'c:/Users/rhodes/projects/proj0012-trec-handoff/owncloud-sync/TREC-HD/Images/TREC_STOP_15_Kristineberg/230805_automic_AI_PA/20230805-122525_AI_PA_successfulrun_recognitiononPLL405cilindionas/Selection'
+ where_output = autonumber_new_directory(
+ 'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0016/output',
+ 'batch-output'
+ )
+
+ px_ilp = Path.home() / 'model-server' / 'ilastik' / 'AF405-bodies_boundaries.ilp'
+
+ params = {
+ 'ilastik_project_file': px_ilp.__str__(),
+ 'pxmap_threshold': 0.25,
+ 'pixel_class': 0,
+ 'zmask_channel': 0,
+ 'patches_channel': 4,
+ 'mask_type': 'boxes',
+ 'zmask_filters': {'area': (1e3, 1e8)},
+ 'zmask_expand_box_by': (128, 3),
+ 'export_pixel_probabilities': True,
+ 'export_2d_patches_for_training': True,
+ 'export_2d_patches_for_annotation': True,
+ 'export_3d_patches': False,
+ 'export_annotated_zstack': True,
+ 'export_patch_masks': True,
+ }
+
+ input_files = get_matching_files(where_czi, 'czi')
+
+ 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/actual_runs/__init__.py b/extensions/chaeo/actual_runs/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/extensions/chaeo/actual_runs/proj0004-exp0038-fixed.py b/extensions/chaeo/actual_runs/proj0004-exp0038-fixed.py
new file mode 100644
index 00000000..436c9edd
--- /dev/null
+++ b/extensions/chaeo/actual_runs/proj0004-exp0038-fixed.py
@@ -0,0 +1,41 @@
+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
+
+if __name__ == '__main__':
+ where_czi = 'z:/rhodes/projects/proj0004-marine-photoactivation/data/exp0038/AutoMic/20230906-163415/Selection'
+ where_output = autonumber_new_directory(
+ 'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0009/output',
+ 'batch-output'
+ )
+
+ px_ilp = Path.home() / 'model-server' / 'ilastik' / 'AF405-bodies_boundaries.ilp'
+
+ params = {
+ 'ilastik_project_file': px_ilp.__str__(),
+ 'pxmap_threshold': 0.25,
+ 'pixel_class': 0,
+ 'zmask_channel': 0,
+ 'patches_channel': 4,
+ 'mask_type': 'boxes',
+ 'zmask_filters': {'area': (1e3, 1e8)},
+ 'zmask_expand_box_by': (128, 3),
+ 'export_pixel_probabilities': False,
+ 'export_2d_patches_for_training': True,
+ 'export_2d_patches_for_annotation': True,
+ 'export_3d_patches': False,
+ 'export_annotated_zstack': False,
+ 'export_patch_masks': True,
+ }
+
+ input_files = get_matching_files(where_czi, 'czi', coord_filter={'P': (0, 10)}, )
+
+ loop_workflow(
+ input_files,
+ where_output,
+ export_patches_from_multichannel_zstack,
+ params,
+ )
+
+ print('Finished')
\ No newline at end of file
diff --git a/extensions/chaeo/examples/batch_run_patches.py b/extensions/chaeo/examples/batch_run_patches.py
index 198348f3..e448b8f4 100644
--- a/extensions/chaeo/examples/batch_run_patches.py
+++ b/extensions/chaeo/examples/batch_run_patches.py
@@ -4,10 +4,11 @@ from extensions.chaeo.util import autonumber_new_directory, get_matching_files,
from extensions.chaeo.workflows import export_patches_from_multichannel_zstack
if __name__ == '__main__':
- where_czi = 'z:/rhodes/projects/proj0004-marine-photoactivation/data/exp0038/AutoMic/20230906-163415/Selection'
-
+ # where_czi = 'z:/rhodes/projects/proj0004-marine-photoactivation/data/exp0038/AutoMic/20230906-163415/Selection'
+ where_czi = 'c:/Users/rhodes/projects/proj0012-trec-handoff/owncloud-sync/TREC-HD/Images/TREC_STOP_15_Kristineberg/230805_automic_AI_PA/20230805-122525_AI_PA_successfulrun_recognitiononPLL405cilindionas/Selection'
where_output = autonumber_new_directory(
- 'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0009/output',
+ # 'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0009/output',
+ 'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0016/output',
'batch-output'
)
@@ -22,7 +23,7 @@ if __name__ == '__main__':
'mask_type': 'boxes',
'zmask_filters': {'area': (1e3, 1e8)},
'zmask_expand_box_by': (128, 3),
- 'export_pixel_probabilities': False,
+ 'export_pixel_probabilities': True,
'export_2d_patches_for_training': True,
'export_2d_patches_for_annotation': True,
'export_3d_patches': False,
@@ -30,6 +31,7 @@ if __name__ == '__main__':
'export_patch_masks': True,
}
+ # input_files = get_matching_files(where_czi, 'czi', coord_filter={'P': (0, 10)}, )
input_files = get_matching_files(where_czi, 'czi', coord_filter={'P': (0, 10)}, )
loop_workflow(
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 49c114a3..f84cf2eb 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -38,7 +38,7 @@ def export_patches_from_multichannel_zstack(
stack = generate_file_accessor(Path(input_zstack_path))
fstem = Path(input_zstack_path).stem
ti.click('file_input')
- assert stack.nz > 1, 'Expecting z-stack'
+ # assert stack.nz > 1, 'Expecting z-stack'
# MIP and classify pixels
mip = InMemoryDataAccessor(
--
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